Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field

Members of the Sphingomonas -related genera ( Sphingomonas , Sphingobium , Novosphingobium and Sphingopyxis ) are dominant in bacterial isolates from the floodwater of Japanese paddy fields. Fifty-eight Sphingomonas / Novosphingobium bacteriophages (phages) were isolated to elucidate their morphology, host range and phylogenetic diversity based on the capsid gene ( g23 ) sequence. All of the phages were siphoviruses with isometric or elongated, icosahedral capsids and a long, non-contractile tail. The genomes were double-stranded DNA measuring either 40, 60, 100 or 160 kb. The host range of the phages was examined by infecting 16 bacterial isolates from the floodwater, belonging to Sphingomonas , Novosphingobium , Sphingopyxis and Porphyrobacter . The host range was widely different and varied between infection of only the host used for isolation and infection of hosts belonging to the three genera of Sphingomonas , Novosphingobium and Porphyrobacter . All phages had g23 , indicating the ubiquity of the g23 gene among Myoviridae and Siphoviridae members. Every g23 sequence of the phages belonged to one of the six uncharacterized Paddy Groups proposed by Fujii et al . (2008 ). The g23 sequences were identical at the nucleotide level for several phages with isometric and elongated capsids with 60 and 160 kb genomes, and between some phages and the clones that were retrieved from distant paddy fields. This indicates the common occurrence of horizontal transfer of g23 in the paddy fields. The g23 sequence does not correlate with the host range of those phages. In addition, a larger degree of divergence of g23 from coliphage T4 in paddy fields compared to marine environments was estimated from the present study.     

Myosin substitution rate is affected by the amount of cytosolic myosin in cultured muscle cells

In striated muscles, approximately 300 myosin molecules form a single thick filament in myofibrils. Each myosin is continuously displaced by another myosin to maintain the thick filament structure. Our previous study using a fluorescence recovery after photobleaching (FRAP) technique showed that the myosin replacement rate is decreased by inhibition of protein synthesis, but myosin is still exchangeable. This result prompted us to examine whether myosin in the cytoplasm is involved in myosin replacement in myofibrils. To address this, FRAP was measured in green fluorescent protein (GFP)‐tagged myosin heavy chain 3 (Myh3) expressing myotubes that were treated with streptolysin‐O (SLO), which forms pores specifically in the plasma membrane to induce leakage of cytoplasmic proteins. Our biochemical data demonstrated that the cytoplasmic myosin content was reduced in SLO‐permeabilized semi‐intact myotubes. Furthermore, FRAP experiments showed a sluggish substitution rate of GFP‐Myh3 in SLO‐permeabilized myotubes. Taken together, these results demonstrate that the myosin substitution rate is significantly reduced by a decreased amount of myosin in the cytoplasm and that cytoplasmic myosin contributes to myosin replacement in myofibrils.     

Comparison of bacterial community structures at main habitats in paddy field ecosystem based on DGGE analysis

Bacterial communities at different habitats in a Japanese paddy field ecosystem were compared to understand the bacterial world in the ecosystem as a whole by analyzing data of the denaturing gradient gel electrophoresis (DGGE) band patterns and the sequenced DGGE bands. The habitats were floodwater, percolating water, microcrustacean inhabiting in floodwater, plow layer soil, rice roots, rice straw and rice straw compost incorporated in soil, rice straw placed on the soil surface, plant residues in paddy fields, and rice straw under composting process. Phylotype (band) richness, diversity, evenness, and stability of the bacterial communities at the respective habitats were evaluated based on the DGGE profile data. Phylotype richness was greater near plant residues, rice straw buried in soil and rice straw placed on soil surface, while it was smaller at microcrustacean and rice straw compost buried in soil. The samples from plow layer soil and rice straw compost buried in soil showed considerably higher index values for diversity, evenness, and stability, while those from rice straw placed on soil surface and microcrustacean had lower values of the indices than other habitats. Sequences of totally 250 DGGE bands were assigned to phyla or classes. Distribution of bacterial members to phylogenetic taxa was different among the respective habitats. Inhabitants in plow layer soil were most widely distributed among the groups (nine phyla: Proteobacteria, Chloroflexi, Chlorobi, Verrucomicrobia, Acidobacteria, Nitrospira, candidate division OP10, Cyanobacteria, and Actinobacteria), while those in floodwater and microcrustacean were restricted to only three phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). Proteobacteria and Bacteroidetes were found at all the habitats and the habitats except for plow layer soil, respectively, whereas abundant members belonged to Chloroflexi and Actinobacteria in plow layer soil. “Comprehensive mapping” of DGGE fragments was conducted by principal component analysis based on evolutionary distances of the fragments to 202 reference bacterial strains to overview phylogenetic relationships of bacterial members among the respective habitats. The score plots with the first and second principal components distinctly characterized bacterial members at the respective habitats, and the similarity between the respective communities was clearly demonstrated. Overall, bacterial communities at the respective habitats were distinct and different in the diversity and stability to each other, which may have contributed to the diversity of overall bacterial communities in the paddy field ecosystem.     

Clindamycin in the treatment of Babesia gibsoni infections in dogs

This report examines the effectiveness of clindamycin for the treatment of babesiosis in dogs (n=10) experimentally infected with Babesia gibsoni (B. gibsoni). Clindamycin (25 mg/kg body weight, per os, q 12 hours for 14 days) gradually reduced parasitemia levels and induced morphological changes that indicated degeneration of parasites (e.g., segmentation; size reduction; localization in the cell limbic and/or torn state of the nucleus; and swelling, decrease, or disappearance of the cytoplasm) in the majority of dogs. Clindamycin treatment reduced the clinical symptoms characteristic of Babesia infection, including anemia, anorexia, and listlessness. Clindamycin might be useful as a medicine for treatment of B. gibsoni infection.     

Residues of aflatoxins in the liver,muscle and eggs of domestic fowls

The residue of aflatoxins in the liver, muscle and eggs of laying ducks, hens and quails and in broiler chickens was examined by conducting 7-day feeding experiments with a diet containing 3 ppm Aflatoxin B1 (AFB1). Birds were sacrificed on the 8th or 11th day of AFB1 feeding. AFB1 and its metabolites in the tissues and eggs were determined by HPLC. The tissue levels of AFB1 and its metabolites were higher in quail than in the other birds. The levels of AFB1 and its metabolites, including acid-hydrolyzable metabolites, were more than 10-fold higher in the liver than in the muscle in all the species. The ratio of AFB1 in the feed to the residual level in the liver was 383 in quail, but was > or = 5769 in the other birds. The corresponding ratios in the egg yolk and albumen of AFB1 were 4615 and 3846, respectively, in chicken hens, and these values were higher than those in the other birds.     

Results of preliminary selection for the second generation plus trees by private foresters in three genetic tests with controlled pollinated progenies of sugi (<Emphasis Type="Italic">Cryptomeria japonica</Emphasis>) in Kyushu

Second-generation plus tree selections were assessed in three genetic tests of sugi (Cryptomeria japonica) in Kyushu: at Kumamoto, Saga, and Miyazaki. The selections were made by private foresters choosing good trees according to their own preferences when the tests were around 30 years of age. A retrospective selection index applied to the results of selection revealed that the foresters had put more emphasis on stem straightness than on growth. This trend was particularly evident at Kumamoto, whereas the foresters at Miyazaki and Saga had allocated nearly the same weight to growth as to stem straightness. Broad-sense heritabilities on dbh, stem straightness and bottom stem crookedness were 0.226, 0.256, and 0.206, respectively. These estimates were regarded as almost the same as narrow-sense heritabilities, because non-additive genetic variances were found to be small. Relative gains, assuming that the selections are propagated with rooted cuttings, were predicted to be around 10% for stem straightness, 7% for bottom-stem crookedness, while the gains on dbh were variable among the tests: ranging from 3% at Kumamoto up to around 8% at Saga and Miyazaki.     

The importance of subfragment 2 and C‐terminus of myosin heavy chain for thick filament assembly in skeletal muscle cells

In skeletal muscle cells, myofibrillar proteins are highly organized into sarcomeres in which thick filaments interdigitate with thin filaments to generate contractile force. The size of thick filaments, which consist mainly of myosin molecules, is strictly controlled. However, little is known about the mechanisms by which myosin molecules assemble into thick filaments. Here, we assessed the ability of each domain of myosin heavy chain (Myh) to form thick filaments. We showed that exogenously expressed subfragment 2 (S2) + light meromyosin (LMM) of Myh was efficiently incorporated into thick filaments in muscle cells, although neither solely expressed S2 nor LMM targeted to thick filaments properly. In nonmuscle COS7 cells, S2+LMM formed more enlarged filaments/speckles than LMM. These results suggest that Myh filament formation is induced by S2 accompanying LMM. We further examined the effects of Myh C‐terminus on thick filament assembly. C‐terminal deletion mutants were incorporated not into entire thick filaments but rather into restricted regions of thick filaments. Our findings suggest that the elongation of myosin filaments to form thick filaments is regulated by S2 as well as C‐terminus of LMM.     

Identification of rRNA gene loci in the wild mouse (Mus musculus molossinus) captured at Hachioji, Tokyo

Mus musculus (M. m.) molossinus has been considered an independent subspecies of Mus musculus. To elucidate the evolutional origin of this subspecies, we carried out double-color FISH using 18s-28s ribosomal DNA and mouse chromosome paint probes. Among eleven rDNA loci detected, five loci on chromosomes 12, 15, 16, 18 and 19 were common to both Mus musculus (M. m.) musculus and M. m. molossinus and the other six loci, on chromosomes 1, 5, 10, 11, 13 and 17, were characteristic in M. m. molossinus. As M. m. molossinus is thought to originate from a hybrid between ancestral colonies of M. m. musculus and Mus musculus castaneus, we supposed that these six rDNA loci might have evolved after geographical isolation of the ancestral hybrid animals from M. m. musculus and M. m. castaneus.     

Carbon fluxes and their response to environmental variables in a Dahurian larch forest ecosystem in northeast China

The Dahurian larch forest in northeast China is important due to its vastness and location within a transitional zone from boreal to temperate and at the southern distribution edge of the vast Siberian larch forest. The continuous carbon fluxes were measured from May 2004 to April 2005 in the Dahurian larch forest in Northeast China using an eddy covariance method. The results showed that the ecosystem released carbon in the dormant season from mid-October 2004 to April 2005, while it assimilated CO2 from the atmosphere in the growing season from May to September 2004. The net carbon sequestration reached its peak of 112 g.m^-2.month ^-1 in June 2004 （simplified expression of g （carbon）.m^-2.month^-1） and then gradually decreased. Annually, the larch forest was a carbon sink that sequestered carbon of 146 g-m^-2.a^-1 （simplified expression of g （carbon）.m^-2.a^-1） during the measurements. The photosynthetic process of the larch forest ecosystem was largely affected by the vapor pressure deficit （VPD） and temperature. Under humid conditions （VPD 〈 1.0 kPa）, the gross ecosystem production （GEP） increased with increasing temperature. But the net ecosystem production （NEP） showed almost no change with increasing temperature because the increment of GEP was counterbalanced by that of the ecosystem respiration. Under a dry environment （VPD 〉 1.0 kPa）, the GEP decreased with the increasing VPD at a rate of 3.0 μmol.m^-2.s^-1kPa -1 and the ecosystem respiration was also enhanced simultaneously due to the increase of air temperature, which was linearly correlated with the VPD. As a result, the net ecosystem carbon sequestration rapidly decreased with the increasing VPD at a rate of 5.2 μmol.m^-2.s-1.kPa^-1. Under humid conditions （VPD 〈 1.0 kPa）, both the GEP and NEP were obviously restricted by the low air temperature but were insensitive to the high temperature because the observed high temperature value comes within the category of the optimum range.