Monday, January 28, 2013

No pain no gain, lots of pain little gain?

Done. That is the final verdict. My manuscript is finally done and I am submitting.

Of course there were a lot of things that needed fixing today:
References didn't look right in Mendeley. The Journal of Neuroscience wants all journal titles to be the official abbreviations, something Mendeley doesn't support out of the box. This means adding and editing several .txt files to get everything working together. After several hours of frustration I decided to tweet to @mendeleysupport and they helped me with my problems. Turned out I am not so smart (d'uh), default.txt actually means default.txt.txt. Meaning that when windows explorer says default.txt it is actually .txt.txt. Silly silly me....
Then all figures should be in RGB and all text as outlines. Of course a quick fix to do, but also needed some attention.
And then of course there is the problem of all authors who need to make small smaller smallest adjustments to the text. At a certain moment I think we arrived at "not better, just different", which signals we're done with it.

Good thing is that it all looks great now. Figures are also done, text is done, ready to submit.

All these problems meant that I have spent yet another day on this paper. Time that was actually meant to go into an awesome experiment today. I still need a few cells in vivo from the cerebellar nuclei; hard experiments that need some time and attention. Both of which are in short supply lately.

So, there you have it. The mad scramble to the finish is already turning into a hectic mad scramble to the finish. I have only five weeks left..... Two papers to finish and a discussion to write.

I'll keep you all posted!
Best, Lau

Tuesday, January 15, 2013

Finish line set! Now for the mad scramble

Weeks, no months ago, I wrote about the "whirlwind that is called finishing your thesis". It has been very quiet here, and now you know why.

Good news is that I did finish one manuscript. It is now on the desk of my professor who is of course tearing it apart again... Still, I do not despair, since the date for my graduation ceremony is set at the end of May (yes, ceremony. PhD-getting in The Netherlands is a piece of theater for the whole family to enjoy!). There's only two more chapters to finish, which will be done (no, really urgently need to be done) in two months or so. To complicate things a little bit I got sick this weekend, which caused me not to work for two days. A complete disaster when on a tight schedule I might say.

So, my dear readers, now you know why I am so quiet lately. I hope to pick up blogging on interesting stuff again when my thesis has left my desk.

Thursday, November 29, 2012

Grant application from hell

Today is the deadline for my grant, or rather: the deadline is in less than seven hours. And I am freaking out!
The grant application is done, looking great and shiny as a pdf on my computer. It has been read by several people, who all had remarks and wise advice. So, why would I freak out you ask?

The Dutch funding agency asks for an acceptance form stating that the host institute accepts the candidate and the grant if the grant is awarded. So far so good you would say, but the form has been on a desk for a week and now needs to be run by several offices in one day. Extra complicating the story is that I am at GMT+1 time, the host institute is at EST time and the deadline is midnight GMT+1. So, it is now past four in the afternoon, people at NWO will probably leave around five, which leaves me only forty-five minutes to fix things here......

Extra complicated is the fact why it is taking so long at the other side of the pond. They need to check the terms and conditions on the grant. One problem there is the Dutch code on animal experiments. The Netherlands has some strict regulations, and the universities have agreed on a code to be open about animal research. Although the document does not have legal value like a law, research funded by NWO still has to adhere to it. And here begin the problems. It states all research should adhere to Dutch animal law. Of course the document was drafted in Dutch and the possibility of non-dutch research applying to the code was not incorporated in the code. So, in principle the strange situation could arise that by agreeing to adhere to the code, Dutch law should take effect when my research is concerned, also abroad. This then causes the Dutch law openbaarheid van bestuur (Openness of Governance) to be applicable to all experiments I do abroad. Something the University probably won't agree to.

I asked NWO, they didn't know directly so I had to email them. They will get back to me today with an answer. Then, hopefully, this answer is 'good enough' for the host institute and they sign the form and email it to me. Then I can send in the grant tonight. When they are not happy, then I have to get back to NWO, if they are still there to answer the phone of course.

That's why I'm freaking out.....

Tuesday, November 13, 2012

They're moving the finishing line!!!

Dear reader,

it's been a while (again) since I last posted here. I have been caught up in the whirlwind that is called "finishing your thesis". I hoped the storm would have died down a little bit, but if anything, the gale has been growing stronger.

Last week I finished the one manuscript that was supposedly between me and a thesis. Unfortunately, it turns out non-finished manuscript #2 also needs to become a finished manuscript. So, my assumption that I would go back to more normal, less frantic, working was false. At the moment I'm in full swing getting insane electrophysiology done. I'm talking 'whole cell in-vivo at 2mm depth with a perfusion electrode nearby' crazy electrophysiology. It's an unpublished thing we developed, so I can't be too specific. But, needless to say these experiments suck b*lls when you're in a hurry finishing things.

Then there's a lot of histology that needs to be done. Some simple recovery of patched neurons and testing a new antibody that we need for immuno-EM. I heard it's always wise to learn a new technique during the last weeks or months of your thesis work (not), so I'm going to do EM now as well (Jeeeej!!!!).

On the bright side, I have been looking for good estimations of the number or density of cells in the cerebellar cortex. After some cries for help and google scholar searched I have come to the conclusion that no-one ever put all things together. So, I compiled an estimate based on a collection of literature. It all seems to point (roughly) to the same estimation: (in cells per cubic millimeter mouse cerebellum)
Purkinje cells: 20,000
Granule cells: 2.63 million
Mol. Layer Intern: 100,000
Golgi cells: 4,500
I was quite surprised with the Golgi cells being so low. Still, they have an amazing axonal branching pattern, so they can provide a large number of granule cells with inhibition. Also, the high number of interneurons in the molecular layer surprised me. So, the ration MLI:PC seem to be 2:1, quite surprising....
Where did I get this knowledge you ask?

Lange (1974) Cell and Tissue Research 153:219-26
Woodruff-Pak (2006) Neuroscience 141:233-43
Dugue (2009) Neuron 61:126-39
Sturrock (1989) Journal fur Hirnforschung 30(4):499-503
Altman (1977) Exp Brain Res 29:265-74

ps. I still love science, don't be alarmed ;-)

Thursday, October 25, 2012

Troubles of a grant virgin....

I am writing, or rather trying to write, a grant application. It is very difficult and quite different from writing a paper. (So I decided to write a blogpost instead first)
I know what is expected from me in a paper. Introduce the study, present your results in a clear way, discuss the results in the context of the scientific field. Also, when appropriate give credit to previous work (references).
But, how does that work in a grant application? There are no results, only plans. So, that means writing an introduction and then present the plans. How far should I take this? The committee is multidisciplinary, so too much details will not help, but maybe there will be some specialists there who would appreciate details. Still, I really wouldn't want to bore any members of the committee. AAAAAARGH!!!!!
Should I use references in the same way as in a paper? I guess not since the grantcommittee will not be interested in all the details. Still, it is good to show that my plans are based in reality and not too outrageously far-fetched.

One thing I picked up from a grant I could use as an example from my boss is that every figure should have a very clear, exciting and colorful message. Maybe I should include some figures from my present work, combined with some figures from papers the lab has published I'm going to work......

Decisions, decisions.....

There must be some people here who have written grants before. What are the do's and don'ts??? I would be eternally grateful ;-)

Saturday, October 6, 2012

People hang on his every word, even the prepositions...

Okay, so that was another embarrassingly long absence from blogging.

The last months have been hectic, both professionally and on a personal level. I have a postdoc (jeej!), so I have to finish my PhD in time. This means: finish my book in November, graduate in April, get to Boston in May. Two papers... two papers is the only thing in between me and my thesis. Two papers to analyse all the data for, two papers to write and then two papers to send off. I know it's ambitious, too ambitious maybe, but I don't really seem to have a choice.

Meanwhile there was a great little conference here in Amsterdam the last few days. The Cerebnet and C7 consortia had a joint meeting right here in our institute. Today was the final day with a few workshops. Together with a colleague I demonstrated in-vivo patch recordings in the cerebellar nuclei. Now I'm waiting for a PCR gel to settle and I can go home and crash. Next week, an old student will visit the lab, so that's another week out of my schedule. Two papers.....

There is one great thing though from the conference I have to share with you. The keynote lectures were done by two emiritus professors: Professor Nieuwenhuys and Professor Voogd.
Rudolph Nieuwenhuys spoke about the evolution of the brain and what that tells us about its function. He is an unbelievable speaker, with his 80+ years he still captures the audience; I never heard our colloquiumroom so quiet. A very clear lecture with clear takehome messages after every few slides.
Jan Voogd then took the audience home, back to the cerebellum. Why is the cerebellum so big in humans? Which zones got bigger? Is this only in primates or also in other mammals? Dolphins for example show a big cerebellum, but this is mainly due to skeletomuscle zones that increased in size. In primates however, the increase is in the non-skeletomuscle parts of the cerebellum.

They must be the two most interesting men in the world!

The best part actually might have been that they both refused to operate the computer, so someone else was advancing the slides for them. This took the pace out of the presentation and it all came across very calm and controlled. Maybe there is a lesson to be learned here for presentation skills!

If you want to learn more about these two absolute legends in neuro-anatomy, you can buy their book! It's a great bargain, just under $100 for about a thousand pages of wonderful diagrams and clear explanations.

Thursday, July 5, 2012

Easy Come, Easy Go

My newspaper has a section called 'Next Question' which contains intriguing questions from readers. This time the question was "How come we never 'forget' how to ride a bike?" The answer was complicated, convoluted and -at best- incomplete. The answer came from a Dutch Neuropsychology professor who explained that when learning to ride a bike you need to couple correct movements to what you see and feel on a bike.
(Not a literal translation, paraphrased)
If you learn it a little bit you are motivated to get better and better. That is why you keep on making the correct movements fitting to the perceptions. This way you produce robust connections between so-called perception cells and action cells. He makes a reference to Hebb: "Cells that fire together wire together". The more you do it, the more ingrained it becomes. Because every bike works (almost) the same, the relation between perception and action is stable. You never experience something completely different on a bike, that's why you never unlearn it.

So, you might think, that's not such a bad answer. And no, it's not. It's a bit unclear on which parts of the brain are involved. What are perception cells and action cells, but other that that it sort of makes sense. But in the last section it goes off a bit:
(again paraphrased)
Less consequent experiences are more susceptible to forgetting. That's why we have problems forgetting what we ate last week for every day. This is because we eat something different almost every day, the memories interfere and we are not able to form strong memorytraces.

Right, so riding a bike is part of declarative memory? It seems that the answer here is solely built on the principle that if a trace is enforced every time in a constant way it becomes stronger. Though true, it doesn't tell you why you never unlearn to ride a bike, even though you haven't done it for years, while you do forget what you ate yesterday!

What about those pesky Dutch spelling rules? We got drilled in school to know where to put d, t or dt. But sometimes I forget.... Why do we forget numbers so easily, but are always able to thump in our pin at an ATM machine? (Honestly, sometimes I can't remember the digits, but when I see a keyboard I can type it!). The same goes with passwords at your computer, sometimes you can't remember, but your fingers can!

The answer of course lies within the cerebellum. If you say coordinated movements, such as riding a bike, you say cerebellar involvement. On the other hand, riding a bike is also very much a sequence that you have learned, so you would expect striatal involvement. It's probably a bit of both; maybe first cerebellar coordination to get the movements right, then striatal consolidation? Why then don't you unlearn how to ride a bike, while you do forget other things? Although we do not know the cellular and molecular mechanisms, this question can be answered via a different route.

Imagine what would happen if you would learn and unlearn movements in the same vivid and thorough way as you remember your lunch. You would step onto the greens of a golfcourse and you would be able to swing the perfect ball within a few trials. Sounds perfect, doesn't it. But a quick learning implies a quick unlearning as well. You would not be able to make that perfect swing again in one go. And that's what you don't want for your movements. You would forget how to walk after sitting for an hour. So, movements are learned very slowly, so they are also unlearned or forgotten very slowly. Why don't you forget how to learn to ride a bike? Because it took long to learn.