Factor analysis of digestive cancer mortality and food consumption in 65 Chinese counties. (41/5127)

Dietary factors were analyzed for the regional difference of GI tract cancer mortality rates in China. Sixty-five rural counties were selected among a total of 2,392 counties to represent a range of rates for seven most prevalent cancers. The dietary data in the selected 65 counties were obtained by three-day dietary record of households in 1983. The four digestive cancer mortality rates (annual cases per 100,000 standardized truncated rates for ages 35-64) and per capita food consumption were analyzed by the principal components factor analysis. Esophageal cancer associated with poor area, dietary pattern rich in starchy tubers, and salt, lack of consumption of meat, eggs, vegetables and rice. Stomach cancer seemed to be less associated with diet in this study because of its small model Kaiser-Meyer-Olkin (KMO) measure of sampling adequacy, suggesting some other carcinogenic factors would play more important role in the development of this cancer in China. The colon and rectal cancer showed close relation to diet; rich in sea vegetables, eggs, soy sauce, meat and fish, while lack in consumption of milk and dairy products. Rapeseed oil was more important risk factor for colon cancer than that of rectum. Rice, processed starch and sugar were closely associated with colon cancer, supporting the insulin/colon cancer hypothesis.  (+info)

Metaphase chromosome accumulation and flow karyotypes in rice (Oryza sativa L.) root tip meristem cells. (42/5127)

Highly efficient cell synchronization and metaphase chromosome accumulation in rice root tip cells were achieved. Flow cytometric analysis was performed for obtaining optimal parameters to synchronize the cell cycles. High mitotic indices (about 57.6% in root tip meristemic area) were obtained by treating seedlings with 0.5 cm length using 0.5 mM hydroxyurea at 30 degrees C for 4 h, incubating in a hydroxyurea-free solution for 30 min, and then treating with 0.3 microM trifluralin for 3 h. After trifluralin treatment, incubation in distilled water for 15 min reduced chromosome clumping on metaphase spread. Uniformity of seed germination at the time of treatment is a critical parameter for obtaining high metaphase index. Isolated rice chromosomes were suitable for flow cytometric analysis and chromosome sorting. The morphology of flow sorted metaphase chromosomes was intact.  (+info)

Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. (43/5127)

Large, publicly available collections of expressed sequence tags (ESTs) have been generated from Arabidopsis thaliana and rice (Oryza sativa). A potential, but relatively unexplored application of this data is in the study of plant gene expression. Other EST data, mainly from human and mouse, have been successfully used to point out genes exhibiting tissue- or disease-specific expression, as well as for identification of alternative transcripts. In this report, we go a step further in showing that computer analyses of plant EST data can be used to generate evidence of correlated expression patterns of genes across various tissues. Furthermore, tissue types and organs can be classified with respect to one another on the basis of their global gene expression patterns. As in previous studies, expression profiles are first estimated from EST counts. By clustering gene expression profiles or whole cDNA library profiles, we show that genes with similar functions, or cDNA libraries expected to share patterns of gene expression, are grouped together. Promising uses of this technique include functional genomics, in which evidence of correlated expression might complement (or substitute for) those of sequence similarity in the annotation of anonymous genes and identification of surrogate markers. The analysis presented here combines the application of a correlation-based clustering method with a graphical color map allowing intuitive visualization of patterns within a large table of expression measurements.  (+info)

Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. (44/5127)

Most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. The highest viable counts (up to 2.5 x 10(8) cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. The total cell count for the soil, as determined by using 4', 6-diamidino-2-phenylindole staining, was 4.8 x 10(8) cells per g (dry weight) of soil. The nine strains isolated from the terminal positive tubes in counting experiments which yielded culturable populations that were equivalent to about 5% or more of the total microscopic count population belonged to the division Verrucomicrobia, the Cytophaga-Flavobacterium-Bacteroides division, clostridial cluster XIVa, clostridial cluster IX, Bacillus spp., and the class Actinobacteria. Isolates originating from the terminal positive tubes of liquid dilution series can be expected to be representatives of species whose populations in the soil are large. None of the isolates had 16S rRNA gene sequences identical to 16S rRNA gene sequences of previously described species for which data are available. Eight of the nine strains isolated fermented sugars to acetate and propionate (and some also fermented sugars to succinate). The closest relatives of these strains (except for the two strains of actinobacteria) were as-yet-uncultivated bacteria detected in the same soil sample by cloning PCR-amplified 16S rRNA genes (U. Hengstmann, K.-J. Chin, P. H. Janssen, and W. Liesack, Appl. Environ. Microbiol. 65:5050-5058, 1999). Twelve other isolates, which originated from most-probable-number counting series indicating that the culturable populations were smaller, were less closely related to cloned 16S rRNA genes.  (+info)

Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. (45/5127)

We used both cultivation and direct recovery of bacterial 16S rRNA gene (rDNA) sequences to investigate the structure of the bacterial community in anoxic rice paddy soil. Isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are described in the accompanying paper (K.-J. Chin, D. Hahn, U. Hengstmann, W. Liesack, and P. H. Janssen, Appl. Environ. Microbiol. 65:5042-5049, 1999). Here we describe the phylogenetic positions of these strains in relation to 57 environmental 16S rDNA clone sequences. Close matches between the two data sets were obtained for isolates from the culturable populations determined by the most-probable-number counting method to be large (3 x 10(7) to 2.5 x 10(8) cells per g [dry weight] of soil). This included matches with 16S rDNA similarity values greater than 98% within distinct lineages of the division Verrucomicrobia (strain PB90-1) and the Cytophaga-Flavobacterium-Bacteroides group (strains XB45 and PB90-2), as well as matches with similarity values greater than 95% within distinct lines of descent of clostridial cluster XIVa (strain XB90) and the family Bacillaceae (strain SB45). In addition, close matches with similarity values greater than 95% were obtained for cloned 16S rDNA sequences and bacteria (strains DR1/8 and RPec1) isolated from the same type of rice paddy soil during previous investigations. The correspondence between culture methods and direct recovery of environmental 16S rDNA suggests that the isolates obtained are representative geno- and phenotypes of predominant bacterial groups which account for 5 to 52% of the total cells in the anoxic rice paddy soil. Furthermore, our findings clearly indicate that a dual approach results in a more objective view of the structural and functional composition of a soil bacterial community than either cultivation or direct recovery of 16S rDNA sequences alone.  (+info)

Dietary prevention of azoxymethane-induced colon carcinogenesis with rice-germ in F344 rats. (46/5127)

The modifying effect of dietary administration of defatted rice-germ and gamma-aminobutyric acid (GABA)-enriched defatted rice-germ on azoxymethane (AOM)-induced colon carcinogenesis was investigated in two experiments with male F344 rats. In the first experiment (the pilot study), the effects of the defatted rice-germ, the GABA-enriched defatted rice-germ and rice-germ on AOM-induced (15 mg/kg body wt once a week for 3 weeks) formation of aberrant crypt foci (ACF) were examined. The latter two preparations (2.5% in the diet) significantly inhibited ACF formation (P < 0.005). In the second experiment, a long-term study of the effects of rice-germ was done. One group was treated with AOM alone, four groups received the carcinogen and were fed the diets containing 2.5% rice-germ or 2.5% GABA-enriched defatted rice-germ for 5 (initiation phase) or 30 weeks (post-initiation phase), two groups were treated with rice-germ or GABA-enriched defatted rice-germ alone and one group was kept on the basal diet. At the termination of the study, dietary exposure to rice-germ during the initiation phase significantly reduced the incidence of colonic adenocarcinoma (71 versus 29%, P < 0.01). GABA-enriched defatted rice-germ or rice-germ during the post-initiation phase also decreased the frequency of colonic adenocarcinoma (71 versus 20%, GABA-enriched defatted rice-germ feeding, P < 0.01; 27%, rice-germ feeding, P < 0.01). These data suggest that constituents of rice-germ are possible dietary preventatives for human colon cancers.  (+info)

Molecular characterization of Oryza sativa 16.9 kDa heat shock protein. (47/5127)

A rice class I low-molecular-mass heat shock protein (LMM HSP) Oshsp 16.9 was overexpressed in Escherichia coli. Oligomerized complexes of Oshsp16.9 were harvested and electron microscopic observations of purified complexes revealed globular structures of 10-20 nm in diameter (with majority of 15-18 nm) and calculated to comprise approx. 12 monomers per complex. In comparison, complexes from native rice class I LMM HSPs were observed as larger ellipsoid- or globular-like random aggregated hetero-oligomers. To characterize the biochemical functions of the hydrophobic N-terminal region of Oshsp16.9, a truncation in the N-terminal region was constructed and introduced into E. coli. Results showed that the N-terminal truncated Oshsp16.9 mutant was capable of forming complexes similar to the full-length Oshsp16.9; however, the deletion protein failed to confer in vitro protein thermostability under elevated temperatures. Protein assays from in vivo treatments at higher temperatures exhibited that non-specific interactions of E. coli cellular proteins only occurred with full-length Oshsp16.9 complexes but not with the mutant complex. In vitro immunoprecipitation of cellular proteins from E. coli overexpressing full-length Oshsp16.9 showed that interactions between plant LMM HSP and E. coli cellular proteins are temperature-dependent. Taken together, the hydrophobic N-terminal region of rice class I LMM HSP is critical in the ability of the protein to interact/bind with its potential substrates.  (+info)

Phylogenetic relationships in the genus Oryza based on mitochondrial RFLPs. (48/5127)

Restriction fragment length polymorphism (RFLP) of mitochondrial DNA in the genus Oryza was surveyed using 20 accessions including 11 species and a single endonuclease, EcoRI. RFLPs were visualized by Southern hybridization with eight rice mitochondrial DNA probes labeled non-radioactively with digoxigenin-dUTP. A total of 66 bands were obtained from all of the accessions. The total number of fragments per plant was higher in diploid A-genome species (an average of 35.3) than that in diploid B- and C-genome species and allotetraploid BC- and CD-genome species (an average of 28.2). The extent of the polymorphism in the RFLP patterns was various depending on the probes used. A diverse polymorphism was observed with most of the probes used, i.e. the cob, cox I, atp6, rrn18, rrn26 and atp9 regions, whereas, no polymorphic band was observed with a probe for the coxII region. The genus Oryza was separated into two large clusters. One cluster was comprised of A-genome species and the other cluster was comprised of B-, BC-, C-, and CD- genome species. Within A-genome species, the genetic variation was relatively high. Even in O. sativa species, the RFLP patterns of japonica and indica subspecies were clearly different from each other when three probes were used. However, there was no polymorphism between O. glaberrima and O. barthii. Within the genomes of B, BC, C, and CD, RFLP patterns were similar to each other and they showed a closer affinity except for O. minuta (BBCC). Within the BC genome species, the patterns of O. punctata and O. minuta were largely different from each other and separated into two different subclusters. Thus, the mitochondrial genomes of the two BC species (O. punctata and O. minuta) apparently evolved independently. Among CD genome species (O. latifolia and O. alta), the patterns of one accession, O. alta W0017 were largely different from those of the other accessions of CD genome species.  (+info)