Gene co-expression network analysis provides a novel insight into the dynamic response of wheat to powdery mildew stress

Powdery mildew (Blumeria graminis f. sp. Tritici, (Bgt)) is an important worldwide fungal foliar disease of wheat (Triticum aestivum) responsible for severe yield losses. The development of resistance genes and dissection of the resistance mechanism will therefore be beneficial in wheat breeding. The Bgt resistance gene PmAS846 was transferred to the hexaploid wheat lines N9134 from Triticum dicoccoides, and it is still one of the most effective resistance genes. Here, by RNA sequencing, we identified three co-expressed gene modules using pairwise comparisons and weighted gene co-expression network analysis during wheat–Bgt interactions compared with mock-infected plants. Hub genes of stress-specific modules were significantly enriched in spliceosomes, phagosomes, the mRNA surveillance pathway, protein processing in the endoplasmic reticulum, and endocytosis. Induced module genes located on chromosome 5BL were selected to construct a protein–protein interaction network. Several proteins were predicted as the key hub node, including Hsp70, DEAD/DEAH box RNA helicase PRH75, elongation factor EF-2, cell division cycle 5, ARF guanine-nucleotide exchange factor GNOM-like, and protein phosphatase 2C 70 protein, which interacted with several disease resistance proteins such as RLP37, RPP13 and RPS2 analogues. Gene ontology enrichment results showed that wheat could activate binding functional genes via an mRNA transcription mechanism in response to Bgt stress. Of these node genes, GNOM-like, PP2C isoform X1 and transmembrane 9 superfamily member 9 were mapped onto the genetic fragment of PmAS846 with a distance of 4.8 Mb. This work provides the foundations for understanding the resistance mechanism and cloning the resistance gene PmAS846

Characteristics of Atmospheric Fine Particulate Matter (PM ) Induced Differentially Expressed Proteins Determined by Proteomics and Bioinformatics Analyses / 生物医学与环境科学（英文）

Objective@#To screen the differentially expressed proteins (DEPs) in human bronchial epithelial cells (HBE) treated with atmospheric fine particulate matter (PM ).@*Methods@#HBE cells were treated with PM samples from Shenzhen and Taiyuan for 24 h. To detect overall protein expression, the Q Exactive mass spectrometer was used. Gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and Perseus software were used to screen DEPs.@*Results@#Overall, 67 DEPs were screened in the Shenzhen sample-treated group, of which 46 were upregulated and 21 were downregulated. In total, 252 DEPs were screened in the Taiyuan sample-treated group, of which 134 were upregulated and 118 were downregulated. KEGG analysis demonstrated that DEPs were mainly enriched in ubiquitin-mediated proteolysis and HIF-1 signal pathways in Shenzhen PM samples-treated group. The GO analysis demonstrated that Shenzhen sample-induced DEPs were mainly involved in the biological process for absorption of various metal ions and cell components. The Taiyuan PM -induced DEPs were mainly involved in biological processes of protein aggregation regulation and molecular function of oxidase activity. Additionally, three important DEPs, including ANXA2, DIABLO, and AIMP1, were screened.@*Conclusion@#Our findings provide a valuable basis for further evaluation of PM -associated carcinogenesis.

Nitrogen doses in topdressing affect vegetation indices and corn yield / Deses de nitrogênio em cobertura afetam índices de vegetação e produtividade de milho

Nitrogen is the main nutrient required by corn crop, especially in Cerrado soils. Remote sensing techniques can be used to generate additional information now of nitrogen fertilization recommendation. This work investigated the association of plant height and dry matter phenological variables together with NDVI, REDEDGE, SAVI, and IV 760/550 vegetation indices (VIs) with corn grain yield, under different N doses. Sowing occurred in November 2016, at a spacing of 0.45 m between rows and a 60,000 ha-1 plant population. Four N doses (0, 80, 160, and 240 kg of N ha-1) were applied at phenological stage V4. The experimental design consisted of randomized blocks, containing four N doses in topdressing and 16 replications. The active optical sensor Crop Circle ACS-470 was used to obtain the VIs. The NDVI, SAVI, and RE indices have a high positive association with each other and with the variables plant height and dry matter. Polynomial regression equations were adjusted between the variables in response as doses of N. Afterwards, they were estimated as correlations between variables and results expressed through the network of correlations. Finally, a multivariate analysis of canonical variables was performed to understand the interrelationship between the variables and each dose of N applied. NDVI and RE have a positive relationship of moderate magnitude with grain yield in corn crops.

O nitrogênio (N) é o principal nutriente requerido pela cultura do milho, principalmente em solos do Cerrado. Técnicas de sensoriamento remoto podem ser usadas para gerar informações adicionais agora sobre a recomendação de fertilização nitrogenada. Este trabalho investigou a associação de variáveis fenológicas de altura de plantas e matéria seca com os índices de vegetação (IVs) NDVI, REDEDGE, SAVI e IV 760/550 com a produtividade de grãos de milho, sob diferentes doses de N. A semeadura ocorreu em novembro de 2016, com espaçamento de 0,45 m entre linhas e 60.000 ha-1 de população de plantas. Quatro doses de N (0, 80, 160 e 240 kg de N ha-1) foram aplicadas no estádio fenológico V4. O delineamento experimental foi o de blocos casualizados contendo quatro doses de N em cobertura e 16 repetições. O sensor óptico ativo Crop Circle ACS-470 foi usado para obter os IVs. Equações de regressão polinomial foram ajustadas entre as variáveis em resposta como doses de N. Posteriormente, foram estimadas como correlações entre variáveis e resultados expressos através da rede de correlações. Por fim, foi realizada uma análise multivariada de variáveis canônicas para entender a inter-relação entre as variáveis e cada dose de N aplicada. Os índices NDVI, SAVI e RE apresentam alta associação positiva entre si e com as variáveis altura de planta e matéria seca. NDVI e REDEDGE têm uma relação positiva de magnitude moderada com a produtividade de grãos na cultura do milho.

Mining hub genes related to liver cancer stage in TCGA database with weighted correlation network analysis method / 中国医师进修杂志

Objective@#Primary liver cancer is a kind of gastrointestinal malignant tumor with high morbidity and mortality. Early diagnosis is difficult, with postoperative high recurrence rate and high metastasis rate, poor prognosis, so it is particularly important to better understand the occurrence and development of liver cancer from the gene level, so as to provide theoretical basis for gene therapy or targeted drug therapy in the future.@*Methods@#TCGA database for liver cancer gene transcriptome data information and clinical phenotype information was downloaded, and R language edgeR package was used to standardize the transcriptome data. The log FC > 1, FDR < 0.01 gene was set to be expressing differences gene, and then the weighted correlation network analysis (WGCNA) methods was used to analyze the relationship between liver cancer stage (stage) and the differentially expressed genes to look for hub genes.@*Results@#Four hub genes related to tumor staging were identified (TPX2, HJURP, KIAA1524, SGO2). Kaplan-meier survival curve was drawn and it was found that their expression level was significantly correlated with patient survival time, and high expression level was an independent prognostic factor.@*Conclusions@#WGCNA method is used to mine the TCGA database information and find the hub genes related to tumor staging. The relationship between TPX2, HJURP, KIAA1524 and liver cancer has been reported in the literature, except SGO2. This study will provide important theoretical basis for the follow-up study of liver cancer.