Network Analysis of a Comprehensive Knowledge Repository Reveals a Dual Role for Ceramide in Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common cause of senile dementia. Many inflammatory factors such as amyloid-β and pro-inflammatory cytokines are known to contribute to the inflammatory response in the AD brain. Sphingolipids are widely known to have roles in the pathogenesis of inflammatory diseases, where the precise roles for sphingolipids in inflammation-associated pathogenesis of AD are not well understood. Here we performed a network analysis to clarify the importance of sphingolipids and to model relationships among inflammatory factors and sphingolipids in AD. In this study, we have updated sphingolipid signaling and metabolic cascades in a map of AD signaling networks that we named “AlzPathway,” a comprehensive knowledge repository of signaling pathways in AD. Our network analysis of the updated AlzPathway indicates that the pathways related to ceramide are one of the primary pathways and that ceramide is one of the important players in the pathogenesis of AD. The results of our analysis suggest the following two prospects about inflammation in AD: (1) ceramide could play important roles in both inflammatory and anti-inflammatory pathways of AD, and (2) several factors such as Sphingomyelinase and Siglec-11 may be associated with ceramide related inflammation and anti-inflammation pathways in AD. In this study, network analysis of comprehensive knowledge repository reveals a dual role for ceramide in AD. This result provides a clue to clarify sphingolipids related inflammatory and anti-inflammatory pathways in AD.     

Multiscale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, interpopulation genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within‐population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.     

Expression of <Emphasis Type="Italic">Ruminococcus albus</Emphasis> Xylanase Gene (<Emphasis Type="Italic">xyn</Emphasis>A) in <Emphasis Type="Italic">Streptococcus bovis</Emphasis> 12-U-1

The objective of this study was to ligate the xylanase gene A (xynA) isolated from Ruminococcus albus 7 into the promoter and signal-peptide region of the lichenase [β-(1,3-1,4)-glucanase] gene of Streptococcus bovis JB1. This fusion gene was inserted into the pSBE11 vector, and the resulting recombinant, plasmid pXA, was used to transform S. bovis 12-U-1 cells. The transformant, S. bovis 12UXA, secreted the xylanase, which was stable against freeze-thaw treatment and long-time incubation at 37°C. The introduction of pXA and production of xylanase did not affect cell growth, and the xylanase produced degraded xylan from oat-spelt and birchwood. Received: 24 June 2002 / Accepted: 7 October 2002     

Effects of inner solution viscosity and membrane stiffness on erythrocyte deformability on passing through a microchannel: prediction by two-dimensional simulation

We studied erythrocyte deformability in an effort to develop diagnostic methods based on its measurement and thus aid in the development of therapies for circulatory diseases. In the reported work, we performed two-dimensional numerical simulations of blood flow through a microchannel (MC) to evaluate erythrocyte deformability, applying the immersed boundary method to simulate erythrocyte movement and deformation. To evaluate deformability, MC transit capacity and shape recoverability were considered, defined as the time required to pass through the MC and the time constant during the shape-recovery process after exiting the MC, respectively. The simulation results showed that the erythrocyte MC transit time increased when the viscosity of the inner solution or the stiffness of the membrane increased. The time constant for erythrocyte shape recovery increased as the inner solution viscosity increased. In contrast, the time constant decreased as the erythrocyte membrane stiffness increased. These time-constant trends were in agreement with a theoretical equation derived using the Kelvin model and with previous experimental results. This diagnostic method of measuring erythrocyte shape recoverability and MC transit capacity is anticipated to have clinical application.     

Birth weight and birth rate of heavy calves conceived by transfer of in vitro or in vivo produced bovine embryos

The aim of this study was to evaluate the difference in birth weight and gestation length between Japanese Black calves obtained from transfer of bovine embryos produced in vitro (IVP) and those developed in vivo (IVD). An additional objective was to clarify the sire effect on birth weight and gestation length and to examine the birth rate of heavier calves. Two Japanese Black bulls breed at our experimental station were used as a semen source for production of IVP and IVD embryos. Thirty-eight Japanese Black heifers and cows of various genetic backgrounds were used as embryo donors for IVD embryos. Ovaries for IVP embryos were collected at random at a local slaughterhouse from Japanese Black cattle of various genetic backgrounds. IVP embryos were produced using co-culturing with cumulus cells in 5% CS+TCM 199. Both the IVD and IVP embryos were transferred non-surgically to Holstein recipients on day 7+/-1 of estrous cycle. In this study, the birth weights and gestation lengths of half-sib single calves for bull A and B were analyzed.The numbers of single calves born by transfer of IVP and IVD embryos for bull A and B were 133 and 121, 243 and 465, respectively. The birth weight of the IVP calves was significantly higher (P<0.01) than that of the IVD (bull A: 31.0+/-0.4 kg versus 27.2+/-0.4 kg and bull B: 29.9+/-0.6 kg versus 26.6+/-0.2 kg). Gestation length of the IVP calves for bull A was significantly longer (P<0.01) than that of the IVD (291.9+/-0.9 days versus 283.6+/-0.5 days). However, for bull B, there were no differences in gestation length between the IVP and IVD calves (285.9+/-0.7 days versus 286.2+/-0.3 days). These results clearly indicated that IVP calves had heavier birth weights than IVD calves but that the average gestation length of IVP calves was not always longer than that of IVD calves. Furthermore, the birth rate of heavier calves and the incidence of stillbirth and perinatal mortality up to 48 h post partum in IVP calves (bull A: 11.3%, bull B: 7.8%) were greater (P<0.05) than those in IVD calves from both bulls (bull A: 4.1%, bull B: 3.7%).     

Formation of Ascorbate Oxidase in Cultured Pumpkin Cells

Ascorbate oxidase activity rapidly increased during callus formationfrom pumpkin fruit tissue. The activity reached a maximum at5 days after transfer and then declined. In callus which hadbeen subcultured at about 4-week intervals for more than oneyear, the activity also increased after transfer to fresh mediumand reached a maximum in the early logarithmic phase of growth.Light had little effect on the appearance of ascorbate oxidaseactivity in pumpkin callus. In the callus grown in the presenceof 10µM CuSO₄, the activity was about 10 times that inthe presence of 0.1 µM CuSO₄, suggesting that the formatonof ascorbate oxidase in pumpkin callus is stimulated by copper,a prosthetic metal of the enzyme. From 45 to 75% of the totalascorbate oxidase activity in pumpkin cell suspension cultureswas found in the medium. Ascorbate oxidase activity in the medium,as well as that in the cells, increased soon after transferto fresh medium, and reached a maximum at about 5 days. (Received July 2, 1987; Accepted November 21, 1987)     

Alkaline phosphatase of <Emphasis Type="Italic">Physarum polycephalum</Emphasis> is insoluble

The plasmodia of Physarum polycephalum grow as multinucleated cells in the presence of sufficient humidity and nutriment. Under non-illuminating conditions, stresses such as low temperature or high concentrations of salts transform the plasmodia into spherules whereas dehydration induces sclerotization. Some phosphatases including protein phosphatase and acid phosphatase have been purified from the plasmodia, but alkaline phosphatase remains to be elucidated. Phosphatase of the plasmodia, spherules and sclerotia was visualized by electrophoresis gel-staining assay using 5-bromo-4-chloro-3-indolyl phosphate. Insoluble fractions of the sclerotia were abundant in phosphatase activity. The phosphatase which was extracted by nonionic detergent was subjected to column chromatography and preparative electrophoresis. Purified phosphatase showed the highest activity at pH 8.8, indicating that this enzyme belongs to alkaline phosphatase. The apparent molecular mass from sodium dodecyl sulfate-polyacrylamide gel electrophoresis under non-reducing condition was estimated to be 100 kDa whereas that under reducing was 105 kDa. An amount of 1% sodium dodecyl sulfate or 0.5 M NaCl had no effects on the activity although the phosphatase showed heat instability, Mg²⁺-dependency and sensitivity to 2-glycerophosphate or NaF. The extracting conditions and enzymatic properties suggest that this alkaline phosphatase which is in a membrane-bound form plays important roles in phosphate metabolism.     

Galactosialidosis: molecular heterogeneity in biosynthesis and processing of protective protein for β-galactosidase

Summary Biosynthesis and processing of the protective protein for -galactosidase in normal and galactosialidosis fibroblasts were investigated using specific antiserum preparations. A 45-kd precursor was processed to a mature 30-kd protein in normal fibroblasts. The mature protective protein was not detected in any of the twelve galactosialidosis fibroblast strains examined in this study. The precursor was not detected in two cases and in the others was of heterogeneous molecular weight, i.e., normal, abnormally low, or abnormally high. These molecular abnormalities were not correlated with clinical manifestations of the patients.