83 research outputs found

    Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

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    <p>Abstract</p> <p>Background</p> <p>The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, <it>Cycas taitungensis</it>, <it>Pinus thunbergii</it>, and <it>Pinus koraiensis </it>have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of <it>Cryptomeria japonica</it>, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.</p> <p>Results</p> <p>The <it>C. japonica </it>cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (<it>trn</it>I-CAU, <it>trn</it>Q-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the <it>C. japonica </it>cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as <it>Cycas </it>and <it>Gingko</it>, and additionally has completely lost its <it>trn</it>R-CCG, partially lost its <it>trn</it>T-GGU, and shows diversification of <it>acc</it>D. The genomic structure of the <it>C. japonica </it>cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the <it>Pinus thunbergii </it>cp genome into that of <it>C. japonica</it>. In the <it>C. japonica </it>cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements.</p> <p>Conclusion</p> <p>The observed differences in genomic structure between <it>C. japonica </it>and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the <it>C. japonica </it>cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.</p

    Pulmonary function after segmentectomy for small peripheral carcinoma of the lung

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    AbstractObjective: The aim of this study is to compare the pulmonary function after a segmentectomy with that after a lobectomy for small peripheral carcinoma of the lung. Patients And Methods: Between 1993 and 1996, segmentectomy and lobectomy were performed on 48 and 133 good-risk patients, respectively. Lymph node metastases were detected after the operation in 6 and 24 patients of the segmentectomy and lobectomy groups, respectively. For bias reduction in comparison with a nonrandomized control group, we paired 40 segmentectomy patients with 40 lobectomy patients using nearest available matching method on the estimated propensity score. Results: Twelve months after the operation, the segmentectomy and lobectomy groups had forced vital capacities of 2.67 ± 0.73 L (mean ± standard deviation) and 2.57 ± 0.59 L, which were calculated to be 94.9% ± 10.6% and 91.0% ± 13.2% of the preoperative values (P = .14), respectively. The segmentectomy and lobectomy groups had postoperative 1-second forced expiratory volumes of 1.99 ± 0.63 L and 1.95 ± 0.49 L, which were calculated to be 93.3% ± 10.3% and 87.3% ± 14.0% of the preoperative values, respectively (P = .03). The multiple linear regression analysis showed that the alternative of segmentectomy or lobectomy was not a determinant for postoperative forced vital capacity but did affect postoperative 1-second forced expiratory volume. Conclusion: Pulmonary function after a segmentectomy for a good-risk patient is slightly better than that after a lobectomy. However, segmentectomy should be still the surgical procedure for only poor-risk patients because of the difficulty in excluding patients with metastatic lymph nodes from the candidates for the procedure. (J Thorac Cardiovasc Surg 1999;118:536-41

    A Comprehensive Study of Repetitive Transcranial Magnetic Stimulation in Parkinson's Disease

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    The clinical benefits of repetitive transcranial magnetic stimulation (rTMS) for Parkinson's disease (PD) remain controversial. We performed a comprehensive study to examine whether rTMS is a safe and effective treatment for PD. Twelve PD patients received rTMS once a week. The crossover study design consisted of 4-week sham rTMS followed by 4-week real rTMS. The Unified Parkinson's Disease Rating Scale (UPDRS), Modified Hoehn and Yahr Stage, Schwab and England ADL Scale, Actigraph, Mini-Mental State Examination, Hamilton Depression Scale, Wechsler Adult Intelligence Scale-revised, and cerebral blood flow (CBF) and cerebrospinal fluid (CSF) examinations were used to evaluate the rTMS effects. Under both drug-on and drug-off conditions, the real rTMS improved the UPDRS scores significantly, while the sham rTMS did not. There were no significant changes in the results of the neuropsychological tests, CBF and CSF. rTMS seems to be a safe and effective therapeutic option for PD patients, especially in a wearing-off state

    Expression of human mutant cyclin dependent kinase 4, Cyclin D and telomerase extends the life span but does not immortalize fibroblasts derived from loggerhead sea turtle (Caretta caretta)

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    Conservation of the genetic resources of endangered animals is crucial for future generations. The loggerhead sea turtle (Caretta caretta) is a critically endangered species, because of human hunting, hybridisation with other sea turtle species, and infectious diseases. In the present study, we established primary fibroblast cell lines from the loggerhead sea turtle, and showed its species specific chromosome number is 2n = 56, which is identical to that of the hawksbill and olive ridley sea turtles. We first showed that intensive hybridization among multiple sea turtle species caused due to the identical chromosome number, which allows existence of stable hybridization among the multiple sea turtle species. Expressions of human-derived mutant Cyclin-dependent kinase 4 (CDK4) and Cyclin D dramatically extended the cell culture period, when it was compared with the cell culture period of wild type cells. The recombinant fibroblast cell lines maintained the normal chromosome condition and morphology, indicating that, at the G1/S phase, the machinery to control the cellular proliferation is evolutionally conserved among various vertebrates. To our knowledge, this study is the first to demonstrate the functional conservation to overcome the negative feedback system to limit the turn over of the cell cycle between mammalian and reptiles. Our cell culture method will enable the sharing of cells from critically endangered animals as research materials

    Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar)

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    A genome-wide association study (GWAS) was conducted on more than 30,000 single nucleotide polymorphisms (SNPs) in unrelated first-generation plus tree genotypes from three populations of Japanese cedar Cryptomeria japonica D. Don with genomic prediction for traits of growth, wood properties and male fecundity. Among the assessed populations, genetic characteristics including the extent of linkage disequilibrium (LD) and genetic structure differed and these differences are considered to be due to differences in genetic background. Through population-independent GWAS, several significant SNPs found close to the regions associated with each of these traits and shared in common across the populations were identified. The accuracies of genomic predictions were dependent on the traits and populations and reflected the genetic architecture of traits and genetic characteristics. Prediction accuracies using SNPs selected based on GWAS results were similar to those using all SNPs for several combinations of traits and populations. We discussed the application of genome-wide studies for C. japonica improvement

    A frameshift mutation of the chloroplast matK coding region is associated with chlorophyll deficiency in the Cryptomeria japonica virescent mutant Wogon-Sugi

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    Wogon-Sugi has been reported as a cytoplasmically inherited virescent mutant selected from a horticultural variety of Cryptomeria japonica. Although previous studies of plastid structure and inheritance indicated that at least some mutations are encoded by the chloroplast genome, the causative gene responsible for the primary chlorophyll deficiency in Wogon-Sugi, has not been identified. In this study, we identified this gene by genomic sequencing of chloroplast DNA and genetic analysis. Chloroplast DNA sequencing of 16 wild-type and 16 Wogon-Sugi plants showed a 19-bp insertional sequence in the matK coding region in the Wogon-Sugi. This insertion disrupted the matK reading frame. Although an indel mutation in the ycf1 and ycf2 coding region was detected in Wogon-Sugi, sequence variations similar to that of Wogon-Sugi were also detected in several wild-type lines, and they maintained the reading frame. Genetic analysis of the 19 bp insertional mutation in the matK coding region showed that it was found only in the chlorophyll-deficient sector of 125 full-sibling seedlings. Therefore, the 19-bp insertion in the matK coding region is the most likely candidate at present for a mutation underlying the Wogon-Sugi phenotype
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