[Evaluation of a Species-specific, Stable, and Endogenous Sequence of Eggplant (Solanum melongena) using LAMP for the Detection of Genetically Modified Eggplants].

Species-specific endogenous reference sequences are indispensable in the development of methods to detect genetically modified (GM) crops for food and feed. We analyzed a partial sequence derived from the ß-fructosidase gene among several solanaceous species and developed a new eggplant specific detection method using loop-mediated isothermal amplification (LAMP). LAMP is a rapid, specific, and cost-effective technique. The species-specificity and stability of the developed method were evaluated using 18 eggplant cultivars and other crops including solanaceous plants. The limit of detection was also evaluated. The developed method showed high specificity for eggplants and stability among the eggplant cultivars tested. These results suggested that the developed method would be useful as a positive control for the detection of GM eggplants with LAMP.

Gastric neuroendocrine tumor arising from heterotopic pancreas.

There are few English reports on secondary tumors from heterotopic pancreas. Here, we describe a case of gastric neuroendocrine tumor (NET) arising from heterotopic pancreas. A 72-year-old woman underwent esophagogastroduodenoscopy as part of a general health check-up. An endoscopic examination revealed a submucosal tumor on the greater curvature of the gastric body. Laparoscopic and endoscopic cooperative surgery was performed. Histological diagnosis concluded that it was a Grade 1 NET arising from heterotopic pancreas. We report this extremely rare case of a NET presenting as a submucosal tumor, considered to have originated from heterotopic pancreatic tissue.

Findings of Retrograde Contrast Study Through Double-balloon Enteroscopy Predict the Risk of Bowel Resections in Patients with Crohn's Disease with Small Bowel Stenosis.

BACKGROUND: Patients with Crohn's disease (CD) with small bowel strictures are at risk of surgery. Double-balloon enteroscopy (DBE) can evaluate the status of the small intestine, and retrograde contrast through the scope enables the surgeon to obtain information beyond the reach of the scope. This study aimed to examine whether a retrograde contrast study through DBE could be used as a predictor of subsequent surgery in patients with CD with small intestinal strictures. METHODS: The findings of DBE with retrograde contrast in 48 patients CD with small bowel strictures were examined. RESULTS: Of the 48 patients, 14 (29%) underwent surgery for small intestinal strictures during a median observation period of 2.4 years (interquartile range: 1.4-3.7 yr). According to the results of the multivariate analysis, a maximum length of strictures ≥20 mm and the ratio of the maximum diameter of prestenotic dilations to the diameter of the normal small intestine ≥1.4 were independent risk factors of surgery for small intestinal strictures (risk ratio = 7.6 [95% confidence interval, 1.8-42.0], P = 0.006; and risk ratio = 52.0 [95% confidence interval, 3.5-2485.1], P = 0.002, respectively). The latter predicted subsequent surgery with 92% sensitivity and 88% specificity. Cumulative surgery-free rates were discriminated significantly according to the presence or absence of these 2 risk factors (log-rank test: P < 0.001). CONCLUSIONS: Findings of retrograde contrast through DBE are helpful to predict risk of surgery in patients with CD with small intestinal strictures.

Comparing reduced-dose sodium phosphate tablets to 2 L of polyethylene glycol: A randomized study.

AIM: To compare the tolerability and quality of bowel cleansing between 2 L polyethylene glycol (PEG) and reduced-dose sodium phosphate (NaP) tablets as a preparation for colonoscopy. METHODS: Two hundred patients were randomly assigned to the PEG or NaP groups at the same ratio. The NaP group patients took 30 tablets with 2 L of clear liquid, while the PEG group patients took 2L of PEG. Tolerability was assessed by a questionnaire about taste, volume, and the overall impression. The bowel cleansing quality was evaluated by colonoscopists. RESULTS: Although NaP showed better tolerability in terms of taste, volume and overall impression (P < 0.01, P < 0.01 and P = 0.02, respectively), the overall cleansing quality was better in the PEG group (P < 0.01). A subgroup analysis, stratified by sex and age, indicated that NaP was associated with better tolerability and equivalent bowel cleansing quality in females of < 50 years of age. CONCLUSION: Despite the better tolerability, the use of 30 NaP tablets with 2 L of clear liquid should be limited due to its lower cleansing quality; however, in certain cases the regimen may deserve consideration, particularly in cases involving young women.

Cooperativity and evolution of Tetrahymena two-domain arginine kinase.

Tetrahymena pyriformis contains two arginine kinases, a 40-kDa enzyme (AK1) with a myristoylation signal sequence at the N-terminus and a two-domain 80-kDa enzyme (AK2). The former is localized mainly in cilia and the latter is in the cytoplasm. AK1 was successfully synthesized using an insect cell-free protein synthesis system and subjected to peptide mass fingerprinting (PMF) analysis. The masses corresponding to unmodified N-terminal tryptic peptide or N-terminal myristoylated peptide were not observed, suggesting that N-terminal peptides were not ionized in this analysis. We performed PMF analyses for two other phosphagen kinases (PKs) with myristoylation signals, an AK from Nematostella vectensis and a PK from Ectocarpus siliculosus. In both cases, the myristoylated, N-terminal peptides were clearly identified. The differences between the experimental and theoretical masses were within 0.0165-0.0583 Da, supporting the accuracy of the identification. Domains 1 and 2 of Tetrahymena two-domain AK2 were expressed separately in Escherichia coli and the extent of cooperativity was estimated on the basis of their kinetic constants. The results suggested that each of the domains functions independently, namely no cooperativity is displayed between the two domains. This is in sharp contrast to the two-domain AK from Anthopleura.

A Randomized Trial of Monopolar Soft-mode Coagulation Versus Heater Probe Thermocoagulation for Peptic Ulcer Bleeding.

BACKGROUND AND AIM: Endoscopic therapy has been demonstrated to be effective in achieving hemostasis for bleeding peptic ulcers. Thermal coagulation is one of the most commonly used methods, with a high success rate. Recently, endoscopic submucosal dissection for early gastric carcinoma was developed and hemostasis with soft coagulation using hemostatic forceps was introduced. The aim of this study was to compare the hemostatic efficacy of soft coagulation with heater probe thermocoagulation for peptic ulcer bleeding. METHODS: Patients who visited our hospital with hematemesis or melena underwent emergency endoscopy. Inclusion criteria were presentation with an actively bleeding ulcer, a nonbleeding visible vessel, or an adherent clot. Patients were excluded if they were unwilling to give written informed consent or had a bleeding gastric malignancy. Patients were randomized to receive endoscopic hemostasis with soft coagulation (Group S) or heater probe thermocoagulation (Group H). The primary endpoint was the primary hemostasis rate and secondary endpoints were rebleeding rate, complications, and the procedure time. RESULTS: Between May 2010 and February 2012, a total of 111 patients (89 gastric ulcers and 22 duodenal ulcers) were enrolled. Primary hemostasis was achieved in 54 patients (96%) in Group S and 37 (67%) in Group H (P<0.0001). Rebleeding occurred in 7 patients in Group H and none in Group S. Of these 7 patients, urgent surgery was performed in 1. Perforation occurred in 2 patients in Group H, which was managed conservatively. CONCLUSIONS: For patients with gastroduodenal ulcer bleeding, soft coagulation using monopolar hemostatic forceps is more effective than heater probe thermocoagulation for achieving hemostasis.

Using miglitol at 30 min before meal is effective in hyperinsulinemic hypoglycemia after a total gastrectomy.

A 45-year-old woman who had undergone total gastrectomy for gastric cancer presented with a history of postprandial hypoglycemic episodes with loss of consciousness after meals. Laboratory findings revealed marked hyperinsulinemia and hypoglycemia after a meal. We first treated the patient with octreotide; however, she was unable to continue the treatment because of adverse effects of the drug, such as nausea and headache. Diazoxide was used next for preventing hyperinsulinemia; however, this was not effective for suppressing the postprandial insulin secretion. Since hypoglycemia following gastrectomy is thought to be caused by rapid delivery of nutrients into the duodenum, we performed a meal tolerance test while varying the timing of administration of miglitol in relation to the meal. Miglitol was administered 30 min before, just before, or both 30 min and just before a meal. In the case of administration just before a meal, insulin secretion was suppressed, although hypoglycemia was not prevented. Administration of the drug 30 min before a meal prevented postprandial hypoglycemia by slowing the increase of the blood glucose and serum insulin levels following the meal to a greater degree than administration just before a meal. Miglitol administration both 30 min and just before a meal caused an even smoother increase in blood glucose and serum insulin levels following the meal. In this report, we propose a new therapeutic approach for reactive hypoglycemia after gastrectomy, namely, administration of miglitol 30 min before meals.

Two arginine kinases of Tetrahymena pyriformis: characterization and localization.

Two cDNAs, one coding a typical 40-kDa arginine kinase (AK1) and the other coding a two-domain 80-kDa enzyme (AK2), were isolated from ciliate Tetrahymena pyriformis, and their recombinant enzymes were successfully expressed in Escherichia coli. Both enzymes had an activity comparable to those of typical invertebrate AKs. Interestingly, the amino acid sequence of T. pyriformis AK1, but not AK2, had a distinct myristoylation signal sequence at the N-terminus, suggesting that 40-kDa AK1 targets the membrane. Moreover, Western blot analysis showed that the AK1 is mainly localized in the ciliary fraction. Based on these results, we discuss the phosphoarginine shuttle, which enables a continuous energy flow to dynein for ciliary movement in T. pyriformis, and the role of AK1 in this model.

[The impact of guidelines for the management of acute cholecystitis in a rural area of Japan].

We monitored the management of acute cholecystitis in a rural area of Japan to determine the effectiveness of new guidelines for the management of acute cholecystitis and cholangitis. Between January 2000 and September 2011, 366 patients were treated for acute cholecystitis. Of these, 59 had common bile duct stones (CBDS) and 307 did not. Patients in both groups were further subdivided into two groups: a before guidelines group (BGG; n=153) and an after guideline group (AGG; n=154). Among the patients without CBDS, early cholecystectomy was more common in the AGG group (n=53) than in the BGG group. Furthermore, the length of hospital stay was four days shorter in the AGG group than in the BGG group (n=23). Among the patients with CBDS, the timing of cholecystectomy after endoscopic retrograde cholangiography was seven days earlier in the AGG group than in the BGG group. Even in a rural area of Japan, early cholecystectomy appears safe and can decrease the length of hospital stay.

[The anxiety and influence factors of care managers who provide a home palliative care for terminal cancer patients--a comparison between nursing staffs and others].

UNLABELLED: In home palliative care, care managers play an important part. But we suspect that care managers, who don't have a medical license, may feel an anxiety. So, we investigated if these care managers felt an anxiety, and would like to report a role of nursing staffs in home palliative care. METHOD: We surveyed care managers who were working in the western part of Hiroshima. The number of care managers was 199. And 129 of them(86.9%)filled out the questionnaire. We used c 2 -test and analyzed the difference of an anxiety between nursing staffs and the others. RESULTS: The care managers felt an anxiety about the patient's condition and the therapy rather than nursing staffs. CONCLUSION: Nursing staffs play an important role by doing a therapeutic management for terminal cancer patients, an explanation for the family of patients, and a cooperation with other staffs.

The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS.

The SMARCAD1/KIAA1122 protein is structurally classified into the SWI2/SNF2 superfamily of DNA-dependent ATPases that are catalytic subunits of chromatin-remodeling complexes. Although the importance of other members of the SWR1-like subfamily in chromatin remodeling (EP400, INOC1, and SRCAP) has already been elucidated, the biological function of SMARCAD1/KIAA1122 in transcriptional regulation remains to be clarified. To gain insight into the role of this protein, we generated a specific antibody against SMARCAD1/KIAA1122 and used it for chromatin and protein immunoprecipitation assays. We employed high-resolution genome tiling microarrays in chromatin immunoprecipitation and found the binding sites of SMARCAD1/KIAA1122 in the vicinity of the transcriptional start site of 69 candidate target genes. In the protein immunoprecipitation assay, we found that endogenous SMARCAD1/KIAA1122 binds with TRIM28, a recently highlighted transcriptional regulator in the cancer field. From these findings, we propose a novel model for gene regulation via the SMARCAD1/KIAA1122 protein complex.

Ultrasound biomicroscopic examination of acute hydrops in patients with keratoconus.

PURPOSE: To investigate the possible factors involved in the development of acute hydrops in patients with keratoconus. DESIGN: Prospective interventional case series. METHODS: Thirteen consecutive keratoconic eyes of 13 patients with acute hydrops were examined by ultrasound biomicroscopy (UBM). RESULTS: Ultrasound biomicroscopy (UBM) examinations revealed a rupture of Descemet membrane and intrastromal clefts in all eyes. In 11 of 13 eyes, the intrastromal clefts were connected to the anterior chamber. CONCLUSIONS: Formation of intrastromal clefts may be an important factor in the development of acute hydrops in keratoconic eyes. The clefts may cause severe corneal edema and delay the closure of Descemet membrane during the resolution of corneal edema.

Influence of the 3'-UTR-length of mKIAA cDNAs and their sequence features to the mRNA expression level in the brain.

We have previously described the sequence features of approximately 1500 mouse KIAA (mKIAA) genes in comparison with those of human KIAA genes (Okazaki, N., Kikuno, R., Inamoto, S., Hara, Y., Nagase, T., Ohara, O., and Koga, H. 2002, DNA Res., 9, 179-188; Okazaki, N., Kikuno, R., Ohara, R., Inamoto, S., Aizawa, H., Yuasa, S., Nakajima, D., Nagase, T., Ohara, O., and Koga, H. 2003, DNA Res., 10, 35-48; Okazaki, N., Kikuno, R., Ohara, R., Inamoto, S., Koseki, H., Hiraoka, S., Saga, Y., Nagase, T., Ohara, O., and Koga, H. 2003, DNA Res., 10, 167-180; and Okazaki, N., F-Kikuno, R., Ohara, R., Inamoto, S., Koseki, H., Hiraoka, S., Saga, Y., Seino, S., Nishimura, M., Kaisho, T., Hoshino, K., Kitamura, H., Nagase, T., Ohara, O., and Koga, H. 2004, DNA Res., 11, 205-218). To validate the orthologous relationship between mKIAA and KIAA genes in detail, we examined their chromosomal positions and evolutionary rate of synonymous substitutions and confirmed that >93% of the mKIAA/KIAA gene pairs are orthologous. During the sequence analysis of mKIAA genes, we found that 3'-untranslated region (3'-UTR) lengths of mKIAA and KIAA genes are extremely long. In the meanwhile, we have also examined the tissue-specific expression of approximately 1700 mKIAA genes using cDNA microarray and verified predominantly their expression in adult brain (Koga, H., Yuasa, S., Nagase, T., Shimada, K., Nagano, M., Imai, K., Ohara, R., Nakajima, D., Murakami, M., Kawai, M., Miki, F., Magae, J., Inamoto, S., Okazaki, N., Ohara, O. 2004, DNA Res., 11, 293-304). To connect these two evidences, we statistically analysed the relationship between them by using the mKIAA genes. Consequently, a positive correlation was observed between the 3'-UTR lengths and the relative expression intensities in adult brain. Furthermore, we searched sequence elements in the 3'-UTR possibly related with their expression and found some candidates regarding the brain-specific expression.

Preparation of a set of expression-ready clones of mammalian long cDNAs encoding large proteins by the ORF trap cloning method.

Although we have so far identified and sequenced >2000 human long cDNAs, known as KIAA cDNAs, half of them have yet to be functionally annotated. Expression-ready cDNA clones derived from these genes, where the open reading frame (ORF) of the gene of interest is placed under the control of an appropriate promoter, are critical for functional characterization of these gene products. In this study, we attempted to systematically convert original cDNA clones to expression-ready forms for native and fusion proteins. For this purpose, we developed a new method for ORF cloning based on a homologous recombination in Escherichia coli to avoid laborious manipulations and artificial introduction of mutations in ORF. Using 1589 putative full-length ORFs (from 1002 KIAA genes, 119 human known genes and 468 mouse genes) with an average size of 2.8 kb, we successfully prepared expression plasmids for 1463 native proteins and for 1343 fusion proteins by this method. The resultant expression-ready clones were examined using an in vitro transcription/translation system followed by SDS-polyacrylamide gel electrophoresis and by transient expression of GFP-fusion proteins in human embryonic kidney (HEK) 293 cells. This set of expression-ready clones of long cDNAs encoding large proteins would open a new route to experimentally analyze their functions on a proteomic scale, since unavailability of expression-ready clones for mammalian large proteins has been a major obstacle to the functional analysis of these cDNAs.

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins.

The inaugural version of the InGaP database (Integrative Gene and Protein expression database; http://www.kazusa.or.jp/ingap/index.html) is a comprehensive database of gene/protein expression profiles of 127 mKIAA genes/proteins related to hypothetical ones obtained in our ongoing cDNA project. Information about each gene/protein consists of cDNA microarray analysis, subcellular localization of the ectopically expressed gene, and experimental data using anti-mKIAA antibody such as Western blotting and immunohistochemical analyses. KIAA cDNAs and their mouse counterparts, mKIAA cDNAs, were mainly isolated from cDNA libraries derived from brain tissues, thus we expect our database to contribute to the field of neuroscience. In fact, cDNA microarray analysis revealed that nearly half of our gene collection is predominantly expressed in brain tissues. Immunohistochemical analysis of the mouse brain provides functional insight into the specific area and/or cell type of the brain. This database will be a resource for the neuroscience community by seamlessly integrating the genomic and proteomic information about the mouse KIAA genes/proteins.

Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have been conducting a mouse cDNA project to predict protein-coding sequences of mouse homologues of human KIAA and FLJ genes since 2001. As an extension of these projects, we herein present the entire sequences of 500 mKIAA cDNA clones and 4 novel cDNA clones that were incidentally identified during this project. We have isolated cDNA clones from the size-fractionated mouse cDNA libraries derived from 7 tissues and 3 types of cultured cells. The average size of the 504 cDNA sequences reached 4.3 kb and that of the deduced amino acid sequences from these cDNAs was 807 amino acid residues. We assigned the integrity of CDSs from the comparison with the corresponding human KIAA cDNA sequences. The comparison of mouse and human sequences revealed that two different human KIAA cDNAs are derived from single genes. Furthermore, 3 out of 4 proteins encoded in the novel cDNA clones showed moderate sequence similarity with human KIAA proteins, thus we could obtain new members of KIAA protein families through our mouse cDNA projects.

Prediction of the coding sequences of mouse homologues of FLJ genes: the complete nucleotide sequences of 110 mouse FLJ-homologous cDnas identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have been conducting a mouse cDNA project to predict protein-coding sequences of mouse KIAA-homologous genes since 2001. As an extension of this project, we also started to accumulate mouse cDNA clones homologous to the human FLJ cDNA clones which are another long cDNA resource produced in our institute. We have isolated the cDNA clones from size-fractionated cDNA libraries derived from five different mouse tissues and natural killer T-cells. Although the human FLJ cDNA clones were originally derived from human spleen libraries, one-third of their mouse homologues were obtained from the brain library. We designated these homologues "mFLJ" plus a 5-digit number and herein characterized 110 mFLJ cDNA clones. We assigned an integrity of the CDSs from the comparison of the 110 cDNA clones with the corresponding human FLJ cDNA clones. The average size of the 110 mouse cDNA sequences was 3.8 kb and that of the deduced amino acid sequences from their longest CDS in each cDNA was 663 amino acid residues. Homology and/or motif search against public databases revealed new domains and/or motifs in 26 mFLJ gene products which provide additional speculation regarding the function of FLJ genes.

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins: generation and evaluation of anti-mKIAA antibodies.

Since December 2001 we have been conducting a project to isolate and determine entire sequences of mouse KIAA cDNA clones which encode polypeptides corresponding to human KIAA proteins. The ultimate goal of this project is the elucidation of the functions of KIAA proteins. A critical step in this project is the generation of antibodies based on the cDNA sequence information. Although antibodies are the most optimal tools for biological analysis, the production and isolation of multiple recombinant proteins for an antigen is a rate-limiting step in antibody production. To address this problem, we established a system utilizing the in vitro recombination-assisted method and shotgun clones that were generated during the sequencing of mouse KIAA cDNAs (DNA Res. 2003, 10, 129-136). The authenticity of the expressed proteins was confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Another critical step for antibody production is the evaluation of the antibodies. Thus, we also made efforts to develop a systematic approach for evaluation of the titer and the specificity of the antibodies. Using these systems, we have produced and evaluated more than 500 antibodies raised against mouse KIAA proteins to date. We are currently generating antibody arrays for analysis of protein expression profiles. We will verify protein-protein interactions using immunoprecipitation and tandem mass spectrometry analysis.

A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier.

Several studies have addressed the importance of various ubiquitin-like (UBL) post-translational modifiers. These UBLs are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. In this report, we describe the identification of a novel ubiquitin-fold modifier 1 (Ufm1) with a molecular mass of 9.1 kDa, displaying apparently similar tertiary structure, although lacking obvious sequence identity, to ubiquitin. Ufm1 is first cleaved at the C-terminus to expose its conserved Gly residue. This Gly residue is essential for its subsequent conjugating reactions. The C-terminally processed Ufm1 is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. Ufm1 forms several complexes in HEK293 cells and mouse tissues, revealing that it conjugates to the target proteins. Ufm1, Uba5, and Ufc1 are all conserved in metazoa and plants but not in yeast, suggesting its potential roles in various multicellular organisms.

HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE.

We have been developing a Human Unidentified Gene-Encoded (HUGE) protein database (http://www.kazusa.or.jp/huge) to summarize results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. At present, HUGE contains 2031 cDNA entries (KIAA cDNAs), for each of which a gene/protein characteristic table has been prepared. Since we have been shifting our research attention from the identification and cloning of novel cDNAs to the functional analysis of the proteins encoded by these cDNAs (KIAA proteins), we have not substantially increased the number of cDNA entries in HUGE for some time. Instead, we have manually curated 451 KIAA cDNAs in order to prepare a set of genetic resources to facilitate the functional analysis of KIAA proteins. In addition, we have updated the contents of the corresponding gene/protein characteristic tables in HUGE and have constructed two subsidiary databases, HUGEppi (http://www. kazusa.or.jp/huge/ppi) and ROUGE (http://www. kazusa.or.jp/rouge), to make available the results from our study of KIAA protein function. HUGEppi shows detailed information on protein-protein interactions detected between 84 pairs of KIAA proteins by yeast two-hybrid screening. ROUGE summarizes the results of computer-assisted analyses of approximately 1000 mouse homologues of human large cDNAs that we identified.