CAGE: cap analysis of gene expression.
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Animals↗
Biomedical subjects
Mari Nakamura
Publications and source records attributed to Mari Nakamura.
[Eighty cases of chronic respiratory failure treated with home noninvasive positive pressure ventilation].
We studied the clinical features and efficacy of home noninvasive positive pressure ventilation (NPPV) therapy in 80 patients to ascertain its indications and problems. The causes of chronic respiratory failure were restrictive thoracic diseases of post-tuberculosis sequelae (40 cases) and kyphoscoliosis (9 cases), COPD (8 cases), bronchiectasis (7 cases), and interstitial pneumonia (4 cases). One year survival rate of the patients with post-tuberculosis sequelae was 76% and most of the patients who started NPPV at their acute exacerbation died within several months. About half of the patients of COPD improved their quality of life (QOL) through NPPV. However, their survival rate 3 months later was only 69%. More than half of the patients with bronchiectasis felt that their QOL was improved by NPPV. Most of the patients with interstitial pneumonia died within 3 months indicating that NPPV is less useful for improving QOL of interstitial pneumonia PaCO2, after home NPPV, decreased significantly in the responder group (70.0 +/- 15.4 vs. 57.6 +/- 10.7[SD]Torr, p < 0.05), while PaCO2 in the non-responder group was unchanged (65.4 +/- 12.1 vs. 64.2 - 10.4 [SD] Torr). Body Mass Index (BMI) in the responder group tended to be higher than in the non-responder group. In conclusion, the restrictive thoracic diseases with post-tuberculosis sequelae and kyphoscoliosis are a good indication for NPPV and the therapy is also useful for patients with bronchiectasis who can dispose of their sputum by themselves. Home NPPV is suitable for patients whose PaCO2 decreases through NPPV and whose BMI is relatively high. QOL of interstitial pneumonia barely improves through NPPV, because interstitial pneumonia with hypercapnia is at the terminal stage.
Aged↗
Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
It is becoming increasingly clear that alternative splicing enables the complex development and homeostasis of higher organisms. To gain a better understanding of how splicing contributes to regulatory pathways, we have developed an alternative splicing library approach for the identification of alternatively spliced exons and their flanking regions by alternative splicing sequence enriched tags sequencing. Here, we have applied our approach to mouse melan-c melanocyte and B16-F10Y melanoma cell lines, in which 5,401 genes were found to be alternatively spliced. These genes include those encoding important regulatory factors such as cyclin D2, Ilk, MAPK12, MAPK14, RAB4, melastatin 1 and previously unidentified splicing events for 436 genes. Real-time PCR further identified cell line-specific exons for Tmc6, Abi1, Sorbs1, Ndel1 and Snx16. Thus, the ASL approach proved effective in identifying splicing events, which suggest that alternative splicing is important in melanoma development.
Alternative Splicing↗
Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR.
We established a medium-scale real-time RT-PCR system focusing on transcription factors and applied it to their expression profiles in the adult mouse 11 brain regions (http://genome.gsc.riken.jp/qRT-PCR/). Almost 90% of the examined genes showed significant expression in at least one region. We successfully extracted 179 region-specific genes by clustering analysis. Interestingly, the transcription factors involved in the development of the pituitary were still expressed in the adult pituitary, suggesting that they also play important roles in maintenance of the pituitary. These results provide unique molecular markers that may account for the molecular basis of the unique functions of specific brain regions.
Aging↗
Composition and structure of the centromeric region of rice chromosome 8.
Understanding the organization of eukaryotic centromeres has both fundamental and applied importance because of their roles in chromosome segregation, karyotypic stability, and artificial chromosome-based cloning and expression vectors. Using clone-by-clone sequencing methodology, we obtained the complete genomic sequence of the centromeric region of rice (Oryza sativa) chromosome 8. Analysis of 1.97 Mb of contiguous nucleotide sequence revealed three large clusters of CentO satellite repeats (68.5 kb of 155-bp repeats) and >220 transposable element (TE)-related sequences; together, these account for approximately 60% of this centromeric region. The 155-bp repeats were tandemly arrayed head to tail within the clusters, which had different orientations and were interrupted by TE-related sequences. The individual 155-bp CentO satellite repeats showed frequent transitions and transversions at eight nucleotide positions. The 40 TE elements with highly conserved sequences were mostly gypsy-type retrotransposons. Furthermore, 48 genes, showing high BLAST homology to known proteins or to rice full-length cDNAs, were predicted within the region; some were close to the CentO clusters. We then performed a genome-wide survey of the sequences and organization of CentO and RIRE7 families. Our study provides the complete sequence of a centromeric region from either plants or animals and likely will provide insight into the evolutionary and functional analysis of plant centromeres.
Base Composition↗
Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags.
The RIKEN expression array database (READ) provides comprehensive gene expression data for the mouse, which were obtained as relative values from microarray double-staining experiments with E17.5 mRNA as common reference. To assign absolute expression values for mouse transcripts within READ, we applied the E17.5 reference sample to CAGE (cap analysis of gene expression) and expressed sequence tag (EST) high-throughput tag sequencing. Newly assigned values within the READ database were validated by comparison to expression data from serial analysis of gene expression, CAGE and EST experiments. These experiments confirmed the great significance of the absolute expression values within the improved READ database. The new Absolute READ database on absolute expression data is available under.
Animals↗
[A pilot study of trastuzumab and vinorelbine-combined therapy for metastatic breast cancer].
We performed combined therapy with trastuzumab-vinorelbine for 6 HER2 positive metastatic breast cancer patients from which informed consent was obtained. As the initial dosage, we administered 4 mg/kg of trastuzumab, followed by a dosage of 2 mg/kg every week thereafter. At the same time, 25 mg/m2 of vinorelbine was administered for 2 weeks, followed by a week of rest. Total administration frequency of trastuzumab was 13-34 times (median: 27 times) and vinorelbine was 8-22 times (median: 17 times). A partial response was seen in 4 patients and no change in 2, for a response rate of 66%. A fixed period effect was recognized in each case, and the TTP was 112-274 days (median: 205 days). The side effects recognized were leukopenia of grade 3 in 1 patient, but she recovered during a withdrawal period. After that, continuous administration was possible. Trastuzumab-vinorelbine combined therapy expanded treatment alternatives for HER2 positive metastatic breast cancer patients and might prolong life.
Aged↗
[Cap analysis gene expression: CAGE].
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Animals↗
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5' end mRNAs. CAGE allows high-throughout gene expression analysis and the profiling of transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), we redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit. The frequency of CAGE tags correlates well with results from other analyses, such as serial analysis of gene expression, and furthermore maps the TSPs more accurately, including in tissue-specific cases. The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression.
Animals↗
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs were enriched in full-length by Cap-Trapper,and in most cases,aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC),which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project,which also include non-protein-coding RNAs,and the lower gene number estimation of genome annotations. Altogether,5'-end clusters identify regions that are potential promoters for 8637 known genes and 5'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.
Animals↗
Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.
The normalization and subtraction of highly expressed cDNAs from relatively large tissues before cloning dramatically enhanced the gene discovery by sequencing for the mouse full-length cDNA encyclopedia, but these methods have not been suitable for limited RNA materials. To normalize and subtract full-length cDNA libraries derived from limited quantities of total RNA, here we report a method to subtract plasmid libraries excised from size-unbiased amplified lambda phage cDNA libraries that avoids heavily biasing steps such as PCR and plasmid library amplification. The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization.
Gene Expression Profiling↗
[A case of breast cancer with lung and bone metastasis treated successfully by oral combination chemotherapy of 5'-deoxy-5-fluorouridine and cyclophosphamide].
The patient was a 52-year-old woman who underwent left partial mastectomy on April 30, 1999. The stage was T0N1bM1 (bone). After operation, adjuvant therapy consisting of 6 cycles of CMF therapy and radiation was performed. On September 2000, the tumor marker (NCC-ST 439) was at a high level. On January 2001, chest CT examination revealed multiple lung metastases of the right lobe. Oral combination chemotherapy of 5'-deoxy-5-fluorouridine (5'-DFUR, 1,200 mg/day) and cyclophosphamide (CPA, 100 mg/day) was thus performed, and definite improvement resulted in the lung. No adverse reactions occurred except for anemia and thrombocytopenia of grade 1. It is suggested that this oral combination chemotherapy may be useful for advanced recurrent breast cancer patients and applicable in ambulatory chemotherapy administered with consideration for the patient's quality of life.
Antineoplastic Combined Chemotherapy Protocols↗
The genome sequence and structure of rice chromosome 1.
The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.
Arabidopsis↗