scholarly journals Expression Analysis Reveals the Association of Several Genes with Pupal Diapause in Bactrocera minax (Diptera: Tephritidae)

Insects ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 169 ◽  
Author(s):  
Jia Wang ◽  
Huan Fan ◽  
Pan Wang ◽  
Ying-Hong Liu
Keyword(s):  
Environmental Conditions ◽  
Real Time Pcr ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Pupal Stage ◽  
Quantitative Real Time Pcr ◽  
Qrt Pcr ◽  
Number Of Genes ◽  
Pupal Diapause ◽  
Solid Foundation

The Chinese citrus fly, Bactrocera minax, is a devastating pest of citrus, which enters the obligatory diapause in overwintering pupae to resist harsh environmental conditions. However, little is known about the molecular mechanisms underlying pupal diapause. The previous transcriptomic analysis revealed that a large number of genes were regulated throughout the pupal stage. Of these genes, 12 and six ones that are remarkably up- and downregulated, respectively, specifically in intense diapause were manually screened out in present study. To validate the expression of these genes throughout the pupal stage, the quantitative real-time PCR (qRT-PCR) was conducted, and the genes displaying different expression patterns with those of previous study were excluded. Then, the expressions of remaining genes were compared between diapause-destined and non-diapause-destined pupae to reveal their association with diapause using qRT-PCR and semiquantitative PCR. Finally, five genes, TTLL3B, Cyp6a9, MSTA, Fru, and UC2, and two genes, KSPI and LYZ1, were demonstrated to be positively and negatively associated with diapause, respectively. These findings provide a solid foundation for the further investigation of molecular mechanisms underlying B. minax pupal diapause.

scholarly journals Transcriptome characterization analysis and molecular profiles of obligatory diapause induction of the Chinese citrus fruit fly,Bactrocera minax(Diptera: Tephritidae)

2019 ◽  
Author(s):  
Zhixiong Zhou ◽  
Xiaolin Dong ◽  
Chuanren Li
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Citrus Fruit ◽  
Pupal Stage ◽  
Fruit Fly ◽  
Diapause Induction ◽  
Regulation Mechanism ◽  
Pupal Diapause ◽  
Specific Stage

AbstractThe Chinese citrus fruit fly,Bactrocera minax, is a devastating citrus pest in China, Bhutan and India. It will enter obligatory pupal diapause in each generation at specific stage, while little is known about the course and the molecular mechanisms of diapause induction. To gain insight into possible mechanisms of obligatory pupal diapause induction, high-throughput RNA-seq data were generated from second-instar larvae (2L), third-instar larvae (3L) and pupal (P, one week after pupating). A total of 116,402 unigenes were assembled and researched against public databases, and 54,781 unigenes matched to proteins in the NCBI database using the BLAST search. Three pairwise comparisons were performed, and significantly differentially regulated transcripts were identified. Several differentially expressed genes (DEGs) expression patterns revealed that those highly or lowly expressed genes in pupal stage were predicted to be involved in diapause induction. Moreover, GO function and KEGG pathway analysis were performed on all DEGs and showed that 20-hydroxyecdysone (20E) biosynthesis, insulin signaling pathway, FoxO signaling pathway, cell cycle and metabolism pathway may be related to the obligatory diapause of the Chinese citrus fruit fly. This study provides valuable information about the Chinese citrus fruit fly transcriptome for future gene function research, and contributes to the in-depth elucidation of the molecular regulation mechanism of insect obligatory diapause induction.

Genome-wide screening of m6A-modified transcript in the Wilms’ tumor

2021 ◽  
Author(s):  
Zhuo Liu ◽  
Feng He ◽  
Jing Liu ◽  
Shengrong OuYang ◽  
Zexi Li ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Real Time ◽  
Real Time Pcr ◽  
Wilms Tumor ◽  
Expression Patterns ◽  
Mrna Levels ◽  
Gene Ontology Analysis ◽  
Quantitative Real Time Pcr ◽  
Related Factors ◽  
Significant Difference

Abstract Background Wilms’ tumor, also called nephroblastoma, is the most common pediatric renal malignancy. The pathogenesis of Wilms’ tumor has been attributed to several genetic and epigenetic factors. However, the most pervasive internal mRNA modification that affects almost every process of RNA metabolism, RNA N6-Methyladenosine (m6A) methylation, has not been characterized in Wilms’ tumor. Methods Wilms’ tumor (WT) and adjacent non-cancerous (NC) tissue samples were obtained from 23 children with nephroblastoma, and the global m6A levels were measured by mass spectrometry. Analyses by m6A-mRNA epitranscriptomic microarray and mRNA microarray were performed, and m6A-related mRNAs were validated by quantitative real-time PCR for input and m6A-immunoprecipitated RNA samples from WT and NC tissues. Gene ontology analysis and KEGG pathway analysis were performed for differentially expressed genes, and expression of RNA methylation-related factors was measured by quantitative real-time PCR. Results The total m6A methylation levels in total RNA of WT samples and NC samples were (0.21 ± 0.01)% and (0.22 ± 0.01)%, respectively, with no statistically significant difference. Fifty-nine transcripts were differentially m6A-methylated between the WT and NC groups, which showed distinct m6A modification patterns. Gene ontology analysis indicated that m6A-modified genes were enriched in cancer-associated pathways, including the mTOR pathway, and conjoint analysis of the unique methylation and gene expression patterns in WT samples suggested an association with metabolic pathways.The mRNA levels of the m6A-related “reader” genes, YTHDF1, YTHDF2 and IGF2BP3, were statistically higher in WT samples than in NC samples. Conclusion This is the first study to determine the m6A modification profiles in Wilms’ tumor. Our data provide novel information regarding patterns of m6A modification that correlate with carcinogenesis in Wilms’ tumor.

scholarly journals Ascorbic acid improves parthenogenetic embryo development through TET proteins in mice

2019 ◽  
Vol 39 (1) ◽  
Author(s):  
Wei Gao ◽  
Xianfeng Yu ◽  
Jindong Hao ◽  
Ling Wang ◽  
Minghui Qi ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Vitamin C ◽  
Embryonic Development ◽  
Real Time Pcr ◽  
Quantitative Real Time Pcr ◽  
Qrt Pcr ◽  
Tet Proteins ◽  
Parthenogenetic Embryo ◽  
Blastocyst Rate

Abstract The TET (Ten-Eleven Translocation) proteins catalyze the oxidation of 5mC (5-methylcytosine) to 5hmC (5-hydroxymethylcytosine) and play crucial roles in embryonic development. Ascorbic acid (Vc, Vitamin C) stimulates the expression of TET proteins, whereas DMOG (dimethyloxallyl glycine) inhibits TET expression. To investigate the role of TET1, TET2, and TET3 in PA (parthenogenetic) embryonic development, Vc and DMOG treatments were administered during early embryonic development. The results showed that Vc treatment increased the blastocyst rate (20.73 ± 0.46 compared with 26.57 ± 0.53%). By contrast, DMOG reduced the blastocyst rate (20.73 ± 0.46 compared with 11.18 ± 0.13%) in PA embryos. qRT-PCR (quantitative real-time PCR) and IF (immunofluorescence) staining results revealed that TET1, TET2, and TET3 expressions were significantly lower in PA embryos compared with normal fertilized (Con) embryos. Our results revealed that Vc stimulated the expression of TET proteins in PA embryos. However, treatment with DMOG significantly inhibited the expression of TET proteins. In addition, 5hmC was increased following treatment with Vc and suppressed by DMOG in PA embryos. Taken together, these results indicate that the expression of TET proteins plays crucial roles mediated by 5hmC in PA embryonic development.

scholarly journals Cloning, Characterization, and Expression Features of Chicken CDS2 Splicing Variants

2020 ◽  
Author(s):  
Yuanyuan Xu ◽  
Shuping Zhang ◽  
Yujun Guo ◽  
Wen Chen ◽  
Yanqun Huang
Keyword(s):  
Adipose Tissue ◽  
Real Time ◽  
Real Time Pcr ◽  
Expression Patterns ◽  
Mrna Levels ◽  
Exogenous Insulin ◽  
Quantitative Real Time Pcr ◽  
Temporal Expression ◽  
Spatio Temporal ◽  
The Brain

Abstract Background: The CDS gene encodes the CDP-diacylglycerol synthase enzyme that catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid. At present, there are no reports of CDS2 in birds. Here, we identified chicken CDS2 transcripts by combining conventional RT- PCR amplification, 5' RACE (Fig. 1A), and 3' RACE, explored the spatio-temporal expression profiles of total CDS2 and the longest transcript variant CDS2-4, and investigated the effect of exogenous insulin on total the mRNA level of CDS2 by quantitative real-time PCR. Results: Four transcripts of chicken CDS2 (CDS2-1, -2, -3, and -4) were identified, which were alternatively spliced at the 3′-untranslated region (UTR). CDS2 was widely expressed in all tissues examined and the longest variant CDS2-4 was the major transcript. Both total CDS2 and CDS2-4 were prominently expressed in adipose tissue and the heart, and exhibited low expression in the liver and pectoralis of 49 day-old chickens. Quantitative real-time PCR revealed that total CDS2 and CDS2-4 had different spatio-temporal expression patterns in chicken. Total CDS2 exhibited a similar temporal expression tendency with a high level in the later period of incubation (embryonic day 19 [E19] or 1-day-old) in the brain, liver, and pectoralis. While CDS2-4 presented a distinct temporal expression pattern in these tissues, CDS2-4 levels peaked at 21 days in the brain and pectoralis, while liver CDS2-4 mRNA levels were highest at the early stage of hatching (E10). Total CDS2 (P < 0.001) and CDS2-4 (P = 0.0090) mRNA levels in the liver were differentially regulated throughout development of the chicken. Exogenous insulin significantly downregulated the level of total CDS2 at 240 min in the pectoralis of Silky chickens (P < 0.01). Total CDS2 levels in the liver of Silky chickens were higher than that of the broiler in the basal state and after insulin stimulation. Conclusion: Chicken CDS2 has multiple transcripts with variation at the 3′-UTR, which was prominently expressed in adipose tissue. Total CDS2 and CDS2-4 presented distinct spatio-temporal expression patterns, and they were differentially regulated with age in liver. Insulin could regulate chicken CDS2 levels in a breed- and tissue-specific manner.

scholarly journals Reference gene selection for quantitative real-time PCR (qRT-PCR) expression analysis in Galium aparine L.

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0226668 ◽  
Author(s):  
Xu Su ◽  
Liuyang Lu ◽  
Yashe Li ◽  
Congai Zhen ◽  
Guilei Hu ◽  
...  
Keyword(s):  
Real Time ◽  
Reference Gene ◽  
Expression Analysis ◽  
Real Time Pcr ◽  
Gene Selection ◽  
Quantitative Real Time Pcr ◽  
Reference Gene Selection ◽  
Qrt Pcr ◽  
Galium Aparine ◽  
Selection For

scholarly journals Comprehensive genomic analysis and expression profiling of the BTB and TAZ (BT) genes in cucumber (Cucumis sativus L.)

2019 ◽  
Vol 56 (No. 1) ◽  
pp. 15-23 ◽  
Author(s):  
Yong Zhou ◽  
Guanghua Li ◽  
Lin Zhang ◽  
Jie Xu ◽  
Lifang Hu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Biological Processes ◽  
Quantitative Real Time Pcr ◽  
Cucumis Sativus L ◽  
Btb Domain ◽  
Qrt Pcr ◽  
Cucumber Genome ◽  
Bt Genes

BTB-TAZ (BT) proteins are plant-specific transcription factors containing a BTB domain and a TAZ domain. They play vital roles in various biological processes and stress responses. In this study, a total of three BT genes (CsBT1–3) were identified from cucumber genome, and they were unevenly distributed in two of the seven chromosomes. Phylogenetic analysis of the BT proteins from cucumber, Arabidopsis, apple, tomato, and rice revealed that these proteins could be distinctly divided into two groups in accordance with their motif distributions. We also determined the structures of BT genes from cucumber, Arabidopsis, and rice to demonstrate their differences. The quantitative real-time PCR (qRT-PCR) results showed that the CsBT genes displayed differential expression patterns in cucumber tissues, and their expression was regulated by cold, salt, and drought stresses. These findings suggest that CsBT genes may participate in cucumber development and responses to various abiotic stresses.

Expression characteristics of ANGPTL-3 and ANGPTL-4 in duck liver and adipose tissues during early post-hatching development

2016 ◽  
Vol 50 (4) ◽  
Author(s):  
Jie Kou ◽  
Yangmei Zhao ◽  
Hehe Liu ◽  
Wanxia Wang ◽  
Jiwei Hu ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Lipid Metabolism ◽  
Tissue Distribution ◽  
Real Time Pcr ◽  
Adipocyte Differentiation ◽  
Expression Patterns ◽  
Quantitative Real Time Pcr ◽  
Adipose Tissues ◽  
Abdominal Adipose Tissue ◽  
Peking Duck

Angiopoietin-like protein 3 and -4 (ANGPTL-3 and -4) are generally related to lipid metabolism as well as angiogenesis in animals, however very less was known about their mRNA expression characterizations in tissue development. In this study, the mRNA expressions of ANGPTL-3 and ANGPTL-4 (ANGPTL-3 and -4) and tissue distribution in Peking duck (Anas platyrhynchos) of 1 to 8 weeks of age were analyzed using quantitative real-time PCR methods. It was observed that ANGPTL-3 and -4 mRNAs were broadly expressed in duck liver and adipose tissues and were most abundant in intra-abdominal adipose tissue (AD). ANGPTL-3 and -4 had different expression patterns in tissues. These data suggested that both duck ANGPTL-3 and -4 could be related to the development of tissues, and ANGPTL-4 may contribute to the development of adipose tissue through promoting adipocyte differentiation.

scholarly journals Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe)

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yuan Li ◽  
Yun Ren ◽  
Ying Zhao ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Mirna Target ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Putative Target ◽  
Genome Wide ◽  
Ginger Rhizome ◽  
Rhizome Development

Abstract Background MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. Results In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. Conclusion This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.

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