Diatrack particle tracking software: Review of applications and performance evaluation

Vallotton, Pascal; Oijen, Antoine M. van; Whitchurch, Cynthia B.; Gelfand, Vladimir I.; Yeo, Leslie; Tsiavaliaris, Georgios; Heinrich, Stephanie; Dultz, Elisa; Weis, Karsten; Grünwald, David

doi:10.1111/tra.12530

Cited by 48 publications

(38 citation statements)

References 106 publications

(98 reference statements)

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“…Aligned EB1 and CENP-A datasets were processed in three sequential steps using the Diatrack software package ( Vallotton et al, 2017 ). First, images were background subtracted and Gaussian filtered with a sigma of 1 pixel to reduce image noise.…”

Section: Methodsmentioning

confidence: 99%

High-resolution imaging reveals how the spindle midzone impacts chromosome movement

Pamula

Carlini

Forth

et al. 2019

Journal of Cell Biology

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In the spindle midzone, microtubules from opposite half-spindles form bundles between segregating chromosomes. Microtubule bundles can either push or restrict chromosome movement during anaphase in different cellular contexts, but how these activities are achieved remains poorly understood. Here, we use high-resolution live-cell imaging to analyze individual microtubule bundles, growing filaments, and chromosome movement in dividing human cells. Within bundles, filament overlap length marked by the cross-linking protein PRC1 decreases during anaphase as chromosome segregation slows. Filament ends within microtubule bundles appear capped despite dynamic PRC1 turnover and submicrometer proximity to growing microtubules. Chromosome segregation distance and rate are increased in two human cell lines when microtubule bundle assembly is prevented via PRC1 knockdown. Upon expressing a mutant PRC1 with reduced microtubule affinity, bundles assemble but chromosome hypersegregation is still observed. We propose that microtubule overlap length reduction, typically linked to pushing forces generated within filament bundles, is needed to properly restrict spindle elongation and position chromosomes within daughter cells.

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Section: Methodsmentioning

confidence: 99%

High-resolution imaging reveals how the spindle midzone impacts chromosome movement

Pamula

Carlini

Forth

et al. 2019

Journal of Cell Biology

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“…The peripheral NS5A foci (which are putative replication complexes) are frequently highly motile and capable of rapid long-range traffic. Hence, advanced models of NS5A will need to incorporate and addresses the motile populations of NS5A foci, for which particle tracking analysis will be an important evaluation tool, cf, e.g., [ 39 ].…”

Section: Methodsmentioning

confidence: 99%

Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface

Knodel

Nägel

Reiter

et al. 2018

Viruses

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Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.

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“…We took advantage of the observation that single NPCs can occasionally be detected in dividing yeast cells where the part of the NE bridging the mother and daughter nuclei elongates and narrows (Movie S1) (36). These NPCs are more separated from their neighbors, allowing us to image and quantify the intensity of individual NPCs in several thousand cells using the Diatrack particle tracking software (37). As an absolute intensity reference, we also imaged in parallel, yeastexpressed rotavirus-like VP2 particles that contain exactly 120 copies of yEGFP (38).…”

Section: Determination Of Absolute Copy Numbers Reveals That Most Yeastmentioning

confidence: 99%

Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy

Rajoo

Vallotton

Onischenko

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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The nuclear pore complex (NPC) is an eightfold symmetrical channel providing selective transport of biomolecules across the nuclear envelope. Each NPC consists of ∼30 different nuclear pore proteins (Nups) all present in multiple copies per NPC. Significant progress has recently been made in the characterization of the vertebrate NPC structure. However, because of the estimated size differences between the vertebrate and yeast NPC, it has been unclear whether the NPC architecture is conserved between species. Here, we have developed a quantitative image analysis pipeline, termed nuclear rim intensity measurement (NuRIM), to precisely determine copy numbers for almost all Nups within native NPCs of budding yeast cells. Our analysis demonstrates that the majority of yeast Nups are present at most in 16 copies per NPC. This reveals a dramatic difference to the stoichiometry determined for the human NPC, suggesting that despite a high degree of individual Nup conservation, the yeast and human NPC architecture is significantly different. Furthermore, using NuRIM, we examined the effects of mutations on NPC stoichiometry. We demonstrate for two paralog pairs of key scaffold Nups, Nup170/Nup157 and Nup192/Nup188, that their altered expression leads to significant changes in the NPC stoichiometry inducing either voids in the NPC structure or substitution of one paralog by the other. Thus, our results not only provide accurate stoichiometry information for the intact yeast NPC but also reveal an intriguing compositional plasticity of the NPC architecture, which may explain how differences in NPC composition could arise in the course of evolution.

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Diatrack particle tracking software: Review of applications and performance evaluation

Cited by 48 publications

References 106 publications

High-resolution imaging reveals how the spindle midzone impacts chromosome movement

High-resolution imaging reveals how the spindle midzone impacts chromosome movement

Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface

Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy

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