Hepatoprotection by L-cysteine-glutathione mixed disulfide,a sulfhydryl-modified prodrug of glutathione

L-Cysteine-glutathione disulfide, a ubiquitous substance present in mammalian cells, was shown to be highly effective in protecting mice against acetaminophen-induced hepatotoxicity. Since the corresponding D-cysteine-glutathione disulfide was totally ineffective in this regard, an enzymatic mechanism that provides glutathione directly to cells is postulated.     

Nutrient intake of highly competitive male and female collegiate karate players

Nutrient intake of 29 male (M Group) and 16 female (F Group) highly competitive collegiate karate players were compared. The results were also compared with the daily energy expenditure (DEE), Japanese recommended dietary allowances (RDAs) or adequate dietary intakes (ADIs). Dietary information was collected using a 3-weekday diet record. Although the M Group showed significantly higher mean %RDAs or %ADIs in iron, vitamin B1, phosphorus, magnesium, and sodium than the F Group, many of the mean %RDAs or %ADIs were below RDAs or ADIs in both groups. The subjects who skipped meals tended to show lower mean %DEE, Japanese %RDAs or %ADIs in minerals and vitamins than the subjects who did not skip in both M and F Groups. The consumption of green and other vegetables and milk and dairy products in both M and F Groups were low. It is concluded that the male and female highly competitive karate players studied in the present study may be at risk of sub-optimal nutrient intake, which increases the potential for nutrient deficiency. The subjects were advised not to skip meals, and to consume a balanced high-carbohydrate, moderate-protein, low-fat diet with increasing green and other vegetables and milk and dairy products to increase mineral, vitamin and dietary fiber intakes.     

Genetic Basis of Nutritional Requirements in Lactobacillus casei

In a study of the genetic basis of multiple nutritional requirements in Lactobacillus casei, systematic attempts were made to isolate mutants that can grow in the absence of a specific nutrient required by the parental organism. Such mutants have successfully been isolated with respect to seven of twelve amino acids (aspartic acid, leucine, isoleucine, lysine, methionine, serine, and threonine) and three of four vitamins (pantothenic acid, nicotinic acid, and pyridoxal) tested, after extensive screenings employing various mutagens. Mutants that can grow without tryptophan were not isolated, but those that can grow on anthranilate or indole as well as on tryptophan were obtained at a frequency expected for single-step mutations. Activity of tryptophan synthetase was demonstrated in extracts of these anthranilate-utilizing mutants, but not in the parental strain. These results suggest that the multiple nutritional requirements of L. casei are often, if not always, due to one or a few small lesions such as base substitution mutations rather than large deletions affecting the genes involved in each biosynthetic pathway. The data would also imply that many of the biosynthetic pathways that are not fully functional in L. casei were active at one time and became nonfunctional during evolution of the present species.     

Differential gene alteration among hepatoma cell lines demonstrated by cDNA microarray-based comparative genomic hybridization

We assayed chromosomal abnormalities in hepatoma cell lines using the microarray-based comparative genomic hybridization (array-CGH) method and investigated the relationship between genomic copy number alterations and expression profiles in these hepatoma cell lines. We modified a cDNA array-CGH assay to compare genomic DNAs from seven hepatoma cell lines, as well as DNA from two non-hepatoma cell lines and from normal cells. The mRNA expression of each sample was assayed in parallel by cDNA microarray. We identified small amplified or deleted chromosomal regions, as well as alterations in DNA copy number not previously described. We predominantly found alterations of apoptosis-related genes in Hep3B and HepG2, cell adhesion and receptor molecules in HLE, and cytokine-related genes in PLC/PRF/5. About 40% of the genes showing amplification or loss showed altered levels of mRNA (p < 0.05). Hierarchical clustering analysis showed that the expression of these genes allows differentiation between alpha-fetoprotein (AFP)-producing and AFP-negative cell lines. cDNA array-CGH is a sensitive method that can be used to detect alterations in genomic copy number in tumor cells. Differences in DNA copy alterations between AFP-producing and AFP-negative cells may lead to differential gene expression and may be related to the phenotype of these cells.     

Analyses on hydrophobicity and attractiveness of all‐atom distance‐dependent potentials

Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all‐atom distance‐dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT‐TS score, but decreased the Z‐score of the native structure. The attractiveness of potential improved both the correlation and Z‐score for template‐based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states.     

High-sensitivity analysis of sialyl-oligosaccharide glycosylation sites in glycoproteins by miniaturized tryptic digestion and microcolumn liquid chromatography.

A highly sensitive analytical procedure was developed to assess the site of glycosylation in a model glycoprotein, bovine fetuin. First, sample cleavage with immobilized trypsin and the peptide map development are accomplished by microcolumn liquid chromatography. Second, the sialic acids content is measured fluorometrically using their precolumn conversion to quinoxaline derivatives. A unique preconcentration system was developed to secure sensitivity of the second measurement.     

Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

Background

Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.

Results

Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.

Conclusions

Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users.