The Experiment

December 19, 2011

“[…] One reaction tube contains much more bacteria than the other one and they want to know why. In their own discussion the students conclude that something went wrong during the procedure. The experiment failed. […] But there is no course with the title “How to do proper Science”. […] Daring to make your own conclusions […]. […] Realizing what you have learned over the years […]. […] It sounds so simple, but it is a giant leap. […] Tomorrow we will do a new experiment. An experiment with an unknown result. Educational objective: There will come a day on which you can beg for an explanation of your results, but your teacher will also not know the correct answer. There will come a day on which you will have to figure it out yourself.”

by Rosanne Hertzberger (excerpt from her column in the Dutch newspaper NRC next, December 19th 2011)

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A brief intro

December 1, 2011

This is what I do during my Master project number one (of two). As you can see, the Sec systemsSecA motor protein is the center of my work. It is the molecular motor which transports proteins which are made within the (bacterial) cell via the membrane to the outside.  Wordle created this nice overview for me by copy/pasting the introduction of my report into it. I actually borrowed the idea to this from Stefan Kowalczyk who is working at Bionanoscience Department of TU Delft in the Netherlands.

Stuff for your mind

September 28, 2011

Once in a while it’s good to develop a new perspective on the things  which surround you. The following artists impression does this in two distinct ways. And it’s funny, too.

I believe that it’s originally from abstrusegoose.com. This site has some pretty hilarious stuff to offer, but I actually found it at Popperfont which is also a nice place. In the first place I only found those pages because I was looking for a descent science blog which could teach me some interesting things in lab-waiting -periods. I found a very nice one here (selection of 60+ good science blogs). To get a first idea, begin reading this blog entry over why neutrino particles may or may not be traveling faster than light. It’s pretty interesting and makes clear that physics is real world science with all the challenges attached to it. Helps to prevent to see the world as depicted above (although this is also fun at times!).

Shortly I will start with an internship at the Department of Molecular Microbiology at Rijksuniversiteit Groningen (Prof. Driessen). There I will deal with the mechanisms of protein secretion in bacteria. I will in more detail concentrate on the Sec-pathway. The dominant part of this process is achieved by a multi-subunit translocase. This protein consists out of a channel (trimeric SecYEG) which penetrates the lipid membrane. In addition SecA protein belongs to the complex which is some sort of molecular motor that mediates the stepwise protein translocation through the channel at the cost of ATP. Other important proteins during translocation are SecD, SecF and YajC which associate to SecYEG). Chaperones such as SecB guide secretory proteins through the channel, while co-translational targeting via the signal recognition particle (SRP) and its receptor SRPR is also possible. The latter case also occurs for membrane proteins.

The reasearch of the department, generally spoken, is to identify structure-function relations of the above named translocase. In order to achieve this it is important to concentrate on the chain of events during the process and the conformational changes of the participating molecules.

Shortly there will be more information on the topic. On the following website more information can be found: http://www.rug.nl/fmns-research/molecular-microbiology/research/proteintranslocation

Inspiring lectures

April 12, 2011

Bob Goldstein (Cell Biology) from the University of North Carolina at Chapel Hill had the great idea to design posters to attract more students to interesting and distinguished lectures about various topics from molecular and cellular biology. The posters are designed and screenprintend in collaboration with the band-poster experienced people at The Merch. 50 copies are printed per event (1). Needless to say they are quite popular among students, so have a look at a compilation of a selection of these interesting and innovative posters (Fig. 1).

Compilation of Goldstein PostersFig 1: A selection of some nice and fascinating posters which originate from the University of North Carolina at Chapel Hill, are used for lecture advertisement purposes, and are highly demanded by students (2).

(1) http://www.zeit.de/studium/uni-leben/2011-04/plakate-wissenschaft (12-04-2011, 00:20 h)

(2) From various sources.

Homology vs. Analogy

October 8, 2010

Inspired by Banksy and the movie “Exit through the giftshop”.

Form follows Function I

September 29, 2010

A nice and simple overview about the basic activation principles and dimerization of RTKs can be found on YouTube

http://www.youtube.com/watch?v=-iBb1sH-Eh4

But Wikipedia can help! Actually it will get easier if you look at the pieces one by one instead of looking at the whole picture. I’ll try my best to explain some of the pathways. Errors might be included, since I also see it as a preparation for my exams in Biochemistry and Cellbiology.

Here a nice quote on stuff many of us encounter during their studies (the mathematics part might be more or less optional):

“Two things are to be noted about a course such as this: the first is that it is not trivial. Even coming to grips with the apparently counter-intuitive results that we shall find is far from easy if you have not yet become used to them by regular exposure. The second is that it is steep: the mathematics grows heavier, and the exercises more complicated, as you progress. This is a useful thing: suffering is good for the soul.

– Prof. Dr. R. Kleiss, Theoretical High Energy Physics, Radboud University Nijmegen

This quote from Richard Dawkins famous book “The Selfish Gene”  is of course highly controversial (at least for non-biologists), but still it highlights two very important ideas: The first one is the fact that we are born to replicate because in a way we are the “slave” of our genes. Genes determine for a surprisingly great amount the kind of person we are. The second and even more interesting fact of life which is included within this quote is the potential our (human) genes offer to us. Via the formation of the brain our genes enable us to reflect our actions and judge our and the decisions of others. They render the potential to us to act in ways that are seemingly contradictory in some situations. They enable use to think in a sustainable way and make future plans. Humans can have intentions. So maybe genes are both: the key and the chains. Being social has brought us to where we are now. Being social seems to be beneficial in evolution. Ooops… genes seem to selfish indeed.

In the following weeks I want to shed some light on the great world of genes. I want to demonstrate that no great clusters of “brain” genes or “attractivity” genes exist, but that genes can be arranged in rather abstract subgroups. Some of the biggest and therefore (probably) important groups I`m planning to present here. I will especially concentrate on the proteins these genes code for. I will start out with protein kinases.

Some more

May 12, 2010

Here I’m planing to publish things I just happen to like… or that have moved my thoughts.