PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies

Bokota, Grzegorz; Sroka, Jacek; Basu, Subhadip; Das, Nirmal K.; Trzaskoma, Paweł; Yushkevich, Yana; Grabowska, Agnieszka; Magalska, Adriana; Plewczynski, Dariusz

doi:10.1101/2020.07.16.206789

Cited by 4 publications

(3 citation statements)

References 27 publications

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“…We have limited our analysis to cells from the meristematic zone of the root because their shape, size and spatial architecture allow easy recognition and cell segmentation, and preservation of the tissue integrity in the squashed material. For image analyses, we used PartSeg, a novel computational tool for image processing, and segmentation described by Bokota et al (2021). Cells were segmented manually on one z ‐slice and projected to the z ‐slices above and below corresponding to the top and bottom edges of the cell.…”

Section: Methodsmentioning

confidence: 99%

Promoter‐pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt

et al. 2023

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Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co‐directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co‐directional transcription in controlling transcriptional dynamics of downstream genes.

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Section: Methodsmentioning

confidence: 99%

Promoter‐pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt

et al. 2023

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“…The minimal distance from the nuclear periphery and Bdnf alleles in neuronal nuclei of animals was calculated using custom-written software, Segmentation Magick, described in Ruszczycki et al (40). For neuronal cultures, custom-written software Partseg was used, described in (41).…”

Section: Quantitative Image Analysismentioning

confidence: 99%

An important role of the interplay between Bdnf transcription and histone acetylation in epileptogenesis

Walczak

Czaban

Skupien

et al. 2020

Preprint

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Brain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation of Bdnf gene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning of Bdnf alleles from the nuclear periphery towards the nuclear center. This change of Bdnf intranuclear position was associated with transcriptional gene activity.In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of the Bdnf allele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of the Bdnf allele at the nuclear periphery correlates with stronger mossy fiber sprouting - an aberrant form of excitatory circuits formation. Moreover, using in vitro hippocampal cultures we showed that Bdnf repositioning is a consequence of the transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blocked Bdnf gene transcription and repositioning observed after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase of Bdnf gene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.

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“…Our contribution. In this work, we present Trapalyzer, a plug-in for the PartSeg software [4] for the analysis and annotation of fluorescent microscopy images of neutrophils double-stained with a cell-permeable and a cell-impermeable fluorescent DNA dye. Our software extends the capabilities of the currently available tools by quantifying more stages of NET formation without the need for large training data sets.…”

Section: Introductionmentioning

confidence: 99%

Trapalyzer: A computer program for quantitative analyses in fluorescent live-imaging studies of Neutrophil Extracellular Trap formation

Ciach

Bokota

Manda-Handzlik

et al. 2022

Preprint

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Neutrophil extracellular traps (NETs), pathogen-ensnaring structures formed by neutrophils by expelling their DNA into the environment, are believed to play an important role in immunity and autoimmune diseases. In recent years, a growing attention has been put into developing software tools to quantify NETs in fluorescent microscopy images. However, current solutions require extensive training data sets, are difficult to use for users without background in computer science, or have limited capabilities. In this work we present Trapalyzer, a computer program for an automatic quantification of NETs in terms of their area and an approximation of their number. In addition, Trapalyzer counts neutrophils at different stages of NET formation, and is the first tool that makes this possible without extensive training data sets. We validate our approach on a publicly available benchmark data set and apply it in a neutrophil-bacteria co-culture experiment. The software and usage tutorials are available at https://github.com/Czaki/Trapalyzer .

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PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies

Cited by 4 publications

References 27 publications

Promoter‐pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt

Promoter‐pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt

An important role of the interplay between Bdnf transcription and histone acetylation in epileptogenesis

Trapalyzer: A computer program for quantitative analyses in fluorescent live-imaging studies of Neutrophil Extracellular Trap formation

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