Courses in English in Biosciences Senior lecturer Tiina Salminen tiina.salminen(at)abo.fi Structural Bioinformatics Laboratory Biochemistry BioCity 3 rd floor Dept. of Biosciences Åbo Akademi University
Courses in English: Biochemistry http://www.abo.fi/institution/biokemistudier (Language=English) Autumn 2014: 211009.0 Computers in bioresearch, 2 sp 282005.0 Applied bioinformatics, 6 sp 213009.0 Physical biochemistry, 6 sp Spring 2015: 212015.0 Protein structure in bioscience, 4 sp 213017.0 Computer aided drug design, 4 sp 213020.0 Membrane biochemistry lipids, 6 sp 212016.0 Industrial biotechnology fermentation, 2 sp 2014-2015: Project work in research groups 12-25 sp 213016.0 Advanced studies in Structural Bioinformatics, 13 sp 212006.0 Literature course in microbiology, 5 sp 213015.0 Glycobiology - Biochemistry of Complex Carbohydrates 6 sp 213021.0 Fluorescence spectroscopy, 8 sp 213022.0 Lipid metabolism, 8 sp 213024.0 The structure of biological membranes, 8 sp
Courses in English: Cell Biology Autumn 2014: 221006.0 Introduction to cell biology, 3 sp 221008.9 Laboratory basic course, 2 sp 223074.0 Advanced microscopy, 5 sp 283007.0 Cell Signaling, 8 sp 222041.0 Histology, 4 sp 22368 The structure and functions of the cytoskeleton, 8 sp: Contact John Eriksson on information: if 2014 and when. Spring 2015: 221007.0 Microscopy and microtechniques, 3 sp 213017.0 Practical microscopy and microtechniques, 2 sp 2014-2015: Work in laboratories: 6-13 sp: Contact: Kid Törnquist
Project work in research groups 12-25 sp Intermediate to advanced level Contents: Laboratory work in selected research groups (check web site for group presentations) during the academic year Contact(s): J Peter Slotte and other group leaders http://www.abo.fi/institution/biokemiforskning To gain experience in laboratory work and research techniques in various scientific disciplines Target audience: Masters level Form of assessment: written laboratory reports Course literature: handouts
Laboratory work at Structural Bioinformatics Laboratory Interested? Contact: tiina.salminen(at)abo.fi From genes to structures! q q q q q q Cloning & transformation Expression Purification Crystallization X-ray diffraction Structure determination Possible to work for some hours/day or some days/week
213016.0 Advanced studies in structural bioinformatics, 13 sp email: tiina.salminen(at)abo.fi Level: Advanced Advanced studies in structural bioinformatics as part of a scientific research project Entry requirements: Basic knowledge in biochemistry Intermediate/advanced level course in structural bioinformatics Form of assessment: Project report Oral presentation of results Contact hours: Supervised research work in structural bioinformatics for eight weeks
Courses in English: Structural bioinformatics https://www.abo.fi/institution/coursesbiosci n Sign-up in advance electronically Autumn 2014: n 211009.0 Computers in bioresearch, 2 sp n 282005.0 Applied bioinformatics, 6 sp Spring 2015: n 212015.0 Protein structure in bioscience, 4 sp n 213017.0 Computer aided drug design, 4 sp 2014-2015: n 213016.0 Advanced studies in structural bioinformatics, 13 sp n Project work in research groups 12-25 sp
211009.0 Computers in bioresearch, 2 sp https://www.abo.fi/institution/coursesbiosci The purpose of this course is to provide: Computing skills and computational terminology needed during courses in structural bioinformatics Basic knowledge in computer science The dual-boot computers in the computer room Windows and Linux operating systems Level: Basic Moodle e-learning platform Important to attend the first lecture: 10.9.2014 Wednesday 10.15-12 Aud. Biokemi in BioCity, 3rd floor Sign-up before 9.9.2014!
282005.0 Applied bioinformatics, 6 sp https://www.abo.fi/institution/coursesbiosci Level :Intermediate 1. Introduction to a large number of biological resources on the Web: 1. Databases Genome related databases and their content Protein sequence and structure databases 2. Data retrieval Nucleic acid and protein sequence Protein structures 3. www-based tools for data analysis 2. Multiple sequence alignment Theory and practise 3. 3D visualization Bodil : graphics PyMol : generating figures
282005.0 Applied bioinformatics, 6 sp https://www.abo.fi/institution/coursesbiosci Entry requirements: Basic knowledge in biochemistry Contact hours: First lecture 22.9 at 13.15 Biochemistry computer room Preliminary timetable: https://www.abo.fi/institution/coursesbiosci Computer exercises (~18h) weeks 39-47 (Computer room) Monday and Wednesday/Thursday (two groups) 13.15-15 Amino acid quiz During contact hours and at your own time Assistance during contact hours and by e-mail 2 Project works with reports Course literature: All notes and materials provided (Moodle) Recommended Jin Xiong (2006) Essential bioinformatics Project 10 % Quiz 10 % Exam 80 % Sign-up before 22.9.2014!
282005.0 Applied bioinformatics, 6 sp https://www.abo.fi/institution/coursesbiosci Projects: Gene project: The idea is to find out as much as possible information about a gene that causes an inherited disease when it has a lesion Protein project: The idea is to identify a protein when its raw amino acid sequence is known search information about the protein compare its sequence to related protein sequences
212015.0 Protein structure in bioscience https://www.abo.fi/institution/coursesbiosci Level: Intermediate The course is based on published structures and their usage in bioscience research, biotechnology and drug design Relationships between sequence, structure and function Learn visualization and analysis of 3D structures Learn to relate published data on protein structures to its biological function
212015.0 Protein structure in bioscience https://www.abo.fi/institution/coursesbiosci Entry requirements: Basic knowledge in biochemistry Contact hours: Lectures (10 h): Week 6: Mon, Tue, Thu 13-15 Week 7: Mon, Tue 13-15 Aud. Biokemi in BioCity, 3rd floor Computer exercises (10 h) in groups Week 6: Wed, Fri and Week 7: Wed, Thu, Fri Project work and report Course literature: All notes and materials provided (Moodle) Sign-up before 16.1.2015! Project 10 % Quiz 10 % Exam 80 %
213017.0 Computer aided drug design, 4 sp https://www.abo.fi/institution/coursesbiosci Level: Advanced Gives an understanding of how drugs interact with macromolecules Stategies for designing novel therapeutics using computational methods Properties of drug target structures (mainly proteins) Properties of drug candidates Drug-protein interactions Display and docking programs HIV-protease as an example target protein Indinavir (green) bound to HIV-protease
213017.0 Computer aided drug design, 4 sp https://www.abo.fi/institution/coursesbiosci Entry requirements: Basic knowledge in biochemistry Contact hours: Lectures (12 h): Week 17: Mon-Fri 13-15 Week 18: Mon, 13-15 Aud. Biokemi in BioCity, 3rd floor Computer exercises (8 h) in groups In one, two or four days Week 18: Tue-Wed Week 19: Mon-Tue Project and report Course literature: All notes and materials provided in Moodle Sign-up before 4.4.2015! Recommended: Höltje et al.(2003) Molecular modeling: basic principles and applications
Courses in English: Biochemistry Autumn 2014: 211009.0 Computers in bioresearch, 2 sp 282005.0 Applied bioinformatics, 6 sp 213009.0 Physical biochemistry, 6 sp Spring 2015: 212015.0 Protein structure in bioscience, 4 sp 213017.0 Computer aided drug design, 4 sp 213020.0 Membrane biochemistry lipids, 6 sp 2014-2015: 213016.0 Advanced studies in Structural Bioinformatics, 13 sp 212016.0 Industrial biotechnology fermentation, 2 sp 212006.0 Literature course in microbiology, 5 sp 213015.0 Glycobiology - Biochemistry of Complex Carbohydrates 6 sp 213021.0 Fluorescence spectroscopy, 8 sp 213022.0 Lipid metabolism, 8 sp 213024.0 The structure of biological membranes, 8 sp Project work in research groups 12-25 sp
213009.0 Physical biochemistry, 6 sp Level: Advanced Autumn (starts week 45 on Tue 13.15-15 aud. Biokemi) Lecturer(s): J Peter Slotte and others To understand the physical basis for macromolecule interaction and function and to become familiar with biophysical techniques used in biosciences Form of assessment: written essays Course literature: handouts during lectures
212016.0 Industrial biotechnology fermentation, 2 sp https://www.abo.fi/institution/coursesbiosci Sign-up 5.8-15.12.2014! Spring 2015: email: johnson4(at)abo.fi Subject:Fermentation Level: Intermediate level Lecturers: Mark Johnson, Tomi Airenne, Jarmo Käpylä Introduce participants: to practical uses of biochemistry and cell biology, through fermentation, to produce ales; to biochemical metabolism by showing how yeast (and even human muscle tissue) reflect the earliest biochemical pathways to produce energy - glycolysis and fermentation. to growing cells, preventing contamination, and how cellular growth and metabolism changes under conditions of high and low concentrations of oxygen. Show participants how the industrial processes like brewing are designed to take advantage of yeast metabolism during the different stages of fermentation. Form of assessment: lectures and group work
213014.0 Membrane biochemistry lipids, 6 sp Level: Advanced Spring 2015 Lecturer(s): J Peter Slotte and others To understand the behavior of lipids i water and in lipid aggregates in aqueous media, to understand the biophysical basis for lipid interactions in lipid assemblies, and to understand research techniques in the field of membrane research Form of assessment: written essays Course literature: handouts during lectures
212006.0 Literature course in microbiology, 5 sp Level: Intermediate Prescott's Principles in Microbiology by Wiley, Sherwood & Woolverton (McGraw-Hill, 2009) BioCity library and the ÅA course book library The exam will be on the general exam dates in Biochemistry (see Biochemistry web-site) Sign-up through Minplan - at least one week before the exam date If you have questions contact Pia Roos- Mattjus (proos(at)abo.fi)
213015.0 Glycobiology - Biochemistry of Complex Carbohydrates, 6 sp Level: Advanced level Self-study course upon agreement during the academic year Contact person: Peter Mattjus (pmattjus(at)abo.fi) To introduce the student to the essentials of glycobiology Form of assessment: written examination Course literature: Essentials of Glycobiology, Second Edition, 2009 Cold Spring Harbor Laboratory Press
213021.0 Fluorescence spectroscopy, 8 sp 213022.0 Lipid metabolism, 8 sp 213024.0 The structure of biological membranes, 8sp Level: Advanced Self-study courses Contact: Peter Slotte (jpslotte(at)abo.fi) Target audience: Master s level Form of assessment: written examination Literature: Fluorescence spectroscopy: Lakowicz: Principles of fluorescence spectroscopy Lipid metabolism: Vance and Vance: Biochemistry of lipids, lipoproteins and membranes The structure of biological membranes: Yeagle: The structure of biological membranes
Courses in English: Cell Biology Autumn 2014: 221006.0 Introduction to cell biology, 3 sp 221008.9 Laboratory basic course, 2 sp 223074.0 Advanced microscopy, 5 sp 283007.0 Cell Signaling, 8 sp 222041.0 Histology, 4 sp 22368 The structure and functions of the cytoskeleton, 8 sp: Contact John Eriksson on information: if 2014 and when. Spring 2015: 221007.0 Microscopy and microtechniques, 3 sp 213017.0 Practical microscopy and microtechniques, 2 sp 2014-2015: Work in laboratories: 6-13 sp: Contact: Kid Törnquist
221008.9 Laboratory basic course, 2 sp Basic bridging course Learning objectives: Learn basic laboratory techniques, including pipetting, weighing, ph measurements, good laboratory practice and laboratory safety issues. Lectures, calculation exercises, lab work, quizzes Course literature: Moodle page open for all. Start 9.9. 2014 13.15 Aud. Wikgren Teacher: Diana Toivola
221006.0 Introduction to cell biology, 3 sp Basic bridging course Learning objectives: introduce the ultra structure of the cell cellular organelles The relationship between structure and functio The basics of cellular metabolism The basics of cell signaling, the principles of cell division and differentiation. Teaching methods: Lectures, exercises. Lectures, calculation exercises, lab work, quizzes. Starts soon, exact schedule to come week37 Questions to tbi-office@bioimaging.fi Lecturer: John Eriksson
223074.0 Advanced microscopy, 5 sp Advanced course on specialized microscopy techniques utilizing Turku Bioimaging high-end equipment. Prerequisite: Good basic knowledge in microscopy Learning objectives: Theoretical and practical knowledge in fluorescence techniques, confocal microscopy and other advanced microscopy techniques. Teaching methods: Lectures, demonstrations, practical laborator work, extensive essay writing Starts 1.9.2014 10-12, Biology Kurssalen, Biocity 2 nd floor Lecturer: Diana Toivola
283007.0 Cell Signaling, 8 sp Prerequisite: Good knowledge in cell biology Advanced course on cellular signaling pathways Learning objectives: Intracellular signal pathways, techniques, studies targeting signal pathways in drug design. Teaching methods: Lectures (~20 h), subject-related seminars representing current research projects in the Turku/Åbo science community, self-studies and web material. Starts: Monday 10-12, week 38, Biology kurssalen Biocity Contact: John Eriksson
222041.0 Histology, 4 sp Prerequisite: Basic cell biology Learning objectives: Learn to identify the basic types of tissues and understand their features and differences. Learn to identify different organs, and how the basic tissue types compose tissues of individual organs linked to their function. Teaching methods: Lectures, microscopy, web-based exercises. Book: Ross and Pawlina: Histology, A text and Atlas Sixth Edition. Starts: Week 43, Tuesday 13-15 Aud. Wikgren, Biocity Can be done as self-studies Lecturer: Diana Toivola
221007.0 Microscopy and microtechniques, 3 sp 213017.0 Practical microscopy and microtechniques, 2 sp Prerequisites: Basic biology, lab skills Learning objectives: Theoretical and practical knowledge in light microscopy. knowledge in the development of modern microscopy, the parts of a microscope, optics and illumination pathways, staining techniques and Köhler illumination. Teaching methods: Lectures, web-based exercises, microscopy, report with figures 221007.0 weeks 14-15 Tue, Wed 10-12 Aud. Wikgren, and weeks 18-21 microscopy in groups. 213017.0, weeks 16-18 in the lab in groups, some work each day. Lecturer: Diana Toivola
Many imaging-related courses on ÅAU and UTU: All courses: http://www.bioimaging.fi/wp-content/uploads/2014/08/bima-coursestructure.pdf http://www.abo.fi/institution/en/biomedical_imaging Questions: tbi-office@bioimaging.fi or Diana Toivola
Thank you for your attention! See you in BioCity!