Workflow-Based Software Environment for Large-Scale Biological Experiments

Kozak, Karol; Bakos, Gábor; Hoff, Antje; Bennett, Emily; Dunican, Dara J.; Davies, Anthony M.; Kelleher, Dermot; Long, Aideen; Csúcs, Gábor

doi:10.1177/1087057110377354

Cited by 13 publications

(10 citation statements)

References 10 publications

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“…A p-value of <0.05 was considered to be statistically significant (GraphPad Prism 4, GraphPad Software, CA, USA). Konstanz Information Miner [101] data exploration platform and the screening module HiTS [102] were used to visualize the data [44-46]. The protein citrullination level induced by the nanomaterials was normalized using the percent of the positive controls.…”

Section: Methodsmentioning

confidence: 99%

Citrullination of Proteins: A Common Post-Translational Modification Pathway Induced by Different Nanoparticles In Vitro and In Vivo

et al. 2012

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Aim Rapidly expanding manufacture and use of nanomaterials emphasize the requirements for thorough assessment of health outcomes associated with novel applications. Post-translational protein modifications catalyzed by Ca2+-dependent peptidylargininedeiminases have been shown to trigger immune responses including autoantibody generation, a hallmark of immune complexes deposition in rheumatoid arthritis. Therefore, the aim of the study was to assess if nanoparticles are able to promote protein citrullination. Materials & methods Human A549 and THP-1 cells were exposed to silicon dioxide, carbon black or single-walled carbon nanotubes. C57BL/6 mice were exposed to respirable single-walled carbon nanotubes. Protein citrullination, peptidylargininedeiminases activity and target proteins were evaluated. Results The studied nanoparticles induced protein citrullination both in cultured human cells and mouse lung tissues. Citrullination occurred via the peptidylargininedeiminase-dependent mechanism. Cytokeratines 7, 8, 18 and plectins were identified as intracellular citrullination targets. Conclusion Nanoparticle exposure facilitated post-translational citrullination of proteins.

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Section: Methodsmentioning

confidence: 99%

Citrullination of Proteins: A Common Post-Translational Modification Pathway Induced by Different Nanoparticles In Vitro and In Vivo

et al. 2012

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“…A p -value of <0.05 was considered to be statistically significant. For the multiparametric analysis, due to the large amount of information acquired a data mining and exploration platform was used (KNIME (http://KNIME.org, 2.0.3) in combination with a screening module HiTS (http://code.google.com/p/hits, 0.3.0) in order to screen and normalised all parameters under investigation, as previously reported [49,50]. All measured parameters were normalised using their respective percent of the positive controls.…”

Section: Methodsmentioning

confidence: 99%

Activation of stress-related signalling pathway in human cells upon SiO2 nanoparticles exposure as an early indicator of cytotoxicity

Mohamed

Verma

Prina-Mello

et al. 2011

Journal of Nanobiotechnology

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BackgroundNanomaterials such as SiO2 nanoparticles (SiO2NP) are finding increasing applications in the biomedical and biotechnological fields such as disease diagnostics, imaging, drug delivery, food, cosmetics and biosensors development. Thus, a mechanistic and systematic evaluation of the potential biological and toxic effects of SiO2NP becomes crucial in order to assess their complete safe applicability limits.ResultsIn this study, human monocytic leukemia cell line THP-1 and human alveolar epithelial cell line A549 were exposed to a range of amorphous SiO2NP of various sizes and concentrations (0.01, 0.1 and 0.5 mg/ml). Key biological indicators of cellular functions including cell population density, cellular morphology, membrane permeability, lysosomal mass/pH and activation of transcription factor-2 (ATF-2) were evaluated utilizing quantitative high content screening (HCS) approach and biochemical techniques. Despite the use of extremely high nanoparticle concentrations, our findings showed a low degree of cytotoxicity within the panel of SiO2NP investigated. However, at these concentrations, we observed the onset of stress-related cellular response induced by SiO2NP. Interestingly, cells exposed to alumina-coated SiO2NP showed low level, and in some cases complete absence, of stress response and this was consistent up to the highest dose of 0.5 mg/ml.ConclusionsThe present study demonstrates and highlights the importance of subtle biological changes downstream of primary membrane and endocytosis-associated phenomena resulting from high dose SiO2NP exposure. Increased activation of transcription factors, such as ATF-2, was quantitatively assessed as a function of i) human cell line specific stress-response, ii) SiO2NP size and iii) concentration. Despite the low level of cytotoxicity detected for the amorphous SiO2NP investigated, these findings prompt an in-depth focus for future SiO2NP-cell/tissue investigations based on the combined analysis of more subtle signalling pathways associated with accumulation mechanisms, which is essential for establishing the bio-safety of existing and new nanomaterials.

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“…However, under optimal conditions this compression factor could be increased to >200 without significant loss of information. This dramatically increases the processing speed for image data analysis overcoming some of the data management bottlenecks that have been encountered with HCS [42]. Furthermore, as cell technologies change, and in particular as 3D culture technologies become incorporated into drug screening programmes, the type of analysis system described in this paper could also support the transition of HCS into high-throughput 3D drug development cell models [43].…”

Section: Discussionmentioning

confidence: 99%

The Use of Multidimensional Image-Based Analysis to Accurately Monitor Cell Growth in 3D Bioreactor Culture

Baradez¹,

Marshall²

2011

PLoS ONE

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The transition from traditional culture methods towards bioreactor based bioprocessing to produce cells in commercially viable quantities for cell therapy applications requires the development of robust methods to ensure the quality of the cells produced. Standard methods for measuring cell quality parameters such as viability provide only limited information making process monitoring and optimisation difficult. Here we describe a 3D image-based approach to develop cell distribution maps which can be used to simultaneously measure the number, confluency and morphology of cells attached to microcarriers in a stirred tank bioreactor. The accuracy of the cell distribution measurements is validated using in silico modelling of synthetic image datasets and is shown to have an accuracy >90%. Using the cell distribution mapping process and principal component analysis we show how cell growth can be quantitatively monitored over a 13 day bioreactor culture period and how changes to manufacture processes such as initial cell seeding density can significantly influence cell morphology and the rate at which cells are produced. Taken together, these results demonstrate how image-based analysis can be incorporated in cell quality control processes facilitating the transition towards bioreactor based manufacture for clinical grade cells.

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Workflow-Based Software Environment for Large-Scale Biological Experiments

Cited by 13 publications

References 10 publications

Citrullination of Proteins: A Common Post-Translational Modification Pathway Induced by Different Nanoparticles In Vitro and In Vivo

Citrullination of Proteins: A Common Post-Translational Modification Pathway Induced by Different Nanoparticles In Vitro and In Vivo

Activation of stress-related signalling pathway in human cells upon SiO2 nanoparticles exposure as an early indicator of cytotoxicity

The Use of Multidimensional Image-Based Analysis to Accurately Monitor Cell Growth in 3D Bioreactor Culture

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