Isolation and characterization of <Emphasis Type="Italic">Bacillus</Emphasis><Emphasis Type="Italic">polyfermenticus</Emphasis> isolated from <Emphasis Type="Italic">Meju,</Emphasis> Korean soybean fermentation starter

Bacteria of the Bacillus species have been reported as an important microorganism in fermented soybean products. In the present study, thirty Bacillus isolates were screened from Meju, a Korean soybean fermentation starter. The comparative analysis of 16S rDNA sequences, 16S-23S internal transcribed spacer sequences, phenotypic, and biochemical characterizations revealed three phylogenetically distinct groups namely Bacillus atrophaeus, Bacillus polyfermenticus and Bacillus subtilis. The isolates were assayed for poly-γ-glutamate production and fibrinolytic activity. Among the isolates, B. polyfermenticus exhibited maximum poly-γ-glutamate production and fibrinolytic activity. Moreover, the soybean products fermented by B. polyfermenticus have increased the time taken for coagulation and hemorrhage in mice. The results of the present study clearly indicate the functional role of B. polyfermenticus in fermented soybean products.     

Promise and pitfalls of the Immunochip

Genomewide association studies (GWAS) have proven a powerful hypothesis-free method to identify common disease-associated variants. Even quite large GWAS, however, have only at best identified moderate proportions of the genetic variants contributing to disease heritability. To provide cost-effective genotyping of common and rare variants to map the remaining heritability and to fine-map established loci, the Immunochip Consortium has developed a 200,000 SNP chip that has been produced in very large numbers for a fraction of the cost of GWAS chips. This chip provides a powerful tool for immunogenetics gene mapping.     

Proteomic analysis of phytopathogenic fungus <Emphasis Type="Italic">Botrytis cinerea</Emphasis> as a potential tool for identifying pathogenicity factors,therapeutic targets and for basic research

Botrytis cinerea is a phytopathogenic fungus causing disease in a substantial number of economically important crops. In an attempt to identify putative fungal virulence factors, the two-dimensional gel electrophoresis (2-DE) protein profile from two B. cinerea strains differing in virulence and toxin production were compared. Protein extracts from fungal mycelium obtained by tissue homogenization were analyzed. The mycelial 2-DE protein profile revealed the existence of qualitative and quantitative differences between the analyzed strains. The lack of genomic data from B. cinerea required the use of peptide fragmentation data from MALDI-TOF/TOF and ESI ion trap for protein identification, resulting in the identification of 27 protein spots. A significant number of spots were identified as malate dehydrogenase (MDH) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The different expression patterns revealed by some of the identified proteins could be ascribed to differences in virulence between strains. Our results indicate that proteomic analysis are becoming an important tool to be used as a starting point for identifying new pathogenicity factors, therapeutic targets and for basic research on this plant pathogen in the postgenomic era.     

环境样品中DNA的分离纯化和文库构建

采用研磨 /冻融和SDS/蛋白酶K热处理等理化方法 ,直接从性质不同的环境样品中提取和纯化混合基因组DNA。所获得纯品DNA的产量为每克样品 2～ 1 6μg。对纯品DNA进行限制性内切酶处理后 ,构建了以pUC1 8为载体的DNA文库。建库效率为从每克环境样品获得约 1 0 3～ 1 0 4 个含 3～ 8kb外源随机插入片段的克隆。通过DNA序列测定和基因注释 ,对从文库中随机选取的克隆进行了分析 ,发现外源插入片段均含序列未见报道的新基因。本文所做的尝试对于保存、研究和开发未培养微生物基因资源具有意义     

Motion Noise Changes Directional Interaction between Transparently Moving Stimuli from Repulsion to Attraction

To interpret visual scenes, visual systems need to segment or integrate multiple moving features into distinct objects or surfaces. Previous studies have found that the perceived direction separation between two transparently moving random-dot stimuli is wider than the actual direction separation. This perceptual “direction repulsion” is useful for segmenting overlapping motion vectors. Here we investigate the effects of motion noise on the directional interaction between overlapping moving stimuli. Human subjects viewed two overlapping random-dot patches moving in different directions and judged the direction separation between the two motion vectors. We found that the perceived direction separation progressively changed from wide to narrow as the level of motion noise in the stimuli was increased, showing a switch from direction repulsion to attraction (i.e. smaller than the veridical direction separation). We also found that direction attraction occurred at a wider range of direction separations than direction repulsion. The normalized effects of both direction repulsion and attraction were the strongest near the direction separation of ∼25° and declined as the direction separation further increased. These results support the idea that motion noise prompts motion integration to overcome stimulus ambiguity. Our findings provide new constraints on neural models of motion transparency and segmentation.     

Oligomeric State and Thermal Stability of Apo- and Holo- Human Ornithine δ-Aminotransferase

Human ornithine δ-aminotransferase (hOAT) (EC 2.6.1.13) is a mitochondrial pyridoxal 5′-phosphate (PLP)-dependent aminotransferase whose deficit is associated with gyrate atrophy, a rare autosomal recessive disorder causing progressive blindness and chorioretinal degeneration. Here, both the apo- and holo-form of recombinant hOAT were characterized by means of spectroscopic, kinetic, chromatographic and computational techniques. The results indicate that apo and holo-hOAT (a) show a similar tertiary structure, even if apo displays a more pronounced exposure of hydrophobic patches, (b) exhibit a tetrameric structure with a tetramer-dimer equilibrium dissociation constant about fivefold higher for the apoform with respect to the holoform, and (c) have apparent T_m values of 46 and 67?°C, respectively. Moreover, unlike holo-hOAT, apo-hOAT is prone to unfolding and aggregation under physiological conditions. We also identified Arg217 as an important hot-spot at the dimer–dimer interface of hOAT and demonstrated that the artificial dimeric variant R217A exhibits spectroscopic properties, T_m values and catalytic features similar to those of the tetrameric species. This finding indicates that the catalytic unit of hOAT is the dimer. However, under physiological conditions the apo-tetramer is slightly less prone to unfolding and aggregation than the apo-dimer. The possible implications of the data for the intracellular stability and regulation of hOAT are discussed.     

Moose summer and winter diets along a large scale gradient of forage availability in southern Norway

Studies on dietary functional responses in large herbivores are traditionally conducted by following individual animals. The method is very time-consuming, and hence, typically provides only a narrow array of forage species compositions. Here we use a range level approach to look at moose (Alces alces) selectivity for and utilization of forage species in relation to availability in both summer and winter. We compare 12 Norwegian ranges representing a large scale gradient in plant communities. The most important forage species in the diet were birches (Betula spp., comprising 43% of all trees browsed in summer and 27% in winter), rowan (Sorbus aucuparia, 25% of trees browsed in summer, 37% in winter), and bilberry (Vaccinum myrtillus, 42% of herbaceous epidermal fragments in summer feces). Selectivity for birches was positively related to its availability and negatively related to availability of rowan, Salix spp., and aspen (Populus tremula) together (all more selected for than birches). Multiple regression models including availability of several forage species were thus superior to single-species models in explaining the diet content of main forage plants. Selectivity for birches was also stronger in summer than in winter, while the opposite pattern was found for rowan. The finding is relevant for our evaluation of the quality of summer and winter ranges, and hence, their relative influence on population productivity. Our study underlines the need to incorporate species composition of available forage when quantifying dietary functional responses in selective herbivores such as moose. Furthermore, care should be taken when extrapolating data on moose diet across ranges or seasons.     

Habitat Use and Ranging Behavior of <Emphasis Type="Italic">Callimico goeldii</Emphasis>

We studied the diet, habitat use, and ranging behavior of 1 group of Callimico goeldii (callimicos) over 12 mo in northwestern Bolivia. The group’s diet was comprised of fungi (39%), fruits (31%), arthropods (14%), exudates (14%), and other matter (2%). Callimicos concentrated their ranging activities in secondary forest (50%), primary forest with dense understory (30%), and bamboo (17%) habitats. The group’s total home range was 114 ha; on average they used 38.4 ha/ mo and had a day range of 925 m. Monthly average day ranges—but not monthly home ranges—increased as frugivory declined, suggesting that subjects foraged on fungi and exudates by rechecking resources within a core area, making their day ranges longer than during months when they concentrated on fruit resources. The callimicos formed polyspecific associations with tamarins (Saguinus labiatus and S. fuscicollis) during 81% of observations. Day ranges increased in months with higher association rates which appears to result from the callimicos using a broader set of habitats when with tamarins than when alone. The ranging pattern of callimicos appears to be influenced primarily by 3 factors: their seasonal shift in diet requires that they forage in a variety of habitats across the year; their depletion of resources causes them to shift their core area over time; and their lack of territorial behavior eliminates the need to patrol boundaries as part of their daily movement. As a result, callimicos differ from many other callitrichids in their low ratio of day range length to home range size.     

Translational machinery of the chaetognath <Emphasis Type="Italic">Spadella cephaloptera</Emphasis>: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

Background  

Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies.