Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images

Ruszczycki, Błażej; Pels, Katarzyna; Walczak, Agnieszka; Zamłyńska, Katarzyna; Such, Michał; Szczepankiewicz, Andrzej A.; Hall, Małgorzata Hanna; Magalska, Adriana; Magnowska, Marta; Wolny, Artur; Bokota, Grzegorz; Basu, Subhadip; Pal, Ayan; Plewczynski, Dariusz; Wilczyński, Grzegorz M.

doi:10.3389/fnana.2019.00081

Cited by 16 publications

(13 citation statements)

References 36 publications

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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: Methodsmentioning

confidence: 99%

The interplay of seizures-induced axonal sprouting and transcription-dependent Bdnf repositioning in the model of temporal lobe epilepsy

et al. 2021

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The 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 transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blocked Bdnf gene transcription and repositioning occurring 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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Section: Methodsmentioning

confidence: 99%

The interplay of seizures-induced axonal sprouting and transcription-dependent Bdnf repositioning in the model of temporal lobe epilepsy

et al. 2021

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“…There is an awareness that algorithms need to be resistant to morphological variability, object densities and variations in staining intensity. It is an active research area, and new algorithms try to address these issues (e.g., Ruszczycki et al, 2019; Shuvaev et al, 2017).…”

Section: Perspectives In Quantitative Morphologymentioning

confidence: 99%

Basic quantitative morphological methods applied to the central nervous system

Slomianka

2020

J of Comparative Neurology

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Generating numbers has become an almost inevitable task associated with studies of the morphology of the nervous system. Numbers serve a desire for clarity and objectivity in the presentation of results and are a prerequisite for the statistical evaluation of experimental outcomes. Clarity, objectivity, and statistics make demands on the quality of the numbers that are not met by many methods. This review provides a refresher of problems associated with generating numbers that describe the nervous system in terms of the volumes, surfaces, lengths, and numbers of its components. An important aim is to provide comprehensible descriptions of the methods that address these problems. Collectively known as designbased stereology, these methods share two features critical to their application. First, they are firmly based in mathematics and its proofs. Second and critically underemphasized, an understanding of their mathematical background is not necessary for their informed and productive application. Understanding and applying estimators of volume, surface, length or number does not require more of an organizational mastermind than an immunohistochemical protocol. And when it comes to calculations, square roots are the gravest challenges to overcome. Sampling strategies that are combined with stereological probes are efficient and allow a rational assessment if the numbers that have been generated are "good enough." Much may be unfamiliar, but very little is difficult. These methods can no longer be scapegoats for discrepant results but faithfully produce numbers on the material that is assessed. They also faithfully reflect problems that associated with the histological material and the anatomically informed decisions needed to generate numbers that are not only valid in theory. It is within reach to generate practically useful numbers that must integrate with qualitative knowledge to understand the function of neural systems.

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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 betweenBdnftranscription 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.

show abstract

Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images

Cited by 16 publications

References 36 publications

The interplay of seizures-induced axonal sprouting and transcription-dependent Bdnf repositioning in the model of temporal lobe epilepsy

The interplay of seizures-induced axonal sprouting and transcription-dependent Bdnf repositioning in the model of temporal lobe epilepsy

Basic quantitative morphological methods applied to the central nervous system

An important role of the interplay betweenBdnftranscription and histone acetylation in epileptogenesis

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