Program-Specific Required Courses
Credit: 3
Theoretical and practical aspects of working in a cell culture laboratory. Maintenance of a cell culture laboratory; problems and solutions.
Credit: 3
This course delves into the fundamental principles of cellular and molecular medicine, offering insights essential for graduate-level exploration of biological function across various organizational levels, from molecules and cells to multicellular organisms, including humans. Key topics include protein function and analysis, nucleic acids, the central dogma of molecular biology, mechanisms governing gene expression, techniques in recombinant DNA, principles of genome editing, subcellular organization, functions of intracellular compartments, and cell signaling. Additionally, the course provides an overview of experimental techniques crucial for cellular and molecular studies. |
Credit: 0
This course is non-credit and is a course in which the advisor evaluates the student’s thesis work. It covers all the studies and research to be carried out on the thesis topic determined with the guidance of the advisor and is graded periodically as S/U by the advisor faculty member.
Credit: 0
This course is non-credit and aims to increase scientific interaction between students and improve students’ presentation skills by ensuring the participation of students from all interdisciplinary programs. The seminar course, which consists of the presentation of the studies and research conducted in front of the community within the framework of the techniques determined with the guidance of the advisor and the question and answer section, is graded periodically as S/U by the program coordinators. The course must be taken at least once and completed successfully within the framework of Council of Higher Education rules. Program-specific rules are determined by program coordinators and shared with students.
General Required Courses
Credit:3
Ethical principles in biomedical research, biosafety, ethics in animal studies, human and patients’ rights, ethics in clinical research, national and international examples in publication ethics and principles will be discussed. Course will be completed via CITI online education program.
Credit: 3
An introduction to important topics in biostatistical concepts and reasoning. Tools for describing central tendency and variability in data; methods for performing inference on population means and proportions via sample data; statistical hypothesis testing and its application to group comparisons. Several statistical methods such as linear regression, ANOVA, logistic regression, survival analysis, nonparametric methods, ROC analysis that are commonly used to study biological problems. In-lab practices on computers and software for statistical analysis, to provide students with the skills to generate, read and interpret the results in their fields of study.
Credit: 0
Foundations and basics of designing effective teaching environments for higher education courses, learning principles, teaching in English, integrating learning technologies into teaching practices, grading, communicating with students and instructors, and superdiversity and gender sensitive pedagogy.
Credit: 0
The following objectives will be met through extensive reading, writing and discussion both in and out of class.Build a solid background in academic discourse, both written and spoken. Improve intensive and extensive critical reading skills. Foster critical and creative thinking. Build fundamental academic writing skills including summary, paraphrase, analysis, synthesis. Master cohesiveness as well as proper academic citation when incorporating the work of others.
Program-Specific Elective Courses
Credit: 3
Fundamental biology and hallmarks of cancer. Genomics of cancer, uncontrolled cell division, cell cycle,angiogenesis, metastasis, evasion of apoptosis, immune evasion, genomic instability, targeted cancer therapies and current developments in cancer. Weekly literature discussions.
Credit: 3
The importance of genetic makeup in controlling and shaping an organism and disease-causing mutations in the human genome. Historical milestones of gene editing from viral therapy to CRISPR/Cas9. Scientific processed behind the discovery of CRISPR-systems. In-depth discussion of the relevant scientific papers.
Credit: 3
Micro and nanoscale biological systems and their applications in regenerative medicine, disease modeling, diagnostics and therapy. Properties of micro and nanoscale building blocks, their assembly processes and their use in synthesizing larger systems to address biological problems. A plethora of biological and chemical structures, design of systems for use in sensing and diagnosing biological phenomena, manipulating cell functions, engineering tissues, modeling pathologies and delivering therapeutics. Bioinspired and biomimetic design of microphysiological systems, tissues and organ-on-a-chip approaches. Technological impact and use of such systems in translational research.
Credit: 3
Design thinking method used to transform real healthcare challenges into business ideas and transform medicine. Discussions on subjects in medicine, technology and enterpreneurship with experts in health IT, intellectual property, medical device regulations and medtech. In-class applications and discussions of real life unmet clinical challenges with small team of students.
Credit: 3
Information regarding cell structure and function, cell signaling, vesicular trafficking, cell-division cycle, and extracellular matrix. Introduction to cell signaling, G-protein coupled receptors, TGF-beta family members and cytokine receptors, receptor tyrosine kinases, pathways involving proteolysis, ingtegration of signals and gene controls, cell division and cell cycle, membrane trafficking, cytoskeleton, cancer and presentations.
Credit: 3
Applied aspects of molecular biology. Introduction and explanation of what is molecular biotechnology as a scientific discipline, which tools of recombinant DNA technologies are applied, and industrial microbiology. The development of molecular biotechnology, DNA, RNA, and protein synthesis, recombinant DNA technology, chemical synthesis, amplification, and sequencing of DNA, bioinformatics, genomics and proteomics, heterologous protein production in eukaryotic cells, directed mutagenesis and protein engineering, protein therapeutics, nucleic acids as therapeutic agents, vaccines, synthesis of commercial products by recombinant microorganisms, transgenic animals, molecular biotechnology and society.
Credit: 3
Mechanisms by which cells respond to external physical forces (tension, compression, shear, pressure) and relevant signaling processes involved in development, regeneration and pathology (i.e. cancer); mechanisms of cell-matrix interactions and physical stimuli-mediated cellular processes such as tissue remodeling. Cell cytoskeleton and mechanics, ECM and cell-matrix interactions, cellular responses to external physical stimuli, cellular responses to external physical stimuli, mechanobiology in development, mechanobiology in regeneration and tissue remodeling, mechanobiology in disease, analysis of cell mechanics, Manipulation of cell mechanics, applications of mechanobiology.
Credit: 3
How rare genetic disease help to understand common diseases, from clinical to in vitro approaches. Genetic to potential causative gene: Description of the essential steps that allow to identify potentially disease-causing genes. How to detect rare mutations: Overview of next generation sequencing technologies. From patients to dish: Generation of primary tissue/cells, culture and storage. How to prepare tools for modeling: Molecular genetic assays: expression cloning, transfection, mutagenesis, gene editing KO/KI. Biochemistry techniques: Western blot, fractionation, Immunoprecipitation. Cells based assay: Viability, proliferation, cytotoxicity, senescence and cell death assays. Power of tissue and cells imaging: Immunofluorescence, histology, confocal, electron microscopy, live imaging. Advantage of Omics techniques: Transcriptomics, Proteomics, Metabolomics. At the bench: Culture and biochemistry techniques. Modeling Neurodegeneration. Cancer In vitro Modeling. From bench to therapeutic: High throughput cellular assay to drug development.
Credit: 3
Aim: to grasp the functional studies that link rare disorders to a potentially disease-causing gene. How to uncover, through specific examples, biological pathways that are necessary and that may contribute to more common pathologies. How to use various animal models such as zebrafish, mice, Xenopus, flies, worms to model human rare genetic diseases and develop new treatment options.
Credit: 3
Biochemical changes in mitochondrial diseases metabolism, alteration of certain enzyme activities, shuttles, biochemical mitochondrial markers. Mitochondria, role of Mitochondria in metabolism, role of mitochondria in energy metabolism, mitochondria and aging, mitochondria and oxidative stress, mitochondria and cell death, guidelines on experimental methods on mitochondria, mitochondrial diseases, manuscript and Review presentation.
Credit: 3
Study of molecular mechanisms of autophagy regulation in health and disease. The basic mechanisms of autophagy and contribution of autophagy abnormalities to disease formation, progression and drug responses. Introduction to autophagy, Molecular mechanisms-I: ULK1/2, ATG13, ATG9 complexes, Molecular mechanisms-II: Beclin 1 complexes, Molecular mechanisms-III: Omegasome complexes, Molecular mechanisms-IV: ATG8/LC3 conjugation systems, Molecular mechanisms-V: Selective autophagy and receptors, Molecular mechanisms-VI: Autolysosomes, Molecular mechanisms-VII: mTOR and AMPK pathways, Autophagy and cancer, Autophagy and neurodegeneration, Autophagy and rare diseases, Autophagy and infection, Autophagy and immunity.
Credit: 3
Aim: to teach the biochemical changes in cancer metabolism, alteration of certain enzyme activities, hormones and growth factors, biochemical tumor markers.
A biochemical approach to the cancer cell, carbohydrate metabolism in cancer, differences of glycolysis in cancer cell and healthy cell, pentose phosphate pathway in cancer cells and healthy cells, tricarboxylic acid cycle in cancer cells and healthy cells, fatty acid metabolism in cancer cells and healthy cells, Impact of fatty acid metabolism on the cancer cells correlated with cell signaling, biochemistry of cell signaling, cell signaling pathways, a biochemical approach to cancer metastasis.
Credit: 3
Aim: to learn the basic concepts of cancer metastasis and recurrence.
Introduction to cancer biology and metastasis, cancer stem cells, epithelial mesenchymal transition (EMT), mechanisms of cancer cell migration, mechanisms of cancer cell survival and death, mechanisms of tissue invasion, intravasation and survival in the circulation, metastasis through lymphatics, metastasis to lymph nodes, autophagy and cancer, tissue tropims and metastasis, cancer recurrence/relapse.
Credit: 3
Aim: to explain mechanism of Nanotechnology-Based Approaches for Targeting and Delivery of Drugs and Genes. Overview of the important aspects of nanomedicine, how to design and develop novel and effective drug delivery systems using nanotechnology and polymers. Main components of targeting and delivery of molecules including drugs and genes, an introduction to nanomedicine and its associated issues with basics of polymers, the latest technologies in nanomedicine, future developments and marketing challenges.
Credit: 3
Aim: understanding database systems concepts and possess the knowledge about how to use available biological databases and data analysis tools efficiently.
Biological databases, database creation and management, introduction to commonly used analysis tools. Extensive use of different biological data types and data formats, biological data editing techniques, Disease-centric databases, data processing and data analysis tools, web-based bioinformatics environments for research and analysis of biological data.
Credit: 3
To imitate the physiological, pathological and extracellular matrix characteristics in health and diseases in in vitro. Introduction to 3D culture systems. Applications of 3D cultures in health and disease. Applications of different synthetic and natural hydrogels for 3D culture. Methods to experimental design of 3D culture systems. Organoids and tissue models. Methods to generate spheroids in in vitro. Blood-brain barrier and neuromuscular junction and neural communication models in 3D cultures. Multiplex cell culture approaches in 3D systems. Drug delivery methods for 3D systems. Microfluidic and organ-on-chip systems.
Credit: 3
Learning basic concepts and translational applications in the Cell Death Research Field. Introduction to Cell Death Mechanisms, Programmed Cell Death or Cellular Suicide. Apoptosis-Caspases. Apoptosis-Extrinsic Pathway and death receptors. Apoptosis-Bcl-2 family members. Apoptosis-Intrinsic Pathway and Mitochondria. Autophagic cell death. Autosis, Necroptosis. Atypical Cell Death Mechanisms-Anoikis-Mitotic catastrophe. Atypical Cell Death Mechanisms-Ferroptosis-Entosis. Atypical Cell Death Mechanisms- Parthanatos-Pyroptosis.
Credit: 3
The broad topics of gene network design, stochasticity in gene expression, and evolution of genes and networks, detailed critiques of the selected current/classic papers in the Systems/Synthetic/Computational Biology fields, data analysis methods, experimental controls, results, and main conclusions.
Credit: 3
This course is a special course given by the student’s advisor for the student’s thesis work. The PhD students who enrolled with a BS degree can count 2 Independent Study course credits, and the PhD students who enrolled with an MS degree and MS students can count 1 Independent Study course credit during the education period. The important thing is that the Independent Study course names and contents that you take must be different to count the credits.
