Detecting nonculturable bacteria in the active mycorrhizal zone of the pine mushroom <Emphasis Type="Italic">Tricholoma matsutake</Emphasis>

The fungus Tricholoma matsutake forms an ectomycorrhizal relationship with pine trees. Its sporocarps often develop in a circle, which is commonly known as a fairy ring. The fungus produces a solid, compact, white aggregate of mycelia and mycorrhizae beneath the fairy ring, which in Japanese is called a ’shiro’. In the present study, we used soil dilution plating and molecular techniques to analyze the bacterial communities within, beneath, and outside the T. matsutake fairy ring. Soil dilution plating confirmed previous reports that bacteria and actinomycetes are seldom present in the soil of the active mycorrhizal zone of the T. matsutake shiro. In addition, the results showed that the absence of bacteria was strongly correlated with the presence of T. matsutake mycorrhizae. The results demonstrate that bacteria, especially aerobic and heterotrophic forms, and actinomycetes, are strongly inhibited by T. matsutake. Indeed, neither bacteria nor actinomycetes were detected in 11.3% of 213 soil samples from the entire shiro area by culture-dependent methods. However, molecular techniques demonstrated that some bacteria, such as individual genera of Sphingomonas and Acidobacterium, were present in the active mycorrhizal zone, even though they were not detected in soil assays using the dilution plating technique.     

Grasses and browsers reinforce landscape heterogeneity by excluding trees from ecosystem hotspots

Spatial heterogeneity in woody cover affects biodiversity and ecosystem function, and may be particularly influential in savanna ecosystems. Browsing and interactions with herbaceous plants can create and maintain heterogeneity in woody cover, but the relative importance of these drivers remains unclear, especially when considered across multiple edaphic contexts. In African savannas, abandoned temporary livestock corrals (bomas) develop into long-term, nutrient-rich ecosystem hotspots with unique vegetation. In central Kenya, abandoned corral sites persist for decades as treeless ‘glades’ in a wooded matrix. Though glades are treeless, areas between adjacent glades have higher tree densities than the background savanna or areas near isolated glades. The mechanisms maintaining these distinctive woody cover patterns remain unclear. We asked whether browsing or interactions with herbaceous plants help to maintain landscape heterogeneity by differentially impacting young trees in different locations. We planted the mono-dominant tree species (Acacia drepanolobium) in four locations: inside glades, far from glades, at edges of isolated glades and at edges between adjacent glades. Within each location, we assessed the separate and combined effects of herbivore exclusion (caging) and herbaceous plant removal (clearing) on tree survival and growth. Both caging and clearing improved tree survival and growth inside glades. When herbaceous plants were removed, trees inside glades grew more than trees in other locations, suggesting that glade soils were favorable for tree growth. Different types of glade edges (isolated vs. non-isolated) did not have significantly different impacts on tree performance. This represents one of the first field-based experiments testing the separate and interactive effects of browsing, grass competition and edaphic context on savanna tree performance. Our findings suggest that, by excluding trees from otherwise favorable sites, both herbaceous plants and herbivores help to maintain functionally important landscape heterogeneity in African savannas.     

GPCR-MPredictor: multi-level prediction of G protein-coupled receptors using genetic ensemble

G protein-coupled receptors (GPCRs) are transmembrane proteins, which transduce signals from extracellular ligands to intracellular G protein. Automatic classification of GPCRs can provide important information for the development of novel drugs in pharmaceutical industry. In this paper, we propose an evolutionary approach, GPCR-MPredictor, which combines individual classifiers for predicting GPCRs. GPCR-MPredictor is a web predictor that can efficiently predict GPCRs at five levels. The first level determines whether a protein sequence is a GPCR or a non-GPCR. If the predicted sequence is a GPCR, then it is further classified into family, subfamily, sub-subfamily, and subtype levels. In this work, our aim is to analyze the discriminative power of different feature extraction and classification strategies in case of GPCRs prediction and then to use an evolutionary ensemble approach for enhanced prediction performance. Features are extracted using amino acid composition, pseudo amino acid composition, and dipeptide composition of protein sequences. Different classification approaches, such as k-nearest neighbor (KNN), support vector machine (SVM), probabilistic neural networks (PNN), J48, Adaboost, and Naives Bayes, have been used to classify GPCRs. The proposed hierarchical GA-based ensemble classifier exploits the prediction results of SVM, KNN, PNN, and J48 at each level. The GA-based ensemble yields an accuracy of 99.75, 92.45, 87.80, 83.57, and 96.17% at the five levels, on the first dataset. We further perform predictions on a dataset consisting of 8,000 GPCRs at the family, subfamily, and sub-subfamily level, and on two other datasets of 365 and 167 GPCRs at the second and fourth levels, respectively. In comparison with the existing methods, the results demonstrate the effectiveness of our proposed GPCR-MPredictor in classifying GPCRs families. It is accessible at .     

HCCR-1, a novel oncogene,encodes a mitochondrial outer membrane protein and suppresses the UVC-induced apoptosis

Background  

The Human cervical cancer oncogene (HCCR-1) has been isolated as a human oncoprotein, and has shown strong tumorigenic features. Its potential role in tumorigenesis may result from a negative regulation of the p53 tumor suppressor gene.     

Biomass accumulations and the distribution of nitrogen and phosphorus within three<Emphasis Type="Italic">Quercus acutissima</Emphasis> stands in central Korea

Above- and belowground biomass and nitrogen (N) and phosphorus (P) distribution within threeQuercus acutissima stands were investigated in central Korea. The average age (year) and diameter at breast height (DBH, cm) were 10.8 and 7.9 for Stand 1, 38.2 and 17.1 for Stand 2, and 44.0 and 20.7 for Stand 3, respectively. Fifteen trees were destructively harvested for dimension analysis of component biomass (stem wood, stem bark, foliage, branches, and roots) plus N and P concentrations. Total biomass (t ha^-1) was 88.7 for Stand 1, 154.9 for Stand 2, and 278.1 for Stand 3 while N and P contents in all tree components (kg ha^-1) were 483.3 and 52.2, 697.1 and 55.0, and 1113.9 and 83.7. Nitrogen concentrations were highest in the foliage, followed by the stem bark, branches or roots, and stem wood. In contrast, P concentrations were greatest in the roots, then foliage, branches, stem bark, and stem wood. In general, N and P concentrations in these components significantly decreased with tree age and DBH, while N and P contents significantly increased with age and size. These relationships were stronger for size than for age. Our current data could be utilized to estimate N and P budgets for silvicultural practices, including fertilization, thinning, and harvesting.     

<Emphasis Type="Italic">Saturnispora serradocipensis</Emphasis> sp. nov. and <Emphasis Type="Italic">Saturnispora gosingensis</Emphasis> sp. nov., two ascomycetous yeasts from ephemeral habitats

Two novel ascomycetous yeast species, Saturnispora serradocipensis and Saturnispora gosingensis, were isolated from leaf detritus in a tropical stream of Southeastern Brazil and a mushroom collected in Taiwan, respectively. Analysis of the D1/D2 domains of the large-subunit of the rRNA gene of these strains showed that these species are related to Saturnispora hagleri, their closest relative. Saturnispora serradocipensis and S. gosingensis differed from S. hagleri, respectively, by seven nucleotide substitutions and two indels and three nucleotide substitutions and three indels in D1/D2 rRNA sequences. The two new species differ from each another by four nucleotide substitutions and one indel in D1/D2 rRNA sequences. However, the ITS sequences of S. serradocipensis, S. gosingensis and S. hagleri were quite divergent, showing that they are genetically separate species. The type strain of S. serradocipensis is UFMG-DC-198^T (=CBS 11756^T = NRRL Y-48717^T), and of S. gosingensis GA4M05^T is (CBS 11755^T = NRRL Y-48718^T).     

Inherited fungal symbionts enhance establishment of an invasive annual grass across successional habitats

Plants infected with vertically transmitted fungal endophytes carry their microbial symbionts with them during dispersal into new areas. Yet, whether seed-borne endophytes enhance the host plant’s ability to overcome colonisation barriers and to regenerate within invaded sites remains poorly understood. We examined how symbiosis with asexual endophytic fungi (Neotyphodium) affected establishment and seed loss to predators in the invasive annual grass Lolium multiflorum (Italian ryegrass) across contrasting successional plots. Italian ryegrass seeds with high and low endophyte incidence were sown into three communities: a 1-year-old fallow field, a 15-year-old grassland, and a 24-year-old forest, which conformed to an old-field chronosequence in the eastern Inland Pampa, Argentina. We found that endophyte infection consistently increased host population recruitment and reproductive output. Endophyte presence also enhanced aerial biomass production of ryegrass in a low recruitment year but not in a high recruitment year, suggesting that symbiotic effects on growth performance are density dependent. Endophyte presence reduced seed removal by rodents, although differential predation may not account for the increased success of infected grass populations. Overall, there was no statistical evidence for an endophyte-by-site interaction, indicating that the fungal endosymbiont benefitted host establishment regardless of large differences in biotic and abiotic environment among communities. Our results imply that hereditary endophytes may increase the chances for host grass species to pass various ecological filters associated with invasion resistance across a broad range of successional habitats.