Zebrafish as a model system to study DNA damage and repair

Indigo dyes: Toxicity, teratogenicity, and genotoxicity studies in zebrafish embryos

Wastewater released by textile dyeing industries is a major source of pollution. Untreated wastewater released from indigo dyeing operations affects aquatic ecosystems and threatens their biodiversity. We have assessed the toxicity of natural and synthetic indigo dye in zebrafish embryos, using the endpoints of teratogenicity, genotoxicity, and histopathology. The zebrafish embryo toxicity test (ZFET) was conducted, exposing embryos to ten concentrations of natural and synthetic indigo dyes; the 96-hour LC50 values were approximately 350 and 300 mg/L, respectively. Both dyes were teratogenic, causing egg coagulation, tail detachment, yolk sac edema, pericardial edema, and tail bend, with no significant difference in effects between the natural and synthetic dyes. Both dyes were genotoxic (using comet assay for DNA damage). Real-time RT-PCR studies showed upregulation of the DNA-repair genes FEN1 and ERCC1. Severe histological changes were seen in zebrafish larvae following exposure to the dyes. Our results show that indigo dyes may be teratogenic and genotoxic to aquatic organisms, underscoring the need for development of sustainable practices and policies for mitigating the environmental impacts of textile dyeing.

Thallium(I) induces a prolonged inhibition of (6-4)photoproduct binding and UV damage excision repair activities in zebrafish (Danio rerio) embryos via protein inactivation

Cyclobutane pyrimidine dimer (CPD) and (6-4)photoproduct (6-4 PP) are two major types of UV-induced DNA lesion and 6-4 PP is more mutagenic than CPD. Activated by lesion detection, nucleotide excision repair (NER) eliminates CPDs and 6-4 PPs. Thallium (Tl) is a toxic metal existing primarily as Tl+ in the aquatic environment. Ingestion of Tl+-contaminated foods and water is a major route of human poisoning. As Tl+ may inhibit enzyme activities via binding to sulfhydryl groups, this study explored if Tl+ could intensify UV mutagenicity by inactivating NER-linked damage recognition factors using zebrafish (Danio rerio) embryo as a model system. Incubation of Tl+ (as thallium nitrate) at 0.1-0.4 μg/mL with zebrafish extracts for 20 min caused a concentration-dependent inhibition of 6-4 PP binding activities as shown by a photolesion-specific band shift assay, while CPD binding activities were insensitive to Tl+. The ability of Tl+ to suppress 6-4 PP detection was stronger than that of Hg2+. Exposure of zebrafish embryos at 1 h post fertilization (hpf) to Tl+ at 0.4-1 μg/mL for 9 or 71 h also specifically inhibited 6-4 PP detection, indicating that Tl+ induced a prolonged inhibition of 6-4 PP sensing ability primarily via its direct interaction with damage recognition molecules. Tl+-mediated inhibition of 6-4 PP binding in embryos at distinct stages resulted in a suppression of NER capacity monitored by a transcription-based DNA repair assay. Our results revealed the potential of Tl+ to enhance UV mutagenicity by disturbing the removal of 6-4 PP through repressing the lesion detection step of NER.

Tritiated thymidine induces developmental delay, oxidative stress and gene overexpression in developing zebrafish (Danio rerio)

Tritium is a betta emitter radionuclide. Being an isotope of hydrogen, it is easily transferred to different environmental compartments, and to human and non-human biota. Considering that tritium levels are expected to rise in the upcoming decades with the development of nuclear facilities producing tritium using fission processes, investigating the potential toxicity of tritium to human and non-human biota is necessary. Tritiated thymidine, an organic form of tritium, has been used in this study to assess its toxicity on fish embryo development. Zebrafish embryos (3.5 hpf; hours post fertilization) have been exposed to tritiated thymidine at three different activity concentrations (7.5; 40; 110 kBq/mL) for four days. These experiments highlighted that zebrafish development was affected by the exposure to organic tritium, with smaller larvae at 3 dpf after exposure to the two lowest dose rates (22 and 170 µGy/h), a delayed hatching after exposure to the two highest dose rates (170 and 470 µGy/h), an increase in the spontaneous tail movement (1 dpf) and a decrease in the heartbeat (3 dpf) after exposure to the highest dose rate. The results also highlighted an increase in ROS production in larvae exposed to the intermediate dose rate. A dysregulation of many genes, involved in apoptosis, DNA repair or oxidative stress, was also found after 1 day of exposure to the lowest tritium dose rate. Our results thus suggest that exposure to tritiated thymidine from a dose rate as low as 22 µGy/h can lead to sublethal effects, with an effect on the development, dysregulation of many genes and increase of the ROS production. This paper provides valuable information on toxic effects arising from the exposure of fish to an organic form of tritium, which was the main objective of this study.

Unraveling DNA Repair Processes In Vivo: Insights from Zebrafish Studies

The critical role of the DNA repair system in preserving the health and survival of living organisms is widely recognized as dysfunction within this system can result in a broad range of severe conditions, including neurodegenerative diseases, blood disorders, infertility, and cancer. Despite comprehensive research on the molecular and cellular mechanisms of DNA repair pathways, there remains a significant knowledge gap concerning these processes at an organismal level. The teleost zebrafish has emerged as a powerful model organism for investigating these intricate DNA repair mechanisms. Their utility arises from a combination of their well-characterized genomic information, the ability to visualize specific phenotype outcomes in distinct cells and tissues, and the availability of diverse genetic experimental approaches. In this review, we provide an in-depth overview of recent advancements in our understanding of the in vivo roles of DNA repair pathways. We cover a variety of critical biological processes including neurogenesis, hematopoiesis, germ cell development, tumorigenesis, and aging, with a specific emphasis on findings obtained from the use of zebrafish as a model system. Our comprehensive review highlights the importance of zebrafish in enhancing our understanding of the functions of DNA repair systems at the organismal level and paves the way for future investigations in this field.

Quality of fish eggs and production of androgenetic and gynogenetic doubled haploids (DHs)

Induced development of haploid embryos (H) with only paternal (androgenesis) or maternal (gynogenesis) chromosomes requires irradiation of eggs before fertilization or activation of eggs with irradiated spermatozoa, respectively. To provide doubled haploids (DHs), androgenetic and gynogenetic haploid zygotes need to be subjected to the thermal or high hydrostatic pressure (HHP) shock to suppress the first mitotic cleavage and to double paternal or maternal haploid set of chromosomes. Androgenesis and mitotic gynogenesis (mito-gynogenesis) result in the generation of fully homozygous individuals in a single generation. DHs have been utilized in selective breeding programs, in studies concerning the phenotypic consequences of recessive alleles and to evaluate the impact of sex chromosomes on the early ontogeny. Moreover, the use of DHs for the NGS approach radically improves de novo the assembly of the genomes. However, reduced survival of the doubled haploids limits the wide application of androgenotes and gynogenotes. The high mortality of DHs may be only partly explained by the expression of recessive traits. Observed inter-clutch variation in the survival of DHs developing in eggs originating from different females make it necessary to take a closer look at the quality of the eggs used during induced androgenesis and gynogenesis. Moreover, the developmental competence of eggs that are subjected to irradiation before fertilization in order to deactivate maternal chromosomes when undergoing induced androgenesis and exposed to the physical shock after fertilization that leads to the duplication of the zygotes in both mito-gynogenesis and androgenesis may be also altered as irradiation and sublethal values of temperatures and hydrostatic pressure are considered as harmful for the cell organelles and biomolecules. Here, recently provided results concerning the morphological, biochemical, genomic, and transcriptomic characteristics of fish eggs showing high and low competence for androgenesis and mito-gynogenesis are reviewed.

Susceptibility of DNA damage recognition activities linked to nucleotide excision and mismatch repair in zebrafish (Danio rerio) early and mid-early embryos to 2.5 to 4.5 °C heat stress

Fish at early life stages are sensitive to temperature change because of their narrower temperature tolerance ranges. Initiated by damage detection, DNA mismatch repair (MMR) and nucleotide excision repair (NER) maintain genome integrity respectively by eliminating mismatched nucleotides and helix-distorting DNA lesions. As discharge of heated effluent from power plants may elevate water temperatures to only 2 to 6 °C higher than ambient, this study explored if temperatures within this range affected MMR and NER-linked damage detection activities in fish embryos using zebrafish (Danio rerio) embryo as a model organism. Exposure of early embryos at 10 h post fertilization (hpf) to a warmer temperature at + 4.5 °C for 30 min enhanced damage recognition activities targeting UV-induced cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts (6-4PPs) that distorted helical structures. Conversely, photolesions sensing activities were inhibited in 24 hpf mid-early embryos under the same stress conditions. A much higher temperature at + 8.5 °C imposed similar effects on UV damage detection. A mild heat stress at + 2.5 °C for 30 min, however, repressed both CPD and 6-4PP binding activities in 10 and 24 hpf embryos. Inhibition of damage recognition under mild heat stress impeded the overall NER capacity evidenced by a transcription-based repair assay. Warmer water temperatures at + 2.5 and + 4.5 °C also inhibited G-T mismatch binding activities in 10 and 24 hpf embryos, but G-T recognition was more sensitive to + 4.5 °C stress. Inhibition of G-T binding partially correlated with a downregulation of Sp1 transcription factor activity. Our results showed the potential of water temperature elevation within 2 to 4.5 °C to disturb DNA damage repair in fish at embryonic stages.

Ecogenotoxicity of environmentally relevant atrazine concentrations: A threat to aquatic bioindicators

Atrazine (ATZ) is a herbicide that is frequently present in surface waters and may result in damage to the health of various organisms, including humans. However, most scientific literature reports injuries caused by ATZ at high concentrations, which are not found in the environment. Therefore, the scope of this study was to investigate the impacts of realistic concentrations of ATZ found in surface waters (1, 2, 5, 10, 15 and 20 μg/L) using the bioindicators Allium cepa, Daphnia magna and zebrafish (Danio rerio). ATZ elicited a genotoxic effect in A. cepa, manifested by the induction of chromosomal aberrations, and a mutagenic effect with increased incidence of micronuclei formation, promotion of cell death and reduction in nuclear size revealed by flow cytometry analysis. D. magna exposed to 10, 15 and 20 μg/L of ATZ showed significant reduction in body size after 21 days, delayed first-brood release, decreased egg production and total offspring, as well as swimming behavioral changes. ATZ exposure promoted physiological and developmental alterations in zebrafish embryos, including an increased spontaneous movement rate, which led to premature hatching at all concentrations investigated. Increase in total body length, decrease of the yolk sac area, pericardial edema and higher heart rate were also detected in ATZ-treated zebrafish. In summary, environmentally relevant concentrations of ATZ can induce substantial alterations in the three bioindicators investigated. This study evidences the deleterious effects of ATZ on three aquatic bioindicators employing established and current techniques, and may contribute to elucidate the risks caused by this widely used herbicide even at low concentrations and short-to-medium-term exposure.

DNA repair genes play a variety of roles in the development of fish embryos

Embryogenesis is one of the most important life stages because it determines an organism's healthy growth. However, embryos of externally fertilizing species, such as most fish, are directly exposed to the environment during development and may be threatened by DNA damaging factors (pollutants, UV, reactive oxygen species). To counteract the negative effects of DNA fragmentation, fish embryos evolved complex damage response pathways. DNA repair pathways have been extensively studied in some fish species, such as zebrafish (Danio rerio). Our literature review, on the other hand, revealed a paucity of knowledge about DNA damage response and repair in non-model aquaculture fish species. Further, several pieces of evidence underlie the additional role of DNA repair genes and proteins in organogenesis, spatiotemporal localization in different tissue, and its indispensability for normal embryo development. In this review, we will summarize features of different DNA repair pathways in course of fish embryo development. We describe how the expression of DNA repair genes and proteins is regulated during development, their organogenetic roles, and how the expression of DNA repair genes changes in response to genotoxic stress. This will aid in addressing the link between genotoxic stress and embryo phenotype. Furthermore, available data indicate that embryos can repair damaged DNA, but the effects of early-life stress may manifest later in life as behavioral changes, neoplasia, or neurodegeneration. Overall, we conclude that more research on DNA repair in fish embryos is needed.

Biocompatible, Biodegradable, and Improved Fluorescent Silicon Quantum Dots for Zebrafish Imaging

One of the greatest benefits of nanomedicine elucidated to date includes the non-invasive tracking and monitoring of living organisms by the selective uptake of harmless metallic nanoparticles. Several nanoscale probes have been employed for biomolecular imaging. Among them, fluorescent nanoscale silicon materials have been recently established with a strong and safe potential for bioimaging and biosensing applications due to their bright fluorescence coupled with strong photostability, biocompatibility and negligible toxicity. Herein, we developed high-quality silicon nanomaterials (4–5 nm; SiNPs) as biological fluorescent probes for bioimaging of living organisms through an easy aquatic synthesis method with a quantum yield of ∼8%. In this regard, we report that the presently synthesized SiNPs-based sensors/probes are attractive materials for solvent-based fluorescence measurements and are biocompatible, non-toxic, highly photo-stable and pH stable. Most importantly, their fluorescence lifetime is much longer than that of native probes in living cells. Thus, these presently formulated SiNPs are improved fluorescent probes for in vivo biological imaging in zebra fish embryos as well as numerous other living organisms and, thus, should be further studied.

2,4-Dichlorophenoxyacetic acid (2,4-D) affects DNA integrity and retina structure in zebrafish larvae

Monitoring the potential risk of herbicides in non-target organisms is a crucial issue for environmental safety. 2,4-D is an herbicide of high environmental relevance that has been shown to exert toxic effects to soil and aquatic biota. In the present study, we investigated the possible genotoxic and retinal development effects of 2,4-dichlorophenoxyacetic acid (2,4-D) herbicide in early life stages zebrafish (Danio rerio). Genotoxicity was evaluated by measuring DNA damage using the comet assay and also by the mRNA expression of genes implicated in apoptosis and/or DNA repair. Retinal development toxicity was evaluated with histological approach. The results obtained revealed that 2,4-D alters DNA integrity of zebrafish larvae. Moreover, transcriptomic data showed a significant induction of p-53 and casp-3 genes and a significant decrease of lig-4 in larvae exposed to the highest tested concentration of 2,4-D (0.8 mg/L). This suggested that p-53 gene regulates the process of DNA repair and apoptosis with increased levels of 2,4-D. The histopathological analysis revealed that early exposure to 2,4-D damaged the structure of larvae retina. Overall, this study is the first to report the DNA damage, casp-3, lig-4 and p-53 regulation, as well as the ocular developmental toxicity in zebrafish larvae at environmentally relevant concentrations of 2,4-D herbicide.

Aluminum (Al) causes a delayed suppression of nucleotide excision repair (NER) capacity in zebrafish (Danio rerio) embryos via disturbance of DNA lesion detection

Aluminum (Al) is extensively used for making cooking utensils and its presence in the aquatic environment may occur through acid mine drainage and wastewater discharge. Al is known to induce genotoxicity in human cells, rodents, and fish. Nucleotide excision repair (NER) eliminates helix-twisting DNA lesions such as UV-induced dipyrimidine photoproducts. Because our earlier investigation revealed the operation of NER in zebrafish (Danio rerio) embryos, this study explored if inhibition of NER could be a mechanism of Al-induced genotoxicity using zebrafish embryo as a model system. An acute fish embryo toxicity test indicated that Al (as aluminum sulfate) at 2-15 mg/L were nonlethal to zebrafish embryos, yet exposure of embryos at 1 h post fertilization (hpf) to Al at 10-15 mg/L for 71 h significantly repressed their NER capacity monitored by a transcription-based DNA repair assay. Band shift analysis indicated a higher sensitivity of (6-4) photoproduct (6-4PP) than cyclobutane pyrimidine dimer (CPD) detecting activities to Al, reflecting the preferential influence of Al on the detection of strongly distorted DNA lesions. Time-course experiments showed a delayed response of NER to Al as repair machinery was unaffected by Al at 15 mg/L following a 35-h exposure, while Al treatment for the same period obviously inhibited 6-4PP binding activities although the gene expression of damage recognition factors remained active. Inhibition of 6-4PP detection blocked downstream lesion incision/excision detected by a terminal deoxy transferase-mediated end labeling assay. As the disturbance of damage sensing preceded that of the overall repair process, Al exposure was believed to downregulate NER capacity by inhibiting the activities of lesion detection proteins. Our results revealed the ability of Al to enhance its genotoxicity by suppressing NER capacity.

Teleost Fish and Organoids: Alternative Windows Into the Development of Healthy and Diseased Brains

The variety in the display of animals’ cognition, emotions, and behaviors, typical of humans, has its roots within the anterior-most part of the brain: the forebrain, giving rise to the neocortex in mammals. Our understanding of cellular and molecular events instructing the development of this domain and its multiple adaptations within the vertebrate lineage has progressed in the last decade. Expanding and detailing the available knowledge on regionalization, progenitors’ behavior and functional sophistication of the forebrain derivatives is also key to generating informative models to improve our characterization of heterogeneous and mechanistically unexplored cortical malformations. Classical and emerging mammalian models are irreplaceable to accurately elucidate mechanisms of stem cells expansion and impairments of cortex development. Nevertheless, alternative systems, allowing a considerable reduction of the burden associated with animal experimentation, are gaining popularity to dissect basic strategies of neural stem cells biology and morphogenesis in health and disease and to speed up preclinical drug testing. Teleost vertebrates such as zebrafish, showing conserved core programs of forebrain development, together with patients-derived in vitro 2D and 3D models, recapitulating more accurately human neurogenesis, are now accepted within translational workflows spanning from genetic analysis to functional investigation. Here, we review the current knowledge of common and divergent mechanisms shaping the forebrain in vertebrates, and causing cortical malformations in humans. We next address the utility, benefits and limitations of whole-brain/organism-based fish models or neuronal ensembles in vitro for translational research to unravel key genes and pathological mechanisms involved in neurodevelopmental diseases.

Zebrafish—An Optimal Model in Experimental Oncology

A thorough understanding of cancer pathogenesis is a necessary step in the development of more effective and safer therapy. However, due to the complexity of the process and intricate interactions, studying tumor development is an extremely difficult and challenging task. In bringing this issue closer, different scientific models with various advancement levels are helpful. Cell cultures is a system that is too simple and does not allow for multidirectional research. On the other hand, rodent models, although commonly used, are burdened with several limitations. For this reason, new model organisms that will allow for the studying of carcinogenesis stages and factors reliably involved in them are urgently sought after. Danio rerio, an inconspicuous fish endowed with unique features, is gaining in importance in the world of scientific research. Including it in oncological research brings solutions to many challenges afflicting modern medicine. This article aims to illustrate the usefulness of Danio rerio as a model organism which turns out to be a powerful and unique tool for studying the stages of carcinogenesis and solving the hitherto incomprehensible processes that lead to the development of the disease.

Transcriptome and Proteome Analyses Reveal Stage-Specific DNA Damage Response in Embryos of Sturgeon (Acipenser ruthenus)

DNA damage during early life stages may have a negative effect on embryo development, inducing mortality and malformations that have long-lasting effects during adult life. Therefore, in the current study, we analyzed the effect of DNA damage induced by genotoxicants (camptothecin (CPT) and olaparib) at different stages of embryo development. The survival, DNA fragmentation, transcriptome, and proteome of the endangered sturgeon Acipenser ruthenus were analyzed. Sturgeons are non-model fish species that can provide new insights into the DNA damage response and embryo development. The transcriptomic and proteomic patterns changed significantly after exposure to genotoxicants in a stage-dependent manner. The results of this study indicate a correlation between phenotype formation and changes in transcriptomic and proteomic profiles. CPT and olaparib downregulated oxidative phosphorylation and metabolic pathways, and upregulated pathways involved in nucleotide excision repair, base excision repair, and homologous recombination. We observed the upregulated expression of zona pellucida sperm-binding proteins in all treatment groups, as well as the upregulation of several glycolytic enzymes. The analysis of gene expression revealed several markers of DNA damage response and adaptive stress response, which could be applied in toxicological studies on fish embryos. This study is the first complex analysis of the DNA damage response in endangered sturgeons.

Combined Effects of Potassium Perchlorate and a Neonicotinoid on Zebrafish Larvae (Danio rerio)

Imidacloprid (IMI) is part of the neonicotinoids family, insecticides widely used by humans and also found in wastewater. This class of compounds, if present in the environment, can cause toxicity to different species such as bees and gammarids, although little is known about vertebrates such as fish. In addition, several substances have been reported in the environment that can cause damage to aquatic species, such as potassium perchlorate (KClO₄), if exposed to high concentrations or for long periods. Often, the co-presence of different contaminants can cause a synergistic action in terms of toxicity to fish. In the present study, we first analyzed different concentrations of IMI (75, 100 and 150 mg/L) and KClO₄ (1, 1.5 and 5 mM) to highlight the morphological effects at 96 hpf and, subsequently, chose two nontoxic concentrations to evaluate their co-exposure and the pathway involved in their co-toxicity. Morphological alteration, mucus production, messenger RNA (mRNA) expression related to intestinal function and oxidative stress were measured. These results suggest that co-exposure to IMI and KClO₄ could affect zebrafish embryo development by increasing gut toxicity and the alteration of antioxidative defense mechanisms.

Species variations in XRCC1 recruitment strategies for FHA domain-containing proteins

DNA repair scaffolds XRCC1 and XRCC4 utilize a phosphopeptide FHA domain binding motif (FBM) of the form Y-x-x-pS-pT-D-E that supports recruitment of three identified FHA domain-containing DNA repair proteins: polynucleotide kinase/phosphatase (PNKP), aprataxin (APTX), and a third protein, APLF, that functions as a scaffold in support of non-homologous end joining (NHEJ). Mammalian dimeric XRCC4 is able to interact with two of these proteins at any given time, while monomeric XRCC1 binds only one. However, sequence analysis indicates that amphibian and teleost XRCC1 generally contain two FHA binding motifs. X1-FBM1, is similar to the single mammalian XRCC1 FBM and probably functions similarly. X1-FBM2, is more similar to mammalian XRCC4 FBM; it is located closer to the XRCC1 BRCT1 domain and probably is less discriminating among its three likely binding partners. Availability of an additional PNKP or APTX recruitment motif may alleviate the bottleneck that results from using a single FBM motif for recruitment of multiple repair factors. Alternatively, recruitment of APLF by X1-FBM2 may function to rescue a misdirected or unsuccessful SSB repair response by redirecting the damaged DNA to the NHEJ pathway, - a need that results from the ambiguity of the PARP1 signal regarding the nature of the damage. Evaluation of XRCC4 FBMs in acanthomorphs, which account for a majority of the reported teleost sequences, reveals the presence of an additional XRCC4-like paralog, distinct from other previously described members of the XRCC4 superfamily. The FBM is typically absent in acanthomorph XRCC4, but present in the XRCC4-like paralog. Modeling suggests that XRCC4 and its paralog may form homodimers or XRCC4-XRCC4-like heterodimers.

Toxicity impact of hydrogen peroxide on the fate of zebrafish and antibiotic resistant bacteria

Hydrogen peroxide (H₂O₂) is applied in various environments. It could be present at concentrations ranging from nanomolar to micromolar in a water system. It is produced through pollutants and natural activities. Since few studies have been conducted about the impact of naturally produced H₂O₂ on aquatic organisms, the objective of the present study was to monitor changes in responses of aquatic model organisms such as zebrafish and antibiotic-resistant bacteria to different exogenous H₂O₂ exposure. Increases in exposure concentration and time induced decreases in the perception of zebrafish larvae (up to 69%) and movement of adult zebrafish (average speed, average acceleration, movement distance, and activity time) compared to the control (non-exposed group). In addition, as a function of H₂O₂ exposure concentration (0-100,000 nM) and time, up to 20-fold increase (p = 5.00*10^-6) of lipid peroxidation compared to control was observed. For microorganisms, biofilm, an indirect indicator of resistance to external stressors, was increased up to 68% and gene transfer was increased (p = 2.00*10^-6) by more than 30% after H₂O₂ exposure. These results imply that naturally generated H₂O₂ could adversely affect aquatic environment organisms and public health. Thus, more careful attention is needed for H₂O₂ production in an aquatic system.

Effect of benzophenone-3 on the blood cells of zebrafish (Danio rerio)

Benzophenone-3 (BP-3) is a common component of organic sunscreen widely used that can affect especially aquatic ecosystems health, including fish. To verify the biological effects of low concentrations of BP-3 on blood cells, one hundred and forty zebrafish (D. rerio) were used and then randomly divided into five groups: control group (water), solvent group (alcoholic water), and BP-3 group (BP-3 at 7 µg L^-1, BP-3 at 70 µg L^-1, and BP-3 at 700 µg L^-1). The blood slices were stained with Panoptic stain and with Giemsa solution for the hematological analysis. During the exposure to BP-3, no behavioral changes were observed. Although no significant difference in total leukocytes occurred, an increase in neutrophils and a reduction of lymphocytes at the highest concentration on both 7th and 14th days were detected. The total and cytoplasmic area of erythrocytes on the 7th day at the highest concentration were reduced. In addition, alterations on the erythrocyte nuclear morphology in fish exposed to BP-3 were usually visualized, mainly when considered the occurrence of blebbed nucleus and micronucleus, indicating that BP-3 exhibits cytotoxic and mutagenic effects. The results indicate that BP-3 can interfere with the morphophysiology of aquatic organisms.

Parp1 promotes sleep, which enhances DNA repair in neurons

The characteristics of the sleep drivers and the mechanisms through which sleep relieves the cellular homeostatic pressure are unclear. In flies, zebrafish, mice, and humans, DNA damage levels increase during wakefulness and decrease during sleep. Here, we show that 6 h of consolidated sleep is sufficient to reduce DNA damage in the zebrafish dorsal pallium. Induction of DNA damage by neuronal activity and mutagens triggered sleep and DNA repair. The activity of the DNA damage response (DDR) proteins Rad52 and Ku80 increased during sleep, and chromosome dynamics enhanced Rad52 activity. The activity of the DDR initiator poly(ADP-ribose) polymerase 1 (Parp1) increased following sleep deprivation. In both larva zebrafish and adult mice, Parp1 promoted sleep. Inhibition of Parp1 activity reduced sleep-dependent chromosome dynamics and repair. These results demonstrate that DNA damage is a homeostatic driver for sleep, and Parp1 pathways can sense this cellular pressure and facilitate sleep and repair activity.

Progress in Gene-Editing Technology of Zebrafish

As a vertebrate model, zebrafish (Danio rerio) plays a vital role in the field of life sciences. Recently, gene-editing technology has become increasingly innovative, significantly promoting scientific research on zebrafish. However, the implementation of these methods in a reasonable and accurate manner to achieve efficient gene-editing remains challenging. In this review, we systematically summarize the development and latest progress in zebrafish gene-editing technology. Specifically, we outline trends in double-strand break-free genome modification and the prospective applications of fixed-point orientation transformation of any base at any location through a multi-method approach.

DNA Damage in Liver Cells of the Tilapia Fish Oreochromis mossambicus Larva Induced by the Insecticide Cyantraniliprole at Sublethal Doses During Chronic Exposure

Cyantraniliprole can effectively control lepidopteran pests and has been used all over the world. In general, the risk of cyantraniliprole seems low for fish, but the toxicity selectivity among different fish species was not clear. Here, we present the methods for the acute toxicity and chronic effects of cyantraniliprole by using juvenile tilapia (Oreochromis mossambicus). Based on this test, 96 h LC₅₀ of cyantraniliprole to tilapia was 38.0 mg/L. After exposed for 28 days, specific growth rates of the blank control, solution control, and the treatments of 0.037, 0.37 and 3.7 mg/L of cyantraniliprole were 1.14, 0.95, 0.93, 0.82, and 0.70% per day, respectively. The results of micronucleus experiment and single cell gel electrophoresis showed that cyantraniliprole damaged DNA in liver cells of tilapia larvae. Quantitative PCR results showed that cyantraniliprole could induce the upregulation of Rpa 3 that is responsible for the DNA repair. The significant downregulation of Chk 2 gene was related to p53 pathway. It is therefore proposed that cyantraniliprole causes DNA damage in liver cells of tilapia and activates DNA damage and repair pathways.

Large-scale generation and phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes

A systematic knowledge of the roles of DNA repair genes at the level of the organism has been limited due to the lack of appropriate experimental approaches using animal model systems. Zebrafish has become a powerful vertebrate genetic model system with availability due to the ease of genome editing and large-scale phenotype screening. Here, we generated zebrafish mutants for 32 DNA repair and replication genes through multiplexed CRISPR/Cas9-mediated mutagenesis. Large-scale phenotypic characterization of our mutant collection revealed that three genes (atad5a, ddb1, pcna) are essential for proper embryonic development and hematopoiesis; seven genes (apex1, atrip, ino80, mre11a, shfm1, telo2, wrn) are required for growth and development during juvenile stage and six genes (blm, brca2, fanci, rad51, rad54l, rtel1) play critical roles in sex development. Furthermore, mutation in six genes (atad5a, brca2, polk, rad51, shfm1, xrcc1) displayed hypersensitivity to DNA damage agents. Our zebrafish mutant collection provides a unique resource for understanding of the roles of DNA repair genes at the organismal level.

Zebrafish (Danio rerio) using as model for genotoxicity and DNA repair assessments: Historical review, current status and trends

Genotoxic pollutants lead to both DNA damage and changes in cell repair mechanisms. Selecting suitable biomonitors is a fundamental step in genotoxicity studies. Thus, zebrafish have become a popular model used to assess the genotoxicity of different pollutants in recent years. They have orthologous genes with humans and hold almost all genes involved in different repair pathways. Therefore, the aim of the current study is to summarize the existing literature on zebrafish using as model system to assess the genotoxicity of different pollutants. Revised data have shown that comet assay is the main technique adopted in these studies. However, it is necessary standardizing the technique applied to zebrafish in order to enable better result interpretation and comparisons. Overall, pollutants lead to single-strand breaks (SSB), double-strand breaks (DSB), adduct formation, as well as to changes in the expression of genes involved in repair mechanisms. Although analyzing repair mechanisms is essential to better understand the genotoxic effects caused by pollutants, few studies have analyzed repair capacity. The current review reinforces the need of conducting further studies on the role played by repair pathways in zebrafish subjected to DNA damage. Revised data have shown that zebrafish are a suitable model to assess pollutant-induced genotoxicity.

Medaka (Oryzias latipes) Embryo as a Model for the Screening of Compounds That Counteract the Damage Induced by Ultraviolet and High-Energy Visible Light

Continuous overexposure to sunlight increases its harmful effects on the skin. For this reason, there is a growing need to characterize economic models more representative of the negative effects and counteracting responses that irradiation causes on human skin. These models will serve for the screening of protective compounds against damage caused by ultraviolet (UV) and high energy visible light (HEV). Therefore, two common in vitro models employed for sunlight irradiation studies, namely human keratinocyte HaCat culture and reconstructed human epidermis (RHE), were compared with the medaka fish embryo model, traditionally used in other scientific disciplines. Using suberythemal doses of UVA and HEV to determine the level of Reactive Oxygen Species (ROS) generation and thymine dimers formed by UVB, we show that medaka embryo responds with a lower damage level, more comparable to human skin, than the other two models, probably due to the protective mechanisms that work in a complete organism. In the same way, the protective effects of antioxidant compounds have the greatest effect on medaka embryos. Taken together, these findings suggest that medaka embryos would be a good alternative in vitro model for sunlight effect studies, and for the screening of molecules with counteracting capacity against the damage caused by UV and HEV.

Cockayne Syndrome: The many challenges and approaches to understand a multifaceted disease

The striking and complex phenotype of Cockayne syndrome (CS) patients combines progeria-like features with developmental deficits. Since the establishment of the in vitro culture of skin fibroblasts derived from patients with CS in the 1970s, significant progress has been made in the understanding of the genetic alterations associated with the disease and their impact on molecular, cellular, and organismal functions. In this review, we provide a historic perspective on the research into CS by revisiting seminal papers in this field. We highlighted the great contributions of several researchers in the last decades, ranging from the cloning and characterization of CS genes to the molecular dissection of their roles in DNA repair, transcription, redox processes and metabolism control. We also provide a detailed description of all pathological mutations in genes ERCC6 and ERCC8 reported to date and their impact on CS-related proteins. Finally, we review the contributions (and limitations) of many genetic animal models to the study of CS and how cutting-edge technologies, such as cell reprogramming and state-of-the-art genome editing, are helping us to address unanswered questions.

Fluoxastrobin-induced effects on acute toxicity, development toxicity, oxidative stress, and DNA damage in Danio rerio embryos

Strobilurin fungicides (SFs), the most commonly used fungicides, pose threats for controlling fungal diseases. The fungicides were monitored in aquatic ecosystems and may have negative effects on nontarget organisms. This project was undertaken to monitor the toxic effects of fluoxastrobin (FLUO) on Danio rerio embryos and to evaluate the SF risks in aquatic ecosystems. The 96-hour median lethal concentration (96 h LC₅₀), hatching rates, and morphological abnormalities were used to analyze acute toxicity and teratogenicity of FLUO to Danio rerio embryos at an FLUO dose of 0.549 mg/L (95% confidence limits: 0.423 to 0.698 mg/L); the results showed that FLUO has high toxicity in embryos that is analogous to the toxicity observed in adult Danio rerio. Fluoxastrobin may lead embryos to delayed hatching at concentrations >0.6 mg/L, and it may lead to teratogenicity (i.e., pericardial edema and spinal curvature). Based on the 96 h LC₅₀ results, the following parameters were evaluated in Danio rerio: development-related indicators (body length and heart rates), reactive oxygen species (ROS) levels, lipid peroxidation (LPO) levels, the levels of three antioxidants, 8-hydroxy-2-deoxyguanosine (8-OHdG), and apoptosis. The results elucidated that FLUO inhibition of spinal and heart development may be induced by oxidative stress. In addition, FLUO induced a notable climb in ROS content, LPO, the activated activity of superoxide dismutase (SOD) and catalase (CAT), and it inhibited glutathione peroxidase (GSH-PX) activity. Fluoxastrobin led to DNA damage (i.e., a notable climb of 8-OHdG contents and apoptotic cells). Collectively, FLUO posed threats to Danio rerio embryos at multiple levels, and this investigation could be a reminder for people to be more judicious in SF-use to avoid or relieve SF toxicity to nontarget organisms.

Methylnitrosourea, dimethylbenzanthracene and benzoapyrene differentially affect redox pathways, apoptosis and immunity in zebrafish

Cancer continues to be a major cause of mortality globally. Zebrafish present suitable models for studying the mechanisms of genotoxic carcinogens. The aim of this study was to investigate the interaction between oxidant-antioxidant status, apoptosis and immunity in zebrafish that were exposed to three different genotoxic carcinogens methylnitrosourea, dimethylbenzanthracene, benzoapyrene and methylnitrosourea + dimethylbenzanthracene starting from early embryogenesis for 30 days. Lipid peroxidation, nitric oxide levels, superoxide dismutase and glutathione-S-transferase activities and mRNA levels of apoptosis genes p53, bax, casp3a, casp2 and immunity genes fas, tnfα and ifnγ1 were evaluated. The disruption of the oxidant-antioxidant balance accompanied by altered expressions of apoptotic and immunity related genes were observed in different levels according to the carcinogen applied. Noteworthy, ifnγ expressions decreased in all carcinogen-exposed groups. Our results will provide basic data for further carcinogenesis research in zebrafish models.

DNA damage in liver cells of the tilapia fish Oreochromis mossambicus larva induced by the insecticide cyantraniliprole at sublethal doses during chronic exposure

Cyantraniliprole can effectively control lepidopteran pests and has been used all over the world. In general, the risk of cyantraniliprole seems low for fish, but the toxicity selectivity among different fish species was not clear. Here the acute toxicity and chronic effects of cyantraniliprole to juvenile tilapia (Oreochromis mossambicus) were assessed. The results showed that 96 h LC₅₀ of cyantraniliprole to tilapia was 38.0 mg/L. After exposed for 28 days, specific growth rates of the blank control, solution control, and the treatments of 0.037, 0.37 and 3.7 mg/L of cyantraniliprole were 1.14, 0.95, 0.93, 0.82 and 0.70% per day, respectively. The results of micronucleus experiment and single cell gel electrophoresis showed that cyantraniliprole damaged DNA in liver cells of tilapia larvae. Quantitative PCR results showed that cyantraniliprole could induce the up-regulation of Rpa 3 that is responsible for the DNA repair. The significantly down-regulation of Chk 2 gene was related to p53 pathway. It is therefore proposed that cyantraniliprole causes DNA damage in liver cells of tilapia and activates DNA damage and repair pathways.

Heat stress modulates nucleotide excision repair capacity in zebrafish (Danio rerio) early and mid-early embryos via distinct mechanisms

Discharge of heated effluent at 8-12 °C above ambient into water areas is known to retard the growth of aquatic organisms due to heat stress. Nucleotide excision repair (NER) maintains genome integrity by removing helix-distorting adducts such as UV-induced DNA lesions. This study explored how NER in zebrafish (Danio rerio) embryos at different hours post fertilization (hpf) responded to + 8.5 °C heat shock for 30 min. Our transcription-based repair assay monitoring the ability of zebrafish extracts to upregulate a UV-suppressed gene expression detected a 2-fold increase of NER capacity in 10 hpf early embryos after heat stress. In contrast, heat stress caused a mild inhibition of NER capacity in 24 hpf mid-early embryos. Heat-treated and untreated 10 hpf zebrafish extracts displayed similar levels of UV-damaged-DNA binding activities, while an apparently weaker (6-4) photoproduct (6-4 PP) binding activity was present in heat-stressed 24 hpf zebrafish extracts. Heat stress enhanced UV-induced NER in 10 hpf embryos by increasing the efficiency of damage incision/excision based on both genomic DNA electrophoresis and terminal deoxytransferase (TdT)-mediated end labeling assay. UV-irradiated embryos preexposed to heat stress produced a significantly larger amount of NER-associated DNA fragments about 20-30 nucleotides in length than embryos only heat-treated or irradiated. Correlated with its inhibitory effect on 6-4 PP damage recognition, heat stress downregulated damage incision/excision activities in 24 hpf embryos. Hence, thermal stress may positively or negatively modulate NER capacity in zebrafish embryos at different stages by targeting at the step of DNA incision/excision or damage recognition.

DNA repair and neurological disease: From molecular understanding to the development of diagnostics and model organisms

In both replicating and non-replicating cells, the maintenance of genomic stability is of utmost importance. Dividing cells can repair DNA damage during cell division, tolerate the damage by employing potentially mutagenic DNA polymerases or die via apoptosis. However, the options for accurate DNA repair are more limited in non-replicating neuronal cells. If DNA damage is left unresolved, neuronal cells die causing neurodegenerative disorders. A number of pathogenic variants of DNA repair proteins have been linked to multiple neurological diseases. The current challenge is to harness our knowledge of fundamental properties of DNA repair to improve diagnosis, prognosis and treatment of such debilitating disorders. In this perspective, we will focus on recent efforts in identifying novel DNA repair biomarkers for the diagnosis of neurological disorders and their use in monitoring the patient response to therapy. These efforts are greatly facilitated by the development of model organisms such as zebrafish, which will also be summarised.

AP endonuclease 1 (Apex1) influences brain development linking oxidative stress and DNA repair

Brain and neurons are particularly sensitive to reactive oxygen species (ROS). Oxidative damage from ROS results in increased 8-oxoguanine in DNA followed by repair through the base excision repair (BER) pathway. We reported earlier that AP endonuclease 1 (Apex1) not only participates directly in BER but also regulates transcription factor Creb1. Here, we investigated how Apex1 affects brain to respond effectively to oxidative damage during zebrafish development. Loss of Apex1 resulted in increased ROS, 8-oxoguanine, and abasic sites as well as loss of Ogg1, which recognizes 8-oxoguanine and is required for its repair. Moreover, knock-down of Apex1 not only resulted in reduction of expression of several major proteins in the BER pathway (Polb and Ogg1), and it also resulted in maldistribution and loss of four key brain transcription factors (fezf2, otx2, egr2a, and pax2a), leading to abnormal brain development. These results were independent of p53 protein level. In contrast, exposure to exogenous H₂O₂ resulted in increased transcription and protein of Apex1 along with other BER components, as well as Creb1. Taken together, these results indicate that oxidative stress increased when the level of Apex1 was reduced, revealing a novel pathway of how Apex1 manages oxidative stress in developing brain.

Knock-In Strategy for Editing Human and Zebrafish Mitochondrial DNA Using Mito-CRISPR/Cas9 System

The mitochondria DNA (mtDNA) editing tool, zinc finger nucleases (ZFNs), transcription activator-like effector nuclease (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) system, is a promising approach for the treatment of mtDNA diseases by eliminating mutant mitochondrial genomes. However, there have been no reports of repairing the mutant mtDNA with homologous recombination strategy to date. Here, we show a mito-CRISPR/Cas9 system that mito-Cas9 protein can specifically target mtDNA and reduce mtDNA copy number in both human cells and zebrafish. An exogenous single-stranded DNA with short homologous arm was knocked into the targeting loci accurately, and this mutagenesis could be steadily transmitted to F₁ generation of zebrafish. Moreover, we found some major factors involved in nuclear DNA repair were upregulated significantly by the mito-CRISPR/Cas9 system. Taken together, our data suggested that the mito-CRISPR/Cas9 system could be a useful method to edit mtDNA by knock-in strategy, providing a potential therapy for the treatment of inherited mitochondrial diseases.

The toxicity of 2,6-dichlorobenzoquinone on the early life stage of zebrafish: A survey on the endpoints at developmental toxicity, oxidative stress, genotoxicity and cytotoxicity

2,6-dichlorobenzoquinone (2,6-DCBQ), an emerging disinfection by-production, frequently occurs in reclaimed water and drinking water. However, limited information was available regarding its toxicity. To evaluate its impact, zebrafish at early life stage were exposed to 0, 10, 30, 60, 90, or 120 μg L^-1 2,6-BDCQ for 72 h. Our results indicated that 2,6-BDCQ decreased zebrafish's survival rate to 65% and 44% at 90 and 120 μg L^-1 treatments and increased its aberration rate to 11% and 26% at 90 μg L^-1 and 120 μg L^-1 treatments. Besides, 2,6-BDCQ had adverse effect on its oxidative stress (elevated superoxide dismutase activity), lipid peroxidation (increased malondialdehyde levels), DNA damage (increased 8-hydroxydeoxyguanosine contents) and apoptosis (increased caspase-3 activity). Although lower concentrations (≤60 μg L^-1) of 2,6-BDCQ didn't exhibit significant effect on its survival development or lipid peroxidation of zebrafish, they induced obvious DNA damage and apoptosis occurrence. These results revealed 2,6-BDCQ caused genotoxicity and cytotoxicity to zebrafish. This study provides novel insight into 2,6-DCBQ-induced toxicity in zebrafish.

Radiobiological effects and proton RBE determined by wildtype zebrafish embryos

The increasing use of proton radiotherapy during the last decade and the rising number of long-term survivors has given rise to a vital discussion on potential effects on normal tissue. So far, deviations from clinically applied generic RBE (relative biological effectiveness) of 1.1 were only obtained by in vitro studies, whereas indications from in vivo trials and clinical studies are rare. In the present work, wildtype zebrafish embryos (Danio rerio) were used to characterize the effects of plateau and mid-SOBP (spread-out Bragg peak) proton radiation relative to that induced by clinical MV photon beam reference. Based on embryonic survival data, RBE values of 1.13 ± 0.08 and of 1.20 ± 0.04 were determined four days after irradiations with 20 Gy plateau and SOBP protons relative to 6 MV photon beams. These RBE values were confirmed by relating the rates of embryos with morphological abnormalities for the respective radiation qualities and doses. Besides survival, the rate of spine bending, as one type of developmental abnormality, and of pericardial edema, as an example for acute radiation effects, were assessed. The results revealed that independent on radiation quality both rates increased with time approaching almost 100% at the 4th day post irradiation with doses higher than 15 Gy. To sum up, the applicability of the zebrafish embryo as a robust and simple alternative model for in vivo characterization of radiobiological effects in normal tissue was validated and the obtained RBE values are comparable to previous finding in animal trials.

Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness

How the environment shapes the function and evolution of DNA repair systems is poorly understood. In a comparative study using zebrafish and the Somalian blind cavefish, Phreatichthys andruzzii, we reveal that during evolution for millions of years in continuous darkness, photoreactivation DNA repair function has been lost in P. andruzzii. We demonstrate that this loss results in part from loss-of-function mutations in pivotal DNA-repair genes. Specifically, C-terminal truncations in P. andruzzii DASH and 6-4 photolyase render these proteins predominantly cytoplasmic, with consequent loss in their functionality. In addition, we reveal a general absence of light-, UV-, and ROS-induced expression of P. andruzzii DNA-repair genes. This results from a loss of function of the D-box enhancer element, which coordinates and enhances DNA repair in response to sunlight. Our results point to P. andruzzii being the only species described, apart from placental mammals, that lacks the highly evolutionary conserved photoreactivation function. We predict that in the DNA repair systems of P. andruzzii, we may be witnessing the first stages in a process that previously occurred in the ancestors of placental mammals during the Mesozoic era.

Injection of an SV40 transcriptional terminator causes embryonic lethality: a possible zebrafish model for screening nonhomologous end-joining inhibitors

Introduction

DNA repair by the nonhomologous end joining (NHEJ) pathway promotes tumor recurrence after chemotherapy and radiotherapy. Discovery of rapid and high-throughput techniques to screen for an effective NHEJ inhibitor drug is imperative for the suppression of NHEJ during tumor treatment. However, traditional screening methods are too cumbersome to meet the current need. Zebrafish is an ideal model for drug screening due to the specificity of its early embryonic development and similarity of tumor cell generation. By exploiting the high frequency of NHEJ in early embryonic development, we established a model that uses a transcriptional terminator signal fragment from the Simian virus 40 (SV40) to cause embryonic lethality. SV40 fragment-induced embryonic lethality was alleviated by 5,6-bis ((E)-benzylideneamino)-2-mercaptopyrimidin-4-ol or C18H14N4OS (SCR7), an NHEJ inhibitor.

Materials and methods

A 122 bp SV40 terminator fragment (10 ng/µL) was microinjected into zebrafish zygotes. SV40 fragment integration into the zebrafish embryonic genome was detected by Southern blot using a DNA probe for the SV40 terminator. Embryonic lethality rates were observed 24 and 48 h after microinjection. A nonhomologous recombinant inhibitor, SCR7 (5 µM), was used to alleviate embryonic lethality.

Results

Microinjection of zebrafish embryos with the SV40 terminator fragment (10 ng/µL) caused a progressive increase in mortality over time. Using Southern blots, we confirmed that SV40 terminator sequences were integrated into the zebrafish embryonic genome. This phenomenon was effectively alleviated by addition of SCR7.

Conclusion

Injection of an SV40 terminator into zebrafish embryos may cause embryonic lethality due to NHEJ during early zebrafish development. The high mortality of zebrafish embryos could be alleviated by using the NHEJ inhibitor, SCR7. The zebrafish model presented here is simpler and more convenient than traditional methods of screening for NHEJ inhibitors and can be utilized in large-scale drug screens for NHEJ inhibitors and for the development of novel anticancer drugs.

Tritiated water exposure disrupts myofibril structure and induces mis-regulation of eye opacity and DNA repair genes in zebrafish early life stages

Tritium (³H) is a radioactive isotope of hydrogen. In the environment, the most common form of tritium is tritiated water (HTO). The present study aimed to identify early biomarkers of HTO contamination through the use of an aquatic model, the zebrafish (Danio rerio). We used the zebrafish embryo-larvae model to investigate the modes of action of HTO exposure at dose rates of 0.4 and 4 mGy/h, dose rates expected to induce deleterious effects on fish. Zebrafish were exposed to HTO from 3 hpf (hours post fertilization) to 96 hpf. The transcriptomic effects were investigated 24 h and 96 h after the beginning of the contamination, using mRNAseq. Results suggested an impact of HTO contamination, regardless of the dose rate, on genes involved in muscle contraction (tnnt2d, tnni2a.4, slc6a1a or atp2a1l) and eye opacity (crygm2d9, crygmxl1, mipb or lim2.3) after 24 h of contamination. Interestingly, an opposite differential expression was highlighted in genes playing a role in muscle contraction and eye opacity in 24 hpf embryos when comparing dose rates, suggesting an onset of DNA protective mechanisms. The expression of h2afx and ddb2 involved in DNA repair was enhanced in response to HTO exposure. The entrainment of circadian clock and the response to H₂O₂ signalling pathways were enriched at 96 hpf at 0.4 mGy/h and in both stages after 4 mGy/h. Genes involved in ROS scavenging were differentially expressed only after 24 h of exposure for the lowest dose rate, suggesting the onset of early protective mechanisms against oxidative stress. Effects highlighted on muscle at the molecular scale were confirmed at a higher biological scale, as electron microscopy observations revealed sarcomere impairments in 96 hpf larvae for both dose rates. Together with other studies, the present work provides useful data to better understand modes of action of tritium on zebrafish embryos-larvae.

Deciphering the Combined Effects of Environmental Stressors on Gene Transcription: A Conceptual Approach

The use of classical mixture toxicity models to predict the combined effects of environmental stressors based on toxicogenomics (OMICS) data is still in its infancy. Although several studies have made attempts to implement mixture modeling in OMICS analysis to understand the low-dose interactions of stressors, it is not clear how interactions occur at the molecular level and how results generated from such approaches can be better used to inform future studies and cumulative hazard assessment of multiple stressors. The present work was therefore conducted to propose a conceptual approach for combined effect assessment using global gene expression data, as illustrated by a case study on assessment of combined effects of gamma radiation and depleted uranium (DU) on Atlantic salmon ( Salmo salar). Implementation of the independent action (IA) model in reanalysis of a previously published microarray gene expression dataset was performed to describe gene expression patterns of combined effects and identify key gene sets and pathways that were relevant for understanding the interactive effects of these stressors. By using this approach, 3120 differentially expressed genes (DEGs) were found to display additive effects, whereas 279 (273 synergistic, 6 antagonistic) were found to deviate from additivity. Functional analysis further revealed that multiple toxicity pathways, such as oxidative stress responses, cell cycle regulation, lipid metabolism, and immune responses were enriched by DEGs showing synergistic gene expression. A key toxicity pathway of DNA damage leading to enhanced tumorigenesis signaling is highlighted and discussed in detail as an example of how to take advantage of the approach. Furthermore, a conceptual workflow describing the integration of combined effect modeling, OMICS analysis, and bioinformatics is proposed. The present study presents a conceptual framework for utilizing OMICS data in combined effect assessment and may provide novel strategies for dealing with data analysis and interpretation of molecular responses of multiple stressors.

Bloom syndrome: research and data priorities for the development of precision medicine as identified by some affected families

Bloom syndrome (BS) is a rare, autosomal recessive genetic disorder characterized by short stature, a skin rash associated with sun exposure, and an elevated likelihood of developing cancers of essentially all types, beginning at an early age. Cancer is the leading cause of death for persons with BS, and its early onset results in a reported median lifespan of <30 years. With fewer than 300 documented cases since BS was first described in 1954, its rarity has challenged progress in advancing both the care of and the cure for persons with BS. Presently, there are no known clinically actionable targets specific to persons with this cancer predisposition syndrome, despite the fact that standard cancer treatments are often contraindicated or must be substantially modified for persons with BS. Herein, Zachary Rogers recounts his experience as a cancer patient with BS contemplating a substantially customized chemotherapy regimen that highlights the need for development of individualized treatments in the BS community. We also outline a patient-centered research and community action road map with the goal of improving and prolonging the lives of persons with Bloom syndrome, including the facilitation of precision medicine development specific to this condition.

Accurate quantification of homologous recombination in zebrafish: brca2 deficiency as a paradigm

Homologous Recombination (HR) repair is essential for repairing DNA double strand breaks (DSB) in dividing cells and preventing tumorigenesis. BRCA2 plays an important role in HR by recruiting the DNA recombinase RAD51 to the DSB. Despite being a popular model organism in genetic and cancer research, knowledge on the conservation of the HR pathway and function of zebrafish Brca2 is limited. To evaluate this, we developed a Rad51 foci assay in zebrafish embryos. We identified the zebrafish embryonic intestinal tissue as an ideal target for Rad51 immunostaining. After inducing DSB through irradiation, Rad51 foci were present in irradiated embryos but not in unirradiated controls. We present a method for accurate quantification of HR. Both morpholino-induced knockdown and knockout of Brca2 lead to almost complete absence of Rad51 foci in irradiated embryos. These findings indicate conserved function of Brca2 in zebrafish. Interestingly, a statistically significant decrease in Rad51 foci was observed in Brca2 heterozygous carriers compared to wild types, indicative of haploinsufficiency, a hypothesised cause of some tumours in patients with a germline BRCA2 mutation. In conclusion, we demonstrated the suitability of zebrafish as an excellent in vivo model system for studying the HR pathway and its functionality.

Mercury (II) impairs nucleotide excision repair (NER) in zebrafish (Danio rerio) embryos by targeting primarily at the stage of DNA incision

Mercuric ion (Hg²⁺) is the most prevalent form of inorganic Hg found in polluted aquatic environment. As inhibition of DNA damage repair has been proposed as one of the mechanisms of Hg²⁺-induced genotoxicity in aquatic animals and mammalian cells, this study explored the susceptibility of different stages of nucleotide excision repair (NER) in zebrafish (Danio rerio) embryos to Hg²⁺ using UV-damaged DNA as the repair substrate. Exposure of embryos at 1h post fertilization (hpf) to HgCl₂ at 0.1-2.5μM for 9h caused a concentration-dependent inhibition of NER capacity monitored by a transcription-based DNA repair assay. The extracts of embryos exposed to 2.5μM Hg²⁺ almost failed to up-regulate UV-suppressed marker cDNA transcription. No inhibition of ATP production was observed in all Hg²⁺-exposed embryos. Hg²⁺ exposure imposed either weak inhibitory or stimulating effects on the gene expression of NER factors, while band shift assay showed the inhibition of photolesion binding activities to about 40% of control in embryos treated with 1-2.5μM HgCl₂. The damage incision stage of NER in zebrafish embryos was found to be more sensitive to Hg²⁺ than photolesion binding capacity due to the complete loss of damage incision activity in the extracts of embryos exposed to 1-2.5μM Hg²⁺. NER-related DNA incision was induced in UV-irradiated embryos based on the production of short DNA fragments matching the sizes of excision products generated by eukaryotic NER. Pre-exposure of embryos to Hg²⁺ at 0.1-2.5μM all suppressed DNA incision/excision in UV-irradiated embryos, reflecting a high sensitivity of DNA damage incision/excision to Hg²⁺. Our results showed the potential of Hg²⁺ at environmental relevant levels to disturb NER in zebrafish embryos by targeting primarily at the stage of DNA incision/excision.

Aptamers for DNA Damage and Repair

DNA is damaged on a daily basis, which can lead to heritable mutations and the activation of proto-oncogenes. Therefore, DNA damage and repair are critical risk factors in cancer, aging and disease, and are the underlying bases of most frontline cancer therapies. Much of our current understanding of the mechanisms that maintain DNA integrity has been obtained using antibody-based assays. The oligonucleotide equivalents of antibodies, known as aptamers, have emerged as potential molecular recognition rivals. Aptamers possess several ideal properties including chemical stability, in vitro selection and lack of batch-to-batch variability. These properties have motivated the incorporation of aptamers into a wide variety of analytical, diagnostic, research and therapeutic applications. However, their use in DNA repair studies and DNA damage therapies is surprisingly un-tapped. This review presents an overview of the progress in selecting and applying aptamers for DNA damage and repair research.

Identification of low-molecular-weight vitellogenin 1 (Vg1)-like proteins as nucleotide excision repair (NER) factors in developing zebrafish (Danio rerio) using a transcription-based DNA repair assay

Nucleotide excision repair (NER) removes helix-distorting DNA lesions such as UV-induced pyrimidine dimers and cisplatin-induced strand crosslinking. Our earlier studies have identified low-molecular-weight proteins homologous to the 150-kDa vitellogenin 1 (Vg1) as UV-damaged DNA-binding factors expressed in developing zebrafish (Danio rerio). This present study explored if Vg1-like proteins also participated in NER in zebrafish. Immunoblot analysis of affinity-captured 12 h post-fertilization (hpf) zebrafish extract proteins showed a transient binding of a 30-kDa Vg1-like polypeptide to UV-damaged DNA. A transcription-based in vitro repair assay revealed a significant up-regulation of UVC or cisplatin-suppressed transcriptional activity of a marker cDNA driven by a SP6 RNA polymerase-regulated promotor after incubating the damaged plasmid with the extracts of 12 hpf embryos or 96 hpf larvae. The up-regulation of UV or cisplatin-suppressed transcription was abolished in the presence of a monoclonal anti-zebrafish Vg1 antibody. The differential sensitivity of UV-induced repair in 12 and 96 hpf zebrafish extracts to exogenous ATP suggested a development-dependent expression of Vg1-like NER factors. A T₄ endonuclease V digestion assay showed no inhibition of the anti-Vg1 antibody on the excision of UV-induced cyclobutane pyrimidine dimers. Our results identified the participation of Vg1-like factors in NER in developing zebrafish, and these factors may function at post-incison steps of NER.

A novel forward osmosis system in landfill leachate treatment for removing polycyclic aromatic hydrocarbons and for direct fertigation

Landfill leachate (LL) is harmful to aquatic environment because it contains high concentrations of dissolved organic matter, inorganic components, heavy metals, and other xenobiotics. Thus, the remediation of LL is crucial for environmental conservation. Here, a potential application of the forward osmosis (FO) filtration process with ammonium bicarbonate (NH₄HCO₃) as a draw solution (DS) was investigated to remediate membrane bioreactor-treated LL (M-LL). After the leachate treatment, the toxicity and removal efficiencies of polycyclic aromatic hydrocarbons (PAHs) were evaluated using zebrafish and cultured human cells. The water recovery rate was improved using the current protocol up to 86.6% and 91.6% by both the pressure retarded osmosis (PRO) mode and the forward osmosis (FO) mode. Water flux increased with the increasing DS concentrations, but solution velocities decreased with the operation time. Toxicity tests revealed that the M-LL treated by NH₄HCO₃ had no toxic effect on zebrafish and human cells. Moreover, green fluorescent protein (GFP) expression in the transgenic zebrafish Tg(cyp1a:gfp) induced by PAHs was very weak compared to the effects induced by untreated M-LL. Since the diluted DS met local safety requirements of liquid fertilizer, it could be directly applied as the liquid fertilizer for fertigation. In conclusion, this novel FO system using NH₄HCO₃ as the DS provides a cheap and efficient protocol to effectively remove PAHs and other pollutants in LL, and the diluted DS can be directly applied to crops as a liquid fertilizer, indicating that this technique is effective and eco-friendly for the treatment of different types of LL.

Oxidative stress intensity-related effects of cadmium (Cd) and paraquat (PQ) on UV-damaged-DNA binding and excision repair activities in zebrafish (Danio rerio) embryos

Our earlier studies showed the inhibitory effects of cadmium (Cd) and paraquat (PQ) on the gene expression of DNA mismatch recognition proteins in zebrafish (Danio rerio) embryos. This study explored the effects of Cd and PQ on nucleotide excision repair (NER) capacity in zebrafish embryos. Exposure of embryos at 1 h post fertilization (hpf) to 3-5 μM Cd or 30-100 μM PQ for 9 h induced a 2-3-fold increase of oxidative stress, while a 6.5-fold increase of oxidative stress was induced by 200 μM PQ. Real-time RT-PCR detected a down-regulated xeroderma pigmentosum C (XPC) and an up-regulated UV-DDB2 gene expression in mildly-stressed embryos, whereas 8-oxoguanine DNA glycosylase (OGG1) gene expression increased with PQ exposure levels. NER of UV-damaged DNA was enhanced in weakly oxidant-stressed embryos as shown by a transcription-based DNA repair assay, yet repair activities of both UV and cisplatin-damaged DNA were inhibited in embryos exposed to 200 μM PQ. Band shift assay showed a suppression of cyclobutane pyrimidine dimer (CPD) binding activity in all stressed embryos. In contrast, (6-4) photoproduct (6-4PP) recognition activity was weakly stimulated except in embryos exposed to 200 μM PQ, revealing a link of NER capacity to 6-4PP binding. Our results showed that Cd and PQ imposed similar inducing effects on UV-DDB2 gene expression, NER of UV-damaged DNA and 6-4PP binding activity in zebrafish embryo under low levels of oxidative stress and NER capacity could be inhibited if the intensity of oxidative stress increased to a critical level.

In vivo characterization of hair and skin derived carbon quantum dots with high quantum yield as long-term bioprobes in zebrafish

Carbon quantum dots (CDs) were widely investigated because of their tunable fluorescence properties and low toxicity. However, so far there have been no reports on in vivo functional studies of hair and skin derived CDs. Here, hair derived CDs (HCDs) and skin derived CDs (SCDs) were produced by using human hair and pig skin as precursors. The quantum yields (QYs) of HCDs and SCDs were quite high, compared to citric acid derived CDs (CCDs). HCDs and SCDs possess optimal photostability, hypotoxicity and biocompatibility in zebrafish, indicating that HCDs and SCDs possess the capacity of being used as fluorescence probes for in vivo biological imaging. The long-time observation for fluorescence alternation of CDs in zebrafish and the quenching assay of CDs by ATP, NADH and Fe3+ ions demonstrated that the decaying process of CDs in vivo might be induced by the synergistic effect of the metabolism process. All results indicated that large batches and high QYs of CDs can be acquired by employing natural and nontoxic hair and skin as precursors. To our knowledge, this is the first time to report SCDs, in vivo comparative studies of HCDs, SCDs and CCDs as bioprobes, and explore their mechanism of photostability in zebrafish.