Multi-omics analysis provides insight into the phytotoxicity of chicken manure and cornstalk on seed germination

Kong, Yan; Wang, Guoying; Tang, Huan; Jun, Yu; Yang, Yan; Wang, Jiani; Li, Guoxue; Li, Yun; Yuan, Jing

doi:10.1016/j.scitotenv.2022.160611

Cited by 15 publications

(3 citation statements)

References 69 publications

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“…Auxin regulates growth and developmental processes by being engaged in cell division and growth, tissue differentiation, organ development, and a range of physiological responses throughout the whole lifetime of all plants [ 35 ]. Auxin also has regulatory functions by promoting the expression of early auxin-responsive genes such AUX/IAA , Gretchen Hagen ( GH3 ), and small growth hormone up-regulated RNA ( SAUR ) genes [ 36 ]. In our study, 84 up-regulated DEGs were significantly enriched in the “plant hormone signal transduction” (ko04075) pathway and a total of 40 DEGs were identified in the auxin pathway ( Figure 5 A and Figure 6 A).…”

Section: Discussionmentioning

confidence: 99%

Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi

Li,

Xi,

Gao

et al. 2023

IJMS

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Hypocotyl length is a critical determinant for the efficiency of mechanical harvesting in pakchoi production, but the knowledge on the molecular regulation of hypocotyl growth is very limited. Here, we report a spontaneous mutant of pakchoi, lhy7.1, and identified its characteristics. We found that it has an elongated hypocotyl phenotype compared to the wild type caused by the longitudinal growth of hypocotyl cells. Different light quality treatments, transcriptome, and proteomic analyses were performed to reveal the molecular mechanisms of hypocotyl elongation. The data showed that the hypocotyl length of lhy7.1 was significantly longer than that of WT under red, blue, and white lights but there was no significant difference under dark conditions. Furthermore, we used transcriptome and label-free proteome analyses to investigate differences in gene and protein expression levels between lhy7.1 and WT. At the transcript level, 4568 differentially expressed genes (DEGs) were identified, which were mainly enriched in “plant hormone signal transduction”, “photosynthesis”, “photosynthesis–antenna proteins”, and “carbon fixation in photosynthetic organisms” pathways. At the protein level, 1007 differentially expressed proteins (DEPs) were identified and were mainly enriched in photosynthesis-related pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network of hypocotyl elongation involving plant hormone signal transduction and photosynthesis-related pathways. The findings of this study help elucidate the regulatory mechanisms of hypocotyl elongation in lhy7.1.

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Section: Discussionmentioning

confidence: 99%

Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi

Li,

Xi,

Gao

et al. 2023

IJMS

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“…The total RNA and protein samples were sent to Allwegene Technology Company Limited (Beijing, China) for further processing and bioinformatics analysis. The detailed process was performed as previously described [ 25 , 26 ]. For RNA-Seq, p value < 0.005 and |log2(fold change)| ≥ 1 were set as the threshold for significantly differential expression.…”

Section: Methodsmentioning

confidence: 99%

Antifungal Activity, Synergism with Fluconazole or Amphotericin B and Potential Mechanism of Direct Current against Candida albicans Biofilms and Persisters

Zou,

Liu,

et al. 2024

Antibiotics

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Candida albicans, as a notorious fungal pathogen, is associated with high morbidity and mortality worldwide due to its ability to form biofilms and persisters that can withstand currently available antifungals. Direct current (DC) has demonstrated a promising antimicrobial effect and synergistic effect with antimicrobials against various infections. Here, we first found DC exerted a killing effect on C. albicans planktonic and biofilm cells. Moreover, DC showed a synergistic effect with fluconazole (FLC) and amphotericin B (AMB). Notably, near-to-complete eradication of AMB-tolerant C. albicans biofilm persisters was achieved upon DC treatment. Next, the mechanism of action of DC was explored through mapping the genes and proteomic profiles of DC-treated C. albicans. The multi-omics analysis, quantitative real-time PCR and assay of reactive oxygen species (ROS) demonstrated DC exerted an antifungal effect on C. albicans by increasing cellular oxidative stress. As revealed by multiple analyses (e.g., protein assay based on absorbance at 280 nm and rhodamine 6G assay), DC was able to enhance membrane permeability, inhibit drug efflux and increase cellular FLC/AMB concentration of C. albicans, thereby mediating its synergism with the antifungals. Furthermore, DC inhibited superoxide dismutase 2 (SOD2) expression and manganese-containing SOD (Mn SOD) activity, leading to ROS production and enhanced killing of C. albicans biofilm persisters. The current findings demonstrate that the adjunctive use of DC in combination with antifungals is a promising strategy for effective control of C. albicans infections and management of antifungal resistance/tolerance in Candida biofilms.

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“…The germination assay is one of the primary measures of seed quality, and it is inextricably related to other seeds and seedlings' vigor tests such as the seedling development test [89,90]. The hydrothermal duration of germination experiments may explain barley seeds' tolerance to abiotic stress, uniformity, and germination viability.…”

Section: Water Availability Experimentsmentioning

confidence: 99%

Effect of Abiotic Stresses from Drought, Temperature, and Density on Germination and Seedling Growth of Barley (Hordeum vulgare L.)

Tarnawa

Kende

Sghaier

et al. 2023

Plants

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Seed germination and seedling growth are highly sensitive to deficit moisture and temperature stress. This study was designed to investigate barley (Hordeum vulgare L.) seeds’ germination and seedling growth under conditions of abiotic stresses. Constant temperature levels of 5, 10, 15, 20, 25, 30, and 35 °C were used for the germination test. Drought and waterlogging stresses using 30 different water levels were examined using two methods: either based at 1 milliliter intervals or, on the other hand, as percentages of thousand kernel weight (TKW). Seedling density in a petri dish and antifungal application techniques were also investigated. Temperature significantly impacted germination time and seedling development with an ideal range of 15–20 °C, with a more comprehensive range to 10 °C. Higher temperatures reversely affected germination percentage, and the lower ones affected the germination and seedling growth rate. Germination commenced at 130% water of the TKW, and the ideal water range for seedling development was greater and more extensive than the range for germination, which means there is a difference between the starting point for germination and the seedling development. Seed size define germination water requirements and provides an objective and more precise basis suggesting an optimal range supply of 720% and 1080% of TKW for barley seedling development. A total of 10 seeds per 9 cm petri dish may be preferable over greater densities. The techniques of priming seeds with an antifungal solution (Bordóilé or Hypo) or antifungal application at even 5 ppm in the media significantly prevented fungal growth. This study is novel regarding the levels and types of abiotic stresses, the crop, the experimental and measurement techniques, and in comparison to the previous studies.

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Multi-omics analysis provides insight into the phytotoxicity of chicken manure and cornstalk on seed germination

Cited by 15 publications

References 69 publications

Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi

Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi

Antifungal Activity, Synergism with Fluconazole or Amphotericin B and Potential Mechanism of Direct Current against Candida albicans Biofilms and Persisters

Effect of Abiotic Stresses from Drought, Temperature, and Density on Germination and Seedling Growth of Barley (Hordeum vulgare L.)

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