Common responses of fish embryos to metals: an integrated analysis of transcriptomes and methylomes in zebrafish embryos under the stress of copper ions or silver nanoparticles

Metallomics ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1452-1464 ◽  
Author(s):  
ZhiPeng Tai ◽  
PengPeng Guan ◽  
ZiYang Wang ◽  
LingYa Li ◽  
Ting Zhang ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Differentially Expressed Genes ◽  
Gene Transcription ◽  
Copper Ions ◽  
Methylation Status ◽  
Integrated Analysis ◽  
Zebrafish Embryos ◽  
Differentially Methylated Regions ◽  
Fish Embryos ◽  
The Common

This study demonstrated the common responses of differentially expressed genes (DEGs) and differentially methylated regions (DMRs) under Cu2+ or AgNPs stresses in zebrafish, and verified the correlation of the gene transcription and the methylation status of some common DMGs.

scholarly journals The Relationship between Dissolution Behavior and the Toxicity of Silver Nanoparticles on Zebrafish Embryos in Different Ionic Environments

Nanomaterials ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 652 ◽  
Author(s):  
Wang Lee ◽  
Eungwang Kim ◽  
Hyun-Ju Cho ◽  
Taejoon Kang ◽  
Bongsoo Kim ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Polyethylene Glycol ◽  
Zebrafish Embryo ◽  
Antibacterial Properties ◽  
Dissolution Behavior ◽  
Aquatic Environments ◽  
Zebrafish Embryos ◽  
Negative Effects ◽  
The Relationship ◽  
Water Filters

A silver nanoparticle is one of the representative engineered nanomaterials with excellent optical, electrical, antibacterial properties. Silver nanoparticles are being increasingly used for medical products, water filters, and cosmetics, etc. However, silver nanoparticles are known to cause adverse effects on the ecosystem and human health. To utilize silver nanoparticles with minimized negative effects, it is important to understand the behavior of silver nanoparticles released to the environment. In this study, we compared toxicity behaviors of citrate-stabilized silver nanoparticles with polyethylene glycol coated silver nanoparticles in two different ionic environments, which are aquatic environments for developing zebrafish embryo. Depending on the composition of the ionic environment, citrate-stabilized silver nanoparticles and polyethylene glycol coated silver nanoparticles exhibited different behaviors in dissolution, aggregation, or precipitation, which governed the toxicity of silver nanoparticles on zebrafish embryos.

Reproducibility-optimized detection of differential DNA methylation

Epigenomics ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 747-755
Author(s):  
Veronika Suni ◽  
Fatemeh Seyednasrollah ◽  
Bishwa Ghimire ◽  
Sini Junttila ◽  
Asta Laiho ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Throughput Sequencing ◽  
State Of The Art ◽  
Methylation Status ◽  
Real Data ◽  
Epigenetic Mechanism ◽  
Methylation Analysis ◽  
Test Statistic ◽  
Differentially Methylated Regions ◽  
Dna Methylation Analysis

Aim: DNA methylation is a key epigenetic mechanism regulating gene expression. Identifying differentially methylated regions is integral to DNA methylation analysis and there is a need for robust tools reliably detecting regions with significant differences in their methylation status. Materials & methods: We present here a reproducibility-optimized test statistic (ROTS) for detection of differential DNA methylation from high-throughput sequencing or array-based data. Results: Using both simulated and real data, we demonstrate the ability of ROTS to identify differential methylation between sample groups. Conclusion: Compared with state-of-the-art methods, ROTS shows competitive sensitivity and specificity in detecting consistently differentially methylated regions.

scholarly journals Identification of the Differentially Expressed Genes of Muscle Growth and Intramuscular Fat Metabolism in the Development Stage of Yellow Broilers

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Dongfeng Li ◽  
Zaixu Pan ◽  
Kun Zhang ◽  
Minli Yu ◽  
Debing Yu ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Developmental Stage ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Intramuscular Fat ◽  
Regulatory Genes ◽  
Breast Muscle ◽  
Differentially Expressed ◽  
The Common

High-quality chicken meat is an important source of animal protein for humans. Gene expression profiles in breast muscle tissue were determined, aiming to explore the common regulatory genes relevant to muscle and intramuscular fat (IMF) during the developmental stage in chickens. Results show that breast muscle weight (BMW), breast meat percentage (BMP, %), and IMF (%) continuously increased with development. A total of 256 common differentially expressed genes (DEGs) during the developmental stage were screened. Among them, some genes related to muscle fiber hypertrophy were upregulated (e.g., CSRP3, LMOD2, MUSTN1, MYBPC1), but others (e.g., ACTC1, MYL1, MYL4) were downregulated from Week 3 to Week 18. During this period, expression of some DEGs related to the cells cycle (e.g., CCNB3, CCNE2, CDC20, MCM2) changed in a way that genetically suggests possible inhibitory regulation on cells number. In addition, DEGs associated with energy metabolism (e.g., ACOT9, CETP, LPIN1, DGAT2, RBP7, FBP1, PHKA1) were found to regulate IMF deposition. Our data identified and provide new insights into the common regulatory genes related to muscle growth, cell proliferation, and energy metabolism at the developmental stage in chickens.

scholarly journals An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability

2019 ◽  
Vol 20 (23) ◽  
pp. 5893 ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Wenzhong Zhang ◽  
Jiping Gao ◽  
Jun Yi ◽  
...  
Keyword(s):  
Root Growth ◽  
Differentially Expressed Genes ◽  
Nitrogen Availability ◽  
Rice Root ◽  
Integrated Analysis ◽  
High Nitrogen ◽  
Rice Roots ◽  
Regulation Mechanisms ◽  
Low Nitrogen ◽  
Nitrogen Conditions

Nitrogen is an essential nutrient for plant growth and basic metabolic processes. Root systems play an important role in the ability of plants to obtain nutrients from the soil, and are closely related to the growth and development of above-ground plants. Root morphology analysis showed that root growth was induced under low-nitrogen conditions and inhibited under high-nitrogen conditions. To better understand the molecular mechanisms and metabolic basis underlying the rice root response to nitrogen availability, an integrated analysis of the rice root transcriptome and metabolome under three environmental conditions (low-, control, and high-nitrogen conditions) was conducted. A total of 262 and 262 differentially level metabolites were identified under low- and high-nitrogen conditions, respectively. A total of 696 and 808 differentially expressed genes were identified under low- and high-nitrogen conditions, respectively. For both the differentially expressed genes and metabolites, KEGG pathway analysis indicated that amino acid metabolism, carbon and nitrogen metabolism, phenylpropanoid metabolism, and phytohormones’ signal transduction were significantly affected by nitrogen availability. Additionally, variable levels of 65 transcription factors (TFs) were identified in rice leaves exposed to high and low nitrogen, covering 22 TF families. These results also indicate that there is a significant difference in the transcriptional regulation mechanisms of rice roots between low and high nitrogen. In summary, our study provides new information for a further understanding of the response of rice roots to low-nitrogen and high-nitrogen conditions.

Toxicity of different-sized copper nano- and submicron particles and their shed copper ions to zebrafish embryos

2014 ◽  
Vol 33 (8) ◽  
pp. 1774-1782 ◽  
Author(s):  
Jing Hua ◽  
Martina G. Vijver ◽  
Farooq Ahmad ◽  
Michael K. Richardson ◽  
Willie J.G.M. Peijnenburg
Keyword(s):  
Copper Ions ◽  
Submicron Particles ◽  
Zebrafish Embryos

scholarly journals Integrated Analysis of mRNA Expression, CpG Island Methylation, and Polymorphisms in the MITF Gene in Ducks (Anas platyrhynchos)

2019 ◽  
Vol 2019 ◽  
pp. 1-9
Author(s):  
Ruiyi Lin ◽  
Weimin Lin ◽  
Shiye Zhou ◽  
Qiaohui Chen ◽  
Jiahua Pan ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Methylation Level ◽  
Cpg Island ◽  
Methylation Status ◽  
Cpg Islands ◽  
Plumage Coloration ◽  
Integrated Analysis ◽  
Nucleotide Polymorphisms ◽  
White Feather ◽  
Black Feather

Microphthalmia-associated transcription factor (MITF) is a key regulator for the development and function of melanocytes in skin, eye, and plumage pigmentations. Thus, the MITF was selected as a candidate gene associated with plumage coloration in ducks. This study analyzed the mRNA expression, promoter methylation, and polymorphisms in the MITF gene in ducks with different plumage colors (Putian Black, Putian White, Liancheng White, and Longsheng Jade-green). No expression of the MITF melanin-specific isoform (MITF-M) was detected in white feather bulbs. By contrast, the mRNA expression levels of MITF-M were high in black feather bulbs. Bioinformatics analysis showed that two CpG islands were present in the promoter region of the MITF gene. The methylation level of the second CpG island was significantly lower in black feather bulbs than in white feather bulbs. However, the methylation level of the first CpG island was not different among the feather bulbs with various colors except Liancheng White feather bulbs. The methylation status of the whole CpG island significantly and negatively correlated with the mRNA expression of MITF-M (P<0.05). Furthermore, four novel SNPs (single nucleotide polymorphisms) were identified in the 5′UTR, exon 4, intron 7, and intron 8 of the MITF gene. Allele T in g.39807T>G and allele G in g.40862G>A were the predominant alleles only found in Putian White, whereas the variant A allele in g.32813G>A exhibited a high allele frequency in Liancheng White. Collectively, these results contributed to the understanding of the function of the MITF gene in duck plumage coloration.

scholarly journals Ontogeny of ornithine-urea cycle gene expression in zebrafish (Danio rerio)

2013 ◽  
Vol 304 (11) ◽  
pp. R991-R1000 ◽  
Author(s):  
Christophe M. R. LeMoine ◽  
Patrick J. Walsh
Keyword(s):  
Gene Expression ◽  
Urea Cycle ◽  
Methylation Status ◽  
Zebrafish Embryos ◽  
Carbamoyl Phosphate ◽  
Differential Gene Regulation ◽  
Urea Production ◽  
Differential Gene ◽  
Waste Handling

Although the majority of adult teleosts excrete most of their nitrogenous wastes as ammonia, several fish species are capable of producing urea early in development. In zebrafish, it is unclear whether this results from a functional ornithine-urea cycle (O-UC) and, if so, how it might be regulated. This study examined the spatiotemporal patterns of gene expression of four major O-UC enzymes: carbamoyl phosphate synthase III (CPSIII), ornithine transcarboxylase, arginosuccinate synthetase, and arginosuccinate lyase, using real-time PCR and whole mount in situ hybridization. In addition, we hypothesized that CPSIII gene expression was epigenetically regulated through methylation of its promoter, a widespread mode of differential gene regulation between tissues and life stages in vertebrates. Furthermore, to assess CPSIII functionality, we used morpholinos to silence CPSIII in zebrafish embryos and assessed their nitrogenous waste handling during development, and in response to ammonia injections. Our results suggest that mRNAs of O-UC enzymes are expressed early in zebrafish development and colocalize to the embryonic endoderm. In addition, the methylation status of CPSIII promoter is not consistent with the patterns of expression observed in developing larvae or adult tissues, suggesting other means of transcriptional regulation of this enzyme. Finally, CPSIII morphants exhibited a transient reduction in CPSIII enzyme activity 24 h postfertilization, which was paralleled by reduced urea production during development and in response to an ammonia challenge. Overall, we conclude that the O-UC is functional in zebrafish embryos, providing further evidence that the capacity to produce urea via the O-UC is widespread in developing teleosts.

Phytogenic Synthesis of Nano Silver from Madagascar Periwinkle Extracts and Their Angiogenic Activities in Zebrafish Embryos (ZFE)

2020 ◽  
Vol 12 (1) ◽  
pp. 79-87
Author(s):  
Govindarajan Kathiravan ◽  
Kosuru Rekha Yamini ◽  
Kalyanaraman Rajagopal ◽  
Sambandam Anandan ◽  
Kwang Jin Kim ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Plant Extracts ◽  
Visible Spectrum ◽  
Inhibitory Effect ◽  
Zebrafish Embryos ◽  
Fragmentation Pattern ◽  
Madagascar Periwinkle ◽  
Plasmon Resonance Peak ◽  
Pathological Conditions ◽  
Vis Spectroscopy

Green biosynthesis of silver nanoparticles utilizing plant extracts is a simple, cost effective system of generating nanoparticles in an ecofriendly environment. In the present study, biosynthesis of silver nanoparticles was carried out using different parts of Madagascar periwinkle plant extracts. The production of the silver nanoparticles (AgNPs) was detected visually by change in color of the reaction mixture from yellow to reddish brown in a 8 h treatment at 37 °C. Further, the AgNPs were analyzed by various standard characterization techniques such UV-Vis spectroscopy, Electron Microscopy (TEM and SEM), FT-IR, and GC-MS analysis. The UV-Visible spectrum showed the plasmon resonance peak for AgNPs at 435 nm, indicating the formation of silver nanoparticles. FTIR analysis showed a good interaction between the plant extract and NPs. The morphology of the NPs varied in shape has observed through TEM with the particle size less than 10 nm. The phytoformulated nanoparticles were found to be well dispersed in solution and stable due to capping molecules present in the reaction mixture. The chromatographic analysis (GC-MS) displayed a prominent fragmentation pattern especially at the higher molecular weight in the range of 280 to 271. Angiogenesis is an important physiological process that plays a crucial role in several pathological conditions (tumor growth and metastasis). The green synthesized AgNPs were assessed for their angiogenic inhibition properties using zebrafish embryos as a model system. The biogenic AgNPs treatment at the dose of 100 μl and 150 μl showed significant anti-angiogenesis (inhibitory effect on angiogenesis), which represents more effectiveness in controlling the vessel formation during pathological conditions.

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