mbiotcurriculum2008.doc.doc

Updated 28.8.2008

Curriculum 2008-2009Master’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 / IV529242 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 credits529230/882503 Final Examination in M.Sc. degree 8-10 2529250/882504 Master´s Thesis and Maturity Essay 40 2529249 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/or529212 Advanced Training in a Research Group, I and II 10 + 10 1-2and/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)

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http://cie.hkkk.fi/28A00210/

http://cie.hkkk.fi/31A00210/

https://cie.hkkk.fi/23A00210/

http://www.helsinki.fi/biosci/biochem/51044%20BioBusiness.htm

http://www.helsinki.fi/biosci/biochem/51044%20BioBusiness.htm

Abbreviations: B = Faculty of Biosciences AF = Faculty of Agriculture and Forestry BI = Institute of Biotechnology NC = Neuroscience Center MBI = Master’s Degree Programme in BioinformaticsBM = 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 Englishf = 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

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ECTS Quota forcredits Period MBIOT

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TRACK 1: BIOINFORMATICS AND SYSTEMS BIOLOGY More information: Liisa Holm (B, BI), [email protected] or Teemu Teeri (AF), [email protected]

Primarily recommended elective courses:52912 (B) Genomes (e) 3 IV -52939 (B) From Genomes to Gene Function (e) 6 IV 2-3529224 (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) 3582606 (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) 881037 (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) 2582604 (MBI) Practical Course in Biodatabases (e) 4 III -------------------------------------------------------------------------------------------------------------------------------------------

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mailto:[email protected]



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TRACK 2: BIOTECHNOLOGY OF NATURAL RESOURCES

TRACK 2a) Microbial and Environmental BiotechnologyMore information: Hannu Saarilahti (B), [email protected], Annele Hatakka (AF), [email protected]

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 4528012 (B) Laboratory Course in Virology and Bioinf.. (f or e) 6 II 2864062 (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 2-3529234 (BI) Recombination Mechanisms (e) 3 IV (in uneven years) -

TRACK 2b) Plant and Forest Genomics and BiotechnologyMore information: Tapio Palva (B), [email protected], Teemu Teeri (AF), [email protected]

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 2-3529225 (B, BI) Laboratory Course on Plant Genomics (e) 5 IV (in even years) 352728 (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) 2830114 (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 2-352747 (B) Advanced Course in Plant Genomics and

Molecular Biology (e) 9 I-IV 2-381039 (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) -

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TRACK 3: CELLULAR BIOTECHNOLOGY AND DEVELOPMENTAL AND STRUCTURAL BIOLOGY

TRACK 3a) Cellular BiotechnologyMore information: Pekka Lappalainen (BI), [email protected], Jussi Jäntti (BI), [email protected]

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 8529222 (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), [email protected], Tapio Heino (BI), [email protected]

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) 352936 (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 BiologyMore information: Dennis Bamford (BI, B), [email protected], Sarah Butcher (BI), [email protected]

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) 12529267 (BI) Lecture and Exercise Course on Electron Microscopy

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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) 8528006 (BI, B) Introduction to Viruses (f ) 3-4 II -528012 (B) Laboratory Course in Virology and Bioinf. (f or e) 6 II 2529234 (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

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TRACK 4: FOOD BIOTECHNOLOGY AND HEALTH BIOTECHNOLOGY

TRACK 4a) Food BiotechnologyMore information: Tapani Alatossava (AF), [email protected]

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) 852773 (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 BiotechnologyMore information: Hannu Saarilahti (B), [email protected]

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 4529232 (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

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TRACK 5: NEUROSCIENCEMore information: Tomi Taira (NC, B), [email protected]

Please find the list of courses given by the Neuroscience Center 2008-2010 here:http://www.helsinki.fi/neurosci/education.htm

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http://www.helsinki.fi/neurosci/education.htm


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 fieldObjective: 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 coordinatorStudy material and literature: MBIOT degree requirements, course descriptions, curriculum, other instructionsCompletion: 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/failResponsible 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 thesisPlace: Will be announced later. Mon 19.1.2009 at 12-15, INFO computer class 170Preceding 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

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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/failResponsible 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 ForestryOther information: More information on the HEBIOT and MBIOT home pages (Return to Major Subject Studies)

529208 Bioethics, 3 ECTS creditsTime: 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 2Target group: MBIOT, MScPPS, MScFood and HEBIOT Master's studentsPreceding studies: Bachelor's degree or equivalent in biotechnology, biology, biochemistry, chemistry or in a related fieldObjective: 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 courseCompletion: Lectures, case studies, panel discussionEvaluation: 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/failResponsible persons: MBIOT, MScPPS, MScFood and HEBIOT coordinatorsOther 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 creditsTime: 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 unitPreceding studies: Bachelor's degree or equivalent in biotechnology or in a related fieldObjective: To acquire practical experience in a company, research institute or government agency operating in the field of biotechnologyContents: As agreedStudy material and literature: Material related to the training

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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 creditsEvaluation: 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/failResponsible 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 creditsTime: 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 unitPreceding studies: Bachelor's degree or equivalent in biotechnology or in a related fieldObjective: 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 trainingCompletion: 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: 0-5Responsible person: Professors in charge of MBIOT (Return to Major Subject Studies)

529230/882503 Final Examination for the Master's Degree, 8-10 ECTS creditsTime: 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 studiesObjective: To deepen the student's knowledge of molecular biology and biotechnology within the chosen specialisation trackContents: Independent study, examinationStudy material and literature: Scientific literature according to the chosen specialisation track

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Completion: Literature examination. 100-150 pages will yield 1 ECTS creditEvaluation: Literature examination. Grading scale: 0-5Responsible 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 creditsTime: 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 subjectStudy material and literature: Scientific literature according to the chosen research topicCompletion: See the instructions of your facultyEvaluation: 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)

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Study unit descriptions:Alternative study units for MBIOT students organized by the Institute of Biotechnology (BI)


529225 Laboratory Course on Plant Genomics, 5 ECTS creditsTime: 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 lecturesObjective: A lab course, in which a student will be introduced to modern methods in the structural and functional analyses of plant genomesContents: Laboratory work, minisymposiumStudy materials and literature: OptionalCompletion: Laboratory courseEvaluation: Laboratory work in practice. Grading scale: 0-5Responsible person: Prof. Ykä HelariuttaOther 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 creditsTime: 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 3108Target group: Designed for MSc students and PhD studentsObjective: 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 FunctionCompletion: 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: 0-5Responsible person: Prof. Sarah Butcher

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http://www.biocenter.helsinki.fi/viikkigs/PlantGenomics08.htm

Relations to other study units: This course is a prerequisite for 529223 Advanced Course in Structural Biology and Biophysics, 10 ECTSOther 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 BiologyObjective: 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 organogenesisContents: 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 creditsTime: 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 spectrometryStudy 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 weekEvaluation: Presentation during class, examination. Grading scale: 0-5Responsible person: Prof. Sarah ButcherRelations 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 creditsTime: 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

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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 processingContents: 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 courseCompletion: Lectures (30 hours), 1 x4 hour EM demonstration, 5 x 4 hour image processing exercises. Evaluation: Presentation during class, exercise reports. Grading scale: 0-5Responsible person: Prof. Sarah ButcherOther 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 creditsTime: 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. SeminaariesitelmätStudy materials and literature: LuentomateriaaliCompletion: Lectures (3 ECTS credits) and seminar presentations (1 ECTS credit) Evaluation: Examination. Grading scale: 0-5Responsible person: Prof. Dennis BamfordOther 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 chemistryObjective: The objective of the course is to introduce the students to some of the central methods in analytical protein chemistryContents: 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), bioinformaticsStudy material and literature: Given literature and laboratory manualsCompletion: Daily lectures followed by practical laboratory work/ demonstrations. 1 ECTS with lectures and exam, 2 ECTS with lectures, exam and laboratory partEvaluation: Examination. Grading scale: 0-5Responsible person: Doc. Nisse KalkkinenOther information: The lectures are open to all. The number of participants for the laboratory part is limited to 8 persons

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(Return to Track 1, 3c, or 4a)


529263 Advanced Laboratory Course in Cellular Biotechnology, 5 ECTS creditsTiming: 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 VartiainenOther 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 creditsTiming: 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 2063Contents: 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 courseEvaluation: Examination. Grading scale: 0-5Responsible person: Doc. Tapio HeinoOther 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 creditsTime: 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 cellsContents: 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

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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 lecturesCompletion: Lecture courseEvaluation: Examination. Grading scale: 0-5Responsible person: Doc. Mikko Frilander (Return to Track 1, 3a, 3b, 3c, or 4b)

529235 Growth Factors and their Receptors, 3 ECTS creditsTime: Spring term, period IV in uneven years (11.3.-6.5.2009, Wed and Thu at 14-16)Place: Biocenter 1, seminar room 3108Preceding 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 lecturesCompletion: Lectures, seminars Evaluation: Examination. Grading scale: 0-5Responsible person: Prof. Mart Saarma (Return to Track 3a, 3b, or 4b)

529234 Recombination Mechanisms, 3 ECTS creditsTime: 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 1041Preceding studies: At least basic knowledge on genetics, biochemistry, and microbiologyObjective: Understanding various forms of recombination reactions and their uses for research and other purposesContents: 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 lecturesCompletion: Lecture courseEvaluation: Examination. Grading scale: 0-5Responsible person: Prof. Harri Savilahti(Return to Track 1, 2a , 2b, 3a, 3b,3c or 4b)

529221 Developmental Biology, Practical Course, 4 ECTS creditsTime: Spring term, period IVTarget 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) recommendedObjective: To learn laboratory skills in modern developmental biology, to learn advantages of different research model organisms

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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: 0-5Responsible person: Doc. Juha Partanen(Return to Track 3b, or 4b)

529233 X-Ray Crystallography Techniques, 2 ECTS creditsTime:Place:Target group:-Preceding studies: Courses 529236 and 529223Objective: 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 courseCompletion: Demonstrations and practicals (hands-on computer work).Evaluation: Lab notebooks. Scale: pass/failedResponsible person: Prof. Adrian Goldman(Return to Track 3c)


529223 Advanced Course in Structural Biology and Biophysics, 10 ECTS creditsTime: 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 groupContents: Written research proposal, laboratory work on a project, written report in the form of a scientific paperStudy material and literature: OptionalCompletion: 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 ButcherOther 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 creditsTime: 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

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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 reportStudy material and literature: OptionalCompletion: 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 VartiainenOther 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 creditsTime: 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 courseObjective: A 9 week period during which a student will be introduced to a genuine research project in a research groupContents: Written research proposal, laboratory work on a project, written report in the form of a scientific paperStudy materials and literature: OptionalCompletion: Will be done in a laboratory of the Program in Developmental biology at the Institute of BiotechnologyEvaluation: 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 ShimmiOther 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 creditsTime: 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 lecturesObjective: A 9 week period during which a student will be introduced to a genuine research project in a research groupContents: Written research proposal, laboratory work on a project, written reportStudy material and literature: OptionalCompletion: 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)/3Responsible person: Prof. Ykä HelariuttaOther information: Please contact the group leader or the responsible person for further information (Return to Track 1)

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Study unit descriptions:Alternative study units for MBIOT students organized by the Faculty of Biosciences (B)


52930 Protein Informatics, 3 ECTS creditsTime: 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 applicationsStudy materials and literature: Lecture material, Literature: Lesk, Introduction to Bioinformatics, OxfordCompletion: Lectures and excercisesEvaluation: Examination. Grading scale: 0-5Responsible person: Prof. Liisa HolmOther 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 creditsTime: Autumn term, period I (1.9. - 17.10.2008, Mon-Fri at 9-17) Place: Biocenter 3, 6th floor laboratoryPreceding studies: Basics in plant anatomy and physiologyContents: 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 assessmentStudy materials and literature: Material provided during the courseCompletion: Laboratory courseEvaluation: Written reports. Grading scale: 0-5Responsible person: Senior researcher Dr. Anthony Bishopp (Return to Track 2b)

52751 Molecular Genetics Laboratory Course, 9 ECTS creditsTime: Autumn term, periods I-II (6.10.-24.10.2008, Mon-Fri at 9-17)Place: Biocenter 1, course lab 1024Preceding 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 courseEvaluation: Examination, poster and lab report. Grading scale: 0-5Responsible person: Univ. lecturer Pekka HeinoOther information: The course language is Finnish and English(Return to Track 2a, 3a or 4b)

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528012 Laboratory Course in Virology and Bioinformatics, 6 ECTS creditsTime: 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 2015Preceding 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 knowledgeObjective 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 courseCompletion: Laboratory exercises, laboratory reports, exercises in bioinformaticsEvaluation: Laboratory report. Grading scale: 0-5Responsible persons: University lecturers Minna Poranen and Janne RavanttiOther 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 creditsTime: Autumn term, period II (29.10-10.12.2008, Wed and Thu at 14-16)Place: INFO 2Contents: 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 geneticsStudy materials and literature: Lecture materialCompletion: Lecture courseEvaluation: Examination. Grading scale: 0-5Responsible person: Univ. lecturer Katarina PelinOther information: The lectures are given in Finnish unless otherwise required (in English)(Return to Track 4b)

52931 Exercises in Protein Informatics, 5 ECTS creditsTime: Autumn term, period II (dates to be announced later)Place: INFO 138 Preceding studies: 53739 Genetic bioinformaticsContents: Practical course where we aim to infer protein function and structure as well as possible from the amino acid sequence. Tools include public web serversStudy materials and literature: Material provided during the courseCompletion: The course contains guided exercises and a group work where a target protein is analyzedEvaluation: Written report. Grading scale: 0-5Responsible person: Prof. Liisa HolmOther information: The exercises are given in Finnish unless otherwise required (in English)(Return to Track 1)


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http://www.helsinki.fi/biosci/ymbo/virologiankurssi.htm

52748 Microbial Genetics and Genomics, 4 ECTS creditsTime: 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 partition2. Phages, plasmids3. Transposons and transposition4. Gene transfer and recombination5. Protein export and secretion in bacteria6. Gene regulation: proteins as regulators7. Gene regulation: regulatory RNA8. Bacterial social communication9. Stress genetics10. Genome research: principles and applications11. Manipulation of gene expression in prokaryotesStudy materials and literature: lecture material and material provided during the courseCompletion: Lecture courseEvaluation: Literature excercises. Grading scale: Pass/failResponsible persons: Univ. lecturer Hannu Saarilahti(Return to Track 2a)

52728/81085 Plant Biotechnology and Molecular Biology (KBIOT300), 5 ECTS creditsTime: Spring term, period III (12.1-26.2.2009, Mon and Thu, at 9-12) Place: Biocenter 2, lecture room 2012Preceding studies: Basics in biochemistry and cell biologyObjective: Learning of different aspects of plant biotechnology and molecular biologyContents: Lectures include: Molecular biology of agrobacterium-mediatedgene 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 ofvegetative-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 biotechnologyStudy 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 essayEvaluation: Short written assignment, final examination. Grading scale: 0-5

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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 1015Contents: 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 articlesCompletion: Lectures and literatureEvaluation: Examination. Grading scale: 0-5Responsible persons: Doc. Minna Nyström(Return to Track 4b)

52739 Genetic Bioinformatics, 3 ECTS creditsTime: Spring term, period III (13.1.-19.2.2009, Tue and Thu at 10-12) Place: Biocenter 2, Auditorium 1041Contents: 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 materialCompletion: Lecture courseEvaluation: Examination. Grading scale: 0-5Responsible persons: Univ. lecturer Päivi OnkamoOther information: The lectures are given in Finnish(Return to Track 1)

52773 Immunobiology, 3 ECTS creditsTime: Spring term, period III (27.1.-19.3.2009, Tue and Thu at 10-12)Place: Biocenter 2, Auditorium 1041Contents: 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 techniquesStudy materials and literature: Lecture materialCompletion: Lecture courseEvaluation: Examination. Grading scale: 0-5Responsible persons: To be announced(Return to Track 2a, 4a, or 4b)

52746 Genetic Analysis, 3 ECTS creditsTime: 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)

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Preceding studies: Basic courses in mathematics and statisticsContents: 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' topicStudy materials and literature: Lecture materialEvaluation: Examination. Grading scale: 0-5Responsible person: Univ. lecturer Päivi OnkamoOther information: The lectures are given in Finnish, one exercise group in English (Return to Track 1)

529264 Practical Training in Cancer Genetics, 5 ECTS creditsTime: Spring term, period III Relations to other study units: The lecture course 52911 Cancer genetics and basic knowledge of gene technologyContents: Functional characterization of mutations found in cancer patients. Experimental design: expression/stability, protein/protein interaction and repair efficiency assaysCompletion: Laboratory courseEvaluation: Examination and laboratory note book. Grading scale: Pass/failResponsible persons: Doc. Minna Nyström and PhD Reetta Kariola(Return to Track 4b)

52518/81028 Laboratory Course in Plant Biotechnology (KBIOT301), 5 ECTS creditsTime: 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 1026Preceding 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 transferContents: 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 articlesCompletion: Laboratory courseEvaluation: Laboratory report. Grading scale: Pass/failResponsible 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 creditsTime: 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 functionStudy materials and literature: Lecture material Completion: Lecture courseEvaluation: Examination. Grading scale: 0-5

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Responsible persons: Doc. Gunter Brader(Return to Track 2a, or 2b)

52912 Genomes, 3 ECTS creditsTime: Spring term, period IV (6.4-18.5.2009, Mon at 12-16) Place: Biocenter 2, Auditorium 1041Preceding studies: Basics in biosciences and molecular geneticsObjective: 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 functionContents: 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 lecturesCompletion: Lecture courseEvaluation: Examination. Grading scale: 0-5Responsible 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 CoECompletion: Requires active student participation, with seminars given by the students and discussed with the expertsEvaluation: Examination. NOTE! Attendance to the seminars is obligatoryResponsible 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 creditsTime: 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 1031Preceding studies: Basics of bioinformatics. The “Genomes” lectures, if not taken previously, need to be completed during the courseContents: A problem-based approach starting with sequence database searches and ending with functional characterization of specific genesStudy materials and literature: Course manual and material distributed during the course Completion: Practical courseEvaluation: Examination and presentations. Grading scale: 0-5Responsible person: Ass. Elina Helenius(Return to Track 1, 2a, 2b, 3a, 3b, 3c, or 5)

52936 Gene Regulation in Eukaryotes, 3 ECTS creditsTime: 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 2012Objective: To provide a general view of regulation in eukaryotesContents: 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

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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 signalsStudy materials and literature: Lecture material and additional material provided during the lecturesCompletion: Lecture courseEvaluation: Examination. Scale: 0-5Responsible person: Univ. lecturer Pekka Heino(Return to Track 2a, 2b, 3a, 3b, 3c, or 4b)


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 CoEPreceding studies: Not recommended before finishing the mandatory laboratory courses and lecturesObjective 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 resultsEvaluation: Written reports. Grading scale: 0-5Responsible persons: PIs of the CoE(Return to Track 2b)

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Study unit descriptions:Alternative study units for MBIOT students organized by the Faculty of Agriculture and Forestry (AF)


81037 Molecular Methods in Applied Plant Genetics (JAL403/KBIOT403), 5 ECTS creditsTime: Autumn term, period I, in even-numbered years (2.9-16.10.2008, Tue and Thu at 8-10)Place: C-building, seminar room 130Objective: 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 courseCompletion: 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 creditsTime: 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 knowledgeObjective: 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 creditsTime: 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+4Objective: To introduce to the common dairy processes covering from the raw milk cold chain to the microbiological quality control and shelf life of dairy productsContents: 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

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microbiology, technology and bioprocessing textbooksStudy materials and literature: Relevant literature and material provided during the courseCompletion: Laboratory course and literature examinationsEvaluation: Examinations and laboratory reports Responsible person: Prof. Tapani Alatossava and Patricia Munsch-Alatossava (Return to Track 4a)

850030 Biofuels (YKEM420), 5 creditsTiming: Autumn term, period I (8.9-15.10.2008, Mon and Wed at 14.15-15.45)Place: INFO 4Preceding studies: Chemically or biotechnically oriented bachelor degree or corresponding knowledge requiredObjective: 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 informedCompletion: Lectures, seminars, independent study Evaluation: ExaminationResponsible person: Prof. Liisa ViikariOther information: The course will be held in English or Finnish (depending on theattending students)(Return to Track 2a)

830114 Basic Biotechnology in Forestry (ME363), 5 creditsTiming: 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 332Contents: Biotechnology and its allied areas of bioresource science and genomics isa rapidly developing field of study with considerable benefits not just for agricultural,environmental and medical sciences but also in forestry. The course however willprimarily 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 ofnutrition and also natural biocides. With the advent of biotechnology, there is anincreasing demand for the use of biomass from forest trees as a renewable energysource as well as carbon sink to control global warming. Additionally, the rootsystems of certain tree species are also adaptable for use in phytoremediation ofpolluted soils or habitats. Equally, some microbes associated to forest trees are ofpotential biotechnological significance in the area of bioremediation of pollutedecosystems, industrial chemical processing and production (bioethanol),pharmaceuticals (antibiotics) and in biological control of pests. Biotechnology furtheroffers opportunities through the use of genetics to expand or improve on many ofthese positive attributes of forest trees and associated organisms. The course willalso address principles and ethical issues on genetical modified organisms (trees).Completion: Lectures, seminars, literature discussions, independent and group workEvaluation: Examination=80%, Report/seminars=20%Responsible person: Prof. Fred Asiegbu(Return to Track 2b)

871074 Food Legislation and Control (EK131), 5 ECTS creditsTime: 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

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Objective: Introduction to food legislation and control systemsContents: 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 LaboratoryStudy materials and literature: Material provided during the courseCompletion: Lectures, excursion to EVIRAEvaluation: Examination and/or a written essayResponsible person: Univ. lecturer Velimatti Ollilainen(Return to Track 4a)

871072 Chemical Risk Factors (EK132), 5 ECTS creditsTime: 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 foodsContents: 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 residuesStudy materials and literature: Material provided during the courseCompletion: Lecture courseEvaluation: Examination and/or a written essayResponsible person: Univ. lecturer Velimatti Ollilainen(Return to Track 4a)

81351 Bacteria, Viruses and Pathogen Diagnostics (KPAT403), 10 ECTS creditsTime: 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: 0-5Responsible person: Prof. Minna Pirhonen and Prof. Jari Valkonen (Return to Track 2a)

8720092 LAB Starters (ETT340), ECTS credirtTime: Autumn term, period II (29.10-12.12.2008, Wed at 13.15-14.45)Place: EE-building, seminar room 3+4

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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 identificationContents: 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 strainsStudy materials and literature: Material provided during the courseCompletion: Laboratory course including a couple of lecturesEvaluation: Examination + laboratory reports Responsible person: Prof. Tapani Alatossava (Return to Track 4a)

830113 Forest Microbiology (ME362), 8 creditsTime: 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 332Objective: 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, literaturediscussions, 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 creditsTime: Autumn term, period II (13.11-17.12, Mon-Thu)Contents: The course will be primarily based on laboratory and individual projectwork sessions. It will cover current advances used in studies related to treepathogens which are made possible with aid of novel and modern biologicaltechniques. Additionally, the course will cover the microbiology of living roots, stems,needles and leaves. Specific focus will be on diseases affecting the various tissueorgans of forest trees. The course will also address the many functions of fungi in theuptake and cycling of nutrients in forest ecosystems, microbial parasitic andsymbiotic 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 wellas the exploitation of forest microorganisms in commercial & industrial processes,including biological control.Completion: Lectures, practical work, demonstrations, seminars, literature discussions, independent and group workEvaluation: 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 creditsTime: Autumn term, period II, every third year (next time in autumn 2010)

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Preceding studies: BSc. level or equivalent requiredObjective: 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 HatakkaOther information: The course is given every third year (NOVA collaboration)(Return to Track 2a)


81576 Molecular Genetic Markers in Animal Breeding (KEJAL/KEBIOT440), 5 ECTS creditsTime: Spring term, period III, in uneven years (12.1-1.3.2009)Place: Course and research laboratories at the Dept. of Animal SciencePreceding studies: Basics in biochemistry and animal biotechnologyObjective: 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 geneticsContents: 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 laboratoryStudy materials and literature: Course material provided during the courseCompletion: Laboratory course, seminarsEvaluation: Participation in journal club, demonstrations and laboratory work and report Responsible person: Univ. lecturer Kari EloOther 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 creditsTime: 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 sessionsStudy 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

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(Return to Track 2a or 2b)

81085/52728 Plant Biotechnology and Molecular Biology (KBIOT300), 5 ECTS creditsTime: Spring term, period III (12.1-26.2.2009, Mon and Thu, at 9-12) Place: Biocenter 2, lecture room 2012Preceding studies: Basics in biochemistry and cell biologyObjective: Learning of different aspects of plant biotechnology and molecular biologyContents: Lectures include: Molecular biology of agrobacterium-mediatedgene 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 ofvegetative-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 biotechnologyStudy 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 essayEvaluation: Short written assignment, final examination. Grading scale: 0-5Responsible 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 creditsTime: Spring term, period III (12.1.-1.3.2009, Mon 12-16 and Wed 14-16)Place: Mon INFO 3 and Wed INFO 4Relations to other study units: Basics in microbiologyObjective: Basics of food and water microbiologyContents: 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 workResponsible person: Prof. Per SarisOther 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 creditsTime: Spring term, period IV (9.3-27.4.2009, Mon 12.15-13.45)Place: EE-building, seminar room 3+4Objective: To get familiar with potential new food processing technologies and to evaluate the possibilities and limitations of these methodsContents: 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 courseCompletion: Group workEveluation: Examination (50%) + report and teaching and acting as an opponent (50%)

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Responsible person: Prof. Lea Hyvönen and Univ. lecturer Kirsi Jouppila (Return to Track 4a)

812010 Laboratory Course in Plant Molecular Biology (KBIOT401), 5 ECTS creditsTime: Spring term, period III, in even years (next time in spring 2010)Preceding studies: Basics in gene technology and plant molecular biology (e.g. BIOT200, BIOT201, KBIOT200 and KBIOT300) Objective: Learning of some key techniques and applications in plant molecular biology and genome-wide analysis Contents: Construction of cDNA libraries; Basics of sequence analysis; Use of microarrays for analysis of gene expression and pathogen diagnostics; Data analysis by means of bioinformatics; Analysis of gene expression using RT-PCR Study materials and literature: Course manual Completion: Laboratory course Evaluation: Laboratory report. Grading scale: Pass/failResponsible person: Prof. Teemu Teeri and Prof Jari Valkonen Other information: Priority in advanced level students. (Return to Track 2b)

81039 Selection Breeding and Experimental Designs (JAL401), 5 ECTS creditsTime: Spring term, period III, in uneven years (next time in spring 2009)Objective: To understand the process of selection breeding and to learn how to plan experiments in plant breeding and forest tree breeding Contents: The role of genotype, environment, G*E interaction and random effects in determining variation in plants. The structure of breeding trials to separate genetic and environmental effects. Applications of selection work Study materials and literature: Relevant literature will be indicated during the course Completion: Lectures and presentationsEvaluation: Examination 70% and presentation 30%. Grading scale: 0-5 Responsible person: Prof. Teemu Teeri (Return to Track 2b)

81028/52518 Laboratory Course in Plant Biotechnology (KBIOT301), 5 ECTS creditsTiming: 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 1026Preceding 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 transferContents: 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 articlesCompletion: Laboratory courseEvaluation: Laboratory report. Grading scale: Pass/failResponsible 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)

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864062 Biotechnology of Fungi and Renewable Natural Materials (YBIOT525), 5 ECTS creditsTime: Spring term, period IV (9.3-17.5.2009, Mon at 14-16, Tue at 12-14, Wed at 10-12)Place: INFO 4Preceding studies: Basics in microbiologyContents: Fungi as living organisms; ecology and biotechnology of fungi; degradation of organic matter by fungi; details of fungal exoenzymes in wood decay; edible fungi; applications and use of fungi in pulp and paper industryStudy materials and literature: Relevant literature will be indicated during the courseCompletion: Lectures, written exercises, oral presentationEvaluation: Home examination, written exercises, oral presentationResponsible person: Prof. Annele HatakkaOther information: The lectures are given in Finnish unless otherwise required (in English) (Return to Track 2a)

8720091 Fermentation Technology (ETT330), 3 ECTS creditsTime: Spring term, period IV (11.3-29.4, Wed at 13.15-14.45)Place: EE-building, seminar room 3+4Objective: Introduction to food and biotechnological fermentations and fermentorsContents: Experimental fermentations: Lactic acid bacteria fermentation and Escherichia coli and insect cell cultures for recombinant protein productionStudy materials and literature: Material provided during the courseCompletion: Lecture series (8 h), demonstrations, three practical laboratory excercises with written reportsEvaluation: Examination + laboratory reports Responsible person: Prof. Tapani Alatossava and Olli Mäentausta (Return to Track 4a)

850029 Biorefineries (YKEM410), 5 creditsTiming: Spring term, period IV (16.3-6.4.2009, Mon and Wed at 9.15-12)Preceding studies: Bachelor degree or corresponding knowledgeObjective: To give an overview on present and future on agroor forestrybased biorefineries and their valuechains with a special emphasis on biotechnologyContents: The focus is on biotechnical methods and processes, but also other relevant methodologies are reviewed (background and drivers, chemistry and biotechnology of raw materials, bioenergy and biofuels, and various biorefinery concepts in agriculture and forestry)Study materials and literature: Lecture material, articles on the topicsCompletion: Lectures, independent study Evaluation: ExaminationResponsible person: Prof. Liisa ViikariOther information: Joint course with HUT, lectures in Viikki and Otaniemi (detailedinformation later). The course will be held in English (or Finnish depending on theattending students)(Return to Track 2a)

81041 Conservation of Plant Genetic Resources (JAL402) 5 ECTS creditsTime: Spring term, period IV, in even years (next time in spring 2010)Objective: Becoming acquainted with the importance of genetic variation and plant genetic resources, to learn methods of assessing and conserving genetic resources. Contents: The nature of biological diversity, applications of ecological genetics to plant breeding, practical management of germplasm. Presentations by students.

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Study materials and literature: Relevant literature will be indicated during the course Completion: Lectures, study diary and presentations. Evaluation: Study diary 70% and presentation 30%. Grading scale: 0-5 Responsible person: Univ. lecturer Helena Korpelainen (Return to Track 2b)

87145 Vitamins and other Bioactive Compounds (EK221), 5 ECTS creditsTime: Spring term, period IV, in even years (next time in spring 2010)Prededing studies: Basics in chemistry and biochemistryObjective: Understanding the chemistry and reaction mechanisms of vitamins and other bioactive compoundsContents: Chemical and biochemical properties, modes of action (bioactivities) and analytical methods of vitamins and other bioactive compounds including carotenoids, flavonoids and phenolic acids, phytoestrogens, purines and phytosterolsStudy materials and literature: Belitz, H.D. & Grosch, W. Food Chemistry,Springler Verlag, Berlin, 1999. Other relevant literature will be indicated during the courseCompletion: Lectures, written exercisesEvaluation: Examination, written exercisesResponsible person: Univ. lecturer Marina Heinonen (Return to Track 4a)

87295 ABS Course on Functional Foods, 3 - 5 ECTS creditsTime: Spring term, period IV, in even years (next time in spring 2010)Objective and contents: The course will give an update on current interest in the field of functional foods and their development including views on scientific evidence to substantiate health claims, legislative boundaries, and existing and up-coming products on the market. Special interest will be given to selected topics: cardiovascular health, gut and bone health, and the importance of weight control in reducing the risk of certain diseases. In addition to information given by experts in their presentations the course include group work targeted for possible development of functional foods. Completion: Lectures, group workResponsible person: Univ. lecturer Marina Heinonen(Return to Track 4a)

871073 Basic Toxicology and Risk Assessment (EK133), 5 ECTS credits Time: In academic year 2009 -2010

Prededing studies: Basics in chemistry and biochemistryObjective: Understanding the principles of safety assessment of food and food ingredientsContents: Basic principles of toxicology (clinical testing, basic consepts), principles of nutritional fysiology, metabolic reactions of chemical risk factors, principles of risk assesment Study materials and literature: Material provided during the courseCompletion: Lecture courseEvaluation: Examination and/or a written essay Responsible person: Univ. lecturer Marina Heinonen(Return to Track 4a)


8720051 Dairy Technology 6 (ETT650), 1 - 9 ECTS creditsTime: Autumn or spring termPrededing studies: Basics in food technologyContents: Advanced lectures, seminars and group work in dairy technologyStudy materials and literature: Relevant literature will be indicated during the courses

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Completion: Lecture series, seminars, group workEvaluation: Examination, written reportsResponsible person: Prof. Tapani AlatossavaOther information: Lectures, seminars and group work in Finnish or English, some parts can also be taken as a literature examination in English(Return to Track 4a)

871066 Basic Studies in Food Science (Elintarviketieteiden perusopinnot), 25 ECTS creditsContents: EK110 Basics of Food Chemistry (Elintarvikekemian peruskurssi), 3 ECTS (in Finnish) ETT140-170 Basics of Food Technology, 2 courses (Elintarviketeknologian

peruskursseja, 2 kurssia), 5 ECTS (in Finnish) RAV090 Introduction to Nutritional Sciences (Johdatus ravitsemustieteeseen), 4 ECTS

(in Finnish) + 13 ECTS elective studies in Food Science (in Finnish or English)

Responsible persons: Prof. Vieno Piironen and Prof. Lea HyvönenOther information: This minor subject package is mainly given in Finnish(Return to Track 4a)

871070 Functional Foods Minor Subject (Funktionaaliset elintarvikkeet –sivuaine), 25 ECTS creditsContents: EK224 Functional Foods and Novel Foods (Funktionaaliset elintarvikkeet ja

uuselintarvikkeet), 5 ECTS (in Finnish) EK130 Food Safety and Control (Elintarvikkeiden turvallisuus ja valvonta), 5 ECTS (in

Finnish) RAV 090 Introduction to Nutritional Sciences (Johdatus ravitsemustieteeseen), 4 ECTS

(in Finnish) A seminar serie in Functional Foods (Seminaari funktionaalisten elintarvikkeiden alalta)

3-5 ECTS (in English) + 8 ECTS elective studies in Functional Foods (in Finnish or English)

Responsible person: Univ. lecturer Marina Heinonen Other information: This minor subject package is mainly given in Finnish(Return to Track 4a)

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Study unit descriptions:Alternative study units for MBIOT students organized by the Neuroscience Center (NC)

Please check the more detailed schedules (times and places) from the NC home pages: http://www.helsinki.fi/neurosci/education.htm

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http://www.helsinki.fi/neurosci/education.htm


Study unit descriptions:Alternative study units for MBIOT students organized by the Master's Degree Programme in Bioinformatics (MBI)

MBI Study Guide: http://www.cs.helsinki.fi/bioinformatiikka/mbi/studies.htmlMBI Teaching programme: http://www.cs.helsinki.fi/bioinformatiikka/mbi/courses.html

582606 Introduction to Bioinformatics, 4 ECTS creditsTime: Autumn term, period I (2.9.-10.10.2008, Tue and Fri 14–16)Place: Exactum C222, KumpulaContents: This course gives an introduction to the central topics in bioinformatics, and gives a foundation for further courses in the Master's Degree Programme in BioinformaticsStudy materials and literature: Richard C. Deonier, Simon Tavare & Michael S. Waterman: Computational Genome Analysis – An Introduction, Springer 2005Completion: Lecture courseEvaluation: Examination (Wed 15.10.2007 at 16-19)Responsible person: Univ. lecturer Esa Pitkänen (Return to Track 1,or 3b)

399671 Practical Bioinformatics, 8-10 ECTS creditsTime: Autumn and spring terms, periods I-IV. The course consists of different modules that are organized in four different periods Place: Biomedicum Helsinki, Haartmaninkatu 8Contents: Practical Bioinformatics approaches various bio-computational analysis methods essential in life sciences from a practical point of view. The course is tailored for undergraduate and graduate students studying biosciences (biology, biochemistry, medicine etc.) and assumes no previous background in bioinformatics or programming. Basic computer skills are required.Completion: Lectures and practical exercises in a computer class. Additionally, the modules will include homework and an exam Responsible persons: Adjunct Prof. Outi Monni and Univ. lecturer Päivi OnkamoOther information: A maximum of 25 students will be accepted for each module. The selection of the students is performed based on the phase of the studies(Return to Track 1,or 3b)

582604 Practical Course in Biodatabases, 4-5 ECTS creditsTiming: Spring term, period III (12.1-17.2.2009, Mon and Tue at 14-16)Place: Exactum D122, Kumpula Contents: Techniques for accessing and integrating data in biological databases are studied. The course contains project workPreceding studies: 582606 Introduction to Bioinformatics, basics of databases, basic programming skills Evaluation: No separate examinationResponsible person: PhD Jarno Tuimala and Adjunct Prof. Siru Varvio(Return to Track 1)

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http://www.cs.helsinki.fi/bioinformatiikka/mbi/courses.html

http://www.cs.helsinki.fi/bioinformatiikka/mbi/studies.html

mbiotcurriculum2008.doc.doc

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