Bacteriophages, the viruses that infect bacteria, are the most abundant biological entities in the biosphere and play a key role in global biogeochemical cycling. All T4-type bacteriophage isolates tested so far have a conserved genetic module that encodes the virion components including gene 23 (g23), the major capsid protein. Molecular analysis of the g23 sequence revealed a remarkable level of diversity of T4-type bacteriophages isolated from rice straw and surface soil in a Japanese rice field. It was found that g23 sequences obtained from the rice field were quite distinctive from those obtained in marine environments. Phylogenetic analysis showed that most of these g23 sequences belonged to two novel subgroups of T4-type bacteriophages, although some of them were related to well-studied subgroups of T4-type bacteriophages, such as marine cyanophage isolates of exoT-evens.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the selective loss of motor neurons. Recent studies have implicated that chronic hypoxia and insufficient vascular endothelial growth factor (VEGF)-dependent neuroprotection may lead to the degeneration of motor neurons in ALS. Expression of apelin, an endogenous ligand for the G protein-coupled receptor APJ, is regulated by hypoxia. In addition, recent reports suggest that apelin protects neurons against glutamate-induced excitotoxicity. Here, we examined whether apelin is an endogenous neuroprotective factor using SOD1G93A mouse model of ALS. In mouse CNS tissues, the highest expressions of both apelin and APJ mRNAs were detected in spinal cord. APJ immunoreactivity was observed in neuronal cell bodies located in gray matter of spinal cord. Although apelin mRNA expression in the spinal cord of wild-type mice was not changed from 4 to 18 weeks age, that of SOD1G93A mice was reduced along with the paralytic phenotype. In addition, double mutant apelin-deficient and SOD1G93A displayed the disease phenotypes earlier than SOD1G93A littermates. Immunohistochemical observation revealed that the number of motor neurons was decreased and microglia were activated in the spinal cord of the double mutant mice, indicating that apelin deficiency pathologically accelerated the progression of ALS. Furthermore, we showed that apelin enhanced the protective effect of VEGF on H2O2-induced neuronal death in primary neurons. These results suggest that apelin/APJ system in the spinal cord has a neuroprotective effect against the pathogenesis of ALS.

Ammonia oxidation to nitrite is the key part in the nitrification–denitrification process that occurs in the oxic–anoxic interface of paddy fields and is, therefore, an important component of the nitrogen cycle. Ammonia oxidation is carried out by autotrophic ammonia oxidizing bacteria (AOB). In this study, we investigated the AOB community in the surface paddy soil layer using polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE) and sequencing methods using amoA‐specific primers targeting a partial stretch of the gene that encodes ammonia monooxygenase A (amoA). DGGE bands with eight different levels of mobility were obtained from the surface soil. The DNA sequences of five bands were identified. All DNA sequences were closely related to Nitrosospira spp. and no Nitrosomonas‐like AOB were identified. The deduced amino acid sequences of the five retrieved DGGE bands were closely related (99–100%) to previously published amoA amino acid sequences of the cultured strains Nitrosospira Ka3 and Nitrosospira CT2F. A phylogenetic tree based on the amoA amino acid sequence revealed that all five AOB sequences were grouped within the amoA cluster 1.

In the meat industry, correct labeling of beef origins or breed is required to assure quality and safety. This paper describes the development of discrimination markers between Japanese domestic and imported beef from the United States (US) and Australia (AUS) based on a bovine 50K single nucleotide polymorphism (SNP) array using a total of 110 samples: Japanese Black (n = 50), Japanese Holstein (n = 50) and US cattle (n = 10). Genotyping information revealed 1081 SNPs as candidate markers that were polymorphic only in US cattle. The genotyping results by PCR-restriction length polymorphism in Japanese Black (n = 300) and Holstein cattle (n = 146) revealed that 11 SNPs had alleles specific to US cattle. Their allelic frequencies in US cattle (n = 108) ranged from 0.097 to 0.250 with an average of 0.178 and the combined identification probability of US cattle was 0.987. In addition, we also verified the applicability of these US-specific markers to AUS cattle. Their allelic frequencies in AUS cattle (n = 280) ranged from 0.063 to 0.224 with an average of 0.137 and the combined identification probability of AUS cattle was 0.963. In conclusion, a set of these markers could be useful for discriminating between Japanese domestic and imported beef and would contribute to identify origins and prevent falsified labeling of beef.

To estimate the bacterial communities in rice straw left on the soil surface of paddy fields, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis was conducted. Rice straw samples were placed on the soil surface in a Japanese paddy field under drained conditions after harvest and under flooded conditions after the transplanting of rice. The residual samples on the soil surface under upland conditions were collected just before spring plowing and were replaced again on the soil surface after transplanting, under flooded conditions. The DGGE patterns of the bacterial communities in rice straw on the surface of paddy field soil were divided into three groups, namely rice straw samples before placement, under drained conditions and under flooded conditions. Sequence analysis of DGGE bands indicated that most of the bacterial members in rice straw during decomposition on the soil surface in the paddy field belonged to Gram-negative bacteria. The bands that commonly existed throughout the periods under flooded and upland conditions were closely related to α-Proteobacteria. The groups of Spirochaetes and δ-Proteobacteria were often observed during flooded periods, although the members of Bacteroidetes, α-Proteobacteria, Gemmatimonadetes and Actinobacteria were also detected under flooded conditions. In contrast, the bands characteristic to the rice straw left on the soil surface of the paddy field under drained conditions belonged to Bacteroidetes and γ-Proteobacteria. This finding clearly indicates that the bacterial communities responsible for rice straw decomposition were determined by the water regime in the paddy field, and various members of Gram-negative bacteria have contributed to the decomposition of rice straw left on the soil surface in a paddy field.