UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl)
UvA-DARE (Digital Academic Repository)
Studies on a bacterial photosensor
Kort, R.
Publication date
1999
Link to publication
Citation for published version (APA):
Kort, R. (1999). Studies on a bacterial photosensor.
General rights
It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons).
Disclaimer/Complaints regulations
If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.
Acknowledgements
My Ph.D-study would not have been possible without the help of many enthusiastic people. First of all, I would like to thank my promotor Prof Hellingwerf. Dear Klaas, the first time we met was at the Department of Microbiology at the Wageningen Agricultural University. You were giving a seminar about an interesting yellow protein, and I had just planned to extend my undergraduate study for another year for a study on the discussion between Vitalists and Materialists at the Institute for the History of Natural Sciences, University of Utrecht. Although it is still not clear what photoactive yellow protein is doing in a bacterium, this protein at least strongly affected my life after hearing about it during your seminar. I told you about my interest and you invited me for an interview. A couple of months later, I went on my way west, but instead of Utrecht, I was going all the way to Amsterdam with a new mission in my pocket: studies on a bacterial photosensor. Soon it became clear to me that your choice to investigate photoactive yellow protein was an excellent one. A relatively new subject with an enormous potential, and great for a Ph.D-study, since the protein guides you from the world of molecular genetics to that of spectroscopy, crystallography and even beyond. Not only your taste for fields of research, where the interdisciplinary character plays a major role, but also your enthusiasm, analytical insight and even your criticism, which divided us at times, have been of crucial importance for succeeding this Ph.D.-study during the past four years.
The journey to the west continued. This time by crossing the Atlantic Ocean to the USA, where the destination was the laboratory of Prof. Spudich in Houston, Texas. Dear John, thank you very much for this great opportunity to work in your lab in such an inspiring environment. Besides the fields of expertise I could use in your lab to study motility and adaptation responses in Rhodobacter
sphaeroides, it was very interesting to get in touch with your work on sensory rhodopsins. The
system you and others developed, which allows studies on light-induced molecular interactions between two proteins and their effect on bacterial swimming behavior, sounds like paradise for a photoactive yellow protein researcher. In addition, I would like to thank Elena Spudich for supervision and a good time in the lab. It was also very nice to work with the other people in the lab, Kevin Jung, Xue-Nong Zhang and Jun Sasaki (thanks a lot for showing me around in Kyoto, it was great to climb that mountain together). And Wouter, we met again in Houston after you introduced me to photoactive yellow protein in Amsterdam. Thanks a lot for coming to my defense in January and for all the excellent work you did, which allowed a great start of my Ph.D-study (I only had to step into this riding train). 1 will never forget our hiking trips through the forests of Texas. Also many thanks to Sam Kaplan and the people working in his impressive lab next door in Houston for their support: Jesus Eraso, Adrian Simmons, Kris Nereng for helping me with TAFE, Chris MacKenzie for assistance with DNA sequencing and Mark Gomelski for being my teacher in Rhodobacter genetics (thank you for the great stolitsnaya evening in a Russian restaurant). I also would like to thank Bastianella Perazzona for looking after me in Houston. Dear Bastianella, thank for you driving me around. This was very convenient, although I never got used to the automatic seat belts in your car T would have been completely lost without you.
From Houston the trip continued to the lab of Prof. Moffat in Chicago, where exciting times were going on. The results from previous experiments carried out in in Grenoble were just roling in. Dear Keith, thanks a lot for introducing me to the exciting field of time-resolved X-ray crystallography. I also would like to thank Ben Perman for the great Chicago-Amsterdam exchange of science and culture.
Also the work of undergraduate students on the project at the Laboratory for Microbiology, Amsterdam, is gratefully acknowledged: Mirjam Hoefkens for Tn5 mutagenesis and construction of
the Rb. sphaeroides pyp deletion, Sally Hoffer for work on the cloning oî Rb. sphaeroides pyp (also 105
for the great trip to San Fransisco after the Gordon conference). Michael van der Horst for construction of Rb. sphaeroides mutants, Vincent Los for work on the overproduction of Rb.
sphaeroides PYP, Micha Rijkenberg for the characterization Alkali spirillum mobilis and Arthur
Kroon for the development of an overproduction system for£. halophila PYP.
Also the conributions of researchers at the faculty of Chemistry from the University of Amsterdam are gratefully acknowledged. From the Department of Organic Chemistry, Jan Geenevasen for NMR-spectroscopy, Hans Bieräugel and Herman Fennema for work on the synthesis of chromophore analogues. From the Department of Biochemistry Louis Hartog for the synthesis of anhydrides and assistance with HPLC, Ton Muisers for protein sequencing, Henk Dekker for mass spectrometry and Antonio Pierik for FTIR-spectroscopy. From the Department of Analytical Chemistry I would like to thank Henk Vonk for chromophore analysis with capillary electrophoresis. I also would like to thank Mariken Jacobs from the Department of Microbiology from the University of Groningen for assistance with the Rb. sphaeroides Chemotaxis plug plate assays, Jack Leunissen from the University of Nijmegen for help with CAMMSA, Willem Reijnders from the Free University of Amsterdam for assistance with DNA sequencing and also for organizing an exciting chess competition (coming monday we will meet!). Mary Phillips-Jones from the University of Leeds, thank you for your contribution by fishing a Rb. sphaeroides pyp clone out of a genomic library. Wander Sprenger, thanks for suggestions on phototaxis assays, Ruslan Grishanin for suggestions on the selection for
Rb. sphaeroides Tn5 mutants, Daan van Aalten, thank you for the construction of a 3-D model of Rb. sphaeroides and Jenny Driessen for sequencing work of 16S rRNA from A. mobilis.
In addition, I would like to thank Prof Armitage for the interesting visit to her laboratory at the University of Oxford. Dear Judy, thank you very much for all your comments on my thesis and for coming to Amsterdam for my defense; I hope there will be a chance for a second visit in order to do some work in your lab in Oxford. Also many thanks to Paul Hamblin for his hospitality and suggestions for knock-out strategies.
My colleagues in Amsterdam, my co-promotor Wim Crielaard, thank you for all your support during the past four years and it was very nice to walk around with you in Vienna, Daniel Verhamme, Ruben Kok, Jasper van Thor, Inge van Nugteren-Roodzant, Betsie Voetdijk, Bart van Rotterdam, thanks a lot for your contributions to this work. I also would like to thank Robert Cordfunke, Andrea Haker and Johny Hendriks for all their help during my Ph.D.-study and I wish them goodluck with the PYP project in the future.
In addition, taking part in a new society for all Ph.D.-students from the University of Amsterdam, called Apollo, has been a great experience during the past 4 years. In spite of extensive campaigns for the interesting lecture evenings we organized on 'academic freedom', 'fraud in science' and 'the consequences of computerization in the process of decision-making', only a limited number of Ph.D.-students showed up. Nevertheless, it has been a very fruitful and joyful time together with the other members of the 'executive committee' of Apollo: Carolien, Corne, Emiel, Esther, Iris, Roel & Wilma thanks a lot!
a kiss for my beautiful friends and my parents zonder jullie was het niks geworden,
Remco ^—,
