obligatory courses -...
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Obligatory Courses
227.4001 Biological Oceanography
Credits: 2
Lecturer: -
Type: Course
221.4001 Experiment planning, Data collecting and results analysing
Credits: 4
Lecturer: Prof. Ido Yitzhaki
Type: Course
Experiment planning, Data collecting and results analyzing: The course's goal is that students will acquire some skills of ecologic experiments planning, sampling and quantitative data collecting methods, processing and computed presenting of the data and conclusion concluding. Planning thesis and experiments, ecologic data analyzing, biotic and a-biotic sampling methods, ecological indexes, population's size evaluation methods, communities analyzing and spatial distribution of communities
227.4011 Geochemical Oceanography
Credits: 2
Lecturer: Prof. Barak Herut, Dr. Revital Bookman and Prof. Michael D. Krom
Type: Course
Geochemical Oceanography::This course will focus on two major aspects: chemical cycles in sea water and geochemical processes in marine sediment, especially the interaction between sea water and the sediment. Main concepts of interactions and processes, fluxes and reservoir, sources and sinks in marine environment, will be discussed. The course chapters will include understanding of chemical composition and properties of water, dynamic equilibrium in the sea water, dissolved gases in water, resistance time and mass balance of several elements. In addition, transportation of dissolved and particle mater from land to sea, distribution and composition of marine sediment precipitation and dissolving, digenesis and subsidence of sediments will be discussed. We shell study about chemical and geochemical processes in sediment, bioturbation, redox processes, and processes in the intermediate sediment-water such as interaction between volcanic rocks and sea water. Final grade will be composed of an exam and tutorials.}Geochemical Oceanography
227.4002 Departmental Seminar
Lecturer: Dr. Tamar Lotan
Type: Seminar
Departmental Seminar: A departmental seminary which is aimed to introduce an updated situation report of research areas by discussing articles from all disciplines of marine biology. Some of the subjects that will be discussed are: Global warming causes and effects, ocean acidification and its impact on flora and fauna, biogeochemical cycles, ecology and evolution, marine viruses and biotechnological developing from marine systems. An interdisciplinary discussion will occur after each lecture. The seminar will function as a workshop for presentation preparing in which a reciprocal feedback will be given.}Departmental Seminar
227.4444 School Seminar
Lecturer: Dr. Nicolas Waldmann
Type: Seminar
227.4007 The Mediterranean A
Credits: 2
Lecturer: Dr. Daniel Sher and Dr. Revital Bookman
Type: Course
The Mediterranean A: "The Mediterranean" course will discuss current topics relating to the Mediterranean, from natural sciences, social sciences and policy. The course will be divided into two semesters. During the first semester we will discuss the geology, geochemistry, oceanography, history and archeology of the Mediterranean. At the second semester we will focus on in-depth discussions of various aspects of pelagic, benthic and coastal ecosystems. We will end with a future outlook on the major challenges facing the Mediterranean, including sustainable fisheries, gas and oil exploration, desalination and other developmental programs. Each lecture will be given by an expert in the field, and will be accompanied by required reading material.
In addition to the lectures, the course will include three one-day field trips.
The course will be graded by two written projects ("home tests"), one for each semester, based on the material learned in the class. Participation in the lectures is mandatory.
227.4017 The Mediterranean B
Credits: 2
Lecturer: Dr. Assaf Yasur-Landau and Dr. Tamar Lotan
Type: Course
227.4003 Research Students' Forum
Credits: 2
Lecturer: Dr. Smadar Ben-Tabu De Leon and Dr. Laura Steindler [email protected] [email protected]
Type: SeminarThe research student forum is a seminar course which aims to increase the exposure of graduate students to
cutting edge research in biology, provide them with tools to critically read research papers, and train them in
analyzing and presenting scientific data.
Every student will give two presentations during the course, one in-depth seminar talk (30 minutes) and one
short conference-like talk (15 minutes). In each talk a student will present a recent paper published in one of
the leading, high-impact journals, including the relevant background to put the paper into context. The
papers will be chosen by the student in consultation with the teachers, and sent to the rest of the class
minimum 5 days before the lesson. A list of high impact papers recommended by the teachers will be
available for the students to pick from. The presentations will be followed by a discussion on both the paper
itself and the manner in which it was presented. The students will send a list of papers they read to prepare
their presentations to the teachers, and include it as a final slide in their talks. 80% attendance in the classes
is required for completion of the course.
Grading is based on the presentations and participation in discussions:
40%- in-depth paper presentation: focus, clarity and speaker proficiency in: question addressed by the
paper, background, methods used, results and their meaning, interpretation and discussion of the results and
significance of the work.
40% - short conference-like presentation: focus, clarity and speaker proficiency in: Scientific question,
background, approach, results, discussion and significance of the work.
20% - participation in discussions and reading the papers presented by other students.
Partial topics list:
1) Cell-cell communication in marine bacteria (e.g. quorum sensing)2) Marine symbiosis3) Marine photosynthesis/ photoheterotrophy 4) Coral reefs (Including corals, sponges, tunicates, echinoderms etc…)
5) Evolution and development 6) Regulation of gene expression7) Genome research (genomes, trasncriptomes, bioinformatics and related topics).
227.4005 Physical Oceanography for Biologists
Credits: 2Lecturer: Smadar Ben-Tabou de-Leon [email protected]
Tutor: Michal Grossowicz [email protected]
Type: Course
The course physical oceanography aims to teach advanced students about the physical properties of ocean
water and the physical processes within them, emphasizing the physical aspects that influence marine
organisms. The course will discuss external (e.g., sun and winds) and internal (e.g., temperature and density)
factors that drive physical processes in the ocean (currents, waves, stratification, ect.). Common
mathematical formalism used to study these processes and get predictions will be introduced and practiced.
The course will also describe the connection between physical factors and processes to biological processes
and ecological systems.
100% completion of the exercised and 80% attendance in the classes is required for completion of the
course.
Grading is based on exercises and a test:
30% - Exercises.
70% - Test.
Lectures and tutorials:
1. Basic aspects of Physical oceanography: Time and space scales. Temperature, salinity, pressure and
density and the relation between them (lecture).
2. Exercise #1: Mathematical basis for the course. Scalars, vectors, Cartesian and spherical coordinates,
scalar and vectorial multiplications, total and partial derivatives (tutorial).
3. Ocean stratification and stability. Basic conservation laws in oceanography, the continuity equation and
the equations of motion (lecture).
4. Exercise #2: Heat and solution to the equation of motion at special cases (tutorial).
5. Molecular diffusion, eddy diffusion, static and dynamic stability and how these processes affect mixing
and thermocline shape. Viscosity and turbulent motion (lecture).
6. Exercise #3: diffusion, stability and viscosity (tutorial).
7. Ocean – atmosphere interaction: wind stress and waves, Ekman layers and transport (lecture).
8. Exersice #4: Ekman dynamics and flow (tutorial).
9. Geostrophic flow, ocean waves and tsunamis (lecture).
10. Exercise #5: Solution of wave equation (tutorial).
11. Ocean tides, light and water (lecture).
12. Exercise #6: tides and light (tutorial).
13. State of the art in physical oceanography (Guest lecture – Hezi Gildor).
227.4014 Research methods in Marine Biology and Biological Oceanography
Credits: 4
Lecturer: Dr. Daniel Sher and Dr. Tali Mass
Type: Workshop
Non Obligatory Courses
227.4100 Marine Biology of Climate Changes
Credits: 2
Lecturer: Dr. Dan Tchernov
Type: Course
Marine Biology of Climate Changes::Climate changes throw the geological history of earth have been the main evolution engine that has designed the living world. The course will instill knowledge of climate influence on physiology, biochemistry, molecular level and evolution of a number of main taxon in the living world.
227.4004 Marine Ecology
Credits: 2
Lecturer: Prof. Baruch Rinkevich
Type: Course
The Marine Ecology course will be engaged with various aspects in the ecology of marine multicellular organisms, including vertebrates and invertebrates. A special attention will be given to ecological parameters and properties distinguishing marine from terrestrial ecosystems. Major chapters and topics:
1. Marine ecosystems : plankton vs. benthos, tidal, intertidal and the deep sea. Highlighting specific ecosystems (marsh tidal, reef corals, mangroves and algal kelps).
2. Marine biogeography : dispersion, distribution, invasion, larval ecological aspects, connectivity, population genetics.
3. Interactions : inter- and intra-specific interactions, predation, parasitism, commensalism, symbiosis.
4. Ecological aspects of : sessile mode of life, living in 3D, chimerism, pattern formation of complex structures
5. The man and the sea : Uses: fishery, mariculture, coastal development, tourism, novel bioactive compounds, marine mines. Anthropogenic impacts: pollution, global changes (El-Ni?o, ozone layer, green-house impacts). Management and restoration of marine biodiversity, marine protected areas.
Textbooks:
1. Kaiser, M. et al., Marine ecology: Processes, systems and impacts. Oxford University press, 2005. IBSN: 0-19-1924975 – X.
2. Barnes, R. and R. N. Hughes, Introduction to marine ecology. Blackwell, 1999. ISBN- 0865428344.
Course schedules and students' assignments:
During the semester we shall have 7 lectures, each 4-h duration. Students should attend at least 6/7 meetings (only military service and documented illness are exempted).
The vast majority of chapters 1,2 and part of chapter 5 material will be delivered through self-reading from the two textbooks.
Each student will deliver a seminar on a topic, provided during the first lecture. Each student will prepare a power-point talk (about ½ h), a summary and 2 key papers (will be delivered to the class 2 weeks before the talk) and written seminar paper.
Grades:
Participation and discussion in the class 10%*Seminar presentation 25%Written seminar 25%*Final exam (including material: the topics of books’ chapters, seminars, content of key papers, frontal lectures) 40%
227.4006 Marine Microbial Ecology
Credits: 2
Lecturer: Dr. Daniel Sher and Dr. Laura Steindler
Type: Course
Marine Microbial Ecology::Microorganisms are the most dominant life form in marine environment and they function in key positions in marine food web and in global geochemical cycles. This course will deal with marine microorganisms – Bacteria, Archaea, Protists and Viruses – from biological point of view, and will discuss their adaptations to life in sea, the diverse interactions among them and the way the microbial population in sea influence life on earth. Some of the subjects that will be included in the course are: physical conditions of microbial world (diffusion, motion and meeting rates in viscous world), phytoplankton as an example of minimal organism, different life strategies of heterotrophic organisms, phages and their complex interactions with their host, eukaryotes' algae in the changing world, interactions between microorganisms and corals, dynamic models of microorganisms distribution etc.
227.4008 From Science to Industry
Credits: 2
Lecturer: Dr. Tamar Lotan
Type: Course
221.4422 Developmental Biology and Evolution of Marine invertebrates
Credits: 2
Lecturer: Dr. Ram Reshef
Type: Course
Developmental Biology and Evolution of Marine invertebrates::tip The course will focus in ontogenesis of marine organisms of several taxonomic levels. The developmental processes from its morphology to its molecular level will be studied. We shell track the development of Cindaria, Mollusca and Echinodermata systems.
227.4013 From genes to oceans: Bioinformatics approaches in Marine Biology
Credits: 4
Lecturer: Dr. Daniel Sher
Type: Course
From genes to oceans: Bioinformatics approaches in Marine Biology::Modern microbial oceanography relies heavily on the analysis of genes and proteins from marine organisms to help understand how these organisms adapt to life in the marine environment. Students will learn the basic concepts, approaches and tools used for bioinformatic analysis of sequence data, and will utilize these tools to analyze genomic and metagenomic data from the oceans. Students will also critically assess the current literature describing genomic, metagenomic and proteomic analyses from the marine environment. We will discuss how microbial genomes are built, and what shapes them in the marine environment; how are genes lost and gained through lateral transfer; viruses and their role in genomic evolution, and how the gene content of different environments can teach us about the selection pressure in that environment. Technical topics covered will include: Selection pressure on DNA, RNA and proteins, genomic architecture, sequence alignment, gene identification and phylogenetic assessment, sequencing and assembly methods, comparative metagenomics and proteomics. The course will include lectures, hands-on computer tutorial and student seminars. The final grade will be composed of 30% seminar and 70% final project.
Sea and Coastal Pollution
Credits: 2
Lecturer: Dr. Dror Angel
Type: Course
Sea and Coastal Pollution::Introduction to marine environmental problems and challenges world-wide, and especially in Israel. Introduction to diverse types and sources of pollution, their behavior in marine environment and way to measure water and sediments quality.
221.4004 Ecology of Populations
Credits: 2
Lecturer: Prof. Ido Yitzhaki
Type: Course
Ecology of Populations::Description of population structure by using life tables; competition between species; population size regulation; population's growth and competition models; prey-predator interaction; strategies; life stroke; introducing computer's software and internet's websites for population modeling..
221.4007 Genetics of Populations
Credits: 2
Lecturer: Dr. Rachel Ben-Shlomo
Type: Course
Genetics of Populations::The course aim is to teach different methods of description of population genetic structure, effecting factors and their evolutionary importance. The course will deal with the following subjects: genetic variance in populations, Hardy-Weinberg steady state, indexes for ecology diversity's assessment, influence of selection types on polymorphism and heterozygotic levels, reproduction and organization methods, populations' characterization, etc.
227.4015 Rocky shore ecology
Credits: 3
Lecturer: Dr. Gil Rilov
Type: Workshop
Topic: the rocky shore is an extreme and fascinating environment that for several decades serves as a test-bed for experimental ecological research and for the development of ecological theory. This course reviews in detail the history, theory and methods of research in this ecosystem and uses hands-on experience to examine several major topics. Among the topics we will discuss are:
The unique conditions of life in the intertidal zone and the way organisms there deal with extreme conditions of desiccation and wave action.
The special patterns that develop in this ecosystem such as vertical zonation and patchiness. Species interactions such as competition, predator-prey interactions and facilitation and how
scientists test the importance of these processes in the system. The important links between coastal oceanography and ecological processes on the shore including
the supply of nutrients and the role of larval transport, settlement and recruitment to the adult populations.
The biogeography of biodiversity and the human impacts on biodiversity and ecosystem structure and function (e.g., bioinvasions, climate change, local stressors).
The Israeli Mediterranean perspective: During the course we will pay special attention to the unique rocky shore ecosystem on the Israeli coast – the vermetid (abrasion) reefs – an ecosystem under an extinction threat. We will discuss recent findings on the ecology of this system from studies conducted in the last 3 years and the present research that is being held at IOLR. The students will participate in biodiversity surveys and will study basic analysis of biodiversity data. They will also conduct short experiments in the lab and possibly field, testing for example the predation rates of crabs and larval settlement variability of invasive mussels. The students will work in small groups on specific projects and will write a short report in a scientific paper format that will be part of the overall course mark.
Format: This is an intensive five-day course that will take place at the National Institute of Oceanography of IOLR in Shikmona, Haifa, and will include every day lectures intermittent with field sampling, lab work, data analysis and interpretation. Several scientific papers will be given to the students for reading prior and during the course (for writing of the reports).
The mark will be based on a final exam (50%), project report (40%) and general participation (10%).
The course is open to 6-12 students
The students must be equipped with basic clothing and gear for working in the marine environment
224.4004 Geology of the Eastern Mediterranean
Credits: 2
Lecturer: Dr. Uri Schattner
Type: Course
Geology of the Eastern Mediterranean::During the course we will discuss the geology processes that have shaped the Mediterranean and especially its eastern part. The course will include several opening and summary lectures in the following subjects: present structure of the Mediterranean, tectonics, Mediterranean's formation, Levantine continental margins, Eratosthenes seamount, the Messinian event, Cyprus arc, the Carmel structure, young tectonics in Levant margin, the Nile and its deposits, Hellenic arc and Aegean sea, tsunami and earthquakes in Mediterranean region.
Final grade will be decomposed of presence and participating in class, frontal presentation (20 minutes) and written work (10 pages) on a Mediterranean geology subject.
221.4405 Advanced Biostatistics
Credits: 2
Lecturer: Prof. Ido Yitzhak
Type: Course
221.4416 Introduction to Phylogenetic Evolution
Credits: 2
Lecturer: Dr. Sagi Snir
Type: Course
227.4018 Biological Regulation in Development: from Genes to Embryos
Credits: 2
Lecturer: Smadar Ben-Tabou de-Leon, Department of Marine Biology
Type: CourseThe course will discuss the various molecular mechanisms that regulate differential gene
expression and cell fate specification and the formation of complex embryonic morphologies. The
course will present: 1. Principles of biological regulation: transcriptional regulation, chromatin
structure, post-transcriptional and post-translational regulation, 2. up to date experimental
techniques in molecular biology, imaging, and high-through put sequencing that is relevant to the
studies of biological regulation, and 3. mathematical models that simulate the kinetics of gene
regulatory circuits through embryogenesis. Specifically, the following aspects of regulatory control
will be covered: basic mechanistic aspects of transcription and gene regulation, dynamics of
transcript synthesis and turnover, enhancer design and function, design principles of regulatory
circuits, gene regulatory networks, whole genome expression profiles and global regulatory
networks, chromatin structure and cellular memory, microRNA and short RNAs, and post-
translational regulation.
The format is lecture plus discussion. Two problems will be assigned during the semester and the
solutions will be presented in the class by students in the following weeks (each presentation will be
15% of the grade). At the end of the semester the students will write a short review paper based on
the material learned in the class and the home assignments (70% of the grade). Participation in the
lectures is mandatory.
Lectures:
1. Overview of the basic mechanistic aspects of the regulation of transcription and translation.
2. Transcription initiation rates: Transcription factor DNA binding affinity, binding and unbinding
kinetics, enhancer logic processing.
3. Regulatory control of spatial gene expression and enhancer spatial processing function.
4. Principles of gene regulatory circuits design – exclusion circuitry and feedforward circuits
(examples and model). Home problem assigned.
5. Regulatory state activation by inductive intercellular signals, lock-down by positive feedback
circuitry and cis-regulatory module switching.
6. Evolutionary conservation in developmental regulatory networks: Axis formation by Wnt and
BMP pathways and Wnt role in endodermal specification.
7. Whole genome transcriptional profile and RNA-seq. Guest speaker, Dr. Noa Sher.
8. Short student presentations presenting their home assignment. Home problem assigned.
9. Post-transcriptional regulation: MicroRNAs, other non-coding RNAs and RNA binding proteins.
Guest speaker: Dr. Hila Toledano.
10. "mRNA coordinators": novel kind of factors that integrate all stages of gene expression into a
system, Guest speaker: Prof. Motti Choder.
11. Post-translational regulation: The proteosome and Ubiquitination. Guest speaker: Dr. Tsvia
Gildor.
12. Short student presentations of home assignments.
13. Course Summary, a model for basic mechanistic aspects of the regulation transcription and
translation.
227.4020 Research Methodologies in Bioinformatics
Credits: 2
Lecturers: Dr. Daniel Sher, Dr. Mickey Kosloff, Dr. Eyal Privman
Type: Course
Modern biological research relies heavily on the analysis of genes and proteins. Recent technological advances (such as next generation sequencing and tandem mass spectrometry) led to exponential growth of biological databases and allow us to analyze whole genomes, together with many thousands of gene expression patterns, protein structures, and protein-protein interactions. Such research requires sophisticated computational tools.
Students will learn basic concepts, approaches and tools used for bioinformatic analysis of sequence data (DNA and protein) and structural data (protein). We will discuss the design principles of prokaryotic and eukaryotic genomes, as well as the environmental and evolutionary forces shaping genomes. Technical topics covered will include: genomic architecture, gene identification, characterization, and annotation, sequence alignment, phylogeny reconstruction, selection pressure on DNA, RNA and proteins, protein 3D structure visualization and comparison, quantitative methods for protein structure analysis, structure prediction, genome/transcriptome sequencing and assembly methods, and gene/protein networks. The course will include lectures and hands-on computer tutorials. Prerequisite courses include biochemistry, molecular biology and genetics.
Grade composition: 70% final exam and 30% written tutorials (the exam can be substituted with a final project if approved)
Environmental genomics and the human microbiome
Credits: 2
Lecturer: Dr. Daniel Sher, Dr. Noa Sher
Type: workshop
The workshop will be not taught every year
Non Obligatory Courses in IUI
Research Methods in Oceanography (in IUI)
Credits: 3
Lecturer: Prof. Boaz Lazar and Prof. Yonatan Erez
Type: Course
Venom Mechanisms and Chemical Protection in the Sea (in IUI)
Credits: 3
Lecturer: Dr. Daniel Sher
Type: Course
Understanding the Ecosystem of the Gulf of Eilat (in IUI)
Credits: 3
Lecturer: Dr. Yeala Shaked
Type: Course
Marine Sedimentology: collecting samples, documentation and analysis of sediments
from the Gulf of Eilat (in IUI)
Credits: 3
Lecturer: Dr. Beverly Goodman and Dr. Timor Katz
Type: Course
-
Rhythmic and cyclical marine systems (in IUI)
Credits: 3
Lecturer: Dr. Oren Levy and Itzik Brinker
Type: Course
Knowing the Plancton (in IUI)
Credits: 3
Lecturer: Prof. Amazia Ganin and Dr. Bracha Farstey
Type: Course
Nano syringes jellyfish and corals - injection system 700 million years old (in IUI)
Credits: 3
Lecturer: Dr. Tamar Lotan
Type: Course
Biogeochemistry of Nutrients in the Open Sea (in IUI)
Credits: 3
Lecturer: Dr. Yeala Shaked
Chapters In the Classification and Biology of the Red Sea Invertebrates (in IUI)
Credits: 3
Lecturer: Dr. Yehuda Benayahu
Type: Course
Quantitive Methods of Marine Ecology (in IUI)
Credits: 4
Lecturer: Prof. Amazia Ganin, Dr. Moshe Kiflawi and Dr. Roi Holtzman
Type: Course
Marine Microbiology (in IUI)
Credits: 4
Lecturer: Prof. Oded Beja, Prof. Aharon Oren and Dr. Rakefet Schwarz
Type: Course
Biology of Corals (in IUI)
Credits: 4
Lecturer: Dr. Dan Tchernov and Dr. Maoz Fine
Type: Course
Geology and Geophysics of the Marine Environment (in IUI)
Credits: 2
Lecturer: Prof. Amotz Agnon
Type: Course
Marine Photosynthesis (in IUI)
Credits: 3
Lecturer: Prof. Sven Beer, Dr. Dan Tchernov
Type: Course
Advanced Methods in neurophysiology (in IUI)
Credits: 4
Lecturer: Prof. Yosi Rom
Type: Course
Biogeochemistry of Coral Reefs
Credits: 3
Type: Course
Topics in Physical Oceanography
Credits: 3
Lecturer: Prof. Hezi Gildor, Prof. Yosi Ashkenazy
Type: Course
Advanced Topics in Physical Oceanography
Credits: 2
Lecturer: Prof. Yosi Ashkenazy, Prof. Yohai Caspi
Type: Course