Jian He’s research while affiliated with Minjiang University and other places

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Publications (42)


Mandarin fish tankyrase 1-like protein regulates the Wnt/β-catenin pathway and facilitates the infectious spleen and kidney necrosis virus replication
  • Article
  • Full-text available

June 2025

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20 Reads

Zhimin Li

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Yashan Wu

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Jian He

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[...]

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Jianguo He
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Figure 1. The workflow of identifying circRNA.
Top 10 enrichments of the gene ontology (GO) analysis of the host DE-circRNA genes.
Cont.
Transcriptome Analysis of Muscle Growth-Related circRNA in the Pacific Abalone Haliotis discus hanna

January 2025

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17 Reads

Genes

(1) Background: Animal growth is a complex process, involving the coordination of a wide variety of genes, non-coding RNAs, and pathways. Circular RNAs (circRNAs) belong to a novel class of functional non-coding RNAs (ncRNAs). They have a distinctive ring structure and are involved in various biological processes, including the proliferation, differentiation, and apoptosis of muscle cells. The Pacific abalone Haliotis discus hannai is an economically valuable mollusk species cultivated in China. However, the modulation of muscle growth by circRNAs in this species is poorly understood. (2) Methods: In this study, we analyzed the muscle transcriptomes of 6 H. discus hannai specimens: three small (S_HD) and three large (L_HD) groups via RNA-seq and bioinformatics technology. (3) Results: The results indicated the presence of 11,744 circRNAs in abalone adductor muscle. Furthermore, the L_HD group had 250 significantly differentially expressed circRNAs (106 upregulated and 144 downregulated) relative to the S_HD group. Moreover, the bioinformatics assessment revealed that circRNAs were related to lipid transporter activity, lipid biosynthetic process, fat digestion and absorption, the single-organism metabolic process, the thyroid hormone signaling pathway, and the hippo signaling pathway, which regulates growth. Seventeen key candidate circRNAs were identified, and a core functional circRNA-miRNA-mRNA network associated with abalone muscle growth was described. Gene expression was verified using qRT-PCR, confirming the accuracy of the RNA-seq data. (4) Conclusion: Overall, this investigation furnishes novel evidence for the potential muscle growth modulatory mechanisms in Pacific abalone. These high-quality circRNA data of abalone muscle provide a reference for functional studies on the abalone genome.


Genome assembly of C. quadricarinatus. Circos plot of the distribution of genomic elements in C. quadricarinatus. a GC content; b Density of tandem repeats; c Density of transposable elements; d Gene density
The evolution of genome sizes in decapod crustaceans. A The comparison of genome sizes, transposable element (TE) content, and tandem repeat (TR) content among decapod species. B The correlation between TE content and genome sizes in decapod species. C The correlation between TR content and genome sizes in decapod species. D Frequency distribution of the synonymous substitution rates (Ks) among syntenic gene pairs of decapod species
The evolution of gene families in decapod crustaceans. A A species tree of 13 arthropod species with D. melanogaster as outgroup. B Gene family expansion and contraction analysis of decapod crustaceans. Numbers of expanded gene families are marked in green, and numbers of contracted gene families are marked in red. The number below the MRCA (most recent common ancestor) represents the total number of orthologs from OrthoMCL analysis used as input for CAFE expansion/contraction analysis. C The comparison of gene numbers within the nine expanded immune-related gene families among arthropod species. D A phylogenetic tree of IgLectin Proteins from C. quadricarinatus, P. clarkii, S. paramamosain, E. sinensis. E Genomic distribution of IgLectin genes in C. quadricarinatus
The role of KDM5A in the hypoxic tolerance of C. quadricarinatus and L. vannamei. A RNA interference (RNAi) of the CqKDM5A gene in C. quadricarinatus. B Survival of wild-type, KDM5A-silenced, and GFP dsRNA treated C. quadricarinatus reared under normoxic and hypoxic conditions. C Quantification of the expression levels of CqKDM5A in adult and juvenile C. quadricarinatus. D Survival of adult and juvenile C. quadricarinatus when exposed to hypoxic stresses
Genome assembly of redclaw crayfish (Cherax quadricarinatus) provides insights into its immune adaptation and hypoxia tolerance

July 2024

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141 Reads

BMC Genomics

Background The introduction of non-native species is a primary driver of biodiversity loss in freshwater ecosystems. The redclaw crayfish (Cherax quadricarinatus) is a freshwater species that exhibits tolerance to hypoxic stresses, fluctuating temperatures, high ammonia concentration. These hardy physiological characteristics make C. quadricarinatus a popular aquaculture species and a potential invasive species that can negatively impact tropical and subtropical ecosystems. Investigating the genomic basis of environmental tolerances and immune adaptation in C. quadricarinatus will facilitate the development of management strategies of this potential invasive species. Results We constructed a chromosome-level genome of C. quadricarinatus by integrating Nanopore and PacBio techniques. Comparative genomic analysis suggested that transposable elements and tandem repeats drove genome size evolution in decapod crustaceans. The expansion of nine immune-related gene families contributed to the disease resistance of C. quadricarinatus. Three hypoxia-related genes (KDM3A, KDM5A, HMOX2) were identified as being subjected to positive selection in C. quadricarinatus. Additionally, in vivo analysis revealed that upregulating KDM5A was crucial for hypoxic response in C. quadricarinatus. Knockdown of KDM5A impaired hypoxia tolerance in this species. Conclusions Our results provide the genomic basis for hypoxic tolerance and immune adaptation in C. quadricarinatus, facilitating the management of this potential invasive species. Additionally, in vivo analysis in C. quadricarinatus suggests that the role of KDM5A in the hypoxic response of animals is complex.


Molecular mechanism of infectious spleen and kidney necrosis virus in manipulating the hypoxia-inducible factor pathway to augment virus replication

April 2024

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29 Reads

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2 Citations

Infectious spleen and kidney necrosis virus (ISKNV), a member of the genus Megalocytivirus in the family Iridoviridae, can infect over 50 fish species and cause significant economic losses in Asia. Our previous study showed that hypoxia triggers the hypoxia-inducible factor pathway (HIF-pathway), leading to increased replication of ISKNV through promoting the upregulation of viral hypoxic response genes like orf077r. This study delved into the molecular mechanism of how ISKNV manipulates the HIF-pathway to enhance its replication. In vitro and in vivo experiments confirmed that ISKNV infection activated the HIF-pathway, which in turn promoted ISKNV replication. These findings suggest that ISKNV actively manipulates the HIF-pathway. Co-immunoprecipitation experiments revealed that the ISKNV-encoded protein VP077R interacts with the Von Hippel−Lindau (VHL) protein at the HIF-binding region, competitively inhibiting the interaction of HIF-1α with VHL. This prevents HIF degradation and activates the HIF-pathway. Furthermore, VP077R interacts with factor-inhibiting HIF (FIH), recruiting FIH and S-phase kinase-associated protein 1 (Skp1) to form an FIH – VP077R – Skp1 complex. This complex promotes FIH protein degradation via ubiquitination, further activating the HIF-pathway. These findings indicated that ISKNV takes over the HIF-pathway by releasing two “brakes” on this pathway (VHL and FIH) via VP077R, facilitating virus replication. We speculate that hypoxia initiates a positive feedback loop between ISKNV VP077R and the HIF pathway, leading to the outbreak of ISKNV disease. This work offers valuable insights into the complex interactions between the environment, host, and virus.


Architecture of the baculovirus nucleocapsid revealed by cryo-EM

November 2023

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172 Reads

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6 Citations

Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) has been widely used as a bioinsecticide and a protein expression vector. Despite their importance, very little is known about the structure of most baculovirus proteins. Here, we show a 3.2 Å resolution structure of helical cylindrical body of the AcMNPV nucleocapsid, composed of VP39, as well as 4.3 Å resolution structures of both the head and the base of the nucleocapsid composed of over 100 protein subunits. AcMNPV VP39 demonstrates some features of the HK97-like fold and utilizes disulfide-bonds and a set of interactions at its C-termini to mediate nucleocapsid assembly and stability. At both ends of the nucleocapsid, the VP39 cylinder is constricted by an outer shell ring composed of proteins AC104, AC142 and AC109. AC101(BV/ODV-C42) and AC144(ODV-EC27) form a C14 symmetric inner layer at both capsid head and base. In the base, these proteins interact with a 7-fold symmetric capsid plug, while a portal-like structure is seen in the central portion of head. Additionally, we propose an application of AlphaFold2 for model building in intermediate resolution density.


Oxygen-Sensing Protein Cysteamine Dioxygenase from Mandarin Fish Involved in the Arg/N-Degron Pathway and Siniperca chuatsi Rhabdovirus Infection

July 2023

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50 Reads

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5 Citations

Mammalia cysteamine (2-aminoethanethiol) dioxygenase (ADO) controls the stability of the regulator of G protein signaling 4 (RGS4) through the Cys branch of the Arg/N-degron pathway, thereby affecting the response of the body to hypoxia. However, the oxygen-sensing function of ADO remains unknown in teleost fish. Mandarin fish (Siniperca chuatsi) is one of the most important freshwater economic fishes in China. As the scale of the rearing density continues to increase, hypoxia has become an important factor threatening the growth of mandarin fish. Herein, the molecular characterization, the oxygen-sensing enzyme function, and the role in virus infection of ADO from mandarin fish (scADO) were explored. Bioinformation analysis results showed that scADO had all the molecular foundations for achieving thiol dioxygenase function: three histidine residues coordinated with Fe(II), PCO/ADO domain, and a “jelly roll” β-barrel structure. The expression pattern analysis showed that scAdo was highly expressed in the immune-related tissues, liver, and kidneys and responded to hypoxia on the expression level. Protein degradation experiment results revealed that scADO could lead to the degradation of RGS4 protein through the Cys branch of the Arg/N-degron pathway. Furthermore, the expression levels of scADO responded to fish virus infection. scADO could significantly promote the replication of Siniperca chuatsi rhabdovirus, and this was associated with its thiol dioxygenase activity. These findings not only demonstrate scADO as an oxygen-sensing protein in teleost fish, but are also of considerable importance for clarifying the contribution of the mechanism of hypoxia to the outbreaks of fish viruses.


Figure 2. scPHD2 inhibited the HIF-1 signaling pathway. (A) The scHIF-1 signaling pathway was inhibited by scPHD2. When the MFF-1 cells reached approximately 70% confluency, they were used for transfection. Four treatments were designed: 0.2 μg pGL4-HREs-luc + 0.2 μg pCMV-Flag + 0.2 μg pCMV-Myc + 0.02 μg pRT-TK; 0.2 μg pGL4-HREs-luc + 0.2 μg Flag-scHIF-1α + 0.2 μg pCMVMyc + 0.02 μg pRT-TK; 0.2 μg pGL4-HREs-luc + 0.2 μg Flag-scHIF-1α + 0.2 μg Myc-scPHD2 + 0.02 μg pRT-TK; 0.2 μg pGL4-HREs-luc + 0.2 μg pCMV-Flag + 0.2 μg Myc-scPHD2 + 0.02 μg pRT-TK. Luciferase activity was measured after 24 h. Firefly luciferase activity value was compared with Renilla luciferase activity. The y-axis represents the relative luciferase activities. Data are presented as the mean ± SD from three independent triplicated experiments. **, p < 0.01 versus the controls. (B) Increased scPHD2 inhibited the scHIF-1 signaling pathway in a dose-dependent manner. MFFFigure 2. scPHD2 inhibited the HIF-1 signaling pathway. (A) The scHIF-1 signaling pathway was inhibited by scPHD2. When the MFF-1 cells reached approximately 70% confluency, they were used for transfection. Four treatments were designed: 0.2 µg pGL4-HREs-luc + 0.2 µg pCMV-Flag + 0.2 µg pCMV-Myc + 0.02 µg pRT-TK; 0.2 µg pGL4-HREs-luc + 0.2 µg Flag-scHIF-1α + 0.2 µg pCMV-Myc + 0.02 µg pRT-TK; 0.2 µg pGL4-HREs-luc + 0.2 µg Flag-scHIF-1α + 0.2 µg Myc-scPHD2 + 0.02 µg pRT-TK; 0.2 µg pGL4-HREs-luc + 0.2 µg pCMV-Flag + 0.2 µg Myc-scPHD2 + 0.02 µg pRT-TK. Luciferase activity was measured after 24 h. Firefly luciferase activity value was compared with Renilla luciferase activity. The y-axis represents the relative luciferase activities. Data are presented as the mean ± SD from three independent triplicated experiments. **, p < 0.01 versus the controls. (B) Increased scPHD2 inhibited the scHIF-1 signaling pathway in a dose-dependent manner. MFF-1 cells were transfected with either Flag-scHIF-1α or increasing doses of Myc-scPHD2, and the firefly luciferase activity value was compared with Renilla luciferase activity. Flag-scHIF-1α and Myc-scPHD2 expression were analyzed by Western blotting after 24 h of transfection (right image). Data are presented as the mean ± SD from three independent triplicate experiments. **, p < 0.01; *, p < 0.05 versus the controls. (C-E) Expression patterns of scvegf, scldha, and scglut-1 genes determined by RT-qPCR after cells were overexpressed with scHIF-1α and scPHD2. The β-actin served as an internal control. The y-axis represents the relative mRNA expression. Asterisks above bars represent statistically significant differences among the control samples. **, p < 0.01.
Molecular Characterization and Functional Analysis of Hypoxia-Responsive Factor Prolyl Hydroxylase Domain 2 in Mandarin Fish (Siniperca chuatsi)

May 2023

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10 Reads

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6 Citations

Animals

With increased breeding density, the phenomenon of hypoxia gradually increases in aquaculture. Hypoxia is primarily mediated by the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Prolyl hydroxylase domain proteins (PHD) are cellular oxygen-sensing molecules that regulate the stability of HIF-1α through hydroxylation. In this study, the characterization of the PHD2 from mandarin fish Siniperca chuatsi (scPHD2) and its roles in the HIF-1 signaling pathway were investigated. Bioinformation analysis showed that scPHD2 had the conserved prolyl 4-hydroxylase alpha subunit homolog domains at its C-terminal and was more closely related to other Perciformes PHD2 than other PHD2. Tissue-distribution results revealed that scphd2 gene was expressed in all tissues tested and more highly expressed in blood and liver than in other tested tissues. Dual-luciferase reporter gene and RT-qPCR assays showed that scPHD2 overexpression could significantly inhibit the HIF-1 signaling pathway. Co-immunoprecipitation analysis showed that scPHD2 could interact with scHIF-1α. Protein degradation experiment results suggested that scPHD2 could promote scHIF-1α degradation through the proteasome degradation pathway. This study advances our understanding of how the HIF-1 signaling pathway is regulated by scPHD2 and will help in understanding the molecular mechanisms underlying hypoxia adaptation in teleost fish.


The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment

February 2023

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161 Reads

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7 Citations

BMC Genomics

Background Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated. Result We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae. Conclusion Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.


The Interaction of Mandarin Fish DDX41 with STING Evokes type I Interferon Responses Inhibiting Ranavirus Replication

December 2022

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23 Reads

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10 Citations

DDX41 is an intracellular DNA sensor that evokes type I interferon (IFN-I) production via the adaptor stimulator of interferon gene (STING), triggering innate immune responses against viral infection. However, the regulatory mechanism of the DDX41-STING pathway in teleost fish remains unclear. The mandarin fish (Siniperca chuatsi) is a cultured freshwater fish species that is popular in China because of its high market value. With the development of a high-density cultural mode in mandarin fish, viral diseases have increased and seriously restricted the development of aquaculture, such as ranavirus and rhabdovirus. Herein, the role of mandarin fish DDX41 (scDDX41) and its DEAD and HELIC domains in the antiviral innate immune response were investigated. The level of scDDX41 expression was up-regulated following treatment with poly(dA:dT) or Mandarin fish ranavirus (MRV), suggesting that scDDX41 might be involved in fish innate immunity. The overexpression of scDDX41 significantly increased the expression levels of IFN-I, ISGs, and pro-inflammatory cytokine genes. Co-immunoprecipitation and pull-down assays showed that the DEAD domain of scDDX41 recognized the IFN stimulatory DNA and interacted with STING to activate IFN-I signaling pathway. Interestingly, the HELIC domain of scDDX41 could directly interact with the N-terminal of STING to induce the expression levels of IFN-I and ISGs genes. Furthermore, the scDDX41 could enhance the scSTING-induced IFN-I immune response and significantly inhibit MRV replication. Our work would be beneficial to understand the roles of teleost fish DDX41 in the antiviral innate immune response.


Genome assembly statistics of four deep-sea vestimentiferan tubeworms 905
The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment

August 2022

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99 Reads

Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in the deep-sea hydrothermal vent and cold seep areas. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to the endemic environments. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, is remained to be investigated. Here we report a high-quality genome of R. piscesae collected at Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis revealed that that the high growth rates of vent-dwelling tubeworms might derive from small genome size. The small genome sizes of these tubeworms are attributed to the repeat content but not the number of genes and intron sizes. Additionally, four genes involved in cell proliferation were subject to positive selection in the genome of R. piscesae, suggesting that, besides apoptosis, cell proliferation is important for regulating growth rate in this species.


Citations (34)


... To understand the provenance and biology of baculo-like viruses, we have determined the structure of the nucleocapsid in the intact BV of the prototypical baculovirus, Autographa californica multiple nucleopolyhedrovirus (AcMNPV). We find that the BV nucleocapsid is a cross-linked tube with a unique molecular organization, and discuss key differences with recent structures of baculovirus nucleocapsids (21,22). In addition, based on a comprehensive structural atlas of the 38 conserved baculovirus proteins, we identify hallmarks in the viral architecture and a set of conserved proteins involved in assembly and virulence that support the independent origin of baculo-like viruses compared to viruses from existing viral realms. ...

Reference:

The nucleocapsid architecture and structural atlas of the prototype baculovirus define the hallmarks of a new viral realm
Architecture of the baculovirus nucleocapsid revealed by cryo-EM

... and SCRV strain NH-2103 (Gen-Bank: PQ066876.1) were separated and stored in our laboratory [16]. For virus infection, cells were infected with the respective viruses at a MOI of 1. ...

Oxygen-Sensing Protein Cysteamine Dioxygenase from Mandarin Fish Involved in the Arg/N-Degron Pathway and Siniperca chuatsi Rhabdovirus Infection

... Subsequently, TBLASTN was performed to the transcriptome database of S. chuatsi with an e-value of e − 10 to collect target genes (accession numbers of NCBI Reference Sequence listed in Supplementary Material 2). Phylogenetic trees were constructed via the Molecular Evolutionary Genetics Analysis (MEGA) v10.0 software, utilizing 1000 bootstrap replicates, as previously described [18]. ...

Molecular Characterization and Functional Analysis of Hypoxia-Responsive Factor Prolyl Hydroxylase Domain 2 in Mandarin Fish (Siniperca chuatsi)

Animals

... The bacteriocyte-containing trophosome is in the trunk. Recently, several vestimentiferan genomes have been released, and this has increased our understanding of the adaptation mechanisms of vestimentiferans to symbiosis [6][7][8][9][10]. For example, certain genes thought to be involved in symbiont − host interactions appear to be expanded [6]. ...

The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment

BMC Genomics

... and Siniperca chuatsi rhabdovirus (SCRV) strain NH-2103 (GenBank: PQ066876.1) were isolated and stored in our laboratory as previously described Qin et al., 2022;. Cells were infected with the respective viruses at a multiplicity of infection (MOI) of 1. ...

The Interaction of Mandarin Fish DDX41 with STING Evokes type I Interferon Responses Inhibiting Ranavirus Replication

... Bias-free solar-to-chemical conversion (SCC) shows promise for establishing a sustainable lowcarbon pathway for energy resource production [1][2][3][4] . Compared with the use of H2 as an energy carrier (2.8 MJ L -1 at 35 MPa), hydrogen peroxide (H2O2) has a comparable energy density (3.0 MJ L -1 for 60% aqueous H2O2) and superior storage, transport, and utilization processes [5][6][7] . ...

Spontaneous exciton dissociation in organic photocatalyst under ambient conditions for highly efficient synthesis of hydrogen peroxide

Proceedings of the National Academy of Sciences

... This unfavorable aquatic habitat can induce fish hypoxia response, which has maximum adverse effects on behavior, physiology, growth and survival [4]. What's worse, fish reduce their resistance versus other environmental stress under hypoxic conditions, such as high temperature, salinity and pathogen infection [5][6][7]. With water pollution and global warming more serious, hypoxia has become increasingly problematic since hypoxia are gradually rising every year in the aquaculture industry. ...

Hypoxia triggers the outbreak of infectious spleen and kidney necrosis virus disease through viral hypoxia response elements

... Antarctic krill samples (58-60° W, 62-64° S) were collected from the East China Sea Fisheries Research Institute (Shanghai, China) in 2016 (Wang et al., 2022). Sample processing was carried out according to our previous methods (Feng et al., 2023;Wang et al., 2021). ...

Environmental risk characteristics of bacterial antibiotic resistome in Antarctic krill

Ecotoxicology and Environmental Safety

... HEC served as a proton donor, thus facilitating a consecutive two-step single-electron reduction of oxygen to produce H 2 O 2 (Fig. 5b). As AQ can increase the selectivity for H 2 O 2 production, it is often used to modify polymer photocatalysts [72][73][74][75]. A two-dimensional catalyst of Co 1 /AQ/C 3 N 4 was developed by strategically positioning a single cobalt atom above the vacant center of C 3 N 4 and affixing AQ molecules along the edges of the C 3 N 4 nanosheets [72]. ...

A solar-to-chemical conversion efficiency up to 0.26% achieved in ambient conditions
  • Citing Article
  • November 2021

Proceedings of the National Academy of Sciences