Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies.

Genebanks provide access to diverse materials for crop improvement. To utilize and evaluate them effectively, core collections, such as the World Rice Core Collection (WRC) in the Genebank at the National Agriculture and Food Research Organization, have been developed. Because the WRC consists of 69 accessions with a high degree of genetic diversity, it has been used for >300 projects. To allow deeper investigation of existing WRC data and to further promote research using Genebank rice accessions, we performed whole-genome resequencing of these 69 accessions, examining their sequence variation by mapping against the Oryza sativa ssp. japonica Nipponbare genome. We obtained a total of 2,805,329 single nucleotide polymorphisms (SNPs) and 357,639 insertion-deletions. Based on the principal component analysis and population structure analysis of these data, the WRC can be classified into three major groups. We applied TASUKE, a multiple genome browser to visualize the different WRC genome sequences, and classified haplotype groups of genes affecting seed characteristics and heading date. TASUKE thus provides access to WRC genotypes as a tool for reverse genetics. We examined the suitability of the compact WRC population for genome-wide association studies (GWASs). Heading date, affected by a large number of quantitative trait loci (QTLs), was not associated with known genes, but several seed-related phenotypes were associated with known genes. Thus, for QTLs of strong effect, the compact WRC performed well in GWAS. This information enables us to understand genetic diversity in 37,000 rice accessions maintained in the Genebank and to find genes associated with different phenotypes. The sequence data have been deposited in DNA Data Bank of Japan Sequence Read Archive (DRA) (Supplementary Table S1).

Identification of qRBS1, a QTL involved in resistance to bacterial seedling rot in rice.

Bacterial seedling rot (BSR), a destructive disease of rice (Oryza sativa L.), is caused by the bacterial pathogen Burkholderia glumae. To identify QTLs for resistance to BSR, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (resistant) and Koshihikari (susceptible). Comparison of the levels of BSR in the CSSLs and their recurrent parent, Koshihikari, revealed that a region on chromosome 10 was associated with resistance. Further genetic analyses using an F5 population derived from a cross between a resistant CSSL and Koshihikari confirmed that a QTL for BSR resistance was located on the short arm of chromosome 10. The Nona Bokra allele was associated with resistance to BSR. Substitution mapping in the Koshihikari genetic background demonstrated that the QTL, here designated as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), was located in a 393-kb interval (based on the Nipponbare reference genome sequence) defined by simple sequence repeat markers RM24930 and RM24944.

Incidence, clinicopathological features, and clinical outcomes of low HER2 expressed, inoperable, advanced, or recurrent gastric/gastroesophageal junction adenocarcinoma.

BACKGROUND: According to the DESTINY-Breast04 trial, treating patients with breast cancer and low human epidermal growth factor receptor 2 expressions (HER2-low) varies from that of those with no HER2 expression. However, it is interesting to know if HER2-low indicates for anti-HER2 therapy in the gastric or gastroesophageal junction (G/GEJ) adenocarcinoma. Hence we conducted this study to assess the incidence, clinicopathological features, and treatment outcomes of patients with HER2-low G/GEJ adenocarcinoma. PATIENTS AND METHODS: This was a single-center, retrospective observational study. Patients with previously untreated G/GEJ adenocarcinoma were classified based on their HER2 status using immunohistochemistry (IHC) with or without in situ hybridization (ISH) as follows: HER2 negative (IHC 0), HER2-low (IHC 1+ or 2+/ISH-), and HER2-positive (IHC2+/ISH+ or 3+). RESULTS: In total, 734 patients with G/GEJ adenocarcinoma were divided into three groups (HER2-negative, n = 410; HER2-low, n = 154, and HER2-positive, n = 170). The intestinal-type histology, peritoneal metastasis, and higher serum carcinoembryonic antigen (CEA) levels differed significantly among patients with negative, low, and positive HER2 statuses: intestinal-type histology (21.0%, 44.2%, and 59.8%, respectively), peritoneal metastasis (56.3%, 44.8%, and 21.8%, respectively), and higher serum CEA level (32.2%, 41.6%, and 56.5%, respectively). Improved survival was observed in the HER2-positive group than in the HER2-negative G/GEJ adenocarcinoma group [hazard ratio (HR) = 0.73, 95% confidence interval (CI) 0.59-0.89; P = 0.002]. However, the prognoses of the HER2-low and HER2-negative groups were similar (HR = 1.01, 95% CI 0.82-1.23; P = 0.843). CONCLUSIONS: Patients with HER2-low G/GEJ adenocarcinoma exhibited intermediate and distinct characteristics than those in the HER2-negative group. Similarly, the HER2-low group's prognosis was worse than that of the HER2-positive group. Therefore developing novel therapeutic strategies targeting HER2-low G/GEJ adenocarcinoma is required.

A multiple gene complex on rice chromosome 4 is involved in durable resistance to rice blast.

Quantitative trait loci (QTLs) for resistance to rice blast offer a potential source of durable disease resistance in rice. However, few QTLs have been validated in progeny testing, on account of their small phenotypic effects. To understand the genetic basis for QTL-mediated resistance to blast, we dissected a resistance QTL, qBR4-2, using advanced backcross progeny derived from a chromosome segment substitution line in which a 30- to 34-Mb region of chromosome 4 from the resistant cultivar Owarihatamochi was substituted into the genetic background of the highly susceptible Aichiasahi. The analysis resolved qBR4-2 into three loci, designated qBR4-2a, qBR4-2b, and qBR4-2c. The sequences of qBR4-2a and qBR4-2b, which lie 181 kb apart from each other and measure, 113 and 32 kb, respectively, appear to encode proteins with a putative nucleotide-binding site (NBS) and leucine-rich repeats (LRRs). Sequence analysis of the donor allele of qBR4-2a, the region with the largest effect among the three, revealed sequence variations in the NBS-LRR region. The effect of qBR4-2c was smallest among the three, but its combination with the donor alleles of qBR4-2a and qBR4-2b significantly enhanced blast resistance. qBR4-2 comprises three tightly linked QTLs that control blast resistance in a complex manner, and thus gene pyramiding or haplotype selection is the recommended strategy for improving QTL-mediated resistance to blast disease through the use of this chromosomal region.

Alveolar bone regeneration using absorbable poly(L-lactide-co-epsilon-caprolactone)/beta-tricalcium phosphate membrane and gelatin sponge incorporating basic fibroblast growth factor.

The aim of this study was to evaluate the effects of combining a porous poly(L-lactide-co-epsilon-caprolactone)/beta-tricalcium phosphate membrane and gelatin sponge incorporating basic fibroblastic growth factor (bFGF) on bone regeneration in mandibular ridges. Four full-thickness saddle-type defects (10 mm long x 5 mm deep) were symmetrically created in both edentulous mandibular alveolar ridges of 6 beagles. The dome-shaped membrane was secured to each defect site, and a gelatin sponge containing 200 microg bFGF was implanted on the left side of each defect (experimental group). Only the membranes (control group) were secured to the defect sites on the right. Three and 6 months later, 3 animals were killed. Bone regeneration was analyzed by soft X-ray photographs, micro-computed tomography (CT) images, and peripheral quantitative CT (pQCT), and then examined histologically. Soft X-ray examination revealed an increase in new bone volume in the experimental group 6 months postoperatively. pQCT showed that immature bone density was higher in the experimental group. Micro-CT images revealed well formed new bone along the original contour of the dome-shaped membrane in the experimental group. Histologically, inflammatory infiltration of tissue surrounding the membranes was slight. These results suggest that combining the poly(L-lactide-co-epsilon-caprolactone)/beta-tricalcium phosphate membrane and bFGF-gelatin sponge is promising for alveolar ridge reconstruction.

Genetic and physical mapping of the partial resistance gene, pi34, to blast in rice.

ABSTRACT Partial resistance to rice blast in the Oryza sativa japonica group cv. Chubu 32 is controlled by Pi34, a major quantitative trait locus (QTL) on chromosome 11, and several uncharacterized QTLs. The objectives of the study were (i) high-resolution genetic and physical mapping of Pi34 and (ii) identification of new QTL imparting resistance to rice blast. Chubu 32 was crossed with a susceptible chromosomal segment substitution line (CSSL) of cv. Koshihikari. From 4,012 of segregating individuals, 213 recombinants in the Pi34 region were screened by using polymerase chain reaction-based markers and tested resistance in the field and greenhouse. The Pi34 locus is located in the 54.1-kb region on the genomic sequence of cv. Nipponbare. We constructed a bacterial artificial chromosome (BAC) library of Chubu 32, selected the clone containing Pi34, and sequenced it. The Pi34 locus consequently was located on an interval of 65.3 kb containing 10 predicted open reading frames (ORFs). Two of these ORFs were predicted only in Chubu 32 and encoded transposable elements. The other eight ORFs were found in both Chubu 32 and Nipponbare and one of them, which encoded an unknown protein, showed significantly different amino acid sequences between two cultivars. The new QTL, Piq6(t), was detected on the short arm of chromosome 6 and the genetic distance of flanking markers was 16.9 centimorgans in Nipponbare. Pi34 and Piq6(t) acted additively on resistance to rice blast but the effect of Piq6(t) was relatively small compared with Pi34.

Molecular cloning and sequences of cDNAs encoding alpha (large) and beta (small) isoforms of human pancreatic zymogen granule membrane-associated protein GP2.

cDNA clones encoding two different (alpha and beta) forms of human pancreatic zymogen granule membrane-associated protein glycoprotein 2 (GP2) (also referred to as ZAP75), a critical component in regulated membrane trafficking along the apical secretory pathway in pancreatic acinar cells, have been isolated. Structural analysis of the clones revealed that the alpha and beta forms of GP2 consist of 527 and 380 amino acid (aa) residues, respectively. The beta form lacks a 147 aa domain that corresponds to the 25-171 region of the alpha form, suggesting that it is a product of an alternative splicing event. Expression of both forms of GP2 in the human pancreas was confirmed. A unique isoform of GP2 is reported for the first time in humans.

Characterization and functional expression of the cDNA encoding human brain quinolinate phosphoribosyltransferase.

Mammalian quinolinate phosphoribosyltransferase (QPRTase) (EC 2.4.2.19) is a key enzyme in catabolism of quinolinate, an intermediate in the tryptophan-nicotinamide adenine dinucleotide (NAD) pathway. Quinolinate acts as a most potent endogenous exitotoxin to neurons. Elevation of quinolinate levels in the brain has been linked to the pathogenesis of neurodegenerative disorders. As the first step to elucidate molecular basis underlying the quinolinate metabolism, the cDNA encoding human brain QPRTase was cloned and characterized. Utilizing partial amino acid sequences obtained from highly purified porcine kidney QPRTase, a human isolog was obtained from a human brain cDNA library. The cDNA encodes a open reading frame of 297 amino acids, and shares 30 to 40% identity with those of bacterial QPRTases. To confirm that the cDNA clone encodes human QPRTase, its functional expression was studied in a bacterial host. Introduction of the human cDNA into a QPRTase defective (nadC) E. coli strain brought about an abrupt increase in QPRTase activity and allowed the cells to grow in the absence of nicotinic acid. It is concluded that the cloned cDNA encodes human QPRTase which is functional beyond the phylogenic boundary.

Localization of pancreatic enzyme secretion-stimulating activity and trypsin inhibitory activity in zymogen granule of the rat pancreas.

The intracellular localization of pancreatic enzyme secretion-stimulating activity in rat pancreas was investigated. We found and purified a pancreatic enzyme secretion-stimulating peptide from rat bile/pancreatic juice. The peptide is trypsin-sensitive (showing temporary trypsin inhibitory activity), and it is hypothesized that it acts as a trypsin-sensitive mediator in the feedback regulation of diet-induced pancreatic enzyme secretion. The zymogen granule fraction was purified 5-fold by ultracentrifugation by the Percoll density gradient method. The purity of the zymogen granule fraction was determined from the specific amylase activity and electron microscopic morphology. The specific enzyme activities of amylase and trypsin and the trypsin inhibitory activity increased in parallel during the purification, and the pancreatic enzyme secretion-stimulating activity was also localized in the zymogen granule fraction. These results suggest that the pancreatic enzyme secretion-stimulating peptide originates from the acinar cells, and that it is secreted through exocytosis of zymogen granules into the small intestine, its ratio to trypsin thus remaining constant. This idea supports our hypothesis that the stimulating peptide acts as a mediator for the feedback regulation of pancreatic enzyme secretion by trypsin.

Physico-chemical analysis of lipid A fractions of lipopolysaccharide from Erwinia carotovora in relation to bioactivity.

Highly purified bisphosphoryl, monophosphoryl and dephosphoryl lipids A from Erwinia carotovora with different acylation patterns were characterized physico-chemically. Applying matrix assisted laser desorption/ionization mass spectrometry, the purity of the lipid A fractions was determined, and from monolayer measurements the molecular space requirement was estimated. Fourier transform infrared spectroscopy allowed the elucidation of the gel to liquid crystalline phase transition of the acyl chains as well as the determination of the tilt angle of the diglucosamine backbone with respect to the acyl chain direction applying dichroitic measurements with attenuated total reflectance. With synchrotron radiation small-angle X-ray diffraction the supramolecular aggregate structure was determined, and with fluorescence resonance energy transfer spectroscopy the lipopolysaccharide binding protein induced intercalation of lipid A into a phospholipid matrix corresponding to that of the macrophage membrane was investigated. From the results, a clear dependence of the physico-chemical parameters on the particular lipid A structure can be followed. Furthermore, these parameters correlate well with the biological activities of the various lipids A as deduced from their ability to induce biological activity (Limulus assay and cytokine induction in mononuclear cells). These results contribute to a closer interpretation of the physico-chemical prerequisites for endotoxic activity as found for enterobacterial lipid A.

Mapping of sequence-tagged sites in rice by single strand conformation polymorphism.

The conditions for efficient single-strand conformation polymorphism (SSCP) detection were examined for its application to mapping of DNA regions in the rice genome. Temperature for electrophoresis and glycerol concentrations in gel affected SSCP patterns significantly. The optimal detection conditions for SSCP also depends on the nucleotide sequences of fragments analyzed. Fragments over 300 bp show complicated patterns depending on their nucleotide sequences and were not suitable for SSCP analysis. Seventy primer pairs were designed from the sequence data available to amplify DNA regions as sequence tagged sites (STSs), and 39 of these STSs were found to generate SSCP between japonica rice (Nipponbare) and indica rice (Kasalath) in at least one of the experimental conditions. The maps of DNA fragments amplified from 186 F2-plant DNAs with 17 primer pairs were successfully determined. This direct mapping method of the amplified DNA fragments with PCR is simple and quite sensitive, and can be used to set markers in the gap regions of a genetic linkage map.

Determination of RAPD markers in rice and their conversion into sequence tagged sites (STSs) and STS-specific primers.

We produced 102 randomly amplified polymorphic DNA (RAPD) markers mapped on all 12 chromosomes of rice using DNAs of cultivars Nipponbare (japonica) and Kasalath (indica) and of F2 population generated by a single cross of these parents. Sixty random primers 10 nucleotides long were used both singly and in random pairs and about 1,400 primer-pairs were tested. Using both agarose gel and polyacrylamide gel electrophoresis enabled us to detect polymorphisms appearing in the range from < 100 bp to 2 kb. The loci of the RAPD markers were determined onto the framework of our RFLP linkage map and some of these markers were mapped to regions with few markers. Out of the 102 RAPD markers, 20 STSs (sequence-tagged sites) and STS-specific primer pairs were determined by cloning, identifying and sequencing of the mapped polymorphic fragments.

Differentiation of intestinal epithelial cell line (IEC-18) by an acid extract of rat small intestine.

A factor which may induce differentiation of intestinal epithelial cell lines in vitro was found in an acid extract of adult rat small intestine. The addition of a partially purified acetic acid extract of rat small intestine to IEC-18 cell culture dishes increased sucrase activity within 48 h. Thymidine incorporation markedly decreased within 24 h. Significant development of microvilli-like structures was observed on the acid extract-treated IEC-18 cells, compared with controls. This activity of rat acid extract was heat-stable and the apparent molecular weight of the factor was 400-800. These findings suggested that the factor may be related to the epithelial differentiation of rat small intestinal crypt cells.

Cerebral hypoperfusion in orthostatic hypotension with globally denervated myocardium.

A 57-yr-old woman had frequent syncope when rising from a seated position. Her blood pressure fell from 140/80 mmHg to 60-70/40 mmHg while changing positions. Iodine-123-metaiodobenzylguanidine ([123I]MIBG) did not accumulate in the heart, whereas 201Tl-Cl (201Tl) did. Raise-up 99mTc-hexamethyl-propyleneamine oxime (99mTc-HMPAO) brain SPECT revealed decreased activity in the bilateral frontal areas, and subsequent supine 99mTc-HMPAO brain SPECT revealed filling in these areas, indicating that the cerebral blood flow (CBF) was transiently decreased in the frontal areas more than others in a standing position. The plasma norepinephrine (NE) level of this patient was normal during supine rest, but when she stood up, failure to increase the plasma level of NE uncovered a sympathetic nervous dysfunction. The CBF abnormality in patients with orthostatic hypotension may be due to a "functional" hemodynamic mechanism that induces orthostatic stress. This patient had transient hypoperfusion in the frontal areas when standing, without organic cerebral arterial stenosis. Only CBF in the frontal areas revealed relative hypoperfusion. These regions might be highly susceptible to a change in blood flow. The causes of orthostatic hypotension of this patient were autonomic failure with a disturbance of the sympathetic nerve endings, which was revealed by 99mTc-HMPAO brain SPECT and cardiac [123l]MIBG imaging.

Functional reconstruction of the jaw bones using poly(l-lactide) mesh and autogenic particulate cancellous bone and marrow.

The goal of the reconstruction of jaw bone defects should be not only to recover deformities, but also to reconstruct the jaw with which the patient can perform normal functions. To achieve this purpose, it is essential that a method of promoting regeneration of physiological bone is developed so that dentures can be accommodated. In this report a new method of functional reconstruction using fresh autogenous particulate cancellous bone and marrow and a poly(L-lactide) mesh tray is presented. This method will make physiological reconstruction of the jaw possible. In the future this method is also expected to assist in the development of simultaneous functional reconstruction of the jaw bone and oral rehabilitation when dental implants are included in the tray.

Pancreatic enzyme secretion mediated by novel peptide: monitor peptide hypothesis.

A new model is proposed for pancreatic enzyme secretion in response to food protein intake in rats. We have found a novel peptide in rat bile-pancreatic juice, which exhibits a trypsin-sensitive, cholecystokinin (CCK)-releasing activity. The amino acid sequence of the peptide purified from rat bile-pancreatic juice is very similar to that of a conservative region in pancreatic secretory trypsin inhibitor (PSTI). The peptide loses its CCK-releasing activity during trypsin digestion, but food protein intake prevents this trypsin digestion. Results of a reconstitution experiment indicate that pancreatic enzyme secretion in response to food protein intake only occurs as a result of interaction between trypsin and our purified peptide. Also, a peptide-specific antibody abolished the response. These findings lead us to hypothesize that this peptide acts as an intraduodenal mediator for CCK release in response to food protein intake.

Rapid and selective cloning of monitor peptide, a novel cholecystokinin-releasing peptide, using minimal amino acid sequence and the polymerase chain reaction.

cDNA transcripts encoding rat monitor peptide (MP) have been cloned from a lambda-ZAP-II phage library using minimal specific amino acid sequence (six residues), the polymerase chain reaction (PCR), and multivalent PCR probes to distinguish MP transcripts from those that encode a closely related peptide, pancreatic secretory trypsin inhibitor. DNA sequence analysis of 3 cDNA transcripts, MP1-3, revealed the complete amino acid sequence of the prepeptide (79 residues) including an 18-residue hydrophobic signal sequence at the NH2 terminus. Sequence divergence in both coding and 3' noncoding regions indicates a potential exon-exon junction with alternative splicing, which results in a truncated peptide with Arg 58 at the COOH terminus as well as alternative selection of poly(A) signals, respectively. The 5' nontranslated region of MP1 mRNA (282 nucleotides (nt] contains four upstream ATGs. Conserved structure between MP and anionic trypsinogen mRNAs within 9 nt immediately upstream of the AUG initiation codon may be involved in coupling the expression of MP with anionic trypsinogen, a condition which appears to be required to monitor the intake of dietary protein in the rat.

Role of the GP2/THP family of GPI-anchored proteins in membrane trafficking during regulated exocrine secretion.

Identification and characterization of the GP2/THP family of GPI-anchored membrane proteins associated with apical secretory membranes suggest that this new class of GPI-linked proteins plays a critical role in regulated protein secretion and ion transport in polarized epithelial cells in pancreas, liver, lung, kidney, and gastrointestinal tract. Based on recent information obtained from the world literature and from our own investigations we present the following two hypotheses capable of unifying previously diverse observations. Hypothesis 1 is that formation of GP2 tetramers in the acidic milieu of the trans-Golgi network (TGN) organizes a GP2/proteoglycan (PG) matrix tightly associated with the luminal surface of zymogen granule (ZG) membranes, and proposes that this matrix functions in (a) membrane sorting during granule assembly in the TGN, (b) inactivation of ZG membranes during the storage phase of secretion, and (c) regulated trafficking of ZG membranes from the apical plasma membrane (APM) after exocytosis. Hypothesis 2 is that the acinar lumen constitutes a distinct physiologic compartment for coupled biochemical reactions between acinar and duct cells. Because the acidic pH of the TGN plays a critical role in condensation of secretory proteins, alkalinization of the acinar lumen is required for (a) neutralization of the acidic pH of exocytic contents and (b) solubilization of aggregated (pro)enzymes. Further alkalinization appears to be required for pH-dependent release of the GP2/PG matrix from the APM, a process that may regulate internalization of ZG membranes for reuse during secretion. Taken together, the two hypotheses suggest that luminal factors including acid-base interactions and matrix assembly and disassembly processes perform critical functions during regulated storage and release of pancreatic (pro)enzymes. The requirement that coupling reactions be coordinated through the actions of separate hormones [cholecystokinin (CCK) and secretin] on divergent epithelial cells (acinar and duct cells, respectively) provides a new appreciation for the importance of combined CCK and secretin stimulation during pancreatic secretion in response to food intake.

Pancreatic dysfunction in cystic fibrosis occurs as a result of impairments in luminal pH, apical trafficking of zymogen granule membranes, and solubilization of secretory enzymes.

Recent progress in understanding the luminal biochemistry of regulated pancreatic exocrine secretion, including acid-base interactions between acinar and duct cells and pH-dependent processes that regulate membrane trafficking (endocytosis) at the apical plasma membrane, have led to the development of in vitro models of cystic fibrosis in the rat exocrine pancreas. Based on investigations in these model systems, a unifying hypothesis is presented that proposes that pancreatic dysfunction in cystic fibrosis occurs as a result of progressive acidification of the acinar and duct lumen, which leads to secondary defects in (i) apical trafficking of zymogen granule membranes and (ii) solubilization of secretory (pro)enzymes. By directly acidifying the pH of the acinar lumen in cholescystokinin-stimulated acini, the early cytological findings observed in cystic fibrosis, including (i) massive dilatation of the acinar lumen, (ii) decreased appearance of zymogen granules, (iii) loss of the apical pole of the acinar cell, and (iv) persistent aggregation of secretory (pro)enzymes released into the luminal space, have been reproduced in primary cultures of pancreatic tissue.

Expression of Bcl-2 and PCNA in duct cells after pancreatic duct ligation in rats.

Obstruction of the pancreatic duct induces acinar cell deletion followed by duct proliferation and interstitial fibrosis. Apoptosis has been reported to be involved in the induction of acinar cell deletion after pancreatic duct ligation (PDL) in rats, however, the mechanism of pancreatic duct cell proliferation is still unknown. We hypothesized that Bcl-2 (antiapoptosis protein) and PCNA (cell cycle-related protein) could be involved in the mechanism of pancreatic duct cell proliferation after PDL. In PDL, rats, acinar cells decreased in number and disappeared completely after duct ligation and duct-lining cells increased in number and formed duct-tubular complexes. Immunohistochemical study showed that PCNA expression appeared in the ductules and centroacinar cells from early stages after duct ligation and that Bcl-2 expression in duct cells, which was faint in normal pancreas, increased significantly when acinar cells were diminishing. Western blotting demonstrated that Bcl-2 was detected as a single band at 26 kDa, and the intensity of Bcl-2 in PDL rats was approximately ninefold stronger than in normal pancreas. Expression of Bcl-2 and PCNA after pancreatic duct ligation may be related to the prevention of apoptosis and cell proliferation of pancreatic duct cells in rats.