Wednesday, January 31, 2007

EMBL and my interests

I like signal transduction and doing fancy light microscopy [1]. Hence, I looked forward talking to Philippe Bastiaens, who did a great deal of sophisticated fluorescent life imaging (FLIM) to elucidate pathways and make useful assertion about physiological levels of proteins, substrates and in one recent paper even about a gradient in vivo [2]. To my displeasedness, Bastiaens was too good to stay in Heidelberg and was offered a leading position at the Max-Plank Institute Dortmund, staying at EMBL only as a visiting group leader. «yeah!»

Fortunately, there are a couple of other quite interesting groups. One of which, led by Carsten Schultz, collaborated with Philippe on several occasions and provided the nifty underlying protective chemistry of the substrates he used [2]. A proposed PhD project leads deeper into signal transduction and by neat approaches allows to more or less dynamically switch parts of a pathway on or off [3]. This would enable analyses of the pathway branch without screwing up the physiological levels.

Other research units are concerned about chromosomal organisation and Matthias Hentze explores the mechanisms of translational repression by RNAi, having a paper submitted for review recently that elaborates on pseudopolysomes being observed on repressed mRNAs (hot stuff).

[1] As I currently do in my final year research project, by exploiting Tom Kerppola's wonderful bimolecular fluorescent complementation assay.
[2] Yudushkin IA, Schleifenbaum A, Kinkhabwala A, Neel BG, Schultz C, Bastiaens PI. Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B. Science. 2007 Jan 5;315(5808):115-9.
[3] Sorry guys and gals, detailed information not to be disclosed. However, some research is aiming to produce switches that may be genomically encoded.

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Monday, January 29, 2007

I'm in Germany!

First of all, (the interviews in) Cold Spring Harbor has been absolutely awesome. I had eleven one-on-one conversations with bright minds ala Jim Watson, Gregory Hannon, Nicholas Tonks, Leemor Joshua-Tor and many more. I think the best part was this morning (well NY morning) when Dr Watson took me and Ralph (college from UCL) on a tour across the campus and even into his house, showing us his art collection and talking about the near future of Cold Spring Harbor Laboratory. He is certainly a very interesting character and surprisingly fit for his 79 years. Did you know he played tennis since he was four?

This morning (NY night?), I reached Frankfurt and merely and hour ago I arrived at a hotel near EMBL Heidelberg. I'm slowly but steadily turning into a globe trotter.

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Tuesday, January 23, 2007

Long Island here I come

I'm leaving good old Britain to participate in the Cold Spring Harbor Laboratory interviews. These people are amazing, they even set up a complete itinerary for my stay and organised a limo to pick me up from JFK.

Just in case you read a post with a big «YIPEEEEIO» in the headline, this means I got an offer.


Saturday, January 20, 2007

I want this article, grrr

The New Scientist reported about a cure for most cancers by a dichloroacetate as a magic bullet and mentions the Michelakis group report in the current «Cancer Cell». The article isn't e-published on PudMed yet and this drives me up the walls! I want to read the details and not the populist New Scientist yada-yada.

The PubMed-abstract:

A mitochondria-k(+) channel axis is suppressed in cancer and its normalization promotes apoptosis and inhibits cancer growth.

Bonnet S, Archer SL, Allalunis-Turner J, Haromy A, Beaulieu C, Thompson R, Lee CT, Lopaschuk GD, Puttagunta L, Bonnet S, Harry G, Hashimoto K, Porter CJ, Andrade MA, Thebaud B, Michelakis ED.

Pulmonary Hypertension Program and Vascular Biology Group, University of Alberta, Edmonton, AB T6G 2B7, Canada.

The unique metabolic profile of cancer (aerobic glycolysis) might confer apoptosis resistance and be therapeutically targeted. Compared to normal cells, several human cancers have high mitochondrial membrane potential (DeltaPsim) and low expression of the K(+) channel Kv1.5, both contributing to apoptosis resistance. Dichloroacetate (DCA) inhibits mitochondrial pyruvate dehydrogenase kinase (PDK), shifts metabolism from glycolysis to glucose oxidation, decreases DeltaPsim, increases mitochondrial H(2)O(2), and activates Kv channels in all cancer, but not normal, cells; DCA upregulates Kv1.5 by an NFAT1-dependent mechanism. DCA induces apoptosis, decreases proliferation, and inhibits tumor growth, without apparent toxicity. Molecular inhibition of PDK2 by siRNA mimics DCA. The mitochondria-NFAT-Kv axis and PDK are important therapeutic targets in cancer; the orally available DCA is a promising selective anticancer agent.

Update: The article is online on ScienceDirect.


Friday, January 19, 2007

Mister Deity

This is too hiarious to be kept secret: Mr. Deity. (Seen at Sandwalk)

Some more heresy: God, Inc. by Francis Stokes.


Wednesday, January 17, 2007

Economic models explained with cows

I received this by email today. Thanks, Mel.

SOCIALISM: You have 2 cows, and you give one to your neighbour.

COMMUNISM: You have 2 cows. The State takes both and gives you some milk.

FASCISM: You have 2 cows. The State takes both and sells you some milk.

NAZISM: You have 2 cows. The State takes both and shoots you.

BUREAUCRATISM: You have 2 cows. The State takes both, shoots one, milks the other, then throws the milk away.

TRADITIONAL CAPITALISM: You have two cows. You sell one and buy a bull. Your herd multiplies, and the economy grows. You sell them and retire on the income.

SURREALISM: You have two giraffes. The government requires you to take harmonica lessons.

AN AMERICAN CORPORATION: You have two cows. You sell one, and force the other to produce the milk of four cows. Later, you hire a consultant to analyse why the cow has dropped dead.

A FRENCH CORPORATION: You have two cows. You go on strike, organise a riot, and block the roads, because you want three cows.

A JAPANESE CORPORATION: You have two cows. You redesign them so they are one-tenth the size of an ordinary cow and produce twenty times the milk.

A GERMAN CORPORATION: You have two cows. You re-engineer them so they live for 100 years, eat once a month, and milk themselves.

AN ITALIAN CORPORATION: You have two cows, but you don't know where they are. You decide to have lunch.

A RUSSIAN CORPORATION: You have two cows. You count them and learn you have five cows. You count them again and learn you have 42 cows. You count them again and learn you have 2 cows. You stop counting cows and open another bottle of vodka.

A SWISS CORPORATION: You have 5000 cows. None of them belong to you. You charge the owners for storing them.

A CHINESE CORPORATION: You have two cows. You have 300 people milking them. You claim that you have full employment, and high bovine productivity, and arrest the newsman who reported the real situation.

AN INDIAN CORPORATION: You have two cows. You worship them.

A BRITISH CORPORATION: You have two cows. Both are mad.

AN IRAQI CORPORATION: Everyone thinks you have lots of cows. You tell them that you have none. No-one believes you, so they bomb the sh*t out of you and invade your country. You still have no cows, but at least now you are part of a Democracy.

A WELSH CORPORATION: You have two cows. The one on the left looks very attractive.

A NEW ZEALAND CORPORATION: You have two cows. Business seems pretty good. You close the office and go for a few beers to celebrate.


Monday, January 15, 2007

Counselling Service

Dear Student,
The Student Counselling Service is running a series of workshops and training programmes this term on the following:
1. Confidence Building;
2. Overcoming Procrastination;
3. Stress Management & Self-Hypnosis.

yada, yada

«Overcoming Procrastination». Hmm, let me think about this one...


Guess what came per mail today

Wrong! It was my GRE Powerprep software. Let me contemplate this: today is the 15th of January 2007 and I sat the exam on the first of November 2006. I registered for the test one month prior to the test-day, on the first of October. So the CD was only one and a half months late to reach me before the exam [1]. Strangely, it was delivered by Deutsche Post and its journey apparently took it through Frankfurt. Even more confusing is the French postmark.

[1] Not that it would have been useful at this time any more.

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Saturday, January 13, 2007

The bitterest compound (for humans) ...

... turns out to be Denatonium. So if somebody keeps stealing your food from the communal fridge, try to season it a little with this unique ingredient [1]. Adding some of it to the saltshaker might result in peculiar/amusing situations as well [2].

[1] We tried everything last year to put off our special friend. However, even laxatives and nasty letters pleading to the thief's social pride (people from Singapore are sometimes so naive) showed no effect.
[2] I doubt anyone would notice here at my halls. Dinner is rubbish most of the days anyway.


Friday, January 12, 2007

World of Warcraft Nerd arrested

This looks pretty fake, nevertheless it amused me. «I wear boots of escaping!» I wish they produced the boots of unfailable lab-experiments.


Thursday, January 11, 2007

Fancy a laugher?

Then click the following links.


Wednesday, January 10, 2007

Research started!

Well, at least the preliminary work. I'm trying to analyse G-protein coupled receptor heterodimerisation [1] via reconstitution of two (enhanced) yellow fluorescent protein fragments. This means that I'll have to construct plasmids for fusion proteins of the appropriate receptors with either the N- or C-terminal part of YFP. In close proximity due to receptor interaction, the two YFP halves should re-associate to form a functional fluorophore. Right now I'm busy with primer design and which restriction enzyme sites to implement. Sounds lovely, doesn't it?

[1] to be precise: neuronal nucleotide and purinergic receptors.



By how much time have you ever missed a flight? A minute (indeed), an hour (certainly), two days (unfortunately). Yes, I managed to miss my last flight by two days. How did I managed that, one might want to ask. Take an itinerary add a good proportion of self-confidence and season with a splash of dyslexia. Et voila, suddenly «Fri, 05Jan07» reads as «Jan07» – «seven zero»... oh yeah, must be 07/01/07 - Sunday. It was not until the day of the alleged departure, when my luggage was packed, the car loaded and ready to leave for the airport that I took another look onto the itinerary and realised my tremendous mistake [1]. I think this falls into the category «You cannot outsmart yourself».

Luckily I managed to get a cheap flight the next day, but I missed two lectures.

[1] Echoing yells of “NOOOOO!” were reported in whole Austria. The epicentre was calculated to be my basement.


Sunday, January 07, 2007

Mobile phone dependency

I planned a small reunion night out with my friends before I fly back to London today. I arranged place and time to meet. Now one bad thing about all my mobiles is that they are pay-as-you-go phones, which is usually a pain in the ass, but the cheapest way of maintaining one UK and one Austrian number. Consequently, this means that I regularly run out of credit [1] and have to top up the damn thing. Actually no biggie, because nowadays one can do this directly at cash-machines by punching numbers.

However, on my way to Vienna I placed my mobile in the middle console of the car, because I hate fumbling the phone out of my pocket while driving [2]. Naturally, I forgot the cursed thing in the car when I used the «tube» [3] to get to the centre. At the meeting point, I realised my forgetfulness and had two problems: my friends weren't there yet and they couldn't call me. Thus, I decided to go back to the car and to fetch the mobile. Now, having a phone without credits and 8 missed calls is another problem - how to call back [4]? Fortunately, people kept calling me, so I had a chance to explain myself and why the hell I was half an hour late [5].

[1] Those text-messages to the US are bloody expensive.
[2] Having calls without a handsfree-set is illegal anyway - hah, I'm a badass outlaw.
[3] Austrian underground (U-Bahn), cheaper, smaller but quicker, more reliable and one can stand upright.
[4] Yepp, I wanted to top it up at the meeting point, outside a Bank.
[5] It's obeying Murphy's law that the underground train is always late when you need it the most.


Saturday, January 06, 2007

Latest time waster

That's what I do instead of finishing my RNAi essay: Laser


Thursday, January 04, 2007

Holiday rhythm

I always fall back into my holiday routine of staying up until 3am and sleeping until at least 1pm (or even worse after nights out). Bad, bad, bad, I need to break free! I've got three more days to adapt to my London rhythm again. Gosh, I'll need intravenous coffee for the 9am lectures. These are the situations when I regret not «borrowing» that bottle of caffeine from my old organic chemistry lab.