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Seed germination, one of the most important stages in a plant's life cycle, can be affected by abiotic stresses, such as salinity. The plant hormone abscisic acid (ABA) and high concentrations of glucose are also known to inhibit germination. In contrast, nitrate is known to stimulate germination in many plants. However, this stimulatory effect has not yet been investigated in the presence of inhibitory effects caused by abiotic stresses, ABA, and glucose. In this study, we show that nitrate can alleviate the inhibitory effects of sodium chloride (NaCl) or high concentrations of glucose on seed germination in Arabidopsis , while it was not able to promote germination that was inhibited by exogenous ABA and mannitol (an inducer of osmotic stress). An analysis of the gene expression involved in the regulation of germination showed that GA20ox1, encoding the gibberellin (GA) synthesis enzyme, SPATULA ( SPT ), encoding a bHLH transcription factor, and CYP707A2, encoding an ABA catabolic enzyme, were significantly upregulated by the addition of KNO 3 in the presence of NaCl or glucose. Our results suggest the possibility that these genes are involved in the nitrate-mediated control of seed germination in the presence of NaCl or glucose.

Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.

HLA-DM is now known to have a major contribution to the selection of immunodominant epitopes. A better understanding of the mechanisms controlling epitope selection can be achieved by examination of the biophysical behavior of major histocompatibility complex (MHC) class II molecules upon binding of antigenic peptides and the effect of DM on the interactions. Using purified soluble molecules, in this chapter, we describe several in vitro methods for measuring peptide binding to HLA-DR molecules and the effects of HLA-DM on the interactions. A simple qualitative method, Gentle SDS-PAGE Assay, would assess the ability of peptides to form tight complexes with MHC class II molecules. Measuring binding kinetics is among the most informative approaches to understanding molecular mechanisms, and here we describe two different methods for measuring binding kinetics of peptide-MHC complexes. In one method, rates of association and dissociation of fluorescently labeled peptides to soluble MHC class II molecules can be determined using G50 spin columns to separate unbound peptides from those in complex with MHC molecules. In another method, association and dissociation of unlabeled peptides and MHC class II molecules can be determined in real time using BIAcore surface plasmon resonance (SPR). We also have described an Intrinsic Tryptophan Fluorescence Assay for studying transient interactions of DM and MHC class II molecules.

Background: To examine the effects of percutaneous endoscopic gastrostomy (PEG) on quality of life (QOL) in patients with dementia., Methods: We retrospectively included 53 Japanese community and tertiary hospitals to investigate the relationship between the newly developed PEG and consecutive dementia patients with swallowing difficulty between Jan 1st 2006 and Dec 31st 2008. We set improvements in 1) the level of independent living, 2) pneumonia, 3) peroral intake as outcome measures of QOL and explored the factors associated with these improvements., Results: Till October 31st 2010, 1,353 patients with Alzheimer's dementia (33.1%), vascular dementia (61.7%), dementia with Lewy body disease (2.0%), Pick disease (0.6%) and others were followed-up for a median of 847 days (mean 805 ± 542 days). A total of 509 deaths were observed (mortality 59%) in full-followed patients. After multivariate adjustments, improvement in the level of independent living was observed in milder dementia, or those who can live independently with someone, compared with advanced dementia, characterized by those who need care by someone: Odds Ratio (OR), 3.90, 95% confidence interval (95%CI), 1.59 - 9.39, P = 0.003. Similarly, improvement of peroral intake was noticed in milder dementia: OR, 2.69, 95%CI, 1.17 - 6.17, P = 0.02. Such significant associations were not observed in improvement of pneumonia., Conclusions: These results suggest that improvement of QOL after PEG insertion may be expected more in milder dementia than in advanced dementia.

A convenient tool for studying metabolism of seminolipid in testis was developed by using mouse isolated seminiferous tubules prepared by collagenase treatment. Because more than 99% of [(35)S]sulfate-incorporation was distributed in seminolipid, its metabolism in seminiferous tubules can be analyzed without disturbance of the other sulfolipids in this assay system. Furthermore, the contents of seminolipid and its precursor, galactosylalkylacylglycerol, which were determined by liquid chromatography-electrospray ionization mass spectrometry, did not change within a few hours, indicating that the incorporations of [(35)S]sulfate into seminolipid solely reflects the turnover rate of this sulfolipid. As an initial application of this system, we characterized heat-susceptibility of the seminolipid turnover rate in mouse seminiferous tubules. Severe heating (44 degrees C for 10 min) of the isolated seminiferous tubules suppressed the (35)S-incorporation into seminolipid to 47% of heating at scrotal temperature (32 degrees C for 70 min). In contrast, pretreatment of the testis in vivo under the same condition (44 degrees C for 10 min) did not decrease the seminolipid turnover rate in the isolated seminiferous tubules. In addition, the activity of galactocerebroside sulfotransferase decreased in the temperature-dependent manner in seminiferous tubules as well as crude tubular homogenates, where the activity is significantly more stable in the former than the latter. The newly developed system could provide useful basic data for further analyses of seminolipid metabolism in the testis.

Background: During tube exchange for percutaneous endoscopic gastrostomy (PEG), a misplaced tube can cause peritonitis and death. Thus, endoscopic or radiologic observation is required at tube exchange to make sure the tube is placed correctly. However, these procedures cost extensive time and money to perform in all patients at the time of tube exchange. Therefore, we developed the "sky blue method" as a screening test to detect misplacement of the PEG tube during tube exchange., Methods: First, sky blue solution consisting of indigocarmine diluted with saline was injected into the gastric space via the old PEG tube just before the tube exchange. Next, the tube was exchanged using a standard method. Then, we checked whether the sky blue solution could be collected through the new tube or not. Finally, we confirmed correct placement of the tube by endoscopic or radiologic observation for all patients., Results: A total of 961 patients were enrolled. Each tube exchange took 1 to 3 minutes, and there were no adverse effects. Four patients experienced a misplaced tube, all of which were detectable with the sky blue method. Diagnostic parameters of the sky blue method were as follows: sensitivity, 94% (95%CI: 92-95%); specificity, 100% (95%CI: 40-100%); positive predictive value, 100% (95%CI: 100-100%); negative predictive value, 6% (95%CI: 2-16%)., Conclusion: These results suggest that the number of endoscopic or radiologic observations to confirm correct replacement of the PEG tube may be reduced to one fifteenth using the sky blue method.

Patterns and contents of major acidic glycosphingolipids in the kidney of three marine mammalian species, the Steller sea lion (Pinnipedia), the rough-toothed dolphin and the broad-beaked dolphin (Odontoceti), were examined, and compared with those of terrestrial mesic mammals. The profile of major acidic glycosphingolipids was not significantly different between the terrestrial and marine mammals: predominant gangliosides were GM3 and GD3, and major sulfoglycolipids were SM4s and SM3. On the other hand, the total concentration (nmol/g wet tissue) of sulfoglycolipids was considerably higher in the marine mammals (2.3-3.0 times) than that in the terrestrial mesic mammals with comparable body weights. In contrast, there was no significant difference in the level of renal glycolipids-bound sialic acid between the marine and the terrestrial mammals. These results suggest that higher expression of renal sulfoglycolipids in marine mammals may contribute to the maintenance of osmotic balance of their body fluid against sea water.

Effects of a glycolytic (glucose) and a gluconeogenic renal nutritional substrate (glutamine) on metabolic turnover of sulfolipids, determined as [(35)S]sulfate incorporation, were compared in renal tubules prepared from well-fed rats. The results showed that the effects of glucose and glutamine, at nearly physiological serum concentration, are quite contrary to each other. Glucose increased the turnover rates of relatively long chain ganglio-series sulfoglycolipids (Gg(3)Cer II(3)-sulfate and Gg(4)Cer II(3),IV(3)-bis-sulfate) (1.7 to 2.4-fold), but not of cholesterol 3-sulfate (0.9-fold). In contrast, glutamine accelerated the turnover rates of relatively short chain sulfoglycolipids (glucosyl sulfatide, galactosyl sulfatide and lactosyl sulfatide) (1.3 to 2.7-fold), as well as cholesterol 3-sulfate (2.4-fold). The possible mechanism which causes these marked differences is also discussed.

We performed an immunohistochemical analysis of cell cycle-regulating protein (p21, p27 and Ki67) expression in endoscopic biopsy samples from the patients with gastroesophageal reflux disease (GERD) using angled -biopsy forceps. Inflammatory cell accumulation into the lamina propria was detected even in patients with modified Los Angeles (LA) system grades N or M. In grade N or M patients with no changes in the epithelium, the area of p21, p27 and Ki67 positive cells was expanded compared to normal mucosa. The area of p21, p27 and Ki67 positive cells tended to expand upward in the epithelium with GERD severity based on the LA classification grading. These indicate that inflammatory cell infiltration into the lamina propria is initial histological change of GERD.

Four unidentified acidic glycolipids (X3-X6) were isolated from the kidney of the Pacific salmon on an anion exchange column and by high performance liquid chromatography using a silica bead (Iatrobeads) column. Based on methylation analysis, chemical and enzymatic degradation, proton nuclear magnetic resonance spectroscopy and mass spectrometry, the glycon structure of X5 and X6 was identified as a unique disialosyl fucosyl-N-acetylgalactosaminyl ganglio-N-tetraose:Fucalpha3GalNAcbeta3Galbeta3GalNAcbeta4[NeuAcalpha8NeuAcalpha3] Galbeta4Glcbeta1Cer. NMR showed that X3 and X4 were analogues of X5 and X6 and contained O-acetyl groups on C4 of the outer N-acetylneuraminic acid, first disialosyl gangliosides containing 4-O-acetyl-N-acetylneuraminic acid. The ceramides of X3 and X5 contained predominantly C24: 1, and X4 and X6 contained saturated fatty acids (C14: 0, C16: 0 and C18: 0), whereas the long chain base was exclusively sphingenine. The concentrations of X3 and X4 were 0.13 and 0.16 nmol/g of kidney respectively and those of X5 and X6, were 0.07 nmol/g each.