scholarly journals Integrated Analysis of the lncRNA/circRNA-miRNA-mRNA Expression Profiles Reveals Novel Insights Into Potential Mechanisms in Response to Root-knot Nematodes in Peanut

2021 ◽  
Author(s):  
Ping Xu ◽  
Hui Li ◽  
Xiaohua Wang ◽  
Ge Zhao ◽  
Xiaofei Lu ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Reduction Process ◽  
Synthesis Process ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis ◽  
Root Knot Nematode ◽  
Root Knot Nematodes ◽  
Oxidation Reduction ◽  
The World

Abstract BackgroundThe high content of oil and protein makes peanut the main oil and edible crop in the world. Root-knot nematode forms root-knot by infecting peanut roots, which lead to poor development of peanut roots and seriously restricts the yield of peanut in the world. With the release of peanut genome, a large number of genetic loci controlling peanut root-knot nematode have been detected, but the molecular mechanism of root-knot nematode is still unclear. ResultsThe whole transcriptome RNA-seq was used to reveal the divergent response to root-knot nematode stress in peanut roots. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs and 123 circRNAs were identified differential expression between infected and no-infected peanut, respectively. To understand the potential mechanisms in response to root-knot nematodes in peanut roots, the expression profiles of lncRNA/circRNA-miRNA-mRNA network were constructed. A total of 10 lncRNAs, 4 circRNAs, 5 miRNAs and 13 mRNAs can regularly the expression of mRNA during root-knot nematodes stress by forming competing endogenous RNA and participate in oxidation-reduction process and other various biological metabolism pathways in peanut. The results gained will reveal the role of ceRNAs of peanut in response to root-knot nematodes.ConclusionThe GO classification and KEGG pathway enrichment analysis of core regulatory networks revealing the ceRNAs participate in oxidation-reduction, peroxidase activity, lignin synthesis in xylem and flavonoid synthesis process. Overall, those results could gain the knowledge of the role of no-coding RNAs in response to root-knot nematodes.

scholarly journals The Role Of Literacy In The Economic Growth Of Cameroon

2018 ◽  
Vol 14 (22) ◽  
pp. 25
Author(s):  
Dudjo Yen G. Boris ◽  
Sonkeng Germain ◽  
Njong Mom Aloysius ◽  
Tafah Edokat O. Edward
Keyword(s):  
Economic Growth ◽  
Significant Relationship ◽  
Poverty Reduction ◽  
Empirical Studies ◽  
Reduction Process ◽  
Literacy Rate ◽  
The World ◽  
The Relationship ◽  
Positive Effect

This paper focuses on how education contributes to economic growth. That is to say that there is a significant relationship between the variables of education and the economic growth of Cameroon. Education is therefore a priority for all nations. This shows the prominent place it occupies in the Constitution of almost every state. There are several studies that have focused on the relationship between education and economic growth of the microeconomic perspective, as macroeconomic, both theoretically and empirically. Empirical studies, which have been carried out everywhere around the world, do not agree with the fact that education has a positive effect on economic growth. The estimation results show that literacy rate, however, remains ambiguous and contradictory when OLS is going to GMM. Investing in Literacy is a challenge for development and it is the heart of poverty reduction process at all levels.

scholarly journals GROWTH AND YIELD RESPONSES OF FIFTEEN CUCUMBER CULTIVARS TO ROOT-KNOT NEMATODE (Meloidogyne incognita)

2019 ◽  
Vol 18 (3) ◽  
pp. 45-52 ◽  
Author(s):  
Tariq Mukhtar ◽  
Muhammad Zameer Kayani
Keyword(s):  
Meloidogyne Incognita ◽  
Growth And Yield ◽  
Root Knot Nematode ◽  
Root Knot Nematodes ◽  
Resistant Cultivars ◽  
Yield Parameters ◽  
Significant Damage ◽  
The World ◽  
Yield Responses ◽  
Moderately Resistant

Root-knot nematodes have become a grave menace to the lucrative production of cucumber throughout the world. These nematodes are mainly controlled by applying nematicides, but their use is often associated with hazards. Alternatively, the use of nematode resistant cultivars is considered to be innocuous and economically feasible. For their fitness as nematode-suppressive crops, the reduction in growth and yield parameters of these cultivars must be assessed. As there is little documented data about the effects of Meloidogyne incognita on the damage of cucumber, therefore, in the present study, the effects of M. incognita were evaluated on growth and yield parameters of fifteen cucumber cultivars. M. incognita significantly negatively affected the growth and yield parameters of all the cucumber cultivars. Shoot and root lengths and shoot weights of all the cultivars were significantly reduced as a result of nematode infection. Maximum reductions in these parameters were recorded in highly susceptible cultivars followed by susceptible ones, while the reductions were minimal in resistant followed by moderately resistant cultivars. On the contrary, the infection by M. incognita resulted in an increase in root weights of all the cultivars. The increase was found to be the maximum in highly susceptible cultivars followed by susceptible and moderately susceptible cultivars. Likewise, the minimum increase was observed in the resistant cultivars followed by moderately resistant cultivars. Similarly, significant variations in yield parameters among fifteen cucumber cultivars were also recorded as a result of M. incognita infection. In the case of highly susceptible cultivars, the reductions in yield parameters were maximum, whereas the reductions in resistant and moderately resistant cultivars were found to be minimum. As cultivars Long Green, Marketmore, Pioneer-II, Dynasty and Summer Green experienced no significant damage compared to susceptible cucumber cultivars and therefore, they are approved for cultivation in nematode infested soils.

scholarly journals Integrated analysis of lncRNA-miRNA-mRNA ceRNA network and the potential prognosis indicators in sarcomas

2020 ◽  
Author(s):  
Ling Zhang ◽  
Lu Gao ◽  
Yu Zhao ◽  
Xuelei Ma
Keyword(s):  
Survival Analysis ◽  
Protein Interactions ◽  
Sequence Data ◽  
Gene Prediction ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis ◽  
Tissue Samples ◽  
Cerna Network

Abstract The ceRNA network has been demonstrated to play crucial roles in multiple biological processes and the development of neoplasms, which have the potential to become diagnostic and prognosis markers and therapeutic targets. In this work, we comparing the expression profiles between sarcoma identified differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs) in sarcomas and normal tissue samples in GEO datasets. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied to investigate the major functions of the overlapping DEGs. Then, lncRNA-miRNA interactions and miRNA-mRNA interactions were predicted, and a ceRNA regulatory network was constructed. In addition, the mRNAs included in ceRNA network were used to construct the protein-protein interactions network, and the survival analysis of sarcomas was performed according to the biomarkers included in the ceRNA network. According to the RNA sequence data from GEO dataset, 1296 DEGs were identified in sarcoma samples by combining the GO and Pathway enrichment analysis, 338 DELs were discovered after re-annotating the probes, and 36 DEGs were ascertained through intersecting two different expression miRNAs sets. Further, 448 miRNA-mRNA interactions and 454 miRNA-lncRNA interactions were obtained through target gene prediction, and then, we constructed a lncRNA-miRNA-mRNA ceRNA network containing 9 miRNAs, 69 lncRNAs and 113 mRNAs. PPI network showed that the hub up-regulated nodes include IGF1, PRKCB and GNAI3, and the hub down-regulated nodes include AR, CYCS and PPP1CB. Survival analysis revealed that the expression levels of 12 RNAs involved in the ceRNA network were associated with overall survival of sarcoma patients. Our study showed that the ceRNA network in sarcomas based on that lncRNA could serve as ceRNA and discovered the potential indicators for prognosis of sarcoma patients.

scholarly journals Integrated microRNA and mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Ebstein’s Anomaly

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1066
Author(s):  
Masood Abu-Halima ◽  
Viktoria Wagner ◽  
Lea Simone Becker ◽  
Basim M. Ayesh ◽  
Mohammed Abd El-Rahman ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Fold Change ◽  
Mrna Abundance ◽  
Ebstein’S Anomaly ◽  
Cellular Interaction ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis ◽  
Ebstein's Anomaly ◽  
Mrna Targets ◽  
Lower Abundance

Little is known about abundance level changes of circulating microRNAs (miRNAs) and messenger RNAs (mRNA) in patients with Ebstein’s anomaly (EA). Here, we performed an integrated analysis to identify the differentially abundant miRNAs and mRNA targets and to identify the potential therapeutic targets that might be involved in the mechanisms underlying EA. A large panel of human miRNA and mRNA microarrays were conducted to determine the genome-wide expression profiles in the blood of 16 EA patients and 16 age and gender-matched healthy control volunteers (HVs). Differential abundance level of single miRNA and mRNA was validated by Real-Time quantitative PCR (RT-qPCR). Enrichment analyses of altered miRNA and mRNA abundance levels were identified using bioinformatics tools. Altered miRNA and mRNA abundance levels were observed between EA patients and HVs. Among the deregulated miRNAs and mRNAs, 76 miRNAs (49 lower abundance and 27 higher abundance, fold-change of ≥2) and 29 mRNAs (25 higher abundance and 4 lower abundance, fold-change of ≥1.5) were identified in EA patients compared to HVs. Bioinformatics analysis identified 37 pairs of putative miRNA-mRNA interactions. The majority of the correlations were detected between the lower abundance level of miRNA and higher abundance level of mRNA, except for let-7b-5p, which showed a higher abundance level and their target gene, SCRN3, showed a lower abundance level. Pathway enrichment analysis of the deregulated mRNAs identified 35 significant pathways that are mostly involved in signal transduction and cellular interaction pathways. Our findings provide new insights into a potential molecular biomarker(s) for the EA that may guide the development of novel targeting therapies.

scholarly journals Integrated analysis of high-throughput sequencing data reveals the key role of LINC00467 in the invasion and metastasis of testicular germ cell tumors

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Hao Bo ◽  
Fang Zhu ◽  
Zhizhong Liu ◽  
Qi Deng ◽  
Guangmin Liu ◽  
...  
Keyword(s):  
Germ Cell ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Germ Cell Tumors ◽  
Differentially Expressed ◽  
Migration And Invasion ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Testicular Germ Cell

AbstractLong noncoding RNAs (lncRNAs) are involved in various physiological and pathological processes. However, the role of lncRNAs in testicular germ cell tumor (TGCT) has been rarely reported. Our purpose is to comprehensively survey the expression and function of lncRNAs in TGCT. In this study, we used RNA sequencing to construct the lncRNA expression profiles of 13 TGCT tissues and 4 paraneoplastic tissues to explore the function of lncRNAs in TGCT. The bioinformatics analysis showed that many lncRNAs are differentially expressed in TGCT. GO and KEGG enrichment analyses revealed that the differentially expressed lncRNAs participated in various biological processes associated with tumorigenesis in cis and trans manners. Further, we found that the expression of LINC00467 was positively correlated with the poor prognosis and pathological grade of TGCT using WGCNA analysis and GEPIA database data mining. In vitro experiments revealed that LNC00467 could promote the migration and invasion of TGCT cells by regulating the expression of AKT3 and influencing total AKT phosphorylation. Further analysis of TCGA data revealed that the expression was negatively correlated with the infiltration of immune cells and the response to PD1 immunotherapy. In summary, this study is the first to construct the expression profile of lncRNAs in TGCT. It is also the first study to identify the metastasis-promoting role of LNC00467, which can be used as a potential predictor of TGCT prognosis and immunotherapeutic response to provide a clinical reference for the treatment and diagnosis of TGCT metastasis.

scholarly journals A Bioinformatics-Based Screening and Analysis of Key Genes in Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Yanfei Wei ◽  
Shengshan Wang ◽  
Wanjun Chen ◽  
Yuning Lin ◽  
Qi Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Reduction Process ◽  
Heme Binding ◽  
Sequencing Technology ◽  
Hub Genes ◽  
Hub Gene ◽  
Oxidation Reduction ◽  
Extracellular Region ◽  
The World ◽  
Key Genes

Abstract Hepatocellular carcinoma (HCC) is considered as the leading killer disease in the world. So far most of the diagnosis of HCC is mainly established on imaging and biopsy. As sequencing technology is developing quite fast, and it has already been widely applied in the medical area, such as cancer diagnosis. In this article, GSE121248, GSE76427 and GSE60502 datasets were chosen to analyze and screen key genes which could affect the development of liver cancer through the bioinformatics method. The results showed up regulated genes mainly reside in cell division, nucleus, protein binding pathway, and down regulated genes are mostly located in the Oxidation-reduction process, Extracellular region, Heme binding, Metabolic pathway. Secondly, hub gene analysis indicated there were twelve critical hub genes found: RFC4, RACGAP1, CCNB2, CDC20, UBE2C, PTTG1, AURKA, PRC1, NCAPG, CDKN3, TOP2A, KIF20A, AURKA and CDKN3. By applying bioinformatic measures , the genes associated with hepatocellular carcinoma can be efficiently analyzed, that would provide invaluable information for translational studies.

Soybean Root-Knot Nematode: A Diagnostic Guide

2021 ◽  
pp. PHP-01-21-0005-
Author(s):  
Adrienne M. Gorny ◽  
Weimin Ye ◽  
Sam Cude ◽  
Lindsey Thiessen
Keyword(s):  
Common Root ◽  
Root Knot Nematode ◽  
Root Knot Nematodes ◽  
Soybean Production ◽  
Soybean Root ◽  
The World ◽  
Plant Parasites ◽  
Meloidogyne Spp

Root-knot nematodes (Meloidogyne spp.) are one of the most economically important plant parasites in the world, and significantly impacts soybean production in places where they are endemic. Several species of root-knot nematode are capable of causing significant damages to soybean and have broad host ranges that include common rotational crops and weeds. Symptoms of root-knot nematode infections may be confused with other diseases, nutritional disorders, or common root features associated with legumes. The purpose of this diagnostic guide is to provide information regarding identification, isolation, storage, and other relevant aspects of this pathosystem.

scholarly journals Integrated Analysis of the Clinical and Molecular Characteristics of IDH Wild-Type Gliomas in the Chinese Glioma Genome Atlas

2021 ◽  
Author(s):  
Peng Wang ◽  
Yanwei Liu ◽  
Lin Zhi ◽  
Xiaoguang Qiu
Keyword(s):  
Genetic Information ◽  
Reduction Process ◽  
Progression Free Survival ◽  
Integrated Analysis ◽  
Molecular Characteristics ◽  
Lower Grade ◽  
Wild Type ◽  
Oxidation Reduction ◽  
Lower Grade Glioma ◽  
Genome Atlas

Abstract Purpose: Current studies and guidelines suggest that the biobehavior of IDH-wild type (IDH-wt) lower-grade glioma (LGG, WHO II-III) is similar to IDH-wt glioblastoma (GBM). However, differences in their clinical and molecular characteristics have not been reported. This study aimed to analyze the clinical and genetic information of gliomas with IDH-wt. Methods: Four hundred patients with IDH-wt were enrolled in the study (LGG = 176, GBM = 224), and their clinical and genetic information was collected from the Chinese Glioma Genome Atlas (CGGA). We conducted an analysis of this information between the two groups of patients and drew conclusions thereof. Results: The median age of the LGG patients was 42 (40–47) years, while that of the GBM patients was 51 (47–53) years (P < 0.05). GBM patients were more likely to undergo total resection (P < 0.05) and had fewer epileptic seizure symptoms (P < 0.01). The median overall survival (OS) was 51.87 months for the LGG patients and only 14.5 months for the GBM patients (P < 0.01). The median progression-free survival (PFS) was 37.6 months for the LGG patients and only 9.3 months for the GBM patients (P < 0.01). LGG patients were more prone to PETN mutations (P < 0.05). Transcriptome analysis showed that the differentially expressed genes in LGG patients were mainly enriched in metabolic pathways and pathways in cancer and in the function of signal transduction and positive regulation of GTPase activity, while in GBM patients, they were mainly enriched in the PI3K-Akt signaling pathway and in the functions of apoptotic process and oxidation-reduction process. Conclusions: Our data indicate that these two groups of patients should be re-evaluated and treated differently, despite both having IDH wild type.

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