BİYOMÜHENDİSLİK YÜKSEK LİSANS PROGRAMI
Biyoproses tasarım, biyokataliz, biyolojik ayırım, doku kültürü mühendisliği, protein mühendisliği, proteomik, biyomateryal ve endüstriyel biyoteknoloji gibi biyomühendisliğin farklı birçok alanında yetkinlik kazanmaktır.
Programın Dili : İngilizce
Bilimsel Hazırlık Programı Gerektiren Bilim Alan ve Dalları
Programa kabul edilen adayların aşağıdaki dersleri veya eşdeğer sayılabilecek dersleri lisans öğretimleri sırasında almış olmaları, almadıkları ders sayısının 3’ün üzerinde olması durumunda Marmara Üniversitesi Lisansüstü Eğitim-Öğretim ve Sınav Yönetmeliği uyarınca Bilimsel Hazırlık Programını tamamlamaları gerekir.
INTRODUCTION TO BIOENGINEERING
Definitions and concepts in biochemical & bioprocess engineering, enzyme kinetics & immobilization, metabolic stoichiometry and energetics, microbial and cell growth kinetics, unstructured and structured growth models, bioreactor design & operation, transport phenomena, downstream processing and product recovery, mixed culture, biosensors
BASIC TECHNIQUES IN BIOPROCESS ENGINEERING
Introduction to the experimental techniques of biology and biochemistry .The research of biological effects of cellular environment. Bioreactor and bioprocess engineering: observation of cell growth kinetics and mass transfer with computer simulation. Ideal bioreactors. Reactor dynamics. Reactors with non ideal mixing. Sterilization. Reactors for immobilized biocatalysts and cells.
MATHEMATICAL APPLICATIONS IN BIOLOGICAL SYSTEMS
Advanced Mathematics and engineering applications, partial differential functions, vectors, optimization of numerical methods.
BASIC TECHNIQUES IN MOLECULAR BIOLOGY
Safety in Mol.Bio. Lab, Basic techniques in microbiology (sterilization, preparation of culturing media, culturing), DNA isolation from bacterial cells, Restriction digestion of DNA, Electrophoresis of isolated DNA, Southern blot, Primer design and Polymerase chain reaction.
Separation and purification of biochemicals. Removal of insolubles by filtration, centrifugation and sedimentation. Isolation of products by adsorption and solvent extraction. Purification by nonlinear multicomponent chromatography , electrophoresis, dialysis and membrane processes. Polishing by drying and crystallization. Mathematical modeling and scale-up of selected operations.
A wide range of microbial processes will be examined and used to illustrate how complex products can be made economically from microorganisms.
BIOMATERIAL SCIENCE AND ENGINEERING
Classification of materials. Atomic bonding in solids. Amorphous and crystalline structure of solids. Imperfections in crystals. Mechanical properties of materials. Deformation and fracture behavior . Phase diagrams and phase transformations. Metal alloys. Thermal processing of metals. Nonmetallic materials. Corrosion and degradation of materials. (Oriented for Chemical and Food Engineering)
Natural occurring polymers are much more frequent than synthetic polymers and they show higher structural and functional complexity .Biopolymers are the main constituents of biological systems, and from a technological point of view , they have particular interest due to their biodegradable properties. In this course, the biosynthetic processes, the structure and the properties of biopolymers with special attention to proteins and polysaccharides, are studied. The biological and technological importance of these natural polymers in relation to their function and structure are examined. The course includes the study of other biotechnological polymers as natural rubbers, polyesters and polyamides, which are outstanding for their industrial importance.
CELL CULTURE METHODS
Biology of Animal Cell; Cellular Interactions, Media Formulations for Cell Culture, Culturing and Sub-Culturing of Animal Cells, Transfection, Cloning of Animal Cells; Functional Assays in Cell Culture Systems. Cell culture, equipment, cell culture media, serum, preparation of primary cells, cryopreservation, specialized techniques, insect and cancer cell lines.
Introduction: General property of enzymes, enzyme activation and its effect factors/ Enzyme- Substrate Relation: Enzyme kinetic, cooperative effect, allosteric effect/ Chemical modification of enzyme: using materials for modification, changing on modification and enzyme molecule properties, practice areas/ Immobilization of enzymes: using materials for immobilizations, changing on immobilization with enzyme molecule properties/ The future of chemical enzymology.
ADVANCED MOLECULAR BIOLOGY
Basic properties of polymers: mechanical, thermal, electrical and optical properties, polymer characterization: determination of molecular weight and weight distrubition, structural analysis, characterization.
Antigensl classifıcations of antigens: antigens of microorganisms (bacteria, virus, toxins etc.), allergens (plant powder, insect waste), blood group antigens (polysaccharides involved peptide), transplantation and tumor antigensl Specifıc structure- immunalogenic relation/ Antigenic determinant! Haptens/ Timus addicted and non timus addictedantigens/ Adjutants/ Regulation immunology of antigens/ Antibodies: its structure, classification, domens, polymerize, isotypes, allotypes, properties/ Immune system: Monoclonal antibodies/ Reactions of antigen-antibody: its theory, precipitation, immunoelectrophoresis, immune diagnostic, activation of complement! Cell immunity and mediators; Regulation of immune answer/ Patalogic immune reaction/lmmunology of infection disease/ Bacterial and viral disease/ immunology of transplantation/ Transplantation of tissue and organs.
Chemical synthesis with solid situation method of peptides (Merrifield method)/ Biosynthesis of peptides and proteins/ DNA technology/ Hybrid technology/ Monoclonal immunoglobulins(antibodies) / Modifications of biomolecules/ Immobilization of peptides and proteins:, latecs and liposome, binding micro encapsulation and polymeric matrix/ The method of preparation adjutants/ Regulation of antigen immunology/ Synthetic vaccine/ Viral vaccine/ Polymeric immunogensand vaccine prototypes: The synthetic vaccine development methods of alum (foot-mouth), hepatic, diabetic, plague tuberculosis, flu, AIDS disease.
Producing Data, Graphing Data, Summarizing Data, Bivariate Relationships, Normal Distribution, Sampling Distributions, Standard Error of the Mean, Confidence Intervals, t-tests, Tests, Chi Square and 2-way Tables, Regression and Correlation, ANOVA.
BIOMEDICAL SIGNAL PROCESSING
Discrete-time signals and systems. Sampling, bandwidth and aliasing, convolution, recursive and nonrecursive difference equations, frequency response. The z-transform and its extensions. Discrete Fourier transform, circular convolution, expansion, Fast Fourier Transform (FFT) algorithms. Spectral analysis and detection. Digital and adaptive filter algorithms. Applications; processing of bioelectric signals; image and speech processing, estimation of echoes.
Reverse engineering in the nervous system; anatomical, physiological and mathematical approaches. Computational action and interaction of brain networks; architecture, performance, learning, memory. Modeling of neural networks. Artificial implementations, static and dynamic networks. Pulse frequency modulation in the nervous system. Learning algorithms, stability, periodic oscillations. Application examples, projected technological developments .
Yeast cell, gene transfer into yeast cell, artifical chromosomes of yeasts and applications, gene transfer into bugs and biotechnological material production, plant biotechnology and applications, techniques for development of transgenic animal and applications.
Immune cells and immune molecules, anticores, polyclonal anticores, production, purtification and usage of polyclonal anticores, biotechnological applications of polyclonal anticores: advantages and disadvantages. Monoclonal anticores, production, purification and usage of monoclonal anticores, biotechnological applications of recombinant anticores: advantages and disadvantages, peptide libraries.
Sterilization and pasteurization; dry and heat sterilization, application of thermal processing in the industry , radiation, gaseous and filtration sterilization, sterilization standards, industrial sterilization methods and technologies, new and emerging technologies, support testing, indicators, clean rooms, cleaning of facilities, personal training, sterility assurance.
MATHEMATICAL MODELLING IN BIOLOGICAL SYSTEMS
Simple mathematical tools will be applied to biological systems in an attempt to express bioprocesses with equations. The results obtained will help the scientist in designing new experiments. This course requires a solid background in mathematics and a knowlegde in basic cellular biology .
Analysis of movement of the musculoskeletal system: anthropometry, link-segment models, kinematics, kinetics. Active and passive mechanical properties of skeletal muscle in relation to its structure. Mechanisms of transmission of muscle force. Effects of myofascial force transmission on muscle function. Motor control and coordination of muscular activity: types of muscle fibers, motor units, size principle, sensory information.
BIOMEDICAL INSTRUMENTATION AND MEASUREMENTS
Biomedical sensors, transducers and electrodes. Instrumentation amplifiers and their applications. Electrical safety in hospitals. Electrocardiography , electroencephalography , electromyography and electroretinography. Pulse oximetry, blood pressure and flow measurements, cardiac output measurements. Cardiac pacing, defibrillators and cardiovascular prostheses and assist devices. Physical therapy equipment. Electrosurgical unit, anesthesia equipment, ventilators and hemodialysis unit.
BIOLOGICAL CONTROL SYSTEMS
Dynamic systems and control. Mathematical modeling of biological control systems. Biological receptors, their characteristics and transfer function models. Examples of biological feedback systems: Pupil control system, visual fixation, thermoregulation, skeletal-muscle servo mechanism, blood pressure control, cardiac output and other biological regulatory systems. Biological performance criteria and adaptive control mechanisms.
Spectroscopic techniques, chromatographic techniques, spectrometric analysis used in biological systems
The human body as a machine; physiological principles, modeling, neural networks; diagnostic techniques and related instrumentation; high technology in patient care and therapy .Computers in medicine; signal and image processing, picture archiving, telemedicine; biomaterials and prostheses; principles of clinical engineering and safety considerations; technology management in hospitals.
SPECIAL TOPICS IN BIOENGINEERING I
Various special topics selected from the branches of bioengineering as proposed by the instructor to address the research interests of the students
INTRODUCTION TO BIOMECHANICS
Structural and physical properties of bone, muscle, tendon and cartilage. Mechanics of joint and muscle action. Body equilibrium. Mechanics of the spinal column, of the pelvis and ofthe hipjoint. Panhomechanics.
Introduction. Biological properties and functions of enzymes and microorganisms, their preparations to biochemical processes. Momentum, heat and mass transfer at the systems microorganisms are used. Designing, operating and controlling of biotechnological systems. Enzyme technology .Immobilized enzyme and microorganisms. The separation procedure in bioprocesses. Sterilization. The classical biotechnological applications about enzymes and microorganisms. Modem biotechnological applications, genetic engineering, the recombinant DNA technologies
BIOLOGICAL REACTION ENGINEERING
Bioreactor modeling, modeling principles, basic reactor concept, biological kinetics, mass transfer inbiological systems, diffusion and biological reaction in immobilized biocatalyst systems
Extra cellular matrix analogs, Extra cellular matrix, synthetic polymers, natural polymers, the organization of cell functions, cell adhering, cell-biomaterial interaction, cellular action and metabolism, tissue development, tissue modeling, tissue regeneration, angiogenesis, drug release, tissue engineering approach, tissue induction (skin, nerve, vessel, tendon, ligament, bone ), cell transplantation (skin, cartilage, tissue, bone, liver, kidney, endothelia, nerve system), biohybrid organs (liver, pancreas), blood formation, gene therapy, tissue engineering products; patents, rules.
ADVANCED CELL BIOLOGY
General structure and functions connection relations on molecular and cellular level 1 Importance of general/ genetic mechanisms/ Control of gene expirations/ The structure of membrane and Cytoplasmic events/ Sub cellular organelles structure, function and biogenesis 1 Today's researches about cell biology
RECOMBINANT DNA TECHNOLOGY
Plasmids and chromosomes, different types of vectors, Blotting techniques, DNA libraries, Site specific mutagenesis, Methods of transferring DNA to different types of cells.
The goal of this course is to introduce students quantitative concepts in understanding and manipulating the behavior of biological cells. We will try to understand the interplay between molecules in cells and cell function. A particular focus is on receptors -cell surface molecules that mediate cell responses. We will also try to understand processes such as adhesion, motility , cytoskeleton, signal transduction, differentiation, and gene regulation.
INTRODUCTION TO BIOINFORMATICS
Sequence Comparison, Multiple Sequence Alignments, Primer Analysis & Sequencing, RNA/DNA Structural Analysis, Protein Secondary Structure, 3D Molecular Modeling, Microarray Technology , Assembly of DNA Pieces, Multivariate Analysis of Large Scale Gene Expression, Metabolic Pathway Analysis, Modelling and Simulation of Biological Processes, Data Mining,
In this course, transport phenomena principles will be applied to biological systems in an attempt to model living systems. This includes the calculation of the rates of diffusion of substrates and nutrients through biological membranes to understand growth characteristics, protein production and metabolism of microorganisms.
METABOLISM AND CELLULAR ADAPTATION
Since the beginning of evolution, cells have developed highly efficient metabolic systems to extract energy in order to carry out biosynthesic reactions. The specific reactions vary in different cell types. The scope of this course is to learn general metabolic pathways and relate the differences in metabolic pathways of different microorganisms to cellular adaptation.
Relationships between materials' science and medicine. Properties of crystalline and noncrystalline materials. Principles in strength of materials. Natural biological materials. Artificial biological materials. Applications of materials science to orthopedic surgery. Cardiology and materials science. Applications of materials science research methods to medicine.
Consideration and principles, binding to the membranes, adsorption, cell and enzyme immobilization technology, mathematical modeling, scale-up gel bead and microcapsule production, living cells and microorganisms immobilization, inverted microcarriers, biorector systems based on microencapsulated cells, emerging techniques, materials and applications
Microbiological risk assessment, biosafety levels 1,2,3, guidelines for laboratory facility. Biosecurity concepts, transport of infectious substances, bİosafety and recombİnant DNA technology , chemical, fire and electrical safety, safety organization and training.
Introduction to Proteomics, the proteom and technology , protein identification, co and post translational modifications, clinical and biomedical applications of proteomics, biological applications of proteomics
SPECIAL TOPICS IN BIOENGINEERING II
An advanced treatment of selected bioengineering topics of current interest .