OsMKK1 is a novel element that positively regulates the Xa21-mediated resistance response to Xanthomonas oryzae pv. oryzae in rice.

KEY MESSAGE: OsMKK1, a MAPK gene, positively regulates rice Xa21-mediated resistance response and also plays roles in normal growth and development process of rice. The mitogen-activated protein kinase (MAPK) cascade was highly conserved among eukaryotes, which played crucial roles in plant responses to pathogen infection. Bacterial blight is the most devastating bacterial disease. Xa21 confers broad-spectrum resistance to Xanthomonas oryzae pv. Oryzae (Xoo). This study identified that the transcription level of OsMKK1 was up-regulated in resistant response against Xoo, thus overexpression (OsMKK1-OX) and RNA interference (OsMKK1-RNAi) transgenic rice lines under the background of Xa21 was constructed. Compared with recipient control plants 4021, the OsMKK1-OX lines significantly enhanced disease resistance to Xoo, on the contrary, the resistance of OsMKK1-RNAi lines was weakened, demonstrated that OsMKK1 played a positive role in Xa21-mediated disease resistance pathway. A number of pathogenesis-related proteins, including PR1A, PR2 and PR10A showed enhanced expression in OsMKK1-OX lines, supported that these PR genes may be regulated by OsMKK1 to participate in the defense responses. In addition, the agronomic traits of OsMKK1 transgenic plants were affected. Overall, these results revealed the role of OsMKK1 in Xa21-mediated resistance against Xoo and in the normal growth and development process in rice.

Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741.

Poplar is an important shelterbelt, timber stand, and city tree species that has been the focus of forestry research. The regulatory role of the long non-coding RNA molecule (lncRNA; length > 200 nt) has been a research hotspot in plants. In this study, seedlings of 741 poplar were irradiated with LED blue and white light, and the Illumina HiSeq 2000 sequencing platform was used to identify lncRNAs. |logFC| > 1 and p < 0.05 were considered to indicate differentially expressed lncRNAs, and nine differentially expressed lncRNAs were screened, the target genes of which were predicted, and three functionally annotated target genes were obtained. The differentially expressed lncRNAs were identified as miRNA targets. Six lncRNAs were determined to be target sites for twelve mRNAs in six miRNA families. LncRNAs and their target genes, including lncRNA MSTRG.20413.1-ptc-miR396e-5p-GRF9, were verified using quantitative real-time polymerase chain reaction analysis, and the expression patterns were analyzed. The analysis showed that the ptc-miR396e-5p expression was downregulated, while lncRNA MSTRG.20413.1 and GRF9 expression was upregulated, after blue light exposure. These results indicate that lncRNAs interact with miRNAs to regulate gene expression and affect plant growth and development.

Dehalogenative Arylation of Unactivated Alkyl Halides via Electroreduction.

Herein, a facile and efficient dehalogenative arylation of unactivated alkyl halides enabled by electrochemical reductive coupling is developed, affording a series of C(sp2)-C(sp3) products in moderate to good yields. This protocol proceeds in the absence of transition metal catalysts and redox mediators. The reaction features mild conditions, broad substrate scope, and high tolerance of functional groups and is demonstrated to be applicable for gram-scale synthesis and late-stage functionalization of natural products.

Electroreduction Enables Regioselective 1,2-Diarylation of Alkenes with Two Electrophiles.

Precisely introducing two similar functional groups into bulk chemical alkenes represents a formidable route to complex molecules. Especially, the selective activation of two electrophiles is in crucial demand, yet challenging for cross-electrophile-coupling. Herein, we demonstrate a redox-mediated electrolysis, in which aryl nitriles are both aryl radical precursors and redox-mediators, enables an intermolecular alkene 1,2-diarylation with a remarkable regioselectivity, thereby avoiding the involvement of transition-metal catalysts. This transformation utilizes cyanoarene radical anions for activating various aryl halides (including iodides, bromides, and even chlorides) and affords 1,2-diarylation adducts in up to 83 % yield and >20 : 1 regioselectivity with more than 80 examples, providing a feasible approach to complex bibenzyl derivatives.

Rice MPK17 Plays a Negative Role in the Xa21-Mediated Resistance Against Xanthomonas oryzae pv. oryzae.

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most serious diseases affecting rice production worldwide. Xa21 was the first disease resistance gene cloned in rice, which encodes a receptor kinase and confers broad resistance against Xoo stains. Dozens of components in the Xa21-mediated pathway have been identified in the past decades, however, the involvement of mitogen-activated protein kinase (MAPK) genes in the pathway has not been well described. To identify MAPK involved in Xa21-mediated resistance, the level of MAPK proteins was profiled using Western blot analysis. The abundance of OsMPK17 (MPK17) was found decreased during the rice-Xoo interaction in the background of Xa21. To investigate the function of MPK17, MPK17-RNAi and over-expression (OX) transgenic lines were generated. The RNAi lines showed an enhanced resistance, while OX lines had impaired resistance against Xoo, indicating that MPK17 plays negative role in Xa21-mediated resistance. Furthermore, the abundance of transcription factor WRKY62 and pathogenesis-related proteins PR1A were changed in the MPK17 transgenic lines when inoculated with Xoo. We also observed that the MPK17-RNAi and -OX rice plants showed altered agronomic traits, indicating that MPK17 also plays roles in the growth and development. On the basis of the current study and published results, we propose a "Xa21-MPK17-WRKY62-PR1A" signaling that functions in the Xa21-mediated disease resistance pathway. The identification of MPK17 advances our understanding of the mechanism underlying Xa21-mediated immunity, specifically in the mid- and late-stages.

Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic.

Novel coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which can be transmitted from person to person. As of September 21, 2021, over 228 million cases were diagnosed as COVID-19 infection in more than 200 countries and regions worldwide. The death toll is more than 4.69 million and the mortality rate has reached about 2.05% as it has gradually become a global plague, and the numbers are growing. Therefore, it is important to gain a deeper understanding of the genome and protein characteristics, clinical diagnostics, pathogenic mechanisms, and the development of antiviral drugs and vaccines against the novel coronavirus to deal with the COVID-19 pandemic. The traditional biology technologies are limited for COVID-19-related studies to understand the pandemic happening. Bioinformatics is the application of computational methods and analytical tools in the field of biological research which has obvious advantages in predicting the structure, product, function, and evolution of unknown genes and proteins, and in screening drugs and vaccines from a large amount of sequence information. Here, we comprehensively summarized several of the most important methods and applications relating to COVID-19 based on currently available reports of bioinformatics technologies, focusing on future research for overcoming the virus pandemic. Based on the next-generation sequencing (NGS) and third-generation sequencing (TGS) technology, not only virus can be detected, but also high quality SARS-CoV-2 genome could be obtained quickly. The emergence of data of genome sequences, variants, haplotypes of SARS-CoV-2 help us to understand genome and protein structure, variant calling, mutation, and other biological characteristics. After sequencing alignment and phylogenetic analysis, the bat may be the natural host of the novel coronavirus. Single-cell RNA sequencing provide abundant resource for discovering the mechanism of immune response induced by COVID-19. As an entry receptor, angiotensin-converting enzyme 2 (ACE2) can be used as a potential drug target to treat COVID-19. Molecular dynamics simulation, molecular docking and artificial intelligence (AI) technology of bioinformatics methods based on drug databases for SARS-CoV-2 can accelerate the development of drugs. Meanwhile, computational approaches are helpful to identify suitable vaccines to prevent COVID-19 infection through reverse vaccinology, Immunoinformatics and structural vaccinology.

Electrodeposited dopamine/strontium-doped hydroxyapatite composite coating on pure zinc for anti-corrosion, antimicrobial and osteogenesis.

Zinc-based biometal is expected to become a new generation of biodegradable implants. Due to its antibacterial and biocompatibility in vivo, zinc metals is recently considered to be the most promising biodegradable metal, However, cytotoxicity is the thorny problem that currently restrict its application, due to the excessive Zn ions released during degradation. In order to solve these problems, dopamine modified strontium-doped hydroxyapatite coating (SrHA/PDA) was fabricated on alkali-treated pure zinc to improve its corrosion rate and cytocompatibility by electrodeposition for the first time. The obtained coating showed a dense structure and high crystallinity, which was attributed to the attraction of Ca2+ ions by polydopamine. The results showed that the SrHA/PDA coating delayedthe degradation rate of zinc metal, which reduced the release of Zn2+, thereby reducing its cytotoxicity. Additionally, electrochemical tests showed that SrHA/PDA coating can reduce the corrosion rate of pure zinc. In vitro cell viability showed that even at high Zn2+ concentrations (3.11 mg/L), preosteoblasts (MC3T3-E1) cells proliferated at a high rate on SrHA/PDA, thus confirming that Sr2+ counteracted the cytotoxic effects of Zn2+ and promoted cell differentiation. Moreover, the SrHA/PDA coating still maintained excellent antibacterial effects against pathogenic bacterial strains (Escherichia coli and Staphylococcus aureus). Mild pH changes had no significant effect on the viability of cells and bacterias. Collectively, the present study elucidated that by coating SrHA/PDA/Zn(OH)2 on Zn, a controllable corrosion rate, original antibacterial properties and better cell compatibility can be achieved. This provided a new strategy for the surface modification of biodegradable Zn.

Construction and Comprehensive Analysis of a ceRNA Network to Reveal Potential Novel Biomarkers for Triple-Negative Breast Cancer.

BACKGROUND: Triple-negative breast cancer (TNBC) is the most common and aggressive type of breast cancer with an unfavourable outcome worldwide. Novel therapeutic targets are urgently required to explore this malignancy. This study explored the ceRNA network and the important genes for predicting the therapeutic targets. METHODS: It identified the differentially expressed genes of mRNAs, lncRNAs and miRNAs between TNBC and non-TNBC samples in four cohorts (TCGA, GSE38959, GSE45827 and GSE65194) to explore the novel therapeutic targets for TNBC. Downstream analyses, including functional enrichment analysis, ceRNA network, protein-protein interaction and survival analysis, were then conducted by bioinformatics analysis. Finally, the potential core protein of the ceRNA network in TNBC was validated by immunohistochemistry. RESULTS: A total of 1,045 lncRNAs and 28 miRNAs were differentially expressed in the TCGA TNBC samples, and the intersections of 282 mRNAs (176 upregulations and 106 downregulations) between the GEO and TCGA databases were identified. A ceRNA network composed of 7 lncRNAs, 62 mRNAs, 12 miRNAs and 244 edges specific to TNBC was established. The functional assay showed dysregulated genes, and GO, DO and KEGG enrichment analysis were performed. Survival analysis showed that mRNA LIFR and lncRNA AC124312.3 were significantly correlated with the overall survival of patients with TNBC in the TCGA databases (P < 0.05). Finally, the LIFR protein was validated, and immunohistochemical results showed the upregulated expression of LIFR in TNBC tissues. CONCLUSION: Thus, our study presents an enhanced understanding of the ceRNA network in TNBC, where the key gene LIFR may be a new promising potential therapeutic target for patients with TNBC.

Catalytic asymmetric de novo construction of dihydroquinazolinone scaffolds via enantioselective decarboxylative [4+2] cycloadditions.

The first de novo construction of enantioenriched dihydroquinazolinones via an intermolecular strategy has been established. This approach also represents the first catalytic asymmetric [4+2] cycloaddition of vinyl benzoxazinanones with sulfonyl isocyanates, which afforded chiral dihydroquinazolinones in high yields and excellent enantioselectivities (up to 98% yield, 99 : 1 er). This reaction not only confronts the great challenge in de novo construction of enantioenriched dihydroquinazolinone skeletons, but also advances the chemistry of decarboxylative cycloadditions involving vinyl benzoxazinanones.

[Screening of three novel antimicrobial peptides with antifungal pathogens].

OBJECTIVE: In order to discover novel antimicrobial peptides against important crop pathogens, we designed and screened a high capacity random peptide library and isolated a number of clones expressing peptides with antifungal activity. We selected 96 peptides from the library and synthesized their sequence, which were used to assay their activity against crop fungal pathogens. METHODS: Using agar diffusion assay, these peptides were assayed for their activity against pathogens that cause cotton Fusarium wilt (Fusarium f. sp, vasinfecum), cotton red rot (Fusarium moniliforme), wheat spot blotch (Bipolaris sorokiniana) and potato early blight (Alternaria solani). RESULTS: The three random peptides, A6, D4 and F10, showed the strongest activity against the above four crop fungal pathogens. Through Blastp analysis, we did not find they have homologous sequences with known antimicrobial peptides. CONCLUSION: The novel antimicrobial peptides will provide gene resources for preventing important crop pathogens.