Biomedical subjects

Yohei Yamada

Publications and source records attributed to Yohei Yamada.

4 recordsLinked to original sources

PubMed2006

Semi-quantitative expression and knockdown of a target gene in single-cell mouse embryonic stem cells by high performance microinjection.

Interactions of multiple genes and associated factors are involved in the differentiation and de-differentiation of embryonic stem (ES) cells. Quantitative analysis of these genes and factors is essential for the elucidation of their mechanism. To meet this requirement, we have investigated various experimental conditions for high performance microinjection into mouse ES cells. A speedy and rhythmic operation was found to be important and was accomplished robotically by using a single-cell manipulation technique and XY-address registrable culture dishes. Among many experimental parameters, the tip size of an injection capillary, the pressure condition, and the DNA concentration in the injection capillary were of critical significance. Their optimum values were 0.5-0.8 microm, 0.7 kgf/cm(2) for 30 ms, and 1-100 ng/microl, respectively. Under these conditions, semi-quantitative control of the EGFP gene expression in mouse ES cells and its knockdown was successfully demonstrated.

Animals↗

PubMed2006

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.

BACKGROUND: Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual affairs, and therefore constitute a major bottleneck in the evolution of computational cell biology. RESULTS: We developed the Genome-based Modeling (GEM) System for the purpose of automatically prototyping simulation models of cell-wide metabolic pathways from genome sequences and other public biological information. Models generated by the GEM System include an entire Escherichia coli metabolism model comprising 968 reactions of 1195 metabolites, achieving 100% coverage when compared with the KEGG database, 92.38% with the EcoCyc database, and 95.06% with iJR904 genome-scale model. CONCLUSION: The GEM System prototypes qualitative models to reduce the labor-intensive tasks required for systems biology research. Models of over 90 bacterial genomes are available at our web site.

Chromosome Mapping↗

PubMed2006

Successful liver transplantation across the ABO incompatibility barrier in 6 cases of biliary atresia.

BACKGROUND: The problem of ABO-incompatible liver transplantation still remains unsolved in older children. In this article, we report on our experience of 6 successful ABO-incompatible liver transplantations in patients with biliary atresia. MATERIAL AND METHODS: Six patients (ABO incompatibility type A-->O:1 case, B-->O:2 cases, A-->B:3 cases) were enrolled in this study; 3 patients were aged approximately 1 year and the other 3 ranged in age from 9 to 24 years at the time of transplantation. Each patient received perioperative plasma exchange, until the anti-donor blood-type antibody titers became less than 1:16, and also systemic multidrug immunosuppressive therapy (cyclophosphamide, prednisolone, and tacrolimus). We applied the protocol of intraportal infusion therapy (local administration of prostaglandin E(1), steroid, and gabexate mesilate via a portal vein catheter), splenectomy, and rituximab administration for the older group. RESULTS: Both the patient and graft survival rates remain at 100%, with the follow-up period of the patients ranging from 12 and 123 months. Acute cellular rejection occurred in 2 cases, and both were steroid sensitive. There was no incidence of humoral rejection. Although all cases developed viral infection, all recovered uneventfully with the administration of antiviral agents. CONCLUSION: ABO-incompatible liver transplantation can be performed with a low risk of humoral rejection or late biliary complications using this combined antirejection strategy, even in older children.

ABO Blood-Group System↗

PubMed2005

KEGG-based pathway visualization tool for complex omics data.

Pathway-level visualization of omics data provides an essential means for systems biology, to capture the systematic properties of the inner activities of cells. Here we describe a web-based resource consisting of a web-application for the visualization of complex omics data onto KEGG pathways to overview all entities in the context of cellular pathways, and databases created with the software to visualize a series of microarray data. The web-application accepts transcriptome, proteome, metabolome, or the combination of these data as input, and because of this scalability it is advantageous for the visualization of cell simulation results. The web server can be accessed at http://www.g-language.org/data/marray/.

Computer Graphics↗