Mitochondrial changes in fish cells in vitro in response to serum deprivation

Fan, Xiaoteng; Yan, Tao; Hou, Tingting; Xiong, Xiaofan; Feng, Leilei; Li, Shiyi; Wang, Zaizhao

doi:10.1007/s10695-022-01088-y

Cited by 4 publications

(2 citation statements)

References 51 publications

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“…The 12S rRNA region in mitochondria is often partially sequenced, and there are many reference sequences, but validated D-loop reference sequences are currently insufficient to support species assignment. The copy number of mitochondria is tens to hundreds of times greater than that of the nuclear genome (Hartmann et al 2011 ; Fan et al 2022 ), and full-length mitochondria can be easily assembled by low-coverage shotgun whole genome sequencing. Therefore, we attempted to add the D-loop sequence of fish species living in the seas around Japan to the database by sequencing the complete mitochondrial genome using thin shotgun whole-genome sequencing (Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Yoshitake

Yanagisawa

Sugimoto

et al. 2023

Funct Integr Genomics

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Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.

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Section: Resultsmentioning

confidence: 99%

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Yoshitake

Yanagisawa

Sugimoto

et al. 2023

Funct Integr Genomics

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“…Whole mtDNA was amplified by long-range PCR and sequencing to identify the mutation bases with nonsense or missense. mtDNA copy number and methylation were in accordance with our published protocols . The cytosolic mtDNA content was measured by the digitonin method with some modifications .…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial DNA Stress-Mediated Health Risk to Dibutyl Phthalate Contamination on Zebrafish (Danio rerio) at Early Life Stage

Fan,

Zhang,

Hou

et al. 2024

Environ. Sci. Technol.

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Plastics contaminations are found globally and fit the exposure profile of the planetary boundary threat. The plasticizer of dibutyl phthalate (DBP) leaching has occurred and poses a great threat to human health and the ecosystem for decades, and its toxic mechanism needs further comprehensive elucidation. In this study, environmentally relevant levels of DBP were used for exposure, and the developmental process, oxidative stress, mitochondrial ultrastructure and function, mitochondrial DNA (mtDNA) instability and release, and mtDNA-cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling pathway with inflammatory responses were measured in zebrafish at early life stage. Results showed that DBP exposure caused developmental impairments of heart rate, hatching rate, body length, and mortality in zebrafish embryo. Additionally, the elevated oxidative stress damaged mitochondrial ultrastructure and function and induced oxidative damage to the mtDNA with mutations and instability of replication, transcription, and DNA methylation. The stressed mtDNA leaked into the cytosol and activated the cGAS-STING signaling pathway and inflammation, which were ameliorated by co-treatment with DBP and mitochondrial reactive oxygen species (ROS) scavenger, inhibitors of cGAS or STING. Furthermore, the larval results suggest that DBP-induced mitochondrial toxicity of energy disorder and inflammation were involved in the developmental defects of impaired swimming capability. These results enhance the interpretation of mtDNA stress-mediated health risk to environmental contaminants and contribute to the scrutiny of mitochondrial toxicants.

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Insight into the health risk implicated in mitochondrial toxicity of dibutyl phthalate exposure on zebrafish (Danio rerio) cells

et al. 2023

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Mitochondrial changes in fish cells in vitro in response to serum deprivation

Cited by 4 publications

References 51 publications

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Mitochondrial DNA Stress-Mediated Health Risk to Dibutyl Phthalate Contamination on Zebrafish (Danio rerio) at Early Life Stage

Insight into the health risk implicated in mitochondrial toxicity of dibutyl phthalate exposure on zebrafish (Danio rerio) cells

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