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Next generation multi-scale biophysical characterization of high precision cancer particle radiotherapy using clinical proton, helium-, carbon- and oxygen ion beams

Ivana Dokic, Andrea Mairani, Martin Niklas, Ferdinand Zimmermann, Naved Chaudhri, Damir Krunic, Thomas Tessonnier, Alfredo Ferrari, Katia Parodi, Oliver Jäkel, Jürgen Debus, Thomas Haberer (+1 others)
2016 OncoTarget  
The cell fluorescence ion track hybrid detector (Cell-Fit-HD) technology was employed to detect particle traverse per cell nucleus.  ...  A high level of agreement was found between the in silico simulations, the physical dosimetry and the clonogenic tumor cell survival.  ...  The support of colleagues in the Medical Physics Department in Radiation Oncology of the Heidelberg University Hospital is greatly acknowledged.  ... 
doi:10.18632/oncotarget.10996 pmid:27494855 pmcid:PMC5302944 fatcat:lugildhjujad7oj6gijipiy5xi

Labelling and imaging of single endogenous messenger RNA particles in vivo

J.-H. Spille, U. Kubitscheck
2015 Journal of Cell Science  
New imaging modalities allow determination of not only lateral but also axial positions with high precision within the cellular context, and across a wide range of specimen from yeast and bacteria to cultured  ...  In this Commentary, we highlight how single molecule imaging and particle tracking can yield further insight into the dynamics of RNA particles in living cells.  ...  Acknowledgements The authors acknowledge Dr. J. P. Siebrasse for critical reading of the manuscript. Competing interests The authors declare no competing or financial interests.  ... 
doi:10.1242/jcs.166728 pmid:26416818 fatcat:ziil5rfd7fhmngnfckuqinjyra

Particles with similar LET values generate DNA breaks of different complexity and reparability: a high-resolution microscopy analysis of γH2AX/53BP1 foci

Lucie Jezkova, Mariia Zadneprianetc, Elena Kulikova, Elena Smirnova, Tatiana Bulanova, Daniel Depes, Iva Falkova, Alla Boreyko, Evgeny Krasavin, Marie Davidkova, Stanislav Kozubek, Olga Valentova (+1 others)
2018 Nanoscale  
Different particles with similar LET and energy may generate different types of DNA damage with consequences for DNA double-strand break repair.  ...  Krylov from the Laboratory of Radiation Biology (JINR) for exposing the cells to radiation with accelerated heavy ions using the U400M cyclotron and V. N.  ...  Acknowledgements The authors thank Y. G. Teterev and A. A. Bezbakh from the Flerov Laboratory of Nuclear Reactions (JINR) and G. N. Timoshenko and V. A.  ... 
doi:10.1039/c7nr06829h pmid:29271466 fatcat:7s37opitevgfrjhlfpbj6vt7zi

Hybrid optical gating for long-term 3D time-lapse imaging of the beating embryonic zebrafish heart [article]

Jonathan M Taylor, Carl J Nelson, Finnius A Bruton, Aryan K Baghbadrani, Charlotte Buckley, Carl S Tucker, John J Mullins, Martin A Denvir
2019 bioRxiv   pre-print
This approach has enabled us to observe detailed developmental, structural, cellular and subcellular processes, including live cell division and cell fate tracking, in the embryonic zebrafish heart using  ...  We show that our approach not only provides high spatial and temporal resolution 3D-imaging, but also avoids phototoxic injury, where alternative approaches induce measurable harm.  ...  This has enabled us, for the first time, to track developmental morphogenesis and patterning in the heart with a high degree of temporal and spatial resolution in 3D, and track individual motile cells,  ... 
doi:10.1101/526830 fatcat:rqryhbvmcjc4ddhzgdcj762hje

Tracking Multiple Genomic Elements Using Correlative CRISPR Imaging and Sequential DNA FISH

Juan Guan, Harrison Liu, Xiaoyu Shi, Siyu Feng, Bo Huang
2017 Biophysical Journal  
Here we introduce an approach to achieve highly multiplexed live recording via correlative CRISPR imaging and sequential DNA fluorescence in situ hybridization (FISH).  ...  Our approach keeps the rest of the color palette open to image other cellular phenomena of interest, as demonstrated by our simultaneous live imaging of genomic loci together with a cell cycle reporter  ...  Single particle tracking The positions of the spots in cell nuclei in live images were determined in CellProfiler (cellprofiler.org).  ... 
doi:10.1016/j.bpj.2017.01.032 pmid:28355536 pmcid:PMC5375138 fatcat:ijld4hvibzaq5bzptm7gdxuqi4

Ion track reconstruction in 3D using alumina-based fluorescent nuclear track detectors

M Niklas, J A Bartz, M S Akselrod, A Abollahi, O Jäkel, S Greilich
2013 Physics in Medicine and Biology  
FNTDs were coated with a confluent human lung adenocarcinoma epithelial cell layer. Carbon ion irradiation of the hybrid detector was performed perpendicular and angular to the detector surface.  ...  Making use of the trajectory information provided by the FNTD the accuracy of 3D track reconstruction of single particles traversing the hybrid detector was studied.  ...  JB participated in the axial geometrical correction. MA developed the crystal (FNTD) material and FNTD imaging technique.  ... 
doi:10.1088/0031-9155/58/18/n251 pmid:23965401 fatcat:3u4lzelezrgqzcrhpawdtmheay

Image analysis for understanding embryo development: a bridge from microscopy to biological insights

MA Luengo-Oroz, MJ Ledesma-Carbayo, N Peyriéras, A Santos
2011 Current Opinion in Genetics and Development  
These tools will be essential to ultimately produce the multilevel in toto reconstruction that combines the cell lineage tree, cells, and tissues structural information and quantitative gene expression  ...  validation methodologies for cell membrane shape identification, single cell gene expression quantification from in situ hybridization data, and multidimensional image registration algorithms for the construction  ...  Acknowledgements This work was supported by TEC2008-06715-C02-02 (Spain), ANR and ARC (France), FP6 New Emerging Science and Technology EC program and European Regional Development Funds (FEDER).  ... 
doi:10.1016/j.gde.2011.08.001 pmid:21893410 fatcat:woaff5emnje4rg64otdqzx6yry

In Vivo Assessment of Stem Cells for Treating Neurodegenerative Disease: Current Approaches and Future Prospects

Byeong-Wook Song
2017 Stem Cells International  
Monitoring stem cell survival and migration and graft-host relationships is a useful strategy to evaluate the therapeutic efficacy of regenerative medicine approaches in neurodegenerative disease.  ...  This review summarizes the recent approaches that have been used for tracking and imaging engrafted stem cells in vivo.  ...  Future Directions An important development in assessing stem cell therapy with brain imaging is the ability to measure the relationship and connectivity between graft and host cells in 3D.  ... 
doi:10.1155/2017/9751583 pmid:28326106 pmcid:PMC5343274 fatcat:4nwh4ou72fe75ivlf7h5rgrn5a

Capturing Chromosome Structural Properties From Their Spatial and Temporal Fluctuations [chapter]

Aurélien Bancaud, Olivier Gadal, Kerstin Bystricky
2017 Epigenetics and Systems Biology  
Intense efforts based on interdisciplinary research at the forefront of physics, mathematics, molecular and cellular biology and biochemistry have contributed to a better understanding of the physical  ...  We describe state of the art chromatin labeling technologies, focusing on optimizing yield of signal-to-noise ratio, high-throughput automated imaging techniques, and physical modeling.  ...  The standard approach to assess the level of localization precision consists in tracking simulated spots at a fixed position with a registered level of SNR.  ... 
doi:10.1016/b978-0-12-803075-2.00012-x fatcat:nrpp53z6afamhidjrn62z2iwrm

Taking Aim at Moving Targets in Computational Cell Migration

Paola Masuzzo, Marleen Van Troys, Christophe Ampe, Lennart Martens
2016 Trends in Cell Biology  
Indeed, 2D in vitro assays [13, 14] have recently given way to more sophisticated two-and-a-half-dimensional (2.5D) and 3D approaches [15, 16] which more faithfully represent the tissue environment.  ...  We review computational approaches for the key tasks in the quantification of in vitro cell migration: image pre-processing, motion estimation and feature extraction.  ...  In the case of cell migration, diffusion measurements are related to the mean squared displacement of a particle undergoing a Brownian motion.  ... 
doi:10.1016/j.tcb.2015.09.003 pmid:26481052 fatcat:yi6aghqtybfmxl3iznz6yhwyoq

Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH [article]

Juan Guan, Harrison Liu, Xiaoyu Shi, Siyu Feng, Bo Huang
2017 bioRxiv   pre-print
Here we introduce an approach to achieve highly multiplexed live recording via correlative CRISPR imaging and sequential DNA fluorescence in situ hybridization (FISH).  ...  Our approach keeps the rest of the color palette open to image other cellular phenomena of interest, as demonstrated by our simultaneous live imaging of genomic loci together with a cell cycle reporter  ...  Single particle tracking The positions of the spots in cell nuclei in live images were determined in CellProfiler.  ... 
doi:10.1101/101444 fatcat:w67mohzgvrhgvfngbumh73osci

Engineering cell-fluorescent ion track hybrid detectors

Martin Niklas, Steffen Greilich, Claudius Melzig, Mark S Akselrod, Jürgen Debus, Oliver Jäkel, Amir Abdollahi
2013 Radiation Oncology  
Conclusions: The Cell-Fit-Hybrid Detector system is a promising platform for a multitude of studies linking biological response to energy deposition at high level of optical microscopy resolution. of a  ...  The ion track information was not compromised in Cell-Fit-HD as compared to the FNTD alone.  ...  Acknowledgements We are grateful to S. Brons for generously providing support and technical irradiation assistance at the Heidelberg Ion-Beam Therapy Center (HIT). We should also like to thank F.  ... 
doi:10.1186/1748-717x-8-141 pmid:23758749 pmcid:PMC3699405 fatcat:kduvh5bmczdc7cuiiexfscok5i

Chromosome dynamics and folding in eukaryotes: Insights from live cell microscopy

Kerstin Bystricky
2015 FEBS Letters  
Even if single cell analyses are beginning to yield precious insights, how can we determine whether a snapshot of position is related to function of the probed locus or cell-type?  ...  and large scale geometrical analysis of multiple loci in 3D.  ...  Acknowledgments Imaging and analysis shown in  ... 
doi:10.1016/j.febslet.2015.07.012 pmid:26188544 fatcat:hkhr5ys3sved7n2ckjh7c6e3xa

Penetrating particle ANalyzer (PAN)

X. Wu, G. Ambrosi, P. Azzarello, B. Bergmann, B. Bertucci, F. Cadoux, M. Campbell, M. Duranti, M. Ionica, M. Kole, S. Krucker, G. Maehlum (+9 others)
2019 Advances in Space Research  
The precise measurement and monitoring of the energetic particles is also a unique contribution to space weather studies.  ...  It can precisely measure and monitor the flux, composition, and direction of highly penetrating particles (> ∼100 MeV/nucleon) in deep space, over at least one full solar cycle ( 11 years).  ...  The TOF detector will measure the charge of the particles, provide a time of flight measurement with a precision of 100 ps, and provide a high rate (up to 10 MHz) counter for particles above 10 MeV, particularly  ... 
doi:10.1016/j.asr.2019.01.012 fatcat:oaedy6j2tjb5jluqt5bfvtntqa

Morphology and dynamics of chromosome territories in living cells

Peter Edelmann, Harald Bornfleth, Daniele Zink, Thomas Cremer, Christoph Cremer
2001 Biochimica et Biophysica Acta. CR. Reviews on Cancer  
Chromosome territories formed by fluorescence-labeled sub-chromosomal foci were analyzed in time-lapse series of 3D confocal data sets of living HeLa and human neuroblastoma cells.  ...  The changes in morphology with time of single chromosome territories were found to be less pronounced than differences in morphology of different chromosome territories in fixed cells.  ...  Stelzer, Light Microscopical Group, European Molecular Biology Laboratory (EMBL) for providing access to a prototype of the Zeiss LSM 5 microscope and for kind help with data acquisition.  ... 
doi:10.1016/s0304-419x(01)00023-3 pmid:11553419 fatcat:lk6qfbuegral3c35ibqpyma4qy
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