Genome-Wide Analysis of Cotton MYB Transcription Factors and the Functional Validation of GhMYB in Response to Drought Stress.

MYB transcription factors play important roles during abiotic stress responses in plants. However, little is known about the accurate systematic analysis of MYB genes in the four cotton species, Gossypium hirsutum, G. barbadense, G. arboreum and G. raimondii. Herein, we performed phylogenetic analysis and showed that cotton MYBs and Arabidopsis MYBs were clustered in the same subfamilies for each species. The identified cotton MYBs were distributed unevenly on chromosomes in various densities for each species, wherein genome-wide tandem and segment duplications were the main driving force of MYB family expansion. Synteny analysis suggested that the abundant collinearity pairs of MYBs were identified between G. hirsutum and the other three species, and that they might have undergone strong purification selection. Characteristics of conserved motifs, along with their consensus sequence, promoter cis elements and gene structure, revealed that MYB proteins might be highly conserved in the same subgroups for each species. Subsequent analysis of differentially expressed genes and expression patterns indicated that most GhMYBs might be involved in response to drought (especially) and salt stress, which was supported by the expression levels of nine GhMYBs using real-time quantitative PCR. Finally, we performed a workflow that combined virus-induced gene silencing and the heterologous transformation of Arabidopsis, which confirmed the positive roles of GhMYBs under drought conditions, as validated by determining the drought-tolerant phenotypes, damage index and/or water loss rate. Collectively, our findings not only expand our understanding of the relationships between evolution and function of MYB genes, but they also provide candidate genes for cotton breeding.

Genome-wide identification and expression analysis of DREB family genes in cotton.

BACKGROUND: Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome­wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species. RESULTS: In total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1-A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress. CONCLUSIONS: Collectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response.

Effects of Different Natural Factors on Rheological Properties of SBS Modified Asphalt.

Typical climatic environments such as UV radiation, high temperature and strong wind in cold and arid regions have a significant effect on asphalt aging. The intent of this work is to reveal the evolution law of natural aging of SBS-modified asphalt under the complex adverse climate environment in cold and arid regions. Furthermore, the contribution rate of various environmental factors of natural aging of asphalt in cold and arid regions was analyzed. Based on rheological parameters, this paper characterized the influence of natural aging on the viscoelastic properties, rutting resistance at a high temperature, fatigue resistance and cracking resistance at a low temperature of SBS-modified asphalt. The evolution law of natural aging performance of SBS-modified asphalt was revealed. A quantitative evaluation index (CIi) of natural aging contribution rate of asphalt was put forward and the contribution rate of various environmental factors to asphalt natural aging was analyzed. The results showed that the effects of simulated aging and natural aging on asphalt properties were similar. After aging, the viscoelastic properties of asphalt were deteriorated, and the risk of fatigue cracking and low temperature cracking was increased. It also enhanced the deformation resistance of asphalt and increased the rutting resistance at high temperature. The aging contribution index CIi obtained based on rheological parameters such as complex modulus and rutting factor could directly reflect the influence of different natural factors on the performance of asphalt during aging. Among them, the effect of thermal oxygen was more obvious on the natural aging of SBS-modified asphalt.

Predicting Dynamic Properties of Asphalt Mastic Considering Asphalt-Filler Interaction Based on 2S2P1D Model.

The relationship between the various phases of asphalt materials, from asphalt binder to mastic and mixture, has received great attention over the years, with efforts being made to establish linkages among these phases. Many methods for predicting the rheology properties of asphalt mastics from those of asphalt and filler volume fractions exist. However, most prediction methods are based on an empirical formula and on the micromechanical model. Very few research studies focus on the constitutive model. In addition, relatively little research has explored the influence of asphalt-filler interaction on mastic's rheology properties, which is believed to be an important factor. In this study, the 2S2P1D (two springs, two parabolic elements, and one dashpot) model was applied to link the behavior of asphalt binder, filler volume fraction, asphalt-filler interaction and asphalt mastic. First, the interaction between asphalt and filler was evaluated, and the interaction parameter C of the Palierne model was used as an assessment indicator to calculate the effective filler volume fraction of asphalt mastic. Then, the relation between the 2S2P1D model parameters of asphalt mastic and those of asphalt binder and the effective filler volume fraction was analyzed. Finally, a simple relationship associating the 2S2P1D model parameters h, log(τ0) of mastic and that of asphalt binder and the effective filler volume fraction was developed. The proposed expression was validated, and the result showed that it was an efficient model for the shear complex modulus prediction of virgin asphalt mastic.

Effects of 5-azaC on Iridoid Glycoside Accumulation and DNA Methylation in Rehmannia glutinosa.

Iridoid glycoside is the important secondary metabolite and the main active component in Rehmannia glutinosa. However, the mechanisms that underlie the regulation of iridoid glycoside biosynthesis remain poorly understood in R. glutinosa. Herein, the analysis of RNA-seq data revealed that 3,394 unigenes related to the biosynthesis of secondary metabolites were identified in R. glutinosa. A total of 357 unigenes were involved in iridoid glycoside synthesis, in which the highly conservative genes, such as DXS, DXR, GPPS, G10H, and 10HGO, in organisms were overexpressed. The analysis of the above genes confirmed that the co-occurrence ratio of DXS, DXR, and GPPS was high in plants. Further, our results showed that under normal and 5-azacytidine (5-azaC) treatment, the expression levels of DXS, DXR, GPPS, G10H, and 10HGO were consistent with the iridoid glycoside accumulation in R. glutinosa, in which the application of the different concentrations of 5-azaC, especially 50 µM 5-azaC, could significantly upregulate the expression of five genes above and iridoid glycoside content. In addition, the changes in the spatiotemporal specificity of degree and levels of DNA methylation were observed in R. glutinosa, in which the hemi-methylation was the main reason for the change in DNA methylation levels. Similar to the changes in 5-methyl cytosine (5mC) content, the DNA demethylation could be induced by 5-azaC and responded in a dose-dependent manner to 15, 50, and 100 µM 5-azaC. Taken together, the expression of iridoid glycoside synthesis gene was upregulated by the demethylation in R. glutinosa, followed by triggering the iridoid glycoside accumulation. These findings not only identify the key genes of iridoid glycoside synthesis from R. glutinosa, but also expand our current knowledge of the function of methylation in iridoid glycoside accumulation.

Response of Wheat DREB Transcription Factor to Osmotic Stress Based on DNA Methylation.

Dehydration-responsive element-binding protein (DREB) plays an important role in response to osmotic stress. In this study, DREB2, DREB6 and Wdreb2 are isolated from wheat AK58, yet they belong to different types of DREB transcription factors. Under osmotic stress, the transcript expression of DREB2, DREB6 and Wdreb2 has tissue specificity and is generally higher in leaves, but their expression trends are different along with the increase of osmotic stress. Furthermore, some elements related to stresses are found in their promoters, promoters of DREB2 and Wdreb2 are slightly methylated, but DREB6's promoter is moderately methylated. Compared with the control, the level of promoter methylation in Wdreb2 is significantly lower under osmotic stress and is also lower at CG site in DREB2, yet is significantly higher at CHG and CHH sites in DREB2, which is also found at a CHG site in DREB6. The status of promoter methylation in DREB2, DREB6 and Wdreb2 also undergoes significant changes under osmotic stress; further analysis showed that promoter methylation of Wdreb2 is negatively correlated with their expression. Therefore, the results of this research suggest the different functions of DREB2, DREB6 and Wdreb2 in response to osmotic stress and demonstrate the effects of promoter methylation on the expression regulation of Wdreb2.

Study on the gene signature related to immune microenvironment on viral and nonviral infections of hepatocellular carcinoma.

ABSTRACT: The pathogenesis of hepatocellular carcinoma (HCC) can be divided into viral infection (VIR) and nonviral (NVIR) infection. Two types of HCC performed different tumor immune microenvironment (TIME) which directly affected prognosis of HCC. This study aimed to identify an effective 2 types of HCC prognostic gene signature that related to immune TIME.The differential expression genes (DEGs) were analyzed by Limma R package from the Cancer Genome Atlas. Immune related genes getting from IMMport database were matched to DEGs for testing prognosis. Prognostic index (PI) consisted of prognostic immune related genes was calculated in different types of HCC by COX regression and the correlation with the abundance of immune infiltrates, including 6 type cells, via gene modules. Tumor immune estimation resource database was applied to analyze TIME. Finally, the correlations between PI of DEGs and TIICs were analyzed by the Spearman method.Results showed that PI consisted of 11 messenger RNAs in VIR and 12 messenger RNAs in NVIR groups. The PI related to HCC prognosis has different correlations with immune infiltrating cells in VIR and NVIR groups. The PI value of DEGs has significant correlations with neutrophils (R = 0.22, P-value = .029) and dendritic (R = 0.21, P-value = .036) infiltration levels in VIR group. However, in NVIR group, the result showed there were no significant correlations between PI and other 5 type cell infiltration levels (P-value > .05).The 11-gene signature in VIR and 12-gene signature in NVIR group selected based on data from the Cancer Genome Atlas database had a different correlation with immune infiltrating cells of HCC patients.

Effects of xipayi mouth rinse combined with minocycline on localized aggressive periodontitis' therapeutic effect and the levels of CRP, TNF-α, IL-6 in serum.

BACKGROUND: Localized aggressive periodontitis is rare periodontitis in clinical practice, which often occurs in young adults under 35 years old, seriously affecting patients' quality of life. As a tetracycline antibacterial drug, minocycline is also considered an essential choice to treat periodontal disease. However, few reports focused on the effect of xipayi mouth rinse combined with minocycline on periodontal pathogens. The goal of this study was to investigate the clinical effect of xipayi mouth rinse combined with minocycline in the treatment of localized aggressive periodontitis and its effect on the levels of CRP, TNF-α, and IL-6. METHODS: Ninety-six patients with limited aggressive periodontitis were selected and randomly divided into two groups. Forty-eight patients in the control group were treated with xipayi mouth rinse after primary periodontal treatment. Then, 48 patients in the experimental group were treated with xipayi mouth rinse combined with minocycline after primary periodontal treatment. The periodontal probe was applied to detect periodontal plaque index (PLI), periodontal pocket depth (PD), sulcus bleeding index (SBI), gingival index (GL), and clinical attachment loss (CAL) before and after treatment in both groups of patients. ELISA was used for detecting the expression levels of CRP, TNF-α, and IL-6 in the serum of patients in two groups before and after treatment. We compared the recurrence rates of the two groups after a 1-year follow-up. RESULTS: Compared with the control group, the PLI, PD, SBI, GL, CAL, and total masticatory efficiency of the experimental group were significantly better than those of the control group. The levels of inflammatory factors CRP, TNF-α, and IL-6 were significantly declined, and the total effective rate of treatment was significantly elevated. After follow-up, it was found there was no noticeable difference in the recurrence rate between the two groups. CONCLUSIONS: Xipayi mouth rinse, combined with minocycline in the treatment of localized aggressive periodontitis, can significantly improve the periodontal gingival condition and reduce the level of inflammatory factors. Also, the efficacy of the treatment was significant. This experiment has provided ideas for improving the clinical treatment of patients with localized aggressive periodontitis.