FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes.

Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness. As a result, FoodPro has accumulated 236 aqueous (extracted in D2O) and 131 hydrophobic (extracted in CDCl3) experimental bench-top 60-MHz NMR spectra, 1753 tastings scored by volunteers, and 139 hardness measurements recorded by a penetrometer, all placed into a core database. The database content was roughly classified into fish and vegetable groups from the viewpoint of different spectrum patterns. FoodPro can query a user food NMR spectrum, search similar NMR spectra with a specified similarity threshold, and then compute estimated tasting and hardness, covariance, and correlation spectra to tasting and hardness. Querying fish spectra exemplified specific covariance spectra to tasting and hardness, giving positive covariance for tasting at 1.31 ppm for lactate and 3.47 ppm for glucose and a positive covariance for hardness at 3.26 ppm for trimethylamine N-oxide.

The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis.

NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites.

SpinCouple: Development of a Web Tool for Analyzing Metabolite Mixtures via Two-Dimensional J-Resolved NMR Database.

A new Web-based tool, SpinCouple, which is based on the accumulation of a two-dimensional (2D) (1)H-(1)H J-resolved NMR database from 598 metabolite standards, has been developed. The spectra include both J-coupling and (1)H chemical shift information; those are applicable to a wide array of spectral annotation, especially for metabolic mixture samples that are difficult to label through the attachment of (13)C isotopes. In addition, the user-friendly application includes an absolute-quantitative analysis tool. Good agreement was obtained between known concentrations of 20-metabolite mixtures versus the calibration curve-based quantification results obtained from 2D-Jres spectra. We have examined the web tool availability using nine series of biological extracts, obtained from animal gut and waste treatment microbiota, fish, and plant tissues. This web-based tool is publicly available via http://emar.riken.jp/spincpl.

Synthesis of biantennary complex-type nonasaccharyl asn building blocks for solid-phase glycopeptide synthesis.

The biantennary complex-type N-glycans bearing LacNAc and LacdiNAc as the nonreducing end motif were synthesized in a protected form suitable to use in the Fmoc solid-phase peptide synthesis studies. Two approaches for the nonasaccharide synthesis were examined by taking advantage of the highly ß-selective glycosylation with GlcNTCA (N-phenyl)trifluoroacetimidate. An earlier approach, which involved the reaction of the trisaccharide donor (Gal-GlcNTCA-Man) and trisaccharide acceptor (Man-GlcNPhth(2)-N(3)), produced a mixture of nonasaccharide isomers. On the other hand, mannosylation of the trisaccharide acceptor (Man-GlcNPhth(2)-N(3)) stereoselectively afforded the known pentasaccharide (Man(3)-GlcNPhth(2)-N(3)), which was reacted with the disaccharyl glycosyl donor (Gal-GlcNTCA or GalNTCA-GlcNTCA) to produce the desired nonasaccharide as a single stereoisomer. Selective dephthaloylation followed by N-acetylation furnished the GlcNAc(2) functionality. The resulting nonasaccharyl azides were condensed with Fmoc-Asp(OPfp)-OBu(t) or Fmoc-Asp(OPfp)-OPac in the presence of Ph(CH(3))(2)P and HOOBt. Finally, the Zn reduction and cleavage of the tert-butyl ester or Zn reduction alone produced the targeted nonasaccharyl Asn building blocks.

Pathogenesis of herpetic stromal keratitis in CCR5- and/or CXCR3-deficient mice.

PURPOSE: Herpetic stromal keratitis (HSK) is an immunopathological reaction to herpes simplex virus type 1 (HSV-1) corneal infection. It has been reported that CD4+ cells play the most important role in the pathogenesis of this disease. In this study, we have focused on two chemokine receptors, CCR5 and CXCR3, which are expressed on CD4+ Th1 cells in mice HSK model. METHODS: CCR5-deficient (CCR5KO), CXCR3-deficient (CXCR3KO), CCR5/CXCR3 double-deficient (DKO), and wild type (WT) mice (C57/BL6 background) were infected intracorneally with HSV-1 (CHR3 strain). The corneas were examined biomicroscopically, and cryosections of the corneas were examined histologically and immunohistochemically. Real-time RT-PCR and RNase protection assay (RPA) were performed, and the virus titers were measured in excised eyes and trigeminal ganglia (TG). RESULTS: The HSK clinical severity in DKO mice was significantly lower than that in WT mice, and this was reversed by transfer of cells from the spleen of WT mice to DKO mice. Histologically, the numbers of T cells (CD4+ and CD8+ cells) and neutrophils infiltrating the cornea were significantly fewer in CCR5KO, CXCR3KO, and DKO mice. Transcript levels of immune-related cell surface marker in the eye by RPA were reduced in DKO mice. The expression of I-TAC was significantly increased in the cornea of CCR5KO mice, and MIP-1alpha and MIP-1beta were significantly lower in CXCR3KO mice than in WT mice by RT-PCR. There were no significant differences of virus titers in the eye and TG among any groups of mice except the increase in the TG of DKO mice on day 5 PI. CONCLUSIONS: The suppression of chemotaxis and activation of CD4+ Th1 cells by the lacking of CXCR3 and CCR5 causes a decrease of other infiltrating cells, resulting in a lower severity of HSK. These results suggest that targeting chemokine receptors is a promising way to treat HSK.

Clinical application of real-time polymerase chain reaction for diagnosis of herpetic diseases of the anterior segment of the eye.

PURPOSE: To assess the value of quantification of herpes simplex virus (HSV) DNA for the differential diagnosis of herpetic diseases of the anterior segment of the eye. METHODS: One hundred forty-four samples from 90 patients with ocular inflammatory diseases were examined for HSV DNA by real-time polymerase chain reaction (PCR) with primers set for the consensus sequence of HSV-1/2 DNA polymerase. The samples included corneal epithelial scrapings, tear fluid (200microl of eye wash), and aqueous humor. RESULTS: In cases of typical herpetic epithelial keratitis, a large number of copies of HSV DNA were detected (mean, 1.0 x 10(7) copies in epithelial scrapings and 3.5 x 10(5) copies in tear fluid). In atypical epithelial keratitis cases, a smaller number of HSV DNA copies were detected. In stromal keratitis cases, the number of copies of HSV DNA in the tear fluid (mean: 4.7 x 10(2) copies) was significantly smaller than in cases of epithelial keratitis. In the aqueous humor, the number of copies was small in endotheliitis cases (mean, 2.9 x 10(2) copies/microl), but the range was great, from (1.2-4.8) x 10(5)/microl in herpetic iridocyclitis. Seventeen percent of cases in which HSV was not suspected to be involved showed a small number of copies of HSV DNA, indicating the unexpected involvement of HSV in these cases. CONCLUSIONS: Real-time PCR is an informative method of diagnosing herpetic eye diseases and evaluating the possible involvement of HSV in other inflammatory ocular diseases.

Transforming growth factor-beta1 induces LMO7 while enhancing the invasiveness of rat ascites hepatoma cells.

We have previously shown that transforming growth factor-beta1 (TGF-beta1) markedly stimulates the invasive capacity of rat ascites hepatoma AH130 W1 cells in vitro and in vivo. A differential hybridization procedure was used to isolate genes that were specifically up-regulated in TGF-beta1 treated W1 cells. Among ten independent cDNA clones, we focused on LMO7 and a variant isoform, LMO7S, that was generated by alternative splicing. LMO7 had PDZ and LIM domains, while LMO7S had only PDZ domain. TGF-beta1 up-regulated expression levels of LMO7 and LMO7S. LMO7 expression was up-regulated in the highly metastatic clone MM1.

Immunohistochemical study of apparently intact coronary artery in a child after Kawasaki disease.

BACKGROUND: Coronary arterial lesions (CAL) due to Kawasaki disease (KD) often show progressive intimal hyperplasia even many years after the disease. However, most patients have no CAL after the acute phase, and it is an important issue whether or not coronary arteries without CAL have significant intimal hyperplasia, and whether or not there is the potential for this to progress to stenosis and/or atherosclerosis. METHODS: The authors examined formalin-fixed specimens of the coronary arteries immunohistochemically, using antibodies against vascular growth factors (GFs), the receptors of transforming growth factor-beta (TbetaRs) and inducible nitric oxid synthesis (iNOS) in a KD patient without CAL, and also in four control patients: two with CAL due to KD and two without a history of KD. RESULTS: Vascular endothelial GFs, Platelet-derived growth factor-A (PDGF-A) and TbetaRs were expressed in the vascular smooth muscle cells of all patients. PDGF-A, transforming Gfbeta1 and iNOS were expressed in the intimal smooth muscle cells of the KD but not the normal coronary artery without a history of KD. The number of TbetaR-II-positive cells were fewer than TbetaR-I-positive cells in the intima of CAL due to KD, but the number was of both almost same in the intima of coronary artery without CAL after KD and in the normal coronary. CONCLUSION: The intact coronary artery 13 months after KD still showed the influence of the inflammation of KD. Although the authors speculate that the intimal proliferation will not continue beyond the acute phase, those patients may have a risk factor for atherosclerosis.

Swimming exercise in infancy has beneficial effect on the hearts in cardiomyopathic Syrian hamsters.

The phenotypic expression of cardiomyopathy is greatly influenced by extrinsic factors other than intrinsic genetic defects, such as environmental stress. Exercise is assumed to be an important extrinsic factor, since sudden death is sometimes seen during exercise in young patients with hypertrophic cardiomyopathy (HCM). However, the long-term effects of mild exercise on phenotypic expression in cardiomyopathy remain unclear. To evaluate the effects of exercise performed during infancy or adolescence in cardiomyopathic patients, cardiomyopathic Syrian hamsters (BIO14.6) were subjected to swimming. BIO14.6 and age-matched congenic normal hamsters (CN) as controls were divided into three groups: sedentary (Sed), and trained during infancy (Inf) and during adolescence (Ado). Histological and biochemical analysis of 41-week-old hamsters revealed that (1) the relative level of beta-myosin heavy chain mRNA was significantly lower in the Inf group than in the Sed and Ado groups of BIO14.6. The level in the Inf group of BIO14.6 was compatible with that in the age-matched Sed group of the CN strain; (2) in BIO14.6, degenerative mitochondrial change in the cardiomyocytes was not seen in the Inf group while it was common in the Sed and Ado groups; (3) calcineurin phosphatase activity in the swimming group in 10-week-old CN was significantly higher than that of the age-matched sedentary group, and was as much as that of the swimming and sedentary groups in 10- and 41-week-old BIO14.6.

Oolong tea increases energy metabolism in Japanese females.

Oolong tea is a traditional Chinese tea that has long been believed to be beneficial to health such as decreasing body fat. We were interested in this assertion and tried to evaluate the effect of oolong tea on energy expenditure (EE) in comparison with green tea. The subjects were eleven healthy Japanese females (age 20+/-1 y; body mass index (BMI) 21.2+/-2.5 kg/m2) who each consumed of three treatments in a crossover design: 1) water, 2) oolong tea, 3) green tea. Resting energy expenditure (REE) and EE after the consumption of the test beverage for 120 min were measured using an indirect calorimeter. The cumulative increases of EE for 120 min were significantly increased 10% and 4% after the consumption of oolong tea and green tea, respectively. EE at 60 and 90 min were significantly higher after the consumption of oolong tea than that of water (P<0.05). In comparison with green tea, oolong tea contained approximately half the caffeine and epigallocatechin galate, while polymerized polyphenols were double. These results suggest that oolong tea increases EE by its polymerized polyphenols.

Expression of S100A6 and S100A4 in matched samples of human colorectal mucosa, primary colorectal adenocarcinomas and liver metastases.

OBJECTIVE: S100A6 and S100A4, two of S100 protein family, have been suggested to be associated with cancer tumorigenesis and metastasis. The aim of this study was to evaluate the expression levels of S100A6 and S100A4 in matched samples of primary human colorectal adenocarcinomas (T), adjacent normal colorectal mucosa (N) and liver metastases (M). This gave us the advantage of directly comparing levels of S100A6 and S100A4 expression within the same genetic background. METHODS: In matched samples of N, T and M from 10 colorectal adenocarcinoma patients, expressions of S100A6 and S100A4 were studied by Western blot and immunohistochemical analyses using specific antibodies against each protein. RESULTS: The expression levels of S100A6 were significantly higher in T than in N (p < 0.05), while those of S100A4 showed no difference between T and N. There were no significant differences in the expression levels of S100A6 or S100A4 between M and T. Similar results were obtained by immunohistochemical analysis. Moreover, S100A6 was stained more intensely in invading fronts than in central portions of both T and M. CONCLUSIONS: The observed differential expression of S100A6 and S100A4 suggests that S100A6, rather than S100A4, is associated with human colorectal adenocarcinoma tumorigenesis and invasion/metastasis.