Bayesian genome-wide association study of nut traits in Japanese chestnut

Japanese chestnut (Castanea crenata Sieb. et Zucc.) has a long juvenile phase, so breeders have to wait many years to evaluate nut traits. Molecular markers associated with genes of interest would accelerate selection in chestnut breeding programs. We evaluated five nut traits (nut harvest date, nut weight, pericarp splitting, insect infestation, and specific gravity) in 99 Japanese chestnut cultivars and selections. A wide range of phenotypic variation was observed for each of the traits, suggesting that the collection harbored sufficient genetic diversity for breeding. A Bayesian genome-wide association study was conducted using 162 simple sequence repeat markers and 741 single nucleotide polymorphism markers. To evaluate the potential of marker-assisted selection, we examined 12 molecular markers found to be associated with nut traits: 4 for nut harvest date, 4 for nut weight, 1 for pericarp splitting, and 3 for insect infestation. The percentages of phenotypic variance explained ranged from 4.8 to 37.1%. Although insect infestation showed only medium heritability (0.672), we obtained two quantitative trait loci (QTLs) with extremely high posterior probabilities (0.93 and 1.00). Out of the 12 molecular markers, 3 of the 4 markers for nut harvest time could be validated in a breeding population. Accuracies of genomic selection were extremely high for nut harvest date (0.841) and moderate for insect infestation (0.604), suggesting that genomic selection based on Bayesian regression would reduce the cost of phenotypic evaluation of these traits and possibly others.     

Promotion of transferrin folding by cyclic interactions with calnexin and calreticulin.

Calnexin, an abundant membrane protein, and its lumenal homolog calreticulin interact with nascent proteins in the endoplasmic reticulum. Because they have an affinity for monoglucosylated N-linked oligosaccharides which can be regenerated from the aglucosylated sugar, it has been speculated that this repeated oligosaccharide binding may play a role in nascent chain folding. To investigate the process, we have developed a novel assay system using microsomes freshly prepared from pulse labeled HepG2 cells. Unlike the previously described oxidative folding systems which required rabbit reticulocyte lysates, the oxidative folding of transferrin in isolated microsomes could be carried out in a defined solution. In this system, addition of a glucose donor, UDP-glucose, to the microsomes triggered glucosylation of transferrin and resulted in its cyclic interaction with calnexin and calreticulin. When the folding of transferrin in microsomes was analyzed, UDP-glucose enhanced the amount of folded transferrin and reduced the disulfide-linked aggregates. Analysis of transferrin folding in briefly heat-treated microsomes revealed that UDP-glucose was also effective in elimination of heat-induced misfolding. Incubation of the microsomes with an alpha-glucosidase inhibitor, castanospermine, prolonged the association of transferrin with the chaperones and prevented completion of folding and, importantly, aggregate formation, particularly in the calnexin complex. Accordingly, we demonstrate that repeated binding of the chaperones to the glucose of the transferrin sugar moiety prevents and corrects misfolding of the protein.     

Simulation of citric acid production by rotating disk contactor

A simple model was presented to describe the time courses of citric acid production by a rotating disc contactor (RDC) using Aspergillus niger. The model is expressed by Monod-type cell growth, Luedeking-Piret-type citric acid production rate equations, and the diffusion equation for oxygen in the biofilm. The model contains five parameters which were determined by the nonlinear least squares method by fitting the numerical solution to the experimental data. In solving the equations, the cell density of the biofilm was estimated from the value of cellular mass per unit of biofilm area using an empirical equation. The experimental time courses in citric acid production period were well simulated with this model. The relation between the specific biofilm surface area and the rate of citric acid production was also explained by the simulation using the average values of five parameters of twelve runs. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 689-696, 1997.     

Primary biliary cirrhosis sera recognize not only gp210 but also proteins of the p62 complex bearing N-acetylglucosamine residues from rat liver nuclear envelope

We have recently observed reactivity of primary biliary cirrhosis (PBC) sera with several proteins bearing N-acetylglucosamine residues from rat liver nuclear envelopes. The aim of this study was to characterize the reactive antigens. Sera from 31 patients with PBC, 30 with rheumatoid arthritis (RA) and 30 with Sjögren's syndrome (SS) were examined. Rim-like immunofluorescence staining was observed in 15 of 31 (48%) sera from patients with PBC, in 1 of 30 with RA and in 1 of 30 with SS. Upon immunoblotting using preparations of whole rat liver nuclear envelopes and their Triton X 100-KCl extract as antigen souces, a 200 kDa protein band was observed in 9 of sera with PBC. Furthermore, upon immunoblotting using the wheat germ aggulutinin-bound fraction of rat liver envelope as antigen, 62, 60 and 54 kDa protein bands corresponding to components of the p62 complex in the nuclear pore complex (Kita et al. Biochem. 113, 377–382) were observed in 7, 5 and 6 samples respectively, of the 31 PBC sera. Our data suggest that PBC sera recognize not only the 210 kDa protein but also the p62 complex proteins.Abbreviations ANA antinuclear antibody - AMA anti-mitochondrial antibodies - IF immunofluorescence - LAP2 lamina-associated polypeptide 2 - LBR lamin B receptor - anti-NBP 60 anti-nuclear localization signal binding protein 60 - NE nuclear envelope - NPC nuclear pore complex - PBC primary biliary cirrhosis - RA rheumatoid arthritis - SLE systemic lupus erythematosus - SS Sjögren's syndrome - WGA wheat germ agglutinin     

Spatial structure of avifauna along urban-rural gradients

We examined the pattern of species composition of breeding birds along urban-rural gradients in the Osaka Prefecture, western Japan. We recorded the proportion of nine types of land-use and the presence/absence of each of 76 breeding birds in 5 km square quadrats on a map of the Prefecture. The proportion of woodland and farmland which increased from urban to rural areas were two major enviornmental gradients according to Principal Component Analysis of the nine types of land-use. Ordination by Canonical Correspondence Analysis (CCA) showed that the breeding bird distribution differentiated along the two major clines, woodland and farmland. The avifauna changed successively along these environmental gradients. There were no discrete boundaries of the distribution of bird species groups. We tentatively classified five groups of quadrats on the ordination plane of the sample score. The geographic position of these five groups on a map preserved the environmental gradient, but showed that water (seashore and river) was a stronger influence on bird species composition than land-use pattern. Although the diversity of land-use seemed to raise species richness in the third group, the less diverse, woodland-rich group contained as many species as the third group. Four groups of bird species, and one group in which species occurred in more than 90% of the quadrats, were classified in the CCA-ordination plane. The occurrence of these bird groups correlated with land-use; the first group with woodland area, the second with scatter woodland, the third with farmland and the fourth with seashore.     

Cyst formation in the red tide flagellate Heterosigma akashiwo (Raphidophyceae)

A natural population of Heterosigma akashiwo was collected andincubated in the dark with autoclaved marine sediment. A portionof the cells in the population changed into cysts, which wereidentical to H.akashiwo cysts found in the field. The cystsrequired at least 2 weeks of mandatory dormancy before germination.     

Epstein-Barr virus infection of human gastric carcinoma cells: implication of the existence of a new virus receptor different from CD21.

Recombinant Epstein-Barr virus (EBV) with a selectable marker successfully infected the human gastric carcinoma cell lines AGS, MKN28, and MKN74. Following incubation in selective media, drug-resistant cell clones were isolated and proved to be infected with EBV. All gastric carcinoma cell clones were positive for EBNA 1 but negative for EBNA 2. LMP 1 expression was negative in most clones, but there were a few exceptions. Gastric carcinoma cells were negative for the EBV receptor CD21, and infection was not inhibited by pretreatment of cells with the anti-CD21 monoclonal antibody OKB7. The results indicate that gastric carcinoma cells are susceptible to EBV infection and that infection is mediated via a new receptor different from CD21.     

The relationship between viability and intracellular pH in the yeast Saccharomyces cerevisiae.

The relationship between viability (cell proliferation activity) and intracellular pH in the yeast Saccharomyces cerevisiae was investigated by using cells that had been deactivated by low-temperature storage, ethanol treatment, or heat treatment. The intracellular pH was measured with a microscopic image processor or a spectrofluorophotometer. At first, the intracellular pH measurements of individual cells were compared with slide culture results by microscopic image processing. A clear correlation existed between the proliferation activity and intracellular pH. Moreover, by spectrofluorophotometry analysis, it was found that there was a relationship between the viability and intracellular pH of brewing yeast under conditions of low external pH (n = 15, r = 0.960, P = 0.001). This relationship was also observed in baker's yeast (n = 13, r = 0.950, P = 0.001). On the other hand, when the fluorescein staining method was used in these experiments, the relationship between viability and staining percentage was not observed. From these results, intracellular pH was found to be a sensitive factor for estimating yeast physiology. The possible role of cell deterioration is also discussed.     

Localization of angiotensin-converting enzyme,prolyl endopeptidase and other peptidases in cultured neuronal or glial cells

To determine the cellular localization of nervous tissue peptidases, 7 peptidases and 2 lysosomal marker enzyme activities were measured in cultured mouse and rat cells. Neuronal cells of both species exhibited higher activities of angiotensin-converting enzyme (ACE) and prolyl endopeptidase (Pro-EP) than glial cells did. In contrast, arginyl endopeptidase and lysosomal enzymes (acid phosphatase, β-glucuronidase) in the neuronal cell lines were lower than those in the glial cell lines. Other peptidases (alanyl aminopeptidase, arginyl aminopeptidase, leucyl aminopeptidase, dipeptidyl aminopeptidase) activities were not specifically localized in either cell lines. The effects of cellular differentiation on these peptidase activities in the PC 12h cell line and rat glioblasts were also examined using nerve growth factor (NGF) and glia maturation factor (GMF), respectively. Neuron specific peptidase (ACE and Pro-EP) activities were decreased in PC12h cells cultured with NGF, and Pro-EP activity was increased in the glioblast cells cultured with GMF. These results support the idea that some of the peptidases are differentially localized in neuronal or glial cells, and play physiological roles in central or peripheral neural tissues.