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91.
92.
Kimiko Saka Maki Tadenuma Shinsuke Nakade Noriko Tanaka Hideaki Sugawara Ken Nishikawa Nobuyuki Ichiyoshi Masanari Kitagawa Hirotada Mori Naotake Ogasawara Akiko Nishimura 《DNA research》2005,12(1):63-68
To facilitate genetic studies of Escherichia coli, we constructed a complete set of mobile plasmid clones of intact open reading frames (ORFs). Their expression is strictly controlled by Ptac / lacI(q). The plasmids carrying each ORF were introduced into an F+ recA strain and stored in 96-well microtiter plates. In this way, 96 clones can be transferred simultaneously to F- bacteria using the conjugative system. This provides a convenient procedure for systematic identification of ORFs that suppress or complement mutations. We created two types of clone sets: the original set contained individual clones in 45 microtiter plates, and a second set contained pools of 48 clones stored in a single microtiter plate. Using these clone sets, we have identified 403 genes that can correct in trans the temperature-sensitive defect of cell division mutants, which would suggest multiple global regulators for bacterial cell division. 相似文献
93.
Nozaki H Matsuzaki M Takahara M Misumi O Kuroiwa H Hasegawa M Shin-i T Kohara Y Ogasawara N Kuroiwa T 《Journal of molecular evolution》2003,56(4):485-497
Abstract
Red algae are one of the main photosynthetic eukaryotic lineages and are characterized by primitive features, such as a lack
of flagella and the presence of phycobiliproteins in the chloroplast. Recent molecular phylogenetic studies using nuclear
gene sequences suggest two conflicting hypotheses (monophyly versus non-monophyly) regarding the relationships between red
algae and green plants. Although kingdom-level phylogenetic analyses using multiple nuclear genes from a wide-range of eukaryotic
lineages were very recently carried out, they used highly divergent gene sequences of the cryptomonad nucleomorph (as the
red algal taxon) or incomplete red algal gene sequences. In addition, previous eukaryotic phylogenies based on nuclear genes
generally included very distant archaebacterial sequences (designated as the outgroup) and/or amitochondrial organisms, which
may carry unusual gene substitutions due to parasitism or the absence of mitochondria. Here, we carried out phylogenetic analyses
of various lineages of mitochondria-containing eukaryotic organisms using nuclear multigene sequences, including the complete
sequences from the primitive red alga Cyanidioschyzon merolae. Amino acid sequence data for two concatenated paralogous genes (α- and β-tubulin) from mitochondria-containing organisms
robustly resolved the basal position of the cellular slime molds, which were designated as the outgroup in our phylogenetic
analyses. Phylogenetic analyses of 53 operational taxonomic units (OTUs) based on a 1525-amino-acid sequence of four concatenated
nuclear genes (actin, elongation factor-1α, α-tubulin, and β-tubulin) reliably resolved the phylogeny only in the maximum
parsimonious (MP) analysis, which indicated the presence of two large robust monophyletic groups (Groups A and B) and the
basal eukaryotic lineages (red algae, true slime molds, and amoebae). Group A corresponded to the Opisthokonta (Metazoa and
Fungi), whereas Group B included various primary and secondary plastid-containing lineages (green plants, glaucophytes, euglenoids,
heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the sister lineage
to Group B. Using 34 OTUs for which essentially the entire amino acid sequences of the four genes are known, MP, distance,
quartet puzzling, and two types of maximum likelihood (ML) calculations all robustly resolved the monophyly of Group B, as
well as the basal position of red algae within eukaryotic organisms. In addition, phylogenetic analyses of a concatenated
4639-amino-acid sequence for 12 nuclear genes (excluding the EF-2 gene) of 12 mitochondria-containing OTUs (including C. merolae) resolved a robust non-sister relationship between green plants and red algae within a robust monophyletic group composed
of red algae and the eukaryotic organisms belonging to Group B. A new scenario for the origin and evolution of plastids is
suggested, based on the basal phylogenetic position of the red algae within the large clade (Group B plus red algae). The
primary plastid endosymbiosis likely occurred once in the common ancestor of this large clade, and the primary plastids were
subsequently lost in the ancestor(s) of the Discicristata (euglenoids, Kinetoplastida, and Heterolobosea), Heterokontophyta,
and Alveolata (apicomplexans and Ciliophora). In addition, a new concept of “Plantae” is proposed for phototrophic and nonphototrophic
organisms belonging to Group B and red algae, on the basis of the common history of the primary plastid endosymbiosis. The
Plantae include primary plastid-containing phototrophs and nonphototrophic eukaryotes that possibly contain genes of cyanobacterial
origin acquired in the primary endosymbiosis. 相似文献
94.
Yuka Hattori Hangsoo Kim Naotake Tsuboi Akihito Yamamoto Shinichi Akiyama Yiqin Shi Takayuki Katsuno Tomoki Kosugi Minoru Ueda Seiichi Matsuo Shoichi Maruyama 《PloS one》2015,10(10)
BackgroundAcute kidney injury (AKI) is a critical condition associated with high mortality. However, the available treatments for AKI are limited. Stem cells from human exfoliated deciduous teeth (SHED) have recently gained attention as a novel source of stem cells. The purpose of this study was to clarify whether SHED have a therapeutic effect on AKI induced by ischemia-reperfusion injury.MethodsThe left renal artery and vein of the mice were clamped for 20 min to induce ischemia. SHED, bone marrow derived mesenchymal stem cells (BMMSC) or phosphate-buffered saline (control) were administered into the subrenal capsule. To confirm the potency of SHED in vitro, H2O2 stimulation assays and scratch assays were performed.ResultsThe serum creatinine and blood urea nitrogen levels of the SHED group were significantly lower than those of the control group, while BMMSC showed no therapeutic effect. Infiltration of macrophages and neutrophils in the kidney was significantly attenuated in mice treated with SHED. Cytokine levels (MIP-2, IL-1β, and MCP-1) in mice kidneys were significantly reduced in the SHED group. In in vitro experiments, SHED significantly decreased MCP-1 secretion in tubular epithelial cells (TEC) stimulated with H2O2. In addition, SHED promoted wound healing in the scratch assays, which was blunted by anti-HGF antibodies.DiscussionSHED attenuated the levels of inflammatory cytokines and improved kidney function in AKI induced by IRI. SHED secreted factors reduced MCP-1 and increased HGF expression, which promoted wound healing. These results suggest that SHED might provide a novel stem cell resource, which can be applied for the treatment of ischemic kidney injury. 相似文献
95.
96.
Nozaki H Matsuzaki M Misumi O Kuroiwa H Hasegawa M Higashiyama T Shin-I T Kohara Y Ogasawara N Kuroiwa T 《Journal of molecular evolution》2004,59(1):103-113
The plastids of red algae, green plants, and glaucophytes may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis. In contrast, the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary endosymbiotic events involving a phototrophic eukaryote and a eukaryotic host cell. Although phylogenetic analyses of multiple plastid genes from a wide range of eukaryotic lineages have been carried out, the phylogenetic positions of the secondary plastids of the Chromista (Heterokontophyta, Haptophyta and Cryptophyta) are ambiguous in a range of different analyses. This ambiguity may be the result of unusual substitutions or bias in the plastid genes established by the secondary endosymbiosis. In this study, we carried out phylogenetic analyses of five nuclear genes of cyanobacterial origin (6-phosphogluconate dehydrogenase [gnd], oxygen-evolving-enhancer [psbO], phosphoglycerate kinase [pgk], delta-aminolevulinic acid dehydratase [aladh], and ATP synthase gamma [atpC] genes), using the genome sequence data from the primitive red alga Cyanidioschyzon merolae 10D. The sequence data robustly resolved the origin of the cyanobacterial genes in the nuclei of the Chromista (Heterokontophyta and Haptophyta) and Dinophyta, before the divergence of the extant red algae (including Porphyra [Rhodophyceae] and Cyanidioschyzon [Cyadidiophyceae]). Although it is likely that gnd genes in the Chromista were transmitted from the cyanobacterium-like ancestor of plastids in the primary endosymbiosis, other genes might have been transferred from nuclei of a red algal ancestor in the secondary endosymbiosis. Therefore, the results indicate that the Chromista might have originated from the ancient secondary endosymbiosis before the divergence of extant red algae. 相似文献
97.
98.
Amiteye S Kobayashi K Imamura D Hosoya S Ogasawara N Sato T 《Journal of bacteriology》2003,185(17):5306-5309
The sn-1,2-diacylglycerol kinase homologue gene, dgkA, is a sporulation gene indispensable for the maintenance of spore stability and viability in Bacillus subtilis. After 6 h of growth in resuspension medium, the endospore morphology of the dgkA mutant by standard phase-contrast microscopy was normal; however, after 9 h, the endospores appeared mostly dark by phase-contrast microscopy, suggesting a defect in the spores. Moreover, electron microscopic studies revealed an abnormal cortex structure in mutant endospores 6 h after the onset of sporulation, an indication of cortex degeneration. In addition, a significant decrease in the dipicolinic acid content of mutant spores was observed. We also found that dgkA is expressed mainly during the vegetative phase. It seems likely that either the DgkA produced during growth prepares the cell for an essential step in sporulation or the enzyme persists into sporulation and performs an essential function. 相似文献
99.
100.