A nerdy post after such a long break. Sorry

Zinc fingers is typically a domain of about 60 amino acids that fold around one or more zinc ions and is found in over 400 eukaryotic proteins, many of which are involved in the regulation of gene expression and in the maintenance of chromatin structure. Zinc fingers typically show a C4HC3 signature (four cysteines, one histidine, three cysteines) with characteristic cysteine spacing and with additional conserved residues, most notably a tryptophan or other aromatic amino acid preceding the final cysteine pair. Studies have suggested a role for zinc fingers as nucleosome interaction determinants. However their functions are still elusive and controversial, as a variety of functions have been suggested, including phosphoinositide binding and E3 ubiquitin ligase activity. In addition to their role as a DNA-binding module,  zinc finger have been shown to mediate protein-protein and protein-lipid interactions as well.

What about the electrostatic surface properties of zinc-finger domains? Here an example with the models of the 4 zinc-fingers of one of the histone methyl-transferase I’m working on. On the figures, blue is positively charged, and red is negative. The large positive (blue) area will bind to the DNA. But, on the other face, there is room for binding to some positively charged partners. Fascinating!

Saturday 21st, I ran the Turkey Trot’09 (10K) in Davis. It was fun as usual and a somewhat easy 10K.  However the weather was not so great: foggy, wet, slippery and cold. But what a great crowd to cheers us up! I just love Davis and I will miss it very much. This year I ran it in 43 minutes, beating my last year time of 48 minutes. I’m happy with that!….do you like my hair?

Since I have some time-off for the next few weeks before staring my new exiting job, I took advantage of today’s great weather to spend some time flying around, just for the heck of flying. I took off KEDU (UC Davis airport called University airport) using runway 17 then I made a 90 right-turn to the west and climb to 4500ft.

The climb to cruising altitude was really smooth, thanks to the temperature inversion. However the downside of a temperature inversion is bad to poor visibility of such air masses. After few minutes I was overflying Winters and decided to head north for a little while. No other aircrafts were around me and the radio was quiet. Perfect!

After some time, I headed back to Davis and started my descent while turning over Winters. I overflew KEDU at 1600ft then descended a bit to 1400ft to stay underneath SMF airspace. After few moments of flying south Davis, I overflew the city to take some photos of downtown Davis. Not easy to fly with one hand and take pictures with the other.

As usual I had a great time. I can’t get enough of that!

Over the last months, I have been monitoring in disbelief the number of “comments-spams ” that hit my website: 4,464 since March 23. Too me, it is way too many for a website that gets an average of 10 legitimate visits per days. I absolutely can’t wrap my mind around the fact that somewhere an army of bots/zombie PC are burning a lot of CPU and bandwidth to vomit a load of nonsense comments on websites…Thankfully, the spam gets caught in powerful filters such as Akismet. So far 99.955% of the comments are junk on my site…It leads to the question: “How much energy can we save if we take down all the spam-servers?, how much bandwidth can we save?

I finally put together a quickly made movie about some of my flights in California. As you may know by now, is that I love flying. But I love even more sharing it with friends. This video is all about the great times I had so far with my friends, flying around just for the heck of flying or for sightseeing from the sky. California is awesome (obviously), but it is even better from high above…

I recently came across this excellent commentary by Brian Matthews on the 5 (five…) papers Chang et al. retracted back in 2006. For those not familiar with X-ray crystallography and the Changs papers withdraw from leading scientific publishers, I give you a bit of explanation. X-ray crystallography is the gold standard in structure determination and it uses a crystal of pure molecular specie(s) shot through an X-ray beam. If the crystal is good, the electron clouds of the atoms diffract the x-ray beam. By recording various diffractions images, one can compute the electron density inside the crystal and trace (build) the molecular specie(s) in it. Sound simple enough? actually no. I’m not talking here about the maths and physics involved and the phasing problem. The essence of  X-ray crystallography is to solve the phase problem leading to having “good” and “reliable” maps of electron density.

What happened to Chang et al., is that they were working with some wrong electron density maps because of a gross error made early-on during the project pipeline. The culprit was an in-house data reduction program that switched critical column of data. Because of this error, they build/trace various proteins with the “wrong” hand.

Brian Matthews commentary is a solid X-ray crystallography 101 lesson. A lot have been said and written about Chang et al. mistake and their consequences. But, Brian Matthews point out that nowadays we are seeing an ever-increasing use of “black-box” procedures for structure determinations. The rapid development of easy to use X-ray crystallography softwares along with massive computing power render the structure determination fairly easy for one with limited X-ray crystallography knowledge. Solving a structure can be fairly straightforward but it can easily become a tricky task. In any cases but especially in tricky cases, one needs to be extremely cautious about the validity of the maps. Brian Matthews gave us a great lesson about the various checking we all should do when dealing with problems encountered by Chang et al.

X-ray crystallography is like anything else, it is an art. It requires experience, failures, learning from failures and constant knowledge update. Like everything else in Science, it is a grave mistake to assume that we master all the whereabouts of a technology/methodology. I guess, Chang et al. learnt it the hard way. However it raises another question: Shall we seek advice from a peer to help solving a problem in case of dealing with a very hot project? All the 5 retracted papers were all hot projects…

The take home message from this is to be über-cautious and don’t take nice looking maps for granted…