Positive and negative regulator Junb : impact on chromatin remodeling and stress response

The AP-1 transcription factor is a central player in a multitude of biological processes from normal development to neoplastic transformation causing cancer. Junb, a subunit of AP-1, is special by the fact that it has at the same time activator and repressor functions. While positively regulated Junb target genes are principally required for proper vascular development, negative regulation of cytokines is of crucial importance to suppress pro-inflammatory and tumorigenic phenotypes. In this work, I approached this double-edge role of Junb by addressing two scientific questions: the mode of operation of Junb as negative transcription regulator and its impact in the ER stress response and apoptosis. First, I could show that, in addition to the general view of being an inhibitor of AP-1 by absorbing Jun activity, Junb also represses genes by epigenetic mechanisms. Although Junb did regulate neither the levels of histone acetylation nor the expression of HDACs, DNMTs and co-repressor complexes, few genes showed differential induction by HDAC inhibitors in wild-type and Junb-deficient fibroblasts. Presumably, these genes may be regulated through a yet to be identified Junb-dependent mechanism involving HDACs. Moreover, Junb regulated the DNA methylation of the imprinting control region of the gene H19. The molecular mechanisms involved in Junb-dependent epigenetic regulation appear to be novel and very unusual for an AP-1 member and remains to be fully solved. Secondly, I investigated the role of Junb in ER stress, a condition that has been described to contribute to hypoxia tolerance and tumor progression. Although Junb deficiency resulted in minor changes in the ER stress-triggered unfolded protein response (UPR), Junb-ablated MEFs were resistant towards apoptosis. Very high levels of activated pro-survival kinases resulted in aberrant post-translational modification of BH3-only proteins Bim and Bad and subsequent failure in mitochondria permeabilization and caspases activation. A soluble factor, most likely Pdgfb, elicited a pro-survival autocrine loop causative for the apoptosis resistance in absence of Junb. In summary, the negative regulation of cytokines and growth factors by Junb accounts for most of the deleterious effects observed in absence of Junb, except for the angiogenesis phenotype. Thus, the understanding of how Junb represses genes and the targeting of this specific mechanism would represent a promising therapeutic approach to treat in the future inflammatory disease and cancer

Computational modeling of motile cilia generated cerebral flow dynamics in zebrafish embryo

Background: Motile cilia are hair-like microscopic structures which move the fluids along the epithelial surfaces. Cilia cover a wide range of regions in the nervous system, such as the nasal cavity, spinal cord central canal, and brain ventricles. Motile cilia-driven cerebrospinal fluid (CSF) flow in the brain ventricles has an important role in the brain development. Embryos lacking motile cilia develop neurological defects due to altered CSF flow. Aim: To investigate the effect of motile-cilia motion on the altered CSF flow, and to understand the role of CSF flow in the brain development and physiology. Methods: The dynamics of motile-cilia driven flow is analyzed employing computational fluid dynamics (CFD) modeling. A 2D model is generated using the time-lapse microscopic movies showing movements of a fluorescently labeled motile-cilia in a zebrafish embryo (48-hour post-fertilization). The effects on the generated flow are elucidated by investigating the cilia beating angle, multiple cilia formations, and the phase difference between different ciliary beats. Results: Ciliary beating generated a directional flow in the form of a circulating vortex. The angle of ciliary beating significantly affected the flow velocity. As the angle between the wall and cilia decreases, the flow becomes more efficient by achieving higher velocities. Multiple cilia formations increased the flow velocity but the significance of multiple cilia is not as critical as the beating angle. Interestingly, phase difference between the multiple cilia beats increased the directional flow velocity. Conclusion: Motile-cilia generated flow dynamics are investigated, and it is concluded that out-of-phase multiple ciliary beating is the optimum form of beating in order to generate a directional flo

Computational Modeling of Motile Cilia-Driven Cerebrospinal Flow in the Brain Ventricles of Zebrafish Embryo.

Motile cilia are hair-like microscopic structures which generate directional flow to provide fluid transport in various biological processes. Ciliary beating is one of the sources of cerebrospinal flow (CSF) in brain ventricles. In this study, we investigated how the tilt angle, quantity, and phase relationship of cilia affect CSF flow patterns in the brain ventricles of zebrafish embryos. For this purpose, two-dimensional computational fluid dynamics (CFD) simulations are performed to determine the flow fields generated by the motile cilia. The cilia are modeled as thin membranes with prescribed motions. The cilia motions were obtained from a two-day post-fertilization zebrafish embryo previously imaged via light sheet fluorescence microscopy. We observed that the cilium angle significantly alters the generated flow velocity and mass flow rates. As the cilium angle gets closer to the wall, higher flow velocities are observed. Phase difference between two adjacent beating cilia also affects the flow field as the cilia with no phase difference produce significantly lower mass flow rates. In conclusion, our simulations revealed that the most efficient method for cilia-driven fluid transport relies on the alignment of multiple cilia beating with a phase difference, which is also observed in vivo in the developing zebrafish brain.Part of this work was supported by a FRIPRO grant from the Research Council of Norway (N.J.-Y. grant number 314189). The publication of this article was funded by the Qatar National Library

Elevated photic response is followed by a rapid decay and depressed state in ictogenic networks

Objective: The switch between nonseizure and seizure states involves profound alterations in network excitability and synchrony. In this study, we aimed to identify and compare features of neural excitability and dynamics across multiple zebrafish seizure and epilepsy models. Methods: Inspired by video-electroencephalographic recordings in patients, we developed a framework to study spontaneous and photically evoked neural and locomotor activity in zebrafish larvae, by combining high-throughput behavioral tracking and whole-brain in vivo two-photon calcium imaging. Results: Our setup allowed us to dissect behavioral and physiological features that are divergent or convergent across multiple models. We observed that spontaneous locomotor and neural activity exhibit great diversity across models. Nonetheless, during photic stimulation, hyperexcitability and rapid response dynamics were well conserved across multiple models, highlighting the reliability of photically evoked activity for high-throughput assays. Intriguingly, in several models, we observed that the initial elevated photic response is often followed by rapid decay of neural activity and a prominent depressed state. Elevated photic response and following depressed state in seizure-prone networks are significantly reduced by the antiseizure medication valproic acid. Finally, rapid decay and depression of neural activity following photic stimulation temporally overlap with slow recruitment of astroglial calcium signals that are enhanced in seizure-prone networks. Significance: We argue that fast decay of neural activity and depressed states following photic response are likely due to homeostatic mechanisms triggered by excessive neural activity. An improved understanding of the interplay between elevated and depressed excitability states might suggest tailored epilepsy therapies. Keywords: astroglia; calcium imaging; depressed state; elevated state; epilepsy; high-throughput behavior; hyperexcitability; photic stimulation; seizure; zebrafis

Notch/Her12 signalling modulates, motile/immotile cilia ratio downstream of Foxjla in zebrafish left-right organizer

undacao para a Ciencia e a Tecnologia PTDC/BEX-BID/1411/2014 Susana Santos Lopes Fundacao para a Ciencia e a Tecnologia FCT-ANR/BEX-BID/0153/2012 Sara Pestana Fundacao para a Ciencia e a Tecnologia PTDC/SAU-OBD/103981/2008 Andreia Vaz Fundacao para a Ciencia e a Tecnologia PD/BD/52420/2013 Raquel Jacinto Fundacao para a Ciencia e a Tecnologia SFRH/BPD/77258/2011 Barbara Tavares Fundacao para a Ciencia e a Tecnologia SFRH/BD/111611/2015 Pedro Sampaio Fundacao para a Ciencia e a Tecnologia IF/00951/2012 Susana Santos Lopes The funders had no role in study design, data collection and interpretation, or the on the decision to submit the work for publication.publishersversionpublishe

Ringers et al, 2021

Novel analytical tools reveal that local synchronization of cilia coincides with tissue-scale metachronal waves in zebrafish multiciliated epitheliaIn this attached zip file, there are1. an example dataset of cilia in the zebrafish nose in Matlab format (03-02-2017_0_0_aligned.mat) and its associated metadata (03-02-2017_0_0.json)2. an example dataset of cilia in the ependymal cells of teh zebrafish brain in Matlab format (06-08-2022_3_8.mat_aligned.mat) and its associated metadata (06-08-2022_3_8.json)3. all Matlab functions needed, downloaded from https://github.com/Jurisch-Yaksi-lab/Ringers-et-al on 12.01.202

Past, present and future of zebrafish in epilepsy research

Animal models contribute greatly to our understanding of brain development and function as well as its dysfunction in neurological diseases. Epilepsy research is a very good example of how animal models can provide us with a mechanistic understanding of the genes, molecules, and pathophysiological processes involved in disease. Over the course of the last two decades, zebrafish came in as a new player in epilepsy research, with an expanding number of laboratories using this animal to understand epilepsy and to discover new strategies for preventing seizures. Yet, zebrafish as a model offers a lot more for epilepsy research. In this viewpoint, we aim to highlight some key contributions of zebrafish to epilepsy research, and we want to emphasize the great untapped potential of this animal model for expanding these contributions. We hope that our suggestions will trigger further discussions between clinicians and researchers with a common goal to understand and cure epilepsy

Ringers et al, 2021

Novel analytical tools reveal that local synchronization of cilia coincides with tissue-scale metachronal waves in zebrafish multiciliated epitheliaIn this attached zip file, there are1. an example dataset of cilia in the zebrafish nose in Matlab format (03-02-2017_0_0_aligned.mat) and its associated metadata (03-02-2017_0_0.json)2. an example dataset of cilia in the ependymal cells of teh zebrafish brain in Matlab format (06-08-2022_3_8.mat_aligned.mat) and its associated metadata (06-08-2022_3_8.json)3. all Matlab functions needed, downloaded from https://github.com/Jurisch-Yaksi-lab/Ringers-et-al on 12.01.2023THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Jeong et al, 2022, Measurement of ciliary beating and fluid flow in the zebrafish adult telencephalon

In this dataset, we are providing MATLAB codes to analyse ciliary beating and cerebrospinal fluid flow in the zebrafish forebrain. Test datasets are also included. Please refer to the manuscript text Jeong et al, STAR protocol, 2022 for more details on how to use the codes and the expected outcomes.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV