Genome-wide analysis of TALE superfamily in Triticum aestivum reveals TaKNOX11-A is involved in abiotic stress response.

BACKGROUND: Three-amino-loop-extension (TALE) superfamily genes are widely present in plants and function directly in plant growth and development and abiotic stress response. Although TALE genes have been studied in many plant species, members of the TALE family have not been identified in wheat. RESULTS: In this study, we identified 70 wheat TALE protein candidate genes divided into two subfamilies, KNOX (KNOTTED-like homeodomain) and BEL1-like (BLH/BELL homeodomain). Genes in the same subfamily or branch in the phylogenetic tree are similar in structure, and their encoded proteins have similar motifs and conserved structures. Wheat TALE genes are unevenly distributed on 21 chromosomes and expanded on the fourth chromosome. Through gene duplication analysis, 53 pairs of wheat TALE genes were determined to result from segmental duplication events, and five pairs were caused by tandem duplication events. The Ka/Ks between TALE gene pairs indicates a strong purification and selection effect. There are multiple cis-elements in the 2000 bp promoter sequence that respond to hormones and abiotic stress, indicating that most wheat TALE genes are involved in the growth, development, and stress response of wheat. We also studied the expression profiles of wheat TALE genes in different developmental stages and tissues and under different stress treatments. We detected the expression levels of four TALE genes by qRT-PCR, and selected TaKNOX11-A for further downstream analysis. TaKNOX11-A enhanced the drought and salt tolerances of Arabidopsis thaliana. TaKNOX11-A overexpressing plants had decreased malondialdehyde content and increased proline content, allowing for more effective adaptation of plants to unfavorable environments. CONCLUSIONS: We identified TALE superfamily members in wheat and conducted a comprehensive bioinformatics analysis. The discovery of the potential role of TaKNOX11-A in drought resistance and salt tolerance provides a basis for follow-up studies of wheat TALE family members, and also provides new genetic resources for improving the stress resistance of wheat.

Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.).

BACKGROUND: VQ motif-containing (VQ) proteins are cofactors of transcriptional regulation that are widely involved in plant growth and development and respond to various stresses. The VQ gene family has been identified and characterized for many plants, but there is little research on VQ gene family proteins in wheat (Triticum aestivum L.). RESULTS: In this study, 113 TaVQ genes (40 homoeologous groups) were identified in the wheat genome. TaVQ proteins all contain the conserved motif FxxhVQxhTG, and most of the TaVQ genes do not contain introns. Phylogenetic analysis demonstrated that TaVQ proteins can be divided into 8 subgroups (I-VIII). The chromosomal location mapping analysis indicated that TaVQ genes are disproportionally distributed on 21 wheat chromosomes. Gene duplication analysis revealed that segmental duplication significantly contributes to the expansion of the TaVQ gene family. Gene expression analysis demonstrated that the expression pattern of TaVQ genes varies in different tissues. The results of quantitative real-time PCR (qRT-PCR) found that TaVQ genes displayed different expression levels under different phytohormones and abiotic stresses. The cis-elements analysis of the promoter region demonstrated that stress responses, hormone responses, growth and development, and WRKY binding elements are all widely distributed. Additionally, a potential regulatory network between TaVQ proteins and WRKY transcription factors was visualized. CONCLUSION: This study systematically analyzed the wheat TaVQ gene family, providing a reference for further functional characterization of TaVQ genes in wheat.

The correlation of EZH2 expression with the progression and prognosis of hepatocellular carcinoma.

BACKGROUND: Enhancer of Zeste homologue 2 (EZH2) is a polycomb group gene and an epigenetic regulator that inhibits transcription, a modification associated with gene silencing. EZH2 plays an essential role in humoral and cell-mediated adaptive immunity. The purpose of the current study is to investigate the prognostic potential of EZH2 and to comprehensively analyse the correlation between EZH2 and immune infiltration in multiple cancer cases, especially liver hepatocellular carcinoma. METHODS: EZH2 expression across cancers was explored through Oncomine, HPA, and GEPIA2. Additionally, the prognostic value of EZH2 analysis across cancers was based on the GEPIA2, TCGA portal, Kaplan-Meier Plotter, and LOGpc databases. Based on GO and KEGG analyses, GSEA helped demonstrate the biological processes through which EZH2 might lead to HCC development. GEPIA and TIMER were adopted to detect the possible relationship of EZH2 expression with tumour-infiltrating immune cells (TIICs). RESULTS: EZH2 overexpression levels were associated with poor prognosis of cancer, especially hepatocellular carcinoma. A high EZH2 expression level is related to a poor prognosis of HCC, especially in disease histology and stage III. The EZH2 expression level was positively correlated with critical gene markers of TAMs, M2 macrophages, M1 macrophages, and monocytes. Further analysis revealed that EZH2 genes were mainly related to DNA recombination, mitotic cell cycle phase transition, and chromosome segregation. CONCLUSION: EZH2 plays an essential role in the immune microenvironment and is a potential prognostic marker and immunotherapy target for hepatocellular carcinoma.

Genome-Wide Analysis of the Peptidase M24 Superfamily in Triticum aestivum Demonstrates That TaM24-9 Is Involved in Abiotic Stress Response.

The peptidase M24 (Metallopeptidase 24, M24) superfamily is essential for plant growth, stress response, and pathogen defense. At present, there are few systematic reports on the identification and classification of members of the peptidase M24 proteins superfamily in wheat. In this work, we identified 53 putative candidate TaM24 genes. According to the protein sequences characteristics, these members can be roughly divided into three subfamilies: I, II, III. Most TaM24 genes are complex with multiple exons, and the motifs are relatively conserved in each sub-group. Through chromosome mapping analysis, we found that the 53 genes were unevenly distributed on 19 wheat chromosomes (except 3A and 3D), of which 68% were in triads. Analysis of gene duplication events showed that 62% of TaM24 genes in wheat came from fragment duplication events, and there were no tandem duplication events to amplify genes. Analysis of the promoter sequences of TaM24 genes revealed that cis-acting elements were rich in response elements to drought, osmotic stress, ABA, and MeJA. We also studied the expression of TaM24 in wheat tissues at developmental stages and abiotic stress. Then we selected TaM24-9 as the target for further analysis. The results showed that TaM24-9 genes strengthened the drought and salt tolerance of plants. Overall, our analysis showed that members of the peptidase M24 genes may participate in the abiotic stress response and provided potential gene resources for improving wheat resistance.

Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response.

BACKGROUND: The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family members have not yet been performed in wheat. RESULTS: In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat. CONCLUSIONS: We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat.

Correlation of MKI67 with prognosis, immune infiltration, and T cell exhaustion in hepatocellular carcinoma.

BACKGROUND: MKI67 plays a vital role in the tumour microenvironment (TME) and congenital immunity. The present work focuses on exploring the prognosis prediction performance of MKI67 and its associations with T cell activity and immune infiltration within numerous cancers, especially hepatocellular liver carcinoma (LIHC). METHODS: Oncomine, GEPIA2, and HPA were adopted to analyse MKI67 levels in different types of cancers. The prognostic prediction performance of MKI67 was evaluated through the TCGA portal, GEPIA2, LOGpc, and Kaplan-Meier Plotter databases. The associations of MKI67 with related gene marker sets and immune infiltration were inspected through TISIDB, GEPIA2, and TIMER. We chose MKI67 to analyse biological processes (BPs) and KEGG pathways related to the coexpressed genes. Furthermore, the gene-miRNA interaction network for MKI67 in liver cancer was also examined based on the miRWalk database. RESULTS: MKI67 expression decreased in many cancers related to the dismal prognostic outcome of LIHC. We found that MKI67 significantly affected the prognosis of LIHC in terms of histology and grade. Increased MKI67 levels were directly proportional to the increased immune infiltration degrees of numerous immune cells and functional T cells, such as exhausted T cells. In addition, several critical genes related to exhausted T cells, including TIM-3, TIGIT, PD-1, LAG3, and CXCL13, were strongly related to MKI67. Further analyses showed that MKI67 was associated with adaptive immunity, cell adhesion molecules (CAMs), and chemokine/immune response signal transduction pathways. CONCLUSION: MKI67 acts as a prognostic prediction biomarker in several cancers, particularly LIHC. Upregulation of MKI67 elevates the degree of immune infiltration of many immune cell subtypes, including functional T cells, CD4+ T cells, and CD8+ T cells. Furthermore, MKI67 shows a close correlation with T cell exhaustion, which plays a vital role in promoting T cell exhaustion within LIHC. Detection of the MKI67 level contributes to prognosis prediction and MKI67 modulation within exhausted T cells, thus providing a new method to optimize the efficacy of anti-LIHC immunotherapy.

Photoinduced Triphenylphosphine and Iodide Salt Promoted Reductive Decarboxylative Coupling.

The transient electron donor-acceptor (EDA) complex has been an emerging area in the photoinduced organic synthesis field, generating radicals without exogenous transition-metal or organic dye-based photoredox catalysts. The catalytic platform to form suitable photoactive EDA complexes for photochemical reduction reactions remains underdeveloped. Herein, a general photoinduced reductive alkylation via the EDA complex strategy is described. A simple yet multifunctional system, triphenylphosphine and iodide salt, promotes the photoinduced decarboxylative hydroalkylation, and reductive defluorinative decarboxylative alkylation of trifluoromethyl alkenes, to access trifluoromethyl alkanes and gem-difluoroalkenes. Moreover, decarboxylative hydroalkylation can be applied to more kinds of electron-deficient alkenes as a general Giese addition reaction.

Composition and sources of particulate matter in the Beijing-Tianjin-Hebei region and its surrounding areas during the heating season.

This paper aimed to analyze the composition and pollution sources of particulate matter (PM) in the Beijing-Tianjin-Hebei region and its surrounding areas (henceforth the BTH region) during the heating season to support the mitigation and control of regional air pollution. Manual monitoring data from the China National Environmental Monitoring Network for Atmospheric PM in the BTH region were collected and analyzed during the 2016 and 2018 heating seasons. The positive definite matrix factor analysis (PMF) model was used to analyze the PM sources in BTH cities during the heating season. The main PM components were organic matter (OM), nitrate (NO3-), sulfate (SO42-) and ammonium salt (NH4+). Direct emission sources have decreased since 2016, indicating the effectiveness of governmental controls on these sources; however, secondary pollution showed an increasing trend, suggesting control measures should be strengthened. Daily regional average concentrations of OM, SO42-, NH4+, elemental carbon (EC), chloride (Cl-) and trace elements all showed similar trends. When air quality worsened, the concentrations of the main PM components increased, but trends of change varied among components. In 2018, concentrations of OM and chloride were highest in the Taihang Mountains, and NO3 concentrations were highest in Anyang, Hebi, Jiaozuo and Xinxiang. The SO42- concentration was highest in the southern section of the Taihang Mountains. The NH4+ and EC concentrations were generally highest in the central and southern regions. The concentration of crustal substances was highest in some cities in the north and central parts of the BTH region. In the 2018 heating season, the pollution level of five transmission channels showed an increasing trend in the Northwest, Southeast, Yanshan, South and Taihang Mountain channels. These findings provide a scientific basis for the continued management of atmospheric PM pollution.

Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems.

The occurrence of antibacterial agents has received increasing concern due to their possible threats to human health. However, the effects of antibacterial residues on the evolution and dynamics between bacteria and bacteriophages in wastewater treatment systems have seldom been researched. Especially for phages, little is known about their response to antimicrobial exposure. In this study, two identical anoxic-aerobic wastewater treatment systems were established to evaluate the responses of bacterial and phage communities to long-term exposure to antimicrobial agents. The results indicated simultaneous exposure to combined antimicrobials significantly inhibited (p < 0.05) the abundance of phages and bacteria. Metagenomic sequencing analysis indicated the community of bacteria and phages changed greatly at the genus level due to combined antibacterial exposure. Additionally, long-term exposure to antimicrobial agents promoted the attachment of receptor-binding protein genes to Klebsiella, Escherichia and Salmonella (which were all members of Enterobacteriaceae). Compared to that in the control system, the numbers of receptor-binding protein genes on their possible phages (such as Lambdalikevirus and P2likevirus) were also obviously higher when the microorganisms were exposed to antimicrobials. The results are helpful to understanding the microbial communities and tracking the relationship of phage-bacterial host systems, especially under the pressure of antimicrobial exposure.

Synthesis of trisubstituted alkenes by Ni-catalyzed hydroalkylation of internal alkynes with cycloketone oxime esters.

A method for Ni-catalyzed hydroalkylation of internal alkynes with cycloketone oxime esters was developed. The reaction has a broad substrate scope. This hydroalkylation shows excellent regio- and stereo-selectivity. This method enables readily available starting materials to be used to access a range of cyano-substituted single-configuration trisubstituted alkenes. These are valuable feedstock chemicals and are widely used in synthetic and medicinal chemistry.

Base-free Ni-catalyzed Suzuki-type cross-coupling reactions of epoxides with boronic acids.

A Ni-catalyzed Suzuki-type cross-coupling of boronic acids with epoxides without an exogenous base and with broad substrate scope has been developed. The product selectivity of styrenyl epoxides is different from that of previous work. This methodology uses readily available starting materials to access a range of substituted alcohols, which are valuable feedstock chemicals.

Pd-Catalyzed decarboxylative cross-coupling reactions of epoxides with α,ß-unsaturated carboxylic acids.

A Pd-catalyzed decarboxylative cross-coupling of α,ß-unsaturated carboxylic acids with cyclic and acyclic epoxides has been developed. Both ß-monosubstituted and ß-disubstituted unsaturated carboxylic acids, as well as conjugated diene unsaturated carboxylic acids are suitable reaction substrates. Substituted homoallylic alcohols were obtained in moderate to good yields. The product was obtained as a mixture of diastereomers favoring the anti diastereomer of the cyclic epoxides. This work provides a method for the modification of complex organic molecules containing α,ß-unsaturated carboxylic acids.