From Subaging to Hyperaging in Structural Glasses.

We demonstrate nonequilibrium scaling laws for the aging and equilibration dynamics in glass formers that emerge from combining a relaxation equation for the static structure with the equilibrium scaling laws of glassy dynamics. Different scaling regimes are predicted for the evolution of the structural relaxation time τ with age (waiting time t_{w}), depending on the depth of the quench from the liquid into the glass: "simple" aging (τ∼t_{w}) applies for quenches close to the critical point of mode-coupling theory (MCT) and implies "subaging" (τ≈t_{w}^{δ} with δ<1) as a broad equilibration crossover for quenches to nearly arrested equilibrium states; "hyperaging" (or superaging, τ∼t_{w}^{δ^{'}} with δ^{'}>1) emerges for quenches deep into the glass. The latter is cut off by non-mean-field fluctuations that we account for within a recent extension of MCT, the stochastic β-relaxation theory (SBR).

AFM imaging and theoretical modeling studies of sequence-dependent nucleosome positioning.

Telomeric chromatin has different features with respect to bulk chromatin, since nucleosomal repeat along the chain is unusually short. We studied the role of telomeric DNA sequences on nucleosomal spacing in a model system. Nucleosomal arrays, assembled on a 1500-bp-long human telomeric DNA and on a DNA fragment containing 8 copies of the 601 strong nucleosome positioning sequence, have been studied at the single molecule level, by atomic force microscopy imaging.

Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor, and RNA polymerase subunit sequences.

The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, and S3 encoded in the S10 operon (833 aa positions); (ii) the joint sequences of the elongation factors Tu(1alpha) and G(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint RNA polymerase beta- and beta'-type subunits encoded in the rpoBC operon (1130 aa positions). Phylogenies of r-protein and EF sequences support with moderate (r-proteins) to high statistical confidence (EFs) the placement of the two hyperthermophiles at the base of the bacterial clade in agreement with phylogenies of rRNA sequences. In the more robust EF-based phylogenies, the branching of Aquifex and Thermotoga below the successive bacterial lineages is given at bootstrap proportions of 82% (maximum likelihood; ML) and 85% (maximum parsimony; MP), in contrast to the trees inferred from the separate EF-Tu(1alpha) and EF-G(2) data sets, which lack both resolution and statistical robustness.

The archaea monophyly issue: A phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions.

A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and protein databases with representative EF-G(2) sequences.

Hebbian learning of context in recurrent neural networks.

Single electrode recording in the inferotemporal cortex of monkeys during delayed visual memory tasks provide evidence for attractor dynamics in the observed region. The persistent elevated delay activities could be internal representations of features of the learned visual stimuli shown to the monkey during training. When uncorrelated stimuli are presented during training in a fixed sequence, these experiments display significant correlations between the internal representations.

Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences.

The gene fus (for EF-G) of the hyperthermophilic bacterium Aquifex pyrophilus was cloned and sequenced. Unlike the other bacteria, which display the streptomycin-operon arrangement of EF genes (5'-rps12-rps7-fus-tuf-3'), the Aquifex fus gene (700 codons) is not preceded by the two small ribosomal subunit genes although it is still followed by a tuf gene (for EF-Tu). The opposite strand upstream from the EF-G coding locus revealed an open reading frame (ORF) encoding a polypeptide having 52.

Influence of DNA superstructural features and histone amino-terminal domains on nucleosome positioning.

Nucleosome positioning has been studied on a strongly curved 268 bp DNA fragment from a Crithidia fasciculata kinetoplast, complexed with a histone octamer either normal or lacking amino-terminal domains. A very similar nucleosome multiple positioning, with the same rotational phasing, has been found, by Exo III mapping, in both cases. The experimental positioning is in fairly good agreement with that predicted using a theoretical method based on DNA distortion energy, derived from the nucleotide sequence.

Mevalonate-derived proteins in liver regeneration.

Sixteen hours after partial hepatectomy in the rat, the synthesis of mevalonate (MVA) is not committed to produce cholesterol and only partially utilized for dolichol formation. In order to investigate the fate of MVA in this replicative system, slices of the remaining liver were incubated with 5-3H-MVA. Labeled proteins from whole liver and purified nuclei were analyzed after extensive delipidation and separation by SDS-PAGE.

Circannual variations in mevalonate utilization in frog (Rana esculenta).

1. The fate of mevalonate, the product of HMGCoA reductase, was studied in male and female frogs (Rana esculenta) in order to explain the circannual variations of enzyme activity. 2.

Changes in lipoprotein binding and uptake by hepatocytes during rat liver regeneration.

The binding and uptake of cholesterol enriched lipoproteins by isolated hepatocytes was decreased at 16 hours after partial hepatectomy, with a tendency to return to control values as the regeneration proceeds. The number of lipoprotein binding sites of total cellular membranes remained similar to control at 16 and 24 hours. The plasma lipoprotein pattern, determined by electrophoretic analysis, showed a lower per cent of very low density lipoproteins (VLDL) and a higher per cent of low density lipoproteins (LDL) at 16 and 24 hours post-partial hepatectomy.

Cholesterol metabolism in frog (Rana esculenta) liver: seasonal and sex-related variations.

Many aspects of lipid metabolism have been studied in amphibians, but seasonal lipid modulation in male and female frogs has not been investigated. We describe here the yearlong patterns of hepatic lipid content and enzyme activities related to cholesterol homeostasis, 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase activity and acyl coenzyme A:cholesterol acyltransferase (ACAT) activity in liver of the male and female frog, Rana esculenta. Lipid storage follows distinct seasonal patterns, with an increase in June that is more pronounced in the female than in the male frog.