Inconspicuous restraint of rice seedling growth by root-infecting fungi in soil of a rice paddy field

 Rice seedling growth, estimated by plant height and root development and discoloration, was better in pasteurized soil than in unpasteurized soil obtained from a flooded rice field. Rice seedlings also grew better in sterilized soil modified by adding roots harvested from the pasteurized soil than in soil modified by adding roots harvested from the unpasteurized soil. The results demonstrate that seedling growth in the rice field soil was inhibited by soil microorganisms, even though no typical symptoms such as seedling blight or damping-off appeared. Pythium aristosporum is suggested to be involved in the inhibition. Thus, it appears that inconspicuous restraint of rice seedling growth could occur in soils of rice paddy fields. Received: May 20, 2002 / Accepted: October 16, 2002 Acknowledgments The authors thank Dr. T. Ichitani, former professor at Osaka Prefectural University, for providing an isolate of Pythium aristosporum for comparison, and Mr. Mitsuaki Sato of Akita Prefectural College of Agriculture for technical assistance.     

Identification of c-kit mutations-independent neoplastic cell proliferation of canine mast cells

Gain-of-function mutations in the proto-oncogene c-kit have been considered the molecular mechanism of neoplastic proliferation of mast cells. However, the importance of c-kit gene mutations is not well evaluated in canine mast cell tumors (MCTs). In the present study, we established and characterized a mast cell line, HRMC, derived from a dog with MCT. We also examined c-kit mutations in HRMC cells and assessed an inhibitory effect of a tyrosine kinase inhibitor, STI571, on HRMC cells. HRMC cells had cytoplasmic metachromatic granules, chymase and tryptase, and expressed both KIT and FcepsilonRI on the cell surface. HRMC cells contained histamine and released beta-hexosaminidase through FcepsilonRI cross-linking and calcium ionophore stimulation. Nucleotide sequence analysis demonstrated no mutations in an open reading frame of c-kit cDNA and genomic DNA of the juxtamembrane domain of c-kit in HRMC cells. STI571 did not show any inhibitory effects on the proliferation of HRMC cells. These findings clearly demonstrated the existence of c-kit mutations-independent neoplastic canine mast cell proliferation. The growth factor-independent mast cell line established in this study might be valuable to explore novel mechanisms of c-kit mutations-independent neoplastic proliferation of mast cells in dogs.     

Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Practical capability of a DNA pool‐based genome‐wide association study using BovineSNP50 array in a cattle population

Genome‐wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome‐wide association studies. However, in DNA pooling design, the additional variance generated by pooling‐specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P‐values estimated by a genome‐wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost‐effectiveness of pool‐based genome‐wide association studies using the BovineSNP50 array in a cattle population.     

Isolation of a human erythrocyte-adapted substrain of Babesia rodhaini and analysis of the merozoite surface protein gene sequences

Babesia rodhaini is a rodent hemoparasite closely related to B. microti, the major causative agent of human babesiosis. We tested the infectivity of B. rodhaini for human erythrocytes by using the SCID mouse model in which the circulating erythrocytes were replaced with those of humans. Initially, parasites grew very poorly in the mouse model, but a variant capable of propagating in human erythrocytes emerged after an adaptation period of three weeks. In an attempt to identify parasite proteins involved in the alteration of host cell preference, an expression cDNA library of B. rodhaini was constructed and screened with immune mouse sera. Although we were able to obtain three merozoite surface protein (MSP) genes, sequences of these genes from both the parental strain and human erythrocyte-adapted substrain were identical. Our results suggest that B. rodhaini has potential ability to infect human erythrocytes, but development of this ability may not be brought about by an amino acid change in MSPs.     

Effects of feeding and animal performance on nitrogen, phosphorus and potassium excretion by Holstein cows

Thirty‐four Holstein dry cows and 16 lactating cows were used in balance trials to identify the effects of feeding and animal performance on nitrogen (N), phosphorus (P) and potassium (K) excretion by dairy cows, and to develop prediction models for these excreta. Orchard grass silage, corn silage, alfalfa silage or timothy hay were offered to dry cows. Orchard grass silage or alfalfa silage, and concentrates were offered to lactating cows. In the statistical analysis, the independent variables were bodyweight (kg), dry matter (DM) intake (kg/day), milk yield (for lactating cows only, kg/day), water intake (free water plus water in feed, kg/day), intake (g/day) of N, P and K and dietary contents (% of DM) of crude protein, P and K. The dependent variables were N, P and K excretion (g/day) in feces and urine. In both dry and lactating cows, intake of N, P and K had large effects on corresponding excretion. The results indicated that a decrease in the intake of N, P and K could decrease the corresponding excretion. Further research by path analysis showed that K intake positively affected urinary N excretion in dry cows indirectly, through water intake and urine volume.     

Hepatic AA amyloidosis in a cat: cytologic and histologic identification of AA amyloid in macrophages

A 3‐year‐old, spayed female, Domestic Shorthair cat presented with anorexia, lethargy, vomiting, probable hemoabdomen, and multiple masses on the right lateral liver lobe. Clinicopathologic and imaging abnormalities included anemia, azotemia, icterus, and hepatomegaly with hypoechoic masses. On cytologic evaluation of a fine‐needle aspiration of a liver mass there was abundant extracellular pink‐ to purple‐colored material between hepatocytes. The amorphous material was stained with direct fast scarlet (DFS), and green birefringent areas were observed under polarized light, confirming the presence of amyloid. A unique finding on the cytologic smear were macrophages containing amorphous and fibrillar amyloid‐like protein. Histopathologic examination using H&E and Congo red staining confirmed amyloid deposits within the space of Disse, along the sinusoids, portal tracts, blood vessel walls, and within the cytoplasm of macrophages. Immunohistochemical staining with anti‐AA amyloid antibodies further confirmed the presence of AA amyloid. To the author's knowledge, this is the first report of the cytologic finding of AA amyloid protein within macrophages and DFS stain detection of amyloid on a cytologic smear.     

The functional-morphological adaptive strategy of digestive organs of decapodiform cephalopods

The digestive organs in decapodiform cephalopod species morphologically vary byindividual lifestyle. We examined the following six species of adult decapodiformescephalopods representing different habitats: Todarodes pacificus, Loligobleekeri, Loligo edulis, Wataseniascintillans (pelagic), Sepia lycidas and Euprymnamorsei (benthic). L. bleekeri and L. edulispossess a bursiform cecal sac connected to the cecum. Pelagic species have a singledigestive gland smaller than in benthic species. T. pacificus has an ovaldigestive gland larger than that of L. bleekeri and L.edulis, which possess withered-looking and smaller digestive glands. Incontrast, the digestive glands in benthic species are paired. S. lycidasand E. morsei have well-developed and larger digestive glands than thoseof the pelagic species. Well-developed digestive duct appendages are found in benthicspecies. In qualification of the mass of digestive organs, pelagic species have smallerstomachs, digestive glands and digestive ducts’ appendages than benthic species. Becausepelagic species need to swim, they may possess smaller stomachs and larger cecums for morerapid digestion. A smaller digestive gland may have the advantage of reducing the bodyweight in pelagic species for rapid swimming. In contrast, since benthic species require alonger time for digestion than pelagic species, they compact more food in their stomachsand absorb nutrients via more organs, such as the digestive grand and digestive ductappendages, in addition to cecum.     

Positional strategy of trunk muscles among aquatic,semi-aquatic and terrestrial species in Urodela

Clarification of the trunk structure in Urodela is important in understanding the locomotive evolution of basal tetrapods. The components of the muscular trunk wall among Urodela using different modes of locomotion were compared. Since the whole trunk may be used for swimming and the effect of limbs may be small in the more aquatic species, they showed smaller differences in the trunk muscles among anterior, middle and posterior sections of the trunk. By contrast, in the more terrestrial species, the dorsal and abdominal muscles are larger in the middle section than those in the anterior and posterior sections. High compressive stresses occur in the supporting limbs and their insertion at the trunk on the ventral side, and spread from the forelimbs along the back to the supporting hindlimbs on the dorsal side. Tensile stresses occur in the middle ventral part. The components of the trunk muscles among the three sections may reflect differences in stresses occurring in the trunk of the more terrestrial species. The findings also suggest that in the middle section, larger dorsal muscles for stiffening the back to maintain posture and larger abdominal muscles are responsible for balancing the body weight while it is supported by the limbs in the more terrestrial species.     

Evaluating environmental impacts of the Japanese beef cow–calf system by the life cycle assessment method

The objectives of this study were to evaluate the environmental impacts of a beef cow–calf system using a life cycle assessment (LCA) method and to investigate the effects of scenarios to reduce environmental impacts on the LCA results. The functional unit was defined as one marketed beef calf, and the processes associated with the cow–calf life cycle, such as feed production, feed transport, animal management, the biological activity of the animal and the treatment of cattle waste were included in the system boundary. The present results showed that the total contributions of one beef calf throughout its life cycle to global warming, acidification, eutrophication and energy consumption were 4550 kg of CO₂ equivalents, 40.1 kg of SO₂ equivalents, 7.0 kg of phosphate (PO₄) equivalents and 16.1 GJ, respectively. The contribution of each process to the total environmental impact in each environmental impact category showed a similar tendency to the contribution of each process in each environmental category reported in the case of the beef fattening system as a whole. The results from this analysis showed that shortening calving intervals by 1 month reduced environmental impacts by 5.7–5.8% in all the environmental impact categories examined in the current study, and increasing the number of calves per cow also reduced environmental impacts in all the categories, although the effects were smaller.