scholarly journals Proteomics and Interspecies Interaction Analysis Revealed Abscisic Acid Signalling to Be the Primary Driver for Oil Palm’s Response against Red Palm Weevil Infestation

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2574
Author(s):  
Nazmi Harith-Fadzilah ◽  
Su Datt Lam ◽  
Mohammad Haris-Hussain ◽  
Idris Abd Ghani ◽  
Zamri Zainal ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Stress Response ◽  
Elaeis Guineensis ◽  
Interaction Analysis ◽  
Insect Pest ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Red Palm Weevil ◽  
Palm Weevil ◽  
Primary Driver

The red palm weevil (RPW; Rhynchophorus ferrugineus Olivier (Coleoptera Curculionidae)) is an invasive insect pest that is difficult to manage due to its nature of infesting the host palm trees from within. A holistic, molecular-based approach to identify proteins that correlate with RPW infestation could give useful insights into the vital processes that are prevalent to the host’s infestation response and identify the potential biomarkers for an early detection technique. Here, a shotgun proteomic analysis was performed on oil palm (Elaeis guineensis; OP) under untreated (control), wounding by drilling (wounded), and artificial larval infestation (infested) conditions at three different time points to characterise the RPW infestation response at three different stages. KEGG pathway enrichment analysis revealed many overlapping pathways between the control, wounded, and infested groups. Further analysis via literature searches narrowed down biologically relevant proteins into categories, which were photosynthesis, growth, and stress response. Overall, the patterns of protein expression suggested abscisic acid (ABA) hormone signalling to be the primary driver of insect herbivory response. Interspecies molecular docking analysis between RPW ligands and OP receptor proteins provided putative interactions that result in ABA signalling activation. Seven proteins were selected as candidate biomarkers for early infestation detection based on their relevance and association with ABA signalling. The MS data are available via ProteomeXchange with identifier PXD028986. This study provided a deeper insight into the mechanism of stress response in OP in order to develop a novel detection method or improve crop management.

scholarly journals Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guilherme B. Dias ◽  
Musaad A. Altammami ◽  
Hamadttu A. F. El-Shafie ◽  
Fahad M. Alhoshani ◽  
Mohamed B. Al-Fageeh ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Control Strategies ◽  
Insect Pest ◽  
Single Copy ◽  
Gene Content ◽  
Rhynchophorus Ferrugineus ◽  
Red Palm Weevil ◽  
Transcriptomic Data ◽  
Palm Trees ◽  
Palm Weevil

AbstractThe red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage ($$\sim$$ ∼ 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.

Quantitative proteomics analysis of FFPE tumor samples reveals the influences of novel targeting nanobubbles conjugated with NET-1 siRNA on tetraspanin protein involved in HCC

2020 ◽  
Author(s):  
Bolin Wu ◽  
Haitao Shang ◽  
Xitian Liang ◽  
Huajing Yang Huajing Yang ◽  
Hui Jing ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Interaction Analysis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Protein Protein Interaction ◽  
Study Results ◽  
Ffpe Tumor

Abstract Background: Hepatocellular carcinoma (HCC) poses a severe threat to human health. The NET-1 protein has been proved to be strongly associated with HCC proliferation and metastasis in our previous study. Methods: Here, we developed a label-free proteome mass spectrometry workflow to analyze formalin-fixed and paraffin-embedded HCC xenograft samples collected in our previous study. Results: The result showed that 78 proteins were differentially expressed after NET-1 protein inhibited. Among them, the expression of 61 proteins up-regulated and the expression of 17 proteins were significantly down-regulated. Of the differentially expressed proteins, the vast majority of Gene Ontology enrichment terms belong to the biological process. The KEGG pathway enrichment analysis showed that the 78 differentially expressed proteins significantly enriched in 45 pathways. We concluded that the function of the NET-1 gene is not only to regulate HCC but also to participate in a variety of biochemical metabolic pathways in the human body. Furthermore, the protein-protein interaction analysis indicated that the interactions of differentially expressed proteins are incredibly sophisticated. All the protein-protein interactions happened after the NET-1 gene has been silenced. Conclusions: Finally, our study also provides a useful proposal for targeted therapy based on tetraspanin proteins to treat HCC, and further mechanism investigations are needed to reveal a more detailed mechanism of action for NET-1 protein regulation of HCC.

scholarly journals Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

2020 ◽  
Author(s):  
Guilherme B. Dias ◽  
Musaad A. Altammami ◽  
Hamadttu A.F. El-Shafie ◽  
Fahad M. Alhoshani ◽  
Mohamed B. Al-Fageeh ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Control Strategies ◽  
Insect Pest ◽  
Single Copy ◽  
Gene Content ◽  
Rhynchophorus Ferrugineus ◽  
Red Palm Weevil ◽  
Transcriptomic Data ◽  
Palm Trees ◽  
Palm Weevil

ABSTRACTThe red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage (~62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6,000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.

scholarly journals Host Factor Interaction Networks Identified by Integrative Bioinformatics Analysis Reveals Therapeutic Implications in COPD Patients With COVID-19

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenjiang Zheng ◽  
Ting Wang ◽  
Peng Wu ◽  
Qian Yan ◽  
Chengxin Liu ◽  
...  
Keyword(s):  
Network Analysis ◽  
Bioinformatics Analysis ◽  
Interaction Analysis ◽  
Clinical Sample ◽  
Enrichment Analysis ◽  
Host Factor ◽  
Interaction Networks ◽  
Host Factors ◽  
Pathway Enrichment Analysis ◽  
Factor Interaction

Background: The COVID-19 pandemic poses an imminent threat to humanity, especially for those who have comorbidities. Evidence of COVID-19 and COPD comorbidities is accumulating. However, data revealing the molecular mechanism of COVID-19 and COPD comorbid diseases is limited.Methods: We got COVID-19/COPD -related genes from different databases by restricted screening conditions (top500), respectively, and then supplemented with COVID-19/COPD-associated genes (FDR<0.05, |LogFC|≥1) from clinical sample data sets. By taking the intersection, 42 co-morbid host factors for COVID-19 and COPD were finally obtained. On the basis of shared host factors, we conducted a series of bioinformatics analysis, including protein-protein interaction analysis, gene ontology and pathway enrichment analysis, transcription factor-gene interaction network analysis, gene-microRNA co-regulatory network analysis, tissue-specific enrichment analysis and candidate drug prediction.Results: We revealed the comorbidity mechanism of COVID-19 and COPD from the perspective of host factor interaction, obtained the top ten gene and 3 modules with different biological functions. Furthermore, we have obtained the signaling pathways and concluded that dexamethasone, estradiol, progesterone, and nitric oxide shows effective interventions.Conclusion: This study revealed host factor interaction networks for COVID-19 and COPD, which could confirm the potential drugs for treating the comorbidity, ultimately, enhancing the management of the respiratory disease.

scholarly journals The Effect of Low Temperature Stress on the Leaves and MicroRNA Expression of Potato Seedlings

2021 ◽  
Vol 9 ◽  
Author(s):  
Chongchong Yan ◽  
Nan Zhang ◽  
Qianqian Wang ◽  
Yuying Fu ◽  
Feng Wang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Low Temperature ◽  
Temperature Stress ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Potato Production ◽  
Low Temperature Stress ◽  
Pathway Enrichment Analysis ◽  
Novel Mirna ◽  
Potato Seedlings

In recent years, with the wanton destruction of the ecological environment by humans and the frequent occurrence of extreme bad weather, many places that should have been warm and blooming in spring have instead experienced the phenomenon of the “April blizzard,” which has seriously affected China's crops, especially spring potato production in most areas. Potato cultivars, especially potato seedlings, are sensitive to frost, and low temperature frost has become one of the most important abiotic stresses affecting potato production. Potato cold tolerance is regulated by a complex gene network. Although some low temperature resistant microRNAs have been identified, little is known about the role of miRNAs in response to low temperature stress in potato. Therefore, the objective of this study is to clarify the influence of low temperature stress on the miRNA expression of potato by comparing the expression differences of miRNA in potato which was treated with different low temperatures. For the study, 307 known miRNAs belonging to 73 small RNA families and 211 novel miRNAs were obtained. When the temperature decreased, the number of both known and novel miRNA decreased, and the minimum temperature was −2°C. Most of the miRNAs respond to low temperature, drought, and disease stress; some conserved miRNAs were first found to respond to low temperature stress in potato, such as stu-miR530, stu-miR156d, and stu-miR167b. The Gene Ontology, Kyoto Encyclopedia of Genes, and Genomes pathway enrichment analysis of 442 different expression miRNAs target genes indicated that there existed diversified low temperature responsive pathways, but Abscisic Acid was found likely to play a central coordinating role in response to low temperature stress in many metabolism pathways. Quantitative real-time PCR assays indicated that the related targets were negatively regulated by the tested different expression miRNAs during low temperature stress. The results indicated that miRNAs may play an important coordination role in response to low temperature stress in many metabolic pathways by regulating abscisic acid and gibberellin, which provided insight into the roles of miRNAs during low temperature stress and would be helpful for alleviating low temperature stress and promoting low temperature resistant breeding in potatoes.

Effects of an entomopathogen nematode on the immune response of the insect pest red palm weevil: Focus on the host antimicrobial response

2016 ◽  
Vol 133 ◽  
pp. 110-119 ◽  
Author(s):  
Simona Binda-Rossetti ◽  
Maristella Mastore ◽  
Marina Protasoni ◽  
Maurizio F. Brivio
Keyword(s):  
Immune Response ◽  
Insect Pest ◽  
Red Palm Weevil ◽  
Palm Weevil

scholarly journals Identification of Four Oxidative Stress-Responsive MicroRNAs, miR-34a-5p, miR-1915-3p, miR-638, and miR-150-3p, in Hepatocellular Carcinoma

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Yong Wan ◽  
Ruixia Cui ◽  
Jingxian Gu ◽  
Xing Zhang ◽  
Xiaohong Xiang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Hepatocellular Carcinoma ◽  
Stress Response ◽  
Clinical Investigation ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Oxidative Stress Response ◽  
Rank Aggregation ◽  
Integrated Analysis ◽  
Pathway Enrichment Analysis

Increasing evidence suggests that oxidative stress plays an essential role during carcinogenesis. However, the underlying mechanism between oxidative stress and carcinogenesis remains unknown. Recently, microRNAs (miRNAs) are revealed to be involved in oxidative stress response and carcinogenesis. This study aims to identify miRNAs in hepatocellular carcinoma (HCC) cells which might involve in oxidative stress response. An integrated analysis of miRNA expression signature was performed by employing robust rank aggregation (RRA) method, and four miRNAs (miR-34a-5p, miR-1915-3p, miR-638, and miR-150-3p) were identified as the oxidative stress-responsive miRNAs. Pathway enrichment analysis suggested that these four miRNAs played an important role in antiapoptosis process. Our data also revealed miR-34a-5p and miR-1915-3p, but not miR-150-3p and miR-638, were regulated by p53 in HCC cell lines under oxidative stress. In addition, clinical investigation revealed that these four miRNAs might be involved in oxidative stress response by targeting oxidative stress-related genes in HCC tissues. Kaplan-Meier analysis showed that these four miRNAs were associated with patients’ overall survival. In conclusion, we identified four oxidative stress-responsive miRNAs, which were regulated by p53-dependent (miR-34a-5p and miR-1915-3p) and p53-independent pathway (miR-150-3p and miR-638). These four miRNAs may offer new strategy for HCC diagnosis and prognosis.

scholarly journals Abscisic Acid Improves Linoleic Acid Accumulation Possibly by Promoting Expression of EgFAD2 and Other Fatty Acid Biosynthesis Genes in Oil Palm Mesocarp

2021 ◽  
Vol 12 ◽  
Author(s):  
Peng Shi ◽  
Wei Hua ◽  
Yin Min Htwe ◽  
Dapeng Zhang ◽  
Jun Li ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Fatty Acid ◽  
Linoleic Acid ◽  
Oil Palm ◽  
Fatty Acid Biosynthesis ◽  
Enrichment Analysis ◽  
Linoleic Acid Content ◽  
Pathway Enrichment Analysis ◽  
Acid Biosynthesis ◽  
Palm Fruit

Abscisic acid plays an important role in fruit development. However, the effect of ABA on fatty acid biosynthesis in oil palm is still unknown. In this study, ABA treatments (CK, A1–A4) were applied to oil palm fruit at 16 WAP (weeks after pollination), and fatty acids in the mesocarp at 24 WAP were analyzed by GC-MS. Results showed that linoleic acid content under treatment A2 (20 μM ABA) was significantly higher (slightly increased by 8.33%) than the control. Therefore, mesocarp samples of A2, and the control at 16, 20, and 24 WAP was sampled for RNA-Seq. KEGG pathway enrichment analysis showed that 43 genes were differentially expressed in the fatty acid biosynthesis pathway, of which expression of EgFAD2 (unigene 105050201) under 20 μM ABA treatment was 1.84-fold higher than in the control at 20 WAP. Further sequence analysis found that unigene 105050201 had more ABA-responsive elements (ABRE), complete conserved domains, and a C-terminal signaling motif among two FAD2 copies. Furthermore, WGCNA and correlation analysis showed co-expression of EgFAD2 (unigene 105050201) with transcription factors (TFs) (WRI1, AP2-EREBP, bZIP, bHLH, C2C2-Dof, MYB, NAC, and WRKY), ABA signaling genes (PYR, PP2C, SnRK, and ABI5), and other genes involved in fatty acid biosynthesis (FATA, FATB, LACS, SAD, Oleosins, and so on). These results indicated that ABA treatment promoted the expression of FAD2 and other genes involved in fatty acid biosynthesis, which possibly resulted in the accumulation of linoleic acid. This study will be helpful for understanding the possible mechanisms through which ABA affects fatty acid biosynthesis and their accumulation in the mesocarp of oil palm.

scholarly journals Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10141
Author(s):  
Sevcan Atay
Keyword(s):  
Pancreatic Ductal Adenocarcinoma ◽  
Interaction Analysis ◽  
Meta Analysis ◽  
Prognostic Significance ◽  
Enrichment Analysis ◽  
Prognostic Biomarkers ◽  
Ductal Adenocarcinoma ◽  
Receptor Interaction ◽  
Pathway Enrichment Analysis ◽  
Adjacent Tissue

A comprehensive meta-analysis of publicly available gene expression microarray data obtained from human-derived pancreatic ductal adenocarcinoma (PDAC) tissues and their histologically matched adjacent tissue samples was performed to provide diagnostic and prognostic biomarkers, and molecular targets for PDAC. An integrative meta-analysis of four submissions (GSE62452, GSE15471, GSE62165, and GSE56560) containing 105 eligible tumor-adjacent tissue pairs revealed 344 differentially over-expressed and 168 repressed genes in PDAC compared to the adjacent-to-tumor samples. The validation analysis using TCGA combined GTEx data confirmed 98.24% of the identified up-regulated and 73.88% of the down-regulated protein-coding genes in PDAC. Pathway enrichment analysis showed that “ECM-receptor interaction”, “PI3K-Akt signaling pathway”, and “focal adhesion” are the most enriched KEGG pathways in PDAC. Protein-protein interaction analysis identified FN1, TIMP1, and MSLN as the most highly ranked hub genes among the DEGs. Transcription factor enrichment analysis revealed that TCF7, CTNNB1, SMAD3, and JUN are significantly activated in PDAC, while SMAD7 is inhibited. The prognostic significance of the identified and validated differentially expressed genes in PDAC was evaluated via survival analysis of TCGA Pan-Cancer pancreatic ductal adenocarcinoma data. The identified candidate prognostic biomarkers were then validated in four external validation datasets (GSE21501, GSE50827, GSE57495, and GSE71729) to further improve reliability. A total of 28 up-regulated genes were found to be significantly correlated with worse overall survival in patients with PDAC. Twenty-one of the identified prognostic genes (ITGB6, LAMC2, KRT7, SERPINB5, IGF2BP3, IL1RN, MPZL2, SFTA2, MET, LAMA3, ARNTL2, SLC2A1, LAMB3, COL17A1, EPSTI1, IL1RAP, AK4, ANXA2, S100A16, KRT19, and GPRC5A) were also found to be significantly correlated with the pathological stages of the disease. The results of this study provided promising prognostic biomarkers that have the potential to differentiate PDAC from both healthy and adjacent-to-tumor pancreatic tissues. Several novel dysregulated genes merit further study as potentially promising candidates for the development of more effective treatment strategies for PDAC.

scholarly journals Physical and Physiological Monitoring on Red Palm Weevil-Infested Oil Palms

Insects ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 407
Author(s):  
Nazmi Harith-Fadzilah ◽  
Mohamad Haris-Hussain ◽  
Idris Abd Ghani ◽  
Azlina Zakaria ◽  
Samsudin Amit ◽  
...  
Keyword(s):  
Stomatal Conductance ◽  
Chlorophyll Content ◽  
Elaeis Guineensis ◽  
Early Stage ◽  
Physical Symptoms ◽  
Red Palm Weevil ◽  
Significant Drop ◽  
Palm Trees ◽  
Palm Weevil ◽  
Physical Changes

The red palm weevil (RPW) is a stem boring Coleoptera that decimates host palm trees from within. The challenge of managing this pest is due to a lack of physical symptoms during the early stages of infestation. Investigating the physiological changes that occur within RPW-infested palm trees may be useful in establishing a new approach in RPW detection. In this study, the effects of RPW infestation were investigated in Elaeis guineensis by observing changes in physical and physiological parameters during the progress of infestation by visual inspection and the comparison of growth, gas exchange, stomatal conductance, and chlorophyll content between the non-infested control, physically wounded, and RPW-infested E. guineensis groups. During the study period, four distinct levels of physical infestation were observed and recorded. The RPW-infested group displayed significantly lower maximum photosynthesis activity (Amax) starting from the third week post-infestation. However, growth in terms of change in plant height and stem circumference, leaves’ stomatal conductance, and chlorophyll content were not significantly different between the three groups during the duration of the study. The significant drop in photosynthesis was observed one week before physical changes appeared. This suggests the promising utilisation of photosynthesis activity as a signal for detecting RPW infestation at the early stage of attacks, which could be useful for integration in integrated pest management (IPM).

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