Investigation of the microbial community in a microbiological additive used in a manure composting process

The objectives of this study were to investigate the fate of microorganisms by using cultivation methods as well as DNA analyses in a commercial microbiological additive (MA) in the course of the composting. Almost all the predominant species in the microbial succession during composting process determined by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were in disagreement with those determined by the clone library method. None of the microbial species in the composting stages corresponded to the microorganisms identified in the MA either by the cultivation method or DNA analysis. The results in regard to predominant microorganisms of the MA detected from the liquid medium by the PCR-DGGE did not correspond with those detected from the MA itself and composting processes. Although no evidence was found that predominant species in the MA itself dominate in the composting process, predominant species diversity in the MA itself was markedly changed after culturing at different thermophilic temperatures. These results suggested that cultivable microorganisms in the MA did not become predominant in the composting process: however, some microorganisms that are detected from the MA itself by the DNA analysis may act effectively in the composting process.     

PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA) INFERRED FROM CLADISTIC ANALYSIS BASED ON MORPHOLOGICAL DATA1

A cladistic analysis was used to deduce the phylogenetic relationships within the colonial Volvocales. Forty-one pairs of characters related to gross morphology and ultrastructure of vegetative colonies as well as asexual and sexual reproduction were analyzed based on parsimony, using the PAUP 3.0 computer program, for 25 species belonging to nine volvocacean and goniacean genera of the colonial Volvocales. Chlamydomonas reinhardtii Dangeard was the outgroup. The strict consensus tree indicated the presence of two monophyletic groups, one composed of all the volvocacean species analyzed in this study and the other containing the goniacean species except for the four-celled species Gonium sociale (Dujardin) Warming. In addition, these two groups constitute a large monophyletic group, to which G. sociale is a sister group. A new combination Tetrabaena socialis (Dujardin) Nozaki et Itoh and a new family Tetrabaenaceae Nozaki et Itoh are thus proposed for G. sociale. In addition, the analysis suggests that the volvocacean genera Eudorina and Pleodorina are paraphyletic groups, respectively, and that the monotypic genus Yamagishiella has no autapomorphic characters and represents primitive features of the anisogamous and oogamous genera of the Volvocaceae. Phylogenetic relationships within the Volvocaceae and the Goniaceae, as well as the various modes of sexual reproduction exhibited by these organisms, are discussed on the basis of the analysis.     

A new approach to three-dimensional reconstructed imaging of hormone-secreting cells and their microvessel environments in rat pituitary glands by confocal laser scanning microscopy.

There has been considerable interest in the relationship between hormone- secreting endocrine cells and their microvessels in human pituitary gland. However, microcirculatory networks have rarely been studied in three dimensions (3D). This study was designed to visualize and to reveal the relationship between hormone-secreting endocrine cells and their microvessel environment in 3D, using rat pituitary glands under various (hyper/hypo) experimental conditions by confocal laser scanning microscopy (CLSM). Female adult Wistar rats were used after bilateral adrenalectomy or ACTH administration for 2 weeks. Clear 3D reconstructed images of ACTH cells, the microvessel network and counterstained nuclei were obtained at a maximal focus depth of 1 mm by CLSM without any background noise. In the hyperfunctional state, slender cytoplasmic processes of hypertrophic stellate ACTH cells frequently extended to the microvessels. In the hypofunctional state, ACTH cells appeared atrophic and round with scanty cytoplasm, and cytoplasmic adhesions to microvessel network patterns were inconspicuous. Therefore, 3D reconstructed imaging by CLSM is a useful technique with which to investigate the microvessel environment of hormone-secreting cells and has the potential to reveal dynamic hormone-secreting pathways.     

Describing size-related mortality and size distribution by nonparametric estimation and model selection using the Akaike Bayesian Information Criterion

When we calculate mortality along a gradient such as size, dividing into size classes and calculating rates for every class often involves a trade-off: fine class intervals produce fluctuating rates along the gradient, whereas broad ones may miss some trends within an interval. The same trade-off occurs when we want to illustrate size distribution by a histogram. This paper introduces nonparametric methods, published in a statistical journal, into forest ecology, in which the fine-class strategy is used in an extreme way: (1) a smoothly changing pattern is approximated by a fine step function, (2) the goodness-of-fit to the data and the smoothness along the gradient are formulated as a weighting sum within a Bayesian framework, (3) the Akaike Bayesian Information Criterion (ABIC) selects the weighting system that most appropriately balances the two demands, and (4) the values of the step function are optimized by the maximum likelihood method. The nonparametric estimates enable us to represent various patterns visually and, unlike parametric modeling, calculations do not demand the determination of a functional form. Mortality and size distribution analyses were conducted on 12-year forest tree monitoring data from a 4 ha permanent plot in an old-growth warm–temperate evergreen broad-leaved forest in Japan. From trees of 11 evergreen species with a diameter at breast height (DBH) greater than 5 cm, we found three types of trend with increasing DBH: decreasing, ladle-shaped and constant mortality. These patterns reflect variations in life history particular to each species.     

Fermentation of soybean meal withAspergillus usamii improves zinc availability in rats

Soybean meal was fermented withAspergillus usamii to improve zinc availability through the degradation of phytic acid. Rats fed a diet containing fermented soybean meal showed greater femoral zinc than did animals fed a diet containing regular soybean meal. Zinc solubility in the small intestine was higher in the rats fed fermented soybean meal than in the rats fed regular soybean meal. These results suggested that fermentation withAspergillus usamii improved zinc availability in dietary soybean meal, which was induced by the increase of zinc solubility in the small intestine. Adding the same amount of phytate that was contained in the regular soybean mealbased diet did not affect the amount of zinc present in rats fed a fermented soybean meal-based diet with sodium phytate. Phytase activity was found in fermented soybean meal, and this activity may degrade added phytate in fermented soybean meal-based diet.     

Novel role of p66Shc in ROS-dependent VEGF signaling and angiogenesis in endothelial cells

p66Shc, a longevity adaptor protein, is demonstrated as a key regulator of reactive oxygen species (ROS) metabolism involved in aging and cardiovascular diseases. Vascular endothelial growth factor (VEGF) stimulates endothelial cell (EC) migration and proliferation primarily through the VEGF receptor-2 (VEGFR2). We have shown that ROS derived from Rac1-dependent NADPH oxidase are involved in VEGFR2 autophosphorylation and angiogenic-related responses in ECs. However, a role of p66Shc in VEGF signaling and physiological responses in ECs is unknown. Here we show that VEGF promotes p66Shc phosphorylation at Ser36 through the JNK/ERK or PKC pathway as well as Rac1 binding to a nonphosphorylated form of p66Shc in ECs. Depletion of endogenous p66Shc with short interfering RNA inhibits VEGF-induced Rac1 activity and ROS production. Fractionation of caveolin-enriched lipid raft demonstrates that p66Shc plays a critical role in VEGFR2 phosphorylation in caveolae/lipid rafts as well as downstream p38MAP kinase activation. This in turn stimulates VEGF-induced EC migration, proliferation, and capillary-like tube formation. These studies uncover a novel role of p66Shc as a positive regulator for ROS-dependent VEGFR2 signaling linked to angiogenesis in ECs and suggest p66Shc as a potential therapeutic target for various angiogenesis-dependent diseases.     

Spatial distribution of the basidiocarps of aphyllophoraceous fungi in a tropical rainforest on Borneo Island, Malaysia

The spatial distribution of basidiocarps provides much information on the dispersal abilities, habitat preferences, and inter- and intraspecific interactions of aphyllophoraceous fungi. To reveal the spatial distribution and resource utilization patterns of aphyllophoraceous fungi in Malaysia, we conducted field observations in a primary forest in 2006 and analyzed the relationships between the abundance of eight dominant fungal species and various environmental factors. The topographical characteristics were significantly patchily distributed at the 100-m scale, whereas woody debris and most fungal species were distributed randomly. Although the dominant fungal species differed among the decay classes and diameters of the woody debris, the abundance of a few dominant species was significantly correlated with environmental factors. Although the latter factors might affect the spatial distribution of these fungi, the effects appear to be so small that they would not create an aggregated distribution at a few 100-m scales.     

Identification of Murine T Cells Reactive with the Bacterial Superantigen Yersinia pseudotuberculosis-Derived Mitogen (YPM) and Factors Involved in YPM-Induced Toxicity in Mice

We previously reported that Yersinia pseudotuberculosis-derived mitogen (YPM) acts as a superantigen to human T cells. In this study, we assessed the superantigenicity and toxicity of YPM using murine experimental models. YPM activated T cells to produce interleukin-2 in a major histocompatibility complex class II molecule-dependent manner. The T-cell blasts induced by YPM expressed T-cell receptor (TCR) β-chain variable region (Vβ)7, VβS.1, Vβ8.2 and Vβ8.3. The injection of YPM into mice pre-sensitized with D-galactosamine induced lethal shock. This shock was blocked by the injection of monoclonal antibodies (mAbs) to CD4, TCR Vβ7 plus Vβ8, tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ), but not by injection to CD8 or unrelated Vβ. These results indicate that YPM-induced shock requires the presence of CD4⁺ T cells bearing TCR Vβ7 and Vβ8, and that endogenous TNF-a and IFN-γ mediate the lethal effects.     

Real-time quantitative PCR assay on bacterial DNA: In a model soil system and environmental samples

Real-time quantitative PCR (RTQ-PCR) was used to quantify the bacterial target DNA extracted by three commonly used DNA extraction protocols (bead mill homogenization, grinding in presence of liquid nitrogen and hot detergent SDS based enzymatic lysis). For the purpose of our study, pure culture of Bacillus cereus (model organism), sterilized soil seeded with a known amount of B. cereus (model soil system) and samples from woodland and grassland (environmental samples) were chosen to extract DNA by three different protocols. The extracted DNA was then quantified by RTQ-PCR using 16S rDNA specific universal bacterial primers. The standard curve used for the quantification by RTQ-PCR was linear and revealed a strong linear relationship (r(2)=0.9968) with a higher amplification efficiency, e5=1.02. High resolution gel electrophoresis was also carried out to observe the effect of these extraction methods on diversity analysis. For the model soil system, the liquid nitrogen method showed the highest target DNA copy number (1.3 x 10(9) copies/microl). However, for both the environmental samples, the bead beating method was found to be suitable on the basis of the high target DNA copy numbers (5.38 x 10(9) and 4.01 x 10(8) copies/ml for woodland and grassland respectively), high yield (6.4 microg/g and 1.76 microg/g of soil for woodland and grassland respectively) and different band patterns on high resolution gel electrophoresis suggesting an overall high extraction efficiency. This difference in the extraction efficiency between the model soil system and environmental samples may be attributed to different affinity of seeded and native DNA to soil particles.