Molecular characterization and expression profiles of GATA6 in tongue sole (Cynoglossus semilaevis)

Luminescent Quantum Dots: Synthesis, Optical Properties, Bioimaging and Toxicity

Luminescent nanomaterials such as semiconductor nanocrystals (NCs) and quantum dots (QDs) attract much attention to optical detectors, LEDs, photovoltaics, displays, biosensing, and bioimaging. These materials include metal chalcogenide QDs and metal halide perovskite NCs. Since the introduction of cadmium chalcogenide QDs to biolabeling and bioimaging, various metal nanoparticles (NPs), atomically precise metal nanoclusters, carbon QDs, graphene QDs, silicon QDs, and other chalcogenide QDs have been infiltrating the nano-bio interface as imaging and therapeutic agents. Nanobioconjugates prepared from luminescent QDs form a new class of imaging probes for cellular and in vivo imaging with single-molecule, super-resolution, and 3D resolutions. Surface modified and bioconjugated core-only and core-shell QDs of metal chalcogenides (MX; M = Cd/Pb/Hg/Ag, and X = S/Se/Te,), binary metal chalcogenides (MInX₂; M = Cu/Ag, and X = S/Se/Te), indium compounds (InAs and InP), metal NPs (Ag, Au, and Pt), pure or mixed precision nanoclusters (Ag, Au, Pt), carbon nanomaterials (graphene QDs, graphene nanosheets, carbon NPs, and nanodiamond), silica NPs, silicon QDs, etc. have become prevalent in biosensing, bioimaging, and phototherapy. While heavy metal-based QDs are limited to in vitro bioanalysis or clinical testing due to their potential metal ion-induced toxicity, carbon (nanodiamond and graphene) and silicon QDs, gold and silica nanoparticles, and metal nanoclusters continue their in vivo voyage towards clinical imaging and therapeutic applications. This review summarizes the synthesis, chemical modifications, optical properties, and bioimaging applications of semiconductor QDs with particular references to metal chalcogenide QDs and bimetallic chalcogenide QDs. Also, this review highlights the toxicity and pharmacokinetics of QD bioconjugates.

Sexually Dimorphic Gene Expression in X and Y Sperms Instructs Sexual Dimorphism of Embryonic Genome Activation in Yellow Catfish (Pelteobagrus fulvidraco)

Paternal factors play an important role in embryonic morphogenesis and contribute to sexual dimorphism in development. To assess the effect of paternal DNA on sexual dimorphism of embryonic genome activation, we compared X and Y sperm and different sexes of embryos before sex determination. Through transcriptome sequencing (RNA-seq) and whole-genome bisulfite sequencing (WGBS) of X and Y sperm, we found a big proportion of upregulated genes in Y sperm, supported by the observation that genome-wide DNA methylation level is slightly lower than in X sperm. Cytokine-cytokine receptor interaction, TGF-beta, and toll-like receptor pathways play important roles in spermatogenesis. Through whole-genome re-sequencing (WGRS) of parental fish and RNA-seq of five early embryonic stages, we found the low-blastocyst time point is a key to maternal transcriptome degradation and zygotic genome activation. Generally, sexual differences emerged from the bud stage. Moreover, through integrated analysis of paternal SNPs and gene expression, we evaluated the influence of paternal inheritance on sexual dimorphism of genome activation. Besides, we screened out gata6 and ddx5 as potential instructors for early sex determination and gonad development in yellow catfish. This work is meaningful for revealing the molecular mechanisms of sex determination and sexual dimorphism of fish species.

Toxic effects of ZnSe/ZnS quantum dots on the reproduction and genotoxiticy of rare minnow (Gobiocypris rarus)

ZnSe/ZnS quantum dots (QDs) have excellent optical properties, but researchers have not clearly determined whether they cause harm to organisms. In the present study, the effect of ZnSe/ZnS QDs on the parents and offspring of rare minnow were evaluated for the first time. Exposure to ZnSe/ZnS QDs altered the testicular structure, caused sperm DNA damage and decreased sperm motility in males. They also suppressed the expression of reproduction-related genes, such as androgen receptor (Ar), DM-related transcription factor 1 (Dmrt1), estrogen receptor (Er), and X-ray repair cross complementing gene 1 (Xrcc1). Continued monitoring of the F1 generation revealed that the embryonic development of the F1 generation was abnormal and the growth index of the F1 generation of adult fish showed hormesis. A comet assay showed that the F1 generation still had DNA damage in the 400 and 800 nmol/L groups at 96 h post-fertilization (hpf). Thus, ZnSe/ZnS QDs damaged the reproductive system of the rare minnow, and this effect continued to the F1 generation.

Integrated lncRNA and mRNA Transcriptome Analyses in the Ovary of Cynoglossus semilaevis Reveal Genes and Pathways Potentially Involved in Reproduction

Long non-coding RNAs (lncRNAs) have been reported to be involved in multiple biological processes. However, the roles of lncRNAs in the reproduction of half-smooth tongue sole (Cynoglossus semilaevis) are unclear, especially in the molecular regulatory mechanism driving ovarian development and ovulation. Thus, to explore the mRNA and lncRNA mechanisms regulating reproduction, we collected tongue sole ovaries in three stages for RNA sequencing. In stage IV vs. V, we identified 312 differentially expressed (DE) mRNAs and 58 DE lncRNAs. In stage V vs. VI, we identified 1,059 DE mRNAs and 187 DE lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DE mRNAs were enriched in ECM-receptor interaction, oocyte meiosis and steroid hormone biosynthesis pathways. Furthermore, we carried out gene set enrichment analysis (GSEA) to identify potential reproduction related-pathways additionally, such as fatty metabolism and retinol metabolism. Based on enrichment analysis, DE mRNAs with a potential role in reproduction were selected and classified into six categories, including signal transduction, cell growth and death, immune response, metabolism, transport and catabolism, and cell junction. The interactions of DE lncRNAs and mRNAs were predicted according to antisense, cis-, and trans-regulatory mechanisms. We constructed a competing endogenous RNA (ceRNA) network. Several lncRNAs were predicted to regulate genes related to reproduction including cyp17a1, cyp19a1, mmp14, pgr, and hsd17b1. The functional enrichment analysis of these target genes of lncRNAs revealed that they were involved in several signaling pathways, such as the TGF-beta, Wnt signaling, and MAPK signaling pathways and reproduction related-pathways such as the progesterone-mediated oocyte maturation, oocyte meiosis, and GnRH signaling pathway. RT-qPCR analysis showed that two lncRNAs (XR_522278.2 and XR_522171.2) were mainly expressed in the ovary. Dual-fluorescence in situ hybridization experiments showed that both XR_522278.2 and XR_522171.2 colocalized with their target genes cyp17a1 and cyp19a1, respectively, in the follicular cell layer. The results further demonstrated that lncRNAs might be involved in the biological processes by modulating gene expression. Taken together, this study provides lncRNA profiles in the ovary of tongue sole and further insight into the role of lncRNA involvement in regulating reproduction in tongue sole.

Toxic effects of dechlorane plus on the common carp (Cyprinus carpio) embryonic development

Dechlorane Plus (DP) is a widely used chlorinated flame retardant, which has been extensively detected in the environment. Although DP content in the surface water is low, it can pose a continuous exposure risk to aquatic organisms due to its strong bioaccumulation. Considering that the related studies on the toxicity mechanism of DP exposure are limited, the effect of DP on carp embryo development was evaluated. In the present work, carp embryos were exposed to different concentrations (0, 30, 60, and 120 μg/L) of DP at 3 h post-fertilization (hpf). The expression levels of neural and skeletal development-associated genes, such as sox2, sox19a, Mef2c and BMP4, were detected with quantitative PCR, and the changes in different developmental toxicity endpoints were observed. Our results demonstrated that the expression levels of sox2, sox19a, Mef2c and BMP4 were significantly altered and several developmental abnormalities were found in DP-exposed carp embryos, such as DNA damage, increased mortality rate, delayed hatching time, reduced hatching rate, decreased body length, and increased morphological deformities. In addition, the activities of reactive oxygen species and malondialdehyde were remarkably higher in 60 and 120 μg/L DP exposure groups than in control group. These results suggest that DP can exhibit a unique modes of action, which lead to aberration occurrence in the early development stage of common carps, which may be related to some gene damage and oxidative stress. Besides, the parameters evaluated here can be used as tools to access the environmental risk for biota and humans exposed to DP.

Gonadal transcriptome analysis of the common carp, Cyprinus carpio: Identification of differentially expressed genes and SSRs

Common carp (Cyprinus carpio) is a world-wide freshwater fish of eutrophic waters. C. carpio, have various reproductive traits, including early sexual maturity, that may make them excellent, large, realistic, aquaculture model species. In the present work, de novo assembly of gonadal (testicular and ovarian) transcriptomes from juvenile common carp was performed to identify genes involved in gonadal development. A total of 81,757 and 43,257 transcripts with average lengths of 769 and 856 bp, were obtained from the immature testicular and ovarian transcriptomes, respectively. About 84,367 unigenes were constructed after removing redundancy involving representation of transcripts in both gonadal transcriptomes. Gene ontology (39,171 unigenes), clusters of orthologous group's analysis (6651 unigenes) and Kyoto encyclopedia of genes, and genomes automatic annotation server analysis (4783 unigenes) were performed to identify potential genes along with their functions. Furthermore, 18,342 (testis) and 8693 (ovary) simple sequence repeats were identified. About 298 differentially expressed genes were identified, of which 171 and 127 genes were up-regulated in testis and ovary, respectively. Quantitative real-time reverse transcription PCR was performed to validate differential expression of selected genes in testis and ovary. Nearly 809 genes related to reproduction were identified, sex-wise expression pattern of genes related to steroid synthesis, endocrine regulation, germ cell maintenance and others factors related to gonadal differentiation was observed, and expression analysis of nanos, ad4bp/sf-1, and gdf9 was performed. The present study identified certain important genes/factors involved in the gonadal development of C. carpio which may provide insights into the understanding of sex-differentiation and gonadal development processes.

Molecular characterization and expression profiles provide new insights into GATA5 functions in tongue sole (Cynoglossus semilaevis)

GATA5 is a member of the GATA transcription factor family, which serves essential roles in varieties of cellular functions and biological processes. In this study, we have accomplished the molecular cloning, bioinformatic analysis and preliminary function study of C. semilaevis GATA5. The full-length cDNA nucleotide sequence is 1955 bp, with a coding sequence of 1167 bp, which encodes a polypeptide of 388 amino acids. Homology, phylogenetic, gene structure and synteny analysis showed that C. semilaevis GATA5 was highly conserved among vertebrates. Tissue distribution pattern exhibited that C. semilaevis GATA5 was significantly expressed in heart, intestine, liver, kidney and gonad, with a sexual dimorphic feature observed in testis and ovary. Embryonic development expression profiles showed that C. semilaevis GATA5 transcripts increased at the blastula stage, and peaked at the heat-beating period. Strong signals were detected at spermatids of male testis and stage III oocytes of female ovary by ISH. The expression of C. semilaevis GATA5 was regulated by 17α-MT and E2 after hormone stimulation to the ovary. Together, all the results pointed out that GATA5 might play a vital role during gonadal maturation and the reproductive cycle of C. semilaevis. This study lays the foundation for further researches on the sex control breeding in tongue sole.

The comet assay in animal models: From bugs to whales - (Part 2 Vertebrates)

The comet assay has become one of the methods of choice for the evaluation and measurement of DNA damage. It is sensitive, quick to perform and relatively affordable for the evaluation of DNA damage and repair at the level of individual cells. The comet assay can be applied to virtually any cell type derived from different organs and tissues. Even though the comet assay is predominantly used on human cells, the application of the assay for the evaluation of DNA damage in yeast, plant and animal cells is also quite high, especially in terms of biomonitoring. The present extensive overview on the usage of the comet assay in animal models will cover both terrestrial and water environments. The first part of the review was focused on studies describing the comet assay applied in invertebrates. The second part of the review, (Part 2) will discuss the application of the comet assay in vertebrates covering cyclostomata, fishes, amphibians, reptiles, birds and mammals, in addition to chordates that are regarded as a transitional form towards vertebrates. Besides numerous vertebrate species, the assay is also performed on a range of cells, which includes blood, liver, kidney, brain, gill, bone marrow and sperm cells. These cells are readily used for the evaluation of a wide spectrum of genotoxic agents both in vitro and in vivo. Moreover, the use of vertebrate models and their role in environmental biomonitoring will also be discussed as well as the comparison of the use of the comet assay in vertebrate and human models in line with ethical principles. Although the comet assay in vertebrates is most commonly used in laboratory animals such as mice, rats and lately zebrafish, this paper will only briefly review its use regarding laboratory animal models and rather give special emphasis to the increasing usage of the assay in domestic and wildlife animals as well as in various ecotoxicological studies.

Klf4 could be activated by Pou5f3/Stat3 to induce the expression of Nanog in Japanese flounder

Krüppel-like factor 4 (Klf4) is a zinc finger protein transcription factor of the KLF family and plays an important role in various important biological process, including cell proliferation, differentiation, embryonic development, and cancer formation. In this study, the full length Klf4 cDNA sequence of Japanese flounder (Paralichthys olivaceus) was analyzed. Phylogenetic, gene structure, and synteny analysis revealed that PoKlf4 was conserved to that of teleost. Transcript of PoKlf4 showed that its expression was high during early embryonic development but reduced when gastrulation began, thus indicating its possible role in embryonic development. Tissue expression pattern showed that PoKlf4 was expressed higher in ovaries than in testes. ISH revealed that PoKlf4 was also expressed in spermatogonium, oocytes, and oogonia and in high levels in epithelial and lamellar epithelial cells of gills. Functional characterization of PoKlf4 gene promoter provided valuable information in understanding the molecular regulatory mechanisms of PoKlf4 gene. PoKlf4 could up-regulate Nanog, a gene that prevents ES cells from differentiating and being up-regulated by Pou5f3 and Stat3 genes that could maintain ES cell self-renewal. These results suggested that PoKlf4 maintains the pluripotency of ES cells. This study provides valuable information in exploring the regulatory network of PoKlf4 and lays the foundation for further research on the function of this gene.

InP/ZnS QDs exposure induces developmental toxicity in rare minnow (Gobiocypris rarus) embryos

We investigated the in vivo toxicity of InP/ZnS quantum dots (QDs) in Chinese rare minnow (Gobiocypris rarus) embryos. The 72 h post-fertilization (hpf) LC₅₀ (median lethal concentration) was 1678.007 nmol/L. Rare minnows exposed to InP/ZnS QDs exhibited decreased spontaneous movement, decreased survival and hatchability rates, and an increased malformation rate. Pericardial edema, spinal curvature, bent tails and vitelline cysts were observed. Embryonic Wnt8a and Mstn mRNA levels were significantly up-regulated after InP/ZnS QDs treatment at 48 hpf (200 nmol/L) (p < 0.05). The superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels at 96 hpf (800 nmol/L) had an increasing trend. Hsp70 mRNA expression was significantly changed at 48 hpf (200 nmol/L), but compared with the blank control, the different InP/ZnS QDs treatments did not significantly change the Olive tail moments (p > 0.05). Thus, InP/ZnS QDs caused teratogenic effects and death during the development of Chinese rare minnow embryos, but InP/ZnS QDs did not cause significant genetic toxicity during Chinese rare minnow development.

Biocompatible Semiconductor Quantum Dots as Cancer Imaging Agents

Approximately 1.7 million new cases of cancer will be diagnosed this year in the United States leading to 600 000 deaths. Patient survival rates are highly correlated with the stage of cancer diagnosis, with localized and regional remission rates that are much higher than for metastatic cancer. The current standard of care for many solid tumors includes imaging and biopsy with histological assessment. In many cases, after tomographical imaging modalities have identified abnormal morphology consistent with cancer, surgery is performed to remove the primary tumor and evaluate the surrounding lymph nodes. Accurate identification of tumor margins and staging are critical for selecting optimal treatments to minimize recurrence. Visible, fluorescent, and radiolabeled small molecules have been used as contrast agents to improve detection during real-time intraoperative imaging. Unfortunately, current dyes lack the tissue specificity, stability, and signal penetration needed for optimal performance. Quantum dots (QDs) represent an exciting class of fluorescent probes for optical imaging with tunable optical properties, high stability, and the ability to target tumors or lymph nodes based on surface functionalization. Here, state-of-the-art biocompatible QDs are compared with current Food and Drug Administration approved fluorophores used in cancer imaging and a perspective on the pathway to clinical translation is provided.

Identification and analysis of the β-catenin1 gene in half-smooth tongue sole (Cynoglossus semilaevis)

β-catenin is a key signalling molecule in the canonical Wnt pathway, which plays a role in cell adhesion, embryogenesis and sex determination. However, little is known about its function in teleosts. We cloned and characterized the full-length β-catenin1 gene from half-smooth tongue sole (Cynoglossus semilaevis), which was designated CS-β-catenin1. The CS-β-catenin1 cDNA consists of 2,346 nucleotides and encodes a protein with 782 amino acids. Although CS-β-catenin1 was transcribed in the gonads of both sexes, the level was significantly higher in ovaries compared to testes. Furthermore, the mRNA level of CS-β-catenin1 was significantly upregulated at 160 days and constantly increased until 2 years of age. In situ hybridization revealed that CS-β-catenin1 mRNA was mainly localized in oocyte cells, especially in stage I, II and III oocytes. When CS-β-catenin1 expression was inhibited by injection of quercetin in the ovaries, levels of CS-Figla and CS-foxl2 mRNA were significantly down-regulated, and CS-dmrt1 was up-regulated, which suggested that CS-β-catenin1 is a potential upstream gene of CS-Figla and is involved in the development of the ovaries, i.e., folliculogenesis.

Roles of GATA6 during Gonadal Development in Japanese Flounder: Gonadogenesis, Regulation of Gender-Related Genes, Estrogen Formation and Gonadal Function Maintenance

GATA-binding protein 6 (GATA6), a highly-conserved transcription factor of the GATA family plays an important role in gonadal cell proliferation, differentiation and endoderm development. In this study, the full-length cDNA of GATA6 of Paralichthys olivaceus (Japanese flounder) was obtained. Phylogenetic, gene structure and synteny analyses demonstrated that GATA6 of P. olivaceus is homologous to that of teleosts and tetrapods. The P. olivaceus GATA6 transcript showed higher expression in testis than in ovary, demonstrating a sexually dimorphic gene expression. During embryonic development, the expression of P. olivaceus GATA6 increased at the blastula stage, demonstrating that GATA6 is involved in morphogenesis. Results of in situ hybridization showed that GATA6 signals were detected in Sertoli cells, oogonia and oocytes. Moreover, 17α methyl testosterone, a male hormone, could moderately upregulate P. olivaceus GATA6 and downregulate P. olivaceus aromatase CYP19A1 in testis cells. These results suggest that GATA6 may play an important role in gonadal development in P. olivaceus. This study provides valuable information on the function of P. olivaceus GATA6, laying the foundation for further development of breeding techniques in this species.