scholarly journals Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanjun He ◽  
Lili Li ◽  
Yixiu Yao ◽  
Yulin Li ◽  
Huiqing Zhang ◽  
...  
Keyword(s):  
Plant Immunity ◽  
Colorimetric Method ◽  
Transcript Level ◽  
Early Response ◽  
Rna Seq ◽  
Differentially Methylated Genes ◽  
Rna Biology ◽  
Regulatory Functions ◽  
And Control

Abstract Background Cucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m6A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m6A modifications in watermelon. Results We measured the global m6A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m6A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m6A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m6A-seq were carried out. Numerous m6A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m6A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m6A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m6A RNA methylation and transcript level in the watermelon transcriptome. Both the m6A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity. Conclusions Our study represents the first comprehensive characterization of m6A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m6A modification in watermelon in early responses to CGMMV.

scholarly journals Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros Lotus)

2020 ◽  
Author(s):  
Francisco Gil_Muñoz ◽  
Nicolas Delhomme ◽  
Ana Quiñones ◽  
Maria del Mar Naval ◽  
Maria Badenes ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Crop Production ◽  
Chloride Transport ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Diospyros Lotus ◽  
And Control

Abstract Background Drought and salinity are two of the main challenges in agriculture. In many areas, crop production needs solutions to adapt the grown species to the increasing salinity. Research on physiological and molecular responses activated by salinity in plants is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. In temperate fruit tree species, tree grafting on salinity tolerant rootstocks is a common method to compensate for the cultivar saline sensitivity. Persimmon species have different levels of tolerance to salinity, knowledge of this variability provides the basics for development of salt tolerant rootstocks.Results In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock, Diospyros lotus, grown under saline and control conditions. Results from characterization of the physiological responses along with gene expression changes in roots and leaves allowed identifying several salt-tolerance mechanisms related to Ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and Chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. Conclusions Results indicate that D. lotus presents a genetic variability for salt tolerance trait related to the regulation of chloride transport, transmembrane electrochemical potential and thermospermine root synthesis. The study provides knowledge on mechanism of salt stress tolerance in persimmon for further breeding of tolerant persimmon rootstocks.

scholarly journals MeRIP-seq and RNA-seq data of mycelium and spore of Ascosphaera apis, a widespread bee fungal pathogen

2020 ◽  
Author(s):  
Yu Du ◽  
Haibin Jiang ◽  
Zhiwei Zhu ◽  
Jie Wang ◽  
Huazhi Chen ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Rna Isolation ◽  
Transcript Level ◽  
Current Data ◽  
List Type ◽  
Rna Seq ◽  
Ascosphaera Apis ◽  
Bee Health ◽  
Intergenic Regions

ABSTRACTAscosphaera apis is widespread fungal pathogen of honeybee larvae, causing chalkbrood, a chronic disease that weakens bee health and colony productivity. In this article, mecylia and spores of A. apis were respectively purified followed by RNA isolation, cDNA library construction, MeRIP-seq and RNA-seq. A total of 62,551,172, 41,773,158, 49,535,092 and 61,569,610 raw reads were produced from Aam_IP, Aas_IP, Aam_input and Aas_input groups, respectively. After quality control, 58,484,368, 37,381,432, 44,655,434 and 58,739,742 clean reads were obtained. Furthermore, 47,706,205, 31,356,690, 35,259,810 and 44,319,061 clean reads were mapped to the reference genome of A. apis, including 39,337,036, 26,731,957, 31,987,396 and 40,017,855 unique mapped reads, and 8,369,169, 4,624,733, 3,272,414 and 4,301,206 multiple mapped reads. Among them, 96.31%, 96.51%, 96.82% and 97.11% of clean reads were mapped to exons; 2.09%, 2.31%,1.83% and 1.81% to introns; 1.60%, 1.18%, 1.35% and 1.08% to intergenic regions.Value of the dataThe data can be used to investigate the relationship between the m6A modification extent and the transcript level in the A. apis transcriptome.This dataset contributes to transcriptome-wide characterization of the m6A distributing patterns in mRNAs and non-coding RNAs in A. apis mycelium and spore.Current data benefits new functions of m6A modification in the transcripts extensively modified by m6A in A. apis mycelium and spore.Our data could be used to characterize differential patterns of the m6A methylation between mycelium and spore of A. apis.

scholarly journals Multiomics Analysis of Transcriptome, Epigenome, and Genome Uncovers Putative Mechanisms for Dilated Cardiomyopathy

2021 ◽  
Vol 2021 ◽  
pp. 1-29
Author(s):  
Li Liu ◽  
Jianjun Huang ◽  
Yan Liu ◽  
Xingshou Pan ◽  
Zhile Li ◽  
...  
Keyword(s):  
Dilated Cardiomyopathy ◽  
Differentially Expressed ◽  
Molecular Characteristics ◽  
Rna Seq ◽  
Frequent Mutation ◽  
Protein Protein Interaction ◽  
Molecular Features ◽  
Differentially Methylated Genes ◽  
And Control ◽  
Control Samples

Objective. Multiple genes have been identified to cause dilated cardiomyopathy (DCM). Nevertheless, there is still a lack of comprehensive elucidation of the molecular characteristics for DCM. Herein, we aimed to uncover putative molecular features for DCM by multiomics analysis. Methods. Differentially expressed genes (DEGs) were obtained from different RNA sequencing (RNA-seq) datasets of left ventricle samples from healthy donors and DCM patients. Furthermore, protein-protein interaction (PPI) analysis was then presented. Differentially methylated genes (DMGs) were identified between DCM and control samples. Following integration of DEGs and DMGs, differentially expressed and methylated genes were acquired and their biological functions were analyzed by the clusterProfiler package. Whole exome sequencing of blood samples from 69 DCM patients was constructed in our cohort, which was analyzed the maftools package. The expression of key mutated genes was verified by three independent datasets. Results. 1407 common DEGs were identified for DCM after integration of the two RNA-seq datasets. A PPI network was constructed, composed of 171 up- and 136 downregulated genes. Four hub genes were identified for DCM, including C3 ( degree = 24 ), GNB3 ( degree = 23 ), QSOX1 ( degree = 21 ), and APOB ( degree = 17 ). Moreover, 285 hyper- and 321 hypomethylated genes were screened for DCM. After integration, 20 differentially expressed and methylated genes were identified, which were associated with cell differentiation and protein digestion and absorption. Among single-nucleotide variant (SNV), C>T was the most frequent mutation classification for DCM. MUC4 was the most frequent mutation gene which occupied 71% across 69 samples, followed by PHLDA1, AHNAK2, and MAML3. These mutated genes were confirmed to be differentially expressed between DCM and control samples. Conclusion. Our findings comprehensively analyzed molecular characteristics from the transcriptome, epigenome, and genome perspectives for DCM, which could provide practical implications for DCM.

scholarly journals Cloning and Characterization of Glycolate Oxidase and NADH-Dependent Hydropyruvate Reductase Genes in Pachysandra terminalis

HortScience ◽  
2006 ◽  
Vol 41 (5) ◽  
pp. 1226-1230 ◽  
Author(s):  
Suping Zhou ◽  
Fur-Chi Chen ◽  
Samuel Nahashon ◽  
Tingting Chen
Keyword(s):  
Cold Treatment ◽  
Transcript Level ◽  
Rubisco Activase ◽  
Glycolate Oxidase ◽  
Oxidase Gene ◽  
Protection Mechanism ◽  
Hydroxypyruvate Reductase ◽  
Targeting Signal ◽  
And Control

Photorespiration provides a protection mechanism in plants by diverting excessive energy accumulated from photochemical reaction, metabolizing toxic products and producing some protective molecules. The authors report cloning and characterization of a glycolate oxidase gene (GOX; NCBI accession DQ442286) and a NADH-dependent hydroxypyruvate reductase gene (HPR; NCBI DQ442287) from Pachysandra terminallis. The DQ442286 had the predicted GOX-like–Riboflavin-5′-phosphate (FMN) conserved domain and the DQ442287 had the predicted adenosine 5′-(alpha-thio)diphospho-5′-ribofuranosylnicotinamide nicotinamide adenine dinucleotide (NAD) binding domain (2-Hacid_DH_C). C-terminal peroxisome targeting signal was predicted to be -ARL for DQ442286 and –SKL for DQ442287. Both genes encoded enzyme proteins that are located in peroxisome and are involved in the photorespiration process. Real-time quantitative reverse-transcriptase polymerase chain reaction was performed to compare transcript level of the cloned genes after cold treatment. The 18s Ribosomal RNA (rRNA) was included to calibrate the data. The relative cycle threshold values (gene/18s rRNA) were 1.4, 1.5, and 1.5 for GOX and 1.2, 1.3, and 1.3 for HPR in the treatments of 4 °C 4 h, 4 °C 12 h, and control. The data revealed that gene expression was enhanced by only short-term (4-h) cold treatment. A ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco) activase gene (DQ 486905) was also cloned and analyzed following the same procedure.

scholarly journals Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.)

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1703
Author(s):  
Francisco Gil-Muñoz ◽  
Nicolas Delhomme ◽  
Ana Quiñones ◽  
Maria del Mar Naval ◽  
Maria Luisa Badenes ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Diospyros Lotus ◽  
And Control ◽  
Different Levels ◽  
Tolerance To Salinity

Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt--tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.

Introduction

2018 ◽  
Author(s):  
Elizabeth S. Radcliffe
Keyword(s):  
Early Modern ◽  
Historical Background ◽  
Consistent Picture ◽  
And Control ◽  
Good And Evil

The Introduction offers, first, a brief historical background to Hume’s theory of the passions, which is further elaborated in the APPENDIX. Foremost among the theses of the early modern rationalists—like Reynolds, Senault, Descartes, Cudworth, and Clarke—to which Hume is responding are: that many passions left unregulated lead to the pursuit of unsuitable objects, that reason can overcome the pernicious influence of the passions and control our actions, and that the passions are states that represent good and evil. Second, the Introduction presents a sketch of Hume’s characterization of reason and passion and his account of their relationship. Third, it explains the method of interpretation used in this book and previews its chapters. The approach is coherentist: to present an intelligible and consistent picture of Hume’s theory of passion and action, accounting for as many of the relevant texts as possible.

scholarly journals Design, Construction, and Control for an Underwater Vehicle Type Sepiida

Robotica ◽  
2020 ◽  
pp. 1-18
Author(s):  
M. Garcia ◽  
P. Castillo ◽  
E. Campos ◽  
R. Lozano
Keyword(s):  
Embedded System ◽  
Closed Loop ◽  
Underwater Vehicle ◽  
Mathematical Representation ◽  
Closed Loop System ◽  
Vehicle Type ◽  
Mathematical Equations ◽  
And Control ◽  
Design Construction

SUMMARY A novel underwater vehicle configuration with an operating principle as the Sepiida animal is presented and developed in this paper. The mathematical equations describing the movements of the vehicle are obtained using the Newton–Euler approach. An analysis of the dynamic model is done for control purposes. A prototype and its embedded system are developed for validating analytically and experimentally the proposed mathematical representation. A real-time characterization of one mass is done to relate the pitch angle with the radio of displacement of the mass. In addition, first validation of the closed-loop system is done using a linear controller.

scholarly journals Clinical characterization of dysautonomia in long COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Barizien ◽  
Morgan Le Guen ◽  
Stéphanie Russel ◽  
Pauline Touche ◽  
Florent Huang ◽  
...  
Keyword(s):  
Mixed Models ◽  
Repeated Measures ◽  
Physical Medicine ◽  
Persistent Symptoms ◽  
Index Changes ◽  
Changes Over Time ◽  
And Control ◽  
Testing Group ◽  
Over Time

AbstractIncreasing numbers of COVID-19 patients, continue to experience symptoms months after recovering from mild cases of COVID-19. Amongst these symptoms, several are related to neurological manifestations, including fatigue, anosmia, hypogeusia, headaches and hypoxia. However, the involvement of the autonomic nervous system, expressed by a dysautonomia, which can aggregate all these neurological symptoms has not been prominently reported. Here, we hypothesize that dysautonomia, could occur in secondary COVID-19 infection, also referred to as “long COVID” infection. 39 participants were included from December 2020 to January 2021 for assessment by the Department of physical medicine to enhance their physical capabilities: 12 participants with COVID-19 diagnosis and fatigue, 15 participants with COVID-19 diagnosis without fatigue and 12 control participants without COVID-19 diagnosis and without fatigue. Heart rate variability (HRV) during a change in position is commonly measured to diagnose autonomic dysregulation. In this cohort, to reflect HRV, parasympathetic/sympathetic balance was estimated using the NOL index, a multiparameter artificial intelligence-driven index calculated from extracted physiological signals by the PMD-200 pain monitoring system. Repeated-measures mixed-models testing group effect were performed to analyze NOL index changes over time between groups. A significant NOL index dissociation over time between long COVID-19 participants with fatigue and control participants was observed (p = 0.046). A trend towards significant NOL index dissociation over time was observed between long COVID-19 participants without fatigue and control participants (p = 0.109). No difference over time was observed between the two groups of long COVID-19 participants (p = 0.904). Long COVID-19 participants with fatigue may exhibit a dysautonomia characterized by dysregulation of the HRV, that is reflected by the NOL index measurements, compared to control participants. Dysautonomia may explain the persistent symptoms observed in long COVID-19 patients, such as fatigue and hypoxia. Trial registration: The study was approved by the Foch IRB: IRB00012437 (Approval Number: 20-12-02) on December 16, 2020.

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