Plant Biology, courses 2011 - 2012 - Department of Biosciences

526031 Physiological plant ecology ( Fysiologinen kasviekologia ) (3 cr)
Timing: 5.9. – 18.10.2011 except 21.9. Monday-Wednesday 8:15–10:00; 19.10. Wednesday 8:15-12:00.
Place: BIO3 6602, except 12.-14.09. and 10.-12.10 BIO3 6406, 19.-20.09. and 3.-5.10 BIO3 5405,
Responsible person: Yliopistonlehtori Pedro Aphalo /KB
Prerequisites: No formal prerequisites, but basic knowledge of ecology recommended.
Aim: To prepare students to be able to comprehend the scientific literature in physiological plant ecology by teaching them the specialized language, research approach and basic concepts of this branch of ecology.
Content: Bases and definition of physiological plant ecology. Adaptation and acclimation of plants to their environment. Carbon balance. Water relations. Mineral nutrition. Dry matter production and growth. Biological interactions. Stress. Adaptation of plants to cold climates.
Literature: Obligatory: material provided during lectures and in Moodle. Supplementary: Larcher, W (2002) Physiological Plants Ecology. Some chapters from Taiz, L and Zeiger, E (2006) Plant Physiology and Gurevitch, J et al. (2006) The Ecology of Plants.
Course home page: http://blogs.helsinki.fi/aphalo/teaching/courses/ecophys-course/
Evaluation: Written home exam, quizzes in Moodle, and participation in discussions in Moodle and during lectures. Scale: 0-5.
Exam: Home exam, repeats by agreement.
Enrolment: Weboodi from 1.8.

52512 Advanced Course on Plant Physiology and Molecular Biology (7 cr)
Time: 6.9. - 17.10.
Place: BIO3, 6th floor
Responsible person: Universitetslektor Mikael Brosché/KB
Prerequisites: Biotieteiden perusteet II sekä Kasvianatomian ja fysiologian harjoitustyöt.
Aim: Learn how to use the latest techniques in plant molecular biology including gene expression analysis, mutant genotyping and protein characterization.
Content: Introductory lectures to the methods to be used. Small group (2-4 people) laboratory projects.
Course tasks: Lectures and laboratory work with obligatory participation, research work in groups, written report and seminar presentation.
Literature: Articles and other publications on the methods used.
Evaluation: Written lab reports and/or oral presentations of the results. Grading scale 0-5.
Exam: none
Enrolment: Deadline for registration is August 30th in Weboodi. Maximum number of students: 8

526114 Cladistics literature seminar (3 ECTS)
Aika: Mon 12.9.2011-27.2.2012 (preliminary, the actual time and number of meetings will be fixed at the first meeting)
Paikka: Seminar rooms of the botanical and zoological museums.
Vastuuhenkilö: Jaakko Hyvönen /KB
Ennakkovaatimukset: 526084 Essential cladistics or equal knowledge of the basic terminology and concepts.
Tavoite: The aim of the seminar is to make participants familiar with some of the most fundamental and central articles of the field, and encourage critical evaluation of the basic concepts.
Kirjallisuus: Important articles of the field, mostly, but not restricted to, those published in the journal Cladistics.
Ilmoittautuminen: By e-mail to jaakko.hyvonen@helsinki.fi 15.8. at latest.

52549 Wood structure, growth and differentiation (4 cr)
Time: 3.10.-14.10., Mon–Fri klo 13–18.
Place: BIO1 1026.
Teacher: Univ. lecturer Kurt Fagerstedt /Plant Biology
Prerequisites: Biotieteiden perusteet I and II and kasvianatomian harjoitustyöt
Aims: To understand how different organic polymers form the plant cell wall and learn to know how the xylem differentiates and what factors affect it. To learn to know the differences in wood anatomical features in various tree species.
Contents: In the lectures we will go through the anatomical structure of different tree species, wood growth and differentiation of the xylem and factors affecting it, and the chemical compounds forming the plant cell wall and their biosynthesis.
In the practical part of the course we will go through stained microscopical slides of a variety of xylem samples of mainly Finnish tree species, and learn to make such sections with the cryomicrotome and stain the sections for light and fluorescent microscopy.
Literature: Fagerstedt, Pellinen, Saranpää & Timonen 2005: Mikä puu – Mistä puusta, Yliopistopaino and other recent articles. The material will be in Moodle.
Marking: Written exam at the end of the course, grading 0-5/5.
Exam: Fri 21.10. 13-15 BIO1 1026
Registration: Weboodi

52537 Lectures in Plant Stress Physiology (3 cr) (KTB403, organized jointly with Faculty of Agriculture and Forestry).
Time: 31.10.-13.12., Mon and Tue 10-12.
Place: LS C2
Teachers: Univ. lecturer Kurt Fagerstedt /PB and Prof. mvs. Mervi Seppänen
Prerequisites: Biotieteiden perusteet I and II and kasvifysiologian ja -anatomian
harjoitustyöt.
Aims: To understand how plants cope with various stress conditions.
Contents: In the lectures given by a bunch of experts material on various stress conditions and how plants adapt to these with anatomical, physiological and genetic means will be dealt with in detail.
Literature: Recent articles and PDF-files of the lectures in Moodle.
Marking: Written exam, grading 0-5/5.
Exam: Tue 13.12.2011, 10-12. LS C1.
Registration: Weboodi

52538 Practical Course in Plant Stress Physiology (2 cr) (KTB404, organized jointly with Faculty of Agriculture and Forestry)
Time: 31.10.-2.12., time table will be negotiated with students.
Place: Introduction Mon 31.10. 12-14 LS C2. Course labs 1026 (BK1) (7.11.-18.11.) and C134 (21.11.-2.12.)
Teachers: Univ. lecturer Kurt Fagerstedt /PB and Prof. mvs. Mervi Seppänen
Prerequisites: Lectures in plant stress physiology (52537)
Aims: Learn to use various methods to determine how plants adapt to different stress conditions on physiological, anatomical and molecular biology levels.
Contents: During the practical course the following topics will be covered: Photosynthesis and ion leakage, cold tolerance, methods for the microscope section preparation, and mitochondrial functions during oxygen stress.
Literature: Course manual and recent books on plant physiology and molecular biology and latest reviews and articles on the topic. All material in Moodle.
Marking: Exam after the end of the course, grading 0-5/5.
Registration: Weboodi

52518 (=81028) Practical course on plant biotechnology (5 cr) updated 7.2.
Dates:
week 8: mon - fri 20.-24.2.
week 9: mon - fri 27.2.-2.3.
week 10: tue - thu 6.-8.3
week 11: tue 13.3. and thu 15.3.
week 12: wed 21.3.
week 14: wed 4.4.
week 16: tue 17.4. and wed 18.4.
Time always 13 - 18
Place: C 144 (Viikki)
Teachers: Univ. lecturer Mika Kotilainen and professor Teemu Teeri
Preceding studies: Plant biotechnology and molecular biology (52728)
Objective: Objective of the course is to learn the basic techniques in plant cell culture and plant gene transfer.
Contents: The laboratory practices include relevant techniques in plant cell culture (callus and suspension cultures, haploid cultures, protoplast isolation and micropropagation) as well as techniques related to plant gene transfer methods (Agrobacterium-mediated and direct gene transfer methods, use and analysis of reporter genes).
Study materials and literature: Course manual and scientific articles
Completion: Laboratory course
Evaluation: Laboratory reports, grading system 0-5
Other information: The course is given jointly by the Department of Biosciences and the Department of Agricultural Sciences (course code 81028, KBIOT301)
Registration: Weboodi registration code for all students is 81028. Maximum 14 students are accepted for the course.

52728 Plant Biotechnology and Molecular Biology (5 ECTS credits) updated 17.1.
Time: 9 Jan– 27 Feb, 2012 Mon and Thu 9-12 a.m.
Place: BIO2, 2012, Viiki campus.
Responsible person: Ykä Helariutta
Teachers: Ykä Helariutta, Alan Schulman, Pekka Heino, Teemu Teeri, Jaakko Kangasjärvi, Nigel Kilby, Sari Tähtiharju
Aims: Learning of different aspects in plant biotechnology and molecular biology.
Contents: Lectures will familiarize students with structures and function of plant genome; Molecular biology of Agrobacterium-mediated gene transfer; Pathways to plant secondary metabolites; Molecular basis of vegetative-reproductive transitions and flower development; Structure and function of cytoskeleton proteins; Molecular biology of light perception and signal transduction in plants; Molecular basis of abiotic and biotic stress responses in plants; Forest biotechnology; Plant secondary metabolism; Basics of plant gene isolation methods and gene transfer methods to plants; Basics for legislation and risk assessment of plant biotechnology; Introduction to applications and ethics of plant biotechnology.
Literature: Lecture material and additional reading given by the lecturers in the net and Buchanan, B.B, Gruissem, W & Jones, R.L, 2002: Biochemistry and Molecular Biology of Plants. 1408 pages (relevant parts).
Marking: Two essays during the course and one written exam at the end of the course, grading 0-5.
Exam: Thu 27.2.2012 10-12 A.M.
Registration: WebOodi; Registration period: 14.09.11 klo 00:01-15.01.12 klo 23:59.
Other information: The course is given jointly by the Department of Biosciences and the Department of Agricultural Sciences (course abbreviation KBIOT300). Registration code for all students is 52728. This year the course will be also organized as a joint course with Aalto University. Please note that if you are planning to take the 52518/KBIOT301 Practical Course in Plant Biotechnology, you have to attend the ‘Vectors for plant transformation’ and the ‘Gene transfer to plants’ lectures in this lecture series.

526040 Ecosystem ecology (Ekosysteemiekologia) (3 cr)
Timing: 12.3.–11.4. Monday–Wednesday 8:15–10:00.
Place: BIO3 6602.
Responsible person: Yliopistonlehtori Pedro Aphalo /KB
Prerequisites: No formal prerequisites, but basic knowledge of Ecology recommended.
Aim: To prepare students to be able to comprehend the scientific literature in ecosystem ecology by teaching them the specialized language, research approach and basic concepts of this branch of ecology.
Content: Energy flow and material cycles in ecosystems. Ecosystem primary production. Trophic levels. Decomposition of organic matter in soils. Climatic factors and ecosystem water economy. World ecosystems. Global carbon cycle. Greenhouse effect and possible ways of slowing the rate of global warming. Readings about ecosystem services to human society.
Literature: Obligatory: material provided during lectures and in Moodle. Reading assignments from Daily, G. C. (1997) Nature’s Services. Supplementary: Some chapters from Gurevitch, J et al. (2006) The Ecology of Plants.
Course home page: http://blogs.helsinki.fi/aphalo/teaching/courses/ecosys-course/
Evaluation: Written exam on lectures and short reports about reading assignments and participation in forum discussions in Moodle. Also quizzes in Moodle. Scale 0-5.
Exam: Home exam, repeats by agreement.
Enrolment: WebOodi from 1.2.

526107 Practical course in physiological plant ecology (3 cr) updated 15.2.: timing
Timing: 23.04.-23.05.2012 Monday-Thursday 8:15-10:00, 24.05.2012 to 8:15-12:00.
Place: BIO3 6602
Responsible person: Yliopistonlehtori Pedro Aphalo /KB
Prerequisites: None enforced but basic knowledge of ecology recommended as well as physiological plant ecology lectures completed.
Aim: Students will learn how to do research in general, and in physiological plant ecology in particular.
Content: Introductory lecture to the focus theme, which will vary from year to year. Introduction to experimental design and statistical testing, Research work in groups.
Course tasks: Lectures (6 h). and practicals (20 h) with obligatory participation, research work in groups (approx. 30 to 40 h), written report and seminar presentation. Lectures in English, reports and presentations in English or Finnish, but use of English strongly encouraged for everybody if there are foreign students enrolled.
Literature: Material in Moodle. Literature on the theme of the year.
Course home page: http://blogs.helsinki.fi/aphalo/teaching/courses/ecopracticals-course/
Evaluation: Written and oral report. Participation in class and in Moodle.
Exam: none
Enrolment: WebOodi from 1.3. Maximum number of students: 12.

525021 Advanced Computer Methods for Biologists (6 ects) updated 29.2.2012