Scale-dependent effects of windthrow disturbance on forest arthropod communities

The effect of disturbance on local communities may operate within the context of the spatial landscape. We examined the scale-dependent effects of windthrow disturbance caused by a large typhoon on three arthropod communities in a temperate forest of Japan. Canopy arthropods were collected by beating foliage, forest-floor arthropods were collected by sweeping the vegetation, and flying arthropods were collected in Malaise traps. To assess the “functional spatial scale” at which arthropods responded to tree-fall disturbance, the gap rate was quantified at different spatial scales by sequentially enlarging the radius of a circular landscape sector in 10-m increments from 10 to 500 m. We then analyzed the responses of order richness and abundance to the gap rate for each arthropod community. The spatial scale of the significant best-fitting model, which was selected from the models fitted to the gap rate at stepwise spatial scales, was regarded as the arthropod-specific functional spatial scale. Arthropod order richness was not dependent on the gap rate. In contrast, arthropod order abundance depended significantly on the gap rate in many orders, but varied in the response direction and functional spatial scale. These order-specific, scale-dependent responses to tree-fall gaps could complicate interactions among organisms, leading to complex community organization. An understanding of the spatial processes that link the use of space by organisms with the spatial scale at which ecological processes are experienced is required to elucidate the responses of populations, communities, and biotic interactions to disturbances in a spatial landscape context.     

Quantitative food webs of lepidopteran leafminers and their parasitoids in a Japanese deciduous forest

Quantitative food webs were constructed to explore the community structure of leaf-mining moths in the family Gracillariidae and their parasitoid wasps in a deciduous forest in Hokkaido, Japan. A whole food web was constructed from data collected from June to October 2001. In the web, 16 leafminer species on seven tree species were attacked by 58 species of hymenopteran parasitoid; 376 links between leafminers and parasitoids were observed. Leafminers were specialist herbivores, but most parasitoids were generalists. Five webs were constructed for the seasonal prevalence of leafminers over the one-year period to reveal the temporal dynamics in community structure. Among the seasonal webs, the first web in June was distinctive because two tree species, Japanese umbrella tree Magnolia obovata and Japanese magnolia M. kobus, supported the community. Second to fourth webs from July to September were dominated by the leafminer species on Japanese oak Quercus crispula, and the fifth web was marked by that on Carpinus cordata. The extent of potential apparent competition among leafminers was evaluated using quantitative parasitoid overlap diagrams. These diagrams suggested that abundant host species are likely to have large indirect effects on less abundant species. Moreover, the potential for apparent competition between leafminer species inhabiting different host tree species can occur, although leafminers sharing the same tree species are prone to interact via shared parasitoids. In this system, particular leafminer species, acting as potential sources of apparent competition, can affect other species as sinks, and control whole-community dynamics. Directed apparent competition may potentially occur around oak trees.     

Beta-diversity of lepidopteran larval communities in a Japanese temperate forest: effects of phenology and tree species

The specialization of herbivores among tree species is poorly understood despite its fundamental importance as a factor regulating diversity. To examine the effect of tree species on larval community structure, the larval communities in 10 temperate deciduous tree species that differed in leaf emergence pattern (flush- vs. intermediate-type) were seasonally surveyed. The newly developed soft, nitrogen-rich leaves of all species became tough and nitrogen-poor as the season progressed. Following the changes in leaf quality, two distinct seasonal lepidopteran larval communities emerged, with a marked turnover in early July. The beta diversity, or dissimilarity, of species composition in the larval communities among tree species was higher in summer than in spring. These results imply that the lepidopteran larval communities as a whole were supported by alpha diversity in spring and by beta diversity in summer, demonstrating that the plant diversity of this forest could support a caterpillar community. We examined the importance of spatio-temporal variations in leaf quality within and among tree species in promoting herbivore diversity, although other factors, such as tree species phylogeny and predators, may also have a large effect on lepidopteran larval communities.     

Molecular cloning and expression of a major surface protein (the 75-kDa protein) of Porphyromonas (Bacteroides) gingivalis in Escherichia coli

A major immunodominant surface protein (the 75-kDa protein) of Porphyromonas (Bacteroides) gingivalis 381 has been purified and its amino-terminal amino acid sequence has been determined. Using oligonucleotide probes corresponding to the sequence, we identified a recombinant plasmid clone carrying a single 4.2-kb BamHI fragment from pUC19 libraries of P. gingivalis. The BamHI fragment transferred to the bacteriophage T7 RNA polymerase/promoter expression vector system produced a slightly larger (77-kDa) protein, a precursor form, immunoreactive to the antibody against the 75-kDa protein, suggesting that the cloned DNA fragment probably carried an entire gene for the 75-kDa protein. Genomic Southern analysis revealed a single copy of the 75-kDa protein gene per genome among all P. gingivalis strains tested, and that no homologous genes are present in other black-pigmented Bacteroides species. These observations suggest that the 75-kDa protein gene may be useful as a specific DNA probe to classify or to detect this organism.     

鸡氨肽酶H在大肠杆菌中的表达、纯化与部分酶学性质分析

氨肽酶H(Aminopeptidase H, APH))是生物组织内一种常见的氨基内肽酶, 但因为天然材料中含量很低, 基本无法深入研究其催化机理、功能与结构的关系及其在生物体内的确切功能。从鸡肝组织克隆了APH的全基因序列, 并把该序列亚克隆到载体pET22b(+)上, 然后转化大肠杆菌Rosetta(DE3), 构建了APH的表达菌株。该菌株经IPTG诱导, 在SDS-PAGE上明显出现一条与天然APH理论分子量一致的新增蛋白带, 该条带的浓度随着表达时间的延长逐渐加深; 6 h基本达到平衡, 此时重组蛋白占总蛋白的16.7%, 表达水平高达94.7 mg/L。对表达产物进行了活性检测、纯化和酶学性质分析, 发现重组蛋白在亚基构成, 热稳定性, 最适pH等方面与天然APH基本相同, 据此可以确认表达产物确实是APH, 发酵液总活力达到1636 u/L。这些结果为APH的催化机理及其在生物体内的功能的阐明奠定了重要的物质基础。     

MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues

Background  

Sequence alignment is one of the most important techniques to analyze biological systems. It is also true that the alignment is not complete and we have to develop it to look for more accurate method. In particular, an alignment for homologous sequences with low sequence similarity is not in satisfactory level. Usual methods for aligning protein sequences in recent years use a measure empirically determined. As an example, a measure is usually defined by a combination of two quantities (1) and (2) below: (1) the sum of substitutions between two residue segments, (2) the sum of gap penalties in insertion/deletion region. Such a measure is determined on the assumption that there is no an intersite correlation on the sequences. In this paper, we improve the alignment by taking the correlation of consecutive residues.     

Effects of Various Growth Conditions in a Chemostat on Expression of Virulence Factors in Porphyromonas gingivalis

Porphyromonas gingivalis, one of the gram-negative organisms associated with periodontal disease, possesses potential virulence factors, including fimbriae, proteases, and major outer membrane proteins (OMPs). In this study, P. gingivalis ATCC 33277 was cultured in a chemostat under hemin excess and presumably peptide-limiting conditions to better understand the mechanisms of expression of the virulence factors upon environmental changes. At higher growth rates, the amounts of FimA and the 75-kDa protein, forming long and short fimbriae, respectively, increased significantly, whereas gingipains decreased in amount and activity. In a nutrient-limited medium, lesser amounts of the above two fimbrial proteins were observed, whereas clear differences were not found in the amounts of gingipains. In addition, two-dimensional electrophoresis revealed that proteins in cells were generally fewer in number during nutrient-limited growth. Under aeration, a considerable reduction in gingipain activity was found, whereas several proteins associated with intact cells significantly increased. However, the expression of major OMPs, such as RagA, RagB, and the OmpA-like proteins, was almost constant under all conditions tested. These results suggest that P. gingivalis may actively control expression of several virulence factors to survive in the widely fluctuating oral environment.     

Binding of a pleurotolysin ortholog from Pleurotus eryngii to sphingomyelin and cholesterol-rich membrane domains

A mixture of sphingomyelin (SM) and cholesterol (Chol) exhibits a characteristic lipid raft domain of the cell membranes that provides a platform to which various signal molecules as well as virus and bacterial proteins are recruited. Several proteins capable of specifically binding either SM or Chol have been reported. However, proteins that selectively bind to SM/Chol mixtures are less well characterized. In our screening for proteins specifically binding to SM/Chol liposomes, we identified a novel ortholog of Pleurotus ostreatus, pleurotolysin (Ply)A, from the extract of edible mushroom Pleurotus eryngii, named PlyA2. Enhanced green fluorescent protein (EGFP)-conjugated PlyA2 bound to SM/Chol but not to phosphatidylcholine/Chol liposomes. Cell surface labeling of PlyA2-EGFP was abolished after sphingomyelinase as well as methyl-β-cyclodextrin treatment, removing SM and Chol, respectively, indicating that PlyA2-EGFP specifically binds cell surface SM/Chol rafts. Tryptophan to alanine point mutation of PlyA2 revealed the importance of C-terminal tryptophan residues for SM/Chol binding. Our results indicate that PlyA2-EGFP is a novel protein probe to label SM/Chol lipid domains both in cell and model membranes.     

Purification and Some Properties of Arthrobacter globiformis Exo-l,6-α-glucosidase

A gram-positive and pleomorphic bacterium (strain I-42) isolated from soil as a producer of exo-l,6-α-glucosidase [EC 3.2.1.70] was identified as Arthrobacter globiformis. This Arthrobacter enzyme, inducible by dextran extracellularly, was partially purified from a cell-free culture supernatant. It was found most active at pH around 6.0 and most stable at pH 6.0~6.5. The enzyme was proved, by several experiments, to attack dextran in the exo-wise fashion to release only glucose leaving a macromolecular limit dextrandextrin. Transglucosylation from dextran to accumulating or added glucose was not observed.     

Apparent Turnover Rate of Diaphragm Proteins in Rats

A new antibiotic, toromycin (antibiotic B-21085) was isolated as yellow crystals from the culture broth of Streptomyces collinus subsp. albescens subsp. nov. The antibiotic has the molecular formula C₂₇H₂₆O₉ and is the polycyclic aromatic hydrocarbon group of antibiotics. Toromycin is active against gram-positive bacteria, mycobacteria, mycoplasma, DNA viruses and some bacteriophages.