The cellular computer DNA: Program or data

The classical metaphor of the genetic program written in the DNA nucleotidic sequences is reconsidered. Recent works on algorithmic complexity and logical properties of computer programs and data are used to question the explanatory value of that metaphor. Structural properties of strings are looked for which would be necessary to apply to DNA sequences if the metaphor is to be taken literally. The notion of sophistication is used to quantify meaningful complexity and to distinguish it from classical computational complexity. In this context, the distinction between program and data becomes relevant and an alternative metaphor of DNA as data to a parallel computing network embedded in the global geometrical and biochemical structure of the cell is discussed. An intermediate picture of an evolving network emerges as the most likely where the output of the cellular computing network can produce, at a different time scale, changes in the structure of the network itself by means of changes in the DNA activity patterns.     

Transient association of MCM complex proteins with the nuclear matrix during initiation of mammalian DNA replication

The minichromosome maintenance complex (MCM2-7) is the putative DNA helicase in eukaryotes, and essential for DNA replication. By applying serial extractions to mammalian cells synchronized by release from quiescence, we reveal dynamic changes to the sub-nuclear compartmentalization of MCM2 as cells pass through late G1 and early S phase, identifying a brief window when MCM2 becomes transiently attached to the nuclear-matrix. The data distinguish 3 states that correspond to loose association with chromatin prior to DNA replication, transient highly stable binding to the nuclear-matrix coincident with initiation, and a post-initiation phase when MCM2 remains tightly associated with chromatin but not the nuclear-matrix. The data suggests that functional MCM complex loading takes place at the nuclear-matrix.     

Carboplatin-containing porphyrin-platinum complexes as cytotoxic and phototoxic antitumor agents

Tetraarylporphyrins of the Ar:Ar′ = 3:1-type were synthesized from pyrrole, 4-hydroxybenzaldehyde and benzaldehydes substituted with ethyleneglycol, hydroxy and quaternary ammonium substituents for solubilization in DMF and, in particular, in water. After etherification with the tosylate of diethyl cyclobutanedicarboxylate and subsequent ester hydrolysis, the resulting carboxylic acid groups were used to bind platinum fragments bearing two ammonia and (RR/SS)-trans-1,2-diaminocyclohexane ligands, respectively, as non-leaving groups. In comparison to hematoporphyrin-platinum complexes, the title compounds show a 30 nm bathochromic shift of their absorption bands increasing the penetration depth of the red light used for irradiation in photodynamic tumor therapy. The antiproliferative activity of 24 new platinum complexes differing in the porphyrin ligands and the platinum fragments were studied in tests with J82 bladder cancer cells. The compounds showed the cytotoxic effect of the platinum moiety and after irradiation the phototoxic effect of the porphyrin system.     

Total synthesis and evaluation of 22-(3-azidobenzoyloxy)methyl epothilone C for photoaffinity labeling of β-tubulin

The total synthesis of 22-(3-azidobenzoyloxy)methyl epothilone C is described as a potential photoaffinity probe to elucidate the β-tubulin binding site. A sequential Suzuki-aldol-Yamaguchi macrolactonization strategy was utilized employing a novel derivatized C1–C6 fragment. The C22-functionalized analog exhibited good activity in microtubule assembly assays, but cytotoxicity was significantly reduced. Molecular modeling simulations indicated that excessive steric bulk in the C22 position is accommodated by the large hydrophobic pocket of the binding site. Photoaffinity labeling studies were inconclusive suggesting non-specific labeling.     

Rapid lake mapping using a portable Laser Rangefinder

A lightweight LRF 104 laser rangefinder was used in lake mapping. As an example, the Malha crater (Darfur, West-Sudan), containing a lake, springs, wells, and vegetation, was mapped.     

Streptocephalus caljoni n.sp. (Crustacea: Anostraca) from Burundi and analysis of its limb structure

Streptocephalus caljoni n. sp. from Burundi is described. It is related to Streptocephalus trifidus, but differs from it and other Streptocephalus in the cheliform hand of the male antenna II. We also analyse the morphology of the setae on the endo- and exopodite of the fifth trunk limb, using light- and scanning electron microscopy. This analysis reveals additional differences between the two related species, and is a useful tool in the study of the taxonomy of the Anostraca.