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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

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

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Article ; Online: ScreenGarden

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

BMC Bioinformatics, Vol 23, Iss 1, Pp 1-

a shinyR application for fast and easy analysis of plate-based high-throughput screens

2022 Volume 15

Abstract: 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 ...

Abstract	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.
Keywords	Genomics ; Yeast ; Automated data analysis ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	005
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Localized immune surveillance of primary melanoma in the skin deciphered through executable modeling.

Howell, Rowan / Davies, James / Clarke, Matthew A / Appios, Anna / Mesquita, Inês / Jayal, Yashoda / Ringham-Terry, Ben / Boned Del Rio, Isabel / Fisher, Jasmin / Bennett, Clare L

Science advances

2023 Volume 9, Issue 15, Page(s) eadd1992

Abstract: While skin is a site of active immune surveillance, primary melanomas often escape detection. Here, we have developed an in silico model to determine the local cross-talk between melanomas and Langerhans cells (LCs), the primary antigen-presenting cells ... ...

Abstract	While skin is a site of active immune surveillance, primary melanomas often escape detection. Here, we have developed an in silico model to determine the local cross-talk between melanomas and Langerhans cells (LCs), the primary antigen-presenting cells at the site of melanoma development. The model predicts that melanomas fail to activate LC migration to lymph nodes until tumors reach a critical size, which is determined by a positive TNF-α feedback loop within melanomas, in line with our observations of murine tumors. In silico drug screening, supported by subsequent experimental testing, shows that treatment of primary tumors with MAPK pathway inhibitors may further prevent LC migration. In addition, our in silico model predicts treatment combinations that bypass LC dysfunction. In conclusion, our combined approach of in silico and in vivo studies suggests a molecular mechanism that explains how early melanomas develop under the radar of immune surveillance by LC.
MeSH term(s)	Mice ; Animals ; Cell Movement ; Skin/metabolism ; Langerhans Cells/metabolism ; Melanoma/metabolism
Language	English
Publishing date	2023-04-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.add1992
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The effects of genetic deletion of Macrophage migration inhibitory factor on the chronically hypoxic pulmonary circulation.

Li, Lili / Xu, Maojia / Rowan, Simon C / Howell, Katherine / Russell-Hallinan, Adam / Donnelly, Seamas C / McLoughlin, Paul / Baugh, John A

Pulmonary circulation

2020 Volume 10, Issue 4, Page(s) 2045894020941352

Abstract: While it is well established that the haemodynamic cause of hypoxic pulmonary hypertension is increased pulmonary vascular resistance, the molecular pathogenesis of the increased resistance remains incompletely understood. Macrophage migration inhibitory ...

Abstract	While it is well established that the haemodynamic cause of hypoxic pulmonary hypertension is increased pulmonary vascular resistance, the molecular pathogenesis of the increased resistance remains incompletely understood. Macrophage migration inhibitory factor is a pleiotropic cytokine with endogenous tautomerase enzymatic activity as well as both intracellular and extracellular signalling functions. In several diseases, macrophage migration inhibitory factor has pro-inflammatory roles that are dependent upon signalling through the cell surface receptors CD74, CXCR2 and CXCR4. Macrophage migration inhibitory factor expression is increased in animal models of hypoxic pulmonary hypertension and macrophage migration inhibitory factor tautomerase inhibitors, which block some of the functions of macrophage migration inhibitory factor, and have been shown to attenuate hypoxic pulmonary hypertension in mice and monocrotaline-induced pulmonary hypertension in rats. However, because of the multiple pathways through which it acts, the integrated actions of macrophage migration inhibitory factor during the development of hypoxic pulmonary hypertension were unclear. We report here that isolated lungs from adult macrophage migration inhibitory factor knockout (
Language	English
Publishing date	2020-10-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2638089-4
ISSN	2045-8940 ; 2045-8932
ISSN (online)	2045-8940
ISSN	2045-8932
DOI	10.1177/2045894020941352
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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
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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
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Article ; Online: Unifying the mechanism of mitotic exit control in a spatiotemporal logical model.

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

PLoS Biology, Vol 18, Iss 11, p e

2020 Volume 3000917

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.
Keywords	Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Executable network of SARS-CoV-2-host interaction predicts drug combination treatments.

Howell, Rowan / Clarke, Matthew A / Reuschl, Ann-Kathrin / Chen, Tianyi / Abbott-Imboden, Sean / Singer, Mervyn / Lowe, David M / Bennett, Clare L / Chain, Benjamin / Jolly, Clare / Fisher, Jasmin

NPJ digital medicine

2022 Volume 5, Issue 1, Page(s) 18

Abstract: The COVID-19 pandemic has pushed healthcare systems globally to a breaking point. The urgent need for effective and affordable COVID-19 treatments calls for repurposing combinations of approved drugs. The challenge is to identify which combinations are ... ...

Abstract	The COVID-19 pandemic has pushed healthcare systems globally to a breaking point. The urgent need for effective and affordable COVID-19 treatments calls for repurposing combinations of approved drugs. The challenge is to identify which combinations are likely to be most effective and at what stages of the disease. Here, we present the first disease-stage executable signalling network model of SARS-CoV-2-host interactions used to predict effective repurposed drug combinations for treating early- and late stage severe disease. Using our executable model, we performed in silico screening of 9870 pairs of 140 potential targets and have identified nine new drug combinations. Camostat and Apilimod were predicted to be the most promising combination in effectively supressing viral replication in the early stages of severe disease and were validated experimentally in human Caco-2 cells. Our study further demonstrates the power of executable mechanistic modelling to enable rapid pre-clinical evaluation of combination therapies tailored to disease progression. It also presents a novel resource and expandable model system that can respond to further needs in the pandemic.
Language	English
Publishing date	2022-02-14
Publishing country	England
Document type	Journal Article
ISSN	2398-6352
ISSN (online)	2398-6352
DOI	10.1038/s41746-022-00561-5
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Article: Psychological outcomes following a nurse-led preventative psychological intervention for critically ill patients trial: Statistical and health economic analysis plan.

Wulff, Jerome / Sadique, Zia / Grieve, Richard / Howell, David / Mouncey, Paul / Wade, Dorothy / Rowan, Kathryn M / Harrison, David A

Journal of the Intensive Care Society

2018 Volume 19, Issue 4, Page(s) 281–286

Abstract: The Psychological Outcomes following a nurse-led Preventative Psychological Intervention for critically ill patients trial is a cluster-randomised controlled trial of the clinical and cost-effectiveness of a complex nurse-led preventative psychological ... ...

Abstract	The Psychological Outcomes following a nurse-led Preventative Psychological Intervention for critically ill patients trial is a cluster-randomised controlled trial of the clinical and cost-effectiveness of a complex nurse-led preventative psychological intervention compared with usual care in reducing patient-reported post-traumatic stress disorder symptom severity, and other reported psychological morbidities, at six months among Level 3 (intensive care) patients in adult general critical care units in England, Wales and Northern Ireland. This paper describes the proposed statistical and health economic analyses for the Psychological Outcomes following a nurse-led Preventative Psychological Intervention for critically ill patients trial. It is important to complete and publish this plan before inspecting and locking the trial data to ensure that post hoc and data-derived decisions are avoided.
Language	English
Publishing date	2018-01-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2701626-2
ISSN	1751-1437 ; 1751-1437
ISSN (online)	1751-1437
ISSN	1751-1437
DOI	10.1177/1751143718755016
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Article: Glioblastoma Recurrence Correlates With Increased APE1 and Polarization Toward an Immuno-Suppressive Microenvironment.

Hudson, Amanda L / Parker, Nicole R / Khong, Peter / Parkinson, Jonathon F / Dwight, Trisha / Ikin, Rowan J / Zhu, Ying / Chen, Jason / Wheeler, Helen R / Howell, Viive M

Frontiers in oncology

2018 Volume 8, Page(s) 314

Abstract: While treatment with surgery, radiotherapy and/or chemotherapy may prolong life for patients with glioblastoma, recurrence is inevitable. What is still being discovered is how much these treatments and recurrence of disease affect the molecular profiles ... ...

Abstract	While treatment with surgery, radiotherapy and/or chemotherapy may prolong life for patients with glioblastoma, recurrence is inevitable. What is still being discovered is how much these treatments and recurrence of disease affect the molecular profiles of these tumors and how these tumors adapt to withstand these treatment pressures. Understanding such changes will uncover pathways used by the tumor to evade destruction and will elucidate new targets for treatment development. Nineteen matched pre-treatment and post-treatment glioblastoma tumors were subjected to gene expression profiling (Fluidigm, TaqMan assays),
Language	English
Publishing date	2018-08-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2018.00314
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