Quantitative proteomic analysis of rat liver for carcinogenicity prediction in a 28-day repeated dose study

The potential of quantitative proteomic analysis to predict carcinogenicity of chemical compounds was investigated. Using 2D-DIGE, we analyzed the effects of 63 chemical compounds on protein expression in the rat liver after 28 daily doses. Types of carcinogens were categorized depending on the species and organ specificity. The carcinogen characteristic proteins for each classification were identified by Welch's t value. For evaluation of the predictive concordance we used support vector machines. The rat hepatic carcinogen-specific classification gave higher concordance than the other classification. The generalization performance was measured by leave-one-out cross-validation. For genotoxic and non-genotoxic compounds, a concordance of 79.3 and 76.5%, respectively, was obtained by the top 30 ranked proteins with Welch's t value. Furthermore, we found that the increase of the expression level of the stress response proteins as the common feature of poorly predicted chemical compounds in the leave-20%-out cross-validation. Quantitative proteomics could be promising technique for developing biomarker panels that can be used for carcinogenicity prediction. The list of proteins identified in this study and the zoomed gel images of the top ranked proteins in statistic analysis are provided in Supplementary Data.     

Flagellum-mediated motility in Pelotomaculum thermopropionicum SI

The basic functions of a propionate-oxidizing bacterium Pelotomaculum thermopropionicum flagellum, such as motility and chemotaxis, have not been studied. To investigate its motility, we compared with that of Syntrophobacter fumaroxidans, an aflagellar propionate-oxidizing bacterium, in soft agar medium. P. thermopropionicum cells spread, while S. fumaroxidans cells moved downward slightly, indicating flagellum-dependent motility in P. thermopropionicum SI. The motility of P. thermopropionicum was inhibited by the addition of carbonyl cyanide m-chlorophenyl hydrazone, a proton uncoupler, which is consistent with the fact that stator protein, MotB of P. thermopropionicum, shared sequence homology with proton-type stators. In addition, 5-N-ethyl-N-isopropyl amiloride, an Na⁺ channel blocker, showed no inhibitory effect on the motility. Furthermore, motAB of P. thermopropionicum complemented the defective swimming ability of Escherichia coli ?motAB. These results suggest that the motility of P. thermopropionicum SI depends on the proton-type flagellar motor.     

Sequence- and seed-structure-dependent polymorphic fibrils of alpha-synuclein

Synucleinopathies comprise a diverse group of neurodegenerative diseases including Parkinson's disease (PD), dementia with Lewy bodies, and multiple system atrophy. These share a common pathological feature, the deposition of alpha-synuclein (a-syn) in neurons or oligodendroglia. A-syn is highly conserved in vertebrates, but the primary sequence of mouse a-syn differs from that of human at seven positions. However, structural differences of their aggregates remain to be fully characterized. In this study, we found that human and mouse a-syn aggregated in vitro formed morphologically distinct amyloid fibrils exhibiting twisted and straight structures, respectively. Furthermore, we identified different protease-resistant core regions, long and short, in human and mouse a-syn aggregates. Interestingly, among the seven unconserved amino acids, only A53T substitution, one of the familial PD mutations, was responsible for structural conversion to the straight-type. Finally, we checked whether the structural differences are transmissible by seeding and found that human a-syn seeded with A53T aggregates formed straight-type fibrils with short protease-resistant cores. These results suggest that a-syn aggregates form sequence-dependent polymorphic fibrils upon spontaneous aggregation but become seed structure-dependent upon seeding.     

First record of the invasive woodwasp,Urocerus albicornis (Hymenoptera: Siricidae), from a local forest in Japan

The woodwasp Urocerus albicornis (Fabricius, 1781) (Hymenoptera: Siricidae) is a forest pest native to North America and occasionally introduced into European countries. One of these invasive woodwasps was collected in a local forest in Nagano Prefecture, Central Japan. The collected individual was an adult female ovipositing on a log from a Japanese larch (Larix kaempferi (Lamb.) Carrière). Although several of these woodwasps have been found on imported logs in Japan, this is the first record of the alien woodwasp in a local forest within Japan and Asia. This finding indicates that a population of this invasive woodwasp may be established in Japanese forests.     

DmGEN, a novel RAD2 family endo-exonuclease from Drosophila melanogaster

A novel endo-exonuclease, DmGEN (Drosophila Melanogaster XPG-like endonuclease), was identified in D.melanogaster. DmGEN is composed of five exons and four introns, and the open reading frame encodes a predicted product of 726 amino acid residues with a molecular weight of 82.5 kDa and a pI of 5.36. The gene locus on Drosophila polytene chromosomes was detected at 64C9 on the left arm of chromosome 3 as a single site. The encoded protein showed a relatively high degree of sequence homology with the RAD2 nucleases, especially XPG. Although the XPG-N- and XPG-I-domains are highly conserved in sequence, locations of the domains are similar to those of FEN-1 and EXO-1, and the molecular weight of the protein is close to that of EXO-1. In vitro, DmGEN showed endonuclease and 3'-5' exonuclease activities with both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), but the endonuclease action with dsDNA was quite specific: 5'-3' exonuclease activity was found to occur with nicked DNA, while dsDNA was endonucleolytically cut at 3-4 bp from the 5' end. Homologs are widely found in mammals and higher plants. The data suggest that DmGEN belongs to a new class of RAD2 nuclease.     

Coexistence of memory patterns and mixed states in a sparsely encoded associative memory model storing ultrametric patterns

Analyzing the coexistence of memory patterns and mixed states gives important information for constructing a model for the face responsive neurons of the monkey inferior-temporal cortex. We analyzed whether the memory patterns coexist with mixed states when the sparse coding scheme is used for the associative memory model storing ultrametric patterns. For memory patterns and mixed states to coexist, there must be sufficient capacity for storing them and their threshold values must be the same. We determined that the storage capacities for all mixed states composed of correlated memory patterns diverge as 1/|flogf| (where f is the firing rate) even when the correlation of the memory patterns is infinitesimally small. We also determined that the memory patterns and the mixed states can become the equilibrium state of the model in the same threshold value. These results mean that they can coexist in this model. These findings should contribute to research on face responsive neurons in the monkey inferior-temporal cortex.     

New monoterpene glucoside from the aerial parts of thyme (Thymus vulgaris L.)

A new monoterpene glucoside (1) was isolated from a methanol extract of the dried aerial parts of thyme (Thymus vulgaris L.), together with known 2- and 5-beta-D-glucopyranosylthymoquinols (2 and 3, respectively), and (-)-angelicoidenol-beta-D-glucopyranoside (4). The structure of 1 was elucidated to be (R)-p-cymen-9-yl beta-D-glucopyranoside by spectral evidence and enantioselective synthesis from (R)- and (S)-p-cymen-9-ol derived from p-cymen-8-ol.     

New brasiliamide congeners, brasiliamides C, D and E, from Penicillium brasilianum Batista JV-379

Three new brasiliamide congeners, brasiliamides C, D and E, were isolated from okara fermented with Penicillium brasilianum Batista JV-379. Their structures were elucidated on the basis of spectral data and chemical evidence. NMR spectra of these brasiliamides exhibited a mixture of four or two conformers due to the restricted rotation of an amide bond in a solution. The (1)H- and (13)C-NMR spectral data were analyzed for a major rotamer at an appropriate temperature, since the signals were broadened at room temperature. Both brasiliamides C and D showed convulsive activity against silkworms with an ED(50) value of 400 microg/g of diet, whereas brasiliamide E showed less activity than the others.     

Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria

A highly sensitive quantitative PCR detection method has been developed and applied to the distribution analysis of human intestinal bifidobacteria by combining real-time PCR with Bifidobacterium genus- and species-specific primers. Real-time PCR detection of serially diluted DNA extracted from cultured bifidobacteria was linear for cell counts ranging from 10(6) to 10 cells per PCR assay. It was also found that the method was applicable to the detection of Bifidobacterium in feces when it was present at concentrations of >10(6) cells per g of feces. Concerning the distribution of Bifidobacterium species in intestinal flora, the Bifidobacterium adolescentis group, the Bifidobacterium catenulatum group, and Bifidobacterium longum were found to be the three predominant species by examination of DNA extracted from the feces of 46 healthy adults. We also examined changes in the population and composition of Bifidobacterium species in human intestinal flora of six healthy adults over an 8-month period. The results showed that the composition of bifidobacterial flora was basically stable throughout the test period.