Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments

Deciphering the mechanism of functioning of DNA as the carrier of genetic information requires identifying inherent factors determining its structure and function. Following this path, our previous DFT studies attributed the origin of unique conformational characteristics of right-handed Watson-Crick duplexes (WCDs) to the conformational profile of deoxydinucleoside monophosphates (dDMPs) serving as the minimal repeating units of DNA strand. According to those findings, the directionality of the sugar-phosphate chain and the characteristic ranges of dihedral angles of energy minima combined with the geometric differences between purines and pyrimidines determine the dependence on base sequence of the three-dimensional (3D) structure of WCDs. This work extends our computational study to complementary deoxydinucleotide-monophosphates (cdDMPs) of non-standard conformation, including those of Z-family, Hoogsteen duplexes, parallel-stranded structures, and duplexes with mispaired bases. For most of these systems, except Z-conformation, computations closely reproduce experimental data within the tolerance of characteristic limits of dihedral parameters for each conformation family. Computation of cdDMPs with Z-conformation reveals that their experimental structures do not correspond to the internal energy minimum. This finding establishes the leading role of external factors in formation of the Z-conformation. Energy minima of cdDMPs of non-Watson-Crick duplexes demonstrate different sequence-dependence features than those known for WCDs. The obtained results provide evidence that the biologically important regularities of 3D structure distinguish WCDs from duplexes having non-Watson-Crick nucleotide pairing.     

PI3K/Akt Cooperates with Oncogenic Notch by Inducing Nitric Oxide-Dependent Inflammation

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Forum – Taxonomic Stability is Ignorance

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990: Syst. Zool. 39, 307–322; 1992: A. Rev. Ecol. Syst. 23, 449–480; 1994: Trends Ecol. Evol. 9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.     

Seasonal changes of the Leydig cells of viscacha (Lagostomus maximus maximus). A light and electron microscopy study

The Leydig cells of viscacha (seasonal rodent) show cytoplasmic hypertrophy and regional distribution during the breeding period (summer-autumn). The dominant organelles are smooth endoplasmic reticulum (SER) and mitochondria. A moderately well-developed Golgi, abundant lipid inclusions, dense bodies like lysosomes in different stages, and centrioles are observed. Extensive or focal desmosome and gap-like junctions between neighbouring Leydig cells are present. These cells exhibit an evident hypotrophy and an increase in the number of dense bodies during the gonadal regression in winter (July and August). Cells in different stages of involution are observed in this period. Their nuclei are irregular and heterochromatic. The cytoplasm contains few mitochondria. The vesicular SER is scarse. Irregular and large intercellular spaces with microvilli and amorphous material are present. The junctional complexes are absent. The nuclear and cytoplasmic volume and development of SER and mitochondria increase during the recovery period (spring). The lipid inclusions decrease. Dilatations of the intercellular space with microvilli and limited by focal desmosome-like junctions are observed. In conclusion, the Leydig cells of Lagostomus maximus maximus show deep changes alongside the reproductive cycle. The photoperiod variations, through pineal hypothalamus pituitary axis and the hormone melatonin, are probably responsible for them. Moreover, the fall of serum and tubular testosterone would be one of the factors responsible for gonadal regression.     

Morpho-histochemical changes in the liver and intestine of young giltheads (fish-nursery), Sparus aurata, L., induced by acute action of the anionic tensioactive alkylbenzene sulphonate.

In the present study we have assessed the effect on the survival and the morpho-histochemical changes in the liver and intestine of young giltheads (fish-nursery), Sparus aurata, L., induced by acute action of the anionic tensioactive, alkyl benzene sulphonate (ABS). Firstly, the LC50 of ABS at 96 hours was found to be 0.6 mg/L. Secondly, lots with 50 young giltheads (fish-nursery) were exposed to ABS concentrations of 0.5, 1, 3 and 5 mg/L, to obtain the surface tension value and exposure time required for 50% mortality of the specimens at each tested concentration. Exposure to ABS caused several forms of histopathological damage in the liver (the radial arrangement of hepatocytes was lost) and intestine (destruction of the structure of villi and increase in thickness of the other three layers). In addition, changes in bio-macromolecule components (proteins in general, siderophile proteins, neutral mucopolysaccharides, glycogen and acid mucopolysaccharides) were observed. The degree of these alterations was dependent upon the ABS concentration. These changes could have detrimental effects on the growth and survival of the species.     

Lifetime philopatry in the blue-footed booby: a longitudinal study

Philopatry over the lifetime and its relationship with reproductivesuccess were examined using longitudinal records of nest locationand reproduction of individual blue-footed boobies. Males showedshorter natal dispersal than females, and natal dispersal distanceof both sexes were unrelated to either first reproductive successor lifetime reproductive success. Throughout the early lifetime,males and females nested closer to their first breeding sitesthan to their natal sites, and comparison with a simulationof successive breeding dispersals in random directions showedthat male and female blue-footed boobies are philopatric tothe first breeding site. Therefore, throughout the early lifetime,the first breeding site seems to function as a point of referencefor breeding site use together with the previous season's site.Males and females with shorter natal dispersal distances showedstronger lifetime philopatry to their first breeding sites,suggesting stable individual variation in competitive abilityor dispersal phenotype. However, early lifetime philopatry tofirst breeding sites was unrelated to annual breeding success.Compared with simple fidelity to previous breeding sites, lifetimephilopatry to first breeding sites should result in increasedkin interactions and greater selection for kin recognition,altruism and inbreeding avoidance, as well as long-term familiaritywith neighbors.     

Trafficking, assembly, and function of a connexin43-green fluorescent protein chimera in live mammalian cells.

To examine the trafficking, assembly, and turnover of connexin43 (Cx43) in living cells, we used an enhanced red-shifted mutant of green fluorescent protein (GFP) to construct a Cx43-GFP chimera. When cDNA encoding Cx43-GFP was transfected into communication-competent normal rat kidney cells, Cx43-negative Madin-Darby canine kidney (MDCK) cells, or communication-deficient Neuro2A or HeLa cells, the fusion protein of predicted length was expressed, transported, and assembled into gap junctions that exhibited the classical pentalaminar profile. Dye transfer studies showed that Cx43-GFP formed functional gap junction channels when transfected into otherwise communication-deficient HeLa or Neuro2A cells. Live imaging of Cx43-GFP in MDCK cells revealed that many gap junction plaques remained relatively immobile, whereas others coalesced laterally within the plasma membrane. Time-lapse imaging of live MDCK cells also revealed that Cx43-GFP was transported via highly mobile transport intermediates that could be divided into two size classes of <0.5 microm and 0.5-1.5 microm. In some cases, the larger intracellular Cx43-GFP transport intermediates were observed to form from the internalization of gap junctions, whereas the smaller transport intermediates may represent other routes of trafficking to or from the plasma membrane. The localization of Cx43-GFP in two transport compartments suggests that the dynamic formation and turnover of connexins may involve at least two distinct pathways.     

Roles for alpha(2)p24 and COPI in endoplasmic reticulum cargo exit site formation.

A two-step reconstitution system for the generation of ER cargo exit sites from starting ER-derived low density microsomes (LDMs; 1.17 g/cc) is described. The first step is mediated by the hydrolysis of Mg(2+)ATP and Mg(2+)GTP, leading to the formation of a transitional ER (tER) with the soluble cargo albumin, transferrin, and the ER-to-Golgi recycling membrane proteins alpha(2)p24 and p58 (ERGIC-53, ER-Golgi intermediate compartment protein) enriched therein. Upon further incubation (step two) with cytosol and mixed nucleotides, interconnecting smooth ER tubules within tER transforms into vesicular tubular clusters (VTCs). The cytosolic domain of alpha(2)p24 and cytosolic COPI coatomer affect VTC formation. This is deduced from the effect of antibodies to the COOH-terminal tail of alpha(2)p24, but not of antibodies to the COOH-terminal tail of calnexin on this reconstitution, as well as the demonstrated recruitment of COPI coatomer to VTCs, its augmentation by GTPgammaS, inhibition by Brefeldin A (BFA), or depletion of beta-COP from cytosol. Therefore, the p24 family member, alpha(2)p24, and its cytosolic coat ligand, COPI coatomer, play a role in the de novo formation of VTCs and the generation of ER cargo exit sites.