Monday, November 28, 2005

Back home update..

Well this promises to become a long post. that's what you get from waiting to long... So what happened between the last post and this moment? Let me think. The Saturday after the Blazer's game we went to OMSI (Oregon Museum of Science and Industry). If Max could move to this place i am sure he wouldn't hesitate a second. It's a do-museum in which some basics of predominatly physics (magnetism, pressure, etc) are explained with little experiments and play-things. At night I packed and Sunday morning insanely early I caught the plane to Washington DC.

Upon arrival there was a taxi waiting to drop me off at the hotel. On the way we passed the Pentagon and Arlington national cemetery, I decided I should try to visit those if I had the time. The hotel was nice, although the room was really small for me and my three colleagues. Ah well, after some arguments we finally had four beds so all of us could sleep. There was no way we would be able to find something else anyway with 34,000 neuroscientists occupying all hotels in DC. I was to late to register that day so I met with my colleagues for dinner in downtown DC. The next days were spend both at the conference and at the many memorials and monuments in DC. I saw many research posters, and listened to a fair amount of talks. I also visited the white house, pentagon, capitol, Arlington, the Vietnam war-, Korean war-, Lincoln- and jefferson memorials and the Washington monument. Pictures at my photoblog.

Well, wednesday afternoon I was on a plane back to the Netherlands. Arriving in Amterdam at 7am I was happy to see my mom, brother and girlfriend that all managed to get up early enough to pick me up. My brother still lives with my parents which means that there are three cars in front of that house. I had 6-months-luggage, so they choose to pick the smallest car to pick me up... After some trouble we managed to get everything and everyone in and I was on my way home. The first couple of daysI did not seem affected by a jetlag but later I couldn't sleep at night or get up in the morning. It's almost back to normal now. We moved all my stuff back to my room in Utrecht on Sunday and after the inital "if-it's-in-a-closet-it's-organized" attitude, I am now really organized and everything is where it should be. I freshly installed my computersystem, and a second time over because the first time I was attacked by some worm that wouldn't be removed with any of the 6 programs I tried, but now everything seems to work just fine. I must say the Netherlands are pretty cold and wet. Tuesday in Washington I had dinner with some other dutchies outside and it was warm enough to just wear a T-shirt. Here the power-lines are collapsing as a result of snow and ice.....

Last friday we had a party at our house for a number of unimportant reasons. It was fun to see some people again and hang out with people of more or less the same age and situation of life. I had a great time in the USA, but at the institute there were hardly people my age. Most were much older. Sunday I wrote my first column for my philosophy, art and culture class. It deals with the god-shaped hole between the world that we observe (science) and the world of which we are part (art). I noticed that my way of thinking is pretty much biased towards a scientific approach. I really like art and everything, it's just that on a day to day basis I deal with science way more. I hope this course will learn me how to balance this and broaden my general knowledge about art, culture and philosophy. Today I dropped by my old work to arrange when I am starting work again. I can start tomorrow night and we planned all the way till new year. It was fun seeing my old colleagues again, they were enthusiastic about me returning to the company. I have not told them that it will probably only be for a couple of months, since I already have a fulltime job at uni for when I have graduated from my masters program. I guess they will understand when I tell them, but in the meanwhile I'll have to pay the rent and avoid the risk of having no job.

I also started writing the official application for my masters thesis. I am confident this will offer no problems with the exam committee so I plan to start working on it any day now. If everything goes according to my plans I will have fullfilled all graduation requirement in early february. The official graduation dates are unfortunately enough on january 27th (can't make that) and april 27th . Ah well, I can start my PhD job in february anyway, it's only a nice trick of uni to squeeze some more tuition money out of poor students.

To conclude:
I'm back, I'm busy and I am on schedule to graduate....

Thursday, November 10, 2005


Two days left in Portland. I am busy finishing up and making sure I don't forget anything. Presented my work for the research group today and it went great. My professor even asked if he could use some of the schematic pictures I made. After the talk we had a nice it-has-been-nice-working-with-you moment. They gave me a OHSU "brain awareness" T-shirt and I gave my direct colleagues a copy of the book "Flowers for Argenon". It's about a neuroscience lab that does an experiment that makes a mouse really intelligent and then they try it on a human being.. Si-fi, but supposedly pretty cool. So tomorrow I'll have to pick up myfinal report at kinkos and hand it in, clean up my desks and do more stuff to deal with leaving. As a nice surprise I was told I am going to go the Rose Garden tomorrow night to see the Portland Trailblazers play the Detroit Pistons. Should be cool to witness an NBA game. Then I need to start packing my suitcases. The six months are almost over. I'll be having dinner in G.W. backyard on sunday and next thursday I'll be in Amsterdam. But first I need to get some sleep; working towards deadlines usually gets me on some sort of adrenaline rush, so I need less sleep. Now that the efforts of 9 months are all done, I can relax and enjoy the last moments in the USA for a while. I really like Oregon so I am sure I'll be back sometime. But it won't be any time soon, 'cause living abroad for nine months witout pay or the right to work is fantastic, but expensive. I am looking forward to going home, but I am sure I will miss the Portland area and my family. Ah well, to quote my colleague Vadim: "Such is life..."

Tuesday, November 08, 2005

For those who (pretend to) care...

For those two people genuinely interested and others faking interest ; the following section is the general abstract that preceeds the research chapters in the report of my nine month internship. It is as short as I can write it down without leaving out the real important information. I wonder if anyone will actually read it, but....

"The cerebellum is the part of the brain that is crucial in the coordination of reflexive movement. For the maintenance of balance by postural adjustment the cerebellum receives information from the vestibular system, the visual system and proprioceptors in muscles and joints. The cerebellum output signal is used for the necessary compensating movements. This output signal is provided by one singe cell type; the Purkinje cell. This means that understanding how the Purkinje cell’s discharge pattern is modulated is an important step towards understanding the cerebellum and its computational circuitry. Purkinje cells have two distinct types of action potential; climbing fiber responses (CFRs) and simple spikes (SSs). CFRs are multi-peaked action potentials with a low frequency and long duration. SSs are single peak action potentials, with a much higher discharge frequency and shorter duration. There are two major input pathways from the vestibular apparatus to the Purkinje cell. Primary vestibular afferents project as mossy fibers on granule cells in the ipsilateral uvula-nodulus of the cerebellar cortex. Granule cell axons form parallel fibers that synapse on Purkinje cell dendrites. One Purkinje cell receives synapses from up to ~150,000 parallel fibers. Primary vestibular afferents also project to the ipsilateral inferior olive through the parasolitary nucleus. From the inferior olive climbing fibers ascend to the contralateral cerebellar cortex where they synapse on only a few Purkinje cell dendrites. Each Purkinje cell only receives input from one climbing fiber. Purkinje cell discharge patterns can be modulated by vestibular stimulation. Sinusoidal oscillations about the longitudinal axis causes CFR frequencies to increase and SS frequencies to decrease in Purkinje cells ipsilateral to the side that is down during stimulation. In contralateral Purkinje cells this modulation in reversed; CFRs decrease and SSs increase. This antiphasic modulation of CFRs and SSs raises the question if those two types of action potentials are modulated independently or correlated. CFRs are evoked by the climbing fibers and their modulation directly reflects climbing fiber activity. SS modulation is less well understood. A first thought might be to attribute SS modulation to the numerous parallel fiber synapses on the Purkinje cell. But vestibular primary afferents are modulated out of phase with SS discharge and there is no inhibitory synapse in the mossy mossy fiber-granule cell-parallel fiber pathway to the Purkinje cell. Furthermore, experiments in the rabbit and mouse show that after elimination of primary vestibular afferents by a unilateral labyrinthectomy, modulation of CFRs and SSs persists. This means the modulation can not be attributed to the mossy fiber-granule cell-parallel fiber input to the Purkinje cell. Lesions in the inferior olive greatly reduce CFR and SS modulation in the contralateral uvula-nodulus suggesting that climbing fiber activity is the driving force behind both CFR and SS modulation. Modulation of climbing fiber activity is also out of phase with SS modulation, which makes a direct modulation unlikely. Besides Purkinje cells there are also interneurons in the cerebellar cortex that might play a role in SS modulation. Stellate cells are the only interneurons that have the suitable characteristics to inhibit SS discharge. They are modulated in phase with climbing fiber activity and have inhibitory synapses on the Purkinje cell. During increased climbing fiber activity the increased stellate cell inhibition could account for the decrease in SS discharge. How the stellate cells are modulated by climbing fiber activity is unknown since there are no climbing fiber synapses on the stellate cell. Glial astrocytes might have something to do with this. The location of Bergmann glial cells at the climbing fiber-Purkinje cell synapse allows them to sense climbing fiber activity by neurotransmitter transients. They secrete glutamate and diazepam binding inhibitor that could increase the excitability of stellate cells. Attempts to model this hypothesized circuitry in a realistic model of the cerebellar cortex have been abandoned for the time being. Ideas to use a realistic compartmental model of Purkinje cell in the GENESIS modeling software have stranded due to an initial misinterpretation of the Purkinje cell model and a lack of time and resources. Purkinje cell discharge in the uvula-nodulus is modulated by stimulation of the vestibular apparatus. The functional role of the nodulus for the execution of compensatory movements can be investigated with a newly proposed behavioral experiment that measures the displacement of the center of mass and compensatory head movements in the mouse, during vestibular and optokinetic stimulation. Also, new cell-specific RNA interference techniques will be developed to knock down the function of specific interneurons in vivo. With this technique the possible necessity for SS modulation of stellate cells and other interneurons can be tested. This might ultimately lead to an explanation of the modulating circuitry behind the cerebellar output signal."

So you skipped it right? Or did you actually read it? In that case; hats off to you! You have earned the reward. You are invited to a party at my house in Utrecht november 25thor 26th. One of my housemates just returned from a long stay in australia and I will be back next week. Enough reason for a party. Or so I was told today when I heard about the party. Must agree though, it will be a great opportunity to catch up with people I haven't seen for the past six months...

Sunday, November 06, 2005

104 Pages, 42 Figures, 140 References...

My report is approaching the finish line. I think I have all the text I want. I just have to make sure I put my references in the text correctly and that will take some time. I think I can manage to hand my report in before I leave for Washington DC, though. I might give a talk next week. Dunno about what yet. The main topic of my internship is a research topic everyone in the research group co-operates in and we all reviewed the recent manuscripts and grants, so I guess everyone knows exactly what 's the deal. I could talk about the possibilities for a model I explored or my ideas on a new behavioral experiments. Or I don't give a talk, we'll see, I don't care.. Monday we will be able to record again if our mouse made it through the weekend. It looked fine friday night, so it should be okay, but you never know.

By the way, I didn't pay attention for a second and all of a sudden it is very fallish. Cold and wet. Guess the Oregon rain season has started again. Well, one more week..time flies..

Saturday, November 05, 2005

Wednesday, November 02, 2005

Writing, rewritig and referring...

Towards the end of the internship it is time to work at my final report real hard. I am getting close to the end. I have most stuff written down, but there is still a lot to do. I have to rewrite a couple of sections, put the references to the literature in the right place and hopefully we will be able to gather some more preliminary data from our recordings in the labyrinthectomized mice. After the incident in which our veterinary "friends" of the animal department euthanised our mice after surgery because they "looked like they weren't alright" we had a talk with them. We explained they were supposed to look like that, they are in no pain, only disoriented because we messed with the vestibular apparatus. And besides they adapt in a couple of days and then the only thing visible is a slightly tilted head. They accepted our explanation, but we still changed our surgical methods a little to try to decrease the impact while maintaining functionality. This seems to work. The mice I have operated on recover faster than before.

That a good surgical session is no guarantee for a good experiment was proven today when we recorded for three hours with zero result. No responsive Purkinje cells were found, which made the experiment useless from the physiological point of view. Luckily enough we had a new histological colouring method we needed to test so there was some use to it. I performed a labyrinthectomy right away to prepare a hopefully slightly more succesful experiment for next monday. In the meantime I will keep working on my report.

Punk in Amsterdam

The time to go back to the Netherlands is getting closer and thanks to my brother I have tickets to some nice upcoming concerts. I am going to see Lagwagon on january 9th. I have seen them many times before, but it was never dissappointing. The best thing is Bo (well, actually Tim) managed to get me tickets for Me First and The Gimme Gimmes. Why is this so great? Well first of all it's an awesome band. A sideproject with members of Swingin' Utters, NOFX, Lagwagon and the Foo Fighters, playing only covers. Second; because it's a project band they don't tour very often. Third; their original tour did Portland in april (when I was in the Netherlands) and Amsterdam in september (when I was in Portland) . But the show in Amsterdam got cancelled and later postponed to may 5th. So luckily now I can go. Oh, and both shows are in De Melkweg in Amsterdam, which is my favourite club of all time.