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Biomedical subjects

D Shibata

Publications and source records attributed to D Shibata.

At least 37 records · Page 2Linked to original sources
PubMed2000

Functional and quality-of-life outcomes in patients with rectal cancer after combined modality therapy, intraoperative radiation therapy, and sphincter preservation.

PURPOSE: Locally advanced primary and recurrent rectal cancers treated with external beam radiation therapy, intraoperative radiation therapy, and chemotherapy represent a complex group of patients in the setting of extensive pelvic surgery and sphincter preservation. We sought to define functional outcome and quality of life in this subset of patients. METHODS: We retrospectively reviewed our experience with locally advanced primary and recurrent rectal cancer patients who underwent intraoperative radiation therapy with either low anterior resection (n = 12) or coloanal anastomosis (n = 6) between 1991 and 1998. Current functional outcome and quality of life were evaluated by a detailed questionnaire. RESULTS: Median time from operation to assessment was 24 (range, 6-93) months. Using a standardized Sphincter Function Scale, incorporating the number of bowel movements per day and degree of incontinence, patients were graded as poor, fair, good, or excellent function. Of all patients, 56 percent reported unfavorable (poor or fair) function. Of the subset of patients with coloanal anastomosis or very low low anterior resection, 88 percent had unfavorable function as compared with 30 percent with standard low anterior resection. (P = 0.02; Fisher's exact probability test). A quality-of-life satisfaction score based on social, professional, and recreational restrictions demonstrated 56 percent of patients to be dissatisfied with their bowel function. CONCLUSIONS: The majority of patients with advanced rectal cancers who require external beam radiation therapy, extensive pelvic surgery, and intraoperative radiation therapy report unfavorable functional and quality-of-life outcomes after sphincter preservation. In this setting patients being considered for coloanal anastomosis or very low anterior resection may be better served by permanent diversion.

Adult↗
PubMed2000

Mutations in the WUSCHEL gene of Arabidopsis thaliana result in the development of shoots without juvenile leaves.

The vegetative growth of Arabidopsis thaliana can be divided into two phases. The transition from the juvenile (early) phase to the adult (later) phase is associated with changes in several morphological features of leaves, such as the shape of leaf blades, the number of trichomes and patterns of venation. In a screening of mutants with altered morphological identities of leaves, we found one which we named juvenile leafless and misshapen shoot apical meristem (jam). The mutation represented a new allele of the WUSCHEL (WUS) gene, and, in its presence, plants produced no juvenile leaves. Analysis of the morphology of mutant plants revealed that all the rosette leaves had characteristics of adult leaves. The formation of the first rosette leaf in the wus(jam) mutant was markedly delayed, and occurred at the almost same time as formation of the third or fourth leaf in wild-type plants. In the wild-type, these leaves correspond to the first adult leaves. Analysis by RT-PCR showed that transcripts of WUS accumulated in shoot apices and roots, but not in cotyledons and leaves. The present results suggest that the WUS gene controls the morphological traits of rosette leaves either directly or indirectly. In view of the predicted function of the WUS gene, namely maintenance of stem cells within the shoot apical meristem, we suggest that the lack of juvenile leaves in the mutant might have been caused by interruption of leaf initiation during the juvenile phase or by halting of an entire process of formation of juvenile leaves.

Arabidopsis↗
PubMed2000

Heterozygous DNA mismatch repair gene PMS2-knockout mice are susceptible to intestinal tumor induction with N-methyl-N-nitrosourea.

PMS2-deficient (PMS2(-/-)) mice are hypersensitive to N-methyl-N-nitrosourea (MNU)-induced thymic lymphomas based on the failure to initiate mismatch repair (MMR) at O(6)-methylguanine:T mismatches formed after MNU exposure. However, heterozygous PMS2 knockout (PMS2(+/-)) mice do not develop spontaneous tumors, suggesting that they have sufficient MMR function to prevent genomic instability. We hypothesized that in PMS2(+/-) mice, exogenous carcinogens may either mutationally knockout the remaining normal allele leading cells to develop tumors or introduce sufficient DNA adducts and mismatches to overload the lower capacity for MMR, leading in either case to an increased rate of tumor production. In the present study, PMS2(+/-) mice and their littermate PMS2(+/+) mice were monitored for tumor incidence following MNU treatment. Mice were given 50 mg MNU/kg i.p. when 5 weeks old. They demonstrated a similar incidence of thymic lymphomas, suggesting that expression of the single normal PMS2 allele is sufficient to protect the thymus and implying that a single dose of MNU may not efficiently knock out the remaining PMS2 allele in the thymus. Surprisingly, PMS2(+/-) mice were significantly more likely to develop intestinal tumors-both adenomas and adenocarcinomas-after MNU than were PMS2(+/+) mice (2.34 +/- 0.34 tumors per mouse versus 1.34 +/- 0.25 tumors per mouse; P < 0.05). The intestinal tumors were located mainly in the small intestine. However, these tumors in both the PMS2(+/-) mice and PMS2(+/+) mice did not show microsatellite instability characteristic of loss of MMR. These results suggest that a single normal PMS2 allele can protect thymus but not intestine from MNU carcinogenesis. Organ-specific factors might influence MMR- mediated resistance to methylating agents. Heterozygous PMS2 knockout mice may be used as a promising animal model for intestinal tumorigenesis studies involving environmental carcinogens.

Adenosine Triphosphatases↗
PubMed2000

Overexpression of mitochondrial citrate synthase in Arabidopsis thaliana improved growth on a phosphorus-limited soil.

The gene for mitochondrial citrate synthase (CS) was isolated from Daucus carota (DcCS) and introduced into Arabidopsis thaliana (strain WS) using Agrobacterium tumefaciens-mediated transformation. Characteristics of citrate excretion were compared between T3 transgenic plants, which were derived from the initial transgenic plants by self-fertilization and homozygous for DcCS, and the control plants that had no DcCS. The highest CS activity 0.78 micromol protein min(-1) exhibited by the transgenic plants was about threefold greater than that found in the control plants (0.23-0.28 micromol protein min(-1)). Western analysis of the transgenic plants showed two CS signals corresponding to signals obtained from both D. carota and A. thaliana. Thus, it appears that the CS polypeptides by ectopic expression of DcCS were processed into the mature form and localized in the mitochondria of A. thaliana. The signal corresponding to the mature form of DcCS were greater in the transgenic plants having higher levels of CS activity. When the transgenic plants were grown in Al-phosphate media, a correlation between the levels of CS activity and the amounts of citrate excreted into the medium. The highest value (5.1 nmol per plant) was about 2.5-fold greater than that from control plants (1.9 nmol per plant). Both growth and P accumulation were greater in transgenic plants with high CS activity than that in control plants when they were grown on an acid soil where the availability of phosphate was low due to the formation of Al-phosphate. It appears that the overexpression of CS in A. thaliana improves the growth in phosphorous limited soil as a result of enhanced citrate excretion from the roots.

Arabidopsis↗
PubMed2000

Genome-wide expression-monitoring of jasmonate-responsive genes of Arabidopsis using cDNA arrays.

Jasmonates are generally considered to mediate signalling, such as defence responses, flowering and senescence. However, factors involved in the jasmonate signal-transduction pathway remain unclear. To clarify the functions and signalling mechanisms of jasmonates on a genome-wide level, we adopted a cDNA macroarray technique. We prepared nylon filters of a cDNA macroarray on which 2880 independent expressed sequence tag clones of Arabidopsis were blotted, and hybridized (33)P-labelled single-strand DNAs synthesized from mRNAs of methyl jasmonate (MeJA)-treated and untreated Arabidopsis plants to the nylon filters. By analysing the data from the cDNA macroarray, we identified many function-known and unknown genes as MeJA-responsive genes, and confirmed that the profiles of the expression showed good agreement with Northern-blot analysis. These results demonstrate the efficiency of the cDNA macroarray for systematically analysing jasmonate-responsive genes on a genome-wide scale.

Acetates↗
PubMed1999

Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning.

To accelerate gene isolation from plants by positional cloning, vector systems suitable for both chromosome walking and genetic complementation are highly desirable. Therefore, we developed a transformation-competent artificial chromosome (TAC) vector, pYLTAC7, that can accept and maintain large genomic DNA fragments stably in both Escherichia coli and Agrobacterium tumefaciens. Furthermore, it has the cis sequences required for Agrobacterium-mediated gene transfer into plants. We cloned large genomic DNA fragments of Arabidopsis thaliana into the vector and showed that most of the DNA fragments were maintained stably. Several TAC clones carrying 40- to 80-kb genomic DNA fragments were transferred back into Arabidopsis with high efficiency and shown to be inherited faithfully among the progeny. Furthermore, we demonstrated the practical utility of this vector system for positional cloning in Arabidopsis. A TAC contig was constructed in the region of the SGR1 locus, and individual clones with ca. 80-kb inserts were tested for their ability to complement the gravitropic defects of a homozygous mutant line. Successful complementation enabled the physical location of SGR1 to be delimited with high precision and confidence.

Agrobacterium tumefaciens↗
PubMed1999

Loss of function of Trp53, but not Apc, leads to the development of esophageal adenocarcinoma in mice with jejunoesophageal reflux.

INTRODUCTION: APC and TP53 are tumor suppressor genes known to be altered frequently in human esophageal adenocarcinoma (EAC), which arises as a complication of reflux disease. To determine the functional role of these genes in the development of EAC, we have created reflux in mice gene-targeted for either Trp53 or Apc. METHODS: Wild-type (WT), p53-knockout (Trp53-/-), or Apc-mutated (ApcMin/+) mice were generated in our breeding colony. Total gastrectomy with esophagojejunostomy was performed at 6 weeks of age, creating jejunoesophageal reflux. Unoperated control mice were maintained under identical conditions. Mice were sacrificed at 30 weeks of age. Histology of the esophagus and jejunal anastamosis or gastroesophageal junction was reviewed by a single pathologist blinded to the genotype of the animal. RESULTS: The esophagus was normal in all of the unoperated mice (6 ApcMin/+, 6 WT, and 6 Trp53-/-). All operated mice (6 ApcMin/+, 12 WT, and 4 Trp53-/-) had esophagitis, with squamous hyperplasia and early focal ulceration. Barrett's metaplasia was identified in 33% of the operated ApcMin/+ (2/6) and 25% of the Trp53-/- (1/4) mice, but not in the WT mice. Of 4 operated Trp53-/- mice, all developed severe dysplasia of the squamous epithelium and 2 (50%) had EAC on histology, although no gross tumors were seen. No severe dysplasia or carcinoma was identified in any of the ApcMin/+ or WT mice. CONCLUSIONS: Loss of either Trp53 or Apc leads to the development of columnar metaplasia, whereas loss of Trp53, but not Apc, leads to development of cancer in mice with jejunoesophageal reflux.

Adenocarcinoma↗
PubMed1999

FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains.

Distinctive from that of the animal system, the basic plan of the plant body is the continuous formation of a structural unit, composed of a stem with a meristem at the top and lateral organs continuously forming at the meristem. Therefore, mechanisms controlling the formation, maintenance, and development of a meristem will be a key to understanding the body plan of higher plants. Genetic analyses of filamentous flower (fil) mutants have indicated that FIL is required for the maintenance and growth of inflorescence and floral meristems, and of floral organs of Arabidopsis thaliana. FIL encodes a protein carrying a zinc finger and a HMG box-like domain, which is known to work as a transcription regulator. As expected, the FIL protein was shown to have a nuclear location. In situ hybridization clearly demonstrated that FIL is expressed only at the abaxial side of primordia of leaves and floral organs. Transgenic plants, ectopically expressing FIL, formed filament-like leaves with randomly arranged cells at the leaf margin. Our results indicate that cells at the abaxial side of the lateral organs are responsible for the normal development of the organs as well as for maintaining the activity of meristems.

Alleles↗
PubMed1999

A sequence-ready contig map of the top arm of Arabidopsis thaliana chromosome 3.

A fine physical map of the top arm of Arabidopsis thaliana chromosome 3 has been constructed by ordering P1, TAC and BAC clones using the sequences of a variety of DNA markers and end-sequences of clones. The marker sequences used in this study were derived from 58 DNA markers, 93 YAC end-sequences, and 807 end-sequences of P1, TAC and BAC clones. The entire top arm of chromosome 3, except for the centromeric and telomeric regions, was covered by a single contig 13.3 Mb long. This fine physical map will facilitate gene isolation by map-based cloning experiments as well as genome sequencing of the top arm of chromosome 3. The map and end-sequence information are available on the web site KAOS (Kazusa Arabidopsis data Opening Site) at [http://www.kazusa.or.jp/arabi/].

Arabidopsis↗
PubMed1999

Transjugular intrahepatic portosystemic shunt for treatment of bleeding ectopic varices with portal hypertension.

PURPOSE: In the setting of hepatic failure and portal hypertension, hemorrhage from stomal and rectal varices is a well-described problem. It has recently been suggested that transjugular intrahepatic portosystemic shunting may be useful in the therapy of bleeding from parastomal or anorectal varices in patients unresponsive to conservative therapy. METHODS: We retrospectively review our institution's experience of five patients with parastomal varices and seven patients with anorectal varices who underwent transjugular intrahepatic portosystemic shunting for hemorrhage refractory to conservative management between 1994 and 1998. RESULTS: The study group consisted of four Child's A, five Child's B, and three Child's C patients. The mean age of the patients was 60.3 (range, 37-85) years. Mean follow-up was 15 (range, 5-27) months. The mean portosystemic pressure gradient before transjugular intrahepatic portosystemic shunting was 17.4+/-3.1 mm Hg. After transjugular intrahepatic portosystemic shunting, the mean portosystemic pressure gradient was reduced to 5.8+/-1.8 mm Hg (P<0.05). Transjugular intrahepatic portosystemic shunting were successful in complete resolution of bleeding in all patients. Three patients had encephalopathic changes after transjugular intrahepatic portosystemic shunting. Two patients died within 30 days of transjugular intrahepatic portosystemic shunting of causes unrelated to the procedure. Four patients required shunt revision within one year of placement. CONCLUSION: The transjugular intrahepatic portosystemic shunting procedure is an effective modality in the therapy of cirrhotic patients with bleeding stomal or anorectal varices unresponsive to conservative management. There is an acceptable procedure-related morbidity and mortality.

Adult↗
PubMed1999

Epstein-Barr virus (EBV) nuclear antigen (EBNA)-4 mutation in EBV-associated malignancies in three different populations.

Different ethnic groups with a high human leukocyte antigen (HLA)-A11 prevalence have been shown to experience a high rate of Epstein-Barr virus (EBV) infection, EBV-associated malignancies, and Epstein-Barr nuclear antigen (EBNA)-4 mutations. The epitopes 399-408 and 416-424 of EBNA-4 are major antigenic epitopes that elicit an HLA-A11 cytotoxic T lymphocyte (CTL) response to EBV infection. Mutations selectively involving one or more nucleotide residues in these epitopes affect the antigenicity of EBNA-4, because the mutant EBV strains are not recognized by the HLA-A11-restricted CTLs. To investigate these mutations in common EBV-associated malignancies occurring in different populations, we studied the mutation rate of epitopes 399-408 and 416-424 of EBNA-4 in 25 cases of EBV-associated Hodgkin's disease (HD), nine cases of AIDS-related non-Hodgkin's lymphoma, and 37 cases of EBV-associated gastric carcinoma (GC) from the United States, Brazil, and Japan. We found one or more mutations in these two epitopes in 50% (6/12) of United States HD, 15% (2/13) of Brazilian HD, 50% (6/12) United States GC and 28% (7/25) Japanese GC, and 22% (2/9) of United States AIDS-lymphoma. Similar mutations were found in 30% (3/10) of United States reactive, 0% (0/6) of Brazilian reactive, and 25% (2/8) Japanese reactive tissues. The most frequent amino acid substitutions were virtually identical to those seen in previously reported isolates from EBV-associated nasopharyngeal carcinomas and Burkitt's lymphomas occurring in high prevalence HLA-A11 regions. However, only 2/28 (7%) mutations occurred in HLA-A11-positive patients. Our studies suggest that: 1) EBNA-4 mutations are a common phenomenon in EBV-associated HD, GC, and AIDS-lymphoma; 2) the mutation rate does not vary in these geographic areas and ethnic groups; 3) EBNA-4 mutations in EBV-associated United States and Brazilian HD, United States and Japanese GC, and United States AIDS lymphomas are not related to patients' HLA-A11 status.

Amino Acid Sequence↗
PubMed1999

Colorectal adenoma and cancer divergence. Evidence of multilineage progression.

Colorectal cancer progression involves changes in phenotype and genotype. Although usually illustrated as a linear process, more complex underlying pathways have not been excluded. The object of this paper is to apply modern quantitative principles of molecular evolution to multistep tumor progression. To reconstruct progression lineages, the genotypes of two adjacent adenoma-cancer pairs were determined by serial dilution and polymerase chain reaction at 28-30 microsatellite (MS) loci and then traced back to their most recent common ancestor. The tumors were mismatch repair deficient, and therefore relatively large numbers of MS mutations should accumulate during progression. As expected, the MS genotypes were similar (correlation coefficients >0.9) between different parts of the same adenoma or cancer, but very different (correlation coefficients <0. 2) between unrelated metachronous adenoma-cancer pairs. Unexpectedly, the genotypes of the adjacent adenoma-cancer pairs were also very different (correlation coefficients of 0.30 and 0.36), consistent with early adenoma-cancer divergence rather than direct linear progression. More than 60% of the divisions occurred after this early adenoma-cancer divergence. Therefore, the tumor phylogenies were not consistent with sequential stepwise selection along a single most "fit" and frequent lineage from adenoma to cancer. Instead, one effective early progression strategy creates and maintains multiple evolving candidate lineages, which are subsequently selected for terminal clonal expansion.

Adenoma↗
PubMed1999

Regional insertional mutagenesis of genes on Arabidopsis thaliana chromosome V using the Ac/Ds transposon in combination with a cDNA scanning method.

For regional insertional mutagenesis of Arabidopsis thaliana genes, we combined a cDNA scanning method (Hayashida et al. Gene 1995; 165:155-161) and an Ac/Ds transposon designed for local mutagenesis, and evaluated this approach with two overlapping yeast artificial chromosome (YAC) clones, CIC7E11 and CIC8B11, on A. thaliana chromosome 5. We applied a previously developed novel cDNA selection method using DNA latex particles (cDNA scanning method) to the two YAC clones and constructed two sub-libraries in which cDNAs for genes on each YAC DNA were concentrated. From each sub-library we isolated cDNAs for genes on each YAC DNA, partially sequenced them, and produced expressed sequence tags (ESTs). In total, 113 non-redundant groups of cDNAs were obtained. Forty-four per cent of these EST clones were novel, and 34% had significant homology to functional proteins from various organisms. In parallel, we transposed Ds from a donor Ds-GUS-T-DNA line, Ds4391-20, already mapped to the CIC7E11/8B11 region. We obtained Ds-transposed lines and recovered their Ds-flanking genomic DNAs by thermal asymmetric interlaced (TAIL) polymerase chain reaction (PCR). Dot-blot analysis indicated that 20% of the lines contained transposed Ds in the CIC7E11/8B11 region, suggesting that this Ac/Ds transposon system is effective for regional insertional mutagenesis. To isolate Ds insertion mutants in the genes identified from the CIC7E11/8B11 region, we carried out PCR screening from 800 Ds-containing lines using Ds-specific and gene-specific primers that were designed from the 113 cDNA sequences identified by the cDNA scanning method. We found that 49 lines contain Ds insertion mutations, and that five lines contain Ds mutations in genes that are mapped to the sequenced CIC7E11/8B11 genomic DNA region. These results indicate that combining the cDNA scanning method and the Ac/Ds transposon gives a powerful tool for regional insertional mutagenesis not only in Arabidopsis but also in other plants or crops whose genomes are not sequenced.

Arabidopsis↗
PubMed1999

Over expression of mitochondrial citrate synthase gene improves the growth of carrot cells in Al-phosphate medium.

A mitochondrial citrate synthase (CS) of Arabidopsis thaliana was introduced into carrot (Daucus carota L. cv. MS Yonsun) cells by Agrobacterium tumefaciens-mediated transformation. Transgenic cell lines had high CS activity, the highest value observed was 0.24 mumol (mg protein)-1 min-1 which was 1.9-fold of that in wild-type cells. Transcript levels of DcCS were similar between transgenic lines, but those of AtCS were increased as the CS activity of cells was increased. Isoelectric focussing revealed that the CS polypeptide of the transgenic lines had a pI value different from that of the wild-type cells, although the molecular mass was the same. These results indicate that the CS polypeptides of A. thaliana were expressed and processed to the mature form in carrot cells. The growth rate and excretion was 2.2-2.8 and 2.8-4.0 fold greater in the transgenic cells than in the wild type cells, respectively. Phosphate uptake from Al-phosphate also increased in transgenic cells. It appears, the overexpression of mitochondrial citrate synthase in carrot cells improves the growth rate in Al-phosphate medium possibly as a result of increased citrate excretion.

Agrobacterium tumefaciens↗
PubMed1999

Regional insertional mutagenesis of specific genes on the CIC5F11/CIC2B9 locus of Arabidopsis thaliana chromosome 5 using the Ac/Ds transposon in combination with the cDNA scanning method.

We have recently developed a novel cDNA selection method (the cDNA scanning method) to select cDNAs for expressed genes in specific regions of the genome [Hayashida et al. (1995) Gene 165: 155, Seki et al. (1997) Plant J. 12: 481]. The gene Ds is known to transpose mainly in its neighborhood. By combining the cDNA scanning method with this trait of Ds, we started functional analysis of region-specific expressed genes on the Arabidopsis thaliana genome. DNA fragments of yeast artificial chromosome (YAC) clones CIC5F11 and CIC2B9 on A. thaliana chromosome 5 were used for the selection of region-specific cDNAs. In total, 50 and 68 cDNA clones were selected from CIC5F11 and CIC2B9, respectively. In parallel, we transposed Ds from a donor T-DNA line, which was mapped on the CIC5F11/CIC2B9 locus of chromosome 5, and obtained Ds-transposed lines. To isolate Ds insertion mutants in the 10 specific genes identified by the cDNA scanning method, we carried out PCR-based screening of 100 Ds-transposed lines and found that 2 lines contain Ds mutations in the genes isolated. We also isolated Ds-flanking genomic DNAs by thermal asymmetric interlaced PCR (TAIL-PCR) in 153 Ds transposon-tagged lines. Southern blot analysis showed that 14% of the lines contained the transposed Ds in the CIC5F11/2B9 region. This suggests that this Ac/Ds transposon system is effective for region-specific insertional mutagenesis.

Arabidopsis↗