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Biological Oceanography: Marine plants and animals. Energy fixation, growth and abundance of organisms. Seasonality of production.
Chemical Oceanography: Chemical properties of sea water, alkalinity, C, N, P and S cycles, oxic and anoxic environments, redox processes.
Geological and Geophysical Oceanography: Evolution of the earth and morphology; minerals, rocks and sediments, basics of echo-sounding, sub-bottom profiling and side-scanning sonar methods.
Physical Oceanography: Physical properties of sea water, oceanic circulation, waves, oceanographic processes in the Turkish Seas.

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This course is intended to serve as an introduction to Geographic Information Systems (GIS) using ArcGIS software. The scope of the course is balanced between theoretical foundations and hands-on practical exercises. The practical exercises will be constructed relevant to marine sciences. The topics of interest include spatial data types, map projections and GPS, spatial operations on raster and vector data as as well as using model builder.

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The seafloor as one of the largest habitats on Earth, origin and properties; organic matter and particle fluxes to seafloor, geochemical properties of sediments, marine sediment biogeochemistry, organic matter degradation pathways in sediments, C, N, P, O, S cycles at the seafloor, benthic fluxes and benthic-pelagic coupling, chemosynthesis-driven ecosystems, deep-sea hydrothermal vents and midocean ridges, cold seep habitats and mud volcanoes, in situ sensors and platforms for seafloor biogeochemistry, effects of global warming on benthic processes, seafloor minearal and hydrocarbon resources and potential ecological effects of their utilization.

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This course is intended to serve as an introduction to R programming as well as statistical concepts and data analysis techniques relevant to students of marine sciences. The statistical topics of interest include descriptive statistics, probability and distributions, hypothesis testing for uni-variate, multivariate and categorical data-sets, regression, correlation and non-linear curve fitting. The R computational environment will be used to analyze oceanographic data sets through the numerical implementation of the methods learned in the lectures.

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This course is intended to provide graduate students of marine sciences an introduction to general ecosystem theory and mathematical concepts about and quantitative representation of trophic relationships between organisms/populations/communities within marine food webs along with the command of a widely-adopted marine ecosystem modelling tool Ecopath with Ecosim (Christensen et al.,2005). The topics of interest include, but not limited to foraging arena theory, ecological network analysis, ecological indicators, and quantification of ecosystem maturity/health.

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Historical perspectives on the development of ocean sciences, qualitative and quantitative approaches in marine research, meaning of data and their interpretation, types of research outputs and their impact, understanding the ethical issues in scientific research, application of research ethics to marine science specific issues.

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The main goal of this course is to give an introduction to theory and algorithms in the field of molecular evolution. Course will cover basic evolutionary theory (common descent, natural selection, genetic drift, models of growth and selection), and the main types of algorithms used for constructing and analysing phylogenetic trees (parsimony, distance based methods, maximum likelihood methods, and Bayesian inference). The role of statistical modelling in science more generally will be discussed also. The course will consist of lectures, computer exercises, and home works. The student will acquire practical experience in the use of a range of computational methods by analysing sequences from the scientific literature.

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General aspects of marine pollution, pollution; pollution from land-based sources; atmospheric input; distribution of pollutants in the marine environment; environmental impacts; strategies of marine pollution monitoring; trend monitoring, legislation.

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Principal physical and chemical properties of water and sea water; chemical composition of sea water; conservative/nonconservative and dissolved/ particulate components of sea water; source and sink terms; processes in the sea; nutrient and carbon cycles in the oceans; standard methods for chemical analysis of sea water.

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Sampling techniques dissolved and particulate chemical constituents in the marine environments (air, seawater, biota, sediment sampling); preservation techniques; in-situ and near real time measurements; instrumentation on board and laboratory; remote sensing techniques; processing interpretation and presentation of chemical data.

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A review of some elementary concepts in analytical chemistry; statistics used for the evaluation of analytical data; ionic equilibria in aquatic environment; solubility of ionic salts; acid dissociation and pH-pC diagrams; redox potential and pH-pE diagrams.

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The optical properties of the upper water column; photosynthetic activity; light adaptation; nutrient availability; nutrient uptake kinetics; primary production; remineralization processes and grazing; general aspects of the ecosystem of the lower trophic levels in the marine environment.

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Speciation of nutrients in seawater; sampling and measurement techniques; sources and removal processes; spatial and temporal distributions in the oceans and enclosed seas; nitrogen and phosphorus cycles in the sea, factors controlling the Redfield ratio (N:P); concepts of preformed and oxidized nutrients.

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The goal of this course is to lay out a frame work of principles that can be used to understand air pollution and global change problems. It will start with defining the basic physical and chemical principles governing the natural and polluted atmosphere. Then they will be applied to specific problems related to pollution and global change such as indoor pollution, urban photochemical smog, acid rain, stratospheric ozone depletion, greenhouse warming and climate forcing due to atmospheric aerosols. The course will also include some elements of air pollution statistics and introduction to the atmospheric chemical transport models.

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Descriptive and quantitative aspects of earth as bio-geochemical system; fundamental study methods of equilibria; transport processes; chemical kinetics; biological processes; their application to carbon, sulfur, nitrogen, phosphorus and other elemental cycles; stability of bio-geochemical systems; nature of human perturbation of their dynamics.

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Physical property fields, currents, waves and tides, general circulation of the oceans, T-S analysis, ocean-atmosphere interaction, oceanographic processes in the Turkish Seas.

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Basic review of calculus, physical properties of fluids, kinematics of the flow field, conservation of mass, forces and deformations in a moving fluid, stress and rate of strain tensors, derivation of the equations of motion, transformation to rotating earth, Bernoulli theorem, vorticity dynamics, viscous and irrotational flow examples for incompressible homogeneous fluids.

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Geophysical fluid dynamics, equations of motion applied to the ocean, Basic balances leading to geostrophic flow, inertial motion. Geostrophic degeneracy and closure. Shallow water equations, inertia-gravity and Kelvin waves, shelf waves, Rossby waves, quasi-geostrophic theory. Wind driven ocean circulation, examples of geophysical fluid dynamics problems.

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Irrotational motions with free boundaries, perturbations, linear and nonlinear theories, periodic and random waves, momentum and energy fluxes. Wave progression, dispersion, modulation, reflection, refraction, scattering, diffraction, radiation and the notions of phase and group velocities. The Cauchy-Poission problem, wave makers, wind waves, capillary and long waves, basin and edge waves, waves on beaches.

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Introduction to large ecosystems of the world oceans; Arctic, Pacific, Atlatic and Southern Oceans; Marginal Seas and Estuaries; El Niño Southern Oscillation and North Atlantic Oscillation, influence of physical properties on ecosystem dynamics, influence of climate variability and climate change on ecosystem dynamics.

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Turbulent motions, equations of motion, turbulent energy, Reynolds stress, energy flow, inhomogeneous fluids, conservation of scalar properties, Richardson number. Fundamentals of boundary layer theory, turbulent boundary layers, similarity theory and statistics. Effects of wall roughness, viscous sub-layers and turbulent skin friction. Oceanic and atmospheric mixed layer dynamics.

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This course is intended to introduce contemporary techniques used for the analyzing spatio-temporal data sets in oceanography. The topics of interest include data acquisition and processing, interpolation, empirical orthogonal functions, spectral analysis, wavelet analysis, digital filters and data assimilation. A high-level computational environment will be used to analyze oceanographic data sets through the practical implementation of the methods learned in the lectures.

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This course focuses on marine coastal eutrophication as one of the most important environmental problem for decades. Students will learn main soruces and impacts of eutrophicatoin, Nutrient levels, Direct and indirect effects of nutrient enrichments, Oxygen depletion (Plankton respiration), Algal blooms. Furthermore, students will learn how to use Eutrophication assesment tools, indexes and trend analysis. Related EU and National regulations will also be discussed to provide management of eutrophication in Turkish Seas.

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This course is aimed at providing a hands-on understanding of the dynamics of water and its ecosystems from headwaters to the sea in the Mediterranean catchments. The main objectives are to discuss water and mass fluxes throughout the catchments to the recipient seas as well as understand how these fluxes are modulated by lacustrine and riparian ecosystems and the vegetation in the catchment. The consequences of anthropogenic effects will also be elaborated. There will be four compulsory full day excursions to the headwaters. the rivers, the coastal wetlands and the wastewaters in the vicinity of Mersin.

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National and international funding opportunities; project life eyele towards; attaining external funding to research ideas; skills for transforming research ideas into granted projects.

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Analysis of periodic and aperiodic signals, discrete and fast Fourier transforms, covariance, spectral analysis of time-series, sampling, aliasing, digitization errors, random signals. Signal filtering, windowing, deconvolution, detection of signals in noise.

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Marine phytoplankton and their pigment structures. The importance of pigment measurements in the sea. Metabolism of plant cells and functions of phytoplankton pigments. Techniques in qualification and quantification of pigments and their temporal and spatial variability in oceans.

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Descriptive statistics, probability distributions, estimation and hypothesis testing. Analysis of variance, correlation and regression. Analysis of frequencies. Diversity indices, similarity-dissimilarity, cluster analysis, multidimensional scaling, principle component analysis.

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Introductory concepts, marine environment. Plankton and primary production, zooplankton, energy flow and mineral recycling, nekton, fish, benthos and benthic communities. Human impact on marine biota.

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Behaviour and orientation of fish. Influences of environmental factors; temperature, light and oxygen. Principles of applied oceanography. Sea surface temperature, mixed layer depth and stratification in the sea. Known links in fisheries oceanography; examples of stock collapse and recovery.

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Introduction and development of marine microbiology, Significance of marine microbiology in oceanography. Marine microorganisms: bacteria, fungi algae, colorless protozoa, their distribution in the sea and in the sediment. Influence of physical, chemical and biological factors on aquatic microorganisms. Microorganisms and water pollution. Role of microorganisms in the water. Economic aspects of water microbiology.

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Definitions, historical development and factors affecting fish stocks. Theory of fishing. Under and over-fishing problems and optimal fishery. Analytical and holistic models in single species fish stock assessments. Recruitment, growth and mortalities. Multi species approach. Data requirement, analysis and some application examples.

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Definition of pollution, kinds and sources of pollution, accumulation, storage and excretion of pollutants, transfer within the food chain, effects on marine organisms: Plankton, invertebrates and vertebrates.

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Definition of primary and secondary production. Phyto and zoo-plankton, sampling design and sampling techniques. Methods for measuring primary and secondary production, factors affecting primary production: nutrients, light and temperature, organic micronutrients and inhibitors, grazing, seasonal changes in primary and secondary production, role of primary production in marine economy.

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Divisions of marine environment. Classification of marine organisms: Phytoplankton, zooplankton, marine plants and invertebrates. Biology of marine organisms: Cnidaria, Ctenophora, Annelida, Mollusca, Arthropoda, Echinodermata, Crustacea and Tunicata, their habitat, feeding, reproduction and respiration.

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Rules of growth of aquatic organisms. Colonization and life conditions of inland waters. Biological self purification. Forecast of water quality. Loading capacity of waters. Performance of organisms in wastewater treatment plants.

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Classification of benthic organisms. Sampling of benthos; sampling methods, treatment and sorting of samples, preservation and storage of samples. Benthic organisms and pollution; effects of pollution on the distribution of benthic organisms in space and time.

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Introduction to marine zooplankton. General characteristics and classification. Sampling and processing techniques. Vertical migration and distributions. Physiology of zooplankton. Interaction with other marine organisms and relation to fisheries.

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Basic concept of marine geology including the structural and oceanographic setting, the ocean margins and oceanic sediments, as well as history and evolution of the ocean basins and Turkish Seas based on the analysis of marine geology and geophysics.

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Marine processes of erosion, transportation and deposition, composition, single-grain, texture and structural relationship of sediments. Consolidation of the water-sediment gas system; diagenesis. Sedimentary environment; examples of sedimentological problems relevant to coastal and seafloor engineering.

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Principles of seismic sequence analysis, seismic reflection configurations and stratigraphic interpretation of seismic facies, application of seismic reflection configuration to global changes of sea-level, sediment-bedrock relationships. Interpretation of tectonic and depositional systems on the continental shelves.

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Principal geochemical cycles and processes in the hydrosphere and lithosphere, radiometric dating.

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Comparison of types of continental margins. Deep and shallow geological structure. Processes of formation and evolution of continental margins. Petroleum and mineral deposits comparison to continental analogues.

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Sources of sediments, classification of ancient and modern sedimentary environment. Relationship between material and environment. Important factors controlling the type of deposited sediments. Structure of depositional environment, types of beddings and the texture of sediments.

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Approval by the Department.

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Approval by the Department.

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Approval by the Department.

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Approval by the Department.

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The course will cover the fundamentals of redox processes occurring in seas, oceans and coastal waters. Emphasis will be on redox reactions of oxygen and sulfur with metals such as iron, manganese and enzymatically important other cofactor metals. Microbial involvement in these processes will be emphasized. Another focus will be on the importance of metal redox biogeochemistry in the co-evolution of Earth and life and search of life in other potentially habitable ocean worlds emphasizing recent hot research topics in these emerging fields.

Course Content

This semester-long course comprehensively explores the design, development, and deployment of
chemical sensors in marine settings. It is structured to impart both theoretical knowledge and practicalskills, achieved through in-depth case studies and potential hands-on experiences. The course is highlybeneficial for students pursuing interests in marine science, environmental monitoring, andadvancements in sensor technology.

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Estuarine dynamics and its impact on ecosystem, and coastal morphology. Tidal and tidally averaged dynamics, lateral processes, influence of atmospheric forcing and morphology on flow patterns, boundary layer dynamics and turbulence, residence time, dispersion mechanisms, sediment transport, estuarine exchange and productivity (nutrients, oxygen, and eutrophication), estuarine ecosystems.

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Energy, Clouds and Climate is a course intended for the graduate students of marine sciences. The main goals of the course are to (a) give information about energy, energy in the biosphere clouds and climate, and (b) bridge the gap between energy and climate variability. The first chapter Energy covers the types of energy while the second chapter covers energy in the biosphere considering solar light, atmosphere, water, greenhouse effect and photosynthesis. The third chapter Clouds defines types and properties of clouds and their basic formation mechanisms. The last chapter Climate focuses on global climates, albedo, energy balance, climate change, past climate (beginning from Hadean), contemporary and future climate.