Friday, October 29, 2010

Hidden code in proteins

There are 64 combinations of DNA-base triplets that code for the 20 amino acids, and STOP codes. As such there exists redundancy in which more than one triplet codes for the same amino acid. So far it was unclear why this could be, and unknown what function it might serve.

In a recent study, it was shown that different triplets actually result in fast or slow transcription, and thus giving mRNA more flexibility. Kashina and co-workers reported in the study that it is possible to change the arginylation of β- and γ-actin by playing around with these triplets. Since slower transcription leads to exposure of a hidden lysine, it results in ubiquitination (degradation of the protein). Thus, this study reveals for the first time the hidden code in protein coding, as described also in this highlight.

Sunday, October 17, 2010

Scientist Impact Factors (SIF)

Nowadays the impact of a scientist's work is as important as the work itself. And of course, there are many many different ways of measuring this impact: (i) number of citations, (ii) h-index, (iii) publish or perish, etc. Of course, for all of these self-citations are an important issue to be taken care of. There are many pro's and con's for any measure, e.g. the h-index has been suggested to be replaced by a g-index. Both the h- and g-index measure the combination of productivity and impact, but the values are calculated differently. A h-index of 20 means that the author has at least 20 papers that are cited at least 20 times. The g-index corresponds to the (unique) largest number such that the top g articles received (together) at least g2 citations.

Another much more simple measure has so far not been discussed, and which is related to the impact factor for journals. For a given year, say 2008, one looks at the total number of citations for papers in the journal from the years 2006 and 2007 (A), and divide it by the total number of papers in the journal for the years 2006 and 2007 (B). The impact factor is then given by A/B.

Of course, the same procedure could be applied to scientists. I have had to update my statistics recently for a research proposal, so was in an unique position to generate the data. In the figure below, I have plotted my Scientist Impact Factor (SIF) for the years 1998-2009 (also indicated is the one for 2010, although there the statistics is not finished yet).


As one can see, there is a gradual improvement of the SIF, reaching a respectable 7.67 (5.25 without self-citations) for 2009. This SIF measure (without self-citations) might thus be used as additional measure for measuring the impact of a scientist's work, and complement the total number of citations and the h-index.

Friday, October 15, 2010

Sílvia Osuna leaving for the States

Today dr. Sílvia Osuna has moved to the USA, for a two-year period as Marie Curie IOF Fellow at the group of prof. Houk (UCLA).


She will be badly missed! But luckily she will return to Girona for her third year of the Marie Curie fellowship.

Monday, October 4, 2010

Lost correspondence of Francis Crick

Francis Crick is best known for his 1953 paper in Nature together with James Watson about the structure of DNA, which they put together with data from Rosalind Franklin and Ray Gosling.
In fact, this was their second attempt after a fatally flawed proposed structure where the phosphates were on the inside. Many books have been written about this period in the UK, because there were many things happening: misappropriation of scientific data, infighting, competition between different research labs, personal antipathies. And of course, the awarding of the Nobel prize to Crick, Watson and Wilkins in 1962: this was the only objective of honest Jim Watson. (unfortunately, the one person who made it all possible, Rosalind Franklin, and without whose data the others would not have been able to propose the DNA structure, by that time had passed away and was therefore not eligible for the Nobel prize).

The best and most objective book about this period is undoubtedly the biography of Rosalind Franklin ("Rosalind Franklin: The Dark Lady of DNA") by Brenda Maddox, which followed decades after the publication of "The Double Helix" by Jim Watson, and "What Mad Pursuit" by Francis Crick.

Much of the details remained however unclear, also because the correspondence of Francis Crick was apparently lost in the 1970s; now it turns out that it just had been misplaced, and many new details about this period has become clear, as reported recently in Nature. An interesting read!
Nature comments

PS. Note also the review in Nature of a play by Anna Ziegler entitled Photograph 51.

Saturday, October 2, 2010

SSB-D functional in NWChem 6.0

Last week the latest version of NWChem (6.0) was announced, which contains the SSB-D functional in it.

After the inclusion in ADF, this is now the second main Quantum-Chemistry program that contains SSB-D, with more to follow (Turbomole, Gamess-US?, Orca?, Gaussian?).

Friday, October 1, 2010

Premi Extraordinari de Doctorat for Mireia Güell

Yesterday the tribunal has decided to award the Premi Extraordinari de Doctorat en Química 2009 to dr. Mireia Güell for her thesis entitled: "Theoretical Studies of Systems of Biochemical Interest Containing Fe and Cu Transition Metals".

For her thesis she had already received the grade excel· lent cum laude.


The official award description can be found here.

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