Biomedical subjects

Atsuko Yamaguchi

Publications and source records attributed to Atsuko Yamaguchi.

4 recordsLinked to original sources

PubMed2005

Modification of skin composition by conjugated linoleic acid alone or with combination of other fatty acids in mice.

The effects of conjugated linoleic acid (CLA), gamma-linolenic acid (GLA), linoleic acid (LA), and their combinations, on skin composition in mice were investigated. Mice (8 weeks old) were orally administered with either LA, GLA, CLA, LA + GLA, LA + CLA, or CLA + GLA for 4 weeks. Then, the skin was analysed for triacylglycerol content, fatty acid composition and collagen content. Additionally, thicknesses of the dermis layer and subcutaneous tissue layer, and the size and number of adipocytes were measured histologically. The skin fatty acid composition was modified depending upon the fatty acid composition of supplemented oils. In each oil-alone group, skin triacylglycerol content was the highest in LA, followed by GLA and CLA treatments. Combinations with CLA had a similar triacylglycerol content compared with the CLA-alone group. No significant changes in collagen content were observed among any treatments. The effects on subcutaneous thickness were similar to the results obtained in the triacylglycerol contents, where groups supplemented with CLA alone or other fatty acids had significantly thinner subcutaneous tissue compared with the LA-alone group. However, no significant difference was detected in the thickness of the dermis layers. The number of adipocytes was highest in the LA + GLA group and tended to be reduced by CLA with or without the other fatty acids. These results suggest that CLA alone or in combination with other fatty acids strongly modifies skin composition in mice.

Administration, Oral↗

PubMed2004

Application of a new probabilistic model for recognizing complex patterns in glycans.

MOTIVATION: The study of carbohydrate sugar chains, or glycans, has been one of slow progress mainly due to the difficulty in establishing standard methods for analyzing their structures and biosynthesis. Glycans are generally tree structures that are more complex than linear DNA or protein sequences, and evidence shows that patterns in glycans may be present that spread across siblings and into further regions that are not limited by the edges in the actual tree structure itself. Current models were not able to capture such patterns. RESULTS: We have applied a new probabilistic model, called probabilistic sibling-dependent tree Markov model (PSTMM), which is able to inherently capture such complex patterns of glycans. Not only is the ability to capture such patterns important in itself, but this also implies that PSTMM is capable of performing multiple tree structure alignments efficiently. We prove through experimentation on actual glycan data that this new model is extremely useful for gaining insight into the hidden, complex patterns of glycans, which are so crucial for the development and functioning of higher level organisms. Furthermore, we also show that this model can be additionally utilized as an innovative approach to multiple tree alignment, which has not been applied to glycan chains before. This extension on the usage of PSTMM may be a major step forward for not only the structural analysis of glycans, but it may consequently prove useful for discovering clues into their function.

Algorithms↗

PubMed2004

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.

KCaM (KEGG Carbohydrate Matcher) is a tool for the analysis of carbohydrate sugar chains, or glycans. It consists of a web-based graphical user interface that allows users to enter glycans easily with the mouse. The glycan structure is then transformed into our KCF (KEGG Chemical Function) file format and sent to our program which implements an efficient tree-structure alignment algorithm, similar to sequence alignment algorithms but for branched tree structures. Users can also retrieve glycan tree structures in KCF format from their local computers for visualization over the web. The tree-matching algorithm provides several options for performing different types of tree-matching procedures on glycans. These options consist of whether to incorporate gaps in a match, whether to take the linkage information into consideration and local versus global alignment. The results of this program are returned as a list of glycan structures in order of similarity based on these options. The actual alignment can be viewed graphically, and the annotation information can also be viewed easily since all this information is linked with KEGG's comprehensive suite of genomic data. Analogously to BLAST, users are thus able to compare glycan structures of interest with glycans from different glycan databases using a variety of tree-alignment options. KCaM is currently available at http://glycan.genome.ad.jp.

Algorithms↗

PubMed2003

Efficient tree-matching methods for accurate carbohydrate database queries.

One aspect of glycome informatics is the analysis of carbohydrate sugar chains, or glycans, whose basic structure is not a sequence, but a tree structure. Although there has been much work in the development of sequence databases and matching algorithms for sequences (for performing queries and analyzing similarity), the more complicated tree structure of glycans does not allow a direct implementation of such a database for glycans, and further, does not allow for the direct application of sequence alignment algorithms for performing searches or analyzing similarity. Therefore, we have utilized a polynomial-time dynamic programming algorithm for solving the maximum common subtree of two trees to implement an accurate and efficient tool for finding and aligning maximally matching glycan trees. The KEGG Glycan database for glycan structures released recently incorporates our tree-structure alignment algorithm with various parameters to adapt to the needs of a variety of users. Because we use similarity scores as opposed to a distance metric, our methods are more readily used to display trees of higher similarity. We present the two methods developed for this purpose and illustrate its validity.

Algorithms↗