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      A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments

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          Abstract

          Motivation: To advance understanding of eukaryotic cell division, it is important to observe the process precisely. To this end, researchers monitor changes in dividing cells as they traverse the cell cycle, with the presence or absence of morphological or genetic markers indicating a cell's position in a particular interval of the cell cycle. A wide variety of marker data is available, including information-rich cellular imaging data. However, few formal statistical methods have been developed to use these valuable data sources in estimating how a population of cells progresses through the cell cycle. Furthermore, existing methods are designed to handle only a single binary marker of cell cycle progression at a time. Consequently, they cannot facilitate comparison of experiments involving different sets of markers.

          Results: Here, we develop a new sampling model to accommodate an arbitrary number of different binary markers that characterize the progression of a population of dividing cells along a branching process. We engineer a strain of Saccharomyces cerevisiae with fluorescently labeled markers of cell cycle progression, and apply our new model to two image datasets we collected from the strain, as well as an independent dataset of different markers. We use our model to estimate the duration of post-cytokinetic attachment between a S.cerevisiae mother and daughter cell. The Java implementation is fast and extensible, and includes a graphical user interface. Our model provides a powerful and flexible cell cycle analysis tool, suitable to any type or combination of binary markers.

          Availability: The software is available from: http://www.cs.duke.edu/~amink/software/cloccs/.

          Contact: michael.mayhew@ 123456duke.edu ; amink@ 123456cs.duke.edu

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          Most cited references25

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          Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae.

          Green fluorescent protein (GFP) has become an increasingly popular protein tag for determining protein localization and abundance. With the availability of GFP variants with altered fluorescence spectra, as well as GFP homologues from other organisms, multi-colour fluorescence with protein tags is now possible, as is measuring protein interactions using fluorescence resonance energy transfer (FRET). We have created a set of yeast tagging vectors containing codon-optimized variants of GFP, CFP (cyan), YFP (yellow), and Sapphire (a UV-excitable GFP). These codon-optimized tags are twice as detectable as unoptimized tags. We have also created a tagging vector containing the monomeric DsRed construct tdimer2, which is up to 15-fold more detectable than tags currently in use. These tags significantly improve the detection limits for live-cell fluorescence imaging in yeast, and provide sufficient distinguishable fluorophores for four-colour imaging. Copyright 2004 John Wiley & Sons, Ltd.
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            Genetic control of the cell division cycle in yeast.

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              Involvement of an Actomyosin Contractile Ring in Saccharomyces cerevisiae Cytokinesis

              In Saccharomyces cerevisiae, the mother cell and bud are connected by a narrow neck. The mechanism by which this neck is closed during cytokinesis has been unclear. Here we report on the role of a contractile actomyosin ring in this process. Myo1p (the only type II myosin in S. cerevisiae) forms a ring at the presumptive bud site shortly before bud emergence. Myo1p ring formation depends on the septins but not on F-actin, and preexisting Myo1p rings are stable when F-actin is depolymerized. The Myo1p ring remains in the mother–bud neck until the end of anaphase, when a ring of F-actin forms in association with it. The actomyosin ring then contracts to a point and disappears. In the absence of F-actin, the Myo1p ring does not contract. After ring contraction, cortical actin patches congregate at the mother–bud neck, and septum formation and cell separation rapidly ensue. Strains deleted for MYO1 are viable; they fail to form the actin ring but show apparently normal congregation of actin patches at the neck. Some myo1Δ strains divide nearly as efficiently as wild type; other myo1Δ strains divide less efficiently, but it is unclear whether the primary defect is in cytokinesis, septum formation, or cell separation. Even cells lacking F-actin can divide, although in this case division is considerably delayed. Thus, the contractile actomyosin ring is not essential for cytokinesis in S. cerevisiae. In its absence, cytokinesis can still be completed by a process (possibly localized cell–wall synthesis leading to septum formation) that appears to require septin function and to be facilitated by F-actin.
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                Author and article information

                Journal
                Bioinformatics
                bioinformatics
                bioinfo
                Bioinformatics
                Oxford University Press
                1367-4803
                1367-4811
                1 July 2011
                14 June 2011
                14 June 2011
                : 27
                : 13
                : i295-i303
                Affiliations
                1Program in Computational Biology and Bioinformatics, 2Department of Computer Science, 3Department of Biology and 4Center for Systems Biology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
                Author notes
                * To whom correspondence should be addressed.
                Article
                btr244
                10.1093/bioinformatics/btr244
                3117372
                21685084
                c508cba2-f809-454c-99ab-67152cb85029
                © The Author(s) 2011. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Pages: 9
                Categories
                Ismb/Eccb 2011 Proceedings Papers Committee July 17 to July 19, 2011, Vienna, Austria
                Original Papers
                Applied Bioinformatics

                Bioinformatics & Computational biology
                Bioinformatics & Computational biology

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