Abstract
Cellular response to stress can be manifested and visualized by measuring induced DNA damage. However, cellular systems can repair the damage through a variety of DNA repair pathways. It is important to characterize the dynamics of DNA repair in a variety of model systems. Such a characterization is another example of the video bioinformatics through harvesting and fixing of a large sample size at different time points. This chapter provides background and motivation for quantifying the dynamics of DNA damage induction and repair in cycling and stationary cells. These model systems indicate that the repair kinetics have a similar profile for gamma radiation; however, following iron ion exposure residual unrepaired damage is noted at longer times when assayed in stationary cells. Repair kinetics are visualized by immunofluorescence staining of phosphorylated histone gamma-H2AX and the DNA repair protein 53BP1. The kinetics are then quantified using cell-based segmentation, which provides a context for repair measurements and colocalization analysis. For enhanced robustness, cell-based segmentation and protein localization leverage geometric methods. Subsequently, cellular profiles are stored in a database, where colocalization analysis takes place through specially design database queries.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Parvin B, Yang Q, Fontenay G, Barcellos-Hoff M (2003) BioSig: an imaging bioinformatics system for phenotypic studies. IEEE Trans Syst Man Cybernetric B33(5):814–824
Rossetto D, Avvakumov N, Côté J (2012) Histone phosphorylation: a chromatin modification involved in diverse nuclear events. Epigenetics 7(10):1098–1108
Bolte S, Cordelieres F (2006) A guided tour into subcellular colocalization analysis in light microscopy. Microscopy 224:213–232
Groesser T, Chang H, Fontenay G, Chen J, Costes S, Barcellos-Hoff M, Parvin B, Rydberg B (2011) Persistent of gamma-H2AX and 53BP1 fori in proliferating and non-proliferating human mammary epithelial cells after exposure to gamma-rays or iron ions. Int J Radiat Res 87(7):696–710
Belyaev I (2010) Radiation-induced DNA repair foci: spatio-temporal aspects of formation, application for assessment of radiosensitivity and biological dosimetry. Mutat Res 704:132–141
Coelho L, Shariff A, Murphy R (2009) Nuclear segmentation in microscope cell images: a hand-segmented dataset and comparison of algorithms. In: IEEE International symposium on biomedical imaging: from nano to macro, Boston, MA
Carpenter A, Jones T, Lamprecht M, Clarke C, Kang I, Friman O, Guertin D, Chang J, Lindquits R, Moffat J, Golland P, Sabatini D (2006) Cell profiler: image analysis software for identifying and quantifying cell phenotype. Gen Bio 7(10)
Han J, Chang H, Andrarwewa K, Yaswen P, Barcellos-Hoff M, Parvin B (2010) Multidimensional profiling of cell surface proteins and nuclear markers. In: IEEE Transactions on computational biology and bioinformatics
Chang H, Yang Q, Parvin B (2007) Segmentation of heterogeneous blob objects through voting and level set formulation. Pattern Recogn Lett 28(13):1781–1787
Yang Q, Parvin B (2003) Harmonic cuts and regualrized centroid transform for localization of subcellular structures. IEEE Trans Bioeng 50(4):469–476
Lin G, Adiga U, Olson K, Guzowski JF, Barnes CA, Roysam B (2003) A hybrid 3-D watershed algorithm incorporating gradient cues & object models for automatic segmentation of nuclei in confocal image stacks. Cytometry Part A 56A(1):23–36
Raman S, Maxwell C, Barcellos-Hoff MH, Parvin B (2007) Geometric approach to segmentation and protein localization in cell-cultured assays. Microscopy 225(a)
Chang H, Wen Q, Parvin B (2015) Coupled segmentation of nuclear and membrane-bound macromolecules through voting and multiphase level set. Pattern Recogn 48(3):882–893
Chang H, Han J, AD B, Loss L, Gray J, Spellman P, Parvin B (2013) Invariant delineation of nuclear architecture in Glioblastoma Multiforme for clinical and molecular association. IEEE Trans Med Imaging 32(4):670–682
Wen Q, Chang H, Parvin B (2009) A Delaunay triangulation approach for segmenting a clump of nuclei. In: IEEE international synposium on biomedical imaging: from nano to macro. Boston, MA
Parvin B, Yang Q, Han J, Chang H, Rydberg B, Barcellos-Hoff MH (2007) Iterative voting for inference of structural saliency and characterization of subcellular events. IEEE Trans Image Proc 16(3):1781–1787
Urbano F, Cagnacci F (2014) Spatial database for GPS wildlife tracking tata: a practical guide to creating a data management system with PostgreSQL/PostGIS and R. Springer, New York
Raman S, Maxwell C, Barcellos-Hoff MH, Parvin B (2007) Geometric approach to segmentation and protein localization in cell culture assays. J Microsc 225(1):22–30
Markova E, Schultz N, Belyaev I (2007) Kinetics and dose-response of residual 53BP1/g -H2AX foci: co-localization, relationship with DSB repair and clonogenic survival. Int J Radiat Biology 83(5):319–329
Asaithamby A, Uematsu N, Chatterjee A, Story M, Burma S, Chen D (2008) Repair of HZE-particle-induced DNA double-strand breaks in normal human fibroblasts. Radiat Res 169(4):437–446
Acknowledgment
Funding: National Institute of Health [grant R01 CA140663] and carried out at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Groesser, T., Fontenay, G.V., Han, J., Chang, H., Pluth, J., Parvin, B. (2015). Quantification of the Dynamics of DNA Repair to Ionizing Radiation via Colocalization of 53BP1 and ɣH2AX. In: Bhanu, B., Talbot, P. (eds) Video Bioinformatics. Computational Biology, vol 22. Springer, Cham. https://doi.org/10.1007/978-3-319-23724-4_14
Download citation
DOI: https://doi.org/10.1007/978-3-319-23724-4_14
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-23723-7
Online ISBN: 978-3-319-23724-4
eBook Packages: Computer ScienceComputer Science (R0)