RESUMEN
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.
Asunto(s)
División Celular , Procesamiento de Imagen Asistido por Computador , Saccharomyces cerevisiae/citología , Programas Informáticos , Procesamiento de Imagen Asistido por Computador/métodos , Microscopía Fluorescente/métodosRESUMEN
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.
Asunto(s)
Genes Fúngicos , Saccharomyces cerevisiae/genética , Levaduras/genética , Actinas/química , Núcleo Celular/metabolismo , Proteínas Fúngicas/genética , Eliminación de Gen , Regulación Fúngica de la Expresión Génica , Técnicas Genéticas , Genoma Fúngico , Genómica , Microscopía Fluorescente , Modelos Genéticos , Mutación , Sistemas de Lectura Abierta , Fenotipo , Recombinación Genética , Factores de TiempoRESUMEN
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/.
Asunto(s)
Bases de Datos Factuales , Saccharomyces cerevisiae/citología , Saccharomyces cerevisiae/genética , Ciclo Celular , Procesamiento de Imagen Asistido por Computador , Internet , Mutación , Programas Informáticos , Interfaz Usuario-ComputadorRESUMEN
Four types of materials, type I collagen coat (Coat), acid-soluble type I collagen gel (Hardgel), pepsin-treated acid-soluble type I collagen gel (Softgel), and an extract of extracellular matrix of the murine Engelbreth-Holm-Swarm sarcoma (Matrigel), were used as matrices to culture rat hepatic parenchymal cells, and their morphological changes and adhesion were compared to the matrices by electron microscopic observations. Hepatic parenchymal cells cultured on Coat and Hardgel were extended and flattened, whereas cells cultured on Softgel and Matrigel assembled and formed aggregates. Such aggregates consisted of several hepatic parenchymal cells, with a recognizable bile duct-like alveolus on the inside. Morphologically, the aggregates were more spherical on Matrigel and oval shaped on Softgel. Microvilli of the cell surface were parallel to the matrix on Matrigel, but invaded into the gel on Softgel. Subsequently, investigation into how these morphological features affected the liver-specific functions, including secretion of albumin and induction of P450 by 3-methylcholanthrene, demonstrated that a high level of liver function was maintained in a long-term culture in hepatic parenchymal cells on Softgel. These results suggest that hepatic parenchymal cell interactions were stronger with Softgel than with Matrigel, and that Softgel appears to closely mimic the in vivo environment.