Siberian Federal University

Objectives and learning outcomes

The course focuses on the application of contemporary concepts and methodology of physical sciences to the solution of biological problems. Students completing the course shall be able to:

• understand the fundamental processes of life by applying the methodology of physics to biological systems;
• apply novel theoretical and experimental methodology for solving particular research problems in biophysics.

Contents

This course is designed to provide students with the knowledge, skills and analytical capabilities needed to reflect on and discuss key problems of biology: biological evolution, origin of life, key characteristics of life as a phenomenon, principles of living beings organization; structure-function relationship in living systems.

During the course practical seminars will be offered which will allow the students to apply modern theoretical and experimental approaches in order to research biological systems at molecular, cellular and other levels.

Course components

• 8 hrs interactive lectures.
• 16 hrs seminars.
• 84 hrs self-study time, including home assignments.

During classes all information is given in an interactive form with the use of various handouts. Focus on reflection and discussion. Short assignments for doing in class or as homework.

Assessment

60% written exam, 40% class participation.

Core reading

Extensive course manual compiled by professors of the Biophysical Department of the Siberian Federal University (Valentina Kratasyuk, Irina Sviderskaya, Irina Siukovataya et al).

The manual includes detailed course program, guidelines for seminars and self-study, various thematic materials, including lecture handouts, PowerPoint presentations as well as other additional materials required to complete the assignments.

Objectives and learning outcomes

The course focuses on exploring basic and applied aspects of bioluminescence.

After successfully completing the course students:

• shall be able to understand basic mechanisms of bioluminescence of various luminous organisms;
• shall have a good knowledge of the main principles and methods of bioluminescent analysis and their application in biology, ecology, medicine etc.

Contents

Specific topics covered in the course include:

1. Overview of bioluminescence: bioluminescence in nature, luciferases and luciferins, photoproteins, biochemistry and biophysics of bioluminescence, spectra in bioluminescence;
2. The luminous bacteria environment and basic properties, structure of their bioluminescent system, biochemistry and molecular biology of bacterial bioluminescence, kinetics of bioluminescent reaction mechanisms;
3. Terrestrial bioluminescence: firefly and insects, bacteria, fungi, mollusks, arthropods and earthworms;
4. Marine Organisms Bioluminescence: luminous fishes, jellyfish, shrimps, etc.;
5. Bioluminescent analysis;
6. Green Fluorescent Protein and other fluorescent proteins and their applications;
7. Applications of Bioluminescence.

Course components

• 10 hrs lectures.
• 20 hrs seminars.
• 78 hrs self-study time.

Assessment

60% test, 40% class participation

Core reading

1. Comprehensive tutorial created specifically for this course by teams of scientists from the two institutions: Siberian Federal University and the Research Institute of Biophysics (Siberian Branch, Russian Academy of Science). The course tutorial consists of three parts: Bioluminescence of bacteria; Coelenterazine-dependent bioluminescent systems; Under-investigated bioluminescent systems.
2. Shimomura, O. Bioluminescence: Chemical Principles and Methods. Singapore: World Scientific, 2006.
3. Five video lectures on Bioluminescence Mechanisms by Professor John Lee (available at the Siberian Federal University website http://tube.sfu-kras.ru/video/1134).

Objectives and learning outcomes

The objective of the course is to enable students to build up their knowledge and skills pertaining to the use of living organisms for solving real-world problems related to the life sciences.

Students will be encouraged to develop their own engineering solutions by means of analytical, synthetic or combined methods.

After completing the course students should be able to apply the principles of biology and engineering tools in order to create tangible bioluminescent products to be used in real-world situations.

Contents

The course begins with an outline of major trends in biological engineering focusing students’ attention on the following topics: biosensors and biochips as a part of the huge and rapidly evolving areas of biomolecular and bioanalytical sciences.

The subsequent chapters of the course concentrate on the various aspects of biosensors design: biological and molecular recognitions systems, transducers for biosensors and bio-array technologies, miniaturized and micro-engineered systems. Special emphasis will be made on current methods of enzymes immobilization and applications of immobilized enzymes for medical diagnostics, environmental monitoring, pharmaceutical and food industries.

Course components

• 16 hrs lectures.
• 32 hrs practical classes.
• 60 hrs self-study time.
• 36 hrs self-preparation for exam.

During classes all information is given in an interactive form with the use of handouts. Focus on reflection and discussion. Short assignments for doing in class or as homework.

Assessment

60% test, 40% class participation.

Core reading

1. Marks, R.S, Lowe, C.R., Cullen, D.C., Weetall, H.H. et al (Eds.). Handbook of Biosensors and Biochips. Hoboken, NJ: John Wiley & Sons, 2007.
2. Serra P.A. (Ed.). New Perspectives in Biosensors Technology and Applications. InTech, 2011.
3. Flynne, W. G. (Ed.). Biotechnology and Bioengineering, NY: Nova Science Publishers, 2008.
4. Cooper, J., Cass T. (Eds.). Biosensors. Oxford: OUP, 2004.

Objectives and learning outcomes

Through this course students will obtain knowledge about the main principles of photobiophysics and all aspects of photoreactions: from the elementary phenomena and laws, through reactions and apparatus review to practical aspects of photochemistry, photobiology. Students will also learn about and acquire the ability to interpret different aspects of photobiophysics in the natural environment.

Contents

• Chapter 1 Introduction to photobiophysics. Primary and secondary photochemical processes;
• Chapter 2 Bio-, photo-, electro-, sono- and chemiluminescence, fluorescence, phosphorescence, absorption of electromagnetic radiation;
• Chapter 3 Kinetics of photoreactions. Stern–Volmer equation. Chain reaction in nature. The types of photoreactions with examples: photodissociation, photocyclization, photoisomerization, photosubstitution;
• Chapter 4 Photosynthesis: photobiochemistry and photobiophysics;
• Chapter 5 Spectroscopical methods: X-ray crystallography; NMR spectroscopy; molecular modelling; computational methods in biochemical systems; protein–DNA interactions and others.

Course components

• 10 hrs lectures.
• 20 hrs seminars.
• 78 hrs self-study time.

During classes all information is given in an interactive form with the use of handouts. Focus on reflection and discussion. Short assignments for doing in class or as homework.

Assessment

60% exam, 40% class participation.

Core reading

Team of scientists led by Professor Valentina Kratasyuk (program leader of Master in Biophysics) has developed a special training kit for this course, which besides detailed methodological guidelines and presentation materials includes a DVD with a set of training tests.

• Smith, K.C. (Ed.). Photobiological Sciences Online. Washington, DC: American Society for Photobiology.
• Lakowicz, J.R. Principles of Fluorescence Spectroscopy, 3rd ed. New York: Kluwer Academic/Plenum Publishers, 2006.
• Björn, L.O. (Ed.). Photobiology. The Science of Life and Light. New York: Springer Science+Business Media, 2008.

Objectives and learning outcomes

The practicum provides an opportunity to master main techniques for measuring bioluminescence in vitro and learn to apply them in such fields as environmental monitoring, medical diagnostics, pharmaceutical and food industries.

The course also allows students to investigate the fundamental principles of physics, chemistry and biology using the phenomenon of bioluminescence, which serves an important tool for science education as it help to visualize many biological and physical processes.

After completing the course students should be able to:

• implement experimentally different types of bioluminescent reactions;
• understand the principles of bioluminescent assays as applied in environmental monitoring, medical diagnostics, pharmaceutical and food industries, etc.;
• formulate his/her own suggestions as regards how various bioluminescent techniques can be used in education (in the fields of biochemistry, microbiology, molecular biology and biotechnology, ecology, etc.)

Contents

The course is built up around three main topics: principles of bioluminescent assays, media effects on bioluminescence efficiency and application of bioluminescence in teaching biochemistry.

During the course students will execute a number of laboratory tasks that envisage performance of various bioluminescent reactions related to the abovementioned topics.

On the basis of one selected task an individual research project is to be developed by each student.

Several examples of laboratory tasks:

1. Proteins of bioluminescent system: preparation and study of their properties;
2. Kinetic of enzymatic reactions based on bacterial bioluminescent system;
3. Enzymes of bacterial bioluminescent system as a tool for investigation of physicochemical and structural properties of proteins;
4. Implementation of enzymes of bioluminescent system of luminous bacteria in biotesting.

Course components

• 4 hrs introductory classes.
• 28 hrs lab practice (experiments).
• 4 hrs problem session (presentation of projects).
• 72 hrs self-study time, including project preparation.

Assessment

Combination of written exam (40%) and project (60%).

Core reading

For students following the course there is a special set of materials available which is prepared by biophysics scientists from the Siberian Federal University as well as the Research Institute of Biophysics (Siberian Branch, Russian Academy of Science). The said educational materials are based upon original research of the authors.

Objectives and learning outcomes

This course is intended for ESL students. The course aims to teach the fundamentals of effective scientific communication in English. Instruction will focus primarily on the process of writing original manuscripts for professional journals and presenting research results at conferences.

Contents

The course will be presented in segments: structure, vocabulary and grammar of scientific papers, scientific English, oral and visual presentations.

Science writing as a story telling. Paper structure: IMRAD and other formats. Writing introduction, methods, results, discussion and conclusion. Challenge, hypothesis, objective. Scientific English (words, sentences, paragraphs). Tables and figures. Writing global science. Abstracts. Preparing slides, text and speech for presentations.

Course components

• 18 hrs lectures.
• 12 hrs individual counseling.
• 34 hrs practical classes.
• 20 hrs problem sessions.
• 26 hrs individual project.

Assessment

Combination of written exam (50%) and project (50%).

Objectives and learning outcomes

The aim of the course is to develop an understanding of ecosystem services and their role in development of different territories and to learn how to transfer the techniques of ecosystem services assessment into policy-making process.

By the end of the course successful students should acquire the concept of “ecosystem services”, their classification and environmental and economic values, and be able to:

• identify ecosystem service providers, major stakeholders and instruments (legislative, economic, educational, social, etc.) of ecosystem services governance;
• apply research-related methods of ecosystem services assessment for different types of territories (forest, wetlands, urban, agro, recreational, protected areas, etc);
• develop an algorithm of ecosystem services assessment for a specific territory and design a lay-out for its implementation in decision-making process;
• identify risks related to ecosystem degradation and propose to local authorities and business possible solutions for restoration and support of ecosystem services.

Contents

This interdisciplinary course aims to introduce students to new instruments of nature conservation and is based on three pillars: 1) Ecosystem Science – studying various ecosystems, their components and elements; 2) Economics – using economic methods of assessment of ecosystem services; and 3) Political Science – applying planning and management instruments in decision-making process.

Emphasis will be placed on implementation of new concepts and instruments to the ecosystems governance. In addition, the course includes sessions with practical exercises on assessment methods, demonstrating good and bad practices. The course also gives a perspective on broader international context of ecosystem services by engaging students into analysis of real cases from Russia, Ukraine and other countries.

Course components

• 10 hrs lectures.
• 20 hrs seminars with group discussions and practical exercises.
• 78 hrs self-study time.

Assessment

60% exam, 40% class participation.

Core reading

Course manual and additional materials.

Objectives and learning outcomes

Practical skills and techniques development, introduction to new research methods, and application of the obtained skills during the experimental work on the modern equipment.

After completing the course student will be able to design and present professionally research and experimental results.

Contents

1. Possibilities and limitations of the various physicochemical methods of biological objects analysis.
2. Learning of traditional and ‘cutting edge’ scientific techniques and procedures.
3. Experimental data processing methods.
4. Presentation of the results in the form of research reports, manuscripts, presentations for scientific conferences.

Course components

• 4 hrs lectures.
• 10 hrs individual or group counseling.
• 70 hrs individual or group research study.
• 8 hrs scientific seminars (presentation of reports on the results of the study; discussion).

Assessment

1. A written report on the results of research study.
2. Presentation of research results at a scientific seminar.

Core reading

Original materials prepared under the guidance of the head of the master's program V.A. Kratasyuk, including instructions and technical specifications.

Objectives and learning outcomes

This course aims to encourage research skills by students through an individual research project in biology, biological engineering or biophysics. Students will follow all steps of research process from the problem statement to the achievement and analysis of experimental results.

Contents

1. Formulation of the goals and objectives of the study.
2. Planning the survey.
3. Evaluation and selection of appropriate methods, development of the new approaches.
4. Obtaining and interpretation of the results.
5. Report of the research project results in the form of scientific work (master’s thesis).

Course components

• 10 hrs individual counseling.
• 70 hrs work on individual research project.
• 4 hrs project presentation.
• 4 hrs problem session.

Assessment

Defense of the master’s research project (draft master’s thesis).