The mcrA gene and 16S rRNA gene in the phylogenetic analysis of methanogens in the rumen of faunated and unfaunated cattle

The influence of rumen protozoa on the composition of rumen methanogens was studied by using seven growing Holstein cattle divided into two groups: four faunated and three unfaunated. 16S ribosomal RNA gene (rDNA) and methyl coenzyme‐M reductase (MCR) α subunit (mcrA) gene clonal libraries were constructed. The results of each analysis showed that Methanobacteriales was dominant in the rumen of both groups. By mcrA gene analysis, 22.1% of unfaunated clones were classified into unfaunated group 1, which was not detected from faunated cattle. The 16S rRNA gene analysis showed that the number of operational taxonomic units was higher in unfaunated than faunated cattle, suggesting the diversity of methanogens tended to be higher by the removal of protozoa. The results of the LIBSHUFF program indicated that the 16S rRNA gene and mcrA gene clone libraries for the faunated group differed from those for the unfaunated group (P = 0.001). It was suggested that the presence of protozoa strongly affected the composition of rumen methanogens.     

Profiling of plasma metabolites in canine oral melanoma using gas chromatography-mass spectrometry

Malignant melanoma is one of the most common and aggressive tumors in the oral cavity of dog. The tumor has a poor prognosis, and methods for diagnosis and prediction of prognosis after treatment are required. Here, we examined metabolite profiling using gas chromatography-mass spectrometry (GC-MS) for development of a discriminant model for evaluation of prognosis. Metabolite profiles were evaluated in healthy and melanoma plasma samples using orthogonal projection to latent structure using discriminant analysis (OPLS-DA). Cases that were predicted to be healthy using the OPLS discriminant model had no advanced lesions after radiation therapy. These results indicate that metabolite profiling may be useful in diagnosis and prediction of prognosis of canine malignant melanoma.     

Genetic analysis of group composition and relatedness in white‐headed langurs

We collected fecal samples of white‐headed langurs from 3 of the 4 remaining habitat fragments (Fa, Fb and CZ) located in southwestern Guangxi, China in Nov 2005, and used 5 microsatellite loci and the SRY gene to assess the relatedness between 46 langurs within and between groups. We observed 2 forms of group structure: one‐male/multi‐female groups (OMGs) and all‐male groups (AMGs). One AMG in Fa was composed of 2 generations, included a father, 2 sons and 1 unrelated male, and all OMGs in all 3 habitats included 1 resident male, several adult females and offspring. Of the 21 identified father‐offspring cases, the resident male fathered 20 (95%) and the non‐resident male sired 1 (5%), suggesting that adult males had overwhelming priority of access to females as the resident male in an OMG, while the non‐resident male may also have the opportunity to adopt surreptitious mating strategies.     

A case report of RccHanTM: WIST rat with multiple neoplastic and non-neoplastic proliferative lesions

It is extremely rare to have multiple spontaneous proliferative lesions in young adult rats. Here, we report the occurrence of different proliferative lesions in multiple tissues of a 7-week-old female rat in a 1-week repeated toxicity study. Grossly, multiple white patches and nodules in the bilateral kidneys, femoral and subcutaneous masses, and a nodule in the liver were observed. Renal lesions were diagnosed as renal mesenchymal tumors. One of the femoral subcutaneous masses was diagnosed as an adenolipoma consisting of mammary epithelial cells and mature adipocytes. The other femoral and abdominal subcutaneous masses were diagnosed as lipomas consisting of mature adipocytes. The liver nodule was diagnosed as non-regenerative hepatocellular hyperplasia, which was characterized by the proliferation of slightly hypertrophic hepatocytes. In the cauda equina, the growth of enlarged Schwann cells around the axon was observed, and this lesion was diagnosed as a neuroma.     

Amino acid nutrition in egg production industry

The egg production industry is facing various problems that need to be solved. For amino acid nutrition to achieve scientific and economical feeding of laying hens, it is necessary to elucidate the content, digestibility, or availability of nutrients of feedstuffs and feeds and the requirement of amino acids for laying hens. In addition, improvement to quality of eggs and meat of spent hens, methods of management and development of new feedstuffs are essential. For sustainable animal production, decrease in excreta and animal welfare should be studied. The real‐time determination of content and digestibility of amino acids in feedstuffs are essential for formation of feeds. Recent advances in the near infrared reflectance analysis will be able to determine the content, digestibility and availability of nutrients in feedstuffs and feeds, if we have a supplemental amount of conventional analysis to define the calibration population. The amino acid requirements are affected by various factors. Therefore the method to quickly and exactly determine amino acid requirements in response to various factors is necessary. By using plasma free amino acid concentration as a criterion, it is possible to determine amino acid requirements in various conditions of laying hens within a short experimental period, repeatedly using the same animals. Because the amino acid requirements differ among individual animals, it should be expressed as grams per hen per day. Practically, it is impossible to formulate various feeds for individual hens. The various expressions have been developed and these expressions have advantages and disadvantages. The nitrogen excretion of laying hens is easily reduced by reducing dietary nitrogen levels and restricting the feed intake. The availability of amino acid may be improved by feeding management, and supplementing enzyme, but the quality of eggs and meat of spent hens and welfare of laying hens are not affected by amino acid nutrition.     

Water-soluble Al inhibits methane oxidation at atmospheric concentration levels in Japanese forest soil

The effect of aluminium on methane oxidation was examined from incubation experiments involving the addition of several concentrations of Al solution (0.1, 0.2, 0.5, 1, 3 and 5 mM) to two soil samples that possessed different CH₄ oxidation potential. Atmospheric CH₄ oxidation activity was inhibited by the addition of as little as 0.1 mM Al solution (approximately 0.5 μg of Al per gram dry weight soil) to a forest soil that contained low water-soluble Al and possessed a high CH₄ oxidation potential. Our results indicate that Al inhibition of CH₄ oxidation activity is concentration-dependant after a certain time and the inhibition increases gradually over time until at least 96 h have elapsed. We also found that relatively small amounts of Al additions, such as 10-20 μg per gram dry weight of soil, halved the CH₄ oxidation rate compared to the control, regardless of the original CH₄ oxidation potential of the soil. Since the Al concentrations used in our experiment are often observed in forest soils, we can assume that Al acts as an important inhibitor of CH₄ oxidation in forest soils under natural conditions. The sharp falls and a continuous decrease in CH₄ oxidation rate in other forest samples with the addition of deionized water implies that the water-soluble Al contained in soils contributes to the inhibition of CH₄ oxidation rate. This result suggests that precipitation causes a relatively prolonged inhibition of CH₄ oxidation in soils containing a high concentration of water-soluble Al.     

In vitro culture conditions using chemically defined media for in vitro matured and intracytoplasmically inseminated porcine oocytes

The present study investigated in vitro culture methods [droplet and Well of the Well (WOW)] using semi-defined and defined media [modified porcine zygote medium (mPZM)] and the additional effects of insulin on in vitro matured and intracytoplasmically inseminated porcine oocytes. In Experiment 1, in vitro matured and intracytoplasmically inseminated porcine oocytes were cultured for 6 days in the following four groups: 1) mPZM-3 (containing bovine serum albumin) + droplet (30 mul), 2) mPZM-3 + WOW, 3) mPZM-4 (containing polyvinyl alcohol) + droplet, and 4) mPZM-4+ WOW. The culture media (mPZM-3 and mPZM-4) and methods (droplet and WOW) did not significantly affect the cleavage rate, but the blastocyst rate of the oocytes cultured in mPZM-3 was significantly (P<0.01) higher than that of mPZM-4 (20.1 and 9.4%, respectively). The blastocyst rates as percentages of the cleaved oocytes (51.8 and 16.9%) and the hatched blastocyst rate as percentages of the number of blastocysts (12.3 and 2.2%) were also significantly (P<0.01) higher in mPZM-3 compared with those in mPZM-4. There was significant interaction (P<0.05) between the two main factors; the effects of the culture media and methods on the rate of hatched blasyocysts as percentages of the blastocysts produced and, the hatched blastocyst rate (20.3%) as percentages of the number of blastocysts produced in mPZM-3 were significantly (P<0.05) higher than in the other groups. In Experiment 2, the additional effects of insulin (100 ng/ml) in mPZM-3 and mPZM-4 media was investigated in the WOW culture system. Insulin addition did not improve cleavage, blastocyst formation, or the number of cells in blastocysts. However, as in Experiment 1, mPZM-3 resulted in a significantly higher blastocyst rate as percentages of the cleaved oocytes than mPZM-4 (33.9 and 18.4%). These results indicate that a chemically defined medium (mPZM-4) needs to be improved to provide more suitable culture conditions for in vitro development of in vitro matured and intracytoplasmically inseminated porcine oocytes. However, the WOW system may be a useful IVC method for blastocyst development of in vitro matured porcine oocytes following ICSI when a semi-defined medium (mPZM-3) is used.     

Relating sulfate adsorption to soil properties in Japanese forest soils

The relationship of sulfate adsorption capacity to the presence of aluminum, iron oxides, and organic carbon in four Japanese forest soils was investigated. Sulfate adsorption capacities were higher in subsoils than in surface soils, and their profiles were the inverse of those of organic carbon content. The black soil derived from volcanic ash had high sulfate adsorption capacity and showed no release of sulfate, while some of the surface horizons of the other soils desorbed sulfate. Oxalate extractable aluminum (Al₀) and iron (Fe₀) and ditionite-citrate-bicarbonate (DCB) extractable iron (Fe_d) were positively correlated with the sulfate adsorption capacity, and their correlation coefficients were almost identical (0.58–0.61). The lack of significant correlation between Al_d and the adsorption capacity suggests that DCB is unsuitable for extracting aluminum compounds which have the ability to adsorb sulfate. In contrast with oxides, organic carbon correlated with sulfate adsorption capacity negatively, and had a negative coefficient in a multiple regression equation, insignificantly. Furthermore, H₂O₂-treated samples containing decomposed organic matter adsorbed more sulfate than untreated samples. These results clearly indicated that organic matter hinders sulfate adsorption. A comparison of theβ value (standard regression coefficient) of organic carbon with that of Al₀ showed that the negative contribution of organic matter to sulfate adsorption capacity was slightly less than the positive contribution of oxides.     

Sat-BSA: an NGS-based method using local de novo assembly of long reads for rapid identification of genomic structural variations associated with agronomic traits

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulked-segregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F₂ progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes.