A population genetics-based approach reveals candidate gene regions important in the determination of resistance specificity for the Pik family of rice blast resistance genes

Allelic resistance (R) genes at the Pik locus for rice blast resistance consist of two genes, designated as the first gene and the second gene, which each have a nucleotide-binding site and a leucine-rich repeat. We investigated allelic nucleotide sequence diversity at this locus in 36 rice lines and searched for gene regions showing high rates of nonsynonymous nucleotide substitutions. We detected such regions within and near the coiled-coil domain of the first gene but detected only a few nucleotide substitutions in the second gene, suggesting the importance of the N-terminal part of the first protein in the determination of R specificity.     

Abundance of sulphate-reducing bacteria in fish farm sediments along the coast of Japan and South Korea

The abundance of sulphate-reducing bacteria (SRB) was investigated in the coastal marine sediments along the coast of Japan and South Korea. Sediment samples were collected from fish and shellfish farms between 2006 and 2008. As non-fish farming reference sites, sediments were also collected from highly eutrophic bays, a highly sulphidogenic saline lake, and the deep sea. A quantitative real-time PCR analysis that targeted the gene coding for a portion of the α-subunit of dissimilatory sulphite reductase (dsrA) was performed to assess the abundance of the SRB in the sediments. Between 2.8 × 10⁷ and 2.5 × 10⁹ copies of the dsrA gene per gram dry sediment were detected. There was no relationship between dsrA gene copy number and total bacterial count in the sediments, whereas organic matter contents (particulate organic carbon and nitrogen, ignition loss and chemical oxygen demand) and acid-volatile sulphide contents were significantly correlated with the dsrA copy number. The data presented demonstrate that organic enrichment of sediment may influence the abundance of SRB communities in coastal marine sediments and that the cell density of SRB may be used as a biological indicator for assessing pollution levels in sediments of marine fish farms.     

Age and maturation of jack mackerel Trachurus japonicus in the East China Sea

Growth and reproductive characteristics of jack mackerel Trachurus japonicus collected in the East China Sea were determined based on otolith readings and gonad histology, respectively. Translucent and opaque zones on sectioned otoliths were identified and opaque rings counted. Von Bertalanffy growth parameters did not significantly differ between males and females, and the combined growth curve was: L _t  = 401{1 ? exp[?0.275 (t + 1.149)]} (0.8 < t < 6.9), where L _t is fork length (mm) at age t. The calculated lengths at age 1 in our study were larger than those reported 50 years ago from the East China Sea. The spawning period was evaluated to be from December to June, but primarily from February to May, based on the monthly changes in the gonadosomatic index and histological observations. The minimum size and age at first maturity were smaller and younger, respectively, than those reported in previous studies.     

Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan

Rice fragrance is an important characteristic for Southeast Asian consumers, and fragrant landraces from Japan were first recorded in the 17th century. Principal component analysis clearly showed that Japanese fragrant landraces were genetically different from non-Japanese fragrant landraces. Japanese fragrant landraces were composed of six clades, none of which carried the most common fragrance mutation, an 8-bp deletion in exon 7 of Badh2. Fragrant landraces comprised two major groups carrying different Badh2 mutations. One group carried a known SNP at exon13 and the other a SNP at the exon1-intron1 junction as splicing donor site. The latter was considered to be a potential splicing mutant group as a novel allele at Badh2. Heterozygosity (He) scores in the two fragrant groups were not significantly different from non-fragrant landraces and modern cultivars. However, lower He scores were found around the Badh2 locus in the two groups. The potential splicing mutant group showed a more extended haplotype than the E13 SNP group. A likely causal factor responsible for loss of function is a novel splicing mutation allele that may have been generated quite recently. The fragrance allele has dispersed as a result of out-crossing under local environmental conditions.     

Prevalence of dogs with intestinal parasites in Tochigi, Japan in 1979, 1991 and 2002

A total of 772 canine fecal specimens were collected in Tochigi in 1979, 1991 and 2001. The frequency of dogs that were kept indoor in 2002 (72.8%) was significantly higher than that for 1979 (21.2%, P < 0.001) and 1991 (40.6%, P < 0.01). The frequency of parasitized dogs in 2002 (18.8%) was significantly lower than that for 1979 (41.9%, P < 0.01). The findings of this study confirm the declining trend in Japan in the prevalence of helminth parasites in dogs, particularly Ancylostoma caninum and Trichuris vulpis. The reduction in the frequency of dogs with helminths may be mainly a result of the improvement in the environment and the routine use of filaricides.     

Changes of leukocyte counts and expression of pro‐ and anti‐inflammatory cytokines in peripheral leukocytes in periparturient dairy cows with retained fetal membranes

In dairy cows, retained fetal membranes (RFM) affect reproductive performance. The aim of this study was to examine the leukocyte counts and the gene expression of tumour necrosis factor α (TNFα), interleukin 1β (IL‐1β), IL‐8, and IL‐10 in polymorphonuclear leukocytes (PMNs) and peripheral blood mononuclear cells (PBMCs) in cows with (n = 5) or without (n = 5) RFM during the peripartum period. The lymphocyte counts in RFM cows were higher than those in control cows throughout the experiment (p < .05). The expression of IL‐8 in PMNs of control cows was higher (p < .05) compared with that of RFM cows postpartum. In cows with RFM, IL‐1β expression was higher (p < .05) in PMNs at 6 weeks postpartum whereas the expression of IL‐1β was lower (p < .05) in PBMCs at 4 weeks postpartum. The expression of IL‐10 in PBMCs of control cows was higher (p < .05) than that of RFM cows at 2 weeks prepartum and 4 weeks postpartum. Taken together, our data indicate that changes of gene expression of pro‐ and anti‐inflammatory cytokines in RFM cows might be associated with the delayed placental separation and development of uterine inflammation in RFM cows.     

Study of the role of the carbohydrate and protein moieties of soy soluble polysaccharides in their emulsifying properties

The objective of this work was to investigate the role played by the protein fraction of soy soluble polysaccharide (SSPS) during its adsorption at oil/water interfaces. SSPS was separated in a high (HMF; 310 kDa) and low (LMF; 20 kDa) molecular weight fraction by gel filtration. SSPS/HMF consisted of 91.6% carbohydrate and 2.2% protein and showed better emulsifying properties than those of the whole SSPS, whereas SSPS/LMF seemed to affect negatively the adsorption behavior of SSPS. SDS-PAGE of the protein fraction obtained from SSPS/HMF showed a molecular mass of 50 kDa, was composed predominantly of proline (23.1%) and glutamic acid (15.2%), and still contained 8.8% of neutral sugar and 5.3% of uronic acid. Results indicated that not all of the protein material present in SSPS contributes to SSPS functionality but that only the material associated with HMF aids in the adsorption of SSPS onto oil/water interfaces.