ParticleStats: open source software for the analysis of particle motility and cytoskeletal polarity

The study of dynamic cellular processes in living cells is central to biology and is particularly powerful when the motility characteristics of individual objects within cells can be determined and analysed statistically. However, commercial programs only offer a limited range of inflexible analysis modules and there are currently no open source programs for extensive analysis of particle motility. Here, we describe ParticleStats (http://www.ParticleStats.com), a web server and open source programs, which input the X,Y coordinate positions of objects in time, and output novel analyses, graphical plots and statistics for motile objects. ParticleStats comprises three separate analysis programs. First, ParticleStats:Directionality for the global analysis of polarity, for example microtubule plus end growth in Drosophila oocytes. Second, ParticleStats:Compare for the analysis of saltatory movement in terms of runs and pauses. This can be applied to chromosome segregation and molecular motor-based movements. Thirdly ParticleStats:Kymographs for the analysis of kymograph images, for example as applied to separation of chromosomes in mitosis. These analyses have provided key insights into molecular mechanisms that are not possible from qualitative analysis alone and are widely applicable to many other cell biology problems.

[1]  E. Wieschaus,et al.  Dynein-mediated cargo transport in vivo. A switch controls travel distance. , 2000 .

[2]  Eric F. Wieschaus,et al.  Dynein-Mediated Cargo Transport in Vivo , 2000, The Journal of cell biology.

[3]  D. McDonald,et al.  Visualization of the intracellular behavior of HIV in living cells , 2002, The Journal of cell biology.

[4]  Michael C. Ridding,et al.  Therapeutic use of rTMS , 2007, Nature Reviews Neuroscience.

[5]  S. R. Jammalamadaka,et al.  Topics in Circular Statistics , 2001 .

[6]  Daniel Zicha,et al.  The Drosophila hairy RNA localization signal modulates the kinetics of cytoplasmic mRNA transport , 2003, The EMBO journal.

[7]  C. Lively,et al.  Kinesin-1 and Dynein are the primary motors for fast transport of mitochondria in Drosophila motor axons. , 2006, Molecular biology of the cell.

[8]  J. Correale,et al.  Staufen recruitment into stress granules does not affect early mRNA transport in oligodendrocytes. , 2004, Molecular biology of the cell.

[9]  Michael J Rust,et al.  Visualizing infection of individual influenza viruses , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[10]  David Ish-Horowicz,et al.  Conserved signals and machinery for RNA transport in Drosophila oogenesis and embryogenesis , 2001, Nature.

[11]  Ilan Davis,et al.  Drosophila wingless and Pair-Rule Transcripts Localize Apically by Dynein-Mediated Transport of RNA Particles , 2001, Cell.

[12]  B. C. Carter,et al.  Tracking single particles: a user-friendly quantitative evaluation , 2005, Physical biology.

[13]  Daniel St Johnston,et al.  Moving messages: the intracellular localization of mRNAs , 2005, Nature Reviews Molecular Cell Biology.

[14]  John Q Trojanowski,et al.  Rapid and Intermittent Cotransport of Slow Component-b Proteins , 2007, The Journal of Neuroscience.

[15]  A. Pestronk,et al.  Altered Axonal Mitochondrial Transport in the Pathogenesis of Charcot-Marie-Tooth Disease from Mitofusin 2 Mutations , 2007, The Journal of Neuroscience.

[16]  Ilan Davis,et al.  Transmitting the message: intracellular mRNA localization. , 2010, Current opinion in cell biology.

[17]  Ilan Davis,et al.  Dynactin suppresses the retrograde movement of apically localized mRNA in Drosophila blastoderm embryos. , 2007, RNA.

[18]  Ilan Davis,et al.  Intracellular mRNA localization: motors move messages. , 2002, Trends in genetics : TIG.

[19]  B. Helfand,et al.  Fast transport of neurofilament protein along microtubules in squid axoplasm. , 2000, Journal of cell science.

[20]  C. Bramham,et al.  Dendritic mRNA: transport, translation and function , 2007, Nature Reviews Neuroscience.

[21]  K. Jaqaman,et al.  Robust single particle tracking in live cell time-lapse sequences , 2008, Nature Methods.

[22]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[23]  Eric C Greene,et al.  Visualizing one-dimensional diffusion of proteins along DNA , 2008, Nature Structural &Molecular Biology.

[24]  Steven P Gross,et al.  Developmental Regulation of Vesicle Transport in Drosophila Embryos: Forces and Kinetics , 1998, Cell.

[25]  Enrico Gratton,et al.  Melanosomes transported by myosin-V in Xenopus melanophores perform slow 35 nm steps. , 2006, Biophysical journal.

[26]  R. Rock,et al.  Unconventional myosin traffic in cells reveals a selective actin cytoskeleton , 2009, Proceedings of the National Academy of Sciences.

[27]  Ilan Davis,et al.  Cohesin cleavage and Cdk inhibition trigger formation of daughter nuclei , 2010, Nature Cell Biology.

[28]  R. Jansen,et al.  mRNA localization: message on the move , 2001, Nature Reviews Molecular Cell Biology.

[29]  P. J. Smith,et al.  Arrangement of radial actin bundles in the growth cone of Aplysia bag cell neurons shows the immediate past history of filopodial behavior. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[30]  R. Fehon,et al.  Microtubule-mediated transport of the tumor-suppressor protein Merlin and its mutants , 2010, Proceedings of the National Academy of Sciences.