Comparative sequence analysis of four myosin heavy chain isoforms expressed in porcine skeletal muscles: Sequencing and characterization of the porcine myosin heavy chain slow isoform

A nucleotide sequence including the full coding region for the myosin heavy chain (MyHC) slow isoform was determined from the longissimus skeletal muscle. The deduced amino acid sequence was 1935 residues, which was the same length as the human and rat MyHC-slow isoforms. The porcine MyHC-slow isoform showed 97.6% and 97.4% amino acid identities to the human and rat isoforms on their entire regions, respectively. The functional regions were also highly conserved among mammalian MyHC-slow isoforms. Amino acid substitutions between the porcine MyHC-slow and MyHC-fast isoforms were concentrated on the functional regions. Loop 1, the controlling region of nucleotide binding and release, was conserved among the fast isoforms, but not between the slow and fast isoforms. Loop 2, a part of the actin binding region, was not conserved among any of the isoform types, and the most substitutions in this region were found in the slow isoform. The myosin essential light chain binding region was conserved among the fast isoforms, except for some substitutions in the 2b isoform, but was clearly different in the slow isoform. The myosin regulatory light chain binding region was conserved among the fast isoforms, but not between the slow and fast isoforms. These results indicate that the functional difference between the porcine MyHC-slow and -fast isoforms are controlled by the sequence diversity at the four functional regions compared.     

First report of fig mosaic virus infecting common fig (Ficus carica) in Japan

For the first time, fig mosaic virus (FMV) was detected in common fig (Ficus carica) trees in Shimane, Japan. These trees exhibited mosaic, ringspots, or distortion, accompanied by chlorosis on leaves and yellow spots on fruits. Some of the symptomatic trees were infested with the eriophyid mite Aceria ficus. The virus was detected based on RT-PCR, followed by sequencing. The amplified 300 base-pair fragments shared 83.5–91.5% identity with the corresponding region of RNA-dependent RNA polymerase gene of FMV isolates previously reported in Turkey, Iran, and Italy.     

Unique viral capsid assembly protein gene (g20) of cyanophages in the floodwater of a Japanese paddy field

In order to evaluate the genetic diversity of cyanophage communities of rice fields, viral capsid assembly protein gene (g20) was amplified with primers CPS1 and CPS8. The DNA was extracted three times from viral concentrates obtained from floodwater samples collected in each of four different plots (no fertilizer; P and K chemical fertilizers; N, P, and K chemical fertilizers; and chemical fertilizers with compost). Denaturing gradient gel electrophoresis (DGGE) gave different g20 clones. The sequencing of DGGE bands revealed that the g20 genes of the floodwater were divergent and that the majority of clones formed several unique groups. However, they were more closely related to g20 sequences from freshwaters than to those from marine waters, suggesting that g20 genes in terrestrial aquatic environments are different from those in marine environments.     

Eukaryotic communities associated with the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis

To estimate the succession and phylogenetic composition of the eukaryotic communities responsible for the decomposition of rice straw compost under flooded conditions during the cultivation period of paddy rice, denaturing gradient gel electrophoresis (DGGE) analysis targeting 18S rDNA followed by sequencing was conducted in a Japanese paddy field. The eukaryotic communities in rice straw compost incorporated into the flooded paddy field were influenced by the mid-season drainage and mainly composed of fungi (Ascomycota, Zygomycota, and Chytridiomycota) and protozoa (Ciliophora, Euglyphida, and Dactylopodida), most of which existed continuously during the cultivation period of paddy rice. The results indicated that these eukaryotic members were associated with the decomposition of rice straw compost in paddy field soil directly or indirectly.     

Polymorphism analysis of Fagaceae and DNA-based identification ofFagus species grown in Japan based on therbcL gene

Fagaceae species in Japan were identified by restriction fragment length polymorphism (RFLP) and sequence comparison of a region ofrbcL. Of nine restriction endonucleases used for digestion, three (MspI,RsaI,HaeIII) produced different restriction patterns in Fagaceae. Digestion byMspI yielded four patterns: Fagus species,Castanea crenata, Pasania glabra, and others. Digestion byRsaI andHaeIII afforded two patterns:Fagus species and others. These facts indicate thatCastanea crenata andPasania glabra can be identified byMspI restriction patterns ofrbcL. Sequence comparison of a region of therbcL gene among 20 species of Fagaceae showed that: (1) they could be divided into seven groups; (2) there is a site mutation betweenFagus crenata andF. japonica. The latter indicates that the wood of both Fagus species are identifiable at the species level, which is not the case using conventional methods. This result indicates the possibility of wood identification based on DNA polymorphism in Fagaceae at the intrageneric level.Part of this paper was presented at the 46th annual meeting of the Japan Wood Research Society, Kumamoto, April 3–5, 1996 and the 47th annual meeting of the Japan Wood Research Society, Kochi, April 3–5, 1997     

Carbon and nitrogen stocks and their mineralization potentials are higher under organic than conventional farming practices in Japanese Andosols

ABSTRACT

This study aimed at understanding whether and how long-term organic rice farming affects soil carbon (C) and nitrogen (N) stocks and their mineralization potentials in submerged rice paddies in Tochigi, Japan. An incubation experiment was carried out to assess the impacts of internal nutrient cycling after organic farming (OF) for 4–5 years (4OF), 8–9 years (8OF), and 12 years (12OF), compared with a conventional rice field (CF). Soil samples were collected at 0–15 cm and 15–20 cm in flooded rice fields after harvest in October 2013. pH and bulk density at 0–15 cm were significantly lower in 12OF fields than in CF fields (by 0.22 unit pH and 17.5%, respectively). Compared with CF, 12OF fields showed significant differences in soil organic carbon (SOC) and total nitrogen (TN), but 4OF and 8OF fields did not. In 8OF fields, the C decomposition (Co) and N mineralization (No) potentials were significantly higher (by 34.0% and 35.6%, respectively, at 0–15 cm, and by 67.1% and 24.5% at 15–20 cm) than in CF fields. Similarly, in 8OF fields at 0–15 cm, the Co:SOC and No:TN ratios were 19.8% and 23.2% higher, respectively, than in CF fields. Co, No, Co:SOC, and No:TN in 12OF fields were higher than those in CF fields, demonstrating the effects of prolonged organic rice farming. Additionally, in 12OF fields, C and N stocks were significantly higher (by 15.5% and 17.2%, respectively, at 0–15 cm, and by 4.8% and 12.1% at 15–20 cm) than in CF fields. Our findings suggest that long-term organic rice farming increases soil C and N stocks as well as C and N mineralization in Japanese Andosols.     

Possible influence of termites (Macrotermes bellicosus) on forms and composition of free sesquioxides in tropical soils

There has been less concern about soil mineralogical alteration than about soil physical, chemical and biological changes induced by termite nest-building activity. Furthermore, much less attention has been paid to free sesquioxides than to phyllosilicate minerals. In the present study, we conducted field morphological observations and selective dissolution analysis to characterize free sesquioxides in termite (Macrotermes bellicosus) mounds as compared with surrounding pedons in different toposequence positions, i.e., seasonally flooded valley bottom, hydromorphic fringe and well-drained upland sites. Distinctive redoximorphic features, such as surface yellowish layers on mound structures from the fringe site, indicate possible alteration of iron sesquioxide forms in the mounds due to the transportation of soil from reductive (aquic subsoil) to oxidative (epigeal mound) environments by the nest-building activity of M. bellicosus. On the other hand, the iron-soluble content in the dithionite-citrate-bicarbonate (DCB) system (Fe_d) was generally higher in the mound structures than at the adjacent sub-surface (Ap2) horizon at each toposequence position, while there was less difference in the content of acid ammonium oxalate (AAO) extractable iron (Fe_o) as compared to Fe_d. As a consequence, the iron activity index (Fe_d/Fe_o ratio) was found for the most part to be lower in the mound structures than in the neighboring Ap2 horizon. In addition, the content of Fe_d, AAO-soluble Al (Al_o) and DCB-extractable Al (Al_d) was significantly correlated with clay content in these soils. These findings suggest that M. bellicosus preferentially collects clay particles, probably from the clay-rich subsoils, such as the argillic horizon, which has been formed by the co-migration of phyllosilicate minerals and relatively crystalline sesquioxides. The species then likely incorporates them into the mounds, which induces an increase in the Fe_d content relative to that of Fe_o, resulting in a decreased iron activity index in the mound structures.     

Spatial–temporal variations in the composition of two <Emphasis Type="Italic">Zostera</Emphasis> species in a seagrass bed: implications for population management of a commercially exploited grass shrimp

We examined spatial and temporal variations in the species composition of two seagrass species, Zostera marina and Z. caespitosa, in a lagoon facing the Sea of Okhotsk. We also considered how those variations affected habitat quality for motile epifauna, especially for a commercial shrimp. A long-interval comparison between 1996 and 2013 showed that seagrass species composition in the lagoon did not vary, while their relative abundances did. A survey in 2012 revealed that the abundance of Z. caespitosa was affected by the abundance of Z. marina, water depth, and location in the lagoon. Although these seagrass species have similar aboveground morphology, differences in their fine structures were detected. Diversities of motile animals inhabiting the seagrass species were the same. Differences in seagrass utilization were observed when we focused on a commercial shrimp, Pandalus latirostris. This shrimp always preferred higher densities of shoots irrespective of the species and seasonally changed their preference for the number of leaves per shoot. They were therefore more abundant in Z. caespitosa, which had those structural characteristics. The results suggest that the management of shrimp resources could be improved by flexibly changing protected areas in accordance with the dynamics of seagrass distribution in the lagoon.