Exact Sciences Master Guide2005/2006



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Part-time studying


In principle this Master's programme is full-time.
    1. Dual training


Under specific conditions, a tailored Master's programme can be composed, in which in-service training is included.
    1. Master Programmes


Students who have chosen to follow the research-oriented variant (O-variant) first have to choose a specialist track. A choice can be made from the programmes in

  • Physics of Life

  • Bioinformatics / Genomics

  • Biomolecular complexity

  • Molecular Medicine

  • Medical Natural Sciences and Business (M-variant)

  • Medical Natural Sciences and Communication / Education (C/E variant)

 

Each track encompasses at least compulsory (theoretical) courses, a research project including Master thesis (Major), literature thesis and colloquium, and optional courses or training (see scheme). Generally spoken these students may aim at continuing their study with PhD education, in order to obtain an executive job as researcher, group leader etcetera at university, research institution, government or (industrial) company.


    1. Physics of Life

      1. Department of Physics and Medical Technology (VUmc)


The master Physics of life deals with the physics that is essential for the understanding of functioning of man in normal and pathological situations (medical and clinical physics) and the physics that forms the basis of all kinds of measuring techniques of bodily parameters (medical technology). The courses and the research of this master variant cover a wide range of topics: from the cellular level to the functioning of the intact human being. Two research projects (minor (21-27 cp) and major (42 cp) need to be carried out. The major project is usually a part of the research projects of one the departments in the VU medical centre (VUmc). Also the possibility exists to carry out the major in one of the laboratories of one of the industrial partners with which the VUmc cooperates. These projects are supervised by one of the staff members of the department of Physics and Medical Technology (PMT).

 

The department of Physics and Medical Technology is a professional organisation for physics and medical technology in education, research and support of patient care in the VUmc. This department covers and supports a wide range of medical care and employs about 25 physicists/engineers and 50 technicians. Research is often carried out in multidisciplinary teams and is related to projects of the department PMT or to one of the other 45 departments in the VUmc or participating industries.



 

Contactperson general/ master coordinator:

prof. dr. R.M. Heethaar, head of the department (rm.heethaar@vumc.nl)

 

Research

The main research projects of the department PMT deal with:


  • cardio-, circulatory and pulmonary physics

  • brain imaging and neuro-physics

  • skeletal physics and tissue engineering

  • ophthalmic physics

  • clinical physics

 

Important techniques that are being developed are:



  • MRI (tagging) techniques (MRI)

  • Image analysis

  • Functional magnetic resonance imaging techniques (fMRI)

  • Magneto-encephalography (MEG)

  • Electrical-impedance tomography (EIT)

  • Tissue engineering

  • Cornea topography

 

Cardio-, circulatory and pulmonary physics:

Cardiovascular and pulmonary diseases are still the major cause of death in the western world. In the VUmc many departments are working in this field and all related research projects are part of the research institute: ICaR-VU (www.icar.med.vu.nl). Also the PMT department has several projects within this theme, among others:



  • Detailed analysis of cardiac contraction in man, obtained with specially developed MRI tagging techniques. This is essential to gain insight in possible deformations in the contraction patterns of the human heart in certain diseases like pulmonary hypertension, infarction, left ventricular hypertrophy and aberrant electrical excitation of the heart.

  • New MRI techniques are being developed to quantify and study the blood flow through the major coronary arteries and the ventricular myocardium in normal and pathological situations.

  • A new non-invasive technique (Electrical Impedance Tomography) is being developed to measure and study the inflation and deflation of the lungs during artificial respiration and some diseases (e.g. pulmonary oedema). Successful termination of this project is of extreme importance to monitor ventilation in neonates and in other Intensive Care situations where no alternative techniques are available.

 

Contact persons: MRI: dr. M.B.M. Hofman (mbm.hofman@vumc.nl), dr. J.T. Marcus (jt.marcus@vumc.nl); EIT: dr. ir. H. van Genderingen (hr.genderingen@vumc.l).

 

Brain imaging and Neurophysics

Also diseases of the brain are an increasing health problem in the world (e.g. Alzheimer disease and multiple sclerosis). In the VUmc all studies in this field are concentrated in the research institute ICEN. The PMT department has important contributions in this field which are mainly concentrated in three areas:



  • Activation studies: aiming at generating certain reproducible responses in the brain which can be measured with the different brain imaging devices in the VUmc: magneto encephalography (MEG), functional magnetic resonance imaging (fMRI) and positron emission tomography (PET).

  • Analysis studies that aim at signal and image analysis of the responses caused by the different stimuli of the activation studies. These studies often require many non standard mathematical procedures to detect and analyse the brain responses out of the often with noise contaminated recorded signals.

  • Integration studies with deal with combining the responses of the brain measured with several of the just mentioned techniques.

 

Contact person: dr. J.C. de Munck (jc.munck@vumc.nl)

 

Skeletal physics and tissue engineering

Diseases of bones and joints are also of great concern, especially in elderly people. The World Health Organisation has pronounced this decade as the bone and joint decade (www.boneandjointdecade.org/). The department of Physics and Medical Technology has several research projects in cooperation with clinical and industrial partners to clarify the physical processes that play a role in these diseases. In the VUmc the projects covering this area are concentrated in the research institute MOVE (www.vumc.nl/hoofdframes/onderzoek/) and the STEGA foundation (www.vumc.nl/stega/). Some of the projects of the department PMT are:



  • The cage project. At increasing age there is a chance that disks between the vertebra degrade and in some cases collapse. In this case a possible solution is the implantation of a device ('cage') in and between two vertebra to take over the mechanical function of the disk. The cage is made of bio-degradable material and is constructed so that after implantation bone should grow in it to form a permanent bridge between the vertebra. To study the bone growth in the cage the department PMT develops in cooperation with the Technical University Delft miniature implantable telemetric electronical devices that measure essential parameters of bone formation.

  • Tissue engineering project, which aims at the study of making bone and cartilage from stems cells that are obtained from fatty tissue. In this project especially a study is made of the basic physical processes that stimulate the growth of bone and cartilage.

 

Contact person: dr. ir. Th. Smit (th.smit@vumc.nl)

 

Ophthalmic physics:

At increasing age the accommodation response of the eye diminishes. Reliable vision is only possible with a properly working refracting system. Optical imperfections substantially decrease the quality of the retinal image. Recently, technical developments like refractive surgery make it possible to interfere with the system. However, essential knowledge about the optical properties of the main components that play a part (i.e. the cornea and the crystalline lens) is missing. Also an adequate theory to understand the process of accommodation and presbyopia is lacking.

 

The department PMT carries out different projects in this field in collaboration with clinical and industrial partners, among others:



  • Modelling the human eye lens during accommodation. This project aims at increasing knowledge about the forces that are acting on the human eye lens during accommodation. The final goal is to provide scientific data to the industry to develop an automatic focussing artificial implantable lens.

  • Backed by the WHO (www.v2020.org/ 'the right to sight') a project has now been started, to design for young children in the developing world spectacles having lenses of special optics that can readily be adjusted to their individual need.

 

Contact person: dr. G.L. van der Heijde (gl.heijde@vumc.nl)

 

Clinical Physics (general)

A special section 'Clinical Physics' in the department PMT is involved in the physics of daily individual patient care. Research projects in this field are often available and diverse in nature, e.g. checking the performance of membrane oxygenators, controlling the position of an swallowed internal camera, calculating a special radiation dose. The majority of the projects are in radiotherapy, radiology and general clinical physics.

 

Contact persons:



general: dr. ir. B.J. ten Voorde (bj.voorde@vumc.nl)

radiotherapy: dr. J. Cuijpers (j.cuijpers@vumc.nl)

 

Compulsory master courses are:


  • Principles of Biophysics

  • Techniques of Biophysics

  • Introduction to lasers and techniques

  • Ethical aspects of MNS

 

Medical Physics 1-6

In the courses Medical Physics 1 to 4 (given in the first year of the master) the book of Hobbie: Intermediate Physics for medicine and biology (ISBN 1-56396-458-9) is studied. This book covers a wide range of topics from the electrical processes at the cell membrane to the physics of modern imaging devices like MRI, Roentgen and ultrasound.

 

Courses Medical Physics 5 and 6, presented in the second year of the master study cover topics like radiation safety, ethical aspects of research on living subjects, the human hearing system and several topics in hemodynamics and hemorheology.



 

In the compulsory literature study (12 cp) the student has to read very critically several papers on a topic related to medical/clinical physics or medical technology, write a comprehensive report about it and give a presentation for a group of specialists. The topic of the study is chosen in consultation with the master coordinator.


    1. Bioinformatics / Genomics

      1. Integrative Bioinformatics Institute VU (FEW, FALW, VUmc)


Bioinformatics research is concerned with the information processes in living systems and with designing and applying methods to analyse and integrate biological (genomic) data. It therefore has a central position among research fields like pharmaceutics, biotechnology, gene technology, anthropology, agriculture, forensic science and chemistry, as well as clinical research and industrial applications. Bioinformatics is a multidisciplinary field encompassing disciplines such as computer science, statistics, medicine, genomics, molecular biology, cell physiology, etc.

 

The Integrative Bioinformatics Institute

In addition to a growing Bioinformatics Department, the VU recently founded a broad-based bioinformatics institute, the Integrative Bioinformatics Institute VU (IBIVU). This is a multidisciplinary institute founded by the Faculty of Sciences and the Faculty of Earth and Life Sciences in collaboration with the VU University Medical Center. The joint aim of the IBIVU is expanding the knowledge of genetic and cellular processes which play a key role in areas such as multifactorial diseases (e.g. cancer), soil ecology (ecogenomics), neurobiology and biocomplexity. The IBIVU combines, in addition to core bioinformatics, expertise from areas including: mathematics (biostatistics, stochastics), artificial intelligence, high-performance computing, scientific visualization, molecular cell physiology, genetic psychology and genomics.

 

An overview of bioinformatics master courses open to MNW students



Sequence Analysis

Course/workshop studying theory and using techniques of sequence database searching, pairwise and multiple alignment, profile searching, and phylogeny (6 cp).



DNA/Protein Structure-Function Analysis and Prediction

Course/workshop studying theory of DNA/protein sequence- structure-function relationships and providing hands-on experience of associated methods (6 cp).



Genome Analysis: Structural and Functional Genomics

Practical course studying theory and methods of genome mining, gene and gene function prediction, gene clustering, and genomic networks (6 cp).



Bioinformatic Data Analysis and Tools

Course offering theory and methods in applied multivariate statistics, MCMC, data mining, and bioinformatics methods development (6 cp).



Intracellular Networks

Theory and practice of integrative approaches and databases focusing on intracellular networks, including E-cell modelling, metabolic pathways (metabolome), and integrative data mining of genome, proteome, metabolome, and physiome data (6 cp). This course is organized in collaboration with and coordinated by the Faculty of Earth and Life Sciences.

 

MNS-Bioinformatics Research project (major) including master thesis

Your traineeships will account for 42 of your credits. The IBIVU's broad, multidisciplinary structure allows you to work on a wide variety of subjects at the VU.

 

Current research themes in tools development within the Bioinformatics Section (FEW) that can be joined include:


  • Multiple sequence alignment (MSA): The most important technique in molecular biology for gaining understanding about a given protein family is constructing a multiple alignment of a set of sequences. The MSA technique is also indispensable in comparative genomics research. We are currently developing the T-COFFEE and PRALINE methods, and work on designing new strategies to improve MSA.  These strategies include novel ways to include evolutionary information and the integration of other bioinformatics prediction techniques (e.g. protein secondary structure prediction, residue accessible surface prediction) to better match the sequences. In addition to better methods we also work on new quality control and visualisation schemes.

  • Homology searching:  By far the most important current technique to get clues about the function of a given query sequence, for which no knowledge (annotation) is available, is by comparing that sequence with annotated sequences residing in sequence databases. The most widely used bioinformatics method worldwide at present is the method BLAST that incorporates a search strategy that leaves room for improvement. We are designing new and improved techniques to recognise homologous sequences for a given query sequence. The research includes the integration of predicted protein structural information, new filtering rules, and novel techniques from computer science (e.g. suffix trees).

  • Gene expression (microarray) data analysis: in collaboration with the national Centre for Medical Systems Biology (CMSB) and the national Ecogenomics consortium we are working on multi-level gene expression analysis techniques, for example for the detection of soil pollutants based on subsequent genomic responses of soil micro-organisms.

  • Molecular mechanics: we are constructing various strategies to enable longer-term molecular mechanics simulations, aimed at gaining a fuller understanding of the dynamic component leading to protein structure and function.

 

Contact person:

prof. dr. Jaap Heringa

Head, Bioinformatics Section / room R4.41

Dir., Centre for Integrative Bioinformatics VU (IBIVU)



Phone: +31 (0) 20 598 7649

Fax +31 (0) 20 598 7653

E-mail: j.heringa@few.vu.nl

Internet: ibivu.cs.vu.nl

 

Mail address: Bioinformatics Section, FEW/Inf, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands



 

Course code

Course name

Cr.

Period

430047

Genome Analysis

6

1

430045

Sequence Analysis

6

2

430046

DNA Protein Structure-Function Analysis and Prediction

6

3

430048

Bioinformatic Data Analysis and Tools

6

5 and 6

470622

Intracellular Networks

6

3 - 28 Apr 2006 (week 14 - 17)



    1. Biomolecular Complexity

      1. MSc Biomolecular complexity (MSc BMC)


Participating sections/groups


  • Biochemistry and Molecular Biology (FEW/BMB)

Coordinator: dr. M.H. Siderius, room KA2.73, phone: +31 (0) 20 59 87564, mh.siderius@few.vu.nl

 


  • Physics of Complex Systems (FEW/FCS)

Coordinator: dr. ir. G.J.L. Wuite,  room T0.61, phone: +31 (0) 20 59 87987, gjl.wuite@few.vu.nl

 


  • Biophysics (FEW/BF)

Coordinator: dr. J.P. Dekker, room S1.30, phone: +31 (0) 20 59 87931, jp.dekker@few.vu.nl

 

Introduction

The research projects that are offered in the MSc Biomolecular Complexity are multi- disciplinary and may take place either in one or more sections (FCS, BMB & BF). The interdisciplinary character of this MSc programme means that students will gain biochemical as well as biophysical experience. The first year of the program will be spend primarily on course work while the second part will be focused on the actual research. The research consists of a major period of 9 months and a minor period of 3 months. The latter part may be done outside the participating sections.

  

List of available research projects



  • Mechanisms of Motor Proteins

  • Dynamics of DNA Enzymes

  • Cytoskeleton / Semi-flexible Polymers

  • Viral structural biology

  • Protein networks  and Signal transduction

  • Biology of Molecular Chaperone Complexes

  • Ribosome assembly

  • Mechanisms of Light Activation in Flavin-Based Photoreceptors

  • Elementary Events in Biology

  • Light-Harvesting and Photoprotective Functions of Carotenoids

  • Mechanisms of Oxidative Stress in Cyanobacteria

 

For more information read the individual descriptions of the projects below. Research subjects often changes in the sections, so for more information on the current projects contact the coordinators.

 

Background

The research programme of the Section of Physics of Complex Systems focuses on experimental studies of biological and biologically inspired systems. Until quite recently, these processes could only be investigated on a bulk level, which meant handling large numbers of molecules simultaneously resulting in the detection of averaged behaviour of these molecules. The stresses and forces that molecules exert on each other in the course of reactions were not directly measurable. This situation has changed rapidly thanks to the development of methods for manipulating single molecules. Methods such as optical tweezers and scanning force microscopy (SFM) make it possible to follow the movements, forces and strains that develop during the course of a reaction in real-time and at a single molecule level. The area of research includes biochemical processes as diverse as protein folding, DNA elasticity, protein-induced bending of DNA, the stress-induced catalysis of enzymes, and the behaviour of molecular motors such as kinesin, myosin, and RNA polymerase. The general theme relating the projects is the study of dynamic physical properties of complex biological macromolecules, using a combination of microscopes and single molecule manipulation techniques, combined with physical modelling.

 

The research programme of the Biochemistry and Molecular Biology group focuses on experimental studies of large protein-containing complex systems, such as molecular chaperone machines, ribosomes and protein networks for signalling. These complex systems have in common that they are composed of large numbers of proteins and/or RNA which have to interact with each other in a unique way and unique sequence, so that protein folding, ribosome assembly and signal transduction occur properly inside a living cell. Correct folding of a newly synthesised amino acid chain is required to obtain an active three-dimensional protein structure. For reason that are unclear proteins sometimes don't fold correctly and end up as aggregates which are found in certain cells of people with Parkinson, Alzheimer and Type II diabetes. Protein networks regulate signal transduction which plays an important role during cell proliferation (cancer), in the immune response (infection) and during adaptation to changes in osmolarity (kidneys), while ribosome assembly has been linked to protein networks that regulate cellular metabolism, the cell cycle and stress adaptation. The complex systems are studied both inside the living cell (in vivo) using two model organisms: Escherichia coli (bacterium) and Saccharomyces cerevisiae (baker's yeast) as well as in well-defined in vitro set-ups with purified components. The total research programme makes use of an elaborate number of genetics, molecular biological, biochemical and biophysical techniques such as: DNA isolation, modification en transformation, PCR, DNA hybridisation, genetic screen technology, gene deletion and/or mutation, Tandem Affinity Purification (TAP) of protein complexes (proteomics), protein chromatography, electrophoresis, immune-detection, fluorescence microscopy and a variety of spectroscopic methods among which Förster Resonance Energy Transfer (FRET) fluorescence. Depending on the project a different selection of these techniques is used.



 

The Biophysics section investigates molecular processes and structures in living matter. The research is aimed at an understanding of the basic principles of light reactions of photoactive proteins (including photosynthesis), and of the role of the (supra)molecular organization of these protein complexes. The research group has biochemical equipment, many advanced spectroscopic setups, and also a microscope set-up to study fluorescence of single molecules. Ultrafast phenomena from about 100 femtoseconds to 1 nanosecond are studied with laser systems that can produce very short light pulses. The research group also has a number of versatile experimental setups that are used to study steady-state, polarized absorption and fluorescence spectroscopy with high resolution and, if necessary, at very low temperatures. Advanced data analysis programs are present as well. The group has a large number of collaborations with biologically, chemically and physically-oriented groups within the Netherlands, Europe and the rest of the world.

 

Description of current projects

1) Mechanisms of Motor Proteins

Lecturers: prof. dr. C.F. Schmidt, dr. ir. E.J. Peterman, room U0.22, phone: +31 (0) 20 59 87576, ejg.peterman@few.vu.nl.

Biological motor proteins are studied in single-molecule experiments with the goal of understanding the physical principles of biological force generation in a multitude of active transport processes. Motor proteins are the ubiquitous nanometer scale mechanical engines at the basis of many crucial processes of life. Examples are intracellular transport processes, cell division, cell locomotion, and in complex large scale assemblies also macroscopic motion, such as muscle contraction, or flagella motion. The non-equilibrium dynamics of these specialised enzymes, usually embedded in a complex regulatory and functional environment, are the essence of their function.

 

2) Dynamics of DNA Enzymes

Lecturers: dr. ir. G.J.L. Wuite, room T0.61, phone: +31 (0) 20 59 87987, gjl.wuite@few.vu.nl, dr. ir. E.J. Peterman.

The research in this project focuses on experimentally exploring the dynamic function of DNA enzymes. For example, many DNA enzymes perform highly complex mechanical tasks in replication, transcription, or packing of DNA, of which the detailed dynamics are not yet understood. Single molecule experiments using optical tweezers technology and scanning force microscopy will be used for the exploration of the highly complex mechanical tasks of these enzymes. Knowing the dynamic physical processes of the interaction of these bio-molecules is a very important part of the understanding of this machinery. The increasingly microscopic and quantitative analysis, possible with single molecule methods, will push the limits towards progressively more exact and physical/mathematical understanding of molecular functions. This goal is spanning boundaries between biology, biochemistry, physics, and mathematics.

 

3) Cytoskeleton / Semiflexible Polymers

Lecturer: prof. dr. C.F. Schmidt, room T0.13, phone: +31 (0) 20 59 87972, cf.schmidt@few.vu.nl.

The mechanical frame work or cytoskeleton of eukaryotic cells consists of a complex assembly of filamentous proteins, interacting with a multitude of accessory proteins, effecting for example cross-linking, length control, bundling, polymerisation control. This composite polymer structure governs the internal organisation of most plant and animal cells, serves as a transport network for active intracellular transport, and drives cellular motility, for example in cell division, cell growth or cell locomotion. It is also responsible for the mechanical rigidity of cells and the response of cells to external mechanical stresses. The network of actin network is a highly dynamic structure, being locally assembled and disassembled, which plays a crucial role in cellular response to stresses. This project focuses on the investigation of these networks of semi-flexible protein, in vitro and also in living cells, with the goal of understanding the functional principles of the cytoskeleton. Semi-flexible polymers are a so far not well-understood new class of polymers also with potential use as technical materials.

 

4) Viral structural biology

Lecturers: dr. ir. G.J.L. Wuite, room T0.61, phone: +31 (0) 20 59 87987, gjl.wuite@few.vu.nl, prof. dr. C.F. Schmidt.

Many complex biological structures and materials, for example bones, spider silk or snail shells, have extraordinary physical properties far superior in certain aspects to man made materials. Understanding the construction principles of these materials is a challenge to physics, and holds the promise of delivering a future generation of bio-mimicking technical materials. Viruses are the simplest, smallest and often most rugged forms of life. Nature had to solve some extraordinary design challenges to construct these nanometer-sized machines. In this project we focus on the investigation of the micro-mechanical properties of viral shells using Scanning Force Microscopy (SFM). The experiments will be performed in collaboration with theoretical modelling as well as finite element numerical modelling.

 

5) Protein networks and Signal transduction

Lecturers: dr. M. Siderius, room KA2.73, phone: +31 (0) 20 59 87569, mh.siderius@few.vu.nl, prof. dr. S.M. van der Vies.

Protein networks such as signal transduction pathways ensure that internal and external stimuli are translated into the proper cellular responses. The major components of the signal transduction pathways are proteins (often kinases) that are found either in an active or a non-active conformation. Some of the 'signalling' proteins function in several different signal transduction pathways (hence the term 'protein networks'). In this project the regulation of signalling will be studied with a focus on the MAPK (Mitogen Activated Protein Kinase) pathways and the role molecular chaperones play in the organisation of the signalling particles. The external stimulus that will be used is increased osmolarity and the organism for this study is yeast. Different techniques such as genetic screen technology, gene deletion and/or mutation, Tandem Affinity Purification (TAP) of protein complexes (proteomics) and fluorescence microscopy will be utilised.

 

 



6) Biology of Molecular Chaperones Complexes

Lecturer: via dr. M.H. Siderius, room KA2.73, phone: +31 (0) 20 59 87569, mh.siderius@few.vu.nl, or dr. E.J.G. Peterman, room T0.68a, phone: +31 (0) 20 59 87576, ejg.peterman@few.vu.nl.

Molecular chaperones are complex biological systems that are usually composed of several different types of protein. These large protein complexes facilitate protein folding, transport of polypeptides across membranes, activation of signalling molecules and protein degradation and are thus very important in all organisms. This project focuses on the GroEL.gp31 chaperone complex that facilitates the folding of a viral capsid protein. We aim to understand the way by which the polypeptide chain is folded inside the chaperone complex and what the physical interactions. Folding of the viral capsid protein will be studied inside the host cell (Escherichia coli) as well as in vitro. Different techniques like DNA isolation, modification en transformation, PCR, protein chromatography, electrophoresis, immune-detection, refolding assays, fluorescence spectroscopy will be used.

 

7) Ribosome assembly

Lecturer: dr. J.C. Vos, room G2.77a, phone: +31 (0) 20 59) 87558, jc.vos@few.vu.nl.

Ribosomes are large RNA/protein complexes that produce amino acid chains of various lengths. A ribosome is composed of 78 different ribosomal proteins and 4 different ribosomal RNAs. In addition about 100 trans-acting factors and several snoRNP complexes are involved in the assembly and the processing of the precursor ribosomal RNA. The aim of this project is to identify and characterise proteins that are needed for the processing of the ribosomal RNA at site A2 in Saccharomyces cerevisiae. In addition, the recently identified trans-acting protein Rio2p kinase, which is required for the processing to the 18S ribosomal RNA, will be characterised. Techniques such as genetic screens, gene deletion and/or mutation, antibiotics sensitivity assays and Tandem Affinity Purification (TAP) of protein complexes (proteomics) will be used.

  

8) Mechanisms of Light Activation in Flavin-Based Photoreceptors

Contact person: dr. John Kennis, room S1.24, phone: +31 (0) 20 59 87937, j.kennis@few.vu.nl.

Recently, two new classes of blue-light photoreceptors, the LOV and BLUF domains, have been discovered in plants and photosynthetic bacteria. These novel receptors bind flavin cofactors as blue-light sensitive chromophores and mediate light-dependent responses of the organisms to optimize their photosynthetic activity. The goal of the project is to get insights into the physical mechanisms that make these photoreceptors work, from the initial light absorption event, the photochemical processes that stabilize the photon information and the functional-structural changes in the protein that communicate the information to the organism. To this end, optical and infrared time-resolved spectroscopy on the femtosecond to millisecond timescales will be applied.

 

9) Elementary Events in Biology

Contact person: dr. Marloes Groot, room S1.24, phone: +31 (0) 20 59 87937, jl.groot@few.vu.nl.

The catalytic action of biological enzymes often requires the transport of electrons, protons in combination with specific protein dynamics. The crucial state where the catalytic action occurs, the transition state is often very difficult to catch due to its short-lived nature, while the process to reach the transition state is intrinsically slow and involves the diffusive motion of the system on its ground state potential energy surface. We study a variety of light-activated enzymes to overcome this problem. We use a short laserpulse to bring the system within less than a picosecond (1 picosecond is 10-12 s) in the transition state and then follow the development in time by passing a second short laser pulse at a fixed time delay through the sample and detect its spectroscopic response. By varying the time delay we obtain the response of the system over a time-window from femtoseconds to seconds. We study the photosynthetic reaction center, which converts the energy of light into a trans-membrane electro-chemical gradient by the transfer of electrons to learn the physical principles of biological electron transfer, a process at the basis of photosynthesis and respiration. We study the light-active enzyme Protochlorophyllide Oxido-Reductase which reduces Protochlorophyllide to Chlorophyllide requiring two protons and two electron to learn the physical principles of biological proton and hydrogen transfer. In both cases the transfer event is coupled to specific protein dynamics. To this end, we apply optical and infrared time-resolved spectroscopy on the femtosecond to second timescale. We collaborate with groups abroad to provide engineered enzymes in which specific amino acids implicated in the catalytic function have been modified.

 

10) Light-Harvesting and Photoprotective Functions of Carotenoids

Contact persons: dr. John Kennis, room S1.24, phone: +31 (0) 20 59 87937, j.kennis@few.vu.nl., or prof. dr. Rienk van Grondelle, room S1.62, phone: +31 (0) 20 59 87930, r.van.grondelle@few.vu.nl.

Carotenoids are indispensable in photosynthetic energy conversion, where they function as light harvesters and photoprotectors. They exert their light harvesting function by absorbing sunlight in the blue and green parts of the solar spectrum, and transferring the energy to nearby chlorophyll molecules. In subsequent steps the excitation energy is transported to the reaction center, where photochemical conversion takes place. The energy of the photons made available this way accounts for a significant fraction of photosynthetic biomass production on earth. In addition to their light-harvesting function, carotenoids assume a number of photoprotective roles. Essentially all antenna and reaction center complexes bind carotenoids to protect the organism from oxidative damage, primarily by quenching harmful chlorophyll triplet and singlet oxygen species. The goal of this project is to assess the mechanisms that underlie the interaction between carotenoids and chlorophyll in photosynthetic light harvesting complexes and the pathways of energy and electron transfer that govern the carotenoid function. To this end, optical and infrared time-resolved spectroscopy on the femtosecond to microsecond timescales will be applied.

 

11) Mechanisms of Oxidative Stress in Cyanobacteria

Contact person: dr. Jan P. Dekker, room S1.30, phone: +31 (0) 20 59 87931, jp.dekker@few.vu.nl.

Many essential life processes are carried out by multiprotein complexes, in which each protein fulfills a specific task. Problems arise when an essential cofactor is not available for biosynthesis. Iron is such a cofactor. It is, for instance, required for the growth of phytoplankton, while in open sea the amount of iron is often limiting the growth. In the absence of iron, or under other conditions of oxidative stress, the organisms start to express a number of new proteins, of which IsiA, a chlorophyll-binding protein, is one of the most prominent. This protein forms giant double-ring structures around the iron-stressed complex, and fulfills at least two roles: light-harvesting for the affected complex and photoprotection. In collaboration with a group from the UvA a combination of biochemical and spectroscopic approaches will be applied to learn more about the ways how cyanobacteria respond to stress conditions.

 

Basic Courses (2 mandatory): 12 cp

Introduction to Bio-Complexity                 

Principles of Biophysics                             

Principles of Molecular Biochemistry

 

Advanced Courses (3 mandatory): 18 cp

Advanced Biophysics                        

Advanced Structural Biology                     

Techniques in Molecular Biophysics           

Molecular Biology                             

Biological Networks and Signal Transduction

 


Course code

Course name

Cr.

Period

430052

Principles of Molecular Biochemistry

6

1

430051

Principles of Biophysics

6

1

430050

Introduction to Bio-Complexity

6

1

420144

Advanced Biophysics

6

2

430054

Advanced Structural Biology

6

2

430055

Techniques in Molecular Biophysics

6

3

430057

Biological Networks and Signal Transduction

6

4

430056

Molecular Biology

6

4

470707

Ethics

3

23.01.2006 - 03.02.2006




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