Self-organized perturbations enhance class IV behavior and 1/f power spectrum in elementary cellular automata

In this paper, we propose a new class of cellular automata based on the modification of its state space. It is introduced to model a computation which is exposed to an environment. We formalized the computation as extension and projection processes of its state space and resulting misidentifications of the state. This is motivated to embed the role of an environment into the system itself, which naturally induces self-organized internal perturbations rather than the usual external perturbations. Implementing this structure into the elementary cellular automata, we characterized its effect by means of input entropy and power spectral analysis. As a result, the cellular automata with this structure showed robust class IV behavior and a 1/f power spectrum in a wide range of rule space comparative to the notion of the edge of chaos.     

Effects of dung beetles on seedling emergence from herbaceous seeds in the dung of sika deer (<Emphasis Type="Italic">Cervus nippon</Emphasis>) in a temperate Japanese grassland ecosystem

The effects of dung form and condition and of dung beetles on the emergence of seedlings from herbaceous seeds in sika deer dung were examined in a temperate grassland ecosystem dominated by Zoysia japonica and Hydrocotyle maritima. I conducted field experiments to compare seedling emergence between dung exposed to dung beetles and intact dung using both dung pellets and pats during a typical rainy month (June) and the hottest, drier month (August), when large numbers of seeds of the dominant species were present in the dung. The exposed dung was immediately attacked and broken up by dung beetles, whereas dung protected from the beetles remained intact. In June, at least 12 herbaceous species, including Z. japonica, H. maritima, Mazus pumilus, and Plantago asiatica, emerged from the dung, versus at least six species in August. Decomposition rates of the pellets in June and decomposition scores of the pats in June and August were positively correlated with the number of emerging seedlings, suggesting that the acceleration of decomposition by dung beetles can positively affect seed germination. In this system of interactions among sika deer, herbaceous plants, and dung beetles, sika deer dung prevented seeds from germinating, and beetles had an indirect positive effect on seedling emergence by accelerating decomposition of the dung, although the extent of the effect may depend on the dung type, plant species, and environmental factors.     

Pioglitazone ameliorates endothelial dysfunction in obese rats with nephropathy

Endothelial dysfunction is a key event in the development of renovascular complications in the metabolic syndrome. The aim of this study was to elucidate the pathogenetic mechanisms involved in renovascular injuries in the Zucker obese rat, a model of the metabolic syndrome, and to examine the therapeutic effects of pioglitazone, a thiazolidinedione. Obese rats fed high-protein diet (OHP) for 12 weeks exhibited nephropathy and endothelial dysfunction, which were improved by pioglitazone. Accumulation of nitrotyrosine, a tracer of nitrative stress, was increased in aorta of the OHP group. The mRNA expressions of NADPH oxidase components and inducible nitric oxide synthase in the aorta were enhanced in the OHP group. Pioglitazone reduced nitrotyrosine in the aorta of the OHP group, inhibiting the augmented expression levels of both. These results suggest that nitrative stress could cause endothelial dysfunction in the rat model of metabolic syndrome with nephropathy, and that pioglitazone ameliorates these injuries, presumably by reducing nitrative stress.     

Engineering the elongation factor Tu for efficient selenoprotein synthesis

Selenocysteine (Sec) is naturally co-translationally incorporated into proteins by recoding the UGA opal codon with a specialized elongation factor (SelB in bacteria) and an RNA structural signal (SECIS element). We have recently developed a SECIS-free selenoprotein synthesis system that site-specifically—using the UAG amber codon—inserts Sec depending on the elongation factor Tu (EF-Tu). Here, we describe the engineering of EF-Tu for improved selenoprotein synthesis. A Sec-specific selection system was established by expression of human protein O⁶-alkylguanine-DNA alkyltransferase (hAGT), in which the active site cysteine codon has been replaced by the UAG amber codon. The formed hAGT selenoprotein repairs the DNA damage caused by the methylating agent N-methyl-N′-nitro-N-nitrosoguanidine, and thereby enables Escherichia coli to grow in the presence of this mutagen. An EF-Tu library was created in which codons specifying the amino acid binding pocket were randomized. Selection was carried out for enhanced Sec incorporation into hAGT; the resulting EF-Tu variants contained highly conserved amino acid changes within members of the library. The improved UTu-system with EF-Sel1 raises the efficiency of UAG-specific Sec incorporation to >90%, and also doubles the yield of selenoprotein production.     

Roles of base excision repair enzymes Nth1p and Apn2p from Schizosaccharomyces pombe in processing alkylation and oxidative DNA damage

Schizosaccharomyces pombe Nthpl, an ortholog of the endonuclease III family, is the sole bifunctional DNA glycosylase encoded in its genome. The enzyme removes oxidative pyrimidine and incises 3' to the apurinic/apyrimidinic (AP) site, leaving 3'-alpha,beta-unsaturated aldehyde. Analysis of nth1 cDNA revealed an intronless structure including 5'- and 3'-untranslated regions. An Nth1p-green fluorescent fusion protein was predominantly localized in the nuclei of yeast cells, indicating a nuclear function. Deletion of nth1 confirmed that Nth1p is responsible for the majority of activity for thymine glycol and AP site incision in the absence of metal ions, while nth1 mutants exhibit hypersensitivity to methylmethanesulfonate (MMS). Complementation of sensitivity by heterologous expression of various DNA glycosylases showed that the methyl-formamidopyrimidine (me-fapy) and/or AP sites are plausible substrates for Nth1p in repairing MMS damage. Apn2p, the major AP endonuclease in S. pombe, also greatly contributes to the repair of MMS damage. Deletion of nth1 from an apn2 mutant resulted in tolerance to MMS damage, indicating that Nth1p-induced 3'-blocks are responsible for MMS sensitivity in apn2 mutants. Overexpression of Apn2p in nth1 mutants failed to suppress MMS sensitivity. These results indicate that Nth1p, not Apn2p, primarily incises AP sites and that the resultant 3'-blocks are removed by the 3'-phosphodiesterase activity of Apn2p. Nth1p is dispensable for cell survival against low levels of oxidative stress, but wild-type yeast became more sensitive than the nth1 mutant at high levels. Overexpression of Nth1p in heavily damaged cells probably induced cell death via the formation of 3'-blocked single-strand breaks.     

Photo-induced DNA cleavage reaction characteristics of propargylic sulfones possessing anthraquinone chromophore

DNA cleavage potency of propargylic sulfones possessing anthraquinone chromophore 1 under UV-irradiation was evaluated in comparison with the dark reaction. 1 showed inefficient DNA cleavage activity, while having considerably strong DNA binding ability. This result is accounted for by spatial conditions that the activated alkylating allenic site of intercalated 1 could not effectively approach to DNA bases, most probably guanine moiety, and thereby led to insufficient DNA strand cleavage. In contrast, the DNA cleavage activity of 1 was notably enhanced upon UV-irradiation (lambda(ex)=365 nm) followed by incubation. Under UV-irradiation, further DNA cleavage were occurred primary at 5'-G of GG steps within DNA. A DNA cleavage mechanism for 1, by which photo-induced one-electron oxidation of 5'-G of GG steps may occur along with ordinary alkylation, has been proposed.     

Minimal model of a cell connecting amoebic motion and adaptive transport networks

A cell is a minimal self-sustaining system that can move and compute. Previous work has shown that a unicellular slime mold, Physarum, can be utilized as a biological computer based on cytoplasmic flow encapsulated by a membrane. Although the interplay between the modification of the boundary of a cell and the cytoplasmic flow surrounded by the boundary plays a key role in Physarum computing, no model of a cell has been developed to describe this interplay. Here we propose a toy model of a cell that shows amoebic motion and can solve a maze, Steiner minimum tree problem and a spanning tree problem. Only by assuming that cytoplasm is hardened after passing external matter (or softened part) through a cell, the shape of the cell and the cytoplasmic flow can be changed. Without cytoplasm hardening, a cell is easily destroyed. This suggests that cytoplasmic hardening and/or sol-gel transformation caused by external perturbation can keep a cell in a critical state leading to a wide variety of shapes and motion.