Identification of Zebrafish Calcium Toolkit Genes and their Expression in the Brain

Loss of Stim2 in zebrafish induces glaucoma-like phenotype

Calcium is involved in vision processes in the retina and implicated in various pathologies, including glaucoma. Rod cells rely on store-operated calcium entry (SOCE) to safeguard against the prolonged lowering of intracellular calcium ion concentrations. Zebrafish that lacked the endoplasmic reticulum Ca2+ sensor Stim2 (stim2 knockout [KO]) exhibited impaired vision and lower light perception-related gene expression. We sought to understand mechanisms that are responsible for vision impairment in stim2 KO zebrafish. The single-cell RNA (scRNA) sequencing of neuronal cells from brains of 5 days postfertilization larvae distinguished 27 cell clusters, 10 of which exhibited distinct gene expression patterns, including amacrine and γ-aminobutyric acid (GABA)ergic retinal interneurons and GABAergic optic tectum cells. Five clusters exhibited significant changes in cell proportions between stim2 KO and controls, including GABAergic diencephalon and optic tectum cells. Transmission electron microscopy of stim2 KO zebrafish revealed decreases in width of the inner plexiform layer, ganglion cells, and their dendrites numbers (a hallmark of glaucoma). GABAergic neuron densities in the inner nuclear layer, including amacrine cells, as well as photoreceptors significantly decreased in stim2 KO zebrafish. Our study suggests a novel role for Stim2 in the regulation of neuronal insulin expression and GABAergic-dependent vision causing glaucoma-like retinal pathology.

Identification of novel genetic loci related to dromedary camel (Camelus dromedarius) morphometrics, biomechanics, and behavior by genome-wide association studies

In the realm of animal breeding for sustainability, domestic camels have traditionally been valued for their milk and meat production. However, key aspects such as zoometrics, biomechanics, and behavior have often been overlooked in terms of their genetic foundations. Recognizing this gap, the present study perfomed genome-wide association analyses to identify genetic markers associated with zoometrics-, biomechanics-, and behavior-related traits in dromedary camels (Camelus dromedarius). 16 and 108 genetic markers were significantly associated (q < 0.05) at genome and chromosome-wide levels of significance, respectively, with zoometrics- (width, length, and perimeter/girth), biomechanics- (acceleration, displacement, spatial position, and velocity), and behavior-related traits (general cognition, intelligence, and Intelligence Quotient (IQ)) in dromedaries. In most association loci, the nearest protein-coding genes are linkedto neurodevelopmental and sensory disorders. This suggests that genetic variations related to neural development and sensory perception play crucial roles in shaping a dromedary camel's physical characteristics and behavior. In summary, this research advances our understanding of the genomic basis of essential traits in dromedary camels. Identifying specific genetic markers associated with zoometrics, biomechanics, and behavior provides valuable insights into camel domestication. Moreover, the links between these traits and genes related to neurodevelopmental and sensory disorders highlight the broader implications of domestication and modern selection on the health and welfare of dromedary camels. This knowledge could guide future breeding strategies, fostering a more holistic approach to camel husbandry and ensuring the sustainability of these animals in diverse agricultural contexts.

Lack of Stim2 Affects Vision-Dependent Behavior and Sensitivity to Hypoxia

Stromal interaction molecules (STIMs) are endoplasmic reticulum-resident proteins that regulate Ca2+ homeostasis and signaling by store-operated calcium entry (SOCE). The different properties and functions of STIM1 and STIM2 have been described mostly based on work in vitro. STIM2 knockout mice do not survive until adulthood. Therefore, we generated and characterized stim2a and stim2b double-knockout zebrafish. The (stim2a;stim2b)-/- zebrafish did not have any apparent morphological phenotype. However, RNA sequencing revealed 1424 differentially expressed genes. One of the most upregulated genes was annexin A3a, which is a marker of activated microglia. This corresponded well to an increase in Neutral Red staining in the in vivo imaging of the (stim2a;stim2b)-/- zebrafish brain. The lack of Stim2 decreased zebrafish survival under low oxygen conditions. Behavioral tests, such as the visual-motor response test and dark-light preference test, indicated that (stim2a;stim2b)-/- larvae might have problems with vision. This was consistent with the downregulation of many genes that are related to light perception. The periodic acid-Schiff staining of retina sections from adult zebrafish revealed alterations of the stratum pigmentosum, suggesting the involvement of a Stim2-dependent process in visual perception. Altogether, these data reveal new functions for Stim2 in the nervous system.

Neuronal Store-Operated Calcium Channels

The endoplasmic reticulum (ER) is the major intracellular calcium (Ca²⁺) storage compartment in eukaryotic cells. In most instances, the mobilization of Ca²⁺ from this store is followed by a delayed and sustained uptake of Ca²⁺ through Ca²⁺-permeable channels of the cell surface named store-operated Ca²⁺ channels (SOCCs). This gives rise to a store-operated Ca²⁺ entry (SOCE) that has been thoroughly investigated in electrically non-excitable cells where it is the principal regulated Ca²⁺ entry pathway. The existence of this Ca²⁺ route in neurons has long been a matter of debate. However, a growing body of experimental evidence indicates that the recruitment of Ca²⁺ from neuronal ER Ca²⁺ stores generates a SOCE. The present review summarizes the main studies supporting the presence of a depletion-dependent Ca²⁺ entry in neurons. It also addresses the question of the molecular composition of neuronal SOCCs, their expression, pharmacological properties, as well as their physiological relevance.

Effects of the herbicide glyphosate on fish from embryos to adults: a review addressing behavior patterns and mechanisms behind them

The use of agrochemicals has grown in recent years following the increase in agricultural productivity, to eliminate weeds that can compromise crop yields. The intensive use of these products combined with the lack of treatment of agricultural wastewater is causing contamination of the natural environments, especially the aquatics. Glyphosate [N-(phosphonomethyl) glycine] is the most commonly used herbicide in agriculture worldwide. Studies have shown that this compound is toxic to a variety of fish species at the concentrations of environmental relevance. Glyphosate-based herbicides can affect fish biochemical, physiological, endocrine, and behavioral pathways. Changes in behaviors such as foraging, escaping from predators, and courtship can compromise the survival of species and even communities. The behavior patterns of fish has been shown to be a sensitive tool for risk assessment. In this sense, this review summarizes and discusses the toxic effects of glyphosate and its formulations on the behavior of fish in different life stages. Additionally, behavioral impairments were associated with other negative effects of glyphosate such as energy imbalance, stress responses, AChE inhibition, and physiological and endocrine disturbances, which are evidenced and described in the literature. Graphical abstract.

6-Gingerol, a Major Constituent of Zingiber officinale Rhizoma, Exerts Anticonvulsant Activity in the Pentylenetetrazole-Induced Seizure Model in Larval Zebrafish

Zingiber officinale is one of the most frequently used medicinal herbs in Asia. Using rodent seizure models, it was previously shown that Zingiber officinale hydroethanolic extract exerts antiseizure activity, but the active constituents responsible for this effect have not been determined. In this paper, we demonstrated that Zingiber officinale methanolic extract exerts anticonvulsant activity in the pentylenetetrazole (PTZ)-induced hyperlocomotion assay in larval zebrafish. Next, we isolated 6-gingerol (6-GIN)-a major constituent of Zingiber officinale rhizoma. We observed that 6-GIN exerted potent dose-dependent anticonvulsant activity in the PTZ-induced hyperlocomotion seizure assay in zebrafish, which was confirmed electroencephalographically. To obtain further insight into the molecular mechanisms of 6-GIN antiseizure activity, we assessed the concentration of two neurotransmitters in zebrafish, i.e., inhibitory γ-aminobutyric acid (GABA) and excitatory glutamic acid (GLU), and their ratio after exposure to acute PTZ dose. Here, 6-GIN decreased GLU level and reduced the GLU/GABA ratio in PTZ-treated fish compared with only PTZ-bathed fish. This activity was associated with the decrease in grin2b, but not gabra1a, grin1a, gria1a, gria2a, and gria3b expression in PTZ-treated fish. Molecular docking to the human NR2B-containing N-methyl-D-aspartate (NMDA) receptor suggests that 6-GIN might act as an inhibitor and interact with the amino terminal domain, the glutamate-binding site, as well as within the ion channel of the NR2B-containing NMDA receptor. In summary, our study reveals, for the first time, the anticonvulsant activity of 6-GIN. We suggest that this effect might at least be partially mediated by restoring the balance between GABA and GLU in the epileptic brain; however, more studies are needed to prove our hypothesis.

Zebrafish as a Model for In-Depth Mechanistic Study for Stroke

Stroke is one of the world's leading causes of death and disability, posing enormous burden to the society. However, the pathogenesis and mechanisms that underlie brain injury and brain repair remain largely unknown. There's an unmet need of in-depth mechanistic research in this field. Zebrafish (Danio rerio) is a powerful tool in brain science research mainly due to its small size and transparent body, high genome synteny with human, and similar nervous system structures. It can be used to establish both hemorrhagic and ischemic stroke models easily and effectively through different ways. After the establishment of stroke model, research methods including behavioral test, in vivo imaging, and drug screening are available to explore mechanisms that underlie the brain injury and brain repair after stroke. This review focuses on the advantages and the feasibility of zebrafish stroke model, and will also introduce the key methods available for stroke studies in zebrafish, which may drive future mechanistic studies in the pursuit of discovering novel therapeutic targets for stroke patients.

Evolutionary context can clarify gene names: Teleosts as a case study

We developed an ex silico evolutionary-based systematic synteny approach to define and name the duplicated genes in vertebrates. The first convention for the naming of genes relied on historical precedent, the order in the human genome, and mutant phenotypes in model systems. However, total-genome duplication that resulted in teleost genomes required the naming of duplicated orthologous genes (ohnologs) in a specific manner. Unfortunately, as we review here, such naming has no defined criteria, and some ohnologs and their orthologs have suffered from incorrect nomenclature, thus creating confusion in comparative genetics and disease modeling. We sought to overcome this barrier by establishing an ex silico evolutionary-based systematic approach to naming ohnologs in teleosts. We developed software and compared gene synteny in zebrafish using the spotted gar genome as a reference, representing the unduplicated ancestral state. Using new criteria, we identified several hundred potentially misnamed ohnologs and validated the principle manually. Also see the video abstract here: https://youtu.be/UKNLa_TvSgY.

Cortisol rapidly stimulates calcium waves in the developing trunk muscle of zebrafish

Glucocorticoids (GCs) play a role in stress coping by activating the glucocorticoid receptor (GR), a ligand-bound transcription factor. GCs also exert rapid effects that are nongenomic by modulating second messenger signaling, including Ca²⁺. However, the mechanism of action of GCs in modulating cytoplasmic free calcium level ([Ca²⁺]i) is unclear. We hypothesized that cortisol increases ([Ca²⁺]i) in zebrafish (Danio rerio) muscle, and this is independent of GR activation. Indeed, cortisol rapidly stimulated ([Ca²⁺]i) rise in the developing trunk muscle (DTM), and this response was not abolished in the GR knockout zebrafish. The rapid cortisol-induced ([Ca²⁺]i) rise was reduced with EGTA, and completely abolished by the pharmacological inhibition of the calcium release-activated calcium channel (CRACC). Also, cortisol stimulation rapidly increased the expression of Orai1, the pore forming protein subunit of CRACC, in the DTM. Altogether, rapid nongenomic action of cortisol on muscle function may involve Ca²⁺ signaling by CRACC gating in zebrafish.

Knockout of stim2a Increases Calcium Oscillations in Neurons and Induces Hyperactive-Like Phenotype in Zebrafish Larvae

Stromal interaction molecule (STIM) proteins play a crucial role in store-operated calcium entry (SOCE) as endoplasmic reticulum Ca²⁺ sensors. In neurons, STIM2 was shown to have distinct functions from STIM1. However, its role in brain activity and behavior was not fully elucidated. The present study analyzed behavior in zebrafish (Danio rerio) that lacked stim2a. The mutant animals had no morphological abnormalities and were fertile. RNA-sequencing revealed alterations of the expression of transcription factor genes and several members of the calcium toolkit. Neuronal Ca²⁺ activity was measured in vivo in neurons that expressed the GCaMP5G sensor. Optic tectum neurons in stim2a^-/- fish had more frequent Ca²⁺ signal oscillations compared with neurons in wildtype (WT) fish. We detected an increase in activity during the visual-motor response test, an increase in thigmotaxis in the open field test, and the disruption of phototaxis in the dark/light preference test in stim2a^-/- mutants compared with WT. Both groups of animals reacted to glutamate and pentylenetetrazol with an increase in activity during the visual-motor response test, with no major differences between groups. Altogether, our results suggest that the hyperactive-like phenotype of stim2a^-/- mutant zebrafish is caused by the dysregulation of Ca²⁺ homeostasis and signaling.

stim2b Knockout Induces Hyperactivity and Susceptibility to Seizures in Zebrafish Larvae

In neurons, stromal interaction molecule (STIM) proteins regulate store-operated Ca²⁺ entry (SOCE) and are involved in calcium signaling pathways. However, STIM activity in neurological diseases is unclear and should be clarified by studies that are performed in vivo rather than in cultured cells in vitro. The present study investigated the role of neuronal Stim2b protein in zebrafish. We generated stim2b knockout zebrafish, which were fertile and had a regular lifespan. Using various behavioral tests, we found that stim2b^−/− zebrafish larvae were hyperactive compared with wild-type fish. The mutants exhibited increases in mobility and thigmotaxis and disruptions of phototaxis. They were also more sensitive to pentylenetetrazol and glutamate treatments. Using lightsheet microscopy, a higher average oscillation frequency and higher average amplitude of neuronal Ca²⁺ oscillations were observed in stim2b^−/− larvae. RNA sequencing detected upregulation of the annexin 3a and gpr39 genes and downregulation of the rrm2, neuroguidin, and homer2 genes. The latter gene encodes a protein that is involved in several processes that are involved in Ca²⁺ homeostasis in neurons, including metabotropic glutamate receptors. We propose that Stim2b deficiency in neurons dysregulates SOCE and triggers changes in gene expression, thereby causing abnormal behavior, such as hyperactivity and susceptibility to seizures.

Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B

Avian pathogenic Escherichia coli (APEC), a pathotype of extraintestinal pathogenic E. coli, causes one of the most serious infectious diseases of poultry and shares some common virulence genes with neonatal meningitis-associated E. coli. TonB-dependent receptors (TBDRs) are ubiquitous outer membrane β-barrel proteins; they play an important role in the recognition of siderophores during iron uptake. Here, in the APEC strain DE205B, we investigated the role of four putative TBDRs-ireA, 0007, 0008, and 2235-in iron uptake. Glutathione-S-transferase pulldown assays indicated that the proteins encoded by these genes directly interact with TonB. Moreover, the expression levels of all four genes were significantly upregulated under iron-depleted conditions compared with iron-rich conditions. The expression levels of several iron uptake-related genes were significantly increased in the ireA, 0007, 0008, and 2235 deletion strains, with the upregulation being the most prominent in the ireA deletion mutant. Furthermore, iron uptake by the ireA deletion strain was significantly increased compared to that by the wild-type strain. Moreover, a tonB mutant strain was constructed to study the effect of tonB deletion on the TBDRs. We found that regardless of the presence of tonB, the expression levels of the genes encoding the four TBDRs were regulated by fur. In conclusion, our findings indicated that ireA, 0007, 0008, and 2235 indeed encode TBDRs, with ireA having the most important role in iron uptake. These results should help future studies explore the mechanisms underlying the TonB-dependent iron uptake pathway.