Biomedical subjects

Ayaka Saka

Publications and source records attributed to Ayaka Saka.

5 recordsLinked to original sources

PubMed2006

Evaluation of image processing programs for accurate measurement of budding and fission yeast morphology.

To study the cellular functions of gene products, various yeast morphological mutants have been investigated. To describe yeast morphology objectively, we have developed image processing programs for budding and fission yeast. The programs, named CalMorph for budding yeast and F-CalMorph for fission yeast, directly process microscopic images and generate quantitative data about yeast cell shape, nuclear shape and location, and actin distribution. Using CalMorph, we can easily and quickly obtain various quantitative data reproducibly. To study the utility and reliability of CalMorph, we evaluated its data in three ways: (1) The programs extracted three-dimensional bud information from two-dimensional digital images with a low error rate (<1%). (2) The absolute values of the diameters of manufactured fluorescent beads calculated with CalMorph were very close to those given in the manufacturer's data sheet. (3) The programs generated reproducible data consistent with that obtained by hand. Based on these results, we determined that CalMorph could monitor yeast morphological changes accompanied by the progression of the cell cycle. We discuss the potential of the CalMorph series as a novel tool for the analysis of yeast cell morphology.

Cell Division↗

PubMed2005

High-dimensional and large-scale phenotyping of yeast mutants.

One of the most powerful techniques for attributing functions to genes in uni- and multicellular organisms is comprehensive analysis of mutant traits. In this study, systematic and quantitative analyses of mutant traits are achieved in the budding yeast Saccharomyces cerevisiae by investigating morphological phenotypes. Analysis of fluorescent microscopic images of triple-stained cells makes it possible to treat morphological variations as quantitative traits. Deletion of nearly half of the yeast genes not essential for growth affects these morphological traits. Similar morphological phenotypes are caused by deletions of functionally related genes, enabling a functional assignment of a locus to a specific cellular pathway. The high-dimensional phenotypic analysis of defined yeast mutant strains provides another step toward attributing gene function to all of the genes in the yeast genome.

Actins↗

PubMed2004

SCMD: Saccharomyces cerevisiae Morphological Database.

To study the global regulation of cell morphology, a number of groups have recently reported genome-wide screening data for yeast mutants with abnormal morphology. Despite the relatively simple ellipsoidal shape of yeast cells, in the past, cell morphology researchers have processed information on cells manually. These time-consuming, entirely subjective tasks motivated us to develop image-processing software that automatically extracts yeast cells from micrographs and processes them to measure key morphological characteristics such as cell size, roundness, bud neck position angle, nuclear DNA localization and actin localization. To date, we have retrieved 960,609 cells from 52,988 micrographs of 2531 mutants using our software, and we have published the results in the Saccharomyces cerevisiae Morphological Database (SCMD), which facilitates the analysis of abnormal cells. Our system provides quantitative data for shapes of the daughter and mother cells, localization of the nuclear DNA and morphology of the actin patches. To search for mutants with similar morphological traits, the system outputs a list of mutants ranked by similarity of average morphological parameters. The SCMD is available at http://yeast. gi.k.u-tokyo.ac.jp/.

Cell Cycle↗

PubMed2004

Development of image processing program for yeast cell morphology.

Every living organism has its own species-specific morphology. Despite the relatively simple ellipsoidal shape of budding yeast cells, the global regulation of yeast morphology remains unclear. In the past, each mutated gene from many mutants with abnormal morphology had to be classified manually. To investigate the morphological characteristics of yeast in detail, we developed a novel image-processing program that extracts quantitative data from microscope images automatically. This program extracts data on cells that are often used by yeast morphology researchers, such as cell size, roundness, bud neck position angle, and bud growth direction, and fits an ellipse to the cell outline. We evaluated the ability of the program to extract quantitative parameters. The results suggest that our image-processing program can play a central objective role in yeast morphology studies.

Computational Biology↗

PubMed2002

Dissection of upstream regulatory components of the Rho1p effector, 1,3-beta-glucan synthase, in Saccharomyces cerevisiae.

In the budding yeast Saccharomyces cerevisiae, one of the main structural components of the cell wall is 1,3-beta-glucan produced by 1,3-beta-glucan synthase (GS). Yeast GS is composed of a putative catalytic subunit encoded by FKS1 and FKS2 and a regulatory subunit encoded by RHO1. A combination of amino acid alterations in the putative catalytic domain of Fks1p was found to result in a loss of the catalytic activity. To identify upstream regulators of 1,3-beta-glucan synthesis, we isolated multicopy suppressors of the GS mutation. We demonstrate that all of the multicopy suppressors obtained (WSC1, WSC3, MTL1, ROM2, LRE1, ZDS1, and MSB1) and the constitutively active RHO1 mutations tested restore 1,3-beta-glucan synthesis in the GS mutant. A deletion of either ROM2 or WSC1 leads to a significant defect of 1,3-beta-glucan synthesis. Analyses of the degree of Mpk1p phosphorylation revealed that among the multicopy suppressors, WSC1, ROM2, LRE1, MSB1, and MTL1 act positively on the Pkc1p-MAPK pathway, another signaling pathway regulated by Rho1p, while WSC3 and ZDS1 do not. We have also found that MID2 acts positively on Pkc1p without affecting 1,3-beta-glucan synthesis. These results suggest that distinct networks regulate the two effector proteins of Rho1p, Fks1p and Pkc1p.

Calcium-Binding Proteins↗