Colocalization coefficients evaluating the distribution of molecular targets in microscopy methods based on pointed patterns

Pastorek, Lukáš; Sobol, Margarita; Hozák, Pavel

doi:10.1007/s00418-016-1467-y

Cited by 13 publications

(16 citation statements)

References 52 publications

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“…Moreover, our novel immunoelectron microscopy studies showed these molecules localize to the triad. To our knowledge, this is the first report on ultrastructural localization of PI3P, PI(3,4)P2 and PI (4,5)P2 at the triad in a vertebrate model, as previous studies focused on culture cell lines [40][41][42][43][44]. Our data add to the growing evidence showing the importance of PIP metabolism in the development and maintenance of this key muscle substructure.…”

Section: Plos Onesupporting

confidence: 66%

De novo phosphoinositide synthesis in zebrafish is required for triad formation but not essential for myogenesis

et al. 2020

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Phosphoinositides (PIPs) and their regulatory enzymes are key players in many cellular processes and are required for aspects of vertebrate development. Dysregulated PIP metabolism has been implicated in several human diseases, including a subset of skeletal myopathies that feature structural defects in the triad. The role of PIPs in skeletal muscle formation, and particularly triad biogenesis, has yet to be determined. CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) catalyzes the formation of phosphatidylinositol, which is the base of all PIP species. Loss of CDIPT should, in theory, result in the failure to produce PIPs, and thus provide a strategy for establishing the requirement for PIPs during embryogenesis. In this study, we generated cdipt mutant zebrafish and determined the impact on skeletal myogenesis. Analysis of cdipt mutant muscle revealed no apparent global effect on early muscle development. However, small but significant defects were observed in triad size, with T-tubule area, inter terminal cisternae distance and gap width being smaller in cdipt mutants. This was associated with a decrease in motor performance. Overall, these data suggest that myogenesis in zebrafish does not require de novo PIP synthesis but does implicate a role for CDIPT in triad formation.

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Section: Plos Onesupporting

confidence: 66%

De novo phosphoinositide synthesis in zebrafish is required for triad formation but not essential for myogenesis

et al. 2020

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“…To facilitate the visualisation of 6 nm gold nanoparticles in images, Adobe Photoshop CS3 Version 10.0 was used to cover the small nanoparticles co-centrically with red dots. To evaluate computationally the spatial distribution and quantitative mutual dependence of the nanoparticles in electron microscopy images, we developed and used the quantitative objective approach (Pastorek et al, 2016), based on the previously published method describing a pair cross-correlation function (PCCF) (Philimonenko et al, 2000). In this study, we used a newly developed plugin (Pastorek et al, 2016) on the Fiji software platform to quantify the relative colocalisation coefficient (RCC).…”

Section: Temmentioning

confidence: 99%

“…To evaluate computationally the spatial distribution and quantitative mutual dependence of the nanoparticles in electron microscopy images, we developed and used the quantitative objective approach (Pastorek et al, 2016), based on the previously published method describing a pair cross-correlation function (PCCF) (Philimonenko et al, 2000). In this study, we used a newly developed plugin (Pastorek et al, 2016) on the Fiji software platform to quantify the relative colocalisation coefficient (RCC). In summary, we analysed 21 cells co-labelled for NM1 and PtdIns(4,5)P 2 , 59 control cells and 213 α-amanitin-treated cells colabelled for BrRNA and PtdIns(4,5)P 2 , 37 cells co-labelled for RNA and PtdIns(4,5)P 2 , 20 cells co-labelled for cholesterol and PtdIns(4,5)P 2 , and 41 cells co-labelled for ceramide and PtdIns(4,5)P 2 .…”

Section: Temmentioning

confidence: 99%

Nuclear phosphatidylinositol 4,5-bisphosphate islets contribute to efficient RNA polymerase II-dependent transcription

Sobol

Krausová

Yıldırım

et al. 2018

Journal of Cell Science

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This paper describes a novel type of nuclear structure - nuclear lipid islets (NLIs). They are of 40-100 nm with a lipidic interior, and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P] molecules comprise a significant part of their surface. Most of NLIs have RNA at the periphery. Consistent with that, RNA is required for their integrity. The NLI periphery is associated with Pol II transcription machinery, including the largest Pol II subunit, transcription factors and NM1 (also known as NMI). The PtdIns(4,5)P-NM1 interaction is important for Pol II transcription, since NM1 knockdown reduces the Pol II transcription level, and the overexpression of wild-type NM1 [but not NM1 mutated in the PtdIns(4,5)P-binding site] rescues the transcription. Importantly, Pol II transcription is dependent on NLI integrity, because an enzymatic reduction of the PtdIns(4,5)P level results in a decrease of the Pol II transcription level. Furthermore, about half of nascent transcripts localise to NLIs, and transcriptionally active transgene loci preferentially colocalise with NLIs. We hypothesize that NLIs serve as a structural platform that facilitates the formation of Pol II transcription factories, thus participating in the formation of nuclear architecture competent for transcription.

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“…Moreover, our novel immunoelectron microscopy studies showed these molecules localize to the triad. To our knowledge, this is the first report on ultrastructural localization of PI3P, PI(3,4)P2 and PI(4,5)P2 at the triad in a vertebrate model, as previous studies focused on culture cells (Watt et al, 2002) (Tabellini et al, 2003) (Mayhew et al, 2004) (Wegner et al, 2014) (Pastorek et al, 2016). Our data add to the growing evidence showing the importance of PIP metabolism in the development and maintenance of this key muscle substructure.…”

Section: Discussionmentioning

confidence: 86%

De NovoPhosphoinositide Synthesis in Zebrafish Is Required for Triad Formation but Not Essential for Myogenesis

Dowling

Smith

Fabian

et al. 2020

Preprint

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25Phosphoinositides (PIPs) and their regulatory enzymes are key players in many cellular 26 processes and are required for aspects of vertebrate development. Dysregulated PIP 27 metabolism has been implicated in several human diseases, including a subset of 28 skeletal myopathies that feature structural defects in the triad. The role of PIPs in 29 skeletal muscle formation, and particularly triad biogenesis, has yet to be determined. 30 CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) catalyzes the formation 31 of phosphatidylinositol, which is the base of all PIP species. Loss of CDIPT should, in 32 theory, result in the failure to produce PIPs, and thus provide a strategy for establishing 33 the requirement for PIPs during embryogenesis. In this study, we generated cdipt 34 mutant zebrafish and determined the impact on skeletal myogenesis. Analysis of cdipt 35 mutant muscle revealed no apparent global effect on early muscle development. 36However, small but significant defects were observed in triad size, with T-tubule area, 37 inter terminal cisternae distance and gap width being smaller in cdipt mutants. This was 38 associated with a decrease in motor performance. Overall, these data suggest that 39 myogenesis in zebrafish does not require de novo PIP synthesis but does implicate a 40 role for CDIPT in triad formation. 3 41 4 64 been implicated in a number of human diseases, such as congenital myopathies, 65 Charcot-Marie-Tooth Disease (CMT), Alzheimer's disease, and some forms of cancer 66 The consideration of a potential role for PIPs in muscle development comes from two 68 areas of study. One is the work surrounding BIN1, a BAR domain-containing protein 69 that is known to recognize and induce membrane curvature (Peter et al., 2004); (Frost 70 et al., 2009). BIN1 has a PIP-binding domain that interacts with PIP2 (one of the seven 71 PIP sub-species), and this interaction plays a critical role in the formation of T-tubules. 72 Recessive mutations in BIN1 result in centronuclear myopathy, a severe congenital 73 muscle disease featuring abnormal muscle structure including disturbance of the T-74 tubule and the triad as a whole. The second line of evidence comes from another form 75 of centronuclear myopathy called X-linked myotubular myopathy or XLMTM (Dowling et 76 al., 2009) (Amoasii et al., 2012). XLMTM is caused by mutations in the PIP 77 phosphatase myotubularin. Mutation in myotubularin causes accumulation of PI3P and 78 leads to abnormalities in the appearance and number of the triad. 79 In this study, we investigated the role of PIPs in skeletal muscle triad development using 80 the zebrafish model system. Zebrafish is an elegant model for studying skeletal muscle 81 development (Gibbs et al., 2013). Skeletal muscle develops rapidly in zebrafish, muscle 82 fibers are already developing by 24 hours post-fertilization (hpf), with elongated fibers 83 visible by 2 days post-fertilization (dpf). Skeletal muscle is highly prominent in embryos 84 and larvae, and the transparency of developing...

show abstract

Colocalization coefficients evaluating the distribution of molecular targets in microscopy methods based on pointed patterns

Cited by 13 publications

References 52 publications

De novo phosphoinositide synthesis in zebrafish is required for triad formation but not essential for myogenesis

De novo phosphoinositide synthesis in zebrafish is required for triad formation but not essential for myogenesis

Nuclear phosphatidylinositol 4,5-bisphosphate islets contribute to efficient RNA polymerase II-dependent transcription

De NovoPhosphoinositide Synthesis in Zebrafish Is Required for Triad Formation but Not Essential for Myogenesis

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