ABSTRACT
Background: Bacterial wilt caused by Ralstonia solanacearum is the most devastating disease in peanut. Planting resistant peanut cultivars is deemed as the sole economically viable means for effective control of the disease. To understand the molecular mechanism underlying resistance and facilitate breeding process, differences in gene expression between seeds of Rihua 1 (a Virginia type peanut variety resistant to bacterial wilt) inoculated with the bacterial pathogen suspension (10(9) cfu ml-1) and seeds of the same cultivar treated with water (control), were studied using the GenefishingTM technology. Results: A total of 25 differentially expressed genes were isolated. Expression of genes encoding cyclophilin and ADP-ribosylation factor, respectively, were further studied by real time RT-PCR, and full length cDNAs of both genes were obtained by rapid amplification of cDNA ends. Conclusions: The study provided candidate genes potentially useful for breeding peanut cultivars with both high yield and bacterial wilt resistance, although confirmation of their functions through transgenic studies is still needed.
Subject(s)
Arachis/genetics , ADP-Ribosylation Factors/genetics , Ralstonia solanacearum/pathogenicity , Immunity, Innate , Real-Time Polymerase Chain Reaction , Sequence AnalysisABSTRACT
PURPOSE: Venous malformation(VM) which often causes pain and discomfort is the most common type of vascular malformations. Although it is presented with disfigured appearance and associated soft tissue or skeletal hypertrophy, the molecular bases of VMs are poorly understood. Differentially expressed genes(DEGs) of VMs were investigated to illuminate the molecular mechanism of the disease entity. METHODS: Gene expressions of VM patients' subcutaneous tissue were studied in comparison with normal persons' by GeneFishing(TM) technique using the annealing control primers (ACPs) to identify DEGs. Candidate genes were sequenced and screened by basic local alignment search tool (BLAST) afterwards. RESULTS: Among seventy DEGs identified, forty DEGs which had shown significantly different expression pattern were sequenced. Twenty eight out of 40 were up- regulated while 12 were down-regulated. BLAST searches revealed that 37 were known genes and 3 were unknown genes. Many genes were involved in the differentiation and remodeling of smooth muscle cells, opposed to the previous hypothesis that a lot of angiogenetic genes would be involved. Furthermore, several transcription factors and related genes, as well as cell signaling and metabolism regulators, were up regulated. CONCLUSION: It suggests that analysis of DEGs in VMs provide basic knowledge about its pathophysiology. and new therapeutic approaches.
Subject(s)
Gene Expression , Genes, vif , Hypertrophy , Metabolism , Myocytes, Smooth Muscle , Subcutaneous Tissue , Transcription Factors , Vascular MalformationsABSTRACT
PURPOSE: The prognosis of bladder cancer is related to tumor grade and stage. Because these pathological changes are preceded by molecular alterations, new molecular markers are needed in early diagnosis. New target molecular biomarkers can be differentially expressed genes(DEGs) between normal and cancer tissues. We tried to find a new DEG and demonstrated that it may be related to the development of the bladder cancer. MATERIALS AND METHODS: Cancer tissues were obtained from 39 patients with urothelial cell carcinoma, treated by transurethral resection of tumor (TURB) since 2002. Normal bladder tissues were obtained from the same patients during TURB. We compared the mRNA profiles between normal and cancer tissues using annealing control primer(ACP)-based Genefishing(TM) PCR to identify the DEGs in normal and cancer tissues of one same patient. To validate the result of ACP-based GeneFishing(TM) PCR, reverse transcription-polymerase chain reaction(RT-PCR) was performed on those of 39 patients. RESULTS: According to the result of ACP-based Genefishing(TM) PCR, EAR-3 gene was only present or markedly upregulated in normal tissue, compared with cancer tissues. The expression pattern that EAR-3 gene was downregulated in cancer tissues, irrespective of the clinicopathologic parameters was confirmed by RT-PCR in 39 patients. CONCLUSIONS: EAR-3 gene was downregulated in cancer tissues, irrespective of clinicopathologic parameters, compared with normal tissues in the bladder of the same patient. Therefore, we suggested that EAR-3 gene may be also play a role in bladder cancer development.
Subject(s)
Humans , Biomarkers , Carcinoma, Transitional Cell , Early Diagnosis , Gene Expression , Polymerase Chain Reaction , Prognosis , Reverse Transcriptase Polymerase Chain Reaction , RNA, Messenger , Urinary Bladder Neoplasms , Urinary BladderABSTRACT
OBJECTIVE: The aim of this study was to investigate the gene expression profiles using GeneFishingTM kit in human placentae and their membranes delivered at preterm caused by preterm labor. METHODS: Specimens were obtained from placenta, chorion, and amnion delivered at preterm and term, respectively. Total RNAs were isolated from each specimen. Thereafter, the profiles of expression genes between preterm and term specimens were compared using a new and accurate reverse transcription-polymerase chain reaction (RT-PCR) that involves annealing control primers (ACPs) to identify the genes expressed differentially and screened by basic local alignment search tool (BLAST) search. RESULTS: Using 20 ACPs, 13 differentially expressed genes (DEGs) were identified and sequenced. 7 of them were expressed up-regulation, while 6 were expressed down-regulation in preterm deliveries. A BLAST searches revealed that 11 were known genes and 2 were unknown genes. Among known genes, up-regulated genes were insulin-like growth factor II associated protein, vigilin, acyl-Coenzyme A dehydrogenase, tissue inhibitor of metalloproteinase 1 (TIMP1), ribosomal protein S26 (RPS26), follistatin-like 1 (FSTL1) and down-regulated genes were two mitochondrial DNAs, ribosomal protein S28 (RPS28), transglutaminase 2 (TGM2), heparin sulfate proteoglycan (HSPG, perlecan). CONCLUSION: This study shows that the ACP system is a good method for the identification of preterm-related genes. Furthermore, this study suggests that further analysis of the differentially expressed genes in preterm we have identified should provide insights into the molecular basis of preterm delivery caused by preterm labor.
Subject(s)
Female , Humans , Pregnancy , Acyl-CoA Dehydrogenase , Amnion , Chorion , DNA, Mitochondrial , Down-Regulation , Heparin , Insulin-Like Growth Factor II , Membranes , Obstetric Labor, Premature , Placenta , Proteoglycans , Ribosomal Proteins , RNA , Tissue Inhibitor of Metalloproteinase-1 , Transcriptome , Up-RegulationABSTRACT
OBJECTIVE: The aim of this study was to investigate the gene expression profiles using GeneFishing(TM) DEG kit in Korean women with cervical squamous cell carcinoma. METHODS: Cervical cancer biopsies were obtained from patients at the Department of Obstetrics and Gynecology, St. Mary's hodpital. In this study, we used a common reference that was mixed with an equal amount of RNA extracted from non-cervical cancer patients. The profiles of expression genes between cervical normal and squamous cell carcinoma tissue were identified using GeneFishing(TM) DEG Kit and screened by BLAST search. RESULTS: Almost 100 differential expressed genes were identified in universal control and cervical squamous cell carcinoma, 53 of differential expressed genes, up-regulated expression of 32 and 21 down-regulated expression was sequenced. Up-regulated genes were calcylin, calgranulin A, TRK oncogene, HLC5, fibrillarin, collagene type I alpha1 etc. and down-regulated genes were galectin 1, PRP8 pre-mRNA precessing factor 8 homology, clusterin etc. CONCLUSION: We identified gene expression profile in cervical squamous cell carcinoma using GeneFishing(TM) Kit in Korean women. The functional genomics of these genes should be further studied.