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941.
Prediction of molecular interaction networks from large-scale datasets in genomics and other omics experiments is an important task in terms of both developing bioinformatics methods and solving biological problems. We have applied a kernel-based network inference method for extracting functionally related genes to the response of nitrogen deprivation in cyanobacteria Anabaena sp. PCC 7120 integrating three heterogeneous datasets: microarray data, phylogenetic profiles, and gene orders on the chromosome. We obtained 1348 predicted genes that are somehow related to known genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. While this dataset contained previously known genes related to the nitrogen deprivation condition, it also contained additional genes. Thus, we attempted to select any relevant genes using the constraints of Pfam domains and NtcA-binding sites. We found candidates of nitrogen metabolism-related genes, which are depicted as extensions of existing KEGG pathways. The prediction of functional relationships between proteins rather than functions of individual proteins will thus assist the discovery from the large-scale datasets. 相似文献
942.
Shimamura M Huang YY Okamoto N Watanabe Y Murakami Y Kinoshita T Hirabayashi Y Murakata C Ito Y Ogawa T 《The FEBS journal》2007,274(11):2921-2932
We have previously demonstrated that alpha-mannosyl ceramide and its derivatives promote immune responses of NK1.1(+) invariant Valpha19-Jalpha33 T cell receptor (TCR) alpha(+) T cells (Valpha19 NKT cells). In this study, attempts were made to determine the structural requirements for natural ligands for Valpha19 NKT cells. Naturally occurring and synthetic glycolipids were analyzed for their ability to stimulate the cells prepared from invariant Valpha19-Jalpha33 TCR transgenic mice, in which development of Valpha19 NKT cells is facilitated. As a result, alpha-mannosyl phosphatidylinositols such as 2,6-di-alpha-mannosyl phosphatidylinositol and alpha-mannosyl-4alpha-glucosaminyl-6-phosphatidylinositol (alpha-Man-GlcNH(2)-PtdIns) as well as alpha-mannosyl ceramide derivatives were found to activate the cells from the transgenic mouse liver, gut lamina propria and spleen in vivo and in vitro. Thus, glycolipids with nonreducing end alpha-mannosyl residues are suggested to be potent antigens for Valpha19 NKT cells. Next, a series of invariant Valpha19-Jalpha33 TCR(+) hybridomas, each with variations in the sequence of the Valpha-Jalpha junction and the TCR beta chain, were tested for responsiveness toward the alpha-mannosyl glycolipids. A loose correlation between the primary structure of the TCR and the reactive glycolipids was observed. For instance, hybridomas expressing TCRs consisting of an alpha chain with a variation in the Valpha19-Jalpha33 junction and a Vbeta6(+)beta chain showed affinity towards alpha-mannosyl ceramide and alpha-Man-GlcNH(2)-PtdIns, whereas those expressing TCRs with an invariant Valpha19-Jalpha33 alpha chain and a Vbeta8(+)beta chain responded to 2,6-di-alpha-mannosyl phosphatidylinositol. Thus, it is suggested that Valpha19 NKT cells with microheterogeneity in the TCR structure have been generated for defense against various antigens expressing alpha-mannosyl glycolipids. 相似文献
943.
944.
To better understand soil carbon cycling in forest ecosystems, we studied the proportion of fungal sheath area (FSA) in the
cross-sectional ectomycorrhizal area in 13 tree species. Ectomycorrhizal samples were collected from subalpine and temperate
forests in Japan. The FSA values were in the range of 12% to 56% across all tree species, tree ages, and fungal species. In
Abies firma and Quercus serrata, the FSA values were larger in mature trees than in seedlings, whereas no such differences were found in Pinus densiflora and Fagus crenata. In broad-leaved trees, because the plant tissue radii lay within a narrow range, the FSA was affected mainly by the fungal
sheath thickness. In conifers, however, the plant tissue radii varied widely among genera, so the FSA was affected by both
the plant tissue radius and the fungal sheath thickness. Our findings suggest that the fungal content of ectomycorrhizal tips
differs among tree species and fungal species, so that both parameters must be considered in studies of forest carbon cycling.
The estimates revealed that data gathering in each type of forest leads to more accurate estimates of the biomass of fungi
in ectomycorrhizal tips. 相似文献
945.
Antigen B in hydatid cyst fluid of Echinococcus granulosus is a polymeric lipoprotein of 160 kDa, and is an aggregate of several different but homologous small proteins with approximately 8 kDa which are encoded by a multigene family. Four genes encoding 8-kDa-subunit monomers of the antigen B have been identified from E. granulosus. Recently, we have isolated another novel gene from Echinococcus multilocularis encoding a fifth 8-kDa-subunit of AgB (named EmAgB8/5), predominantly transcribed in the adult worm, but not in vesicles of metacestodes. In this study, we cloned and characterized two EmAgB8/5 homologue genes from E. granulosus genotypes 1 and 6 by PCR, and named as EgG1AgB8/5 and EgG6AgB8/5, respectively. The phylogenetic relationship of these genes with other genes encoding the antigen B 8-kDa-subunit monomers was also discussed. 相似文献
946.
Background
High-throughput techniques have multiplied the amount and the types of available biological data, and for the first time achieving a global comprehension of the physiology of biological cells has become an achievable goal. This aim requires the integration of large amounts of heterogeneous data at different scales. It is notably necessary to extend the traditional focus on genomic data towards a truly functional focus, where the activity of cells is described in terms of actual metabolic processes performing the functions necessary for cells to live. 相似文献947.
Background
The ability to regulate metabolism is a fundamental process in living systems. We present an analysis of one of the mechanisms by which metabolic regulation occurs: enzyme inhibition and activation by small molecules. We look at the network properties of this regulatory system and the relationship between the chemical properties of regulatory molecules. 相似文献948.
Tomokazu Amano Emiko Jeffries Misa Amano Akihiro C. Ko Hong Yu Minoru S. H. Ko 《DNA research》2015,22(5):331-342
Aneuploidy, an abnormal number of chromosomes, has previously been considered irremediable. Here, we report findings that euploid cells increased among cultured aneuploid cells after exposure to the protein ZSCAN4, encoded by a mammalian-specific gene that is ordinarily expressed in preimplantation embryos and occasionally in stem cells. For footprint-free delivery of ZSCAN4 to cells, we developed ZSCAN4 synthetic mRNAs and Sendai virus vectors that encode human ZSCAN4. Applying the ZSCAN4 biologics to established cultures of mouse embryonic stem cells, most of which had become aneuploid and polyploid, dramatically increased the number of euploid cells within a few days. We then tested the biologics on non-immortalized primary human fibroblast cells derived from four individuals with Down syndrome—the most frequent autosomal trisomy of chromosome 21. Within weeks after ZSCAN4 application to the cells in culture, fluorescent in situ hybridization with a chromosome 21-specific probe detected the emergence of up to 24% of cells with only two rather than three copies. High-resolution G-banded chromosomes further showed up to 40% of cells with a normal karyotype. These findings were confirmed by whole-exome sequencing. Similar results were obtained for cells with the trisomy 18 of Edwards syndrome. Thus a direct, efficient correction of aneuploidy in human fibroblast cells seems possible in vitro using human ZSCAN4. 相似文献
949.