RiceXPro version 3.0: expanding the informatics resource for rice transcriptome.

A wide range of resources on gene expression profiling enhance various strategies in plant molecular biology particularly in characterization of gene function. We have updated our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp/), to provide more comprehensive information on the transcriptome of rice encompassing the entire growth cycle and various experimental conditions. The gene expression profiles are currently grouped into three categories, namely, 'field/development' with 572 data corresponding to 12 data sets, 'plant hormone' with 143 data corresponding to 13 data sets and 'cell- and tissue-type' comprising of 38 microarray data. In addition to the interface for retrieving expression information of a gene/genes in each data set, we have incorporated an interface for a global approach in searching an overall view of the gene expression profiles from multiple data sets within each category. Furthermore, we have also added a BLAST search function that enables users to explore expression profile of a gene/genes with similarity to a query sequence. Therefore, the updated version of RiceXPro can be used more efficiently to survey the gene expression signature of rice in sufficient depth and may also provide clues on gene function of other cereal crops.

RiceFREND: a platform for retrieving coexpressed gene networks in rice.

Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs and tissues at different developmental stages, mature organs throughout the growth from transplanting until harvesting in the field and plant hormone treatment conditions, using a single microarray platform. The database is provided with two search options, namely, 'single guide gene search' and 'multiple guide gene search' to efficiently retrieve information on coexpressed genes. A user-friendly web interface facilitates visualization and interpretation of gene coexpression networks in HyperTree, Cytoscape Web and Graphviz formats. In addition, analysis tools for identification of enriched Gene Ontology terms and cis-elements provide clue for better prediction of biological functions associated with the coexpressed genes. These features allow users to clarify gene functions and gene regulatory networks that could lead to a more thorough understanding of many complex agronomic traits.

Usefulness of the Preoperative Images Supporting Mechanical Thrombectomy Based on Susceptibility-Weighted Image for Stroke.

Objective: This is a report on the usefulness of 3D fusion imaging with susceptibility-weighted imaging (SWI) as preoperative imaging for mechanical thrombectomy (MT) for acute ischemic stroke (AIS). Case Presentations: Among 17 cases of patients who underwent MT in AIS between March 2021 and April 2022, 14 patients who underwent MRI with SWI (shortened SWI for stroke) and 3D T2-weighted sampling perfection with application-optimized contrasts using different flip angle evolution were targeted in the study. Three cases with motion artifacts due to body movement were excluded from the images.After imaging, 3D fusion images were constructed to visualize thrombi and occluded vessels. SWI for stroke obtained thrombus information in 11 of the 14 cases (78.5%) and 3D images of the thrombi could be created in all 11 cases. 3D fusion images could be created in nine of the 14 cases (64.2%). Conclusion: 3D fusion images, using SWI for stroke, can visualize thrombi and occluded vessels and may be effectively used as preoperative images for MT.

Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.

Here we present the genomic sequence of the African cultivated rice, Oryza glaberrima, and compare these data with the genome sequence of Asian cultivated rice, Oryza sativa. We obtained gene-enriched sequences of O. glaberrima that correspond to about 25% of the gene regions of the O. sativa (japonica) genome by methylation filtration and subtractive hybridization of repetitive sequences. While patterns of amino acid changes did not differ between the two species in terms of the biochemical properties, genes of O. glaberrima generally showed a larger synonymous-nonsynonymous substitution ratio, suggesting that O. glaberrima has undergone a genome-wide relaxation of purifying selection. We further investigated nucleotide substitutions around splice sites and found that eight genes of O. sativa experienced changes at splice sites after the divergence from O. glaberrima. These changes produced novel introns that partially truncated functional domains, suggesting that these newly emerged introns affect gene function. We also identified 2451 simple sequence repeats (SSRs) from the genomes of O. glaberrima and O. sativa. Although tri-nucleotide repeats were most common among the SSRs and were overrepresented in the protein-coding sequences, we found that selection against indels of tri-nucleotide repeats was relatively weak in both African and Asian rice. Our genome-wide sequencing of O. glaberrima and in-depth analyses provide rice researchers not only with useful genomic resources for future breeding but also with new insights into the genomic evolution of the African and Asian rice species.

Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries.

Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare 'Haruna Nijo') under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.

DaizuBase, an integrated soybean genome database including BAC-based physical maps.

Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and genome sequencing are the most effective approaches towards understanding the structure and function of the soybean genome. We constructed bacterial artificial chromosome (BAC) libraries from the Japanese soybean cultivar, Enrei. The end-sequences of approximately 100,000 BAC clones were analyzed and used for construction of a BAC-based physical map of the genome. BLAST analysis between Enrei BAC-end sequences and the Williams82 genome was carried out to increase the saturation of the map. This physical map will be used to characterize the genome structure of Japanese soybean cultivars, to develop methods for the isolation of agronomically important genes and to facilitate comparative soybean genome research. The current status of physical mapping of the soybean genome and construction of database are presented.

Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.).

BACKGROUND: Microarray technology is limited to monitoring the expression of previously annotated genes that have corresponding probes on the array. Computationally annotated genes have not fully been validated, because ESTs and full-length cDNAs cannot cover entire transcribed regions. Here, mRNA-Seq (an Illumina cDNA sequencing application) was used to monitor whole mRNAs of salinity stress-treated rice tissues. RESULTS: Thirty-six-base-pair reads from whole mRNAs were mapped to the rice genomic sequence: 72.0% to 75.2% were mapped uniquely to the genome, and 5.0% to 5.7% bridged exons. From the piling up of short reads mapped on the genome, a series of programs (Bowtie, TopHat, and Cufflinks) comprehensively predicted 51,301 (shoot) and 54,491 (root) transcripts, including 2,795 (shoot) and 3,082 (root) currently unannotated in the Rice Annotation Project database. Of these unannotated transcripts, 995 (shoot) and 1,052 (root) had ORFs similar to those encoding the amino acid sequences of functional proteins in a BLASTX search against UniProt and RefSeq databases. Among the unannotated genes, 213 (shoot) and 436 (root) were differentially expressed in response to salinity stress. Sequence-based and array-based measurements of the expression ratios of previously annotated genes were highly correlated. CONCLUSION: Unannotated transcripts were identified on the basis of the piling up of mapped reads derived from mRNAs in rice. Some of these unannotated transcripts encoding putative functional proteins were expressed differentially in response to salinity stress.

Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels.

The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species O. officinalis, and draft genomes for two other C genome diploid species Oryza eichingeri and Oryza rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated Oryza sativa, mostly due to proliferation of Gypsy type long-terminal repeat transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B, and F). Draft genome assemblies of the two other C genome diploid species, Oryza eichingeri and Oryza rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and long-terminal repeat transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes and a genomic resource for the exploitation of the Oryza tertiary gene pool.

[Secondary myelodysplasia and leukemia following carboplatin and paclitaxel-containing chemotherapy for ovarian cancer].

Platinum is the key drug in current treatment of ovarian cancer. The overall survival rate of patients with advanced ovarian cancer has improved. Recently, therapy-related myelodysplastic syndrome(T-MDS)and therapy-related leukemia( TRL)have been reported with increasing frequency in the literature. In this paper, we report two cases of TMDS followed by TRL after chemotherapy(TC therapy consisting of carboplatin and paclitaxel)with ovarian cancer stageIIIc. The interval from the primary chemotherapy to TMDS was 23 months or 90 months. The abnormal karyotype was observed in chromosomal analysis. Neither cases were given chemotherapy for TMDS, and died of the immunodeficiency. TRL and T-MDS are the most serious complications of chemotherapy. If pancytopenia is detected, bone marrow and cytogenetic examinations should be performed to rule out TMDS.

Structural analysis of epolactaene derivatives as DNA polymerase inhibitors and anti-inflammatory compounds.

Epolactaene (compound 1), a neuritogenic compound found in human neuroblastoma cells, was found to show anti-inflammatory activity in vivo in this study. DNA polymerases and DNA topoisomerase II (topo II) were some of the major molecular targets of compound 1. Since the agent seems to be a potential pharmaceutical medicine, we synthesized derivatives chemically and obtained seven compounds, 1 to 7 to screen clinically more efficient epolactaene derivatives. A comparison of its structural derivatives revealed that the long alkyl side chain seemed to have an important role in the inhibitory effect. Notably, C18-alkyl chain conjugated epolactaene (compound 5) was the strongest inhibitor of DNA polymerase alpha, beta, lambda (pol alpha, beta, lambda) and topo II, with IC50 values of 13, 135, 4.4 and 5 microM, respectively, and 500 microg of compound 5 caused a marked reduction in TPA (12-O-tetradecanoylphorbol-13-acetate)-induced inflammation (inhibitory effect, 65.0%). Compound 5 did not influence the activities of plant or prokaryotic DNA polymerases, or of other DNA metabolic enzymes such as telomerase, RNA polymerase and deoxyribonuclease I. Based on these results, the relationship among the three-dimensional structure of epolactaene derivatives and the inhibition of polymerases and topo II, and anti-inflammation is discussed.

The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars.

We elucidated the genome sequence of Glycine max cv. Enrei to provide a reference for characterization of Japanese domestic soybean cultivars. The whole genome sequence obtained using a next-generation sequencer was used for reference mapping into the current genome assembly of G. max cv. Williams 82 obtained by the Soybean Genome Sequencing Consortium in the USA. After sequencing and assembling the whole genome shotgun reads, we obtained a data set with about 928 Mbs total bases and 60,838 gene models. Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean. The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome. The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide.

The radish genome and comprehensive gene expression profile of tuberous root formation and development.

Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.

Diagnosis of vasospastic angina by hyperventilation and cold-pressor stress echocardiography: comparison to I-MIBG myocardial scintigraphy.

OBJECTIVES: We assessed the usefulness of hyperventilation and cold-pressor stress echocardiography in the diagnosis of vasospastic angina compared with that of iodine-123 metaiodobenzylguanidine (123I-MIBG) myocardial scintigraphy. BACKGROUND: Various noninvasive methods have been used to detect vasospastic angina, but they are not very sensitive in the diagnosis of vasospastic angina. 123I-MIBG images and stress echocardiography have recently been proposed as a useful tool for detecting vasospastic angina. METHOD: Thirty patients (21 males and 9 females, mean age: 52 +/- 14 years) who complained of rest angina were enrolled for this study. The hyperventilation and cold-pressor stress echocardiography test consisted of hyperventilation for 6 minutes, followed by cold water pressor for 2 minutes under continuous electrocardiographic and echocardiographic monitoring. Left ventricular regional wall motion by echocardiogram was analyzed by using the 16-segment model, and wall motion ranging from normokinesis to dyskinesis was evaluated visually in each segment. Single-photon emission computed tomography images of 123I-MIBG myocardial scintigraphy were divided into 26 segments. Defect scores were established using the 4 grades. The echocardiographic criteria for coronary spasm was worsening wall motion and the scintigraphic criteria was defect score more than moderately reduced. Acetylcholine was selectively injected into the right coronary artery (20 microg and 50 microg) and left coronary artery (20 microg, 50 microg, and 100 microg). RESULTS: Of 30 patients, 20 patients had coronary spasm on coronary angiography with an intracoronary injection of acetylcholine, whereas 10 patients showed no spasm. Multivessel spasms were observed in 15 patients. Sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of hyperventilation and cold-pressor stress echocardiography for diagnosing in patients with vasospastic angina were 90%, 90%, 95%, 82%, and 90%, respectively. However, those of 123I-MIBG myocardial scintigraphy for diagnosing in patients with vasospastic angina were 90%, 40%, 75%, 67%, and 73%, respectively. The specificity of hyperventilation and cold-pressor stress echocardiography was significantly higher than that of 123I-MIBG myocardial scintigraphy (P <.05). CONCLUSION: The specificity of hyperventilation and cold-pressor stress echocardiography in diagnosing coronary spasm were higher than that shown by 201I-MIBG myocardial scintigraphy.

Inhibitory action of conjugated C18-fatty acids on DNA polymerases and DNA topoisomerases.

We reported previously that unsaturated linear-chain FA of the cis-configuration with a C18-hydrocarbon chain such as linoleic acid (18:2delta9c,12c) could potently inhibit the activities of mammalian DNA polymerases and DNA topoisomerases, but their saturated forms could not. There are chemically two classes of unsaturated FA, normal and conjugated, but only the conjugated forms show potent antitumor activity. In this report, we study the inhibitory effects of chemically synthesized conjugated C18-FA on mammalian DNA polymerases and DNA topoisomerases as compared with normal unsaturated FA. The conjugated alpha-eleostearic acid (18:3delta9c,11t, 13t) was the strongest of all the FA tested. For the inhibition, the conjugated form is crucially important. The energy-minimized 3-D structures of the FA were calculated, and both a length of less than 20 A and a width of 8.13-9.24 A in the C18-FA structure were found to be important for enzyme inhibition. The 3-D structure of the active site of both DNA polymerases and topoisomerases must have had a pocket to join alpha-eleostearic acid, and this pocket was 12.03 A long and 9.24 A wide.

Diagnosis of ischemic heart disease with exercise echocardiography: Comparison of images obtained at peak- and post-exercise.

Peak-and post-exercise stress echocardiography were compared with respect to ability to detect coronary artery disease in 138 consecutive patients undergoing supine bicycle stress echocardiography. Sixty of these patients had single-vessel disease; 37, double-vessel disease; and 19, triple-vessel disease. Exercise was performed in the 20- to 30-degree left decubitus position on an echo-bed with an ergometer. Exercise started at 50 watts and was increased in 25-watt every 3 minutes and to a maximum of 150 watts. Two-dimensional echocardiographic images were digitized and assigned in a quad-screen format for nonbiased interpretation. Total wall motion score (TWMS) was the sum of the wall motion score, from normokinesis (0) to dyskinesis (4), of 16 segments. Image quality score index (IQSI) was the mean of the image quality scores in all views. All of the patients underwent coronary arteriography. Significant coronary stenosis was defined as≧75% stenosis of the large coronary arteries. Two-dimensional echocardiographic studies were adequate for analysis in 133 patients during the peak-exercise stage (peak-exercise) and in 137 patients 30 to 60 seconds after the end of exercise (post-exercise). TWMS at peak-exercise was higher than at post-exercise, while IQSI at peak-exercise was lower than at post-exercise. Sensitivity at peak-exercise versus that at post-exercise was 91% versus 79% (p<0.05); specificity, 76% versus 85%; and diagnostic accuracy, 88% versus 80% (p<0.05), respectively. We conclude that despite poor image quality on exercise echocardiography, better diagnostic accuracy was attained by assessing wall motion changes at peak-exercise than at post-exercise.

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

Gene duplication occurs by either DNA- or RNA-based processes; the latter duplicates single genes via retroposition of messenger RNA. The expression of a retroposed gene copy (retrocopy) is expected to be uncorrelated with its source gene because upstream promoter regions are usually not part of the retroposition process. In contrast, DNA-based duplication often encompasses both the coding and the intergenic (promoter) regions; hence, expression is often correlated, at least initially, between DNA-based duplicates. In this study, we identified 150 retrocopies in rice (Oryza sativa L. ssp japonica), most of which represent ancient retroposition events. We measured their expression from high-throughput RNA sequencing (RNAseq) data generated from seven tissues. At least 66% of the retrocopies were expressed but at lower levels than their source genes. However, the tissue specificity of retrogenes was similar to their source genes, and expression between retrocopies and source genes was correlated across tissues. The level of correlation was similar between RNA- and DNA-based duplicates, and they decreased over time at statistically indistinguishable rates. We extended these observations to previously identified retrocopies in Arabidopsis thaliana, suggesting they may be general features of the process of retention of plant retrogenes.

Asymmetric distribution of gene expression in the centromeric region of rice chromosome 5.

There is controversy as to whether gene expression is silenced in the functional centromere. The complete genomic sequences of the centromeric regions in higher eukaryotes have not been fully elucidated, because the presence of highly repetitive sequences complicates many aspects of genomic sequencing. We performed resequencing, assembly, and sequence finishing of two P1-derived artificial chromosome clones in the centromeric region of rice (Oryza sativa L.) chromosome 5 (Cen5). The pericentromeric region, where meiotic recombination is silenced, is located at the center of chromosome 5 and is 2.14 Mb long; a total of six restriction-fragment-length polymorphism markers (R448, C1388, S20487S, E3103S, C53260S, and R2059) genetically mapped at 54.6 cM were located in this region. In the pericentromeric region, 28 genes were annotated on the short arm and 45 genes on the long arm. To quantify all transcripts in this region, we performed massive parallel sequencing of mRNA. Transcriptional density (total length of transcribed region/length of the genomic region) and expression level (number of uniquely mapped reads/length of transcribed region) were calculated on the basis of the mapped reads on the rice genome. Transcriptional density and expression level were significantly lower in Cen5 than in the average of the other chromosomal regions. Moreover, transcriptional density in Cen5 was significantly lower on the short arm than on the long arm; the distribution of transcriptional density was asymmetric. The genomic sequence of Cen5 has been integrated into the most updated reference rice genome sequence constructed by the International Rice Genome Sequencing Project.

Desensitization treatment with cisplatin after carboplatin hypersensitivity reaction in gynecologic cancer.

Platinum-based chemotherapy is the standard regimen for the treatment of gynecologic cancers; however, hypersensitivity reactions (HR) to platinum often lead to discontinuation of this effective treatment. Here we performed a desensitization protocol for platinum infusion in 3 patients who required platinum re-administration after developing HR. Two patients (Case 1 and 2) were treated with the desensitization protocol successfully without developing HR during the subsequent 3 courses. Case 3 tolerated desensitization well for 2 courses, but in the 3(rd) course, she developed severe HR immediately after the initiation of cisplatin infusion because the desensitization protocol was unintentionally omitted. These cases show the usefulness and effectiveness of the desensitization protocol for the continuation of platinum treatment in patients who have undergone an extended number of treatments.

A huge ovarian smooth muscle tumor: a case report.

Ovarian smooth muscle tumors are a very rare type of ovarian tumor. In this paper, we report the case of a 62-year-old woman who had a huge smooth muscle tumor of the right ovary. The values of all the serum tumor markers were within normal limit. The tumor measured 25 cm in diameter and weighed 6,200 g. Histological examination revealed that coagulative cellular atypia was moderate to severe, necrosis was not present and mitotic index was low. According to the criteria for the evaluation of the uterine smooth muscle tumors, this huge tumor was diagnosed as atypical leiomyoma. However, we finally made a diagnosis of this tumor as a smooth muscle tumor of uncertain malignant potential (STUMP) because of its huge size. Further information is required regarding the characteristics of ovarian smooth muscle tumor and the propriety to introduce uterine tumor histological criteria to ovarian tumors.