In recent years, the research and development of genome editing technology have been progressing rapidly, and the commercial use of genome-edited soybean started in the United States in 2019. A preceding study's results found that there is public concern with regard to the safety of high-tech foods, such as genetically modified foods and genome-edited foods. Twitter, one of the most popular social networks, allows users to post their opinions instantaneously, making it an extremely useful tool to collect what people are actually saying online in a timely manner.
View Article and Find Full Text PDFFermented milk products are rising in popularity throughout the world as a result of their health benefits, including improving digestion, normalizing the function of the immune system, and aiding in weight management. This study applies an in situ quantitative nuclear magnetic resonance method to monitor chemical changes in three kinds of fermented milk products, Bulgarian yogurt, Caspian Sea yogurt, and kefir, during fermentation. As a result, the concentration changes in nine organic compounds, α/β-lactose, α/β-galactose, lactic acid, citrate, ethanol, lecithin, and creatine, were monitored in real time.
View Article and Find Full Text PDFFenugreek is a dietary supplement for anti-aging and human health. (2S,3R,4S)-4-hydroxyisoleucine (4-HIL), which is extracted from fenugreek seeds, is expected to be a promising orally active drug for diabetes and diabetic nephropathy because of its insulinotropic effect. Although several chemical synthesis methods of 4-HIL have been proposed, these methods require multistep reactions to control the stereochemistry of 4-HIL.
View Article and Find Full Text PDFThe proportion of the elderly population in most countries worldwide is increasing dramatically. Therefore, social interest in the fields of health, longevity, and anti-aging has been increasing as well. However, the basic research results obtained from a reductionist approach in biology and a bioinformatic approach in genome science have limited usefulness for generating insights on future health, longevity, and anti-aging-related research on a case by case basis.
View Article and Find Full Text PDFMore than 800 G protein-coupled receptor (GPCR) genes have been discovered in the human genome. Towards the next step in GPCR research, we performed a knowledge-driven analysis of orphan class-A GPCRs that may serve as novel targets in drug discovery. We examined the relationship between 61 orphan class-A GPCR genes and diseases using the Online Mendelian Inheritance in Man (OMIM) database and the DDSS tool.
View Article and Find Full Text PDFJ Struct Funct Genomics
December 2016
Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments.
View Article and Find Full Text PDFGenome-wide analysis for determining RNA turnover is an advanced method in RNA biology that examines the specific half-life of nuclear noncoding RNA (ncRNA). In particular, a pulse-labeling method using uridine analogs enables the determination of RNA stability under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromo-uridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing.
View Article and Find Full Text PDFBackground: Detection of significant differentially expressed genes (DEGs) from DNA microarray datasets is a common routine task conducted in biomedical research. For the detection of DEGs, numerous methods are proposed. By such conventional methods, generally, DEGs are detected from one dataset consisting of group of control and treatment.
View Article and Find Full Text PDFBiochem Biophys Res Commun
November 2010
A novel member of the human ppGalNAc-T family, ppGalNAc-T20, was identified and characterized. Amino acid alignment revealed a high sequence identity between ppGalNAc-T20 and -T10. In the GalNAc transfer assay towards mucin-derived peptide substrates, the recombinant ppGalNAc-T20 demonstrated to be a typical glycopeptide GalNAc-transferase that exhibits activity towards mono-GalNAc-glycosylated peptide EA2 derived from rat submandibular gland mucin but no activity towards non-modified EA2.
View Article and Find Full Text PDFDNA Data Bank of Japan (DDBJ) provides Web-based systems for biological analysis, called Web APIs for biology (WABI). So far, we have developed over 20 SOAP services and several workflows that consist of a series of method invocations. In this article, we present newly developed services of WABI, that is, REST-based Web services, additional workflows and a workflow navigation system.
View Article and Find Full Text PDFA sequence highly homologous to beta1,4-N-acetylgalactosaminyltransferase III (beta4GalNAc-T3) was found in a database of human expressed sequence tags. The full-length open reading frame of the gene, beta4GalNAc-T4 (GenBank accession number AB089939), was cloned using the 5' rapid amplification of cDNA ends method. It encodes a typical type II transmembrane protein of 1039 amino acids having 42.
View Article and Find Full Text PDFWe found, using a BLAST search, a novel human gene (GenBank trade mark accession number BC029564) that possesses beta3-glycosyltransferase motifs. The full-length open reading frame consists of 500 amino acids and encodes a typical type II membrane protein. This enzyme has a domain containing beta1,3-glycosyltransferase motifs, which are widely conserved in the beta1,3-galactosyltransferase and beta1,3-N-acetylglucosaminyltransferase families.
View Article and Find Full Text PDFBiochem Biophys Res Commun
October 2003
In order to investigate the relationship between glycosyltransferase families and the motif for them, we classified 47 glycosyltransferase families in the CAZy database into four superfamilies, GTS-A, -B, -C, and -D, using a profile Hidden Markov Model method. On the basis of the classification and the similarity between GTS-A and nucleotidylyltransferase family catalyzing the synthesis of nucleotide-sugar, we proposed that ancient oligosaccharide might have been synthesized by the origin of GTS-B whereas the origin of GTS-A might be the gene encoding for synthesis of nucleotide-sugar as the donor and have evolved to glycosyltransferases to catalyze the synthesis of divergent carbohydrates. We also suggested that the divergent evolution of each superfamily in the corresponding subcellular component has increased the complexities of eukaryotic carbohydrate structure.
View Article and Find Full Text PDFRecently, it has become evident that chondroitin sulfate (CS) glycosyltransferases, which transfer glucuronic acid and/or N-acetylgalactosamine residues from each UDP-sugar to the nonreducing terminus of the CS chain, form a gene family. We report here a novel human gene (GenBank trade mark accession number AB086062) that possesses a sequence homologous with the human chondroitin sulfate synthase-1 (CSS1) gene, formerly known as chondroitin synthase. The full-length open reading frame consists of 882 amino acids and encodes a typical type II membrane protein.
View Article and Find Full Text PDFChondroitin sulfate is found in a variety of tissues as proteoglycans and consists of repeating disaccharide units of N-acetylgalactosamine and glucuronic acid residues with sulfate residues at various places. We found a novel human gene (GenBank accession number AB086063) that possesses a sequence homologous with the human chondroitin sulfate glucuronyltransferase gene which we recently cloned and characterized. The full-length open reading frame encodes a typical type II membrane protein comprising 775 amino acids.
View Article and Find Full Text PDFHeparan sulfate d-glucosaminyl 3-O-sulfotransferases (3-OSTs) catalyze the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to position 3 of the glucosamine residue of heparan sulfate and heparin. A sixth member of the human 3-OST family, named 3-OST-5, was recently reported (Xia, G., Chen, J.
View Article and Find Full Text PDFThe hinge region of human immunoglobulin A1 (*IgA1) possesses multiple O-glycans, of which synthesis is initiated by the addition of GalNAc to serine or threonine through the activity of UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferases (pp-GalNAc-Ts). We found that six pp-GalNAc-Ts, pp-GalNAc-T1, -T2, -T3, -T4, -T6, and -T9, were expressed in B cells, IgA-bearing B cells, and NCI-H929 IgA myeloma cells. pp-GalNAc-T activities of these six enzymes for a synthetic IgA hinge peptide, which has nine possible O-glycosylation sites, were examined using a reversed phase-high performance liquid chromatography, a matrix-assisted laser desorption ionization time of flight mass spectrometry, and peptide sequencing analysis.
View Article and Find Full Text PDFWe found a novel glycosyltransferase gene having a hypothetical beta 1,4-galactosyltransferase motif (GenBank accession number ) by a BLAST search and cloned its full-length open reading frame using the 5'-rapid amplification of cDNA ends method. The truncated form was expressed in insect cells as a soluble enzyme. It transferred N-acetylgalactosamine, not galactose, to para-nitrophenyl-beta-glucuronic acid.
View Article and Find Full Text PDF