1


                                                                                                          Updated 28.8...
2
Abbreviations:
B     = Faculty of Biosciences
AF    = Faculty of Agriculture and Forestry
BI    = Institute of Biotechno...
3

                                                                                      ECTS                             ...
4




                                                                                      ECTS                          ...
5
                  and Image Reconstruction                              3                 II (in even years)     -
52922...
6

                                                                                      ECTS                             ...
7

                                                                                      ECTS                             ...
8
                                                             Academic year 2008-2009

Study unit descriptions:
Obligator...
9
Completion: Participation in the seminar, written and oral presentation, acting as an
opponent
Evaluation: Written and o...
10
Completion: Placement in biotechnological research or applications in a company or
research institute. The practical tr...
11
Completion: Literature examination. 100-150 pages will yield 1 ECTS credit
Evaluation: Literature examination. Grading ...
12


                                                             Academic year 2008-2009

Study unit descriptions:
Altern...
13
Relations to other study units: This course is a prerequisite for 529223 Advanced Course
in Structural Biology and Biop...
14
Preceding studies: Prerequisite course: 529236 or Short laboratory course on structural
biology (529266) or book exam.
...
15
(Return to Track 1, 3c, or 4a)


SPRING TERM (period III and IV)

529263 Advanced Laboratory Course in Cellular Biotech...
16
expression by small RNAs and the coupling of mRNA processing with other processes along
gene expression pathway
Study m...
17
Contents: Genetic and experimental approaches to mouse, chicken, Drosophila and
Caenorhabditis elegans development, his...
18
Objective: A 9 week period during which a student will be introduced to a genuine research
project in a research group
...
19
                                                               Academic year 2008-2009

Study unit descriptions:
Altern...
20



528012 Laboratory Course in Virology and Bioinformatics, 6 ECTS credits
Time: Autumn term, period II (13.10.-7.11.20...
21
52748 Microbial Genetics and Genomics, 4 ECTS credits
Time: Spring term, period III (9.1.-27.2.2009, Wed and Fri at 8.3...
22
Responsible persons: Prof. Teemu Teeri (Faculty of Agriculture and Forestry), Univ.
Lecturer. Pekka Heino and Prof. Jaa...
23
Preceding studies: Basic courses in mathematics and statistics
Contents: This course considers classical genetics, like...
24
Responsible persons: Doc. Gunter Brader
(Return to Track 2a, or 2b)

52912 Genomes, 3 ECTS credits
Time: Spring term, p...
25
relation of gene expression, transcriptional regulators and their mode of action, post-
transcriptional gene regulation...
26
                                                                Academic year 2008-2009

Study unit descriptions:
Alter...
27
microbiology, technology and bioprocessing textbooks
Study materials and literature: Relevant literature and material p...
28
Objective: Introduction to food legislation and control systems
Contents: European regulations on food, action of Europ...
29
Objective: Introduce the students to most common lactic acid bacteria (LAB) used as
starters in food industry and to th...
30
Preceding studies: BSc. level or equivalent required
Objective: To learn the major steps in the process of discovery of...
31
(Return to Track 2a or 2b)

81085/52728 Plant Biotechnology and Molecular Biology (KBIOT300), 5 ECTS credits
Time: Spri...
mbiotcurriculum2008.doc.doc
mbiotcurriculum2008.doc.doc
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  1. 1. 1 Updated 28.8.2008 Curriculum 2008-2009 Master’s Degree Programme in Biotechnology (MBIOT) The Master’s Degree Programme in Biotechnology (MBIOT) aims to provide students with the knowledge and skills they need for modern biotechnology research and employment in the industry. Topics of instruction range from the latest developments in recombinant DNA technology to non-technical issues such as business and bioethics. Studies are based on a personal study plan. You may choose your studies from a wide range of course options, from molecular biology to systems biology. Teaching is mainly arranged in English. MBIOT offers five specialisation tracks under the major subject Biotechnology: 1) Bioinformatics and Systems Biology; 2) Biotechnology of Natural Resources; 3) Cellular Biotechnology and Developmental and Structural Biology; 4) Food Biotechnology and Health Biotechnology; and 5) Neuroscience. MBIOT consists of general studies (8-12 ECTS credits), obligatory major subject studies (51-53 ECTS credits, including Master’s Thesis 40 ECTS credits), elective major subject studies related to the chosen specialisation track (30-47 ECTS credits), and elective (free-choice) studies (8-31 ECTS credits). The estimated duration of studies is two years. Degree Requirements and Recommendations 2008-2009 MASTER’S DEGREE, 120 ECTS credits credits year / period ______________________________________________________________________________ ♦GENERAL STUDIES, 8-12 ECTS credits xxxxx Business Economics* 4-8 1 529208 Bioethics 3 1 / IV 529242 Personal Study Plan 1 1/I *Various business economics courses are offered by the faculties and Helsinki School of Economics (JOO-studies). Alternatives include e.g.: - at the Faculty of Biosciences: 510010 Principles of Business, 4 ECTS credits (autumn term 2008, period I)→ RECOMMENDED! - at the Faculty of Biosciences: 51044 Biobusiness, 3+4 ECTS credits (spring term 2009, period IV) - as JOO-studies at HSE: 23A00210 Introduction to Marketing, 6 ECTS credits (autumn term 2008, period II) - as JOO-studies at HSE: 31A00210 Principles of Economics, 6 ECTS credits (spring term 2009, period I) - as JOO-studies at HSE: 28A00210 Introduction to Finance, 6 ECTS credits (spring term 2009, period II) ♦MAJOR SUBJECT STUDIES OBLIGATORY STUDIES, 51-53 ECTS credits 529230/882503 Final Examination in M.Sc. degree 8-10 2 529250/882504 Master´s Thesis and Maturity Essay 40 2 529249 Advanced Seminar in Biotechnology 3 2 / III ELECTIVE STUDIES ACCORDING TO THE SPECIALISATION TRACK, 30-47 ECTS credits At least 20 ECTS credits from the following practical study units: 529260/882505 Practical Training max 10 1-2 (or summer) and/or 529212 Advanced Training in a Research Group, I and II 10 + 10 1-2 and/or xxxxxx Laboratory/practical courses offered by the faculties and institutes (see the recommendations below) 1-2 At least 10 ECTS credits from other elective courses 1-2 (see the recommendations below) ♦ELECTIVE (FREE-CHOICE) STUDIES, 8-31 ECTS credits (see the recommendations below)
  2. 2. 2 Abbreviations: B = Faculty of Biosciences AF = Faculty of Agriculture and Forestry BI = Institute of Biotechnology NC = Neuroscience Center MBI = Master’s Degree Programme in Bioinformatics BM = Biomedicum - = No quota (a lecture course) (-) = No quota, but the student number is limited (a laboratory course or an exercise group), that is, if the course is full, the selection of students for the course is based on their previous studies e = The course is given in English f = The course is given in Finnish f or e = The course is given in Finnish unless otherwise required (in English) f or le = The course is given in Finnish , but can be taken as a literature examination in English MBIOT reserves the right to change the course informations when new updatings are coming in relation to the courses ------------------------------------------------------------------------------------------------------------------------------------------- ECTS Quota for credits Period MBIOT ------------------------------------------------------------------------------------------------------------------------------------------- TRACK 1: BIOINFORMATICS AND SYSTEMS BIOLOGY More information: Liisa Holm (B, BI), liisa.holm@helsinki.fi or Teemu Teeri (AF), teemu.teeri@helsinki.fi Primarily recommended elective courses: 52912 (B) Genomes (e) 3 IV - 52939 (B) From Genomes to Gene Function (e) 6 IV 2-3 529224 (BI) Advanced Course in Bioinformatics and Systems Biology (e) 10 I-IV - 529225 (B, BI) Laboratory Course on Plant Genomics (e) 5 IV (in even years) 3 582606 (MBI) Introduction to Bioinformatics (e) 4 I - 399671 (B, BM) Practical Bioinformatics (e) 8-10 I-IV (-) Other recommended elective courses: 52739 (B) Genetic Bioinformatics (f) 3 III - 52746 (B) Genetic Analysis (f) 3 III-IV - 52930 (B) Protein Informatics (f or e) 3 I (next time 2008) - 52931 (B) Exercises in Protein Informatics (f or e) 5 II (-) 529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) - 529232 (BI) mRNA Processing in Eukaryotes (e) 3 III (in even years) - 529231 (BI) Analytical Protein Chemistry (e) 2 II (in uneven years) 8 81037 (AF) Molecular Methods in Applied Plant Genetics (e) 5 I (in even years) - 81576 (AF) Molec. Genetic Markers in Animal Breeding (f or e) 5 III (in uneven years) 2 582604 (MBI) Practical Course in Biodatabases (e) 4 III - ------------------------------------------------------------------------------------------------------------------------------------------
  3. 3. 3 ECTS Quota for credits Period MBIOT ------------------------------------------------------------------------------------------------------------------------------------------- TRACK 2: BIOTECHNOLOGY OF NATURAL RESOURCES TRACK 2a) Microbial and Environmental Biotechnology More information: Hannu Saarilahti (B), hannu.saarilahti@helsinki.fi, Annele Hatakka (AF), annele.hatakka@helsinki.fi Primarily recommended elective courses: 52748 (B) Microbial Genetics and Genomics (f or le) 4 III - 52751 (B) Molecular Genetics Lab Course (e+f) 9 I-II 4 528012 (B) Laboratory Course in Virology and Bioinf.. (f or e) 6 II 2 864062 (AF) Biotechnology of Fungi and Renewable Natural Materials (f or e) 5 IV - 81351 (AF) Bacteria, Viruses and Pathogen Diagnostics (e) 10 II (-) 81331 (AF) Epidemiology and Ecol. of Plant Pathogens (e) 5 I - 81352 (AF) Plant-Microbe Interac. and Mol. Defence of Plants (e)10 III (-) 830113 (AF) Forest Microbiology (e) 8 II - 850030 (AF) Biofuels (f or e) 5 I - 850029 (AF) Biorefineries (f or e) 5 IV - 864050 (AF) Forest Microbes as Resources in Biotechnology (e) 5 I (every third year) 5-10 Other recommended elective courses: 52948 (B) Chemical Genetics (e) 3 III - 52773 (B) Immunobiology (e) 3 III - 52912 (B) Genomes (e) 3 IV - 52936 (B) Gene Regulation in Eukaryotes (e) 3 IV - 52939 (B) From Genomes to Gene Function (e) 6 IV 2-3 529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) - TRACK 2b) Plant and Forest Genomics and Biotechnology More information: Tapio Palva (B), tapio.palva@helsinki.fi, Teemu Teeri (AF), teemu.teeri@helsinki.fi Primarily recommended elective courses: 52912 (B) Genomes (e) 3 IV - 52936 (B) Gene Regulation in Eukaryotes (e) 3 IV - 52939 (B) From Genomes to Gene Function (e) 6 IV 2-3 529225 (B, BI) Laboratory Course on Plant Genomics (e) 5 IV (in even years) 3 52728 (B, AF) Plant Biotechnology and Molecular Biology (e) 5 III - 52518 (B, AF) Laboratory Course in Plant Biotechnology (e) 5 III 2 81037 (AF) Molecular Methods in Applied Plant Genetics (e) 5 I (in even years) - 812010 (AF) Laboratory Course in Plant Molecular Biology (e) 5 III (in even years) 2 830114 (AF) Basic Biotechnology in Forestry (e) 5 I - 81406 (AF) Advanced Forest Mycology & Pathology (e) 10 II - Other recommended elective courses: 52948 (B) Chemical Genetics (e) 3 III - 52986 (B) Innate Immunity of Plants (e) 3 IV - 52512 (B) Advanced Course on Plant Physiology and Molecular Biology (e) 7 I 2-3 52747 (B) Advanced Course in Plant Genomics and Molecular Biology (e) 9 I-IV 2-3 81039 (AF) Selection Breeding and Experimental Designs (e) 5 III (in uneven years) - 81041(AF) Conservation of Plant Genetic Resources (e) 5 IV (in even years) - 81352 (AF) Plant-Microbe Interac. and Mol. Defence of Plants (e)10 III (-) 529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) - ------------------------------------------------------------------------------------------------------------------------------------------
  4. 4. 4 ECTS Quota for credits Period MBIOT ------------------------------------------------------------------------------------------------------------------------------------------- TRACK 3: CELLULAR BIOTECHNOLOGY AND DEVELOPMENTAL AND STRUCTURAL BIOLOGY TRACK 3a) Cellular Biotechnology More information: Pekka Lappalainen (BI), pekka.lappalainen@helsinki.fi, Jussi Jäntti (BI), jussi.jantti@helsinki.fi Primarily recommended elective courses: 529232 (BI) mRNA Processing in Eukaryotes (e) 3 III (in even years) - 529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) - 529235 (BI) Growth Factors and Their Receptors (e) 3 IV (in uneven years) - 529237 (BI) Stem Cells and Organogenesis (e) 3 I (in uneven years) - 529263 (BI) Advanced Laboratory Course in Cellular Biotech. (e) 5 III 8 529222 (BI) Advanced Course in Cellular Biotechnology (e) 10 I-IV - 52936 (B) Gene Regulation in Eukaryotes (e) 3 IV - 52751 (B) Molecular Genetics Lab Course (e+f) 9 I-II 4 Other recommended elective courses: 52912 (B) Genomes (e) 3 IV - 52939 (B) From Genomes to Gene Function (e) 6 IV 2-3 TRACK 3b) Developmental Biology More information: Juha Partanen (BI), juha.m.partanen@helsinki.fi, Tapio Heino (BI), tapio.heino@helsinki.fi Primarily recommended elective courses: 910050 (BI) From Cell to Organism – Developmental Biology (e) 3 IV - 529232 (BI) mRNA Processing in Eukaryotes (e) 3 III (in even years) - 529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) - 529237 (BI) Stem Cells and Organogenesis (e) 3 I (in uneven years) - 529221 (BI) Developmental Biology, lab practicals (e) 4 IV - 529268 (BI) Advanced Course in Developmental Biology (e) 10 I-IV - 52937 (B) Geenit ja yksilönkehitys (f) 3 III - 52932 (B) Seminar in Developmental Genetics (e) 3 I - 52912 (B) Genomes (e) 3 IV - 52939 (B) From Genomes to Gene Function (e) 6 IV 2-3 Other recommended elective courses: 529235 (BI) Growth Factors and Their Receptors (e) 3 IV (in uneven years) - 529225 (BI) Laboratory Course on Plant Genomics (e) 6 IV (in even years) 3 52936 (B) Gene Regulation in Eukaryotes (e) 3 IV - 582606 (MBI) Introduction to Bioinformatics (e) 4 I - 399671 (MBI) Practical Bioinformatics (e) 8-10 I- IV (-) TRACK 3c) Structural Biology More information: Dennis Bamford (BI, B), dennis.bamford@helsinki.fi, Sarah Butcher (BI), sarah.butcher@helsinki.fi Primarily recommended elective courses: 529236 (BI) Introduction to Structural Biology and Biophysics(e) 4-5 I (in uneven years) - 529266 (BI) Short Lab Course on Structural Biology and Biophys.1+4 I (in even years) 12 529267 (BI) Lecture and Exercise Course on Electron Microscopy
  5. 5. 5 and Image Reconstruction 3 II (in even years) - 529223 (BI) Advanced Course in Structural Biology and Biophysics (e) 10 I-IV - 529233 (BI) X-ray Crystallography Techniques (e) 2 ? ? 529231 (BI) Analytical Protein Chemistry (e) 2 II (in uneven years) 8 528006 (BI, B) Introduction to Viruses (f ) 3-4 II - 528012 (B) Laboratory Course in Virology and Bioinf. (f or e) 6 II 2 529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) - Other recommended elective courses: 529232 (BI) mRNA Processing in Eukaryotes (e) 3 III (in even years) - 52912 (B) Genomes (e) 3 IV - 52936 (B) Gene Regulation in Eukaryotes (e) 3 IV - 52939 (B) From Genomes to Gene Function (e) 6 IV 2-3 ------------------------------------------------------------------------------------------------------------------
  6. 6. 6 ECTS Quota for credits Period MBIOT ------------------------------------------------------------------------------------------------------------------------------------------- TRACK 4: FOOD BIOTECHNOLOGY AND HEALTH BIOTECHNOLOGY TRACK 4a) Food Biotechnology More information: Tapani Alatossava (AF), tapani.alatossava@helsinki.fi Primarily recommended elective courses: 864065 (AF) Food Microbiology (f or le) 5 I-IV - 87145 (AF) Vitamins and Other Bioactive Compounds (e) 5 IV (in even years) - 871074 (AF) Food Legislation and Control (e) 5 I-II - 871072 (AF) Chemical Risk Factors (e) 5 II - 871073 (AF) Basic Toxicology and Risk Assessment (e) 5 ? - 8720024(AF) Potential Novel Processing Technologies (e) 5 IV - 8720091(AF) Fermentation Technology (e) 3 IV - 8720092 (AF) LAB Starters (e) 3 II (-) 8720094 (AF) Dairy Bioprocessing (e) 6 I-IV (-) 8720051 (AF) Dairy Technology 6 (e) 1-9 I-IV - 87295 (AF) ABS Course on Functional Foods (e) 3-5 IV (in even years) (-) 529231 (BI) Analytical Protein Chemistry (e) 2 II (in uneven years) 8 52773 (B) Immunobiology (e) 3 III - Other recommended elective courses: 81037 (AF) Molecular Methods in Applied Plant Genetics (e) 5 I (in even years) - 871066 (AF) Basic Studies in Food Science (f) 25 I-IV - 871070 (AF) Functional Foods Minor Subject (f) 25 I-IV - TRACK 4b) Health Biotechnology More information: Hannu Saarilahti (B), hannu.saarilahti@helsinki.fi Primarily recommended elective courses: 52773 (B) Immunobiology (e) 3 III - 52936 (B) Gene Regulation in Eukaryotes (e) 3 IV - 52911 (B) Cancer Genetics (f ) 3 III - 529264 Practical Training in Cancer Genetics (e) 5 IV (in even years) (-) 52714 (B) Human Genetics (f or e) 3 II - 529235 (BI) Growth Factors and Their Receptors (e) 3 IV (in uneven years) - 529237 (BI) Stem Cells and Organogenesis (e) 3 I (in uneven years) - 910050 (BI) From Cell to Organism – Developmental Biology (e) 3 IV - 529221 (BI) Developmental Biology, lab practicals (e) 4 IV - + Other relevant courses on human genetics or genomics from Meilahti, FGC and the future Molecular Medicine Research Center Other recommended elective courses: 52751 (B) Molecular Genetics Lab Course (e+f) 9 I-II 4 529232 (BI) mRNA Processing in Eukaryotes (e) 3 III (in even years) - 529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) - + Some relevant neuroscience courses -------------------------------------------------------------------------------------------------------------------------------------------
  7. 7. 7 ECTS Quota for credits Period MBIOT ------------------------------------------------------------------------------------------------------------------------------------------- TRACK 5: NEUROSCIENCE More information: Tomi Taira (NC, B), tomi.taira@helsinki.fi Please find the list of courses given by the Neuroscience Center 2008-2010 here: http://www.helsinki.fi/neurosci/education.htm
  8. 8. 8 Academic year 2008-2009 Study unit descriptions: Obligatory study units for all MBIOT students AUTUMN TERM (period I and II) 529242 Personal Study Plan for the Master’s Degree, 1 ECTS credits Time: Autumn term, period I+ updating of the study plan as necessary (3.9.-15.10. 2008 Wednesdays at 12-14, except 1.10 at 10-12) Place: Biocenter 2, lecture room 2012, except 1.10 C-building, seminar room 130 , 8.10 INFO computer class 170 and 15.10 Biocenter 2, lecture room 2063 Preceding studies: Bachelor's degree or equivalent in biotechnology or in a related field Objective: To devise an individual plan for the Master’s degree studies to be completed and a timetable for their completion Contents: Discussions and group work organised and supervised by the coordinator and the teachers, after which students will independently write their plans and return them to the coordinator Study material and literature: MBIOT degree requirements, course descriptions, curriculum, other instructions Completion: Participation in the study plan meetings, discussions with the coordinator and teachers, independent writing Evaluation: A signed, written plan for the completion of studies. Grading scale: Pass/fail Responsible person: MBIOT coordinator Viola Niklander-Teeri Other information: More information on the MBIOT home pages and on the Blackboard (Return to General Studies) SPRING TERM (period III and IV) 529249 Advanced Studies Seminar in Biotechnology, 3 ECTS credits (1 ECTS credits of ICT skills studies integrated) Time: Spring term, period III (first meeting on 12.1.2009). Recommended to be completed during or after the experimental phase of the Master’s thesis Place: Will be announced later. Mon 19.1.2009 at 12-15, INFO computer class 170 Preceding studies: Bachelor's degree or equivalent in biotechnology or in a related field and completion of most of the Master's degree studies Objective: The seminar introduces students to the writing and presentation techniques of written and oral presentations based on experimental research. Students will prepare seminar presentations on the topic of their own Master’s thesis, covering the background, objectives, methodology and the most important findings, and will discuss the topic in a manner similar to a presentation at a scientific conference, taking into account, however, the audience's level of expertise. Furthermore, students will practice giving and receiving feedback by acting as opponents to their fellow students’ presentations and by actively engaging in discussion. Contents: Students will prepare a one-page summary of their research topic in English and a 20-minute oral presentation making use of the ICT equipment available. They will also act as opponents to their fellow students and engage in discussions in the seminar. Attendance in the seminar is compulsory. Study material and literature: Source material for the student’s research, written presentations produced for the seminar
  9. 9. 9 Completion: Participation in the seminar, written and oral presentation, acting as an opponent Evaluation: Written and oral communication, active participation in the seminar. Grading scale: Pass/fail Responsible person: Prof. Sarah Butcher, Institute of Biotechnology and Professors in charge of MBIOT Relations to other study units: Substitutive completions: participation in the advanced seminar series related to biotechnology organized by genetics, biochemistry or microbiology major subjects at the Faculty of the Biosciences or by the five departments in charge of HEBIOT/MBIOT at the Faculty of Agriculture and Forestry Other information: More information on the HEBIOT and MBIOT home pages (Return to Major Subject Studies) 529208 Bioethics, 3 ECTS credits Time: Spring term, period IV (Tue 28.4.2009 at 9-16, Wed 29.4.2009 at 9-14, Tue 19.5.2009 at 9-16 and Wed 20.5.2009 at 9-16) Place: INFO 2 Target group: MBIOT, MScPPS, MScFood and HEBIOT Master's students Preceding studies: Bachelor's degree or equivalent in biotechnology, biology, biochemistry, chemistry or in a related field Objective: The aim is to familiarise students with ELSA (Ethical, Legal and Social Aspects) of biological sciences. Contents: The course comprises 2 + 2 days of lectures, student presentations and a panel discussion divided by a period when students prepare small case studies on the ELSA of chosen research projects. The course will provide basic information on ethical principles in science, the role of science in society (and society in science), good scientific practice and misconduct of research, bioresearch legislation, gene patents in biomedical research and information on the ELSA of agricultural practices, environmental matters and on current questions in developing countries. Study material and literature: Relevant literature will be indicated during the course Completion: Lectures, case studies, panel discussion Evaluation: Attendance in the lectures, active participation in the case studies and the panel discussion, a learning diary and a case study report. Grading scale: Pass/fail Responsible persons: MBIOT, MScPPS, MScFood and HEBIOT coordinators Other information: The number of students is limited to 80. Priority is given to MBIOT, MScPPS and MScFood Master's Degree Programme students and HEBIOT Master's -level students. More information on the MBIOT home pages and on the Blackboard (Return to General Studies) AUTUMN OR SPRING TERM 529260/882505 Practical Training (for the Master’s Degree), max 10 ECTS credits Time: Recommended to be completed during the first or second year, but before the Master’s thesis. Completion according to an advance agreement with the person responsible for this study unit Preceding studies: Bachelor's degree or equivalent in biotechnology or in a related field Objective: To acquire practical experience in a company, research institute or government agency operating in the field of biotechnology Contents: As agreed Study material and literature: Material related to the training
  10. 10. 10 Completion: Placement in biotechnological research or applications in a company or research institute. The practical training is to be agreed upon in advance with the person responsible for this study unit. Duration: 3 months of full-time work will yield 10 ECTS credits Evaluation: The basis of assessment will be agreed upon before the beginning of the placement period with a responsible person of this study unit. Alternatives include a case book, learning diary, work specification, examination, or assessment of professional skills. Grading scale: Pass/fail Responsible person: Professors in charge of MBIOT (Return to Major Subject Studies) 529212 Advanced Laboratory Training in a Research Group (I and II), 10 + 10 ECTS credits Time: Recommended to be completed during the first or second year, but before the Master’s thesis. Completion according to an advance agreement with the person responsible for this study unit Preceding studies: Bachelor's degree or equivalent in biotechnology or in a related field Objective: To engage students in scientific thinking through small-scale projects and to develop their ability for independent work and the reporting of results. This course can be completed in two separate sections and preferably in two different research groups. Contents: Laboratory training in a research group or equivalent group operating in a company or research institute. The training is to be agreed upon in advance with the person responsible for this study unit. Study material and literature: Scientific literature related to the training Completion: The person responsible for this study unit and the director of the relevant research group will approve in advance the student’s work plan, which must indicate the scientific problems, methodology to be applied and include supervision arrangements related to the training. An approved case book and a written report in article form are also required, as is succesful completion of an oral or written examination. Duration: 7 weeks of full-time work Evaluation: The basis of assessment will be agreed upon with the person responsible for this study unit before the beginning of the placement period. Alternatives include a case book, learning diary, work specification, examination, or assessment of professional skills. Grading scale: 0-5 Responsible person: Professors in charge of MBIOT (Return to Major Subject Studies) 529230/882503 Final Examination for the Master's Degree, 8-10 ECTS credits Time: Recommended to be completed during the second year of the Master’s degree studies. Completion according to an advance agreement with the person responsible for this study unit on a general examination day for Biotechnology at 12.00-16: - Autumn term: 2.9., 7.10., 4.11. or 2.12.2008 - Spring term: 13.1., 3.2., 3.3., 7.4. or 5.5.2009 - Summer term: 3.6. or 5.8.2009 (Note time: at 10-14) Registration via Weboodi at the latest on Monday a week before the examination (Note: registration to the summer examinations by the end of May) Place: Biocenter 2, Auditorium 1041 Preceding studies: Bachelor's degree or equivalent in biotechnology or in a related field and completion of most of the Master's degree studies Objective: To deepen the student's knowledge of molecular biology and biotechnology within the chosen specialisation track Contents: Independent study, examination Study material and literature: Scientific literature according to the chosen specialisation track
  11. 11. 11 Completion: Literature examination. 100-150 pages will yield 1 ECTS credit Evaluation: Literature examination. Grading scale: 0-5 Responsible person: Professors in charge of MBIOT Other information: Some of the relevant literature for the final examination is listed on the HEBIOT and MBIOT home pages (Return to Major Subject Studies) 529250/882504 Master’s Thesis, 40 ECTS credits Time: Recommended to be completed during the second year of the Master’s degree studies after advanced laboratory training and laboratory courses. Completion according to an advance agreement with the person responsible for this study unit. Preceding studies: Bachelor's degree or equivalent in biotechnology or in a related field and completion of most of the Master's degree studies Objective: The Master’s thesis must demonstrate the student’s ability to think scientifically, mastery of the necessary research methods, familiarity with the research topic and competence required for scientific communication in the field. The thesis work can be completed independently or, alternatively, by participating in group work or in a wider research project, provided that the student’s independent input can be verified and assessed. Each student must write the thesis independently. Contents: See the instructions of your faculty or major subject Study material and literature: Scientific literature according to the chosen research topic Completion: See the instructions of your faculty Evaluation: Verbal assessment on the Latin scale laudatur – approbatur (improbatur) Responsible person: Professors in charge of MBIOT Other information: More information on the HEBIOT and MBIOT home pages (Return to Major Subject Studies)
  12. 12. 12 Academic year 2008-2009 Study unit descriptions: Alternative study units for MBIOT students organized by the Institute of Biotechnology (BI) AUTUMN TERM (period I and II) 529225 Laboratory Course on Plant Genomics, 5 ECTS credits Time: This year: 25.8-5.9.2008. Minisymposium in 25.8.2008, practicals in 26.8.-5.9.2008 (normally organized in spring term, period IV, in even years) Place: Minisymposium Biocenter 2, Auditorium 1041, Practicals: see the course program Preceding studies: Not recommended before finishing the mandatory laboratory courses and lectures Objective: A lab course, in which a student will be introduced to modern methods in the structural and functional analyses of plant genomes Contents: Laboratory work, minisymposium Study materials and literature: Optional Completion: Laboratory course Evaluation: Laboratory work in practice. Grading scale: 0-5 Responsible person: Prof. Ykä Helariutta Other information: Course program: http://www.biocenter.helsinki.fi/viikkigs/PlantGenomics08.htm (Return to Track 1, 2b, or 3b) 529266 Short Lab Course on Structural Biology and Biophysics, 1 + 4 ECTS credits Time: Autumn term, period I, in even years (29.9.-17.10.2008, every day at 8-18) Place: 29.9.-3.10.2008 at 8-18 INFO meeting room 511. 6.10.-17.10.2008 at 8-10 Biocenter 3, seminar room 1401, except 7.10; 15.10, and 16.10. in Biocenter 1, seminar room 3108 Target group: Designed for MSc students and PhD students Objective: Our goal is that, by the end of the course, the student will have a basic understanding of all of the techniques of modern structural biology and biophysics, so that he or she can then both read the relevant scientific literature critically and also understand laboratory work in the field. Contents: The course introduces all the key structural biology and biophysical techniques. Topics covered include the basic mathematics behind the techniques, including Fourier Transforms and symmetry, wave properties as applied to electromagnetic radiation, energy levels and the interaction of radiation with matter. There is also a discussion of macromolecules, macromolecular assemblies and their properties in biology. Specific techniques discussed and carried out in the practicals are X-ray crystallography, electron microscopy, nuclear magnetic resonance, kinetics Study material and literature: Material provided on the course, Whitford, Proteins structure and function, Serdyuk Zaccai & Zacchai, Methods in molecular biophysics Petsko & Ringe, Protein Structure and Function Completion: Lectures (at 8-10), background reading and practicals (at 10-16) 5 times a week for two weeks. First week full time lectures and essay (1 ECTS, max. 30 participants), weeks 2 & 3 daily methods lectures (at 8-10) followed by labwork, groupwork and presentation (at 10-18) (4 ECTS, max. 12 participants). Evaluation: Essay, presentation during class, lab reports. Grading scale: 0-5 Responsible person: Prof. Sarah Butcher
  13. 13. 13 Relations to other study units: This course is a prerequisite for 529223 Advanced Course in Structural Biology and Biophysics, 10 ECTS Other information: Dead-line for registration 10th September in even years. (Return to Track 3c) 529237 Stem Cells and Organogenesis, 3 ECTS credits Time: Autumn term, period I, in uneven years (next time in autumn 2009) Preceding studies: Preferentially 910050 From Cell to Organism – Developmental Biology Objective: The objective of this lecture series is to give the students a thorough view of the development of different organs, similarities in development and the special features of each organ. It also aims to describe the different tissue-specific stem cells and their contribution to stem cell based therapies. A crucial part is to understand how different genes guide organogenesis Contents: Based on books “Kehitysbiologia, Solusta yksilöksi” in Finnish and “Developmental biology” by Scott Gilbert in English Completion: Lecture course Study materials and literature: Developmental biology (Scott Gilbert) and lecture copies Evaluation: Examination. Grading scale: 0-5 Responsible person: Doc. Marjo Salminen Other information: The lectures are given in English, book material also in Finnish (Return to Track 3a, 3b, or 4b) 529236 Introduction to Structural Biology and Biophysics, 4 - 5 ECTS credits Time: Autumn term, period I, in uneven years (next time in autumn 2009) Objective: Our goal is that, by the end of the course, the student will have a basic understanding of all of the techniques of modern structural biology and biophysics, so that he or she can then both read the relevant scientific literature critically and also understand laboratory work in the field. Contents: The course introduces all the key structural biology and biophysical techniques at a level designed for beginning Master´s students. Topics covered include the basic mathematics behind the techniques, including Fourier Transforms and symmetry, wave properties as applied to electromagnetic radiation, energy levels and the interaction of radiation with matter. There is also a discussion of macromolecules, macromolecular assemblies and their properties in biology. Specific techniques discussed are X-ray crystallography, electron microscopy, nuclear magnetic resonance, kinetics and mass spectrometry Study material and literature: Material provided on the course, Whitford, Proteins structure and function, Serdyuk Zaccai & Zacchai, Methods in molecular biophysics, Petsko & Ringe, Protein Structure and Function Completion: Lectures 3-4 times a week Evaluation: Presentation during class, examination. Grading scale: 0-5 Responsible person: Prof. Sarah Butcher Relations to other study units: This course is a prerequisite for 529223 Advanced Course in Structural Biology and Biophysics, 10 ECTS (Return to Track 3c) 529267 Lecture and Exercise Course on Electron Microscopy and Image Reconstruction, 3 ECTS credits Time: Autumn term, period II, in even years (27.10.-18.11.2008 at 9-12, except on 10.11.-14.11. at 12-15) Place: Biocenter 3, computer classroom 4403 Target group: Designed for MSc and PhD students specializing in structural biology
  14. 14. 14 Preceding studies: Prerequisite course: 529236 or Short laboratory course on structural biology (529266) or book exam. Objective: Our goal is that, by the end of the course, the student will have a basic understanding of electron microscopy and image processing Contents: The course goes into detail about high resolution electron microscopy, data collection and processing. Topics covered include the basic mathematics behind the techniques, including Fourier Transforms and symmetry, wave properties as applied to electromagnetic radiation. Study material and literature: Material provided on the course Completion: Lectures (30 hours), 1 x4 hour EM demonstration, 5 x 4 hour image processing exercises. Evaluation: Presentation during class, exercise reports. Grading scale: 0-5 Responsible person: Prof. Sarah Butcher Other information: Enrolment on the course by 30th October in even years. Max 12 participants (Return to Track 3c) 528006 Introduction to Viruses (Johdanto viruksiin), 3 - 4 ECTS credits Time: Autumn term, period II (27.10.-10.12.2008, Mon and Wed at 10-12) Place: Biocenter 2, lecture room 2012) Preceding studies: Basics in biosciences/ Biotieteiden perusteet I (529001) ja Biotieteiden perusteet II (529002) Objective: Perustiedot viruksista ja keskeisimmistä virologian käsitteistä ja tekniikoista. Seminaariesitelmä: tieteellisen ajattelun kehittäminen, kirjallisuuteen tutustuminen ja suullinen esitystaito. Contents: Virusten rakenne, luokittelu, elinkierto ja replikaatio, virukset biosfäärissä, virusten evoluutio. Seminaariesitelmät Study materials and literature: Luentomateriaali Completion: Lectures (3 ECTS credits) and seminar presentations (1 ECTS credit) Evaluation: Examination. Grading scale: 0-5 Responsible person: Prof. Dennis Bamford Other information: The lectures are mainly given in Finnish. More information: http://www.helsinki.fi/biosci/ymbo/virusluennot.htm (Return to Track 3c) 529231 Analytical Protein Chemistry, 2 ECTS credits (1+1 ECTS credits) Time: Autumn term, period II, in uneven years (next time in autumn 2009) Preceding studies: Basic knowledge in protein biochemistry and chemistry Objective: The objective of the course is to introduce the students to some of the central methods in analytical protein chemistry Contents: This lecture and practical course will deal with the use of electrophoretic, chromatographic and mass spectrometric methods in protein and peptide purification and analysis. Chromatographic methods (gel permeation-, ion exchange- and reversed phase chromatography), electrophoretic methods (1D- and 2D-PAGE), protein and peptide sequencing (Edman and MS), mass spectrometry (MALDI-TOF/TOF and ESI-MS/MS), bioinformatics Study material and literature: Given literature and laboratory manuals Completion: Daily lectures followed by practical laboratory work/ demonstrations. 1 ECTS with lectures and exam, 2 ECTS with lectures, exam and laboratory part Evaluation: Examination. Grading scale: 0-5 Responsible person: Doc. Nisse Kalkkinen Other information: The lectures are open to all. The number of participants for the laboratory part is limited to 8 persons
  15. 15. 15 (Return to Track 1, 3c, or 4a) SPRING TERM (period III and IV) 529263 Advanced Laboratory Course in Cellular Biotechnology, 5 ECTS credits Timing: Spring term, period III (23.2.-6.3.2009, at 8-16) Place: First meeting Mon 23.2.2009 at 8-13, Biocenter 1, seminar room 3106. Practical work in Biocenter 1, 1st floor. Final meeting Tue 24.3.2009 at 8-12. Preceding studies: 510012 Molecular Cell Biology or 850008 Molecular Cell Biology (these lectures are given in Finnish) recommended Objective: To learn laboratory skills in experimental cellular biotechnology Contents: Mammalian cell culture, transfection, immunofluorescence staining, fluorescence microscopy, yeast transformation and multicopy suppression of a mutant, Western blotting of yeast cell lysates, preparation of yeast cells for scanning electron microscopy, SEM, preparation of cultured mammalian cells for transmission microscopy, TEM Completion: Practical course. Lectures, demonstrations and practical work Evaluation: Active participation, poster and oral reports, no examination. Grading scale: Pass/failed Responsible persons: Doc. Eija Jokitalo, Doc. Jussi Jäntti and Doc. Maria Vartiainen Other information: Max 16 students accepted, priority to HEBIOT / MBIOT advanced level students (Return to Track 3a) 910050 From Cell to Organism – Developmental Biology, 3 ECTS credits Timing: Spring term, period IV (9.3.-7.4.2008, Mon and Tue, at 10 -12, and 20.4 Mon 10-12) Place: Biocenter 2, lecture room 2063 Contents: Introduction to basic mechanisms of animal development and to central research trends in developmental biology. Based on books ‘Kehitysbiologia, Solusta yksilöksi, pp. 1-152’ in Finnish and ‘Developmental biology’ by Scott Gilbert or ‘Essential Developmental biology’, 2nd edition by Jonathan Slack in English Study materials and literature: Based on the book: Sariola, H., Frilander, M., Heino, T., Jernvall, J., Partanen, J., Sainio, K., Salminen, M. ja Thesleff, I. (2003) Solusta yksilöksi – Kehitysbiologia (kirjan osa I, yleinen osa), Kustannus Oy Duodecim, and also on Gilbert, S. Developmental Biology, 8th Edition (specific parts only) Completion: Lecture course Evaluation: Examination. Grading scale: 0-5 Responsible person: Doc. Tapio Heino Other information: The lectures are given in English, book material also in Finnish (Return to Track 3b,or 4b) 529232 mRNA Processing in Eukaryotes, 3 ECTC credits Time: Spring term, period III, in even years (next time in spring 2010) Preceding studies: Basic understanding of eukaryotic gene expression (transcription, translation etc), and cellular and molecular biology Objective: The objective of this lecture series is to give the students a thorough view of the mechanisms and regulation of mRNA processing in eukaryotic cells Contents: This advanced lecture series will concentrate on the mechanisms and regulation of mRNA processing in eukaryotic cells. The main focus is on the molecular machines involved in mRNA processing (such pre-mRNA splicing, polyadenylation, capping and editing). Further topics are mechanisms and regulation of alternative pre-mRNA splicing, mechanisms and regulations of alternative polyadenylation, mRNA quality control (esp. nonsense mediated decay), translation and translational control, regulation of gene
  16. 16. 16 expression by small RNAs and the coupling of mRNA processing with other processes along gene expression pathway Study material and literature: Will be provided during the lectures Completion: Lecture course Evaluation: Examination. Grading scale: 0-5 Responsible person: Doc. Mikko Frilander (Return to Track 1, 3a, 3b, 3c, or 4b) 529235 Growth Factors and their Receptors, 3 ECTS credits Time: Spring term, period IV in uneven years (11.3.-6.5.2009, Wed and Thu at 14-16) Place: Biocenter 1, seminar room 3108 Preceding studies: The course requires basic knowledge on genetics, biochemistry, and microbiology, and complements the course 910050 From Cell to Organism – Developmental Biology. Objective: The objective of this lecture series is to give the students a thorough view of the structure and function of the growth factors. It aims to describe the roles of growth factors in development and disease their use in biotechnology and biomedicine. Contents: The lecture course will deal with the structure and function of growth factors, analysis of signaling pathways, roles of growth factors in development, pathology and diseases. Growth factors functioning in different tissues and organs will be presented. Biotechnological and biomedical applications of growth factors will be discussed. Study materials and literature: Will be provided during the lectures Completion: Lectures, seminars Evaluation: Examination. Grading scale: 0-5 Responsible person: Prof. Mart Saarma (Return to Track 3a, 3b, or 4b) 529234 Recombination Mechanisms, 3 ECTS credits Time: Spring term, period IV, in uneven years (18.3.-23.4.2009, Wed and Thu at 12-14) Place: INFO 2, except 25.3. in Biocenter 2, Auditorium 1041 Preceding studies: At least basic knowledge on genetics, biochemistry, and microbiology Objective: Understanding various forms of recombination reactions and their uses for research and other purposes Contents: Essential features of the structures of nucleic acids, protein-DNA complexes as mediators of recombination reactions, DNA topology, homologous recombination, site- specific recombination, DNA transposition and integration reactions (DNA transposons, retrotransposons and retroviruses), illegitimate recombination, RNA-mediated reactions (e.g. mobile introns), telomerase, in vitro recombination reactions as molecular tools, advanced genome engineering, gene therapy requirements and problems. Study material and literature: Will be provided during the lectures Completion: Lecture course Evaluation: Examination. Grading scale: 0-5 Responsible person: Prof. Harri Savilahti (Return to Track 1, 2a , 2b, 3a, 3b,3c or 4b) 529221 Developmental Biology, Practical Course, 4 ECTS credits Time: Spring term, period IV Target group: Master and Graduate students planning to carry out thesis projects in developmental biology. Priority to MBIOT, GSBM and VGSB students Preceding studies: Principles in Developmental Biology (910050) recommended Objective: To learn laboratory skills in modern developmental biology, to learn advantages of different research model organisms
  17. 17. 17 Contents: Genetic and experimental approaches to mouse, chicken, Drosophila and Caenorhabditis elegans development, histology, immunohistochemistry and mRNA in situ hybridization techniques Completion: Full-day practical course. Lectures, demonstrations and group work. Evaluation: Examination and report. Grading scale: 0-5 Responsible person: Doc. Juha Partanen (Return to Track 3b, or 4b) 529233 X-Ray Crystallography Techniques, 2 ECTS credits Time: Place: Target group:- Preceding studies: Courses 529236 and 529223 Objective: Our goal is that, by the end of the course, the student will be able to solve, unaided, a simple protein or macromolecular structure by x-ray crystallography. Contents: The course consists of demonstrations and practicals using key crystallography programs (e.g. XDS for data reduction, CCP4i for crystallography data handling and refinement, SOLVE for MAD phasing, COOT for model building). Study material and literature: Material provided on the course Completion: Demonstrations and practicals (hands-on computer work). Evaluation: Lab notebooks. Scale: pass/failed Responsible person: Prof. Adrian Goldman (Return to Track 3c) AUTUMN OR SPRING TERM 529223 Advanced Course in Structural Biology and Biophysics, 10 ECTS credits Time: At any time after an agreement with one of the group leaders of the Research Program in Structural Biology and Biophysics at BI. Preceding studies: Not recommended before finishing the mandatory laboratory courses and lectures. 529236 “Introduction to structural biology and biophysics” is a mandatory preceding course. Objective: A 9 week period during which a student will be introduced to a genuine research project in a research group Contents: Written research proposal, laboratory work on a project, written report in the form of a scientific paper Study material and literature: Optional Completion: Will be done in a laboratory of the Program in Structural Biology and Biophysics at the Institute of Biotechnology Evaluation: A. Research proposal, laboratory work in practice, and note book B. Report C. Exam (oral or written). Grading scale: 0-5, (A+B+C)/3 The student must pass each module. Responsible person: Prof. Sarah Butcher Other information: Please contact the group leader or the responsible person for further information (Return to Track 3c) 529222 Advanced Course in Cellular Biotechnology, 10 ECTS credits Time: At any time after an agreement with one of the group leaders of the Research Program in Cellular Biotechnology at BI. Preceding studies: Not recommended before finishing the mandatory laboratory courses and lectures. Introduction to virology
  18. 18. 18 Objective: A 9 week period during which a student will be introduced to a genuine research project in a research group Contents: Written research proposal, laboratory work on a project, written report Study material and literature: Optional Completion: Will be done in a laboratory of the Program in Cellular Biotechnology at the Institute of Biotechnology Evaluation: A. Research proposal, laboratory work in practice, and note book B. Report C. Exam (oral or written). Grading scale: 0-5, (A+B+C)/3 The student must pass each module. Responsible person: Doc. Maria Vartiainen Other information: Please contact the group leader or the responsible person for further information (Return to Track 3a) 529268 Advanced Course in Developmental Biology, 10 ECTS credits Time: At any time after an agreement with one of the group leaders of the Research Program in Developmental Biology in the BI. Preceding studies: Not recommended before finishing the mandatory laboratory courses and lectures. “910050 From Cell to Organism – Developmental Biology” is a mandatory preceding course Objective: A 9 week period during which a student will be introduced to a genuine research project in a research group Contents: Written research proposal, laboratory work on a project, written report in the form of a scientific paper Study materials and literature: Optional Completion: Will be done in a laboratory of the Program in Developmental biology at the Institute of Biotechnology Evaluation: A. Research proposal, laboratory work in practice, and note book B. Report C. Exam (oral or written). Grading scale: 0-5, (A+B+C)/3 The student must pass each module. Responsible person: Osamu Shimmi Other information: Please contact the responsible person for further information and to set up the agreement. (Return to Track 3b) 529224 Advanced Course in Bioinformatics and Systems Biology, 10 ECTS credits Time: At any time after an agreement with one of the group leaders of bioinformatics and systems biology at BI. Preceding studies: Not recommended before finishing the mandatory laboratory courses and lectures Objective: A 9 week period during which a student will be introduced to a genuine research project in a research group Contents: Written research proposal, laboratory work on a project, written report Study material and literature: Optional Completion: Will be done in a laboratory of bioinformatics and systems biology at the Institute of Biotechnology Evaluation: A. Research proposal, laboratory work and note book B. Report(s) C. Examination (oral or written). Grading scale: 0-5, (A+B+C)/3 Responsible person: Prof. Ykä Helariutta Other information: Please contact the group leader or the responsible person for further information (Return to Track 1)
  19. 19. 19 Academic year 2008-2009 Study unit descriptions: Alternative study units for MBIOT students organized by the Faculty of Biosciences (B) AUTUMN TERM (period I and II) 52930 Protein Informatics, 3 ECTS credits Time: Autumn term, period I (dates to be announced later) Preceding studies: Geneettinen bioinformatiikka (52739) Contents: Protein sequence and structure analysis based on Mount: Bioinformatics - sequence and structure analysis. Focus is on biological applications Study materials and literature: Lecture material, Literature: Lesk, Introduction to Bioinformatics, Oxford Completion: Lectures and excercises Evaluation: Examination. Grading scale: 0-5 Responsible person: Prof. Liisa Holm Other information: The course is given in Finnish unless otherwise required (in English) (Return to Track 1) 52512 Advanced Course on Plant Physiology and Molecular Biology, 7 ECTS credits Time: Autumn term, period I (1.9. - 17.10.2008, Mon-Fri at 9-17) Place: Biocenter 3, 6th floor laboratory Preceding studies: Basics in plant anatomy and physiology Contents: The course will familiarise students with the central components of plant physiology and plant molecular biology along with research methods and topical research subjects. Practical work to be completed in research groups to familiarise students with laboratory work, reporting and assessment Study materials and literature: Material provided during the course Completion: Laboratory course Evaluation: Written reports. Grading scale: 0-5 Responsible person: Senior researcher Dr. Anthony Bishopp (Return to Track 2b) 52751 Molecular Genetics Laboratory Course, 9 ECTS credits Time: Autumn term, periods I-II (6.10.-24.10.2008, Mon-Fri at 9-17) Place: Biocenter 1, course lab 1024 Preceding studies: Geenitekniikan työt (52729) ja joku seuraavista: Mikrobigenetiikan työt (52721), Eukaryoottien molekyyligenetiikan ja molekyylisytogenetiikan työt (52913). Suositellaan Bioinformatiikan töiden (52920) suorittamista. Objective: Tavoitteena on pienimuotoisten projektien avulla harjaannuttaa opiskelijaa tieteelliseen ajatteluun sekä kehittää kykyä itsenäiseen työskentelyyn ja tulosten raportointiin. Contents: Ajankohtaisia mikrobien ja kasvien tutkimuksen ongelmanasetteluja ja niihin liittyen sekä laboratoriotyöskentelyä että tietokantahakuja ja analyysejä. Study materials and literature: Course manual and material provided during the course Evaluation: Examination, poster and lab report. Grading scale: 0-5 Responsible person: Univ. lecturer Pekka Heino Other information: The course language is Finnish and English (Return to Track 2a, 3a or 4b)
  20. 20. 20 528012 Laboratory Course in Virology and Bioinformatics, 6 ECTS credits Time: Autumn term, period II (13.10.-7.11.2008, Mon-Fri at 9-17 (the laboratory part during 13.10.-31.10. and the bioinformatics part during 3.11.-7.11.)) Place: Biocenter 1, course lab 2015 Preceding studies: Basics of Biosciences I (529001), Introduction to Viruses (528006), Methods in Microbiology and Microbial Genetics (529004), Gene technology (52729) and Methods in Microbiology (52807) or corresponding knowledge Objective and Contents: During the course we get acquainted with the basic techniques in molecular virology and bioinformatics using the well known bacteriophage PRD1 as an example. Study materials and literature: Laboratory manual, other reading material given during the course Completion: Laboratory exercises, laboratory reports, exercises in bioinformatics Evaluation: Laboratory report. Grading scale: 0-5 Responsible persons: University lecturers Minna Poranen and Janne Ravantti Other information: Course web-pages: http://www.helsinki.fi/biosci/ymbo/virologiankurssi.htm The course is given in Finnish unless otherwise required (in English) (Return to Track 2a or 3c) 52714 Human Genetics, 3 ECTS credits Time: Autumn term, period II (29.10-10.12.2008, Wed and Thu at 14-16) Place: INFO 2 Contents: The lecture series will cover the inheritance of both normal properties, and disease in man. Different modes of inheritance will be highlighted with relevant diseases, where an integrated description from the symptoms of the disorders, to molecular pathology will be covered. Special attention will also be paid to prenatal diagnosis and cancer genetics Study materials and literature: Lecture material Completion: Lecture course Evaluation: Examination. Grading scale: 0-5 Responsible person: Univ. lecturer Katarina Pelin Other information: The lectures are given in Finnish unless otherwise required (in English) (Return to Track 4b) 52931 Exercises in Protein Informatics, 5 ECTS credits Time: Autumn term, period II (dates to be announced later) Place: INFO 138 Preceding studies: 53739 Genetic bioinformatics Contents: Practical course where we aim to infer protein function and structure as well as possible from the amino acid sequence. Tools include public web servers Study materials and literature: Material provided during the course Completion: The course contains guided exercises and a group work where a target protein is analyzed Evaluation: Written report. Grading scale: 0-5 Responsible person: Prof. Liisa Holm Other information: The exercises are given in Finnish unless otherwise required (in English) (Return to Track 1) SPRING TERM (period III and IV)
  21. 21. 21 52748 Microbial Genetics and Genomics, 4 ECTS credits Time: Spring term, period III (9.1.-27.2.2009, Wed and Fri at 8.30-10) Place: INFO 3 Preceding studies: Basics in biosciences, gene expression, molecular biology and molecular genetics Objective and contents: This course intends to describe the structure and function of the bacterial genome, as well as to have a look at the ways employed by modern genome research.. Initially, the constituents of the genome, its organization, reproduction and partition to progeny cells will be reviewed. Attention will be paid to mechanisms causing gene flow between bacterial cells, strains and species, as well as to mechanisms potentially interfering with the gene transfer. A major topic will be the aspect of stress in bacteria, i.e. what is stress, what does it cause in bacteria, how do they sense stress and how do they adapt to it. This part will shed light to the cooperative action of various regulatory mechanisms of gene expression, capable of forming delicate regulatory networks. These networks enable sensing of extracellular as well as intracellular signals to cause timely response and adaptation of the gene expression to the prevailing conditions and to ensure the bacterial growth, or at least survival, in conditions far for optimum. Finally, some ways to manipulate prokaryotic gene expression in a controlled way will be reviewed. Tentative subject areas: 1. Genome structure, reproduction and partition 2. Phages, plasmids 3. Transposons and transposition 4. Gene transfer and recombination 5. Protein export and secretion in bacteria 6. Gene regulation: proteins as regulators 7. Gene regulation: regulatory RNA 8. Bacterial social communication 9. Stress genetics 10. Genome research: principles and applications 11. Manipulation of gene expression in prokaryotes Study materials and literature: lecture material and material provided during the course Completion: Lecture course Evaluation: Literature excercises. Grading scale: Pass/fail Responsible persons: Univ. lecturer Hannu Saarilahti (Return to Track 2a) 52728/81085 Plant Biotechnology and Molecular Biology (KBIOT300), 5 ECTS credits Time: Spring term, period III (12.1-26.2.2009, Mon and Thu, at 9-12) Place: Biocenter 2, lecture room 2012 Preceding studies: Basics in biochemistry and cell biology Objective: Learning of different aspects of plant biotechnology and molecular biology Contents: Lectures include: Molecular biology of agrobacterium-mediated gene transfer; Gene transfer methods and vectors for plant transformation; Plant genome structures; Molecular biology of light perception and signal transduction in plants; Pathways to plant secondary metabolites; Molecular basis of vegetative-reproductive transitions and flower development; Molecular basis of abiotic and biotic stress responses in plants; Applications in plant biotechnology; Forest biotechnology; Basics of legislation and risk assessment in plant biotechnology Study materials and literature: Lecture material + additional reading given by the lecturers in the net (Bb). Literature: Buchanan, B.B, Gruissem, W & Jones, R.L, 2002: Biochemistry and Molecular Biology of Plants. 1408 pages (relevant parts) Completion: Lectures, short essay Evaluation: Short written assignment, final examination. Grading scale: 0-5
  22. 22. 22 Responsible persons: Prof. Teemu Teeri (Faculty of Agriculture and Forestry), Univ. Lecturer. Pekka Heino and Prof. Jaakko Kangasjärvi (Faculty of Biosciences) Other information: The lectures are given jointly by the Faculty of Agriculture and Forestry and the Faculty of Biosciences (Return to Track 2b) 52911 Cancer Genetics, 2-3 ECTS credits Time: Spring term, period III (12.1-9.2.2009, Mon and Wed, at 8.30-10. Examination on Mon 9.2.2009 at 8.00 – 10 Biocenter 2, Auditorium 1041) Place: Biocenter 2, lecture room 1015 Contents: The lecture course will cover the basic concepts in cancer genetics: mutations and their mechanism in genome, control of the cell growth, familial cancer syndromes and the genetic testing in cancer. The examination of the lecture material (2 ECTS), together with extra literature (3 ECTS). Study materials and literature: Lecture material and review articles Completion: Lectures and literature Evaluation: Examination. Grading scale: 0-5 Responsible persons: Doc. Minna Nyström (Return to Track 4b) 52739 Genetic Bioinformatics, 3 ECTS credits Time: Spring term, period III (13.1.-19.2.2009, Tue and Thu at 10-12) Place: Biocenter 2, Auditorium 1041 Contents: This lecture course presents all the basic tools and data banks used in bioinformatics – what every biologist or scientist working in close contact with biology should know. The emphasis is more on applicatory side of the methods, though the basic principles how the tools work are presented (e.g., Needleman-Wunsch algorithm). The topics include e.g. BLAST, EMBOSS package (sequence analysis), multiple sequence alignment, molecular phylogenetics methods, promoter analysis, basics of gene expression analysis and biodatabanks. Study materials and literature: Lecture material Completion: Lecture course Evaluation: Examination. Grading scale: 0-5 Responsible persons: Univ. lecturer Päivi Onkamo Other information: The lectures are given in Finnish (Return to Track 1) 52773 Immunobiology, 3 ECTS credits Time: Spring term, period III (27.1.-19.3.2009, Tue and Thu at 10-12) Place: Biocenter 2, Auditorium 1041 Contents: The lecture will cover the basics of immunology, antigen recognition, antigen receptors,cellular immunology, antigen-antibody interactions, phylogeny and ontogeny of immune response and immunochemical techniques Study materials and literature: Lecture material Completion: Lecture course Evaluation: Examination. Grading scale: 0-5 Responsible persons: To be announced (Return to Track 2a, 4a, or 4b) 52746 Genetic Analysis, 3 ECTS credits Time: Spring term, period III-IV (Lectures: Mon 9.2.2009, Wed 11.2.2009 and Fri 13.2.2009 at 10 – 12; Excercise group I: 19.2.-27.2.2009 at 13-17; Excercise group II: April-March, to be announced later (one exercise group in English)
  23. 23. 23 Preceding studies: Basic courses in mathematics and statistics Contents: This course considers classical genetics, like Mendelian inheritance, pedigree/family tree analysis, hybridization experiments, linkage and basics of population genetics. The course consists of three lectures (basic maths and statistics only, aimed for biologists) and seven math exercises with short recaps of the days' topic Study materials and literature: Lecture material Evaluation: Examination. Grading scale: 0-5 Responsible person: Univ. lecturer Päivi Onkamo Other information: The lectures are given in Finnish, one exercise group in English (Return to Track 1) 529264 Practical Training in Cancer Genetics, 5 ECTS credits Time: Spring term, period III Relations to other study units: The lecture course 52911 Cancer genetics and basic knowledge of gene technology Contents: Functional characterization of mutations found in cancer patients. Experimental design: expression/stability, protein/protein interaction and repair efficiency assays Completion: Laboratory course Evaluation: Examination and laboratory note book. Grading scale: Pass/fail Responsible persons: Doc. Minna Nyström and PhD Reetta Kariola (Return to Track 4b) 52518/81028 Laboratory Course in Plant Biotechnology (KBIOT301), 5 ECTS credits Time: Spring term, period IV (23.2.-27.2.2009 at 13-18; 2.3.-6.3.2009 at 13-18; 10.3.-12.3.2009 at 13-18; 17.3.2009 at 13-18; 19.3.2009 at 13-18; 25.3.2009 at 13-18; 8.4.2009 at 13-18; 21.4-22.4.2009 at 13-18) Place: Biocenter 1, course lab 1026 Preceding studies: 525002 Kasvifysiologian ja –anatomian harjoitustyöt and 52728/81085 (KBIOT300) Plant biotechnology and molecular biology lecture serie obligatory 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 report. Grading scale: Pass/fail Responsible person: Prof. Teemu Teeri (Faculty of Agriculture and Forestry) and Univ. lecturer Mika Kotilainen (Faculty of Biosciences) Other information: The course is given jointly by the Faculty of Agriculture and Forestry and the Faculty of Biosciences. Maximum 14 students are accepted to the course. (Return to Track 2b) 52948 Chemical Genetics, 3 ECTS credits Time: Spring term, period III, in even years Contents: The course will focus on the role of chemical signals in plant and bacteria. Emphases will be on: Plant hormones; identification and function; Metabolomics; Communication in bacterial communities; Communication between different species; Small chemical ligands as tools in the investigation of signaling and protein and gene function Study materials and literature: Lecture material Completion: Lecture course Evaluation: Examination. Grading scale: 0-5
  24. 24. 24 Responsible persons: Doc. Gunter Brader (Return to Track 2a, or 2b) 52912 Genomes, 3 ECTS credits Time: Spring term, period IV (6.4-18.5.2009, Mon at 12-16) Place: Biocenter 2, Auditorium 1041 Preceding studies: Basics in biosciences and molecular genetics Objective: To understand the structure and dynamic nature of genomes and understand the basic methods that are used in genome level analysis of gene structure and function Contents: The lectures will focus on organization and function of genetic material. The following topics will be covered: Genome elements. Structure and organization of genomes. Single genes vs. multigene families. Large scale EST and genomic sequencing. Functional genomics. Study materials and literature: Lecture material and additional material provided by the lectures Completion: Lecture course Evaluation: Examination. Grading scale: 0-5 Responsible person: Prof. Tapio Palva (Return to Tracks 1, 2a, 2b, 3a, 3b, or 3c) 52986 Innate Immunity of Plants, 2 ECTS credits Time: Spring term, period IV (Within the period April 27-29, 2009) Contents: The course will be organised as a seminar series covering different aspects of plant defence mechanisms and defence signalling. Lectures will be given by invited experts as well as speakers from the CoE Completion: Requires active student participation, with seminars given by the students and discussed with the experts Evaluation: Examination. NOTE! Attendance to the seminars is obligatory Responsible persons: Prof. Tapio Palva and Prof. Thorsten Nürnberger Other information: Limited attendance. Organised together with the FGSPB (Return to Track 2b) 52939 From Genomes to Gene Function, 6 ECTS credits Time: Spring term, period IV (4.5.-29.5.2009, Tue-Fri at 13-17, 25.5.2009, Mon at 13-17) Place: Biocenter 1, course lab 1031 Preceding studies: Basics of bioinformatics. The “Genomes” lectures, if not taken previously, need to be completed during the course Contents: A problem-based approach starting with sequence database searches and ending with functional characterization of specific genes Study materials and literature: Course manual and material distributed during the course Completion: Practical course Evaluation: Examination and presentations. Grading scale: 0-5 Responsible person: Ass. Elina Helenius (Return to Track 1, 2a, 2b, 3a, 3b, 3c, or 5) 52936 Gene Regulation in Eukaryotes, 3 ECTS credits Time: Spring term, period IV (17.4.-19.5.2009 Tue and Thu at 14-16. No lectures on 9.4, 14.4 or 30.4.2009) Place: Biocenter 2, lecture room 2012 Objective: To provide a general view of regulation in eukaryotes Contents: The lectures will focus on expression of genetic material in eukaryotic cells, especially on regulation of gene expression on different levels. Topics covered by the lecture include: Transcriptional complexes and initiation of transcription, chromatin structures in
  25. 25. 25 relation of gene expression, transcriptional regulators and their mode of action, post- transcriptional gene regulation, genetic networks and their coordinated regulation by internal and external signals Study materials and literature: Lecture material and additional material provided during the lectures Completion: Lecture course Evaluation: Examination. Scale: 0-5 Responsible person: Univ. lecturer Pekka Heino (Return to Track 2a, 2b, 3a, 3b, 3c, or 4b) AUTUMN OR SPRING TERM 52747 Advanced Course in Plant Genomics and Molecular Biology, 9 ECTS credits Time: At any time after an agreement with one of the group leaders of the CoE Preceding studies: Not recommended before finishing the mandatory laboratory courses and lectures Objective and contents: The course will familiarise students with the central methods and approaches in plant genomics and molecular biology along with topical research subjects. Practical work to be done in research groups of the CoE and will include experimental planning, laboratory work, reporting and assessment of the results Evaluation: Written reports. Grading scale: 0-5 Responsible persons: PIs of the CoE (Return to Track 2b)
  26. 26. 26 Academic year 2008-2009 Study unit descriptions: Alternative study units for MBIOT students organized by the Faculty of Agriculture and Forestry (AF) AUTUMN TERM (period I and II) 81037 Molecular Methods in Applied Plant Genetics (JAL403/KBIOT403), 5 ECTS credits Time: Autumn term, period I, in even-numbered years (2.9-16.10.2008, Tue and Thu at 8-10) Place: C-building, seminar room 130 Objective: To learn the range of molecular applications available. To understand their principles and the methodology used Contents: Recent advances in the use of molecular methods in plant and forest tree breeding. Marker-assisted selection, genetic transformation and genomics approaches are discussed in detail. Case studies prepared and presented by the students. Study materials and literature: Relevant literature will be indicated during the course Completion: Lecture course, case studies Evaluation: Examination, case studies. Grading scale: 0-5 Responsible person: Prof. Teemu Teeri (Return to Track 1, 2b, or 4a) 81331 Epidemiology and Ecology of Plant Pathogens (KPAT401/ME460), 5 ECTS credits Time: Autumn term, period I (5.9-7.10.2008, see the detailed schedule in Weboodi) Preceding studies: KPAT121 or ME104, ME260 and ME361 or equivalent knowledge Objective: To understand the factors and processes behind plant disease epidemics in forest and agricultural ecosystems. Contents: Basic epidemiology and examples. The biological background for epidemics, risk assessment, epidemiological mechanisms and modelling. Study materials and literature: Wolfe, M.S. & Caten, C.E. eds. 1987. Populations of Plant Pathogens, Their Dynamics and Genetics. Blackwell Scientic Publications. B.M. Cooke, D. Gareth Jones and B. Kaye (eds).2006: The Epidemiology of Plant Diseases.Springer, Dordrecht. Completion: Lectures, practical work, independent study. Evaluation: Examination 70%, lab report 15%, individual project 15%. Grading scale: 0-5 Responsible person: Univ. lecturer Risto Kasanen and Prof. Minna Pirhonen (Return to Track 2a) 8720094 Dairy Bioprocessing (ETT360), 6 ECTS credits Time: Autumn and spring term, period I-IV (8.9-13.10.2008, Mon at 13.15-14.45, then literature examination) Place: EE-building, seminar room 3+4 Objective: To introduce to the common dairy processes covering from the raw milk cold chain to the microbiological quality control and shelf life of dairy products Contents: The course consists of two parts equal in sizes: Part I (period I) (3 credits): Raw milk microbiology, a laboratory course containg basic microbiological methods to enumerate total, aerobic, anaerobic, psychrotrophic, lipolytic and proteolytic spoilage bacteria and particular pathogens in raw milk, dairy process and product samples, and further isolate and preliminary identify the obtained isolates. Part II (periods I - IV) (3 credits): A literature examination, relevant chapters from three dairy
  27. 27. 27 microbiology, technology and bioprocessing textbooks Study materials and literature: Relevant literature and material provided during the course Completion: Laboratory course and literature examinations Evaluation: Examinations and laboratory reports Responsible person: Prof. Tapani Alatossava and Patricia Munsch-Alatossava (Return to Track 4a) 850030 Biofuels (YKEM420), 5 credits Timing: Autumn term, period I (8.9-15.10.2008, Mon and Wed at 14.15-15.45) Place: INFO 4 Preceding studies: Chemically or biotechnically oriented bachelor degree or corresponding knowledge required Objective: To give an overall insight into biotechnical methods for the production of biofuels from renewable resources. Biofuels include ethanol, butanol, biodieseloils, hydrogen and methane. Contents: Utilization of biotechnical methodologies for the production of biofuels: enzymology and fermentation of of renewables into various fuels. Study materials and literature: To be informed Completion: Lectures, seminars, independent study Evaluation: Examination Responsible person: Prof. Liisa Viikari Other information: The course will be held in English or Finnish (depending on the attending students) (Return to Track 2a) 830114 Basic Biotechnology in Forestry (ME363), 5 credits Timing: Autumn term, period I (15.9-15.10.2008, Mon and Wed at 9-12) Place: Mon A-building seminar room 203, Wed B-building, seminar room 332 Contents: Biotechnology and its allied areas of bioresource science and genomics is a rapidly developing field of study with considerable benefits not just for agricultural, environmental and medical sciences but also in forestry. The course however will primarily cover much of the applied aspects of biotechnology relevant to forestry. Traditionally, humans have for centuries exploited forest organisms (trees & microbes) for their own benefits particularly in timber and fiber production, as a source of nutrition and also natural biocides. With the advent of biotechnology, there is an increasing demand for the use of biomass from forest trees as a renewable energy source as well as carbon sink to control global warming. Additionally, the root systems of certain tree species are also adaptable for use in phytoremediation of polluted soils or habitats. Equally, some microbes associated to forest trees are of potential biotechnological significance in the area of bioremediation of polluted ecosystems, industrial chemical processing and production (bioethanol), pharmaceuticals (antibiotics) and in biological control of pests. Biotechnology further offers opportunities through the use of genetics to expand or improve on many of these positive attributes of forest trees and associated organisms. The course will also address principles and ethical issues on genetical modified organisms (trees). Completion: Lectures, seminars, literature discussions, independent and group work Evaluation: Examination=80%, Report/seminars=20% Responsible person: Prof. Fred Asiegbu (Return to Track 2b) 871074 Food Legislation and Control (EK131), 5 ECTS credits Time: Autumn term, period I-II (22.9-11.12.2008, Wed at 15.15-17.45, Thu at 12.15-14.45) Place: B-building, lecture hall 5
  28. 28. 28 Objective: Introduction to food legislation and control systems Contents: European regulations on food, action of European Food Safety Authority (EFSA,) Food control system in Finnish Food Safety Authority (EVIRA), Finland, case type studies (incl. national and EU legislations), Case study; food control systems in the retail market chains, Control of imported goods, action of Finnish Custom Laboratory Study materials and literature: Material provided during the course Completion: Lectures, excursion to EVIRA Evaluation: Examination and/or a written essay Responsible person: Univ. lecturer Velimatti Ollilainen (Return to Track 4a) 871072 Chemical Risk Factors (EK132), 5 ECTS credits Time: Autumn term, period II (28.10-9.12.2008, Tue at 12.15-15.00, 30.10-11.12.2008, Thu at 9.15-12.00, 18.11.2008, Tue at 12.15-14.00, 25.11.2008, Tue at 12.15-15.00) Place: on 28.10-9.12.2008 D-building, lecture hall D, on 30.10-11.12 B-building, lecture hall 4, on 18.11.2008 and 25.11.2008 B-buildng, lecture hall 6 Objective: Introduction to the chemical hazards and risks related to foods Contents: Chemical hazards:structures, reactivity, analytical methods, occurrance in foods or feeds. Significant for human health i.e chemical safety (occurrence, intake, ADI). Environmental aspects. Course deals with heavy metals, POPs, "the Dirty Dozen" compounds, nitrate, allergenes, natural born toxins, medicine residues, food additives, dietary supplements, hazardous compounds derived from food processing or foor packaging, pesticide residues Study materials and literature: Material provided during the course Completion: Lecture course Evaluation: Examination and/or a written essay Responsible person: Univ. lecturer Velimatti Ollilainen (Return to Track 4a) 81351 Bacteria, Viruses and Pathogen Diagnostics (KPAT403), 10 ECTS credits Time: Autumn term, period II (27.10-12.12.2008, see the detailed schedule in Weboodi) Preceding studies: Basic knowledge in plant or forest pathology, microbiology and gene technology required (KTB121, MIKRO200, MIKRO220, BIOT200, BIOT201 or equivalent knowledge). Objective: To learn to know the common bacterial and viral diseases of cultivated plants in our country, their control, infection cycles and the molecular and taxonomic features of the microbes causing them. To learn the different diagnostic methods that are used in control of plant diseases and the disease-causing organisms. Contents: Identification, biology, morphology, spread and control of bacteria and viruses causing plant diseases in cultivated plants in Finland. Diagnostics, especially serological, biochemical and molecular diagnostic methods, are included in practical laboratory exercises. Study materials and literature: Schaad, N.W., Jones, J.B. & Chun, W. 2001 (eds.) Laboratory Guide for Identification of Plant Pathogenic Bacteria. APS Press. Agrios, G.N. 2006. Plant Pathology. 5th ed. Academic Press Hull, Roger 2002. Matthews’ Plant Virology. 4th ed. Academic Press. Completion: Lecture course, laboratory work, independent study Evaluation: Examination and reports. Grading scale: 0-5 Responsible person: Prof. Minna Pirhonen and Prof. Jari Valkonen (Return to Track 2a) 8720092 LAB Starters (ETT340), ECTS credirt Time: Autumn term, period II (29.10-12.12.2008, Wed at 13.15-14.45) Place: EE-building, seminar room 3+4
  29. 29. 29 Objective: Introduce the students to most common lactic acid bacteria (LAB) used as starters in food industry and to the basic methods used for LAB cultivation and identification Contents: Basic microbiological methods to cultivate, enumerate and isolate lactococci, streptococci and lactobacilli. Identification of LAB starter strains isolated from various fermented foods. Analysis of commercial probiotic Lactobacillus strains Study materials and literature: Material provided during the course Completion: Laboratory course including a couple of lectures Evaluation: Examination + laboratory reports Responsible person: Prof. Tapani Alatossava (Return to Track 4a) 830113 Forest Microbiology (ME362), 8 credits Time: Autumn term, period II (3.11-17.12.2008, Mon-Fri 9-12) Place: Mon A-building seminar room 203, Tue B-building, seminar room 332 Objective: The course covers the many functions of microorganisms in the uptake and cycling of nutrients in forest ecosystems, microbial parasitic and symbiotic interactions with trees, decomposition of forest litter and wood debris. Specifically, the microbiology of living roots, stems, needles and leaves of forest trees will be addressed. Systematics of microbes involved in nutrient cycling will also be discussed. Emphasis will be placed on the genetics, biochemistry, physiology, evolutionary biology and population dynamics of the microorganisms involved, as well as the exploitation of forest microorganisms in commercial & industrial processes, including phytoremediation and biological control. Current advances in these fields of study, made possible by use of novel and modern biological techniques will be demonstrated. Completion: Lectures, practical work, demonstrations, seminars, literature discussions, independent and group work Evaluation: Exam= 80%, project report= 20% Responsible person: Prof. Fred Asiegbu and Univ. lecturer Risto Kasanen (Return to Track 2a) 81406 Advanced Forest Mycology & Pathology (ME463), 10 credits Time: Autumn term, period II (13.11-17.12, Mon-Thu) Contents: The course will be primarily based on laboratory and individual project work sessions. It will cover current advances used in studies related to tree pathogens which are made possible with aid of novel and modern biological techniques. Additionally, the course will cover the microbiology of living roots, stems, needles and leaves. Specific focus will be on diseases affecting the various tissue organs of forest trees. The course will also address the many functions of fungi in the uptake and cycling of nutrients in forest ecosystems, microbial parasitic and symbiotic interactions with trees, decomposition of forest litter and wood debris. Strong emphasis will be placed on the genetics, biochemistry, physiology, evolutionary biology & population dynamics of the microorganisms involved, as well as the exploitation of forest microorganisms in commercial & industrial processes, including biological control. Completion: Lectures, practical work, demonstrations, seminars, literature discussions, independent and group work Evaluation: Examination=80% Project report/seminars=20% Responsible person: Prof. Fred Asiegbu (Return to Track 2b) 864050 Forest Microbes as Resources in Biotechnology: Discovery, Methodology and Utilization (YBIOT570), 5 ECTS credits Time: Autumn term, period II, every third year (next time in autumn 2010)
  30. 30. 30 Preceding studies: BSc. level or equivalent required Objective: To learn the major steps in the process of discovery of new biocompounds Contents: Isolation, identification and characterization of micro-organisms, their cultivation in laboratory as pure cultures, enzyme detection and purification, metabolite and enzyme analysis using biochemical and molecular biology tools, fungal enzymes in degradation of environmental pollutants, fungal metabolites in medication. Completion: Lecture course, demonstrations, field trip and a symposium Evaluation: Active participation, written and oral reports, examination. Grading scale: 0-5 Responsible person: Prof. Annele Hatakka Other information: The course is given every third year (NOVA collaboration) (Return to Track 2a) SPRING TERM (period III and IV) 81576 Molecular Genetic Markers in Animal Breeding (KEJAL/KEBIOT440), 5 ECTS credits Time: Spring term, period III, in uneven years (12.1-1.3.2009) Place: Course and research laboratories at the Dept. of Animal Science Preceding studies: Basics in biochemistry and animal biotechnology Objective: Students learn to work in a DNA laboratory and how to use molecular genetic markers in DNA diagnostics and in other applications of animal breeding and genetics Contents: Journal club, principles of working in a DNA laboratory, collecting samples and extracting DNA, the utilization of DNA sequences, selection of genetic markers, DNA amplification, genotyping of microsatellite markers, parentage testing and pedigree checking, construction of linkage map, visit to a DNA diagnostics laboratory Study materials and literature: Course material provided during the course Completion: Laboratory course, seminars Evaluation: Participation in journal club, demonstrations and laboratory work and report Responsible person: Univ. lecturer Kari Elo Other information: The lectures are given in Finnish unless otherwise required (in English). The number of students is restricted to 8. (Return to Track 1) 81352 Plant-Microbe Interactions and Molecular Defence of Plants (KPAT501/ME560), 10 ECTS credits Time: Spring term, period III (12.1-1.3.2009, see the detailed schedule in Weboodi) Preceding studies: This is an advanced course in molecular plant pathology and therefore previous knowledge of plant pathology and/or plant or molecular biology is required (for example KPAT401, KPAT402, KPAT403 and BIOT200) Objective: To understand the molecular mechanisms of pathogenesis and virulence in plant pathogens, the molecular basis of symbiotic interactions, and the genetic basis and molecular mechanisms of disease resistance in plants. Contents: The biology of pathogen infections, plant defence responses and symbiotic interactions at the molecular level. The course includes laboratory work sessions Study materials and literature: Will be given during the course Completion: Lectures, laboratory exercises, group work and independent study Evaluation: Examination and report. Grading scale: 0-5 Responsible person: Prof. Minna Pirhonen Relations to other study units: The course will be organised jointly and taught simultaneously with the Swedish University of Agricultural Sciences (SLU). It is also included as PhD course within Viikki Graduate School in Molecular Biosciences Other information: For the arrangements, see the course home page: http://www.mm.helsinki.fi/MMSBL/english/research/Kpat/CPPE/Index.htm
  31. 31. 31 (Return to Track 2a or 2b) 81085/52728 Plant Biotechnology and Molecular Biology (KBIOT300), 5 ECTS credits Time: Spring term, period III (12.1-26.2.2009, Mon and Thu, at 9-12) Place: Biocenter 2, lecture room 2012 Preceding studies: Basics in biochemistry and cell biology Objective: Learning of different aspects of plant biotechnology and molecular biology Contents: Lectures include: Molecular biology of agrobacterium-mediated gene transfer; Gene transfer methods and vectors for plant transformation; Plant genome structures; Molecular biology of light perception and signal transduction in plants; Pathways to plant secondary metabolites; Molecular basis of vegetative-reproductive transitions and flower development; Molecular basis of abiotic and biotic stress responses in plants; Applications in plant biotechnology; Forest biotechnology; Basics of legislation and risk assessment in plant biotechnology Study materials and literature: Lecture material + additional reading given by the lecturers in the net (Bb). Literature: Buchanan, B.B, Gruissem, W & Jones, R.L, 2002: Biochemistry and Molecular Biology of Plants. 1408 pages (relevant parts) Completion: Lecture course, short essay Evaluation: Short written assignment, final examination. Grading scale: 0-5 Responsible persons: Prof. Teemu Teeri (Faculty of Agriculture and Forestry), Univ. lecturer. Pekka Heino and Prof. Jaakko Kangasjärvi (Faculty of Biosciences) Other information: The lectures are given jointly by the Faculty of Agriculture and Forestry and the Faculty of Biosciences (Return to Track 2b) 864065 Food Microbiology (MIKRO231), 5 ECTS credits Time: Spring term, period III (12.1.-1.3.2009, Mon 12-16 and Wed 14-16) Place: Mon INFO 3 and Wed INFO 4 Relations to other study units: Basics in microbiology Objective: Basics of food and water microbiology Contents: Water and food standard methods of analysis, food pathogens, microbiological spoilage of food, fermentation products. Microbiological safety in food production. Microbiological quality of drinking water. Study materials and literature: J.M Jay et al. Modern Food Microbiology, seventh edition. Springer Science + Business media Inc. 2005, NY, USA. Parts I, II, III,V and VI. In addition the materials of the lectures are found on the Blackboard platform. Completion: Lecture course, group work Responsible person: Prof. Per Saris Other information: The lectures are given in Finnish, but the course can be taken as a literature examination in English (Return to Track 4a) 8720024 Potential Novel Processing Technologies (ETT425), 5 ECTS credits Time: Spring term, period IV (9.3-27.4.2009, Mon 12.15-13.45) Place: EE-building, seminar room 3+4 Objective: To get familiar with potential new food processing technologies and to evaluate the possibilities and limitations of these methods Contents: Working in small teams, students will study the literature related to a potential novel food processing method, write a report on the method and teach it to other students in the class. Study materials and literature: Material provided during the course Completion: Group work Eveluation: Examination (50%) + report and teaching and acting as an opponent (50%)

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