A genome-wide analysis of the GRAS gene family in upland cotton and a functional study of the role of the GhGRAS55 gene in regulating early maturity in cotton.

The members of the GRAS gene family play important roles in regulating plant growth and development, but their functions in regulating early plant maturity traits are still unknown. In this study, we used a series of bioinformatics tools to identify GRAS gene family members and investigate the function of the gene family (GhGRAS55) using a genome-wide database of upland cotton samples. A total of 58 members of the GRAS gene family were identified and screened, which were distributed on 21 chromosomes within the whole cotton genome. The results of the phylogenetic analysis showed that the genes of upland cotton, island cotton, African cotton, Raymond cotton, and Arabidopsis were distributed in subfamilies I-VIII, although subfamily II did not contain any upland cotton or Arabidopsis GRAS family members. The structures and other characteristics of the genes in this family were clarified using bioinformatics technology. The transcriptomic sequencing results for early and late maturing cotton species showed that the expression of most GRAS family genes, such as GhGRAS10, GhGRAS5511, and GhGRAS55, was lower in early maturing species than late maturing species. We also found that cotton plants with GhGRAS55 genes that were silenced by virus-induced gene silencing (VIGS) technology showed early bud emergence phenotypes, so it could be speculated that the GhGRAS55 gene has the function of regulating early maturity in cotton.

The prediction model of nitrogen nutrition in cotton canopy leaves based on hyperspectral visible-near infrared band feature fusion.

Hyperspectral remote sensing technology is becoming increasingly popular in various fields due to its ability to provide detailed information about crop growth and nutritional status. The use of hyperspectral technology to predict SPAD (Soil and Plant Analyzer Development) values during cotton growth and adopt precise fertilization management measures is crucial for achieving high yield and fertilizer efficiency. To detect the nitrogen nutrition in cotton canopy leaves quickly, a non-destructive nitrogen nutrition retrieval model was proposed based on the spectral fusion features of the cotton canopy. The hyperspectral vegetation index and multifractal features were fused to predict the SPAD value and identify the amount of fertilizer applied at different levels. The random decision forest algorithm was used as the model predictor and classifier. A method was introduced which was widely used in the fields of finance and stocks (MF-DFA) into the field of agriculture to extract fractal features of cotton spectral reflectance. Comparing the fusion feature with multi-fractal feature and vegetation index, the results showed that the fusion feature parameters had higher accuracy and better stability than using a single feature or feature combination. The R2 was as high as 0.8363, and the RMSE was 1.8767%. Our intelligent model provides a new idea for detecting nitrogen nutrition in cotton canopy leaves rapidly.

Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears.

Background: Rotator cuff tears (RCT) is the most common cause of shoulder dysfunction, however, its molecular mechanisms remain unclear. Non-coding RNAs(ncRNAs), such as long ncRNA (lncRNA), microRNA (miRNA) and circular RNA (circRNA), are involved in a variety of diseases, but little is known about their roles in RCT. Therefore, the purpose of this study is to identify dysregulated ncRNAs and understand how they influence RCT. Methods: We performed RNA sequencing and miRNA sequencing on five pairs of torn supraspinatus muscles and matched unharmed subscapularis muscles to identify RNAs dysregulated in RCT patients. To better comprehend the fundamental biological processes, we carried out enrichment analysis of these dysregulated mRNAs or the co-expressed genes of dysregulated ncRNAs. According to the competing endogenous RNA (ceRNA) theory, we finally established ceRNA networks to explore the relationship among dysregulated RNAs in RCT. Results: A total of 151 mRNAs, 38 miRNAs, 20 lncRNAs and 90 circRNAs were differentially expressed between torn supraspinatus muscles and matched unharmed subscapularis muscles, respectively. We found that these dysregulated mRNAs, the target mRNAs of these dysregulated miRNAs or the co-expressed mRNAs of these dysregulated ncRNAs were enriched in muscle structure development, actin-mediated cell contraction and actin binding. Then we constructed and analyzed the ceRNA network and found that the largest module in the ceRNA network was associated with vasculature development. Based on the topological properties of the largest module, we identified several important ncRNAs including hsa_circ_0000722, hsa-miR-129-5p and hsa-miR-30c-5p, whose interacting mRNAs related to muscle diseases, fat and inflammation. Conclusion: This study presented a systematic dissection of the expression profile of mRNAs and ncRNAs in RCT patients and revealed some important ncRNAs which may contribute to the development of RCT. Such results could provide new insights for further research on RCT.

Cell cycle arrest is an important mechanism of action of compound Kushen injection in the prevention of colorectal cancer.

Compound Kushen injection (CKI) is the most widely used traditional Chinese medicine preparation for the comprehensive treatment of colorectal cancer (CRC) in China, but its underlying molecular mechanisms of action are still unclear. The present study employed a network pharmacology approach, in which we constructed a "bioactive compound-target-pathway" network. Experimental RNA sequencing (RNA-Seq) analysis was performed to identify a key "bioactive compound-target-pathway" network for subsequent experimental validation. Cell cycle, proliferation, autophagy, and apoptosis assays and a model of azoxymethane/dextran sodium sulfate-induced colorectal carcinogenesis in mice were employed to detect the biological effect of CKI on CRC. Real-time reverse-transcription polymerase chain reaction, Western blot, and immunohistochemistry were performed to verify the selected targets and pathways. We constructed a predicted network that included 82 bioactive compounds, 34 targets, and 33 pathways and further screened an anti-CRC CKI "biological compound (hesperetin 7-O-rutinoside, genistein 7-O-rutinoside, and trifolirhizin)-target (p53 and checkpoint kinase 1 [CHEK1])" network that targeted the "cell cycle pathway". Validation experiments showed that CKI effectively induced the cell-cycle arrest of CRC cells in vitro and suppressed the development of CRC in vivo by downregulating the expression of p53 and CHEK1. Our findings confirmed that inducing cell-cycle arrest by CKI is an important mechanism of its anti-CRC action, which provides a direct and scientific experimental basis for the clinical application of CKI.

Enhancement of edeine production in Brevibacillus brevis X23 via in situ promoter engineering.

Edeines, a group of cationic antimicrobial peptides produced by the soil bacterium Brevibacillus, have broad biological effects, such as antimicrobial, anticancer and immunosuppressive activities. However, the yield of edeines in wild-type (WT) Brevibacillus is extremely low, and chemical synthesis of edeines is a time-consuming process. Genetic engineering has proven to be an effective approach to produce antibiotics with high yield. In this study, the edeine biosynthetic gene cluster (ede BGC), which is involved in edeine production, was identified and characterized in Brevibacillus brevis X23. To improve edeine production in B. brevis X23, the ede BGC promoter was replaced with six different promoters, Pmwp , Pspc , PxylA , Pshuttle-09 , Pgrac or P43 , through double-crossover homologous recombination. The new promoters significantly increased the expression of the ede BGC as well as edeine production by 2.9 ± 0.4 to 20.5 ± 1.2-fold and 3.6 ± 0.1to 8.7 ± 0.7-fold respectively. The highest yield of edeines (83.6 mg l-1 ) was obtained in B. brevis X23 with the Pmwp promoter. This study provides a practical approach for producing high yields of edeines in B. brevis.

Genome-Wide Investigation of the NAC Transcription Factor Family in Miscanthus sinensis and Expression Analysis Under Various Abiotic Stress.

The NAC transcription factor family is deemed to be a large plant-specific gene family that plays important roles in plant development and stress response. Miscanthus sinensis is commonly planted in vast marginal land as forage, ornamental grass, or bioenergy crop which demand a relatively high resistance to abiotic stresses. The recent release of a draft chromosome-scale assembly genome of M. sinensis provided a basic platform for the genome-wide investigation of NAC proteins. In this study, a total of 261 M. sinensis NAC genes were identified and a complete overview of the gene family was presented, including gene structure, conserved motif compositions, chromosomal distribution, and gene duplications. Results showed that gene length, molecular weights (MW), and theoretical isoelectric points (pI) of NAC family were varied, while gene structure and motifs were relatively conserved. Chromosomal mapping analysis found that the M. sinensis NAC genes were unevenly distributed on 19 M. sinensis chromosomes, and the interchromosomal evolutionary analysis showed that nine pairs of tandem duplicates genes and 121 segmental duplications were identified, suggesting that gene duplication, especially segmental duplication, is possibly associated with the amplification of M. sinensis NAC gene family. The expression patterns of 14 genes from M. sinensis SNAC subgroup were analyzed under high salinity, PEG, and heavy metals, and multiple NAC genes could be induced by the treatment. These results will provide a very useful reference for follow-up study of the functional characteristics of NAC genes in the mechanism of stress-responsive and potential roles in the development of M. sinensis.

Physiological and transcriptomic analyses to reveal underlying phenolic acid action in consecutive monoculture problem of Polygonatum odoratum.

BACKGROUND: The root rot of fragrant solomonseal (Polygonatum odoratum) has occurred frequently in the traditional P. odoratum cultivating areas in recent years, causing a heavy loss in yield and quality. The phenolic acids in soil, which are the exudates from the P. odoratum root, act as allelochemicals that contribute to the consecutive monoculture problem (CMP) of the medicinal plant. The aim of this study was to get a better understanding of P. odoratum CMP. RESULTS: The phenolic acid contents, the nutrient chemical contents, and the enzyme activities related to the soil nutrient metabolism in the first cropping (FC) soil and continuous cropping (CC) soil were determined, and the differentially expressed genes (DEGs) related to the regulation of the phenolic acids in roots were analyzed. The results showed that five low-molecule-weight phenolic acids were detected both in the CC soil and FC soil, but the phenolic acid contents in the CC soil were significantly higher than those in the FC soil except vanillic acid. The contents of the available nitrogen, available phosphorus, and available potassium in the CC soil were significantly decreased, and the activities of urease and sucrase in the CC soil were significantly decreased. The genomic analysis showed that the phenolic acid anabolism in P. odoratum in the CC soil was promoted. These results indicated that the phenolic acids were accumulated in the CC soil, the nutrient condition in the CC soil deteriorated, and the nitrogen metabolism and sugar catabolism of the CC soil were lowered. Meantime, the anabolism of phenolic acids was increased in the CC plant. CONCLUSIONS: The CC system promoted the phenolic acid anabolism in P. odoratum and made phenolic acids accumulate in the soil.

MicroRNA-Mediated Responses to Chromium Stress Provide Insight Into Tolerance Characteristics of Miscanthus sinensis.

Chromium (Cr) is a heavy metal in nature, which poses a potential risk to toxicity to both animals and plants when releasing into the environment. However, the regulation of microRNA (miRNA)-mediated response to heavy metal Cr has not been studied in Miscanthus sinensis. In this study, based on high-throughput miRNA sequencing, a total of 104 conserved miRNAs and 158 nonconserved miRNAs were identified. Among them, there were 45 differentially expressed miRNAs in roots and 13 differentially expressed miRNAs in leaves. The hierarchical clustering analysis showed that these miRNAs were preferentially expressed in a certain tissue. There were 833 differentially expressed target genes of 45 miRNAs in roots and 280 differentially expressed target genes of 13 miRNA in leaves. After expression trend analysis, five significantly enriched modules were obtained in roots, and three significantly enriched trend blocks in leaves. Based on the candidate gene annotation and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function analysis, miR167a, novel_miR15, and novel_miR22 and their targets were potentially involved in Cr transportation and chelation. Besides, miR156a, miR164, miR396d, and novel_miR155 were identified as participating in the physiological and biochemical metabolisms and the detoxification of Cr of plants. The results demonstrated the critical role of miRNA-mediated responses to Cr treatment in M. sinensis, which involves ion uptake, transport, accumulation, and tolerance characteristics.

The roles and prognostic significance of ABI1-TSV-11 expression in patients with left-sided colorectal cancer.

Abnormally expressed and/or phosphorylated Abelson interactor 1 (ABI1) participates in the metastasis and progression of colorectal cancer (CRC). ABI1 presents as at least 12 transcript variants (TSVs) by mRNA alternative splicing, but it is unknown which of them is involved in CRC metastasis and prognosis. Here, we firstly identified ABI1-TSV-11 as a key TSV affecting the metastasis and prognosis of left-sided colorectal cancer (LsCC) and its elevated expression is related to lymph node metastasis and shorter overall survival (OS) in LsCC by analyzing data from The Cancer Genome Atlas and TSVdb. Secondly, ABI1-TSV-11 overexpression promoted LoVo and SW480 cells adhesion and migration in vitro, and accelerated LoVo and SW480 cells lung metastasis in vivo. Finally, mechanism investigations revealed that ABI1-isoform-11 interacted with epidermal growth factor receptor pathway substrate 8 (ESP8) and regulated actin dynamics to affect LoVo and SW480 cells biological behaviors. Taken together, our data demonstrated that ABI1-TSV-11 plays an oncogenic role in LsCC, it is an independent risk factor of prognosis and may be a potential molecular marker and therapeutic target in LsCC.

The Gut Microbial Signature of Gestational Diabetes Mellitus and the Association With Diet Intervention.

Gestational diabetes mellitus (GDM) is a high-risk pregnancy complication that is associated with metabolic disorder phenotypes, such as abnormal blood glucose and obesity. The link between microbiota and diet management contributes to metabolic homeostasis in GDM. Therefore, it is crucial to understand the structure of the gut microbiota in GDM and to explore the effect of dietary management on the microbiota structure. In this study, we analyzed the composition of the gut microbiota between 27 GDM and 30 healthy subjects at two time points using Illumina HiSeq 2500 platform. The taxonomy analyses suggested that the overall bacteria clustered by diabetes status, rather than diet intervention. Of particular interest, the phylum Acidobacteria in GDM was significantly increased, and positively correlated with blood glucose levels. Moreover, Partial least-squares discriminant analysis (PLS-DA) revealed that certain genera in the phyla Firmicutes, Bacteroidetes, Proteobacteria, and Lentisphaerae characterized the GDM gut microbiota. Correlation analysis indicated that blood glucose levels and BMI index were correlated with the relative abundance of SCFAS-producing genera. Through the comparison between the GDM and healthy samples with or without diet intervention, we discovered that the role of short-term diet management in GDM processes is associated with the change in the Firmicutes/Bacteroidetes ratio and some specific taxa, rather than an alternative gut microbial pattern. Our study have important implications for understanding the beneficial effects of diet intervention on the specific gut microbiota and thus possibly their metabolism in pregnant women with GDM.

Integrated transcriptome and microRNA profiles analysis reveals molecular mechanisms underlying the consecutive monoculture problem of Polygonatum odoratum.

Polygonatum odoratum is a historically traditional Chinese medicine plant. However, the consecutive monoculture problem (CMP) widespread in other Chinese medicine limiting their cultivation on a large scale. In this study, the physiological data showed the adverse effect of CMP on the growth of P. odoratum under the consecutive cropping (CC) compared with the first cropping (FC). Then the high-throughput sequencing of miRNA and mRNA libraries of leaves and roots from FC and CC P. odoratum plants identified 671 differentially expressed genes (DEGs) and 184 differentially expressed miRNAs and revealed that the DEGs and target genes of the miRNAs were mainly involved in starch and sucrose metabolism, phenylpropanoid and brassinosteroid biosynthesis. The KEGG analysis revealed that the DEGs between CC and FC roots were enriched in the plant-pathogen interaction pathway. This study provided the expression regulation of genes related to CMP of P. odoratum but also suggested that CMP may result in the serious damage of pathogens to roots and cause the slow growth in the consecutive cropping plants.

SAG expression associates with COPB2-related signaling and a poorer prognosis in breast cancer.

SAG is an essential RING component of the Cullin-RING ligase (CRL) E3 ubiquitin ligase complex, which regulates diverse signaling pathways and biological processes, including cell apoptosis, embryonic development, angiogenesis, and tumorigenesis. In the present study, we revealed that SAG gene expression is upregulated in breast cancer cells and that SAG overexpression is associated with significant poorer survival in breast cancer, especially the luminal A subtype. We also detected highly correlated co-overexpression of SAG and COPB2 in breast cancers. Subsequent in vitro experiments demonstrated that SAG and COPB2 act cooperatively to stimulate breast cancer cell proliferation, migration and invasion. Our findings suggest that levels of SAG and COPB2 expression may be useful prognostic indicators in breast cancers and that SAG may be involved in COPB2-related signaling during breast cancer development.

Association of mRNA expression levels of Cullin family members with prognosis in breast cancer: An online database analysis.

Cullin proteins couple with RING-finger proteins, adaptor proteins and substrate recognition receptors to form E3 ubiquitin ligases for recognizing numerous substrates and participating in a variety of cellular processes, especially in genome stability and tumorigenesis. However, the prognostic values of Cullins in breast cancer remain elusive.A "Kaplan-Meier plotter" (KM plotter) online survival analysis tool was used to evaluate the association of individual Cullin members' mRNA expression with overall survival (OS) in breast cancer patients.Our results revealed that elevated mRNA expression of CUL4A and PARC were significantly associated with poor OS for breast cancer patients. While high mRNA expression of CUL2, CUL4B, and CUL5 were correlated with better survival for breast cancers.The associated results suggested that some Cullin members could serve as new predictive prognostic indicators for breast cancer.

Inactivating the ubiquitin ligase Parkin suppresses cell proliferation and induces apoptosis in human keloids.

Keloids are a common type of pathological skin healing, characterized by the destruction of the vascular network. Thus, keloids often exhibit anoxic conditions. Hypoxia-inducible factor-1α (HIF-1α) is a core factor that mediates hypoxia stress responses and allows the cells to adapt to low-oxygen conditions. In the current study, we identified that Parkin acted as an E3 ubiquitin ligase, contributing to the degradation of HIF-1α in keloid fibroblasts (KFs). Silencing of Parkin in KFs upregulated HIF-1α expression and prolonged its protein half-life. Furthermore, Parkin influenced transforming growth factor ß (TGF-ß)/Smad signaling by targeting HIF-1α. Under hypoxic conditions, silencing Parkin enhanced KF proliferation and inhibited apoptosis through the TGF-ß/Smad signaling pathway. Notably, metformin, an antidiabetic drug, could significantly induce Parkin expression and enhance the interaction between Parkin and HIF-1α. As a result, we revealed an important mechanism for Parkin in keloid development and suggested that targeting Parkin could be an alternative method for keloid treatment.