Cloning of down-regulated genes under cold stress and identification of important genes related to cold tolerance in zebrafish (Danio rerio).

Low-temperature stress poses a significant risk to the survival of both cultivated and wild fish populations. Existing studies have found that the pre-acclimation of fishes to moderate cold stress can stimulate the activation of acclimation pathways, thereby enhancing their tolerance to cold stress. The fitness of fish relies heavily on appropriately controlled transcriptional reactions to environmental changes. Despite previous characterization of gene expression profiles in various fish species during cold acclimation, the specific genes responsible for essential functions in this process remain largely unknown, particularly the down-regulated genes induced by cold acclimation. To investigate the genes involved in cold acclimation, this study employed real-time quantitative PCR (RT-qPCR), molecular cloning, microinjection techniques, and cold stress experiments to determine the genes that play an essential part in cold acclimation. Consequently, 18 genes were discovered to be down-regulated in larval zebrafish experiencing cold stress. All 18 genes successfully detected overexpression in zebrafish at 96 and 126 hpf (fold change ≥3), which declined with the growth of zebrafish. Following microinjection, it was observed that her8a, cyp51, lss, txnipb, and bhlha9 had an adverse impact on the survival rate of zebrafish larvae under cold stress. These genes have been identified to play significant roles in various biological processes. For instance, bhlha9 has been found to be involved in both limb development and temperature sensing and her8a has been implicated in neural development. Additionally, cyp51 and lss have been identified as participants in the cholesterol synthesis pathway. Txnipb has been reported to induce cell apoptosis, thereby potentially influencing the survival rate of zebrafish larvae under cold stress. These findings offered crucial data for the analysis of molecular processes related to cold tolerance and the development of cold-resistant fish breeding.

Enhancment of zebrafish (Danio rerio) immune and antioxidant systems using medicinal plant extracts encapsulated in alginate-chitosan nanocapsules with slow sustained release.

This study aimed to screen 10 medicinal plant extracts on zebrafish (Danio rerio), evaluating their impact on the complement system, immunoglobulin M (IgM) levels, lysozyme, and peroxidase activity, while also enhancing their efficacy through the gradual release using alginate-chitosan nanocapsules. The prepared methanolic extracts were combined with fish feed. The fish were divided into 12 groups, including 10 treatment groups, a positive and a negative control group. Results showed varying impacts of the extracts on the immune and antioxidant systems, with Cinnamon (Cinnamon cassia) and Hypericum (Hypericum perforatum) extracts demonstrating the most significant effects. Subsequently, Cinnamon and Hypericum extract were encapsulated in alginate-chitosan nanocapsules to assess their impact on zebrafish immune parameters, separately and synergistically. Gradual release of the extracts from the nanocapsules was observed, with slower release at pH 2 compared to pH 7. Overall, Cinnamon and Hypericum extracts exhibited substantial immune system enhancement, and their encapsulation in nanocapsules improved their effects on zebrafish immune parameters. These findings suggest using these encapsulated extracts to enhance immune responses in aquatic organisms.

Effects of dietary indispensable amino acid deficiencies on feed intake in stomachless fish.

Evidence suggests that fish are more tolerant than mammals to imbalanced dietary amino acid profiles. However, the behavioral and physiological responses of fish to individual deficiencies in dietary indispensable amino acids (IDAA) remain unclear. This study examined how stomachless fish respond to diets deficient in limiting IDAA (lysine, methionine, and threonine), using Zebrafish (Danio rerio) as a model. The response to deficient diets was assessed based on; 1) growth performance and feeding efficiency; 2) feed intake; 3) expression of appetite-regulating hormones and nutrient-sensing receptors; and 4) muscle postprandial free amino acid (FAA) levels. There were 6 treatments, each with 3 replicate tanks. A semi-purified diet was formulated for each group. The CG diet was based on casein and gelatin, while the FAA50 diet had 50 % of dietary protein supplied with crystalline amino acids. Both were formulated to contain matching, balanced amino acid profiles. The remaining diets were formulated the same as the FAA50 diet, with minor adjustments to create deficiencies in selected IDAA. The (-) Lys, (-) Met, and (-) Thr diets had lysine, methionine, and threonine withheld from the FAA mix, respectively, and the Def diet was deficient in all three. The juvenile Zebrafish were fed to satiation 3 times daily from 21 to 50 days-post-hatch. Results showed that 50 % replacement of dietary protein with crystalline amino acids significantly reduced growth of juvenile Zebrafish. There were no significant differences in growth between the FAA50 group and groups that received deficient diets. The deficiency of singular IDAA did not induce significant changes in feed intake; however, the combined deficiency in the Def diet caused a significant increase in feed intake. This increased feed intake led to decreased feeding efficiency. A significant decrease in feeding efficiency was also observed in the (-) Lys group. There was an observed upregulation of neuropeptide Y (NPY), an orexigenic hormone, in the Def group. Overall, results from this study suggest stomachless fish increase feed intake when challenged with IDAA-deficient diets, and the regulation of NPY might play a role in this response.

Lessons in cognition: A review of maze designs and procedures used to measure spatial learning in fish.

The use of different mazes to assess spatial learning has become more common in fish behavior studies in recent decades. This increase in fish cognition research has opened the door to numerous possibilities for exciting and diverse questions, such as identifying ecological drivers of spatial cognition and understanding the role individual variation plays in navigational abilities. There are many different types of mazes, each with its own specific considerations, making it challenging to determine exactly which spatial test is the most relevant and appropriate for a particular experiment. Many spatial mazes, such as the T-maze and Y-maze, have been successfully adapted from rodent studies, particularly with respect to zebrafish, a widely accepted non-mammalian model in biomedical studies. Standardization across studies is increasing with these easily accessible maze designs, validating them for use in fish; however, variations in design (e.g., length of arms and scale) and procedure still exist, and the impact of these variations on results is largely unknown. The efforts to standardize mazes outside zebrafish work are also more limited. Other mazes have been developed specifically for use on fish, with design modifications varying widely, making it difficult to draw comparisons. In this review, we have highlighted the many design and procedural elements that should be considered for the acquisition of reliable behavioral data, with the goal of drawing readers' attention to aspects of experimentation that are often not given the careful consideration that they deserve. We then argue that additional focused research and reporting is needed to produce more reliable methods in spatial learning research across a broader range of subjects.

Toxicokinetics of a developmental toxicity test in zebrafish embryos and larvae: Relationship with drug exposure in humans and other mammals.

To study the effects of drugs on embryo/fetal development (EFD), developmental and reproductive toxicity studies in zebrafish (Danio rerio) embryos is expected to be an accepted alternative method to animal studies using mammals. However, there is a lack of clarity in the relationship between the concentration of developmental toxicity agents in whole embryos or larvae (Ce) and that in aqueous solution (Cw), and also between the amount of drug exposure required to cause developmental toxicity in zebrafish embryos or larvae and that required in mammals. Here, we measured Ce for developmental toxicity agents every 24 h starting at 24 h post fertilization (hpf). We found a high correlation (R 2: 0.87-0.96) between log [Ce/Cw] and the n-octanol-water distribution coefficient at pH 7 (logD) of each drug at all time points up to 120 hpf. We used this relationship to estimate the Ce values of the 21 positive-control reference drugs listed in ICH guidelines on reproductive and developmental toxicity studies (ICH S5). We then calculated the area under the Ce-time curve in zebrafish (zAUC) for each drug from the regression equation between log [Ce/Cw] and logD and compared it with the AUC at the no-observed-adverse-effect level in rats and rabbits and at the effective dose in humans described in ICH S5. The log of the calculated zAUC for the 14 drugs identified as positive in the zebrafish developmental toxicity test was relatively highly positively correlated with the log [AUC] for rats, rabbits, and humans. These findings provide important and positive information on the applicability of the zebrafish embryo developmental toxicity test as an alternative method of EFD testing. (267 words).

Skin mucosal immune parameters and expression of the immune-relevant genes in Danio rerio treated by white button mushroom (Agaricus bisporus).

This study evaluates using different levels of the white button mushroom powder (WBMP) on some mucosal innate immune parameters (lysozyme, protease, esterase, alkaline phosphatase activities, and total immunoglobulin levels), and the relative expression of some principal immune-relevant genes (lysozyme, TNF-α, and IL-1ß) in the zebra danio intestine. Zebrafish specimens (1.75 ± 0.25 g) were divided into experimental units based on the additives to a diet including 5, 10, and 20 g of WBMP per kilogram of food weight, alone or in conjunction with the antibiotic (10 mg/kg BW), and the AGRIMOS (1 g/kg food weight). Following the 11-day experimental duration, the skin mucus and intestine were sampled. To assess the immune gene expression, the real-time PCR detection system was conducted according to the ΔΔCt method using the IQ5 software (Bio-RAD). Results showed that all groups had a significant increase in terms of mucosal lysozyme activity compared to the control group. Examination of total immunoglobulin, protease, esterase, and ALP activity in fish under experimental treatment showed that there was no significant difference between the trial groups and the control groups. The most expression of the lysozyme gene was related to the group that was separately taken the lower concentration (5 g per kg of FW) of WBMP. In conclusion, the amount of 1% mushroom powder in the diet can improve its immune function. Our recommendation is that given the positive effects that mushroom powder added on the diet alone, avoid taking antibiotics for this purpose.

Effects of antimony on antioxidant system, damage indexes of blood-brain barrier and ultrastructure of zebrafish (Danio rerio).

Antimony (Sb) and its compounds can be harmful to people and are known to cause cancer, so they are a key pollutant to control. This study investigated the influence of antimony on non-enzymatic antioxidants and the blood-brain barrier (BBB) in zebrafish(Danio rerio), a model organism that shares a high degree of genetic similarity with humans. Zebrafish were exposed to different doses of antimony in water for 7, 18, and 30 days. The results indicated that antimony accumulated most in the liver, followed by the gills, flesh, and brain, with the accumulation increasing as the exposure duration extends. Additionally, under identical antimony concentrations, the buildup in the four tissues was positively correlated with the duration of exposure. After 18 days of exposure, the total antioxidant capacity (T-AOC) and endogenous non-enzymatic antioxidants vitamin C (VC) and vitamin E (VE) decreased as a result of antimony ingestion in zebrafish, although cysteine secretion was increased in the liver, gills, and brain. The structural integrity of the BBB was compromised by the elevation of ApoE4 and MMP-9 levels as a result of antimony exposure, which led to the breakdown of the basal lamina, tight junctions, and nerve fibers in the brain. At this injured region, 5-HT and MBP were also able to easily enter and leave the BBB, albeit at variable rates. Additionally, when the antimony exposure level reached 16.58 mg·L-1, antimony penetrated the BBB and bound to erythrocytes, causing their lysis.

Combined effects of polyethylene terephthalate and abamectin on enzymatic activity and histopathology response in juvenile zebrafish (Danio rerio).

One of the most pressing global environmental issues is the widespread abundance and distribution of microplastics (MPs). MPs can act as vectors for other contaminants in the environment making these small plastic particles hazardous for ecosystems. The presence of MPs in aquatic environments may pose threats to aquatic organisms that ingest them. This study examined effects of abamectin (ABM) and polyethylene terephthalate (PET) MP fragments on histopathological and enzymatic biomarkers in zebrafish (Danio rerio). Zebrafish were exposed for 96 h to pristine PET-MPs at concentrations of 5 mg/L and 10 mg/L, ABM alone at 0.006 mg/L, and the same concentration of ABM in the presence of PET-MPs in aquaria. Histopathological analysis revealed tissue content changes in liver and kidney in the presence of ABM individually and in combination with MPs. Results of enzymatic analysis showed that MPs increased the bioavailability and toxicity of pesticides due to inhibition of catalase (CAT) and acid phosphatase (ACP) enzymes. However, MPs did not affect the toxicity of ABM for glutathione s-transferase (GST) enzyme. Despite the inhibition of acetylcholinesterase (AChE) in MPs or ABM treatments, and some neurotoxicity, no change in activity of this enzyme and neurotoxicity was observed in the combined MPs and ABM treatments, although toxicity effects of MPs and ABM on zebrafish require more detailed studies.

Effects of 2-ethylhexyl diphenyl phosphate (EHDPP) on glycolipid metabolism in male adult zebrafish revealed by targeted lipidomic analyses.

The present study aims to evaluate the effects of 2-ethylhexyldiphenyl phosphate (EHDPP) on glycolipid metabolism in vivo. Adult male zebrafish were exposed to various concentrations (0, 1, 10, 100 and 250 µg/L) of EHDPP for 28 days, and changes in lipid and glucose levels were measured. Results indicated significant liver damages in the 100 and 250 µg/L EHDPP groups, which both exhibited significant decreases in hepatic somatic index (HSI), elevated activities of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in serum and liver, as well as hepatocyte vacuolation and nuclear pyknosis. Exposure to 100 and 250 µg/L EHDPP led to significant reductions in serum and liver cholesterol (TC), triglycerides (TGs), and lipid droplet deposition, indicating a significant inhibition of EHDPP on hepatic lipid accumulation. Lipidomic analyses manifested that 250 µg/L EHDPP reduced the levels of 103 lipid metabolites which belong to glycerides (TGs, diglycerides, and monoglycerides), fatty acyles (fatty acids), sterol lipids (cholesterol, bile acids), sphingolipids, and glycerophospholipids, and downregulated genes involved in de novo synthesis of fatty acids (fas, acc, srebp1, and dagt2), while upregulated genes involved in fatty acid ß-oxidation (pparα and cpt1). KEGG analyses revealed that EHDPP significantly disrupted glycerolipid metabolism, steroid biosynthesis and fatty acid biosynthesis pathways. Collectively, the results showed that EHDPP induced lipid reduction in zebrafish liver, possibly through inhibiting lipid synthesis and disrupting glycerolipid metabolism. Our findings provide a theoretical basis for evaluating the ecological hazards and health effects of EHDPP on glycolipid metabolism.

Anticonvulsant and anxiolytic-like potential of the essential oil from the Ocimum basilicum Linn leaves and its major constituent estragole on adult zebrafish (Danio rerio).

The Ocimum species present active compounds with the potential to develop drugs for treating chronic disease conditions, such as anxiety and seizures. The present study aims to investigate the anticonvulsant and anxiolytic-like effect of the essential oil from O. basilicum Linn (OEFOb) leaves and its major constituent estragole (ES) in vivo on adult zebrafish (aZF) and in silico. The aZF were treated with OEFOb or ES or vehicle and submitted to the tests of toxicity, open-field, anxiety, and convulsion and validated the interactions of the estragole on the involvement of GABAergic and serotonergic receptors by molecular docking assay. The results showed that the oral administration of OEFOb and ES did not have a toxic effect on the aZF and showed anxiolytic-like effects with the involvement of GABAA, 5-HT1, 5-HT2A/2C and 5-HT3A/3B as well on anxiety induced by alcohol withdrawal. The OEFOb and ES showed anticonvulsant potential attenuating the seizures induced by pentylenetetrazole (PTZ) by modulation of the GABAA system. Both anxiolytic and anticonvulsant effects were corroborated by the potential of the interaction of ES by in silico assay. These study samples demonstrate the pharmacological evidence and potential for using these compounds to develop new anxiolytic and anticonvulsant drugs.

Design and Synthesis of Novel N-Benzylidene Derivatives of 3-Amino-4-imino-3,5-dihydro-4H-chromeno[2,3-d]pyrimidine under Microwave, In Silico ADME Predictions, In Vitro Antitumoral Activities and In Vivo Toxicity.

The synthesis of a series of new N-benzylidene derivatives of 3-amino-4-imino-3,5-dihydro-4H-chromeno[2,3-d]pyrimidine 10(a-l) bearing two points of molecular diversity is reported. These new compounds were synthesized in five steps including two steps under microwave dielectric heating. They were fully characterized using 1H and 13C NMR, FTIR and HRMS. The in silico physicochemical properties of compounds 10(a-l) were determined according to Lipinski's rules of five (RO5) associated with the prediction of their bioavailability. These new compounds 10(a-l) were tested for their antiproliferative activities in fibroblasts and eight representative human tumoral cell lines (Huh7 D12, Caco2, MDA-MB231, MDA-MB468, HCT116, PC3, MCF7 and PANC1). Among them, the compounds 10h and 10i showed sub-micromolar cytotoxic activity on tumor cell lines (0.23 < IC50 < 0.3 µM) and no toxicity on fibroblasts (IC50 > 25 µM). A dose-dependent inhibition of Store-Operated Ca+2 Entry (SOCE) was observed in the HEK293 cell line with 10h. In vitro embryotoxicity and angiogenesis on the mCherry transgenic zebrafish line showed that 10h presented no toxic effect and no angiogenic effect on embryos with a dose of 5 µM at 72 hpf.

Comparison of developmental toxicity of graphene oxide and graphdiyne to zebrafish larvae.

Graphdiyne (GDY) is a new member of family of carbon-based 2D nanomaterials (NMs), but the environmental toxicity is less investigated compared with other 2D NMs, such as graphene oxide (GO). In this study, we compared with developmental toxicity of GO and GDY to zebrafish larvae. It was shown that exposure of zebrafish embryos from 5 h post fertilization to GO and GDY for up to 5 days decreased hatching rate and induced morphological deformity. Behavioral tests indicated that GO and GDY treatment led to hyperactivity of larvae. However, blood flow velocity was not significantly affected by GO or GDY. RNA-sequencing data revealed that both types of NMs altered gene expression profiles as well as gene ontology terms and KEGG pathways related with metabolism. We further confirmed that the NMs altered the expression of genes related with lipid droplets and autophagy, which may be account for the delayed development of zebrafish larvae. At the same mass concentrations, GO induced comparable or even larger toxic effects compared with GDY, indicating that GDY might be more biocompatible compared with GO. These results may provide novel understanding about the environmental toxicity of GO and GDY in vivo.

Combined toxic effects of polyethylene microplastics and lambda-cyhalothrin on gut of zebrafish (Danio rerio).

Microplastics (MPs), which are prevalent and increasingly accumulating in aquatic environments. Other pollutants coexist with MPs in the water, such as pesticides, and may be carried or transferred to aquatic organisms, posing unpredictable ecological risks. This study sought to assess the adsorption of lambda-cyhalothrin (LCT) by virgin and aged polyethylene MPs (VPE and APE, respectively), and to examine their influence on LCT's toxicity in zebrafish, specifically regarding acute toxicity, oxidative stress, gut microbiota and immunity. The adsorption results showed that VPE and APE could adsorb LCT, with adsorption capacities of 34.4 mg∙g-1 and 39.0 mg∙g-1, respectively. Compared with LCT exposure alone, VPE and APE increased the acute toxicity of LCT to zebrafish. Additionally, exposure to LCT and PE-MPs alone can induce oxidative stress in the zebrafish gut, while combined exposure can exacerbate the oxidative stress response and intensify intestinal lipid peroxidation. Moreover, exposure to LCT or PE-MPs alone promotes inflammation, and combined exposure leads to downregulation of the myd88-nf-κb related gene expression, thus impacting intestinal immunity. Furthermore, exposure to APE increased LCT toxicity to zebrafish more than VPE. Meanwhile, exposure to PE-MPs and LCT alone or in combination has the potential to affect gut microbiota function and alter the abundance and diversity of the zebrafish gut flora. Collectively, the presence of PE-MPs may affect the toxicity of pesticides in zebrafish. The findings emphasize the importance of studying the interaction between MPs and pesticides in the aquatic environment.

Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums.

Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (ß) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.

Current Status of the Zebrafish Euthanasia and Humane Endpoint in the Republic of Korea and Guideline Suggestion from Nationwide Expert Elicitation: A Model for Other Countries.

Since its introduction as a model organism in the 1980s, the use of zebrafish (Danio rerio) in research has expanded worldwide. Despite its now widespread use in research, guidelines to safeguard the ethical treatment of zebrafish, particularly with regard to euthanasia and humane endpoint practices, remain inadequate. One well-recognized example is the use of excess tricaine methanesulfonate (MS-222) as a means to euthanize zebrafish, regardless of life stage. In this study, through nationwide expert elicitation, we provide a detailed account of zebrafish research practices within the Republic of Korea and the challenges of implementing appropriate methods for euthanasia as a humane endpoint, with many opting for hypothermic shock. We report a local expert consensus for establishing national guidelines to improve zebrafish welfare and good research practice. Suggestions and recommendations for national guidelines were offered. Taken together, our findings raise awareness broadly among zebrafish research practitioners in the field, offer an accurate account of the welfare and treatment of zebrafish in research within the Republic of Korea, and advocate for the development and implementation of national guidelines. As such, our study is useful as a model to adopt the expert elicitation approach to investigate, quantify, and address welfare concerns in zebrafish research, and to establish best practice guidelines.

Potential of the Blue Calm® food supplement in the treatment of alcohol withdrawal-induced anxiety in adult zebrafish (Danio rerio).

Alcohol use disorder (AUD) is characterized by a set of behavioral, cognitive, nutritional, and physiological phenomena derived from the uncontrolled use of alcoholic beverages. There are cases in which AUD is associated with anxiety disorder, and when untreated, it requires careful pharmacotherapy. Blue Calm® (BC) is a food supplement indicated to aid restorative sleep, which has traces of medicinal plant extracts, as well as myo-inositol, magnesium bisglycinate, taurine, and L-tryptophan as its main chemical constituents. In this context, this study aimed to evaluate the potential of the BC in the treatment alcohol withdrawal-induced anxiety in adult zebrafish (aZF). Initially, BC was submitted to antioxidant activity against 2,2-diphenyl-1-picrylhydrazyl radical. Subsequently, the aZF (n = 6/group) were treated with BC (0.1 or 1 or 10 mg/mL; 20 µL; p.o.), and the sedative effect and acute toxicity (96 h) were evaluated. Then, the anxiolytic-like effect and the possible GABAergic mechanism were analyzed through the Light & Dark Test. Finally, BC action was evaluated for treating alcohol withdrawal-induced anxiety in aZF. Molecular docking was performed to evaluate the interaction of the major chemical constituents of BC with the GABAA receptor. BC showed antioxidant potential, a sedative effect, was not toxic, and all doses of BC had an anxiolytic-like effect and showed potential for the treatment of alcohol withdrawal-induced anxiety in aZF. In addition to the anxiolytic action, the main chemical constituents of BC were confirmed in the molecular docking, thus suggesting that BC is an anxiolytic that modulates the GABAergic system and has pharmacological potential for the treatment of alcohol withdrawal-induced anxiety.

The uses of zebrafish (Danio rerio) as an in vivo model for toxicological studies: A review based on bibliometrics.

An in vivo model is necessary for toxicology. This review analyzed the uses of zebrafish (Danio rerio) in toxicology based on bibliometrics. Totally 56,816 publications about zebrafish from 2002 to 2023 were found in Web of Science Core Collection, with Toxicology as the top 6 among all disciplines. Accordingly, the bibliometric map reveals that "toxicity" has become a hot keyword. It further reveals that the most common exposure types include acute, chronic, and combined exposure. The toxicological effects include behavioral, intestinal, cardiovascular, hepatic, endocrine toxicity, neurotoxicity, immunotoxicity, genotoxicity, and reproductive and transgenerational toxicity. The mechanisms include oxidative stress, inflammation, autophagy, and dysbiosis of gut microbiota. The toxicants commonly evaluated by using zebrafish model include nanomaterials, arsenic, metals, bisphenol, and dioxin. Overall, zebrafish provide a unique and well-accepted model to investigate the toxicological effects and mechanisms. We also discussed the possible ways to address some of the limitations of zebrafish model, such as the combination of human organoids to avoid species differences.

Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies.

PURPOSE OF REVIEW: GWAS, as a largely correlational analysis, requires in vitro or in vivo validation. Zebrafish (Danio rerio) have many advantages for studying the genetics of human diseases. Since gene editing in zebrafish has been highly valuable for studying embryonic skeletal developmental processes that are prenatally or perinatally lethal in mammalian models, we are reviewing pros and cons of this model. RECENT FINDINGS: The true power for the use of zebrafish is the ease by which the genome can be edited, especially using the CRISPR/Cas9 system. Gene editing, followed by phenotyping, for complex traits such as BMD, is beneficial, but the major physiological differences between the fish and mammals must be considered. Like mammals, zebrafish do have main bone cells; thus, both in vivo stem cell analyses and in vivo imaging are doable. Yet, the "long" bones of fish are peculiar, and their bone cavities do not contain bone marrow. Partial duplication of the zebrafish genome should be taken into account. Overall, small fish toolkit can provide unmatched opportunities for genetic modifications and morphological investigation as a follow-up to human-first discovery.

Validating post-enrichment steps in environmental RNA analysis for improving its availability from water samples.

Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish (Danio rerio) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring.

Identification and characterization of long non-coding RNA (lncRNA) in cypermethrin and chlorpyrifos exposed zebrafish (Danio rerio) brain.

Pesticides, such as cypermethrin (CYP) and chlorpyrifos (CPF), are widely used around the world and are known to cause toxicological effects in the brains of fish and other non-target organisms. Long non-coding RNAs (LncRNAs) are a new class of non-coding RNAs that are highly expressed in the brain and play crucial roles in brain function by regulating gene expression. Many studies have investigated the toxic effects of CYP and CPF on the brain. However, no study has been conducted on the relationship between LncRNAs and the toxicity caused by these chemicals. Therefore, this study aimed to determine changes in the lncRNA expression profile in the brains of fish exposed to CYP and CPF. Out of a total of 482 lncRNAs that were differentially expressed between control and CPF groups, 53 were found to be up-regulated, and 429 were down-regulated. Similarly, among the 200 lncRNAs differentially expressed between the control and CYP groups, 71 were up-regulated, and 129 were down-regulated. Additionally, 268 differentially expressed lncRNAs were identified between CYP and CPF groups, with 240 being up-regulated and the rest being down-regulated. In addition, LncRNAs expressed from fish brains exposed to CYP and CPF were found to regulate multiple signaling pathways, including MAPK, FoxO, PPAR, TGF-ß, and Wnt signaling pathways.