How do nitrogen and phosphorus deficiencies affect strigolactone production and exudation?

Plants exude strigolactones (SLs) to attract symbiotic arbuscular mycorrhizal fungi in the rhizosphere. Previous studies have demonstrated that phosphorus (P) deficiency, but not nitrogen (N) deficiency, significantly promotes SL exudation in red clover, while in sorghum not only P deficiency but also N deficiency enhances SL exudation. There are differences between plant species in SL exudation under P- and N-deficient conditions, which may possibly be related to differences between legumes and non-legumes. To investigate this possibility in detail, the effects of N and P deficiencies on SL exudation were examined in Fabaceae (alfalfa and Chinese milk vetch), Asteraceae (marigold and lettuce), Solanaceae (tomato), and Poaceae (wheat) plants. In alfalfa as expected, and unexpectedly in tomato, only P deficiency promoted SL exudation. In contrast, in Chinese milk vetch, a leguminous plant, and in the other non-leguminous plants examined, N deficiency as well as P deficiency enhanced SL exudation. Distinct reductions in shoot P levels were observed in plants grown under N deficiency, except for tomato, in which shoot P level was increased by N starvation, suggesting that the P status of the shoot regulates SL exudation. There seems to be a correlation between shoot P levels and SL exudation across the species/families investigated.     

Habitat structure determines spider diversity in highland ponds

Wetlands (e.g. ponds, meadows) can be found in many landscapes, playing an important role in maintaining regional biodiversity and supporting heterogeneous communities. Spiders are diversified predators that are highly influenced by changes in plant community structure, heterogeneous habitats sustain high spider diversity and abundance. We investigated the characteristics of spider biodiversity in ponds with different habitat structures, by examining patterns across habitats of ponds with different vegetation levels. Sampling took place in four occasions over a year. We compared spider abundance, species richness and composition among ponds including distinct vegetation variables, related to life form, type of leaves, coverage and height. Overall 1174 individuals (194 adults) of 11 families and 37 morphospecies were sampled. We found mostly expected differences in the manner that communities were structured between different habitats. Thus, higher variability of abundance was explained for higher habitat structure of ponds. We also found differences in species composition between ponds with low emergent vegetation and higher habitat structures. Additionaly, spiders were consistently structured more by turnover than nestedness components, with a greater beta diversity of web-builders. Our results suggest varying levels of habitat structures and species substitution shape pond spider communities, depending on habitat heterogeneity and spider guild. Those findings demonstrate the clear role of spatial habitat structure, with more spider species preferring to build webs or actively hunt at vegetated environments on ponds.     

Evolutionary change of the numbers of homeobox genes in bilateral animals

It has been known that the conservation or diversity of homeobox genes is responsible for the similarity and variability of some of the morphological or physiological characters among different organisms. To gain some insights into the evolutionary pattern of homeobox genes in bilateral animals, we studied the change of the numbers of these genes during the evolution of bilateral animals. We analyzed 2,031 homeodomain sequences compiled from 11 species of bilateral animals ranging from Caenorhabditis elegans to humans. Our phylogenetic analysis using a modified reconciled-tree method suggested that there were at least about 88 homeobox genes in the common ancestor of bilateral animals. About 50-60 genes of them have left at least one descendant gene in each of the 11 species studied, suggesting that about 30-40 genes were lost in a lineage-specific manner. Although similar numbers of ancestral genes have survived in each species, vertebrate lineages gained many more genes by duplication than invertebrate lineages, resulting in more than 200 homeobox genes in vertebrates and about 100 in invertebrates. After these gene duplications, a substantial number of old duplicate genes have also been lost in each lineage. Because many old duplicate genes were lost, it is likely that lost genes had already been differentiated from other groups of genes at the time of gene loss. We conclude that both gain and loss of homeobox genes were important for the evolutionary change of phenotypic characters in bilateral animals.     

Active accumulation of gold nanorods in tumor in response to near-infrared laser irradiation

Gold nanorods, rod-shaped gold nanoparticles, have strong absorbance in the near-infrared region, and the absorbed light energy can be converted to heat, the so-called photothermal effect. The gold nanorods were coated with thermoresponsive polymers, which have different phase transition temperatures that were controlled by adding comonomers, N,N-dimethylacrylamide (DMAA) or acrylamide (AAm) to N-isopropylacrylamide (NIPAM). The phase transition temperatures of poly(NIPAM-DMAA) and poly(NIPAM-AAm)-coated gold nanorods were 38 and 41 °C, respectively, while polyNIPAM-coated gold nanorods showed phase transition at 34 °C. Irradiation of the coated gold nanorods using the near-infrared laser induced a decrease in their sizes due to a phase transition of the polymer layers. Poly(NIPAM-AAm)-coated gold nanorods stably circulated in the blood flow without a phase transition after intravenous injection. Irradiation of near-infrared light at a tumor after the injection resulted in the gold specifically accumulating in the tumor. This novel accumulation technique which combines a thermoresponsive polymer and the photothermal effect of the gold nanorods should be a powerful tool for targeted delivery in response to light irradiation.     

Structural basis of free reduced flavin generation by flavin reductase from Thermus thermophilus HB8

Free reduced flavins are involved in a variety of biological functions. They are generated from NAD(P)H by flavin reductase via co-factor flavin bound to the enzyme. Although recent findings on the structure and function of flavin reductase provide new information about co-factor FAD and substrate NAD, there have been no reports on the substrate flavin binding site. Here we report the structure of TTHA0420 from Thermus thermophilus HB8, which belongs to flavin reductase, and describe the dual binding mode of the substrate and co-factor flavins. We also report that TTHA0420 has not only the flavin reductase motif GDH but also a specific motif YGG in C terminus as well as Phe-41 and Arg-11, which are conserved in its subclass. From the structure, these motifs are important for the substrate flavin binding. On the contrary, the C terminus is stacked on the NADH binding site, apparently to block NADH binding to the active site. To identify the function of the C-terminal region, we designed and expressed a mutant TTHA0420 enzyme in which the C-terminal five residues were deleted (TTHA0420-ΔC5). Notably, the activity of TTHA0420-ΔC5 was about 10 times higher than that of the wild-type enzyme at 20-40 °C. Our findings suggest that the C-terminal region of TTHA0420 may regulate the alternative binding of NADH and substrate flavin to the enzyme.     

The Shigella OspC3 Effector Inhibits Caspase-4, Antagonizes Inflammatory Cell Death,and Promotes Epithelial Infection

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MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.     

Genetic variability maintained by mutation and overdominant selection in finite populations

Mathematical properties of the overdominance model with mutation and random genetic drift are studied by using the method of stochastic differential equations (Itô and McKean 1974). It is shown that overdominant selection is very powerful in increasing the mean heterozygosity as compared with neutral mutations, and if 2Ns (N = effective population size; s = selective disadvantage for homozygotes) is larger than 10, a very low mutation rate is sufficient to explain the observed level of allozyme polymorphism. The distribution of heterozygosity for overdominant genes is considerably different from that of neutral mutations, and if the ratio of selection coefficient (s) to mutation rate (ν) is large and the mean heterozygosity (h) is lower than 0.2, single-locus heterozygosity is either approximately 0 or 0.5. If h increases further, however, heterozygosity shows a multiple-peak distribution. Reflecting this type of distribution, the relationship between the mean and variance of heterozygosity is considerably different from that for neutral genes. When s/v is large, the proportion of polymorphic loci increases approximately linearly with mean heterozygosity. The distribution of allele frequencies is also drastically different from that of neutral genes, and generally shows a peak at the intermediate gene frequency. Implications of these results on the maintenance of allozyme polymorphism are discussed.