General curriculum specifications Courses: Masters and Ph

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In the name of God

Tehran University

Institute of Biochemistry & Biophysics

General curriculum specifications

Courses: Masters and Ph.D.

Field: Biochemistry

Revision of MSc and Ph.D. program in Biochemistry - 1396

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Chapter One: General Curriculum Specifications

Masters and Ph.D. courses in Biochemistry

Definition of the field:

Graduate studies in biochemistry include two master’s and Ph.D. degrees. A master's degree

course is one of the higher education courses beyond the undergraduate degree, which

then runs and eventually leads to the award of a master's degree in the relevant field.

Ph.D. is the highest university degree in this field that will give a degree in biochemistry and

includes a coordinated collection of educational and research activities in the field of cell

and molecular biochemistry in the microbial, animal and plant fields.

The purpose of the field:

The aim of the MSc course is to develop and train specialists and researchers who acquire

the necessary skills for education, research and services through the acquisition of

necessary education and familiarity with scientific research methods. Also, the important

goals of the Ph.D. course are to provide faculty for educational and research centers and

educate people who have creative thinking and can understand the scientific problems of

society and solve them.

Necessity and importance of the field:

Innovation, creation of scientific infrastructures for the production of technical know-how,

and the extension of knowledge boundaries in the field of biochemistry, in accordance with

the goals of the Islamic Republic's holy system in the planning of 20 years, customary in Iran

1400, and training of human resources to carry out the assigned tasks in the future. Since

sciences such as biology and technologies such as intelligence with biotechnology and

nanotechnology require a scientific basis in biochemical knowledge, therefore, in order to

achieve the above goals, biochemistry has a special importance and forms the special

mission of graduates.

The role and ability of graduates:

Graduates of the biochemistry will acquire a set of knowledge and abilities by passing a

theoretical (educational) and a scientific course (Thesis). These courses are expected to

empower graduates in educational, developmental, manufacturing, quality control,

consulting, biochemical industries, pharmaceuticals, government agencies and regulatory

agencies.

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Course length and system form:

A) Master:

The master's degree in biochemistry is 2 years old and has two educational and research

stages. It should be noted that according to the length of the research affairs, the student's

dissertation can be added to the course at the request of the supervisor and the approval of

the supervisory board for two semesters.

B) Ph.D.:

The duration of the doctoral degree in biochemistry is 4 academic years, according to the

regulations of the doctoral program, which has been approved by the Supreme Council of

Planning and has two educational and research stages. It should be noted that according to

the length of the research affairs of the student's dissertation and at the request of the

supervisor, three semesters can be added.

Number and type of Units:

A) Master:

To complete a biochemistry course, the student should have 10 specialized courses, 10 units

of optional courses, 2 seminars and 6 units of thesis. A total of at least 28 curricula for

graduation is required.

B) Ph.D.:

To complete a Biochemistry Ph.D., the student must Succeeding to pass at least 36 credits

and research as follows.

Optional courses=12 units; Seminar (1) and (2) =1 + 1 unit; Project (thesis) =22 units

Student Admission Requirements:

A) Master:

Acceptance of undergraduate encyclopedia holders from one of the accredited universities

in or outside the country is based on the terms and conditions of the Ministry of Science,

Research and Technology.

B) Ph.D.:

The volunteer will initially participate in the Ministry of Science’s test and will be introduced

to the University if the grade is accepted for conducting a specialized interview. After

conducting a specialized interview by the Jury and notifying the volunteer score to the

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assessment organization; the total score of the interview and the written test; is the final

score of the volunteer. If the bidders have earned the necessary points, they will be

introduced to the university on the basis of the student's assessment organization.

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Chapter Two: Course Tables

Table 1 - Compensatory courses for Biochemistry in Master's Degree

Ind

ex

Course Title Number of units

Total Hours Prerequisite

Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l

1 Biochemistry Basics 2 0 2 32 0 32

2 Elemental molecular biology 2 0 2 32 0 32

TOTAL 4 0 4 64 0 64

Table 2 - Compensatory courses for Biochemistry in Ph.D. Degree

Ind

ex



Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l

1 Enzymology 2 0 2 32 0 32

2 Advanced Molecular Biology 2 0 2 32 0 32

3 Metabolic Regulation 2 0 2 32 0 32

TOTAL 6 0 6 96 0 96

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Table 3. Specialized courses for Biochemistry in Master's Degree

Ind

ex



Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l

1 Enzymology 2 0 2 32 0 32

2 Advanced Molecular Biology 2 0 2 32 0 32

3 Biochemistry of Nucleic acids 2 0 2 32 0 32

4 Structure and function of proteins

2 0 2 32 0 32

5 Metabolic Regulation 2 0 2 32 0 32

6 Seminar I 1 0 1 16 0 16

7 Seminar II 1 0 1 16 0 16

TOTAL 12 0 12 192 0 192

Table 4. Specialized courses for Biochemistry in Ph.D. Degree

Ind

ex



Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l

1 Seminar I 1 0 1 16 0 16

2 Seminar II 1 0 1 16 0 16

TOTAL 2 0 2 32 0 32

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Table 5. Optional courses for Biochemistry in Master's & Ph.D. Degree

Ind

ex



Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l

1 Immunobiology 2 0 2 32 0 32

2 Immunochemistry 2 0 2 32 0 32

3 Biochemistry of neural systems

2 0 2 32 0 32

4 Biochemistry of Cognitive Networks

2 0 2 32 0 32

5 Cell Signaling Biochemistry 2 0 2 32 0 32

6 Membrane Biochemistry 2 0 2 32 0 32

7 Chromatin and epigenetics 2 0 2 32 0 32

8 Stem Cell Biology 2 0 2 32 0 32

9 Proteomics 2 0 2 32 0 32

10 Structural and functional studies of proteins involved in health and disease

2 0 2 32 0 32

11 Regulation of signal transduction pathways

2 0 2 32 0 32

12 Chaperones 2 0 2 32 0 32

13 Recombinant DNA methods 2 0 2 32 0 32

14 Chemical Biology of Peptides 2 0 2 32 0 32

15 Chemical Synthetic Biology 2 0 2 32 0 32

16 Medicinal Chemistry: DNA Targeting Drugs

2 0 2 32 0 32

17 Bioinorganic Chemistry 2 0 2 32 0 32

18 Design of Enzyme Inhibitors 2 0 2 32 0 32

19 Introductory Macromolecular X-ray Crystallography

2 0 2 32 0 32

20 Macromolecular X-ray Crystallography 2

2 0 2 32 0 32 Introductory Macromolecular

X-ray Crystallography

21 Cellular and Molecular Mechanism of Cancer

2 0 2 32 0 32

22 Tissue Engineering 2 0 2 32 0 32

Continue Table 5.

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Ind

ex



Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

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23 Principle and Techniques of Electron Microscopy

2 0 2 32 0 32

24 Advanced Topics in Biochemistry

2 0 2 32 0 32

25 Methods in Genetic Engineering

2 0 2 32 0 32

26 Methods of extraction and identification of biological macromolecules

2 0 2 32 0 32

27 Biomedical mass spectrometry

2 0 2 32 0 32

28 Membrane Biophysics 2 0 2 32 0 32

29 Molecular Biophysics 2 0 2 32 0 32

30 Methods of Biophysics 2 0 2 32 0 32

31 Enzymes Kinetics 2 0 2 32 0 32

32 Cellular Biophysics 2 0 2 32 0 32

33 Biosensors 2 0 2 32 0 32

34 Mathematical Models in Biological Issues

2 0 2 32 0 32

35 Methods and Research Logic 2 0 2 32 0 32

36 Biothermodynamics 2 0 2 32 0 32

37 Physical Chemistry of Proteins

2 0 2 32 0 32

38 Topics in Biophysics 2 0 2 32 0 32

39 Biospectroscopy 2 0 2 32 0 32

40 Ligand Protein Interaction 2 0 2 32 0 32

41 Pharmaceutical Biophysics 2 0 2 32 0 32

42 Bio-electromagnetics 2 0 2 32 0 32

43 Biophysics and Tissue Engineering

2 0 2 32 0 32

44 Environmental Biophysics 2 0 2 32 0 32

45 Topics in radiation Biology 2 0 2 32 0 32

46 Computational Biophysics 2 0 2 32 0 32

47 Topics in the Philosophy of Biology

2 0 2 32 0 32

Continue Table 5.

Ind

ex Course Title Number of

units Total Hours Prerequisite

1

Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l

48 X-Ray scattering from Biological Macromolecule

2 0 2 32 0 32

49 Bioelectrochemistry of proteins and nucleic acids

2 0 2 32 0 32

50 Biophysics of ion channels 2 0 2 32 0 32

51 Computational Genomics 1 1 2 16 32 48

52 Structural Bioinformatics 2 0 2 32 0 32

53 Computational Drug Design 2 0 2 32 0 32

54 Chemoinformatics 2 0 2 32 0 32

55 Chemometrics 2 0 2 32 0 32

56 Machine Learning 2 0 2 32 0 32

57 Complex Networks 2 0 2 32 0 32

58 Modeling Metabolic Networks

2 0 2 32 0 32

59 Molecular Evolution and Phylogenetics

2 0 2 32 0 32

60 Molecular Modeling 2 0 2 32 0 32

61 Stochastic Processes 2 0 2 32 0 32

62 Introcuction to Dynamical Systems

2 0 2 32 0 32

63 DNA Computing 2 0 2 32 0 32

64 Evolutionary Algorithms 2 0 2 32 0 32

65 Bayesian Statistics 2 0 2 32 0 32

66 Pattern Recognition 2 0 2 32 0 32

67 Design and Analysis of Algorithms

2 0 2 32 0 32

68 Multivariate Analysis 2 0 2 32 0 32

69 Genomics and Gene Regulation

2 0 2 32 0 32

70 Biomolecular Recognition 2 0 2 32 0 32

71 Special Topics in Bioinformatics

2 0 2 32 0 32

72 Advanced Data Mining 2 0 2 32 0 32

Continue Table 5.

Ind

ex Course Title Number of

units Total Hours Prerequisite

1

Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l

73 Cell and Molecular Mechanism of Cancer

2 0 2 32 0 32

74 Data Mining in Medical Systems

2 0 2 32 0 32

75 Modeling of Biological Systems

2 0 2 32 0 32

TOTAL 149 1 150 2384 32 2416 - MSc student is required to pass 10 units from the table above.

Table 6. Optional courses for Biochemistry in Ph.D. Degree

Ind

ex



Theo

reti

cal

Pra

ctic

al

Tota

l

Theo

reti

cal

Pra

ctic

al

Tota

l 1 Glycolipobiology 2 0 2 32 0 32

2 Advanced Biochemistry of Proteins and Nucleic acids

2 0 2 32 0 32

3 Mechanism of enzyme action 2 0 2 32 0 32

TOTAL 6 0 6 96 0 96 - Ph.D. student is allowed to select at least 12 units in 6 courses as a total of courses in

Tables 5 and 6, and endorsed by their supervisor.

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Chapter Three: Course Descriptions

Courses: Masters and Ph.D.

Field: Biochemistry

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Course title: Enzymology Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Specialized Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Students familiarity with the mechanism of action of enzymes and their qualitative and quantitative comparison with chemical catalysts, the role and importance of enzymes in industrial production and the necessity of their engineering in this regard

Headlines: Introduction: Illustrating the impact of enzymology on our lives through some examples

from medical and biotechnological industries

Enzyme nomenclature

Understanding the mechanisms used by enzymes to increase reaction rate through

examples from simple chemical reactions

Mechanistic basis of chemical reactions catalyzed by cofactors

Chemical nature of enzymatic reactions catalyzed by serine proteases, cysteine proteases,

metalloproteases, aspartic proteases, ribonucleases, glycosidases

Mechanisms of enzyme inhibitors

Michaelis–Menten equations, Lineweaver–Burk plot, Eadie–Hofstee diagram

Site directed mutagenesis of enzymes and its role in deciphering the mechanism of

enzyme action

Application of Recombinant DNA technology to enzyme engineering

Evaluation method: Continuous evaluation

(To be specified in percentage) midterm

(To be specified in percentage) Final Test

(To be specified in percentage) Project

(To be specified in percentage)

30% ______ Written Test: 70% __ _____

Practical: -

References: 1. An Introduction to Enzyme and Coenzyme Chemistry, by T. Bugg, John Wiley 2012

2. Athel Cornish – Bowden, Fundamentals of Enzyme Kinetics, Portland press, 2004.

Course title: Advanced Molecular Biology Number of units: 2 The number of hours: 32

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Unit type: Theoretical Course type: Specialized Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Promotion of students’ knowledge on the field of molecular biology. In this course students will get familiar with the history and the experiments which led to the discovery of discussed biological phenomena. At the end they will be able to compare molecular mechanisms of replication, transcription and translation in the prokaryotic and eukaryotic system.

Headlines: History and philosophy of molecular biology; The concept of the gene; Forward and

reverse genetics

Genome and its organization in prokaryotes and eukaryotes; introducing of the epigenetic modifications in eukaryotic systems.

DNA replication and its regulation in prokaryotes and eukaryotes with emphasis on the fate of chromatin modifications after DNA replication

Mutations and DNA damage and repair in prokaryotes and eukaryotes; Genome elimination and its biological implications; Molecular mechanisms of genome instability

Transcription and its regulation in prokaryotes

Transcription and its regulation in eukaryotes (Chromatin structure and its effects on transcription, post-transcriptional events including RNA processing and post-transcriptional control of gene expression) and introducing of different DNA binding proteins

Translation and its regulation in prokaryotes and eukaryotes

Brief description of main molecular methods which have been used in the study of central

dogma discussed in each session.






20% ______ Written Test: 80% __ _____

Practical: -

References: 1. Robert F. Weaver, Molecular Biology, latest edition, McGraw Hill; (currently 5th ed. 2012).

2. Brue Alberts, Molecular Biology of the Cell, latest edition, Garland Science; (currently 6th

ed. 2015.

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Course title: Biochemistry of Nucleic Acids Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Specialized Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Students' familiarity with rotations, links, structural diversity and space building of proteins and nucleic acids RNA, DNA

Headlines: Definition of nucleic acids, torsion angles in nucleotides, sugar puckering, helical

parameters.

Ionization of bases, tautomeric and modified bases.

Structure and conformation of bases, sugar and phosphate.

Contor-diatance map, allowed and disallowed structures.

Forces stabilizing nucleic acids, base pairing, hydrogen binding and stacking.

Spectroscopic, thermodynamic description of base pairing.

Polymorphism of DNA structure, Hydration, A, B, C, … H, G and Z structures.

DNA supercoiling, nucleosomes

Classification of RNA, Stem, Loop, and buldge structures

RNA structures, primary, secondary, and tertiary structures, U-turn and stability.

Degradation of nucleic acids

Nucleoside drugs and antisense






5% ______ Written Test: 85% 10%

Practical: -

References: 1. Saenger W, Principles of Nucleic Acids Structure, Springer, 1984

2. Cantor CR and Schimmel PR, Biophysical Chemistry Part 1 Freeman, 1980

1

Course title: Structure and Function of Proteins Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Specialized Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Promotion of student’s knowledge in the field of structure and function of proteins, and its relation to organism’s functions.

Headlines: Amino acids as the basis for structure and function.

Primary structure: peptide bound and its chemical and physical characters.

Secondary structure: Helical structures, and structures and random structures.

Tertiary structure: proteins three dimensional formation Domain and motifs

Quaternary structure: proteins with number of subunits.

Structure and function of fibrous proteins.

Structure of membrane proteins.

Structure of active proteins.

Mechanism of protein folding.

Proteins structure prediction.

Biological function of proteins.

Proteins biotechnology.






5% 30% Written Test: 65% __ _____

Practical: -

References: 1. Engelbert Buxbaum, Fundamental of Protein Structure and Function, Wiley, 2007. 2. David Whitford, Protein Structure and Function, Wiley, 2005.

1

Course title: Metabolic Regulation Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Specialized Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To familiarize graduate students with various mechanisms of enzyme regulation involved in a cell’s metabolism and how the signaling elements are involved.

Headlines: Introduction: a survey on the significance of metabolic control and regulation on well-

being of biological system

Enzymatic reactions: kinetic and thermodynamics

Diversity of regulatory mechanisms: short/long term regulation of enzymes, influence of

hormones and cell signals, influx/outflux of metabolites through biological membranes,

tissue variation

A survey on fuel digestion and absorption from the gut and lipoproteins metabolism

Regulation in integrated metabolism of carbohydrates, lipids and proteins under different

physiological conditions (fed state, hunger, work load and exercise)

How some of the cell signaling elements influence metabolic regulation?






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Keith N. Frayn, Metabolic Regulation: a Human Perspective, 3rd ed, Wiley-Blackwell, 2010. 2. David M. Gibson and Robert A. Harris, Metabolic Regulation in Mammals, Taylor and Francis, 2003.

1

Course title: Immunobiology Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The basic principles of the components and mechanisms of working with the immune system on human immune responses against infectious agents are outlined.

Headlines: Introduction to Immunobiology

Innate Immunology

Hematoposis

Antigens

Antibodies and B cell developments

The Major Histocompatibility Complex and its Function

T cell Receptor and T cell developments

Antigen Processing and Presentation

Cell Mediated Immunity

The Humoral Immune Response

Immune Regulation

Immunological Tolerance and Autoimmunity






0% 50% Written Test: 50% __ _____

Practical: -

References: 1. Janeway’s Immunobiology, Edited by K. Murphy, P. Travers and Walport, 2012.

2. Immunology, Edited by Kuby, 2013

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Course title: Immunochemistry Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The description of how the antigen and antibody are prepared, the determination of the antibody's characteristics and the kinetics of the antigen-antibody response, and hence the principles of immunosuppression will be discussed.

Headlines: Introduction to the Immune System and classification of Immune Assay

Antigens and the binding protein-protein (hapten to carrier or enzymes ,fluorochromes or

radioactive to antibody)

Antibody, Preparation of polyclonal and monoclonal antibody, Isolation and purification

of antibody and antibody fragments and antigen-antibody complex disassembly

Reaction kinetics of antigen - antibody

Methods of Immuno Assay in the broth, jelly or using antibodies attached to lable

(Agglutination, precipitation, RIA, ELISA, PCR ELISA, Elispot, Dot ELISA, Western

blotting)

Immunohistochemistry

Immunocytochemistry Evaluation method: Continuous evaluation





10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Principles and practice of immunoassay, Edited by C.P. Price, D.J. Newman, 1997. 2. Immunochemical protocols, Edited by R. Brun, 2005.

3. Immunochemistry, Edited by D. M. Weir, 1986.

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Course title: Biochemistry of Neuronal System Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Improving student’s knowledge in the field of neuron cells, glia, cellular and molecular structures and also the effect of neural system on the organism’s behavior.

Headlines: Brain and neuronal systems anatomy.

Limbic, cortex, spinal cord and peripheral.

Structure of neuronal system structure and function of neural cell, structure and function

of glial cells.

Action potential, excitation, sodium – potassium pumps function.

Functional of synapses, interaction mechanism of neurotransmitters with receptors,

acetylcholine and acetylcholine esterase.

Catecholamine’s mechanism, Dopamine, Serotonin, …., Amino acids neurotransmitters,

prostaglandins.

Carbohydrates, amino acids, lipids, proteins and steroids in brain.

PNS neural system, visual, tactile and taste.

Introduction to neural networks in the brain.






10% 10% Written Test: 80% __ _____

Practical: -

References: 1. Dale Purves, George J, Augustine, Neuroscience, Sinauer Associate Inc, 2004.

2. Eric R. Kandel, Principal of Neural Science, 5th ed. Mac Grow Hill, 2013.

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Course title: Biochemistry of Cognitive Networks Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Improving student’s information in the field of semantic interaction of biomolecules such as proteins, metabolites, and their activity on organism’s intelligence.

Headlines: The anatomy of CNS such as Hippocampus Amygdale, Cortex layers and brain stem, ….

Neural connections of interbrain cells definition of glia cells, neurons, axon, Dendrite cell

membrane functions.

Biochemical factors in brain functional networks. Neurotransmitters (acetylcholine,

glutamate, GABA, Dopamine, Serotonin, Melatonin, peptides.

Neuroprotective factors, short peptides, insulin.

Physical factors: Electromagnetic fields.

Behaves related to functional neuronal networks in brain, normal, neurodegenerative.

Environmentally affected connections visual Hearing, Touch, ….

Neurodegenerative diseases, Alzheimer, Parkinson metabolic disorders, Epilepsy.






5% 20% Written Test: 75% __ _____

Practical: -

References: 1. Edmund T.Rolls and Alexandro Trevis, Neural Network and Brain Function, 4th ed.

MTT Press, 2009.

2. Sangeetha Menon Brain, Self and Consciousness, Springer, 2014.

1

Course title: Cell Signaling Biochemistry Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Description of the structural and biochemical properties of cellular symptoms and their regulation. The tools used by the cell in transmitting messages, based on the messaging organization and the interaction of the messenger paths.

Headlines: Basic of cell signaling

o Cell signaling: Why, When and Where?

o Tools for Cell signaling

o Modular Structure of Signaling Proteins and Signaling Complexes

o Regulatory Modification

o Organization of Signaling

o Signaling Networks

o Spatial and Temporal Aspects of Signaling

Receptors in cell signaling

o Structure and Function of Nuclear Receptors

o Structure and Function of Trans membrane Receptors

G-protein –coupled receptor

Receptors with Tyrosine- specific protein kinase activity

Receptor with Ser/Thr-specific protein kinases activity

Intracellular Messenger Substances:”Second Messengers”

o cAMP

o Calciun

o Lipid messengers

o Reactive Oxygen Species

o Reactive Nitrogen Species

Mtor signaling regulation of protein synthesis and degradation

Methods used in studying cell signaling






1

------------ ______ Written Test: 80% 20%

Practical: -

References: 1. Cell Signaling Biology, Edited by Michael J. Berridge 2014

2. Biochemistry of Signal Transduction and Regulation5th

Edition, Edited by G. Krauss

2014

1

Course title: Membrane Biochemistry Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The purpose of this course is to introduce students to the most important biological organization, namely cell membrane, lipid and protein structures of membrane, various applications and internal and external communications of membranes.

Headlines: Introduction to biological membranes

Bio membranes, Structural Organization and Basic Function

Biosynthesis of phospholipids

Biosynthesis of membrane proteins

Mobility of lipids and proteins in bio membranes

Fluidity of membranes

Cellular cytoskeleton (Microtubule, Intermediate filament, Actin)

Cell-Cell adhesion and communication

Protein sorting

Transport across cell membrane

Passive and active transport

Molecular mechanisms of vesicular traffic






5% 10% Written Test: 60% 25%

Practical: -

References: 1. Harvey Lodish, et al., Molecular Cell Biology, 6th ed. Freeman Company, 2008.

2. Stillwell W., An Introduction to Biological membrane: From Bilayers to Rafts, Elsevier,

2013.

Course title: Chromatin and epigenetics Number of units: 2

1

The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Identification of genetic material compositions, including structural levels and their function in transcription and replication

Headlines: Chromatin definition and its building blocks.

Histone proteins, classification, structure, motifs, their variants, Histone Like proteins.

Interaction of histones with DNA, different levels of chromatin structure (solenoid, Zig-

Zag, Helical ribbon, irregular model, chromatids, Centromere, telomere

Non-histone proteins, HMGs structure and their role in chromatin structure and function.

Epigenetic definition: histones acetylation, methylation, phosphorylation, Ubiquitination,

ADP-ribosylation, DNA methylation, microRNAs (miRs).

Active and inactive chromatin, epigenetic and histones cross-talk, histone code, HPs,

SiRNA, polycombs…

Chromatin and transcription: remodeling factors, models and epigenetic.

Chromatin and replication, histone chaperones and histones assembly

Chromatin and signaling, cancer and diseases.

Seminars






10% 10% Written Test: 70% 10%

Practical: -

References: 1. Workman TL and Abmayr SM, Fundamentals of Chromatin, Springer, 2014. 2. Allis CD et al, Epigenetics , CSHL press Europe , 2015

1

Course title: Stem Cell Biology Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Familiarity with stem cell biology and their applications

Headlines: Introduction to Early Stem Cell Concepts and Definitions - Related Research – History

Embryonic stem cells - embryonic development, production and manipulation of

embryonic stem cells

Stem Cells: Skeletal Muscle - Heart - Hepatic - Pancreas - Stomach - Intestine – Neuronal

Stem cells and amniotic fluid - Cord blood stem cells

Induced pluripotent stem cells - Cell reprogramming

Cellular Mechanisms - Self-Loss

Stem Cell Nitrix - Extracellular Matrix

Epigenetic, differentiation and plasticization of stem cells

Cancer Stem Cells

Ethical considerations in stem cell research

Stem Cell Therapy: Stem Cell Transplantation






5% ______ Written Test: 95% __ _____

Practical: -

References: 1. Robert Lanza, et al. Essential of Stem Cell Biology, 2nd ed. James Thomson and Sir,

2009.

1

Course title: Proteomics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Students' familiarity with the application of mass spectrometers in determining the structure and function of proteins

Headlines: Introduction including the definitions, history and importance of proteomics and its

comparison with genomics and transcriptomics

The outline of proteomics projects

Section 1: Mass spectrometry based proteomics

Two-dimensional gel electrophoresis including isoelectric focusing and SDS-PAGE

Protein staining strategies in proteomics

DIFFERENTIAL GEL ELECTROPHORESIS (DIGE)

Analysis of stained 2D gels

In-gel protein digestion

Principles of mass spectromers used in proteomics: MALDI-TOF, ESI-MS, ESI-Tandem

MS

Protein and peptide separation in proteomics including reverse phase and MudPIT

Protein identification

o Peptide Mass Fingerprinting

o Protein sequencing using Tandem MS

Studying protein modifications using mass spectrometers

Tissue scanning by mass spectrometry

Surface enhanced Mass spectrometry

Isotope coated affinity Tag and its application in analytical and functional proteomics

Section 2: Mass spectrometry independent proteomics

Application of the affinity chromatography in identifying novel protein-protein

interactions

Yeast two hybrid

Phage display technology

DNA micro array

Protein and peptide microarray

Self-assembling protein microarray

1






30% ______ Written Test: 70% __ _____

Practical: -

References: 1. Introduction to proteomics by D. Libler, (2002)

2. Principals of proteomics (R. Twyman), (2013)

3. Methods in protein biochemistry H. Tschesche (2012)

4. Current protocols in protein science G. P. Taylor (2016)

5. Protein-Protein Interactions: A Molecular Cloning Manual, Second Edition by E. Golemis

and P. D. Adams (2005)

1

Course title: Structural and functional studies of proteins involved in health and disease Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: Familiarity with the structure and function of proteins that contribute to health and disease. Also, the knowledge and use of useful sites and software for analyzing the sequence and structure and function of proteins

Headlines: An introduction to amino acids and the post-translational modifications of proteins Protein structure: from primary to quaternary structure

Protein function: protein with varying functions

Structural and functional studies of proteins involved in: o Diet and health

o Human diseases caused by bacteria (e.g. Listeria monocytogenes and Shigella

flexneri) o Crop spoilage caused by bacteria (e.g. Bacillus subtilis) o Biosynthesis of Vitamin B12 by bacteria (e.g. Rhodobacter capsulatus) o Angiogenesis and neurogenesis in humans

A brief introduction into a valuable structural method for studying proteins:

o X-ray Crystallography

Common softwares for protein structure visualisation, analysis and interpretation

Protein data bank






5% ______ Written Test: 80% 15%

Practical: -

References: 1. Arthur M. Lesk, Introduction to Protein Science, Architecture, Function and Genomics

2nd ed. Oxford University Press, 2010.

1

Course title: Regulation of signal transduction pathways Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: In this course, cell communications under normal and abnormal physiological conditions will be emphasized. In addition, signaling-based therapeutic approaches in modern medicine will be discussed.

Headlines: Introduction: How cells communicate?

What are the good and bad signals?

Various ways of cell death

The main regulators of cell signals under normal and abnormal physiological conditions

Cell signaling-based sensitization of resistant cells to the thepentical drugs

Invension of new ways of anti-cancer therapy based on structure and function of

Apoptosomes

Invension of new therapeutical strategies based on lysozyme function under abnormal

physiological conditions






5% ______ Written Test: 80% 15%

Practical: -

References: 1. K.M. Debatin, S. Fulda, Apoptosis and cancer therapy, Wiley-VCH, Vol 1, 2006.

2. Francessco. Cecconi, Marcello D’Amelio, Apoptosome: and up-and-coming therapeutical

tool, Springer, 2010.

1

Course title: Chaperones Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Familiarity with the main role of chaperones in terms of structure, interference in the folding, transfer, assembly of proteins and nucleic acids.

Headlines: Proteins synthesis, quality control, proteins folding and unfolding.

Classification of chaperones in prokaryotes and eukaryotes.

Heat shock proteins (GroEL, TRiC, HSP60. 70. 90, ……).

Co-chaperones and protein folding.

ER chaperones and glycoproteins folding.

Chaperones in proteins aggregation/disaggregation, assembly, transport, ….

Nucleic acids chaperones.

Chemical chaperones and pharmacochaperones.

Chaperones and Diseases, signaling…






10% ______ Written Test: 80% 10%

Practical: -

References: 1. Jackson S, Molecular Chaperones, Springer 2013. 2. Macario AJL, et al., The chaperonopathies , Springer, 2013.

1

Course title: Recombinant DNA methods Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: Students' acquaintance with new molecular biology methods related to purification, alteration, and placement of DNA in different carriers for transfer to the cells and expression of target DNA.

Headlines: Different methods of separating DNA containing recombinant components, Southern Blot

technique and PCR technique

Vectors (definition, isolation and maintenance methods, plasmids, lambda virus, cosmids,

single-stranded phages, animal and plant viruses

Enzymes used, restricting enzymes, other enzymes

Probes and their application

Separating mRNA, making cDNA and Northern Blot, Western blot and Microarray

techniques

DNA binding to the carrier

Carriers entering the host cells

Recombinant Recognition (R-Mapping, PCR) methods.

Expression of foreign genes in hosts other than E.coli

Entry and expression of external genes in eukaryotic host (yeast, etc.)

Entry and expression of external genes in plant cells. Examples of using the above

methods, and a look at the future






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Karl Drlica, Understanding DNA and Gene Cloning: A Guide for the Curious, 4th Ed,

Wiley and sons, 2006.

2. Dominic W. S. Wong, the ABCs of Gene Cloning, 2nd ed., Springer, 2006.

1

Course title: Chemical Biology of Peptides Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The teaching of basic and applied topics in peptides and pseudo-peptides science

Headlines: Introduction to structure and function of peptides

Peptides combinatorial synthesis

Determination of the peptide sequences using the mass spectrometry

Introduction to the click chemistry and its applications in biology

Structure and function of glycopeptides, lipopeptides, and pegylated peptides

Peptidomimetics: Introduction, structure and function

Peptide foldamers






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Andrew B. Hughes, Amino Acids, Peptides and Proteins in Organic Chemistry, Volume 1-

5, Wiley- VCH Press, 2009-2012.

1

Course title: Chemical Synthetic Biology Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Understanding the primary and key biochemical requirements in the design and construction of natural systems and new components synthesized in the laboratory containing the minimum living conditions based on biochemical and biophysical studies.

Headlines: Investigation of the probiotic chemistry and the homochirality reasons in biological

macromolecules

Self-assembly and self-replication in biological systems

Vesicles based biological models

Design and preparation of ribonucleic acids and proteins composed of unnatural

monomers

Design and study of routes resulted in systems with limited life conditions

Ethical issues in chemical synthetic biology






10% ______ Written Test: 70% 20%

Practical: -

References: 1. Pier L. Luisi and Cristiano Chiarabelli, Chemical Synthetic Biology, Wiley-VCH Press,

2011.

1

Course title: Medicinal Chemistry: DNA Targeting Drugs Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To familiarize the students with the most recent strategies and in drug designs against nucleic acids

Headlines: Introduction: a survey on the progress of drug designs against nucleic acids

A review on analytical tools for investigation drug: DNA interaction

The anti-proliferative effects of some intercalating drugs

New strategies used for design and production of mustards

Cross-linking agents used on anticancer drugs

Enediyene antibiotics used against DNA

Nucleic acid sequence reading drugs

New strategies in design of artificial restriction enzymes against nucleic acids

New strategies in design of artificial transcription factors to block gene expression

A survey on the application of siRNA and micRNAs to silence gene translation






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Robert E. Smith, Medicinal Chemistry-Fusion of Traditional and Western Medicine: pp

452-468, 2nd Ed, Betham Science, 2014.

2. David Klussmann, The aptamer Handbook: Functional Oligonucleotides and their

Applications, Wiley-VCH, 2006.

1

Course title: Bioinorganic Chemistry Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The study of fundamental principles in biological inorganic chemistry and the study of the structure and function of metalloproteins, metalfoldamer and the study of the role of metals in health and disease

Headlines: Introduction to inorganic chemistry

Chemistry of metalloproteins

Metallo-foldamers

Metal ion coordination

Metals in health and disease






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Gerard Jaouen, Bioorganometallics, John Wiley Press, 2006.

2. Games C. Dabrowiak, Metals in Medicine, John Wiley Press, 2013.

1

Course title: Design of Enzyme Inhibitors Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To familiarize graduate students with the common strategies applied in designing enzyme inhibitors for application in pharmaceutical, biomedical and agricultural fields.

Headlines: Introduction: a survey on the industrial significance of enzyme inhibitor

Classification of various strategies used in enzyme inhibitor designs

Design of affinity-based reagents on enzyme inhibitors

Design of photoaffinity-based reagents on enzyme inhibitors

Design of multisubstrate-based analogues on enzyme inhibitors

Design of transition-state-based analogues on enzyme inhibitors

Diversity and efficacy of mechanism-based enzyme inhibitor






20% ______ Written Test: 80% __ _____

Practical: -

References: 1. Hsiu-Chung Yang, et al. Enzyme Technologies: Pluripotent Players in Discovering

Therapeutic Agents. John Wiley and Sons, 2014.

2. Robert A. Copeland, Evaluation of Enzyme Inhibitors in Drug-Discovery: A guide for

Medicinal Chemists and Pharmacologists, 2nd Ed. John Wiley and Sons Inc. 2013.

1

Course title: Introductory Macromolecular X-ray Crystallography Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Introduction to familiarity with the macromolecular crystallographic technique and the steps required to obtain a three-dimensional protein structure from the start, that is, the expression and purification of proteins to the end, that is, the insertion of a protein structure into a protein database.

Headlines: An introduction to X-ray crystallography

Expression and purification of proteins for crystallography

Protein crystallization

Crystal preparation for crystallography

Sources and detectors for data collection

Diffraction and symmetry

Data collection and processing

Introduction to phasing

Necessary softwares for data analysis and structure determination:

o Mosflm, Scala , Molrep or PHASER, Refmac5 and Coot

Validation and structure deposition in the Protein Data Bank






5% 5% Written Test: 90% __ _____

Practical: -

References: 1. David Blow, Outline of Crystallography for Biologists, Oxford University Press, First

Published, 2002 reprinted 2010.

2. Gale Rhodes, Crystallography Made Crystal Clear, 3rd ed. Academic Press, 2006.

1

Course title: Macromolecular X-ray Crystallography 2 Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: Introductory Macromolecular X-ray Crystallography Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: After familiarization with the macromolecular crystallographic technique in the lesson "Introductory Macromolecular X-ray Crystallography", this tutorial will provide you with more details and familiarity with the programs necessary to process the data, complete its review and obtain the final structure. This lesson sets out the necessary details for someone who wants to apply crystallography.

Headlines: A reminder on the 'Introductory Macromolecular X-ray crystallography' course

X-ray diffraction from protein crystals and the use of Mosflm program

Evaluation of data quality and information given through Scala, pointless and Mathews

Routine methods used to determine protein structure; SAD, MAD, MR

An example of a structure solved with MR using Molrep and Phaser

Electron density map and validation using Coot program

Refinement of data using Refmac in CCP4 program

Validation of the final model using the Ramachandran plot

Deposition of the final structure in the Protein Data Bank

Assessing and visualizing the final structure using Pymol and Chimera






5% 5% Written Test: 80% 10%

Practical: -

References: 1. David Blow, Outline of Crystallography for Biologists, Oxford University Press, Fist

Published 2002, reprinted 2010.

2. Gale Rhodes, Crystallograph Made Crystal Clear, 3rd ed. Academic Press 2006.

1

Course title: Cellular and Molecular Mechanism of Cancer Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Introduction of Graduates to Molecular Topics and Cell Signaling in Health and Disease (Cancer)

Headlines: Introduction of various types of cancer in terms of tissue origin

The molecular mechanism of colorectal cancer (colon) as a model for explaining the

cellular and molecular process of carcinogenesis

Senescence and cancer together with an explanation of the role of telomeres and

telomerase enzyme in genomic stability and carcinogenesis

Cancer is a cell cycle disease

Cancer resistance mechanisms against cell death (apoptosis)

Cancer cell invasion (metastasis)

Angiogenesis

Student Seminars






5% ______ Written Test: 95% __ _____

Practical: -

References: 1. Bert Vogelstein &Keneth W. Kinzler, The Genetic Basis of Human Cancer, 2nd ed.

McGraw-Hill, 2002.

2. Lauren Percorino, Molecular Biology of Cancer, 2nd ed. Oxford University Press, 2008.

1

Course title: Tissue Engineering Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Familiarity with the medical science of regeneration and tissue engineering

Headlines: History of Tissue engineering, current and future, industry and market, concepts and

definitions.

Biomaterials and tissue engineering - Scaffolding and properties - Scaffolding

construction methods - Nanostructured scaffolds.

Biomolecules used in tissue engineering, growth factors and tissue engineering - drug

delivery

Bioreactors.

Stem cells and isolated primer cells from tissue.

Epithelial, connective, cartilage, bone, nervous system, bone marrow, cardiovascular

structure and function. Cell-cell interactions.

Skin, bone, cartilage, nervous, tendon, liver, pancreatic, heart tissue engineering.

Ethical considerations.






5% ______ Written Test: 95% __ _____

Practical: -

References: 1. Robert Lanza, et al. Principles of Tissue Engineering, 3rd ed. Academic Press, 2007.

1

Course title: Principle and Techniques of Electron Microscopy Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Due to the considerable application of different techniques of electron microscopes in most researches, especially in biology, biochemistry and medicine, the purpose of this course is to familiarize students with the principles, concepts and application of different techniques of electron microscopy in research, especially in biological fields.

Headlines: Introduction- Historical Milestones of EM

Electromagnetic Radiation, Diffraction Phenomenon, Electrons, Waves and Resolution

Design of Electromagnetic lenses, Design of the TEM

Basic system making up a TEM and major operational modes of the TEM

Specimen preparation for TEM (fixation, dehydration, infiltration of resin, Embedding,

Curing of the embedment)

Ultramicrotomy and the sectioning process, Cryo-ultramicrotomy

Specimen staining and contrast method for TEM

Production of the electron micrograph

Autoradiography

Immunocytochemistry

Enzyme Cytochemistry

The scanning Electron Microscope

Specimen preparation for SEM

Intermediate and High voltage microscopy

Interpretation of micrographs Evaluation method: Continuous evaluation





10% ______ Written Test: 80% 10%

Practical: -

References:

1

1. John J. Bozzola and Lonine D. Russell, Electron Microscopy, Principles and Techniques for Biologist, 2nd ed. Jones and Bartlett Publishers, 1999.

2. MA Hayat, Principles and Techniques of Electron Microscopy, Biological Application,

4th ed. Cambridge University Press, 2006.

1

Course title: Advanced Topics in Biochemistry Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: Students' acquaintance with molecular types and basis of cell death

Headlines: A-Programmed cell death

o Introduction including the history, cell death as the basis of life in vertebrates, its role

in embryogenesis and post birth

o Intrinsic apoptosis pathway

o Extrinsic apoptosis pathway

o Caspases

o Inhibitor of Apoptosis Proteins and their antagonist

o The mechanism of action of Bcl-2 family of proteins

o Necroptosis, lysosomal cell death, and Autophagy

o Unfolded protein response and ER stress

o Cancer treatment based on apoptosis

B- Protein degadation

o Definition, quality control, and classification.

o Proteasomal degradation: Ub structure, Ub enzymes (E1, E2, E3….) and their

mechanism of action.

o Proteasome structure and the role of each subunit in protein degradation.

o Mechanism of lysosomal degradation. Chaperones and protein degradation.

o Ubiquitination of membrane proteins, lysosomal and proteasomal degradation.

o ESCORTs in membrane proteins degradation.

o Degradation and disease.






30% ______ Written Test: 70% __ _____

Practical: -

References: 1. Apoptosis Senescence and Cancer by Gewirtz, Holt, and Grant (2007)

2. Mayer RJ et al. (2006, latest ed) Protein degradation, Vols 1-3, Wiley

1

1

Course title: Methods in Genetic Engineering Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Students' acquaintance with conventional and new methods of molecular biology and genetics to make changes in DNA and genome

Headlines: Introduction: Definitions of genetic engineering and b biotechnology and their importance

DNA separation technologies

Viral and non-viral vectors and promoters

Enzymes used in molecular biology

o Nucleases

o Ligases

o Polymerases

o Others

Probes and their applications

Preparation of cDNAs

Strategies for Primer design

PCR including Hot start, touch down, Real time, and digital PCR

DNA sequencing, dideoxy and next generation

Site directed mutagenesis

Gene synthesis

DNA transfer into viral and non-viral vectors

Transformation of cells by vectors

Host selection

Identification of transformed cells using blotting techniques and PCR

Gene expression in eukaryotic and prokaryotic hosts

Cre-Lox technology in genetic engineering

Genetic modification using Zinc Finger nucleases

Clustered regularly interspaced short palindromic repeats (CRISPR) technology and its

applications

Biotechnology and genetic engineering applications

Practical section: Growing bacteria – PCR - DNA isolation - DNA digestion and

horizontal electrophoresis

1






30% ______ Written Test: 70% __ _____

Practical: -

References: 1. An Introduction to Genetic Engineering 3rd Edition, by Desmond S. T. Nicholl (2008)

2. Transgenic Mouse Methods and Protocols (Methods in Molecular Biology) 2nd ed. by M.

H. Hofker and J. Van Deursen (2011)

3. Current Protocols in Molecular Biology (2016)

1

Course title: Methods of extraction and identification of biological macromolecules Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Student’s familiarity with conventional biochemical methods for purification and identification of biochemical macromolecules. Students' acquaintance with the foundations of common spectroscopic methods used in biochemistry and their application in vital sciences studies.

Headlines: Different methods of extraction of biomolecules from natural sources (microbes, plant

tissues and animals); Construction of solutions and buffers; Primary extraction of

materials from raw extracts by distribution between water / organic phase, Salt

precipitation, Sedimentation by organic solvents, Condensation, Isolation Filtration and

centrifuges

Purification of extractives by chromatography: General principles include Partition

coefficient, Diffusion effect, Retardation factor, Retention (V, T), Column capacity,

efficiency, resolution

Types of chromatography, ion exchange, gel filtration, hydrophobic, reluctance,

chromatofocusing, TLC thin film chromatography, HPLC, FPLC, etc.

Electrophoresis: General principles of electrophoretic power, acrylamide gel (with and

without) SDS, molecular weight determination, iso-electrophoresis, agar gel, two-

dimensional electrophoresis, Northern, Western, Southern, Immuno-electrophoresis and

identification by viscometry, calcium photometric and fractometry

Introduction to basic concepts in spectroscopy including: HOMO and LUMO electron

balance, vibrational levels, electromagnetic interactions and electrons in molecular

orbitals, types of interactions of matter and electromagnetic waves, and the introduction

of spectroscopic absorption and diffusion, UV-Visible spectroscopy, spectroscopic

fluorescence, Spectroscopy Circular Dichroism, Spectroscopy FT-IR, NMR

Introduction to Fluorescence Energy Transfer (FRET) and its Application in Vital

Sciences Introduction to Light Scattering and its Application in Biochemistry Some Examples of Using Spectroscopic Methods in Vital Sciences

1






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. R. Katoch, Analytical Techniques in Biochemistry and Molecular Biology, Springer-

verlag, 2011.

2. Gordon G. Hammes, Spectroscopy for the Biological Sciences, Wiley, 2005.

3. A. Hofmann, Methods of Molecular Analysis in the Life Sciences, Cambridge University

Press, 2014.

1

Course title: Biomedical mass spectrometry Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To familiarize the graduate students with mass spectrometer used in biomedical fields.

Headlines: Basics of mass spectrometry techniques

Main differences of mass spectrometer used by chemists and biochemists

Advances in molecular ionization techniques of mass spectrometer

Mass spectrometry in characterization of biological small molecules

Therapeutic drug monitoring by mass spectrometry

Quantitative mass spectrometry

Imaging mass spectrometry: Application in Oncology and Neurobiology






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Kenzo Hiraoka, Fundamentals of Mass Spectrometry, Springer, 2013.

2. Alisa G. Woods & Costel C. Darie, Advancements of Mass Spectrometry in Biomedical

Research, Springer, 2014.

1

Course title: Membrane Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: Considering the biological membranes acting as the first barrier and center for the processing of the incoming information and triggering signals, the current course has tailored to address the fact by discussing structure and function of the biological membranes, and defining corresponding electronic elements and systems for further quantitative modeling and evaluation purposes. In this course, different physical, electrical, mechanical and chemical characteristics as well as techniques to study the membrane and constituted proteins are discussed. Understanding the mentioned aspects provides the basis to learn different mechanisms involved and assists one to monitor and manipulate the malfunctioning ones in different related diseases and also to apply them for design of biosensors.

Headlines: Water and biological buffers

o Structures and dynamics of water molecules

o Polarity, dielectrics, spatial and temporal charge distributions

o Viscosity, density, molecular phases, Kosmotrope and Chaotropes

o Thermodynamics, energy transfer and heat capacity

o Conductivity, transmittance, compressibility, electron hopping, electron wire

o Hydration

Lipids

o Hydrophilicity and hydrophobicity

o Structures and dynamics

o Distributions in different part of membranes and cells

o Micelles, CMC, surfactants, Hysteresis, Kraft point

o Conductivity, turbidity, surface tension

o Heat, pressure, water ratio and ionic strength effects

o Phases (L, H, Q), polymorphisms

Biological and artificial lipid membranes

o Structure and dynamics

o Lipid and protein distributions, rafts, micro-domains

o Lateral, rotational, translational diffusion, flip flop

o Fluidity, thickness, order, packing

o Protein translocation, folding, protein-lipid interaction,

Interfaces, means of diffusion and transportation o Diffusion and electro-transference and permeation

1

o Osmosis, electro-osmosis, hydrostatic permeation

o Ion channels, carriers, pumps, pores

o Selectivity, specificity, flux rate

Bio-electric and biomechanics of lipid membranes

o Capacitance, conductance, dielectric, surface charge density, breakage voltage

o Potential layers (Stern, Helmholtz, Deby-Huckle)

o Membrane potentials (Donnan, Nernst, Zeta, Goldman-Hodgkin-Katz)

o Effects of electric, magnetic, electromagnetic and ultrasonic fields

Theoretical and practical techniques

o Artificial planar bilayer, supported bilayer, liposomes,

o Liposome Swelling Assay (LSA), Langmuir, Electroporation

o Fluorescent Recovery after Photobleaching (FRAP)

o AFM, STM, ssNMR,

o Patch clamp, Voltage clamp, Pat, Electophysilogic data acquisition

o MatLab, MD, HOLE, CHARMM, Hydropathy, RasMol, Protein Explorer

Applications of the discussed subjects

o Drug and gene delivery (Packaging, smart and targeted delivery and release)

o Tissue engineering and cell membrane fusion, repair (Wound healing, SCI, …)

o Complimentary medicine (Biophysical application of Laser, electric, magnetic,

electromagnetic, IR and plasma for pain relief, drug delivery, surgery, and monitoring

of targeted cell and organ)

o Immunotherapy (Allergy and Ab-Ag interactions, kits, monitoring, treatments)

o Biosensors design and fabrication (Based on membrane and reconstituted proteins)






60% ______ Written Test: 40% __ _____

Practical: -

References: 1. Jones, M.N. and Chapman, D. (1995), Micelles, Monolayers. And Biomembranes 2. Tien, T.H. (2000) Membrane Biophysics

3. Kotyk A. Jemacek (1996) Biophysical Chemistry of Membrane Functions

4. Hoppe W. (1983) Biophysics

5. Aidley, D.J. and Stanfield, P.R. (1996) Ion Channels, Molecules in Action

6. Silver, B.L. (1985) The Physical Chemistry of Membranes

7. Weiss T.F. (1996) Cellular Biophysics: Vol I, MIT Press

1

Course title: Molecular Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The purpose of this course is to familiarize students with the principles of the formation and structure of biological macromolecules. In this lesson, in addition to familiarity with the topic of interactions between atoms and molecules, familiarity with the experimental methods of determining the structure of macromolecules is also introduced.

Headlines: Introduction: Biophysical definitions

Chemical and physical links:

o Covalent and ion bond

o Types of inter-molecular forces

o Special water structure

o Hydrogen interactions and their role in molecular self-heal

Physics of bio macromolecules

First structure of proteins

Physical Methods of Determining the structure

Second structure of Proteins

Third structure of proteins

Structure of nucleic acids

The first structure in DNA and RNA.

Second and third structures in DNA and RNA






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Jackson, M.B., Molecular and Cellular Biophysics, Cambridge University Press, 2006 2. Volekenstein, MV, Molecular Biophysics, Academic Press, New York, 1977.

1

1

Course title: Methods of Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is that the students could become familiar with those physical methods which are applicable in separation, and identification of bio-macro-molecules specially proteins and enzymes. In this course in addition to the theoretical base of each method, their limitation and potential for studding the bio-macro-molecules is taught.

Headlines: Chapter I: chromatography

o Thin layer chromatography: The method for preparation of thin layers, sample

preparation and replacement on thin layer, localization and detection of the

ingredients beside the examples for separation of lipids, amino acids and natural

substances

o Column chromatography: Classification based on the phases and mechanism of

action, linear chromatography and their deviations, theory of chromatography (theory

of theoretical plates, theory of speed) column efficiency and the related factors,

resolution, Van Dimter Equation and factors contributing to the widening the peaks,

Scale up of column chromatography

o Liquid chromatography and high performance liquid chromatography: System

components including pumps and solvent gradient, stationary phase, the factors

affecting on the separation yield such as grain and functional group

o Application of liquid chromatography in protein separation:

Ion exchange chromatography, Ion exchange polymers, factors affecting on protein

separation such as ionic strength, pH and pI

Focusing chromatography, chromatography based on hydrophobic interactions,

covalent binding chromatography, affinity chromatography, supercritical fluid

chromatography

o Detectors for LC & HPLC: UV-Vis, electrochemical and Mass

o Gas chromatography: System components, the open column and their functions, the

error caused by injection, narrowing of the bands by split and splitless injections,

solvent trappings, detector for GC (FID, TCD, ECD), advantages and limitations

Chapter II: Electrophoresis for proteins and nucleic acids separation: o The factors affecting on the electrophoresis performance such as electrophoretic

mobility, field, charge, time and temperature

o Operation of electrophoresis: Buffer systems (continuous and batch), band sharpening

(Stacking), the medium for electrophoresis (buffer, paper, starch, polyacrylamide and

agar)

1

o Methods of electrophoresis: PAGE for separation of proteins in natural structure,

SDS-PAGE for determination of molecular weight, gradient gel electrophoresis,

isoelectric focusing, two-dimensional electrophoresis, capillary electrophoresis,

pulsed field gel electrophoresis for separation of nucleic acids, blotting for

transmission of bands

Chapter III: Mass Spectrometry

o Mass as a detector for LC, HPLC, GC and electrophoresis

o Mass techniques: (a) magnetic sector, (b) chemical ionization, (c) time of flight

spectrometry, (d) quadrupole Mass: the principles of separation and detection,

patterns to identify the molecular ions and other molecular components, examples of

applications

Chapter IV: UV-Vis spectroscopy for amino acids and proteins

o Electron excitation in UV-Vis wavelength, the Bear low and its applications and

limitations, types of chromophores in organic compounds, proteins and nucleic acids,

the instrumentation of single-beam, dual-beam and Diode Array

o Determination of protein concentration and studying the factors affecting the UV-Vis

absorption such as solvent, temperature, molecular orientation, pH and ligand

Chapter V: Fluorescence spectroscopy

o The theory of fluorescence: The excitation, relaxation and fluorescence processes,

resonance bands and Stokes shift, quantum yield, relationship between the excitation

and fluorescence spectra, the correlation between fluorescence and structure of

aromatic compounds, the relationship between concentration and fluorescence

intensity,

o Application of fluorescence for studying the protein conformation, comparing the

fluorescence and UV-Vis instrumentation, Intrinsic fluorescence of amino acids and

proteins, examples

Chapter VI: Circular Dichroism (CD) spectroscopy

o Physical basis of circular dichroism, plain and circularly polarized light, optical

activity

o Instrumentation of CD

o Studies of protein structure: CD of the far UV (peptide bond), the near UV (aromatic

amino acids), visible and near UV (cofactor and ligand), the study of the process of

protein folding and unfolding

Chapter VII: Surface Plasmon Resonance

o Physical principle

o Application in the analyzing the following bio-macromolecules interactions:

o Protein-Ligand

o Protein-Protein

o Protein-DNA

o Protein-Membrane

o Antibody-Antigen






1

10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Daniel C. Harris, Quantitative Chemical Analysis, 7th Edition, W H Freeman & Co (2006) -

ISBN 0716761254 2. Douglas A. Skoog, F. James Holler, Stanley R. Crouch, Principles of instrumental analysis -

Thomson Brooks/Cole (2007), 1039 pages - ISBN 0495012017

3. Bengt Nolting, Method in Modern Biophysics, (2003) Springer.

1

Course title: Enzymes Kinetics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To familiar students by kinetics of enzymatic simple and complex reactions; Ligand binding of metal ions and small molecules to an enzyme and their effects on the catalytic activity of the enzyme; Design and study of inhibitors for enzyme

Headlines: Chapter 1: Kinetics of enzymatic simple reactions

o Kinetics of enzymatic reaction by one active site

o Rapid equilibrium and steady state methods

o The initial rate and the Michaelis-Menton equation

o limitations of the Michaelis-Menton equation

o Enzymatic assays

o Graphical methods to determine the enzymatic kinetic constants

o Dixon method to determine the enzymatic kinetic constants

o Michaelis constants for substrates and products and the overall speed of reaction

o Enzymes dimorphism (active and passive)

Chapter 2: Kinetics of enzymatic reactions by several active sites

o Kinetics of enzymatic reactions by several identical and noncooperative active sites

o Kinetics of enzymatic reactions by several identical and cooperative active sites: Hill

equation

o Kinetics of enzymatic reactions with two substrates (Random and ordered

mechanism)

o Kinetics of enzymatic reactions with two substrates (Ping pong mechanism)

Chapter 3: Kinetics reactions of enzyme inhibition

o Reversible and irreversible inhibitors

o Partial and complete inhibitors

o Competitive, noncompetitive, uncompetitive and mixed type inhibitors

o The General Theory of inhibitory

o The degree of inhibition and activity of an enzyme

o Substrate and product inhibition of the enzyme

o competition between two different inhibitor and substrate

o Enzyme inhibition by different binding sites

o Application of isothermal titration calorimetry in studies of enzyme inhibition

Chapter 4: Kinetics of enzyme reactions by activator

o Essential and nonessential activators for an enzyme

o Substrate activators

1

o Competition of activation by inhibitor in enzymatic reactions

o The General Theory of enzyme inhibition and activation

Chapter 5: Effects of temperature and pH on kinetics of enzymatic reactions

o The effect of temperature on the enzyme activity

o The activation energy and Arrhenius equation.

o Effects of buffer and acidity (pH) environment on the enzyme activity

o Kinetics of inactivation of the enzyme by affected of pH

o Logarithmic plots of Dixon - Web

o The effect of pH on the acid and base groups effective on the enzyme activity

o inhibition of the enzymatic reaction by changing the pH






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Enzyme Kinetics, I. H. Segel, John Wiley & Sons, New York, 1993.

2. Enzyme Kinetics: Principles and Methods, H. Bisswanger (Translated by L. Bubenheim),

Wiley, Weinheim: Germany, 2002.

3. Enzyme Kinetics, V. Leskovac, Plenum Pub., New York, 2003.

4. Enzymes & Their Inhibitory: Drug Development, H. J. Smith and C. Simons, CRC Press,

Boca Raton, 2005.

5. Enzyme Kinetics, Ali Akbar Saboury and Ali Akbar Moosavi-Movahedi, University of

Tehran Press, 2006 (Persian Book)

6. Articles published during recent 10 years in the subject of enzyme kinetics

1

Course title: Cellular Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: In this course, based on the physics of the membrane, cytoplasm and organelles constituent molecules and according to the laws of electricity, magnetism, and mechanics, temporal and spatial forces and fields that define the structure and function of the cells are discussed. Further to the intrinsic fields and forces, their possible susceptibility to the extrinsic fields is elaborated and possible consequent effects on the intracellular traffic, dynamics, motility, migration and living status of the cells are evaluated. Understanding the physics of the cells at atomic and molecular levels, students will be able to tailor novel monitoring and manipulative means for pharmaceutical, environmental as well as clinical diagnostic and treatment purposes.

Headlines: Water and biological buffers

o Structures and dynamics of water molecules

o Polarity, dielectrics, spatial and temporal charge distributions

o Viscosity, density, molecular phases, Kosmotrope and Chaotropes

o Thermodynamics, energy transfer and heat capacity

o Conductivity, transmittance, compressibility, electron hopping, electron wire

o Hydration

Lipids

o Hydrophilicity and hydrophobicity

o Structures and dynamics

o Distributions in different part of membranes and cells

o Micelles, CMC, surfactants, Hysteresis, Kraft point

o Conductivity, turbidity, surface tension

o Heat, pressure, water ratio and ionic strength effects

o Phases (L, H, Q), polymorphisms

Biological and artificial lipid membranes o Structure and dynamics

o Lipid and protein distributions, rafts, micro-domains

o Lateral, rotational, translational diffusion, flip flop

o Fluidity, thickness, order, packing

o Protein translocation, folding, protein-lipid interaction,

Interfaces, means of diffusion and transportation

o Diffusion and electro-transference and permeation

o Osmosis, electro-osmosis, hydrostatic permeation

1

o Ion channels, carriers, pumps, pores

o Selectivity, specificity, flux rate

Bio-electric and biomechanics of lipid membranes

o Capacitance, conductance, dielectric, surface charge density, breakage voltage

o Potential layers (Stern, Helmholtz, Deby-Huckle)

o Membrane potentials (Donan, Nernst, Zeta, Goldman-Hodgkin-Katz)

o Effects of electric, magnetic, electromagnetic and ultrasonic fields

Theoretical and practical techniques

o Artificial planar bilayer, supported bilayer, liposomes,

o Liposome Swelling Assay (LSA), Langmuir, Electroporation

o Fluorescent Recovery after Photobleaching (FRAP)

o AFM, STM, ssNMR,

o Patch clamp, Voltage clamp, Pat, Electophysilogic data acquisition

o MatLab, MD, HOLE, CHARMM, Hydropathy, RasMol, Protein Explorer

Applications of the discussed subjects

o Drug and gene delivery (Packaging, smart and targeted delivery and release)

o Tissue engineering and cell membrane fusion, repair (Wound healing, SCI, …)

o Complimentary medicine (Biophysical application of Laser, electric, magnetic,

electromagnetic, IR and plasma for pain relief, drug delivery, surgery, and monitoring

of targeted cell and organ)

o Immunotherapy (Allergy and Ab-Ag interactions, kits, monitoring, treatments)

o Biosensors design and fabrication (Based on membrane and reconstituted proteins)






60% ______ Written Test: 40% __ _____

Practical: -

References: 1. Hoppe W. (1983) Biophysics 2. Weiss T.F. (1996) Cellular Biophysics: Vol I" MIT Press 3. Raicu, V. and Popescu, A. (2008) Integrated Molecular and Cellular Biophysics, Springer

Science 4. Merighi, A. and Carmignoto, G. (2002) Cellular and Molecular Methods in Neuroscience

Research, Springer-Verlag New York, 5. Meyer, B. Jackson (2006) Molecular and Cellular Biophysics, Cambridge University Press 6. Nelson, P. (2006) Biological Physics 7. Philips, R. (2009) Physical Biology of the cell

Course title: Biosensors Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional

1

Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is that the students become familiar with the fundamentals of chemical sensing in living organisms and the methods for mimicking them in such a way that leads to the construction of bio-sensors. Learning the variety of physical transducers to convert biological function of receptor to electrical signals and studying the techniques for developing the biosensors are of the other objectives of this course

Headlines: Chapter I: 1. Definition, principal and the classifications of biosensors, 2. Signaling in

living organisms, 3. Designing the mimetic biosensors

Chapter II: Applications of biosensors in various fields including medical diagnosis,

industrial sample analysis, automation of industrial processes, environmental control and

military purposes

Chapter III: Examples of biosensors: Biosensor for detection of Blood glucose, Biosensor

for detection of Warfare agents, Biosensors for detection of viruses, Biosensors for on

line applications

Chapter IV: Biological receptors: 1. enzymes, antibodies, nucleic acids and receptors, 2.

plant or animal tissues, micro-organisms, cell components (mitochondria)

Chapter V: Immobilization of biological components (techniques of making biosensors):

1. physical methods: adsorption, microencapsulation, entrapment, 2. Chemical methods:

crosslinking and covalent binding, 3. Different supports for protein immobilizations, 4.

The methods for surface modifications, 5. Nanoparticles and nanocomposites as supports

for protein immobilizations

Chapter VI: Physical transducers: 1. Electrochemical methods: potentiometry,

voltammetry, conductometry, and field effect transistors, 2. Optical methods:

spectroscopic approaches, fiber optic biosensors, and surface plasmon resonance (SPR),

3. Piezoelectric transducers including EQCM, QCM, SAW and BAW, 4. Thermal

biosensors

Chapter VII: Factors affecting on the performance of biosensors: Selectivity, linear range,

detection limit, calibration curve, reproducibility, repeatability, response time and life

time, operational and storage stability






10% 30% Written Test: 60% __ _____

Practical: -

References:

1

1. Brian R. Eggins, Biosensors: an Introduction, Springer, 1996

2. J. Cooper, T. Cass, Biosensors, Oxford University Press, 2004.

3. D. M. Fraser, Biosensors in the Body, John Wiley & Sons 1997

1

Course title: Mathematical Models in Biological Issues Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: This lesson focuses on mathematical modeling of biological processes based on population growth and dynamics models.

Headlines: Syllabus: Introduction to mathematical methods

o Ordinary and partial differential equations

o Linear algebra

o Game theory

Evolutionary dynamics: deterministic methods

o Growth dynamics

o Introduction to evolution

o Evolutionary dynamics

o Evolutionary games

Evolutionary dynamics: Stochastic models

o Moran process

o Agent Based Modeling

o Cellular Automata

Dynamical models for cancer

o Tumor growth models

o Angiogenesis

o Metastasis

Dynamical models for infection






20% 30% Written Test: 50% __ _____

Practical: -

References: 1. Evolutionary Dynamics, Nowak, President and Fellows of Harvard College (2006)

1

2. Dynamics of Cancer, Wodarz and Komarova, World Scientific (2014)

1

Course title: Methods and Research Logic Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: This course aims to familiarize students with research methods and methodology, define research projects, rights and values involved in group activities, intellectual property, methods of searching for articles and scientific data and scientific publications, collections and stories writing research papers at international level, is taught.

Headlines: Methods and research methodology

Defined principles, writing proposal

Intellectual property

Principles of group activities

Introduce scientific and literary ethics violations and plagiarism

Principles of data collection and compilation thesis

Methods of compiling progress reports

Principles of participation in scientific conferences and writing reports and poster

The rules and regulation of the research paper for journal submission, thesis, scholarly

book chapters, articles and abstracts extension or the full proceeding for presentation at

scientific conferences

Writing scientific articles for international publications

Software resources and scientific texts

Introducing the prestigious international issues and evaluation criteria and indexing

journals

Familiarity with Digital Library of University of Tehran

Introduction to the position of papers citation and documentation and new approaches in

the analysis of them

Basic understanding of Web of Science citation and other websites and its application in

research and scientific publications Evaluation method:

1

Continuous evaluation (To be specified in percentage)

midterm (To be specified in percentage)

Final Test (To be specified in percentage)

Project (To be specified in percentage)

50% ______ Written Test: 50% __ _____

Practical: -

References: 1. Martyn Shuttleworth "How to Write a Research Paper", Experiment-Resources Publisher,

2010

2. A.A.Saboury, A.A. Moosavi-Movahedi and et al. “Handbook: A Practical Guide to

International Journal” University of Tehran Press (2008)

1

Course title: Biothermodynamics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: The aim of this study was to determine protein stability, protein thermal denaturation via various methods such Differential Scanning Calorimetry, Isothermal Titration Calorimetry, thermal spectroscopy

Headlines: Cold and thermal protein denaturation

Theoretical and experimental thermodynamic study on Cold and thermal protein

denaturation

The analysis of protein thermal profiles

Comparative states of intermediates for protein thermal denaturation

Comparative study on thermodynamic and non-thermodynamic parameters for protein

structure

Protein Calorimetry: Isothermal Titration Calorimetry and Differential Scanning

Calorimetry study for protein –ligand interaction, protein structure deconvolution,

measurement of energetic domains for protein, study the reversibility and irreversibility

states for protein denaturation

Protein stability measurements by different methods






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. J.T. Edsall and H. Gutfrund, "Biothermodynamics", John Wiley, New York, 1983. 2. J.E. Ladbury and M.L. Doyle, "Biocalorimetry", John Wiley, New York, 2004. 3. M.N. Jones, "Biochemical Thermodynamics", Elsevier, 1984. 4. J. Chamani and A.A. Moosavi-Movahedi “Biothermodynamics “University of Tehran

Press, 2009

1

Course title: Physical Chemistry of Proteins Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is the understanding of the pathways and intermediates of protein folding/unfolding and relation with protein structure and function is taught

Headlines: Protein folding and its stages

The role of intermediates in protein folding

The role of molten globule in protein folding

The role of disulfide bond in protein folding

The role of temperature in protein folding

The role of ionic strength, pH, solvent, pressure, temperature, salts in protein folding The role of conformational states in protein folding

The role of domain assembly in protein folding

The kinetic pathways in protein folding

Forecast and prediction in protein folding






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. R.H. Pain, "Mechanisms of protein folding", IRL Press, Oxford, 1994.

2. B.A. Shirley, "Protein stability and folding", Humana Press, New Jersey, 1995

3. A.A. Moosavi–Movahedi and et al. “ Protein Structure”, University of Tehran Press, In

Persian, 2004

1

Course title: Topics in Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The purpose of this course is to review the latest biophysical papers and achievements. In this class, students will discuss their research topics with other students.

Headlines: Course categories each time the lesson is presented, the resources and articles and the

various topics that have been considered in the past years will be examined. Presenting

the results of the students' work is to provide written reports and oral presentations.






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Protein Stability and Folding: Theory and Practice (Methods in Molecular Biology) by

Bret A. Shirley, 1995, Springer

http://www.amazon.com/Bret-A.-Shirley/e/B00JCV80SC/ref=dp_byline_cont_book_1

1

Course title: Biospectroscopy Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Teaching Different Spectrometry Techniques and Its Applications in Biological Sciences

Headlines: Chapter 1: Principles of Spectroscopy

o Quantum view of the interaction between light and matter, Atomic and molecular

spectroscopy, Different parts of spectroscopy devices, using computer in spectroscopy

Chapter 2: UV-Visible Spectroscopy

o Device principles, Principles of quantitative and qualitative analysis, Quantitative and

qualitative assays in biomacromolecules, Biomacromolecule ligand interaction and

ligand binding in different systems, Protein stability measurements, Enzyme assays

Chapter 3: Infrared and Raman Spectroscopy

o Device principles, principles of quantitative analysis and identification of functional

groups, Determine of secondary structure of proteins, Structural studies of biological

macromolecules by Raman and Infrared spectroscopies

Chapter 4: Mass Spectrometry

o Device principles, principles of fragmentation of molecules and identify

quantitatively, Roles of isotopes in identifying qualitatively, Different biological

applications

Chapter 5: Circular Dichroism Spectroscopy

o Device principles, Study of proteins secondary structures, Study of proteins tertiary

structure, Application in structural studies of nucleic acids

Chapter 6: Fluorescence Spectroscopy

o Device Principles, intrinsic and extrensic fluorescence, Protein stability and tertiary

structure, Protein folding and unfolding, Thermodynamic studies of ligand binding to

biomacromolecules, other biological applications

Chapter 7: Nuclear Magnetic Resonance (NMR) Spectroscopy

o Device Principles, Nuclear Magnetic Resonance of different elements, Chemical shift

and analysis qualitatively, Principles of interpretation of spectra to identify materials,

Study of protein structure, Ligand- biomacromolecule interaction, Different biological

applications

Evaluation method:

1

Continuous evaluation (To be specified in percentage)

midterm (To be specified in percentage)

Final Test (To be specified in percentage)

Project (To be specified in percentage)

Short student lecture ______ Written Test: Persistent questioning

Practical: -

References: 1. Biological Applications of Infrared Spectroscopy, B. H. Stuart, John Wiley, 1997.

2. Spectroscopy for the Biological Sciences, Gordon G. Hammes, Wiley, New York, 2005

3. Principles and Applications Fluorescence Spectroscopy, J. Albani (Translated by A.A.

Saboury and M. Saeidifar), University of Tehran Press, 2013

4. Different published articles during last 10 years on the biospectroscopy subjects.

1

Course title: Ligand Protein Interaction Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: Education of various ligand transplantation theories and its empirical methods

Headlines: Chapter One: The linkage of the ligand to the biomacromolecule

o Ligand transplantation to a transplantation site, ligand transplantation to a linkage site,

Scachrard, Clouds and Hill equations, and their relationship, ligand transplantation to

multiple linkage sites, a variety of equilibrium constants in the study of multiple

equilibria, competition in the conjugation of two simultaneous ligands

Chapter Two: Abnormal Biomacromolecule

o Abnormalities with heat and cold, abnormalities with surfactants, abnormalities with

chemicals, abnormalities under environmental factors

Chapter Three: Determination of Biomacromolecule Stability

o Definition of stability, thermodynamic stability and kinetic stability, determination of

thermodynamic stability, determination of kinetic stability, concept and determination

of thermal stability of biomacromolecules, differential calorimetry scanning, use of

rotary exponential doping in determining the structure and stability of

biomacromolecules

Chapter Four: Determination of ligand transplantation parameters

o Equilibrium Dialysis, Spectrophotometry, Homogeneous Titration Thermometer,

Thermodynamic Parameters of Transplantation






Continuous questions ______ Written Test: * Provide short student presentations

Practical: -

References: 1. Protein-Ligand Interactions, First Edition, Holger Gohlke, Wiley, New York, 2012. 2. Protein–Ligand Interactions, G. Ulrich Nienhaus, Humana Press, New Jersey, 2005.

1

Course title: Pharmaceutical Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Considering the extensive development of nanotechnology, in this course different aspects such as identification of structure, migration and interactions between drug-polymeric carrier, drug-membrane, drug-cell, and drug-serum molecule complexes, and corresponding half-life in the physiological condition of the cell and body as well as shelf time will be discussed. Accordingly, tracing of the drug in body and tissue as well as different parts of target cells will be evaluated based on the physical and electronic remote sensing to tailor efficient proscription with minimum dose, fastest effects, precise targeting and minimal side effects. The approaches presented at atomic and molecular levels, together with novel practical considerations, will provide students with some basis to design, produce, monitor, track and have more efficient drugs.

Headlines: Biophysics of water (Structures, dynamics, dielectrics)

Membrane biophysics (structure, dynamics, lipid diversity, electrical characteristics)

Cellular biophysics (Bio-electrics, bio-impedance, biomechanics)

Chemico-physical status of biological fluids

Drug carriers (Inorganic, polymeric, metal-based, composites, biological)

Fundamentals and techniques in drug encapsulation and packaging (CMC, Lipid phases,

Order parameter, Packing parameter, Polarity)

Stability, release, half-life, dose, solubility Targeted drugs (destination factors, carrier elements)

Smart drug delivery (Nanoparticle based, controlled rate, concentration release rate)

Practical biophysical techniques in pharmaceutics

o Modern techniques in drug delivery (Electrical, Thermal, ultrasonic, electromagnetic,

IR, UV, Magnetic)

o Modern techniques for drug tracking (MRI, PET, Electrophysiological impedance-

metery, Gama counter, Fluorescent base, Bio-resonance)

o Microfluidic, Lab-on-chip،Cell-on-chip, Organ-on-chip for drug effect analysis

o Confocal Fluorescent Microscope and its application in time-lapse intracellular traffic

monitoring

o Thermodynamic analysis of interactions, structural and dynamics of the drug effects

on nucleic acids, soluble and membrane proteins

Theoretical methods

1

o Modeling of drug release, diffusion and interaction

o Simulation of the drug targets on the target molecules (Auto dock)

Application of discussed subjects

o Design and production of drug packages with efficient targeting and release rate

o Proposing novel optimum methods of drug tracking in body and cell

o Tailoring novel and more efficient means of drug administration






60% ______ Written Test: 40% __ _____

Practical: -

References: 1. Seetharama D. Sat yanarayanajois. Drug Design and Discovery Methods and Protocols,

Springer Science+Business Media, LLC, 2011.

2. Li, X., Jasti, BR. Design of Controlled Release Drug Delivery Systems, The McGraw-

Hill Companies, Inc., 2006.

3. W. Mark Saltzman, DRU G DELIVERY, Engineering Principles for Drug Therapy,

Oxford University Press, Inc., 2001.

4. AJAY K.BANGA, Electrically Assisted Transdermal and Topical Drug Delivery, Taylor

& Francis e-Library, 2003.

5. Betageri, GV, Jenkins, SA, Parson, DL. Liposome Drug Delivery Systems, Tectonic

publishing Company, 2003.

6. Hans Schreier, Drug Targeting Technology, Physical, Chemical and Biological Methods,

Marcel Dekker, Inc., 2001.

7. Beard, DA, Qian, H, CHEMICAL BIOPHYSICS, Quantitative Analysis of Cellular

Systems Cambridge University Press, 2008

8. Oren M., Becker, Alexander, D. MacKerell, Jr. Benoi, Roux, Masakatsu Watanabe.

Computational Biochemistry and Biophysics, Marcel Dekker, Inc. UK, 2001.

1

Course title: Bio-electromagnetics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The optimum function of biological systems is achieved by unique structural and dynamics of their constituent molecules in the polar and dynamic water medium and in the presence of charged and radical elements. This situation causes intrinsic electric, magnetic and electromagnetic fields in the biological system in first place and makes them susceptible to the extrinsic ones in return. Exposure of the biological molecules to the fields, changes their atomic orientation, conformation, binding constant of ligands, channel conductivity, enzyme activity and ultimate function of tissue, organ, and whole body. In this course, the bioelectric and bioelectronics nature of biological molecules will be discussed and the consequent effects of the intrinsic and extrinsic fields on the structure and function of the host system at atomic, molecular, cellular and tissue levels will be elaborated.

Headlines: Biophysics of water (Structures, dynamics, dielectrics, EM absorption)

Life definition based on stochastic and deterministic events at molecular and atomic

levels

Sources and characteristics of electric, magnetic and electromagnetic fields

Structure and dynamics of biological macromolecules and intracellular polyelectrolytes

Dielectrics and charge distribution in living cell and constituent organelles and

consequent electric, magnetic and electromagnetic fields

Spatial and temporal electromagnetic polarization in cells at different stages of cell cycle

Bio-resonance of molecules, cells and tissues, basics and susceptibilities

Quantum biology and means of non-thermal field effects at low KbT

Bone piezoelectric at atomic, molecular and cellular levels

Magneto-proteins, and magneto-susceptibility of bio-macromolecules

Molecular oscillators and source of electric and electromagnetic fields in the cells

Effects of extrinsic fields on the living status, division, orientation, formation of podia

and migration of cells

Practical techniques

o Identification of the interaction between external and intracellular sources of electric,

magnetic and electromagnetic fields (real time analysis of morphology,

differentiation, orientation and migration)

o Real time recording of the effects of the extrinsic magnetic and electromagnetic fields

on the activity of single ion channel (Patch clamp, Voltage clamp, Fluorescent

Recovery After Photobleaching)

1

Theoretical approaches

o Simulation of electromagnetic bio-fields caused by the ion channel activities

o Computational methods in determination of the electric and magnetic fields caused by

ionic motion and diffusions

Application of the discussed subjects

o Identification of environmental effects of the fields caused by telecommunication, cell

phones, satellites and electric and electronic systems

o Development of diagnostics and therapeutics application of bio-resonance, energy

medicine, AURA, Telepathy and so on.






60% ______ Written Test: 40% __ _____

Practical: -

References: 1. Cynthia Furse, Douglas A. Christensen, Carl H. Durney, Basic Introduction to

Bioelectromagnetics, CRC Press, Taylor & Francis Group LLC 2009.

2. Thomas F. Valone, BIOELECTROMAGNETIC HEALING, A RATIONALE FOR ITS

USE A nonprofit 501(c) 3 organization Washington DC USA 2007.

3. Paul J. Rosch, Marko S. Markov, Bioelectromagnetic Medicine, Taylor & Francis e-

Library, 2005.

4. An Introduction to Environmental Biophysics. Springer Verlag, N.Y., 1998.

5. Ben Greenebaum, Frank S. Barnes, Bioengineering and Biophysical Aspects of

Electromagnetic Fields 2006


Computational Biochemistry and Biophysics, Marcel Dekker, Inc., UK, 2001.

7. Edward L. Alpen, Radiation Biophysics, Second Edition, ACADEMIC PRESS, 1998.

1

Course title: Biophysics and Tissue Engineering Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Cell is a complex system which continuously interacts with the physico-chemical conditions of its media that should be considered in tissue engineering based on the structural, electrical, and functional means of cells at atomic, molecular and cellular levels. In this course, following discussion on the electrical and mechanical characteristics of cells and neighboring medium and scaffolds, roles of physico-chemical condition of the electrolyte substrate on the attraction of migrating cells and their settlement to form a graft is elaborated. Learning this aspects not only provides students with the evaluation of cell-media interactions at molecular level needed for cell culture, tissue engineering and graft formation, familiarizes them with the possibility of real-time monitoring of cell activities inside and outside of host body, and helps them to define noninvasive biophysical approaches for clinical treatment purposes.

Headlines: Biophysics of water

Membrane Biophysics (Bioelectric, mechanics, permeability, surface tension)

Biophysics of biological cells and tissues

Physical chemistry of the biological electrolytes

Cell and tissue culture (slice culture, whole organ culture)

Polymeric scaffolds, fabrication, mechanical and electrostatic interaction

(Electrospinning, Hydrogel, Self-casting polymer)

Bio-composites, structure, stability, porosity, mechanical strength, surface change

Biophysical approaches to create grafts inside host body, biocompatibility,

biodegradability of polymer scaffolds, bio-metals, bio-ceramics

Practical methods

o Microscopic monitoring and real time identification of density, migration growth and

confluency

o Electronic and impedance based indirect means of monitoring and documentation of

cell activities inside and outside of the host body

o Microfluidic systems, natural and artificial ones, in tissue engineering

o Application and tailoring of Lab-on–Chip, Cell-on-Chip systems in tissue engineering

o Precise and ultrasensitive online bioreactors, as a pilots for cell culture and tissue

factories

o Scan and 3D print of scaffolds and cells for creation of cellular grafts

1

Theoretical approaches

o Modeling and calculation methods of tissue and organs

o Application of the biological cells data banks in tissue engineering


o Design, approaches and construction of bioreactors and real time monitoring for mass

tissue production purposes

o Engineering and monitoring of new tissues in the host bodies






60% 10% Written Test: 30% __ _____

Practical: -

References: 1. Park, JB, Bronzino, JD. Biomaterials PRINCIPLES and APPLICATIONS, CRC Press

LLC, 2003.

2. Bin He. Modeling and Imaging of Bioelectrical Activity, Principles and Applications.

Kluwer Academic/Plenum Publishers, New York, USA 2004.

3. Artmann, GM, Chien, S. Bioengineering in Cell and Tissue Research, Springer-Verlag

Berlin Heidelberg, 2008.

4. Beard, DA, Qian, H, CHEMICAL BIOPHYSICS, Quantitative Analysis of Cellular

Systems Cambridge University Press, 2008

5. Robin Leatherbarrow, R H TemplerCampbell G.S., J.M. Norman. Biophysical Chemistry

a. Biophysical Chemistry Group,

6. Chaudhuri, J., Al-Rubaei, M. BIOREACTORS FOR TISSUE ENGINEERING, Springer

2005.

7. Ma, PX., Eleesseff, J. Scaffolding in Tissue Engineering, Taylor & Francis Group, LLC.

2006.

1

Course title: Environmental Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Significant industrial progress in the living environment of human being and increasing presence of physical, electrical, electromagnetics, sonic, and radiation polluting sources has endangered susceptible molecules and systems in human and other living systems. In this course considering physico-chemical, electrochemical and electronic nature of the polluting sources, possible targets and incurred changes in the structure and function of target molecules, cells and eventually tissues and organs that have already been manifested by genetic, metabolic and behavior deviation will be discussed. The involved mechanism of most of these events has still remained unknown and as no specific expertise has yet defined to address the fact at molecular and cellular levels, biophysical approaches can play critical roles. Having the advanced high-tech facilities and approaches together with novel molecular atomic and nano techniques, has practically made it possible to reveal the involved mechanisms through practical and theoretical approaches.

Headlines: Biophysics of living systems activity in the natural condition

Biophysics of Earth gravity and magnetic field

Earthquake biophysics and the way some living creatures detect it

Magnetic navigation of birds and distorting effects

Biophysics of ionized atmosphere and charged clouds

Sound biophysics, effects of sound pollution and plant based control and challenges

Biophysics of radioactive radiations (possibility of safe living at high doses, Ramsar)

Biophysics of non-ionizing , electric, magnetic and electromagnetic radiations

Biophysics of traveling dusts (settlement, sedimentation and filtration approaches)

Biophysics of air polluting hydrocarbon, Pb, and other facile fuel burned side products

Biophysics of magnetic water, formation, stability and effects

Biophysics of greenhouse effect and increased temperature

Practical methods

o Molecular, cellular, tissue and whole body analysis of the effects of the gravity,

electric, magnetic and electromagnetic fields

o Monitoring, recording and analysis means of global monitoring and data collection

(satellites)

o Recording and analysis of the living patterns at different geographical locations and

forming data banks

Theoretical methods

1

o Modeling of electrical and magnetic fields and analysis of their effects on the

conformation and dynamics of targeted molecule

o Bioinformatics and computational biophysics of correlations between living patterns

and status of their correlated area


o Defining the standard safety and environmental conditions for living creatures across

globe

o Identification of the means to tackle with the side effects where the situation is

inevitable






60% ______ Written Test: 40% __ _____

Practical: -

References: 1. Campbell G.S., J.M. Norman. An Introduction to Environmental Biophysics. Springer

Verlag, N.Y., 1998

2. Cancer and the Environment, Research, and Medicine. Roundtable on Environment

Health Sciences, NATIONAL ACADEMY PRESS Washington, D.C. 2002

3. Friedl, A.A. Rühm, W. Radiation and Environmental Biophysics


Computational Biochemistry and Biophysics, Marcel Dekker, Inc. , UK, 2001

5. Waigh T. Applied Biophysics - Molecular Approach for Physical Scientists, John Wiley

& Sons Ltd, TheWest Sussex PO19 8SQ, England, 2007

6. Edward L. Alpen, Radiation Biophysics, Second Edition, ACADEMIC PRESS, 1998.

7. Roland Glaser, Biophysics, Gustav Fischer Verlag, Jena Germany 1999

1

Course title: Topics in radiation Biology Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: The purpose of this course is to review the latest scientific papers and achievements in the field of Biophysics of Beams and Biology of Radiation. In this class, students will discuss their research topics with other students.

Headlines: Introduction

An overview of the biophysics of the beams

Radiation chemistry

Survival Curves: Models and Experiences

Repair of radiation damage

Changes in beam effects

Biodegradation of normal body tissues

Biodegradable tumors

Immediate effects of the beams

Long-term effects of beams

Hyperthermia






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Radiobiology for the Radiologist, Hall, E.J. 5th ed. LIPPINCOTT WILLIAMS &

WILKINS, Philadelphia, 2000.

2. Radiation Biophysics, Alpen, E.L., 2nd ed. Academic Press, Boston 1998.

3. Perez and Brady’s Principles and practice of Radiation Oncology, 5th ed. Halperin, E.C.,

Perez, C.A., and Brady, L.W., Lippincott Williams & Wilkins, New York 2008.

1

Course title: Computational Biophysics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The purpose of this course is to familiarize students with theoretical foundations and common approaches to computational biophysics. In this lesson, students will be introduced to the use of static and dynamic mechanics and other simulation and modeling techniques with the broad application of these methods in modeling biological structures.

Headlines: Introduction to computational biophysics

Atomic models and force fields

Monte Carlo

Molecular Dynamics

Long range force fields

Implicit solvent models for molecular simulations

Normal state calculations

Free energy calculations

Quantum Mechanics/ Molecular Mechanics Methods

Other computational methods






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Becker, CM., Mackerell, Jr. AD, Roux, B., Watanabe, M. Computational Biochemistry

and Biophysics, Marcell Dekker, New York, 2001.

2. Jensen, F. Introduction to computational chemistry. 2ed edition, John Wiley & Sons,

Chichester, 2007.

1

Course title: Topics in the Philosophy of Biology Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The purpose of this course is to study different views on the philosophy of science in general, and in particular the philosophy of life sciences.

Headlines: The course syllabus will be explored every time the lesson is presented, resources and

articles and various topics that are considered in the fields of logic and philosophy of

science, and some philosophical schools and philosophy of biological sciences.

Presenting the results of the students' work is to provide written reports and oral

presentations.






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Ayala, FJ, and Arp, R. eds. contemporary debates in Philosophy of Biology, Wiley-

Blackwell, 2010.

1

Course title: X-Ray scattering from Biological Macromolecule Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: The purpose of this course is to familiarize students with theoretical foundations and the theory of X-ray diffraction from biological macromolecules.

Headlines: Overview of Protein Crystalography

Protein Crystals, Characteristics and Procedures

X-rays and special features necessary for use in diffraction from biological

macromolecules

Problem of diffraction and interference of waves

Collect the diffraction data

From diffraction to electron density

The issue of phase

Preparation and evaluation of molecular models

Other diffraction methods






10% ______ Written Test: 90% __ _____

Practical: -

References: 1. Crystallography Made Crystal Clear, Third Edition: A Guide for Users of

Macromolecular Models. Rhodes, G. Academic Press, NY, 2002.

2. X-Ray Crystallography of Biomacromolecules: A Practical Guide. Messerschmidt, A.

Wiley-VCH, 2007. Weinheim, Germany.

3. Biophysical Chemistry, Part 2: Techniques for the Study of Biological Structure and

Function. Cantor, C.R. and Schimmel. P.R. W. H. Freeman and Company; 1st edition, 1980. San Francisco, USA.

4. Selected papers on the subject.

1

Course title: Bioelectrochemistry of proteins and nucleic acids Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: In this lesson, students will find useful information on how to use these methods in the study of biological molecules, including proteins and nucleic acids, while familiarizing them with the principles and types of electrochemical methods.

Headlines: Introduction to Electrochemical: Electrochemical Tubules, Conductivity in Solutions,

Types of Electrodes.

Electrochemical methods: Potentiometry, voltammetry, impedance, capacitance, and field

effect transistors.

Correction of electrode surfaces for direct electrochemical studies of proteins and nucleic

acids using a variety of functional groups and a range of nanoparticles.

Electrochemistry of free and stabilized proteins.

Electrochemistry NAD (P) + / NAD (P) H

Electron Transfer in Proteins: Direct Transfer and Transmission via Intermediate

Materials.

Kinetics of electron transfer in redox proteins.

Study of nucleic acid by electrochemical methods.

Single cell electrochemistry, Membrane electrochemistry.

Scanning Electrochemical Microscopy.

Bioelectronics

Commercialization of bio-electrochemical instruments based on potentiometric,

voltammetric, capacitive, impedance methods and field effect transistors.






10% 30% Written Test: 60% __ _____

Practical: -

References:

1

1. George S. Wilson Bioelectrochemistry, Volume 9; in Allen J. Bard and Martin

Stratmann, (Editor) Encyclopedia of Electrochemistry, Wiley-VCH, Weinheim, 2002.

2. Itamar Wilner and Eugenii Katz, Bioelectronics from theory to applications, Wiley-VCH,

Weinheim, 2005.

http://eu.wiley.com/WileyCDA/Section/id-302479.html?query=George+S.+Wilson

http://eu.wiley.com/WileyCDA/Section/id-302479.html?query=Allen+J.+Bard

http://eu.wiley.com/WileyCDA/Section/id-302479.html?query=Martin+Stratmann

http://eu.wiley.com/WileyCDA/Section/id-302479.html?query=Martin+Stratmann

1

Course title: Biophysics of ion channels Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Ion channels with known atomic structure provide the basis to study the molecular dynamics and activity of single biological nano-molecules in real time in the presence and absence of different physical and chemical effectors. The aim of this course is to familiarize students with the practical and theoretical aspects of ion channels, their structure, dynamics and functions as controllable influx and efflux molecular gates that control the traffic of different ions and molecules across the membrane. The provided information can transfer the capability of channel application in the design, fabrication of biosensors and molecular switches, control and challenge with pathogenic viruses and bacteria as well as treatment of diseases caused by the malfunction of channels in a non-chemical manner.

Headlines: Biological membranes (Composition, structure, thickness, fluidity, surface charge)

Membrane proteins (channels, receptors, carriers, pumps)

Ion channels (structure, distribution)

Identification, extraction, purification and structure definition of ion channels

Mechanisms of gating in channels (ligand, pH, potential difference, pressure)

Role of channels as oscillators in the establishment of direct and alternative fields

Ion channels and biological electrical resonance (bioresonance)

Application of channels as controllable nano-valves (electrical, chemicals, mechanicals)

Means of mounting and reconstitution of ion channels on supported bilayers for biosensor

activity

Application of ion channels in next generation nucleotide sequencing

Ion channels as unique targets to overcome failure caused in certain diseases

Ion channels as a means for targeted drug delivery and tackle with pathogenic

microorganisms

Practical methods

o Patch clamp, Voltage clamp, AFM, STM, FRAP, Single-Unit, LSA

o Application of (Macro Electro-Mechanical Systems), MEMS, NEMS Theoretical methods

o Simulation and modeling of channel activities based on current traces

o Application of HOLE, CHARMM, AMBER, PAT softwares


o Biophysical targeting and manipulation of channels as substitute for chemical and

pharmaceutical treatments

1

o Application of channels as bio-transistors to identify the positive and negative

biological effects of electric, magnetics and electromagnetic fields at molecular levels

in real time






60% ______ Written Test: 40% __ _____

Practical: -

References: 1. Aidley, D.J. and Stanfield, P.R. (1996) Ion Channels, Molecules in Action

2. Tien, T.H. (2000) Membrane Biophysics

3. Hoppe W. (1983) Biophysics

4. Molleman A. (2003) Patch clamping (An Int. to Patch Clamp Electrophysiology)

5. Molnar P. and Hichman, JJ (2007) Patch clamp methods and protocols

6. Luchtag HR (2008) Voltage-sensitive ion channels (Biophysics of Molecular Excitability)

1

Course title: Computational Genomics Number of units: 2 The number of hours: 48 Unit type: 1 theoretical unit and 1 practical unit Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: This course is a practical aspect of topics in mandatory courses and along that practical projects will be accomplished in various bioinformatics subjects. The aim is to prepare students for doing research about their thesis.

Headlines: Principles, definitions, and ideas in Genome-wide projects

Principles of appropriate data collecting and handling in genome-wide projects

Principles of genomic data refinement

Genomic data analysis and classification and creating appropriate data for computations

Principles of genome-wide computations

Principles of genome-wide data analysis and interpretation

Weekly seminars (every student gives two presentations per term)

Project






- ______ Written Test: - 80%

Practical: 20%

References: 1. Cristianini N., Hahn M.W. Introduction to Computational Genomics: A Case Studies

Approach, Cambridge University Press, London 2007.

2. Introduction to Genomics, Arthur M. Lesk, 2012, Oxford University Press; UK

3. Computational Genomics, Srinivas Aluru, 2016, 2nd edition, Chapman & Hall, USA

1

Course title: Structural Bioinformatics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: To make the students familiar with analysis and prediction of biomolecular structures and primary structural databases.

Headlines: Historical introduction to development of methods and problems in structural

bioinformatics

Potential energy surface, energy minimization methods or molecular structure

optimization

Elements of proteins and nucleic acids structure

Introduction to experimental methods for biomolecular structure determination.

Review on protein folding problem and models for describing this phenomenon.

Main file formats for representation, record, and storage of biomolecular structures e.g.

PDB, mmCIF, XML

Important databases for record and storage of protein and nucleic acid structure

information.

Methods and algorithms in biomolecular structure analysis e.g. structure comparison,

structural similarity, superposition of structures, and classification of structures.

Methods in Proteins and nucleic acids secondary structure determination and prediction.

Methods of protein structural domain identification and prediction.

Protein-protein and protein-ligand interaction analysis and prediction and their networks.

Methods of Protein structure prediction e.g. homology modeling, fold recognition and Ab

initio methods

Knowledge-based and physics-based approaches in scoring function and force fields

design.

Evaluation Method Continuous evaluation




(To be specified in percentage) 40% 30% Written Test: 30% 0%

Practical: -

References: 1. Structural Bioinformatics, Jenny Gu, Philip E. Bourne, John Wiley & Sons, 2011.

1

2. Computational Methods for Protein Structure Prediction and Modeling, Ying Xu, Dong

Xu, Jie Liang, John Wooley, Springer, 2007.

3. Protein Structure Prediction, Daisuke Kihara, Springer (Humana Press), 2014.

1

Course title: Computational Drug Design Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: An introduction to drug design by computational methods.

Headlines: Definition of drug and its receptor

History and discovery of novel drugs

Drug development process

Main issues in drug discovery process

Drug design process

Ligand-based drug design

Structure-based drug design

Tools and computational techniques (homology modeling, molecular mechanics, protein

folding, docking, pharmacophore models, QSAR, 3D-QSAR, Chemoinformatics)

ADMET

Virtual Screening

Fragment-based drug design






20% 20% Written Test: 30% 30%

Practical: -

References: 1. Young D.C. Computational Drug Design: A Guide for Computational and Medicinal

Chemists. Wiley-Interscience. 2009

2. Bultinck P., Tollenaere J.P., Langenaeker W., Winter H.D. Computational Medicinal

Chemistry for Drug Discovery. CRC. 2003.

3. Zheng, Y., Rational Drug Design Methods and Protocols, Springer. 2012.

4. Tari, L. W. Structure-Based Drug Discovery, Springer. 2012.

1

Course title: Chemoinformatics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To make the students familiar with elements of chemoinformatics and modeling the activity of chemical and biological molecules.

Headlines: Molecular concepts and molecular representation

Chemical compounds and drug databases

Searching chemical and drug structures

Chemical and biological compounds structure optimization and conformational search

Calculation of Physical and chemical descriptors of biological and chemical compounds

Calculation of structure descriptors

Calculation of Quantitative structure and activity relationships

Methods for chemical and biological data analysis

Classification of chemical and biological data

Statistical evaluation of chemoinformatics results

Applications of chemoinformatics study in bioinformatics






Practical: -

References: 1. Gastiger, J. Cheminformatics, WILEY-VCH Verlag GmbH & Co.,Germany, 2003.

2. Leach, A.R., An introduction to cheminformatics, Springer, Netherlands, 2007.

3. Bunin, B. A., Siesel, B., Morales, G. A, Bajorath, J., Chemoinformatics: Theory, practice,

& Products, Springer, Netherlands, 2007.

4. Bajorath, J., Chemoinformatics and Computational Chemical Biology, Springer, London,

2011.

1

Course title: Chemometrics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is to make the students familiar with various methods of chemometrics that are used for processing and extracting information from experimental data.

Headlines: Introduction to chemometrics, its relation to other fields, introducing different branches of

chemometrics

Definitions and concepts e.g. normal distribution, F-Test, t-Test, 𝜒2-test, one and two

way analysis of variance

Linear algebra, vectors, and matrices, different mathematical operations on vectors and

matrices

Newton method, Levenberg-Maquardt method

Multivariate calibration methods(MVC), classical least squares (CLS), inverse least

squares (ILS), multivariate linear regression(MLR), Principal component

regression(PCR), and model Cross-validation.

Working with Excel, including data analysis, regression, correlation

Working with Matlab, including concepts and elementary commands, using various

Matlab toolboxes and performing Chemometrics methods using them, and Matlab

programming.

Methods of modeling chemical data, including hard-modeling methods, soft-modeling

methods, multivariate curve resolution methods(MCR)

Factor analysis (FA), FA steps, target factor analysis(TFA), evolutionary factor

analysis(EFA)

Experimental design methods

Full factor design (Full FD), parameters interaction

Fractional factor design (Fractional FD), resolution of the design

Central composite design(CCD), and response surface methodology (RSM)






Practical: 10%

1

References: 1. Richard G. Brereton. Chemometrics.John Wiley2003

2. Howard Mark, Jerry Workman Jr. Chemometrics in Spectroscopy. Elsevier, 2007

3. James N. Miller, Jane C. Miller. Statistics and Chemometricsfor AnalyticalChemistry,

2010

1

Course title: Machine Learning Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: In this course, the student will be familiarized with various approaches to machine learning and after completing the course has skills for design an efficient strategy to solve problems using existing tools or implement a new one.

Headlines: Course introduction and elementary concepts

Learning theory, supervised learning, unsupervised learning, and semi-supervised

learning

Supervised learning methods and regression

Various parameter estimation methods

Artificial neural networks and deep learning

Evaluating machine learning models

Various methods of feature generation and selection

Various methods of unsupervised learning and their evaluation

Semi-supervised learning methods

Graphical models and Bayesian networks

Ensemble methods






Practical: -

References: 1. Sergios Theodoridis, Konstantinos Koutroumbas, “Pattern Recognition”, 3rd Edition,

Elsevier Academic Press, 2006.

2. Cristopher M. Bishop, “Pattern Recognition and Machine Learning”, Springer, 2006.

3. Richard O. Duda, Peter E. Hart, David G. Stork, “Pattern Classification”, 2nd Edition,

John Wiley & Sons, 2001.

4. Ethem Alpaydin, “Introduction to Machine Learning”, the MIT Press, 2004.

1

Course title: Complex Networks Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: This course surveys mathematical theories of emergence and evolution of networks, especially biological systems. Applying network analysis to deepen the understanding of the natural phenomenon is one of the primary objectives. Studies on existing real-world networks (biological, social, and computer), node interaction surveys, static and dynamic models of network emergence will be covered. In this course, the student shall further learn to model complex systems and design algorithms for network data analysis.

Headlines: Course Introduction and basic concepts

Complex systems, hierarchical structures, percolation theory, and random walk on

networks

Introducing biological intracellular networks and their properties

Various models of dynamic complex networks, introducing phase transition concept

Random networks, watts-Strogatz model, small-world networks

Local-world evolving networks

Network controllability and visibility






Practical: -

References: 1. Networks: An Introduction, M. E. J. Newman, Oxford University Press, Oxford (2010)

2. Reuven Cohen and Shlomo Havlin, Complex Networks: Structure, Robustness and

Function, Cambridge University Press, Cambridge (2010). Quite a short book, but it

covers most of the topics of the course, at least to some extent, and some others that are

not in the book by Newman.

3. S.N. Dorogovtsev, Lectures on Complex Networks, Oxford University Press, Oxford

(2010).

4. R. K. Ahuja, T. L. Magnanti, and J. B. Orlin, Network Flows: Theory, Algorithms, and

Applications, Prentice Hall, Upper Saddle River, NJ (1993)

1

5. A. Barrat, M. Barthelemy, and A. Vespignani, Dynamical Processes on Complex

Networks, Cambridge University Press, Cambridge (2008)

6. G. Caldarelli, Scale-Free Networks: Complex Webs in Nature and Technology, Oxford

University Press, Oxford (2007)

7. C. D. Meyer, Matrix Analysis and Applied Linear Algebra, SIAM, Philadelphia, PA

(2000)

8. M. E. J. Newman, A.-L. Barabasi, and D. J. Watts, The Structure and Dynamics of

Networks, Princeton University Press (2006)

1

Course title: Modeling Metabolic Networks Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Introducing various methods of modeling metabolic networks and their practical applications in biology and biotechnology

Headlines: Review on network biology

Review on linear algebra and convex analysis

Review on basic concepts in metabolism (metabolite, interaction, metabolic flux,

reversibility of reactions, … )

Metabolic network reconstruction

Constraint-based modeling of metabolic networks

Flux balance analysis

Flux coupling analysis and flux correlation analysis

Flux variability analysis and alternative optima analysis

Mutation effects studies (MOMA and ROOM)

Strain Design

Pathway analysis in metabolic networks

Modeling of regulation in metabolic networks

Metabolic control analysis

Metabolic flux analysis

Principles of metabolic engineering






Practical: -

References: 1. Palsson, B. O. (2006) Systems Biology: Properties of Reconstructed Networks.

Cambridge University Press.

1

Course title: Molecular Evolution and Phylogenetics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is to make the student familiar with the relevant molecular evolution processes, concepts and methods of phylogenetics and using them in data analysis related to molecular evolution processes.

Headlines: Introduction to relation between population genetics, molecular evolution, and

bioinformatics

Natural selection

Molecular basis of evolution

Evolutionary changes of DNA sequences and proteins

Molecular clock

Phylogenetic trees

Phylogenetic inference

Applications of molecular phylogenetics

Molecular evolution and population genetics

Genome evolution

Weekly seminars






Practical: -

References: 1. Molecular Evolution and phylogenetics by Masatoshi Nei and Sudhir Kumar, 2000.

2. Evolution by Carl T. Bergstrom and Lee Alan Dugatkin, 2012.

3. The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene V.

Koonin, 2011.

1

Course title: Molecular Modeling Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To make the students familiar with basic topics in molecular modeling with emphasis on biological systems.

Headlines: Historical introduction to the development of methods and issues in molecular modeling.

The mathematical expression of molecular structures, coordinate systems for describing

molecular movements, coordinate and internal variables.

Introduction to quantum approaches in molecular modeling e.g. Hartree-Fock, density

function, and semi-empirical methods.

Concepts related to potential energy surface of simple and complex molecules, minimum

and saddle points.

Energy minimization methods and algorithms, and structure optimization e.g. steepest

descent, and conjugate gradient methods.

Molecular mechanic approaches and force fields.

Force fields for biological systems e.g. CHARMM, and AMBER.

Methods and algorithms of analysis and searching conformations e.g. simulated

annealing, and evolutionary algorithms.

Elements of molecular dynamics simulation

Concepts and methods of molecular structure analysis, structural similarity measurement,

structural superposition, coarse-grained coordinate calculation e.g. radius of gyration,

RMSD, number of atom contacts, accessible surface area, …

Methods for the description of the solvent and its effects on molecular modeling,

including implicit and explicit solvent models, generalized Born model and multicenter

models

Methods of analysis and prediction of protein-ligand binding e.g. molecular docking.






Practical: -

References:

1

1. Molecular Modeling Principles and Applications, Andrew R. Leach, Pearson Education,

2001.

2. Molecular Modeling of Proteins, Andreas Kukol, Springer (Humana Press), 2008.

3. New Algorithms for Macromolecular Simulation, T. J. Barth, M. Griebel, D. E. Keyes, R.

M. Nieminen, D. Roose, T. Schlick, Springer, 2006.

1

Course title: Stochastic Processes Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this Optional course is familiarity with discrete time stochastic processes. Nowadays, researchers are using Markov and hidden Markov models frequently. In this course, this topic will be covered.

Headlines: Introduction: short review on concepts, properties of random variables, distribution

functions, and definition of stochastic process.

Markov chains: transition function, calculations using transition function, collision times,

transition matrices, transient and recurrent states, absorption probabilities, martingales,

birth-death chains, branching chains.

Stationary distributions for a Markov chain: elementary properties of a stationary

distribution, examples of stationary distributions, positive recurrent and null states,

irreducible chains, queuing chain.

Jump Markov Processes: birth-death processes, Poisson processes, pure jump Markov

Processes properties, second order processes, Gaussian processes, Bayesian processes






Practical: -

References: 1. Stochastic Processes: Theory for Applications, Robert G. Gallager, 2014, Cambridge

University Press.

2. Pierr Bremoud, (1999) Markov Chains, Monte Carlo Simulations and Queues.

3. Karlin, S. and Taylor, M.H. (1975) A first course in Stochastic Process.

1

Course title: Introduction to Dynamical Systems Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is to make familiar the students with principles of dynamical systems.

Headlines: lagrangians and Euler's equations, vector fields, bifurcation concepts with examples from

physics and biomathematics, Lorenz system, logistic system, stationary points , stable

manifolds , limit cycles , α-limit and β-limit sets and some fundamental theorems e.g.

stable manifolds theorem, Poincare-Bendixon theorem, hatman-grobman theorem and

Lyapunov's theorems, bifurcation theory and codim 1 and 2, normal forms theorem,

structural stability and hyperbolicity, bifurcation diagrams and bifurcation without

parameters, Lyapunov methods and laSalle’s principle, some analytical problems of

numerical methods in dynamical systems.






Practical: -

References: 1. Applications of Dynamical Systems in Biology and Medicine, Trachette Jackson and Ami

Radunskaya, 2015, Springer, USA

2. Differential Equations, Dynamical Systems, and an Introduction to Chaos, Third Edition,

2012, Morris W. Hirsch and Stephen Smale, Academic Press, USA

3. y.a. kuzenetsav, elements of applied bifurration theory, spiringer, 1998.

4. h, khalili, nonlinear systems and control-hall, 1996

5. v.i. arnold, ordinary differential equations, the mit press, 1998.

1

Course title: DNA Computing Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this Optional course is learning algorithms that have been designed based on DNA computing.

Headlines: Molecular computing

Introduction to molecular computing

Biomolecular basis

Adleman’s experiment

Molecular algorithms for solving NP problems

Molecular algorithms for solving Hamiltonian circuit and traveling salesman problems.

Molecular algorithms for solving shortest path problem

Memory modeling

Molecular computing algorithms for logical and computational operators

Automata modeling

Turing machine modeling

Applying dynamic programming on DNA computers.






Practical: -

References: 1. Paun, G., Rosenberg, G. and Saloma, A., DNA computing, Springer Verlag, 1998

2. DNA Computing and Molecular Programming, Satoshi Murata and Satoshi Kobayashi,

2014,Springer, USA

3. Theoretical and Experimental DNA Computation, Martyn Amos, 2010, Springer, USA

1

Course title: Evolutionary Algorithms Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this Optional course is algorithm design based on an evolutionary method that applies to solving problems which cannot be solved in polynomial time.

Headlines: A survey on combinatorial optimization algorithms

Introduction to genetic algorithms

Genetic algorithms in natural evolution

Tabu search annealing simulation

Artificial neural networks

Neural networks evolution, genetic algorithms implementation






Practical: -

References: 1. Evolutionary Optimization Algorithms, Dan Simon, 2013, Wiley, USA

2. A Field Guide to Genetic Programming, Riccardo Poli and William B. Langdon, 2008,

Wiley, USA

3. Multimodal Optimization by Means of Evolutionary Algorithms, Mike Preuß, 2016,

Springer, USA

4. Goldberg, “Genetic Algorithms”, in Search, Optimization and Machine Learning.

Addison Wisley 1989.

5. Mitchell, “An introduction to genetic algorithms”, MIT Press 1998.

1

Course title: Bayesian Statistics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this Optional course is familiarity with Bayesian philosophy vs frequentist methods. Computational methods, such as MCMC will be introduced to take advantage of Bayesian methods.

Headlines: Elements

Probability and Bayes's theorem: examples, random variables, expectation and variance

Bayesian inference for normal distribution and likelihood function, HDR, normal

distribution variance, conjugate distributions, a normal distribution with unknown

expectation and variance, the conjugate prior for normal distribution.

Other statistical distributions: binomial, reference prior for binomial likelihood function,

Jeffrey's rule, uniform distribution

Hypothesis tests: one-way tests, Lindley's method, point null hypotheses with prior

information, point null hypotheses for normal distribution






Practical: -

References: 1. Kendall’s Advance theory of Statistics. (1994) Bayesian Inference, Vol.2B.

2. Bayesian Data Analysis, Andrew Gelman and John B. Carlin, 2013, Third Edition,

Chapman & Hall/CRC, USA

3. Introduction to Bayesian Statistics, William M. Bolstad, 2007, 2nd Edition Aug 15,

Wiley-Interscience, USA

4. Doing Bayesian Data Analysis, John Kruschke, 2014, 2nd Edition, Academic Press, USA

1

Course title: Pattern Recognition Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is familiarity with pattern recognition in systems.

Headlines: Introduction to pattern recognition, classification problems, clustering, statistical and

fuzzy approach to classification and clustering, neural networks as a tool for nonlinear

pattern recognition

Statistical pattern recognition

o Bayesian decision theory, optimized Bayesian classifiers with minimum probability of

error, minimum risk

o Optimized Gaussian classifiers, classifier evaluation, and confusion matrix

o Density function estimation using parametric and nonparametric methods

o Linear classifiers and minimum sum of square errors

o Introduction to classification using support vector machines and kernel-based methods

Pattern recognition using artificial neural networks

o Nonlinear classification and k-nearest neighbor method

o MLP and RBF neural nets as tools for classification and clustering

o Neural nets issues: training, number of neurons in hidden layers, convergence,

normalization, data partitioning, weight initialization, weight drifting, stopping rules,

excitatory functions

Clustering

o Introduction to clustering

o Cluster types and cluster separation measures

o Sequential, Hierarchical and C-means clustering

o Fuzzy clustering: fuzzy C-means, Gustafson-Kessel, gath-geva methods

o Cluster validity

o Introduction to feature extraction and feature selection

o PCA using SVD of covariance or separability matrix






1

Practical: -

References: 1. Pattern Recognition, Sergios Theodoridis (Author), Konstantinos Koutroumbas, 2008, 4th

Edition, Academic Press, USA

2. Introduction to Pattern Recognition, Sergios Theodoridis, Aggelos Pikrakis, Konstantinos

Koutroumbas, Dionisis Cavouras, 2010, Academic Press, USA

3. Statistical Pattern Recognition, Andrew R. Webb, Keith D. Copsey, 2011, 3rd Edition,

Wiley, USA

1

Course title: Design and Analysis of Algorithms Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this Optional course is learning different methods of algorithm design for solving problems in polynomial and nonpolynomial time.

Headlines: Algorithm design

Methods of computational complexity calculation

Different problem-solving techniques

o Divide and conquer

o Dynamic programming

o Greedy

o Backtrack

o Branch and bound

P, NP, NP-hard, and NP-complete problems

Recognizing NP problems e.g. Hamiltonian circuit, and SAT

Problem-solving using approximation and heuristic algorithms and some examples

Problem-solving using parallel algorithms and some examples






Practical: -

References: 1. Corman. Liserson and Reivest, Introduction to algorithms, Academic Press.Brassard, G.

and Bratley, G., Algorithms: Theory and Practice, Prentice Hall, 1988.

2. Introduction to the Design and Analysis of Algorithms, Anany Levitin, 2011, 3rd

Edition), Pearson publisher, USA

3. Algorithms, Robert Sedgewick and Kevin Wayne, 2011, 4th Edition, Addison-Wesley

Professional, USA

1

Course title: Multivariate Analysis Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives:

Headlines: Multivariate and marginal distributions, famous multivariate families (exponential,

hyperbolic, …), multivariate normal distribution and its properties, univariate or

multivariate distributions derived from multivariate normal distribution (…), Principles of

multivariate hypotheses test, principles of multivariate parameter estimation, confidence

intervals, designs with multivariate regression…, multivariate normal hypotheses test, and

other distributions.






Practical: -

References: 1. Anderson, T.W. (1984), An Introduction to Multivariate Analysis, John Wiley, New York

2. Bilodeau, M. and Brener, D. (1999), Theory of Multivariate Statistics, Springer.

3. Mardia, K., Kent, J.T. and Bibby, J. (1979), Multivariate Analysis, Academic Press

1

Course title: Genomics and Gene Regulation Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this Optional course is to make the students familiar with basic topics in organism’s genome and the role of various pieces of the genome in gene expression.

Headlines: Structural genomics: genome size in organisms, mechanism of genome size variation,

genome organization, genome rearrangement

Epigenomics: principles and concepts of epigenetics in gene expression

Functional genomics: cis and trans elements in gene expression regulation, biological

variations in gene expression, genomic disorders

Students seminar presentation (two weeks) in selected topics: personal genomics and

medicinal genetics, pharmacogenomics, genome evolution, …

Lab: basic techniques of DNA and RNA extraction, polymerase chain reactions, ...






Practical: -

References: 1. Human molecular genetics (2003), Read & Astrachan, Bios.

2. The evolution of the genome (2005), T. Ryan Gregory (editor), Elsevier.

3. Genoms (2007), Brown.

4. Gene ExpressionAug, G. S. Miglani, 2013, Alpha Science, USA

5. Gene Expression and its Regulation: Laying the Foundation for Molecular Biology,

Werner Maas, 2013, XLIBRIS, USA

1

Course title: Biomolecular Recognition Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To make the students familiar with the rules of interaction and targeted binding of biological macromolecules with other related molecules.

Headlines: Importance of biomolecular recognition in biological processes

Physical basis of molecular interaction and related molecular properties

Different types of molecular forces e.g. van der Waals, electrostatic, hydrogen, halogen,

hydrophobic, …

Solvent effects on molecular recognition and its calculation methods

Molecular recognition in protein-protein, protein-nucleic acid, and nucleic acid-nucleic

acid interactions.

Molecular recognition in receptor-ligand systems.

Peptide design and drug design based on principles of molecular recognition

The role of molecular recognition in the immune system and antigen-antibody

interactions.

Molecular recognitions mechanisms in biological networks

Databases related to biomolecular recognition






Practical: -

References: 1. Principles of Molecular Recognition, A.D. Buckingham, A.C. Legon, S.M. Roberts,

Springer, 2012.

2. Molecular recognition mechanisms, Michel Delaage, VCH Publishers, 1991.

3. Protein-Ligand Interactions: From Molecular Recognition to Drug Design, Hans-Joachim

Böhm, Gisbert Schneider, Wiley, 2003.

4. Cellular and Biomolecular Recognition, Raz Jelinek, John Wiley & Sons, 2009.

5. Pharmacological Aspects of Molecular Recognition, F. S. Dukhovich, Nova Publishers,

2005.

1

1

Course title: Special Topics in Bioinformatics Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is presenting new topics in bioinformatics that have not proposed as standard courses yet. New subjects will be introduced in the format of seminars based on scientific papers, and the students will be familiar with nature of these investigations.






30% ______ Written Test: - 40%

Practical: 30%

1

Course title: Advanced Data Mining Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Data analysis of text, graphs (biological, social, web networks, and …), spatial, temporal, and time series has more complexities than common methods in data mining. In this course methods for mining complex data will be explored. Also, we will review clustering methods completely. Dealing with big data is another topic.

Headlines: Introduction

Review on probability, decision, and information theories.

Unsupervised learning (clustering)

K-means clustering

Distribution based clustering (EM)

Link-based clustering (hierarchical)

Density-based clustering

Graph-based clustering (Chameleon, …)

High dimensional clustering (subspace clustering, …)

Clustering validation techniques

Dimensionality reduction and review on some techniques e.g.

o Filter-type methods, F-test, mutual information

o Max-relevance min-redundancy algorithm, feature stability algorithms

o Wrapper methods, search methods, floating search methods

Sequence and time series mining (models for time series and sequence data)

Mining methods in biological networks

Mining methods in graphs and trees

Applications in the web (e.g. web advertising, viral marketing, recommender systems, …

)

Working with RapidMiner, Matlab, R, …






1

20% 20% Written Test: 30% 30%

Practical: -

References: 1. Anand Rajaraman, Jure Leskovek, Jeffery D. Ullman, Mining of massive Datasets,

Cambridge University Press, 2012.

2. Jiawei Han, Micheline Kamber, Jian Pei, Data Mining: Concepts and Techniques, Third

Edition, the Morgan Kaufmann Series in Data Management Systems, 2011.

3. Lei Tang, Huan Liu, Community Detection and Mining in Social Media, Morgan and

Claypool Publishers, 2012.

4. Mehryar Mohri, Afshin Rostamizadeh, and Ameet Talwalker. Foundations of Machine

Learning. MIT Press, 2012.

5. Kevin Murphy, Machine Learning: a Probabilistic Perspective, 2012.

6. Christopher M. Bishop, Pattern Recognition and Machine Learning, Springer

1

Course title: Cell and Molecular Mechanism of Cancer Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: To make the students familiar with cell and molecular mechanisms of cancer

Headlines: Introduction: including cell transformation steps and molecular properties of colorectal

tissue

Molecular mechanisms of cell Epithelial- mesenchymal transition

Intercellular connections and their relations to cancer

Deregulation of 𝐺1 → 𝑆 phase of cell cycle

Deregulation of 𝐺2 → 𝑀 phase of cell cycle

Senescence cancer cells

Cell apoptosis and cancer

Oncogenes and their activation mechanism in human cancers

Super Surgen tumors and their mechanisms of inactivity in human cancers

Introducing the most important methods of signal transduction and mechanisms of their

deregulation in human cancers

Genetic instability in cancer

Angiogenesis mechanisms

Cell and molecular mechanisms of metastasis

Novel approaches in human cancer therapy

Seminar presentation





(To be specified in percentage) 10% - Written Test: 70% 20%

Practical: -

References: 1. Volgelstein B and kinzler, KW the Genetic Basis of Human cancer. Mc Graw Hill, 2nd

edition.

2. Research and Review articles. (Nature Review cancer)

1

Course title: Data Mining in Medical Systems Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: The aim of this course is to make the student familiar with novel topics in data mining in medicine and healthcare

Headlines: Introduction to classification rule and association rule

Making decision tree using OneR algorithm

Entropy

Regression

Logistic function

Naïve Bayes method

Likelihood calculation

Precision and recall measures in classification

A priori algorithm for finding frequent itemset

A_close algorithm

GSP algorithm

K_means, DBSCAN, and hierarchical methods for clustering

CLIQUE algorithm

Calculation of Closeness and Interconnectivity between clusters






Practical: -

References: 1. Data Mining: Practical Machine Learning Tools and Techniques Third Edition. Ian H.

Witten, Eibe Frank Mark A. Hall .2011. Elsevier. USA

2. Data Mining and Medical Knowledge Management: Cases and Applications. Petr Berka,

Jan Rauch, Djamel Abdelkader Zighed. 2009. IGI Global. USA

1

Course title: Modeling of Biological Systems Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: In this course at first various standard methods and tools for modeling physiological systems will be introduced, and then novel approaches of modeling complex biological systems will be proposed.

Headlines: Introduction: needs, concepts, importance and applications, and various modeling

approaches

Modeling biological systems process

Modeling biological systems, methods, and applications

Methods of model identification: parametric and nonparametric models

Model validation

Case studies: cell, neurological system, blood flow, respiration, muscle

Methods and novel concepts in modeling biological systems: computational intelligence-

based methods, cellular automata, expert systems, and modular structures.





(To be specified in percentage) 20% - Written Test: 50% 30%

Practical: -

References: 1. C. Cobelli, E. Carson, Introduction to Modeling in Physiology and Medicine, Academic

Press (Elsevier), 2008.

2. J. Keener, J. Sneyd, Mathematical Physiology, Springer, 2009.

3. J. Haefner, Modeling of Biological System: Principles and Application, Springer, 2005.

4. U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits,

Chapman & Hall/CRC, 2006.

5. MCK Khoo, Physiological Control Systems: Analysis, Simulation and Estimation,

Willey-Black Well, 1999.

Course title: Glycolipobiology Number of units: 2

1

The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Familiarity with the Structure and Importance of Glycoproteins and Proteolipids in Biology and Major Applications in Biology of Glycans and Lipoproteins

Headlines: Introduction: Biological role of Glycan

The diversity and common structural features of glycoproteins and glycolipids

Cell position(s) of Glycosylation of proteins in different physiological conditions

Enzymes involved in glycosylation of proteins

Glycans detecting proteins, their categorization and their diagnostic principles

The most modern methods of structural analysis of glycoproteins and glycolipids

Glycans involvement in bacterial, viral and other human diseases, especially cancer and

metastases

The position of Glycans in the pharmaceutical industry

The position of biotechnology in the production of Glycans






20% ______ Written Test: 80% __ _____

Practical: -

References: 1. Susan A. Brooks et al., Functional and molecular Glycobiology, Bios scientific

publishers, 2002. 2. Ajit Varki, et al., Essential of Glycobiology, 2nd Ed, Cold Spring Harbor, 2009.

1

Course title: Advanced Biochemistry of Proteins and Nucleic acids Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D. Course Objectives: Study of chemical changes in proteins by binding small molecules and macromolecules and interacting proteins with nucleic acids

Headlines: Introduction to protein and nucleic acids structure and function, structural and functional

motifs.

Proteins modifications through binding of small molecules, methyl, acetyl….

Modifications of proteins through glycosylation, acylation, ADP-ribosylation.,

Ubiquitination, motifs, structure and function.

Interaction of proteins with nucleic acids at amino acids and nucleotides level.

Structural motifs SPK, HMG-box…..

Interaction of regulatory proteins with DNA, HTH, HLH, Zinc finger, Leu-zipper and

other motifs

Interaction of proteins with RNAs, RRM, KH and …. Motifs.

Seminars






20% ______ Written Test: 80% __ _____

Practical: -

References: 1. Branden & Tooze (latest edition) Introduction to protein structure, Garland Pub.

2. Walsh CT (2006) Post translation modification of proteins, RC Pub.

3. Rice PA, Correl CC (2008) Protein-Nucleic acid interactions, Structural biology, RSC

Pub.

1

Course title: Mechanism of enzyme action Number of units: 2 The number of hours: 32 Unit type: Theoretical Course type: Optional Prerequisite: - Practical training: has it doesn’t have Scientific journey Workshop Laboratory Seminar Degree: MSc Ph.D. MSc & Ph.D.

Course Objectives: Familiarity with the required techniques and the way of study the mechanism of action of enzymes and interpreting the results of the studies with several examples with the aim of capability in the design of drugs, insecticides and other materials of industrial value.

Headlines: The importance of studying the mechanism of action of enzymes

Different and general methods of Chemistry of enzymes:

o Catalysis by approximation

o Catalysis by covalent modification

o Acid/base catalysis

o Strain catalysis

Important methods for determining the mechanism of action of enzymes:

o Kinetic tools o Use of labeled materials

o Use of inhibitors

o Use of various Spectroscopic Techniques

o Use of Space Chemistry

A comprehensive review of the mechanisms of action of the enzymes from the following

groups:

o Isomerization reactions

o Molecular displacement reaction

o Exclusion and elimination reactions

o Carboxylation and dicarboxylation reactions

o Oxidation and resuscitation reactions






30% ______ Written Test: 70% __ _____

Practical: -

References: 1. Christopher Walsh, Enzymatic reaction mechanisms; Freeman and Co., N. Y., 1979.

1

2. Perry A. Frey and Adrian D. Hegeman, Enzyme Reaction Mechanism, Oxford university

press, 2007.

Documents

General curriculum specifications Courses: Masters and Ph