Circlize package in R and Analytic Hierarchy Process (AHP): Contribution values of ABCDE and AGL6 genes in the context of floral organ development

Whole transcriptome sequencing identifies key lncRNAs,circRNAs, and mRNAs for exploring the pathogenesis and therapeutic target of mouse pneumoconiosis

BACKGROUND

Pneumoconiosis is a kind of lung dysfunction caused by the inhalation of mineral dust. However, the potential molecular mechanism of pneumoconiosis have not been fully elucidated.

METHODS

In this study, the silica-treated pneumoconiosis mice model was constructed and the transcriptome sequencing data including lncRNA, circRNA, and mRNA were obtained. Firstly, differentially expressed lncRNA, circRNA, and mRNA (DElncRNA, DEcircRNA, DEGs) between control and pneumoconiosis/silicosis samples were screened, the target miRNAs (co-pre-miRNAs) were obtained by intersecting the miRNAs predicted by DElncRNA and DEcircRNA, respectively, and the target mRNAs (co-mRNA) were obtained by intersecting the mRNAs predicted by target miRNA and DEGs. Then, the lncRNA/circRNA-miRNA-mRNA networks were constructed by Cytoscape. Next, the key mRNAs were obtained by protein-protein interaction (PPI) analysis, and the key lncRNAs/circRNAs were selected by correlation analysis. Moreover, the expression of the key lncRNAs, circRNAs and mRNAs on chromosome were studied by the "circlize" package. Furthermore, the TFs-miRNA-mRNA network was constructed and the function of DEGs were explored by Ingenuity Pathway Analysis (IPA). To demonstrate the feasibility and value of the constructed ceRNA networks, we validated key genes and mmu-miR-682 pathway. Finally, We used the Drug-Gene Interaction database to predict potential drugs that could interfere with key genes,which may help to find promising treatment.

RESULTS

There were 427 DElncRNAs, 107 DEcircRNAs and 1,597 DEGs between silicosis and control groups. Totals of 77 co-pre-miRNAs and 96 co-mRNA were screened, and the lncRNA/circRNA-miRNA-mRNA networks were constructed with 27 lncRNA/25 circRNAs, 74 miRNAs and 96 mRNAs. Then, 6 key mRNAs including Igf1, Klf4, Ptgs2, Epas1, Gnao1, and Il1a were obtained by PPI, and all of these key mRNAs and 10 key lncRNAs and 8 circRNAs were significantly different between the pneumoconiosis and normal groups, in which 10 lncRNAs and 9 circRNA that have not been previously studied in pneumoconiosis/silicosis can be used as new potential therapeutic targets. Moreover, the TFs-miRNA-mRNA network were constructed with 11 TFs, 1 key miRNA (mmu-miR-682) and 3 key mRNAs (Igf1, Epas1, Ptgs2). And the validation of key genes revealing by RNA-seq through experimental approaches shows the the predictive power of this study. Finally, IPA results indicated that 41 pathways were activated and 2 pathways were suppressed in pneumoconiosis/silicosis groups, and Pathogen Induced Cytokine Storm Signaling Pathway was the most significant pathway affected by pneumoconiosis/silicosis. In addition, 93 drugs were screened out by Drug-Gene Interaction database. Among them, Hydroxychloroquine was a kind of drug which associated with Il1a and Ptgs2, may be a promising treatment.

CONCLUSION

This study constructed the lncRNA/circRNA-miRNA-mRNA and TFs-miRNA-mRNA networks, which could deepen the potential molecular regulatory mechanism of pneumoconiosis/silicosis.

Constructing a student development model for undergraduate vocational universities in China using the Fuzzy Delphi Method and Analytic Hierarchy Process

As the industrial structure changes, the severe shortage of high-quality technical and skilled talent in China is one of the most significant factors affecting the high-quality development of China's economy. Bridging the gap between cultivating talent from new undergraduate vocational universities and the demand for industrial talent is regarded as an efficient strategy to address the talent shortage. In addressing the gap, China is hindered by a lack of clarity regarding student development goals and effective assessment instruments. Thus, this study aimed to use the Fuzzy Delphi Method (FDM) and the Analytical Hierarchy Process (AHP) to overcome the above challenges. Specifically, we used the FDM to establish a five-level undergraduate vocational education student development model with two 2nd-level indicators, three 3rd-level indicators, eight 4th-level indicators, and 33 5th-level indicators to clarify student development goals. Then, the AHP was applied to determine the indicator weights, and a student development assessment instrument was developed to help universities acquire student development data and improve the matching degree between talent supply and demand. This study could help undergraduate vocational universities cultivate high-quality technical and skilled talent quickly to meet the demand for China's new economic system and to promote industry independence and global competitiveness.

Two Growing-Season Warming Partly Promoted Growth but Decreased Reproduction and Ornamental Value of Impatiens oxyanthera

Climate warming profoundly affects the vegetative growth, flowering phenology and sexual reproduction of plants; therefore, it affects the ornamental value of wild flowers. Despite this, the extent and mechanism of the impact remain unclear. Here, we conducted a warming experiment for two growing seasons (increases of 1.89 °C in 2017 and 2.37 °C in 2018) with infrared heaters to examine the effects of warming on the ornamental value of the wild flower Impatiens oxyanthera, endemic to China, in Mount Emei. We evaluated the comprehensive ornamental value based on plant morphology and flowering characteristics using the analytic hierarchy process (AHP) and disentangled the impact of the two traits on ornamental value using principal component analysis (PCA) and the partial least squares structural equation model (PLS-SEM) under ambient and warming treatments. We hypothesized that warming would reduce the ornamental value of I. oxyanthera in terms of plant morphology and flowering traits. Our results showed that warming significantly decreased plant height and crown width and increased branch number and single-leaf area. Warming also decreased vexillum length, corolla tube length, nectar spur length and pedicel length. In addition, warming shortened flowering duration per plant and reduced flower number, while there was no significant effect on flower longevity and flower color at full-bloom stage between the control and warming treatment. Therefore, the comprehensive ornamental value under warming was lower than that under the control. Pedicel length, flower color, flower longevity and flowering duration per plant were the main factors affecting the comprehensive ornamental value. The PLS-SEM showed that warming had an indirect negative effect on ornamental value via direct negative effects on flowering traits. Collectively, these results indicate that, although promoting vegetative growth, short-term warming significantly decreased the ornamental value of I. oxyanthera due to warming-caused smaller flowers and shorter flowering duration.

The NAC Transcription Factor PgNAC41-2 Gene Involved in the Regulation of Ginsenoside Biosynthesis in Panax ginseng

Ginseng (Panax ginseng C.A. Meyer) is a perennial herb of the Araliaceae family, a traditional and valuable Chinese herb in China. The main active component of ginseng is ginsenoside. The NAC transcription factors belong to a large family of plant-specific transcription factors, which are involved in growth and development, stress response and secondary metabolism. In this study, we mapped the NAC gene family on 24 pairs of ginseng chromosomes and found numerous gene replications in the genome. The NAC gene PgNAC41-2, found to be highly related to ginsenoside synthesis, was specifically screened. The phylogeny and expression pattern of the PgNAC41-2 gene were analyzed, along with the derived protein sequence, and a structure model was generated. Furthermore, the PgNAC41-2 gene was cloned and overexpressed by a Rhizobium rhizogenes mediated method, using ginseng petioles as receptor material. The saponin content of the transformed material was analyzed to verify the function of the NAC transcription factor in ginseng. Our results indicate that the PgNAC41-2 gene positively regulates the biosynthesis of saponins.

Advance in sex differentiation in cucumber

Cucumber belongs to the family Cucurbitaceae (melon genus) and is an annual herbaceous vegetable crop. Cucumber is an important cash crop that is grown all over the world. From morphology to cytology, from canonical genetics to molecular biology, researchers have performed much research on sex differentiation and its regulatory mechanism in cucumber, mainly in terms of cucumber sex determination genes, environmental conditions, and the effects of plant hormones, revealing its genetic basis to improve the number of female flowers in cucumber, thus greatly improving the yield of cucumber. This paper reviews the research progress of sex differentiation in cucumber in recent years, mainly focusing on sex-determining genes, environmental conditions, and the influence of phytohormones in cucumber, and provides a theoretical basis and technical support for the realization of high and stable yield cultivation and molecular breeding of cucumber crop traits.

Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation

Kiwifruit (Actinidia chinensis Planch.) is a functionally dioecious plant, which displays diverse morphology in male and female flowers. MADS-box is an ancient and huge gene family that plays a key role in plant floral organ differentiation. In this study, we have identified 89 MADS-box genes from A. chinensis Red 5 genome. These genes are distributed on 26 chromosomes and are classified into type I (21 genes) and type II (68 genes). Overall, type II AcMADS-box genes have more complex structures than type I with more exons, protein domains, and motifs, indicating that type II genes may have more diverse functions. Gene duplication analysis showed that most collinearity occurred in type II AcMADS-box genes, which was consistent with a large number of type II genes. Analysis of cis-acting elements in promoters showed that AcMADS-box genes are mainly associated with light and phytohormone responsiveness. The expression profile of AcMADS-box genes in different tissues showed that most genes were highly expressed in flowers. Further, the qRT-PCR analysis of the floral organ ABCDE model-related genes in male and female flowers revealed that AcMADS4, AcMADS56, and AcMADS70 were significantly expressed in female flowers. It indicated that those genes may play an important role in the sex differentiation of kiwifruit. This work provided a comprehensive analysis of the AcMADS-box genes and may help facilitate our understanding of the sex differentiation regulatory mechanism in kiwifruit.