Download BIOJ106 Philosophy and Ethics in Biology (2 ECTS cr.) , 16.1.2013

BIOJ106 Philosophy and Ethics in Biology (2 ECTS cr.) , 16.1.2013 - 1.2.2013
Leona Gilbert, Leena Lindström
Contents: In English. Aimed at post-graduate students to increase their awareness of the
philosophy and ethics behind their own biological research. Based on discussions on a
reading material given at the beinning of the course. Attendance necessary for the credits.
Prerequisites: Master of Science, or experience on own research
Modes of study: Discussion based on literature.
Completion mode: Attendance to all lectures
Literature:Will be given out before the course begins.
BIOJ910 Reserch Seminar (1 - 2 ECTS cr.) , 6.9.2012 - 16.5.2013
Jari Syväranta
Contents: Departmental seminar series in which we have talks delivered by world class
scientists from all fields of biology and environmental sciences. Each visitor is asked to start
with general background understandable to educated audience baring in mind that in the
audience we have scientists who may not be specialists of the particular field.
Learning outcomes: We will educate ourself and broaden our mind about cutting edge
international biological and environmental research that is not nesessarily in our own area of
expertise.
Completion mode: Listening the seminar, asking questions and partisipating in the
discussions after the seminar. Attending 15 seminars will give 1 credit point.
EKOS142 Winter Ecology (2 ECTS cr.) , 12.2.2013 - 16.2.2013
Hannu Ylönen
Contents: The course deals with dynamics in physical and biotic environment in boreal and
subarctic winter, individual and population level adaptation to cold environment and effects
of climate change on individuals and populations.
Specifically lectures, demonstrations and field work focus on snow ecology, plant adaptations
to winter conditions and effects of climate change on boreal and arctic vegetation, small
mammal and bird adaptations to winter and life under ice.
The course week includes an excursion to a national park using cross-country skis (skis for
foreign participants are available at site, possibility for walking exists if skiing is not familiar)
and every student should prepare a short presentation on a selected topic related to
seasonality and winter in the students’ home country.
Prerequisites: Ecology course (Summer part) completed
Selection procedure: In total max. 20 students, including students external to the University
of Jyväskylä. Students from outside of the university do not apply in Korppi.
Modes of study: Lectures, presentations, demonstrations and field work
EKOS144 Evolutionary Biology (5 ECTS cr.) , 4.3.2013 - 17.5.2013
Tapio Mappes
Contact information: Tapio Mappes [email protected]
EKOS160 Community and ecosystem ecology (3 ECTS cr.) , 2.4.2013 7.5.2013
Minna-Maarit Kytöviita
Current events: The course is offered every second year.
Contents: This course focuses on ecosystem processes, trophic dynamics and how diversity
is created and maintained in ecosystems and how diversity and ecosystem function interact.
Modes of study: Attendance to lectures + exam
EKOS308 Wildlife Ecology and Game Research (2 ECTS cr.) , 18.2.2013 21.2.2013
Heli Siitari
Contents: The course provides an excellent overview of the research in wildlife biology and
game in Finland and Northern Europe. Finnish game research is of highest international rank
and students will be guided to use of long-term game biological data, wildlife monitoring and
large game biology, ecology and life-histories. The three-day lecturing period will be
followed by a modeling part, based on northern boreal wildlife data sets.
Schedule:
The course is a part of the three week international Jyväskylä Winter School of Ecology
2013.
EKOS311 Introduction to evolutionary ecology modeling (5 - 6 ECTS cr.) ,
15.1.2013 - 28.2.2013
Lutz Fromhage
Learning outcomes: After completing the course, the participants should:
(i) understand the utility, limitations, and philosophical basis of formal modelling in
evolutionary ecology; (ii) be familiar with common modelling approaches, including
optimisation, game theory, and population genetic dynamics; (iii) be able to write and
evaluate simple models in matlab.
Modes of study: 15 lectures and 15 exercise sessions of 2 h each =60 contact hours
SMBA109 Basics in Microscopy (1 ECTS cr.) , 7.3.2013 - 8.3.2013
Sami Willman
SMBS110 Bioinnovations and business (4 ECTS cr.) , 2.4.2013 - 18.4.2013
Leona Gilbert
Contents: The course will provide insight to intellectual property rights and international
patent laws. The bio-business aspect of life sciences will be discusses with special focus on
biomedical product development. Problem-based learning strategies within the course will
provide knowledge for the student to develop a realistic business plan.
Learning outcomes: To develop a sound understanding of the special characteristics needed
in biobusiness and product development.
Modes of study: 16 h of activating lectures, 4 hours of interactive discussion groups Use of
current case studies in biobusness, lecture series and interactive discussions will be the modes
of instructions.
Completion mode: 25% participation, including exercises and discussion groups + 75%
exam.
Course workload: This course will implement problem-based learning strategies so the
student adopts skills in problem solving and critical thinking. These strategies will allow
students to develop the ability to think critically, analyze problems, find and use appropriate
learning resources.
Literature: Selected content will be provided in the course.
SMBS112 Advanced course in virology (4 ECTS cr.) , 9.4.2013 - 7.5.2013
Jaana Bamford
Contents: A lecture course on virus structures and life cycles. Structural methods for virus
research. Each student gives a short presentation on a particular virus species.
Prerequisites: MOBA310 tai SMBA310.
Modes of study: Lectures and short presentations given by the participants.
SMBS502 Electron microscopy practical course (6 ECTS cr.) , 12.2.2013 22.3.2013
Varpu Marjomäki
Contents: The course focuses on the theory of TEM and SEM, preparation of
immunofluorescent samples, and imaging. Students will also prepare a presentation on a
selected subject and based on given literature.
Learning outcomes:After passing the course, the student knows the theory of the basics in
TEM and SEM, the sample preparation for those techniques, as well as immunolabeling on
cryo sections (Tokyasu method). The student knows the basice terms and can plan and
excecute EM experiments.
Prerequisites: SMBA101, SMBA103, SMBA104
Registration: 12 students are allowed to enter the course.
Literature: Lounatmaa,K. & Rantala, I. 1991: Biologinen elektronimikroskopia.
Yliopistopaino. ISBN 951-570-069-8. LIsäksi muuta kurssilla annettavaa lisämateriaalia.
SMBS503 Advanced light microscopy practical course (4 ECTS cr.) , 8.1.2013
- 7.2.2013
Nina Rintanen, Maija Vihinen-Ranta
Contents: The course focuses on multidimensional confocal microscopy, preparation of
immunofluorescent samples, live imaging and quantitative data analysis of the microscopic
data.
SMBS510 Computer-aided drug discovery (4 ECTS cr.) , 29.4.2013 - 17.5.2013
Sanna Niinivehmas, Olli Pentikäinen
Contents: Introduction and usage of protein and ligand based methods in drug discovery.
During the course, drug candidates are searched for the selected target protein (done in small
teams).
Learning outcomes: Understand the pros and cons of methods used in computer-aided drug
discovery (CADD). Can use CADD-software in linux-OS. Shows ability to work in a drug
discovery-team.
Prerequisites: SMBA110, SMBA111, SMBA502; preferably also: SMBS509, SMBA303,
KEMP101, KEMP105, (or similar knowledge)
Registration: Normal registration in Korppi, selection of participants is done as described
below.
Selection procedure: Based on previous courses taken (see prerequisites) 12 students are
selected (students from at least SMB, chemistry, and physics are considered). It is also
possible that interviews are held to select the participants for this course.
Modes of study: Lectures (~10 hours), practises (~100 hours), and presentation of the project
work.
Completion mode: Project and critical self-evaluation, exam. OBS! compulsory
participation (3 weeks Mo-Fr 8-16).
Course workload: Approximately 150 hours.
Literature: Material is gathered together from lecturers own material and e.g. from the
following books: Patrick: An introduction to medicinal chemistry (3rd - 4th edition)
Schneider, Baringhaus: Molecular design Young: Computational drug design Young:
Compuattional chemistry Leach, Gillet: An introduction to chemoinformatics Ng: Drugs,
from discovery to approval Rang: Drug discovery ad development Leach: Molecular
modelling (2nd edition) Werth: The billion-dollar molecule
Key words: Computer-aided drug discovery, protein structure-based drug discovery, ligandbased drug discovery, molecular dynamics simulations, three dimensional quantitative
structure-activity relationship model, protein-ligand docking, pharmacophore, visualization,
virtual high-throughput screening.
SMBS813 Fundamentals of Nanoscience (6 - 7 ECTS cr.) , 8.10.2012 17.2.2013
Janne Ihalainen
Current events: Nanoscience days: All participants should attend to Nanoscience Days 8.9.10.2012.
Contents: Fundamentals of nanoscience. The goal of this course is to introduce the student to
general ideas and concepts of nanoscience. Topics include physical, chemical and biological
aspects of nanoscience and nanotechnology. The course is taught by three specialists from
fields of physics, chemistry and biology. It starts by visiting the lectures on Nanoscience
Days from which a report is provided. After this, every week includes 2 h lectures followed
by 1 h discussion on the previous home work, which can be a problem, or a topic essay. An
estimated time for the home work is 8 h weekly.
Learning outcomes: After passing this course the student recognizes the size-classes and the
main properties of nano-objects. He/she can fundamentals of the theoretical and experimental
techniques in nanoscience. After the course has a clear picture about scientific literature in
nanoscience and he/she can fluently provide short concise reports from various themes in
nanoscience.
Prerequisites: Knowledge from physics, chemistry and biology
SMBS814 Seminar in Nanoscience (3 - 4 ECTS cr.) , 1.10.2012 - 13.5.2013
Janne Ihalainen
Contents: Introduction of the M.Sc.-thesis project, first a general discussion about the thesis
projects, and finally at the end of the semester a presentation about the results of the master
thesis. During the seminar some scientific publications and master thesis´ are examined and
writing styles, of both a master thesis and a scientific publication, is practiced. Also tips for
oral presentations are given. The students are encouraged to visit Nano-seminar series
(mostly on Friday afternoons)
Learning outcomes: After passing this course the student can fluently provide reports from
various themes in nanoscience. He/she has the skills writing scientific text and provide clear
oral presentations from his/her expertise.
Prerequisites: At least a starting phase of the MSc-thesis-project.
Modes of study:
- Attendance in all sessions highlighted in red is obligatory in order to pass the course.
- Turning in excercises (both during sessions and homeworks) on time is obligatory in order
to pass the course.
- In addition, attendance and reviews from three Nanoseminars (Fridays at 13:15-14:00) are
required. (Optionally one talk from Nanoscience Days and 2 Nanoseminars.) These three
Nanoseminars can be chosen freely throughout the duration of the course. However, it
cannot be a Nanoseminar given by the course attendees.
- Attendance at Nanoscience Days is not obligatory, but highly recommended, as the talks
given there will serve as a base for discussions later during the course.
- Grading will be given right after the feedback session of each students presentation or when
the last review from a Nanoseminar is turned in, whichever comes last. Therefore the first
students may get their credits in February-March, while the last students may get their credits
in September.
-Grading will be on a scale 1 through 5, with 50% of the grade based on reading and writing
scientific text, and the remaining 50% of the grade based on the oral presentation.
SMBS815 Practical course in nanoscience - imaging (4 ECTS cr.) , 21.1.2013 22.2.2013
Janne Ihalainen
Contents: In this course the students get familiar with scientific work in different disciplines
within nanosciences. Especially in this course various imaging techniques in different
disciplines in the nanosciences are introduced. The aim is to understand the basic principles
of each technique and their benefits and drawbacks. During the first week (standard) nano
particles are provided and they will be used as versatile as possible for imaging later on. The
lab work will be done in the groups. The teaching takes place both in English and in Finnish.
Learning outcomes: After passing this course the student recognizes the size-classes of
nano-objects and the basic principles of major imaging techniques. He/she knows the pros
and cons of each used technique. After the course the student is also able to provide simple
nano-particles and choose the most optimal imaging technique for his/her purposes. After the
course the student can interpret the obtained results and is able to report the results in a clear
manner.
Prerequisites: Some laboratory experience is required for the course.
Registration: [Not translated.] [Ei käännetty kuvausta.] [Not translated.] The course is only
for nanoscience students. The course is not recommended for the first year Bachelor students.
Selection procedure: The course is only for nanoscience students. The course is not
recommended for the first year Bachelor students.
WETS201 Phytoplankton ecology (2 ECTS cr.) , 21.1.2013 - 4.2.2013
Roger Jones
Contents: The main themes of this lecture course are: types of phytoplankton and
phylogenetic characteristics; light and photosynthesis; primary production in lakes; relation
between production and growth; nutrients and growth; controls on population development;
seasonality of phytoplankton; eutrophication and management of phytoplankton.
Learning outcomes: By the end of this lecture course students should be familiar with the
main taxonomic groups of net population growth represents a balance between the rate of
increase (controlled by resource availability) and various factors that cause losses of cells
from the population. Students should be able to explain how the different responses by
various phytoplankton types to changes in resource availability and loss factors contribute to
determining phytoplankton community structure and its spatial and temporal variability.
Students should know the principles of measuring phytoplankton photosynthetic production
and the difference between gross and net production. Students should appreciate why
excessive phytoplankton growth can be problematic in lakes, and what measures are available
to tackle this problem.
Completion mode: Final examination based on course material, but additional reading of
selected papers is recommended.
WETS202 Phytoplankton identification (2 ECTS cr.) , 18.2.2013 - 22.2.2013
Roger Jones
Contents: Demonstrations and practical exercises to introduce the main types of freshwater
phytoplankton and their identification.
Completion mode: Identification of test samples at end of course.
WETS302 Winter Limnology Course (3 ECTS cr.) , 7.1.2013 - 21.5.2013
Roger Jones
Current events: The course is jointly arranged by Helsinki and Jyväskylä Universities. Only
the students of the University of Jyväskylä register via Korppi system.
Contents: The students are introduced to large and small lakes. Various determinations are
made in the field and in the laboratory. Warm field clothes are necessary.
Learning outcomes: To learn about conditions that prevail in lakes during the winter, to
have idea of variation between lakes and to further develop field and laboratory skills
acquired earlier.
Prerequisites: WETA104, WETA303, WETS202, WETS305
Selection procedure: In total max. 14 students, including students outside the University of
Jyväskylä. Students from outside of the university do not apply in Korppi.
Modes of study: The course consists of lectures, field and laboratory work and a conclusive
seminar.
Schedule: The schedule will be announced later.
WETS307 Principles of Palaeolimnology (2 ECTS cr.) , 26.4.2013 - 24.5.2013
Jarmo Meriläinen
Contents: Introduction (Sediment: an ecosystem’s memory); Coring and subsampling;
Dating; Physical, Chemical and Biological Properties; Palaeoclimatology; Surface sediment
calibration sets (“Training sets”); Acidification; Metals and Stable Isotopes; Persistent
Organic Pollutants; Nutrients and Eutrophication; Erosion; Environmental history of lakes
(Case Studies)
Completion mode: Exam
WETS402 Assessment and Monitoring of the Ecological Quality of Surface
Waters (2 ECTS cr.) , 28.1.2013 - 15.2.2013
Heikki Hämäläinen
Learning outcomes:
By the end of this course a student should know the objectives and obligations of legislative
assessment, monitoring and management of the ecological condition of surface waters,
particularly in Europe. She/he understands the principles, problems and uncertainties of
measurement, classification and monitoring of the ecological status, and gets familiar with
the associated Finnish procedures in more detail. Hence the student has sufficient background
knowledge to adopt professional law enforcement, consulting tasks or research related to
ecological status assessments. She/he should also have a capability to consider the legislative
restrictions and rationales in all activities touching surface water ecosystems.
WETS920 Guidance for Master's Thesis, part A (1 ECTS cr.) , 25.2.2013 14.3.2013
Jouni Taskinen
Contents: Planning of Master's thesis project. Questions, hypotheses, experimental and
sampling designs, supervisors.
YMPA209 Climate change and global warming (4 ECTS cr.) , 7.3.2013 18.4.2013
Prasad Kaparaju
Contents: Earth’s climate system; Physical & chemical factors affecting climate change;
Impacts of climate change on the society and environment; National and international
policies to mitigate and/or adapt to climate change; Role of UN Framework Convention on
Climate Change and Intergovernmental Panel on Climate Change. Substitute YMPA207.
Learning outcomes: Students should be able to explain the Earth’s climate system, physical
& chemical factors affecting climate change. In addition, the students should be able to
explain the impacts of climate change on the society and environment and various national
and international policies to mitigate and/or adapt to climate change.
Prerequisites: YMPP115,YMPP125 and YMPP151 to recommend
Modes of study:Classroom lectures, exercises and other relavent literature
Completion mode: Written examination
Literature: Houghton (2004) Global Warming: The Complete Briefing, Cambridge.
Relevant reading materials are provided in the course optima pages. Web pages of UN
Framework Convention on Climate Change and Intergovernmental Panel on Climate Change
(www.ipcc.ch).
YMPS464 Waste to Energy (4 ECTS cr.) , 15.1.2013 - 22.2.2013
Prasad Kaparaju
Current events: The course will be given only every second year.