scholarly journals Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rongfa Chen ◽  
Yegeng Fan ◽  
Huiwen Zhou ◽  
Shanping Mo ◽  
Zhongfeng Zhou ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Gibberellin Biosynthesis ◽  
Rna Seq ◽  
Control Groups ◽  
Illumina Hiseq ◽  
Mepiquat Chloride ◽  
System A ◽  
Significant Gene ◽  
Internode Growth

Abstract Background Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. Results In the present study, we first obtained high-quality long transcripts from the internodes of sugarcane using the PacBio Sequel System. A total of 72,671 isoforms, with N50 at 3073, were generated. These long isoforms were used as a reference for the subsequent RNA-seq. Afterwards, short reads generated from the Illumina HiSeq 4000 platform were used to compare the differentially expressed genes in both the DPC and the control groups. Transcriptome profiling showed that most significant gene changes occurred after six days post DPC treatment. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating that DPC affected multiple pathways, in addition to suppressing gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the 36 constructed modules, the top positive correlated module, at the stage of six days post spraying DPC, was sienna3. Notably, Stf0 sulfotransferase, cyclin-like F-box, and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. Furthermore, the qPCR validated the high accuracy of the RNA-seq results. Conclusion Taken together, we have demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

scholarly journals Global Transcriptome Changes of Elongating Internode of Sugarcane in Response to Mepiquat Chloride

2020 ◽  
Author(s):  
Rongfa Chen ◽  
Yegeng Fan ◽  
Huiwen Zhou ◽  
Shanping Mo ◽  
Zhongfeng Zhou ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Gibberellin Biosynthesis ◽  
Rna Seq ◽  
Control Groups ◽  
Illumina Hiseq ◽  
Mepiquat Chloride ◽  
System A ◽  
Internode Growth ◽  
And Control

Abstract Background: Mepiquat chloride (DPC) is an extensively used chemical to control internode growth and compact canopies in cultured plants. Previous studies suggested that DPC could inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. Results: In the present study, we first obtained the high-quality long transcripts from internode of sugarcane by PacBio Sequel System. A total of 72,671 isoforms with N50 as 3,073 were generated. These long isoforms were used for the following RNA-seq as reference. Subsequently, short reads generated from Illumina Hiseq 4000 platform were used for comparing the differentially expressed genes in DPC and control groups. The transcriptome profiling showed the 6 days post DPC treatment had the most significant changed genes. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating DPC affected multiple pathways beside depressed gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the constructed 36 modules, the top positive correlated module with stage of 6 day post spraying DPC was sienna3. Stf0 sulphotransferase, cyclin-like F-box and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. The qPCR demonstrated the high accuracy of RNA-seq result. Conclusion: Taken together, we demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

scholarly journals Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

2020 ◽  
Author(s):  
Rongfa Chen ◽  
Yegeng Fan ◽  
Huiwen Zhou ◽  
Shanping Mo ◽  
Zhongfeng Zhou ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Gibberellin Biosynthesis ◽  
Rna Seq ◽  
Control Groups ◽  
Illumina Hiseq ◽  
Mepiquat Chloride ◽  
System A ◽  
Internode Growth ◽  
And Control

Abstract Background: Mepiquat chloride (DPC) is an extensively used chemical to control internode growth and compact canopies in cultured plants. Previous studies suggested that DPC could inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. Results: In the present study, we first obtained the high-quality long transcripts from internode of sugarcane by PacBio Sequel System. A total of 72,671 isoforms with N50 as 3,073 were generated. These long isoforms were used for the following RNA-seq as reference. Subsequently, short reads generated from Illumina Hiseq 4000 platform were used for comparing the differentially expressed genes in DPC and control groups. The transcriptome profiling showed the 6 days post DPC treatment had the most significant changed genes. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating DPC affected multiple pathways beside depressed gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the constructed 36 modules, the top positive correlated module with stage of 6 day post spraying DPC was sienna3. Stf0 sulphotransferase, cyclin-like F-box and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. The qPCR demonstrated the high accuracy of RNA-seq result. Conclusion: Taken together, we demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

scholarly journals A mutation in transmembrane protein 135 impairs lipid metabolism in mouse eyecups

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael Landowski ◽  
Vijesh J. Bhute ◽  
Tetsuya Takimoto ◽  
Samuel Grindel ◽  
Pawan K. Shahi ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Mutant Mouse ◽  
Transmembrane Protein ◽  
Retinal Disease ◽  
Age Related Macular Degeneration ◽  
Rna Seq ◽  
Wild Type ◽  
Age Related ◽  
Significant Gene

AbstractAging is a significant factor in the development of age-related diseases but how aging disrupts cellular homeostasis to cause age-related retinal disease is unknown. Here, we further our studies on transmembrane protein 135 (Tmem135), a gene involved in retinal aging, by examining the transcriptomic profiles of wild-type, heterozygous and homozygous Tmem135 mutant posterior eyecup samples through RNA sequencing (RNA-Seq). We found significant gene expression changes in both heterozygous and homozygous Tmem135 mutant mouse eyecups that correlate with visual function deficits. Further analysis revealed that expression of many genes involved in lipid metabolism are changed due to the Tmem135 mutation. Consistent with these changes, we found increased lipid accumulation in mutant Tmem135 eyecup samples. Since mutant Tmem135 mice have similar ocular pathologies as human age-related macular degeneration (AMD) eyes, we compared our homozygous Tmem135 mutant eyecup RNA-Seq dataset with transcriptomic datasets of human AMD donor eyes. We found similar changes in genes involved in lipid metabolism between the homozygous Tmem135 mutant eyecups and AMD donor eyes. Our study suggests that the Tmem135 mutation affects lipid metabolism as similarly observed in human AMD eyes, thus Tmem135 mutant mice can serve as a good model for the role of dysregulated lipid metabolism in AMD.

scholarly journals Transcriptome Profiling Provides Insights Into Potential Antagonistic Mechanisms Involved in Chaetomium globosum Against Bipolaris sorokiniana

2020 ◽  
Vol 11 ◽  
Author(s):  
K. Darshan ◽  
Rashmi Aggarwal ◽  
Bishnu Maya Bashyal ◽  
Jagmohan Singh ◽  
V. Shanmugam ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Glycosyl Hydrolase ◽  
Draft Genome ◽  
Transcriptome Profiling ◽  
Bipolaris Sorokiniana ◽  
Chaetomium Globosum ◽  
Rna Seq ◽  
Illumina Hiseq

Chaetomium globosum Kunze is recognized as a potential biocontrol fungus against spot blotch of wheat caused by Bipolaris sorokiniana. Its molecular mechanism of biocontrol activity and the biosynthetic pathways involved have not been yet elucidated. Here, global transcriptome profiling of C. globosum strain Cg2 during interaction with B. sorokiniana isolate BS112 using RNA-seq was performed in order to gain insights into the potential mechanisms of antagonism. The Illumina HiSeq platform (2 × 150 bp) yielded an average of 20–22 million reads with 50–58% GC. De novo assembly generated 45,582 transcripts with 27,957 unigenes. Transcriptome analysis displayed distinct expression profiles in the interaction (Cg2–BS112), out of which 6,109 unique differentially expressed genes were present. The predominant transcripts classified as genes involved in “catalytic activity” constituted 45.06%, of which 10.02% were associated with “hydrolytic activity” (GO:0008152), and similarly, in the biological process, 29.18% of transcripts were involved in “metabolic activity” (GO:0004096 and GO:0006979). Heat map and cluster categorization suggested an increase in the expression levels of genes encoding secondary metabolites like polyketide synthase (GO:0009058), S-hydroxymethyl glutathione dehydrogenase (GO:0006069), terpene cyclase (EC 4.2.3.-), aminotran_1_2 domain-containing protein (GO:0009058), and other hydrolytic CAZYmes such as the glycosyl hydrolase (GH) family (GH 13, GH 2, GH 31, and GH 81; GO:0005975), cellulase domain-containing protein, chitinases, β-1, 3-glucanases (GO:0004565), glucan endo-1,3-beta-glucanase (GO:0052861), and proteases (GO:0004177). The obtained RNA-seq data were validated by RT-qPCR using 20 randomly chosen genes, showing consistency with the RNA-seq results. The present work is worldwide the first effort to unravel the biocontrol mechanism of C. globosum against B. sorokiniana. It generated a novel dataset for further studies and facilitated improvement of the gene annotation models in the C. globosum draft genome.

The SORS Decision-Making Support System: A statistical tool for better policy making in the Republic of Serbia

2021 ◽  
pp. 1-11
Author(s):  
Miladin Kovačević ◽  
Katarina Stančić
Keyword(s):  
Policy Making ◽  
Modern Society ◽  
Monitoring And Evaluation ◽  
Public Debate ◽  
Statistical Tool ◽  
The Public ◽  
System A ◽  
The Republic ◽  
Trusted Data

Modern society is witnessing a data revolution which necessarily entails changes to the overall behavior of citizens, governments and companies. This is a big challenge and an opportunity for National Statistics Offices (NSOs). Especially after the outbreak of COVID-19, when the public debate about the number of mortalities and tested and infected persons escalated, trusted data is required more than ever. Which data can modern society trust? Are modern societies being subjected to opinion rather than fact? This paper introduces a new statistical tool to facilitate policy-making based on trusted statistics. Using economic indicators to illustrate implementation, the new statistical tool is shown to be a flexible instrument for analysis, monitoring and evaluation of the economic situation in the Republic of Serbia. By taking a role in public policy management, the tool can be used to transform the NSO’s role in the statistical system into an active participant in public debate in contrast to the previous traditional, usually passive role of collecting, processing and publishing data. The tool supports the integration of statistics into public policies and connects the knowledge and expertise of official statisticians on one side with political decision makers on the other.

scholarly journals RNA-seq Characterization of Melanoma Phenotype Switch in 3D Collagen after p38 MAPK Inhibitor Treatment

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 449
Author(s):  
Vladimír Čermák ◽  
Aneta Škarková ◽  
Ladislav Merta ◽  
Veronika Kolomazníková ◽  
Veronika Palušová ◽  
...  
Keyword(s):  
P38 Mapk ◽  
Rna Seq ◽  
Differentiation Markers ◽  
Illumina Hiseq ◽  
Invasive Phenotype ◽  
Mesenchymal Transition ◽  
Phenotype Switch ◽  
3D Collagen ◽  
Phenotype Plasticity

Melanoma phenotype plasticity underlies tumour dissemination and resistance to therapy, yet its regulation is incompletely understood. In vivo switching between a more differentiated, proliferative phenotype and a dedifferentiated, invasive phenotype is directed by the tumour microenvironment. We found that treatment of partially dedifferentiated, invasive A375M2 cells with two structurally unrelated p38 MAPK inhibitors, SB2021920 and BIRB796, induces a phenotype switch in 3D collagen, as documented by increased expression of melanocyte differentiation markers and a loss of invasive phenotype markers. The phenotype is accompanied by morphological change corresponding to amoeboid–mesenchymal transition. We performed RNA sequencing with an Illumina HiSeq platform to fully characterise transcriptome changes underlying the switch. Gene expression results obtained with RNA-seq were validated by comparing them with RT-qPCR. Transcriptomic data generated in the study will extend the present understanding of phenotype plasticity in melanoma and its contribution to invasion and metastasis.

scholarly journals VEGF as a potential molecular target in periodontitis: a meta-analysis and microarray data validation

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Bo Ren ◽  
Que Feng ◽  
Shan He ◽  
Yanfeng Li ◽  
Jiadong Fan ◽  
...  
Keyword(s):  
Growth Factor ◽  
Clinical Sample ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Therapeutic Drug ◽  
Data Validation ◽  
Control Groups ◽  
Vegf Expression ◽  
Healthy Control

Abstract Background Anti-vascular endothelial growth factor (VEGF) has been used as a therapeutic drug for the treatment of some human diseases. However, no systematic evidence is performed for assessing the role of VEGF in periodontitis. We carried out a comprehensive analysis to explore the role of VEGF in patients with periodontitis. Methods Multiple databases were searched for eligible studies. The pooled standardized mean difference (SMD) and odds ratio (OR) with the corresponding 95% confidence interval (CI) were applied to evaluate the effect sizes. Clinical data validation from microarray analysis was used. Pathway and process enrichment analysis were also investigated. Results Finally, 16 studies were included in this analysis. Overall, there was a significantly higher level of VEGF expression in periodontitis than in healthy control groups (OR = 16.64, 95% CI = 6.01–46.06, P < 0.001; SMD = 2.25, 95% CI = 1.25–3.24, P < 0.001). Subgroup analysis of ethnicity showed that VEGF expression was still correlated with periodontitis in the Asian and European populations. No correlation was observed between VEGF expression and age, gender, and pathological type. A large clinical sample data (427 periodontitis patients and 136 healthy controls) further validated that VEGF expression was higher in periodontitis than in healthy control groups (P = 0.023). VEGF was involved in many functions such as blood vessel development, response to growth factor, cell proliferation, and cell adhesion. Conclusions High levels of VEGF were credible implications for the development of periodontitis. Anti-VEGF therapy may be valuable for the treatment of periodontitis in clinical management.

Similar use of intonation structure in early implanted children and hearing children: The case of Italian

2021 ◽  
pp. 014272372098605
Author(s):  
Paola Zanchi ◽  
Laura Zampini ◽  
Luca Pancani ◽  
Roberta Berici ◽  
Mariapaola D’Imperio
Keyword(s):  
Chronological Age ◽  
Typically Developing ◽  
Control Groups ◽  
Generation Task ◽  
Story Generation ◽  
Italian Children ◽  
Children's Stories ◽  
Hearing Children ◽  
First Time

This work presents an analysis of the intonation competence in a group of Italian children with cochlear implant (CI). Early cochlear implantation plays a crucial role in language development for children who were born deaf in that it favours the acquisition of complex aspects of language, such as the intonation structure. A story-generation task, the Narrative Competence Task, was used to elicit children’s stories. Narrations produced by 8 early implanted children and by 16 children with typically hearing (TH) (8 one-to-one matched considering the chronological age, TH-CA, and 8 considering the hearing age, TH-HA) were analysed considering intonation features (pitch accent distribution, edge tones and inner breaks). Results show that children with CI produce intonation patterns that are similar to those of both TH-CA and TH-HA control groups. Few significant differences were found only between children with CI and children matched for TH-HA in the use of rising edge tones. These results are discussed in light of the role of cognitive development in using prosody and intonation and the importance of early CI implantation. This study shows for the first time that intonation use of early implanted children is not different from that of typically developing children with the same chronological age.

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