Induction of DNA damage, including abasic sites, in plasmid DNA by carbon ion and X-ray irradiation

DNA from plasmid pUC18 was irradiated with low-LET (13 keV/μm) or high-LET (60 keV/μm) carbon ions or X-rays (4 keV/μm) in solutions containing several concentrations of Tris (0.66–200 mM) to determine the yield of abasic (AP) sites and the effect of scavenging capacity. The yield of AP sites, detected as single-strand breaks (SSB) after digestion with E. coli endonuclease IV (Nfo), was compared with that of SSB and base lesions. At higher concentrations of Tris, the yields of single or clustered AP sites were significantly lower than those of single or clustered base lesions. The relative yields of single AP sites and AP clusters were less than 10 and 7 %, respectively, of the total damage produced at a scavenger capacity mimicking that in cells. The dependence of the yield of AP sites on scavenging capacity was similar to that of prompt strand breaks. The ratios of the yield of isolated AP sites to that of SSB induced by carbon ion or X-ray irradiation were relatively constant at 0.45 ± 0.15 over the tested range of scavenger capacity, although the ratio of SSB to double-strand breaks (DSB) showed the characteristic dependence on both scavenging capacity and radiation quality. These results indicate that the reaction of water radiolysis products, presumably OH radicals, with the sugar-phosphate moieties in the DNA backbone induces both AP sites and SSB with similar efficiency. Direct ionization of DNA is notably more involved in the production of DSB and base lesion clusters than in the production of AP site clusters.     

Genetic and family structure in a group of 165 common bottlenose dolphins caught off the Japanese coast

The biological and genetic structure of common bottlenose dolphins (Tursiops truncatus) that migrate seasonally near Japan remains largely unknown. We investigated the genetic and family structure in a group of 165 common bottlenose dolphins caught off the coast of Japan using mitochondrial DNA (mtDNA) and 20 microsatellite DNA markers. Phylogenetic analysis of the mtDNA control region sequences suggested that the dolphins were related more closely to oceanic types from Chinese waters than other geographic regions. The information on sex, sexual maturation and age together with the genetic markers revealed a strong likelihood for 37 familial relationships related mostly to maternity and an under‐representation of juvenile female offspring. The maternal dolphins had a similar offspring‐birth interval as the coastal types from North Atlantic Ocean, but a slightly younger first‐progeny age. The sex bias in the captured group was particularly marked towards an over‐representation of males among the young and immature dolphins, whereas the mature adults had an equal number of males and females. These results should be useful for future comparative biological, genetic and evolutionary investigations of bottlenose dolphins from the North Pacific Ocean with those from other regions.     

Crystal structure of deltarhodopsin‐3 from Haloterrigena thermotolerans

Deltarhodopsin, a new member of the microbial rhodopsin family, functions as a light‐driven proton pump. Here, we report the three‐dimensional structure of deltarhodopsin (dR3) from Haloterrigena thermotolerans at 2.7 Å resolution. A crystal belonging to space group R32 (a, b = 111.71 Å, c = 198.25 Å) was obtained by the membrane fusion method. In this crystal, dR3 forms a trimeric structure as observed for bacteriorhodopsin (bR). Structural comparison of dR with bR showed that the inner part (the proton release and uptake pathways) is highly conserved. Meanwhile, residues in the protein–protein contact region are largely altered so that the diameter of the trimeric structure at the cytoplasmic side is noticeably larger in dR3. Unlike bR, dR3 possesses a helical segment at the C‐terminal region that fills the space between the AB and EF loops. A significant difference is also seen in the FG loop, which is one residue longer in dR3. Another peculiar property of dR3 is a highly crowded distribution of positively charged residues on the cytoplasmic surface, which may be relevant to a specific interaction with some cytoplasmic component.Proteins 2013; © 2013 Wiley Periodicals, Inc.     

The strepsipteran parasite <Emphasis Type="Italic">Elenchus japonicus</Emphasis> (Strepsiptera,Elenchidae) of planthoppers consists of three genotypes

The twisted-wing parasite Elenchus japonicus is a major parasitoid of rice planthoppers (Hemiptera: Delphacidae), including the brown planthopper Nilaparvata lugens, the white-backed planthopper Sogatella furcifera, and the small brown planthopper Laodelphax striatellus. Another Elenchus species, E. yasumatsui, which is considered to be synonymous with E. japonicus, has also been described in southern Asia. However, limited biological and molecular data on this important parasitoid of rice planthoppers are available. In this study, E. japonicas-stylopized planthoppers were obtained from various regions in Asia and Japan. Sequences of the nuclear 18S ribosomal RNA gene and the mitochondrial cytochrome oxidase I gene of the strepsipterans were analyzed from 40 samples of E. japonicus: 14 from N. lugens, 6 from S. furcifera and 20 from L. striatellus. Sequence analysis of these samples revealed three genotypes of E. japonicus. Of the three types of E. japonicus, one was isolated only from L. striatellus from northern Japan. The other two types were found in all three rice planthopper species collected from a wide area in Asia. These results suggest that the three different genotypes of Elenchus can be associated with a particular geographical region and/or planthopper species. The relationship between two previously described Elenchus species and the present three genotypes needs to be elucidated.     

Rapamycin treatment causes developmental delay, pigmentation defects, and gastrointestinal malformation on Xenopus embryogenesis

Rapamycin is a drug working as an inhibitor of the TOR (target of rapamycin) signaling pathway and influences various life phenomena such as cell growth, proliferation, and life span extension in eukaryote. However, the extent to which rapamycin controls early developmental events of amphibians remains to be understood. Here we report an examination of rapamycin effects during Xenopus early development, followed by a confirmation of suppression of TOR downstream kinase S6K by rapamycin treatment. First, we found that developmental speed was declined in dose-dependent manner of rapamycin. Second, black pigment spots located at dorsal and lateral skin in tadpoles were reduced by rapamycin treatment. Moreover, in tadpole stages severe gastrointestinal malformations were observed in rapamycin-treated embryos. Taken together with these results, we conclude that treatment of the drug rapamycin causes enormous influences on early developmental period.