The added value of 3D cell culture

Friday, September 24th, 2010 by hinrich

3D cell culture

You can hear many talks about the limited translatability of results from experiments done with cell cultures that were grown in 2D ("in plastic"). Often you will then here that 3D culturing where cells can form structures (similar to e.g., tumor tissues, breast tissues, etc.) should lead to much better and much more predictive models.

While this sounds sensible, I am wondering: how much closer are we to the human situation? If 2D cell culture would represent 5% and the conditions in humans were 100%, are we now at 50% with 3D culturing? Or only at 10%? Or even less? Or do we simply swap one bias (as introduced by culturing cells in 2D) for another?

I believe that it will likely be what common sense suggests: most things have advantages and disadvantages. In the end, they are both models that will reflect the human situation better for some aspects but might have trade-offs for other things (e.g., which cells can form 3D structures / how fast you can grow them / how reliably they form 3D structures, how comparable and reproducible such structures form, etc.).

Let's not over promise things with 3D culturing, but rather thoroughly study and investigate this approach so that we can expand our scientific toolbox!

Posted in Science

TOG concert 2010

Monday, September 20th, 2010 by hinrich

Jan van den Brandt

After last year's successful Efteling concert, we have chosen to continue with music linked to a theme. This year's main concert will be about Disney music. Beginning of October (Saturday, 2nd, at 20:00 and Sunday, 3rd, at 14:00 at the Engelenburcht), we invite you to join us for more than two hours of famous Disney music during our Disney Sing-A-Long Proms concert. The songs include titles from Lion King, Hercules, Little Mermaid, Tarzan, and many others.

We have just completed two repetitions checking most of the music together with singers, choir (Crevekoor) and orchestra (TOG Engelen, supported by several musicians from the neighborhood). Now only two more repetitions with the orchestra and a final general repetition...

Our conductor Jan van den Brandt has arranged most of the music himself. Tickets (7,50 Euro) can still be ordered via the web page of TOG Engelen.

Posted in Misc

The IT support paradox

Tuesday, September 14th, 2010 by hinrich

IT support paradox

Why does it not strike people as odd that in many large corporations you can observe the opposite of what common sense should demand? As you go up the managerial ladder (indicated by the vertical arrow) you see an increase in IT support (blue triangle) up to even special dedicated VIP IT support. At the same time the actual computing demands (storage space, computing power, etc.) decreases (green arrow).

The level and responsiveness of IT support should reflect the IT needs and not the position in the managerial hierarchy.

When was the last time that a corporate CEO had to use the same help desk support as the majority of company employees have to rely upon?

Posted in Computer

GeneTitan artifacts

Friday, September 10th, 2010 by hinrich

GeneTitan well array

Ben Bolstad has created a while ago a gallery of images that illustrates various artifacts that can be seen when generating microarray data using Affymetrix' cartridge arrays. The images are generated by running functions that are included in Ben's affyPLM package for R. For the most current version have a look at the BioConductor web site.

A little while ago, Affymetrix has launched the GeneTitan instrument which can process up to two 96-well plates per day. However, as the processing of the arrays is completely different from the cartridge arrays, different problems can occur. We can see gradients / edge effects across the plate, but we can also see effects within a single well array (see icon - this documents a problem with the CCD camera that takes a number of smaller individual images to create a final composite image of the whole array).

Maybe we should start documenting the GeneTitan specific artifacts that we observe? Of course, this could in turn help the producer to optimize the instrumentation.

Posted in Molecular Profiling

We will rock you?

Wednesday, September 01th, 2010 by hinrich

We will rock you

Yesterday we have been to the commercially exploited general repetition of the Dutch version of the Queen musical “We will rock you” at the Beatrix Theater in Utrecht (premiere on September 3rd). What promised to be an entertaining story combined with popular Queen songs turned out to be largely disappointing.

Shortly after the beginning technical difficulties produced something reminiscent of what we know as a dead pixel on a LCD screen. However, it looked like a completely defective screen that continuously distracted the attention away from the performance on stage. Yes, the music was great, but the story reminded me a lot of the German saying “Reim dich oder ich fress' dich”: a story had to be invented to fit the most popular songs.

For a long time I was wondering whether the intention of the author of the story (Ben Elton) was to make fun of the musical genre. Then there were times when the performance seemed very serious. I am not sure. I will settle for a bad story.

The evening set us back 50 Euro per ticket. My recommendation: buy a good Queen CD and invest the rest in a good music system. You will enjoy it much more than visiting this show.

And if this represents contemporary entertainment (completely scripted / no interaction with the audience / no spontaneity / even the encore is planned and performed irrespective of the response of the audience), I do not want to see it.

Posted in Misc