scholarly journals Generation and Analysis of Expressed Sequence Tags fromChimonanthus praecox(Wintersweet) Flowers for Discovering Stress-Responsive and Floral Development-Related Genes

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Shunzhao Sui ◽  
Jianghui Luo ◽  
Jing Ma ◽  
Qinlong Zhu ◽  
Xinghua Lei ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Real Time ◽  
Expressed Sequence Tags ◽  
Floral Development ◽  
Expression Patterns ◽  
Read Length ◽  
Rt Pcr ◽  
Protein Database ◽  
Blast Analysis ◽  
Expressed Sequence

A complementary DNA library was constructed from the flowers ofChimonanthus praecox, an ornamental perennial shrub blossoming in winter in China. Eight hundred sixty-seven high-quality expressed sequence tag sequences with an average read length of 673.8 bp were acquired. A nonredundant set of 479 unigenes, including 94 contigs and 385 singletons, was identified after the expressed sequence tags were clustered and assembled. BLAST analysis against the nonredundant protein database and nonredundant nucleotide database revealed that 405 unigenes shared significant homology with known genes. The homologous unigenes were categorized according to Gene Ontology hierarchies (biological, cellular, and molecular). By BLAST analysis and Gene Ontology annotation, 95 unigenes involved in stress and defense and 19 unigenes related to floral development were identified based on existing knowledge. Twelve genes, of which 9 were annotated as “cold response,” were examined by real-time RT-PCR to understand the changes in expression patterns under cold stress and to validate the findings. Fourteen genes, including 11 genes related to floral development, were also detected by real-time RT-PCR to validate the expression patterns in the blooming process and in different tissues. This study provides a useful basis for the genomic analysis ofC. praecox.

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.

Expression patterns of Doppel gene in golden hamster: Quantification using real-time RT-PCR

2008 ◽  
Vol 22 (4) ◽  
pp. 255-258 ◽  
Author(s):  
Y.R. Li ◽  
Q. Li ◽  
J.M. Yang ◽  
X.M. Zhou ◽  
X.M. Yin ◽  
...  
Keyword(s):  
Real Time ◽  
Golden Hamster ◽  
Expression Patterns ◽  
Rt Pcr

scholarly journals Involvement of Inflammatory Chemokines in Survival of Human Monocytes Fed with Malarial Pigment

2010 ◽  
Vol 78 (11) ◽  
pp. 4912-4921 ◽  
Author(s):  
Giuliana Giribaldi ◽  
Mauro Prato ◽  
Daniela Ulliers ◽  
Valentina Gallo ◽  
Evelin Schwarzer ◽  
...  
Keyword(s):  
Real Time ◽  
Expression Patterns ◽  
Human Monocytes ◽  
Rt Pcr ◽  
Necrosis Factor Alpha ◽  
Monocyte Chemoattractant Protein 1 ◽  
Inflammatory Protein ◽  
Tnf Α ◽  
Inflammatory Chemokines ◽  
Factor Alpha

ABSTRACT Hemozoin (HZ)-fed monocytes are exposed to strong oxidative stress, releasing large amounts of peroxidation derivatives with subsequent impairment of numerous functions and overproduction of proinflammatory cytokines. However, the histopathology at autopsy of tissues from patients with severe malaria showed abundant HZ in Kupffer cells and other tissue macrophages, suggesting that functional impairment and cytokine production are not accompanied by cell death. The aim of the present study was to clarify the role of HZ in cell survival, focusing on the qualitative and temporal expression patterns of proinflammatory and antiapoptotic molecules. Immunocytochemical and flow cytometric analyses showed that the long-term viability of human monocytes was unaffected by HZ. Short-term analysis by macroarray of a complete panel of cytokines and real-time reverse transcription (RT)-PCR experiments showed that HZ immediately induced interleukin-1β (IL-1β) gene expression, followed by transcription of eight additional chemokines (IL-8, epithelial cell-derived neutrophil-activating peptide 78 [ENA-78], growth-regulated oncogene α [GROα], GROβ, GROγ, macrophage inflammatory protein 1α [MIP-1α], MIP-1β, and monocyte chemoattractant protein 1 [MCP-1]), two cytokines (tumor necrosis factor alpha [TNF-α] and IL-1receptor antagonist [IL-1RA]), and the cytokine/chemokine-related proteolytic enzyme matrix metalloproteinase 9 (MMP-9). Furthermore, real-time RT-PCR showed that 15-HETE, a potent lipoperoxidation derivative generated by HZ through heme catalysis, recapitulated the effects of HZ on the expression of four of the chemokines. Intermediate-term investigation by Western blotting showed that HZ increased expression of HSP27, a chemokine-related protein with antiapoptotic properties. Taken together, the present data suggest that apoptosis of HZ-fed monocytes is prevented through a cascade involving 15-HETE-mediated upregulation of IL-1β transcription, rapidly sustained by chemokine, TNF-α, MMP-9, and IL-1RA transcription and upregulation of HSP27 protein expression.

scholarly journals Real-time quantitative RT-PCR identifies distinct c-RET, RET/PTC1 and RET/PTC3 expression patterns in papillary thyroid carcinoma

2004 ◽  
Vol 84 (12) ◽  
pp. 1557-1570 ◽  
Author(s):  
Kerry J Rhoden ◽  
Chaline Johnson ◽  
Guillerme Brandao ◽  
John G Howe ◽  
Brian R Smith ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Real Time ◽  
Expression Patterns ◽  
Papillary Thyroid ◽  
Rt Pcr

scholarly journals IDENTIFICACIÓN DE cDNAs DE Agave tequilana Weber Var. azul SIMILARES A FUROSTANOL GLICÓSIDO 26-O-β-GLUCOSIDASAS

2019 ◽  
Vol 42 (4) ◽  
pp. 439-447
Author(s):  
Zurisadaí Monroy-González ◽  
Aída Martínez-Hernández
Keyword(s):  
Expressed Sequence Tags ◽  
Asparagus Officinalis ◽  
Agave Tequilana ◽  
Rt Pcr ◽  
Expresión Génica ◽  
Expressed Sequence

La furostanol glicósido 26-O-β-glucosidasa (F26G) participa en el último paso de la biosíntesis de saponinas esteroidales, lo que escinde la glucosa unida al hidroxilo del C26 del furostanol glucósido para permitir la formación del espirostano. A pesar de la existencia de numerosos estudios que muestran la diversidad estructural y actividad biológica de las saponinas de plantas, así como su reconocido potencial biotecnológico y farmacológico, pocas enzimas participantes en la ruta de biosíntesis de las saponinas esteroidales han sido estudiadas y sólo una enzima nativa tipo F26G ha sido purificada y caracterizada funcionalmente. En este estudio, mediante búsqueda por BLASTX en una base de datos de Agave tequilana Weber var. azul (Agave DB), se identificaron 46 ESTs (Expressed Sequence Tags) de DNA complementario (cDNAs) similares a la F26G de Asparagus officinalis, la mayoría provienen de cDNAs clonados a partir de tejidos florales (anteras y ovarios) o raíz; ambos órganos son productores de saponinas. Entre ellos, se identificaron seis ESTs cuyo alineamiento indica que representan a tres cDNAs diferentes entre sí. Estos ESTs se registraron en la base de datos dbEST de NCBI (National Center for Biotechnology Information), el cual fue el primer registro de secuencias nativas de cDNAs potencialmente codificantes similares a F26G en Agave. El tamaño de los cDNAs clonados y su alineamiento hacia el lado 5’ de las F26G conocidas sugieren que son cDNAs completos. Se diseñaron iniciadores diferenciales específicos para cada tipo de cDNA y se analizó por RT-PCR su expresión en tejidos vegetativos de A. tequilana. Se establecieron protocolos de PCR cuantitativo (qPCR) para estudios posteriores de regulación de su expresión génica. La información aquí reportada servirá como base para estudiar la función, regulación y actividad enzimática de las enzimas clonadas de Agave similares a F26G.

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