LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 3 of total 3

Search options

  1. Article ; Online: ScreenGarden: a shinyR application for fast and easy analysis of plate-based high-throughput screens.

    Klemm, Cinzia / Howell, Rowan S M / Thorpe, Peter H

    BMC bioinformatics

    2022  Volume 23, Issue 1, Page(s) 60

    Abstract: Background: Colony growth on solid media is a simple and effective measure for high-throughput genomic experiments such as yeast two-hybrid, synthetic dosage lethality and Synthetic Physical Interaction screens. The development of robotic pinning tools ... ...

    Abstract Background: Colony growth on solid media is a simple and effective measure for high-throughput genomic experiments such as yeast two-hybrid, synthetic dosage lethality and Synthetic Physical Interaction screens. The development of robotic pinning tools has facilitated the experimental design of these assays, and different imaging software can be used to automatically measure colony sizes on plates. However, comparison to control plates and statistical data analysis is often laborious and pinning issues or plate specific growth effects can lead to the detection of false-positive growth defects.
    Results: We have developed ScreenGarden, a shinyR application, to enable easy, quick and robust data analysis of plate-based high throughput assays. The code allows comparisons of different formats of data and different sized arrays of colonies. A comparison of ScreenGarden with previous analysis tools shows that it performs, at least, equivalently. The software can be run either via a website or offline via the RStudio program; the code is available and can be modified by expert uses to customise the analysis.
    Conclusions: ScreenGarden provides a simple, fast and effective tool to analyse colony growth data from genomic experiments.
    MeSH term(s) Culture Media ; Genomics ; High-Throughput Screening Assays ; Saccharomyces cerevisiae ; Software
    Chemical Substances Culture Media
    Language English
    Publishing date 2022-02-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-022-04586-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: Synthetic Physical Interactions with the Yeast Centrosome.

    Howell, Rowan S M / Csikász-Nagy, Attila / Thorpe, Peter H

    G3 (Bethesda, Md.)

    2019  Volume 9, Issue 7, Page(s) 2183–2194

    Abstract: The yeast centrosome or Spindle Pole Body (SPB) is an organelle situated in the nuclear membrane, where it nucleates spindle microtubules and acts as a signaling hub. Various studies have explored the effects of forcing individual proteins to interact ... ...

    Abstract The yeast centrosome or Spindle Pole Body (SPB) is an organelle situated in the nuclear membrane, where it nucleates spindle microtubules and acts as a signaling hub. Various studies have explored the effects of forcing individual proteins to interact with the yeast SPB, however no systematic study has been performed. We used synthetic physical interactions to detect proteins that inhibit growth when forced to associate with the SPB. We found the SPB to be especially sensitive to relocalization, necessitating a novel data analysis approach. This novel analysis of SPI screening data shows that regions of the cell are locally more sensitive to forced relocalization than previously thought. Furthermore, we found a set of associations that result in elevated SPB number and, in some cases, multi-polar spindles. Since hyper-proliferation of centrosomes is a hallmark of cancer cells, these associations point the way for the use of yeast models in the study of spindle formation and chromosome segregation in cancer.
    MeSH term(s) Biomarkers ; Centrosome/metabolism ; Computational Biology/methods ; Fungal Proteins ; Gene Ontology ; Models, Biological ; Protein Interaction Mapping ; Spindle Apparatus/metabolism ; Spindle Pole Bodies/metabolism ; Yeasts/physiology
    Chemical Substances Biomarkers ; Fungal Proteins
    Language English
    Publishing date 2019-07-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.119.400117
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Unifying the mechanism of mitotic exit control in a spatiotemporal logical model.

    Howell, Rowan S M / Klemm, Cinzia / Thorpe, Peter H / Csikász-Nagy, Attila

    PLoS biology

    2020  Volume 18, Issue 11, Page(s) e3000917

    Abstract: The transition from mitosis into the first gap phase of the cell cycle in budding yeast is controlled by the Mitotic Exit Network (MEN). The network interprets spatiotemporal cues about the progression of mitosis and ensures that release of Cdc14 ... ...

    Abstract The transition from mitosis into the first gap phase of the cell cycle in budding yeast is controlled by the Mitotic Exit Network (MEN). The network interprets spatiotemporal cues about the progression of mitosis and ensures that release of Cdc14 phosphatase occurs only after completion of key mitotic events. The MEN has been studied intensively; however, a unified understanding of how localisation and protein activity function together as a system is lacking. In this paper, we present a compartmental, logical model of the MEN that is capable of representing spatial aspects of regulation in parallel to control of enzymatic activity. We show that our model is capable of correctly predicting the phenotype of the majority of mutants we tested, including mutants that cause proteins to mislocalise. We use a continuous time implementation of the model to demonstrate that Cdc14 Early Anaphase Release (FEAR) ensures robust timing of anaphase, and we verify our findings in living cells. Furthermore, we show that our model can represent measured cell-cell variation in Spindle Position Checkpoint (SPoC) mutants. This work suggests a general approach to incorporate spatial effects into logical models. We anticipate that the model itself will be an important resource to experimental researchers, providing a rigorous platform to test hypotheses about regulation of mitotic exit.
    MeSH term(s) Cell Cycle/genetics ; Cell Cycle/physiology ; Cell Cycle Proteins/metabolism ; Cell Cycle Proteins/physiology ; Cell Nucleus Division/physiology ; M Phase Cell Cycle Checkpoints/genetics ; M Phase Cell Cycle Checkpoints/physiology ; Mitosis/physiology ; Phosphorylation ; Protein Tyrosine Phosphatases/genetics ; Protein Tyrosine Phosphatases/metabolism ; Protein Tyrosine Phosphatases/physiology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; Saccharomycetales/genetics ; Saccharomycetales/metabolism ; Spindle Apparatus/physiology
    Chemical Substances CDC14 protein, S cerevisiae ; Cell Cycle Proteins ; Saccharomyces cerevisiae Proteins ; Protein Tyrosine Phosphatases (EC 3.1.3.48)
    Language English
    Publishing date 2020-11-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3000917
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6193: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top