Rhododendron simsii(Ericaeae:Rhododendron) has high ornamental value and ecological value.In this study,7 pairs of novel EST-SSR markers were developed from the genomic sequence of R.simsii,and they were used to in...Rhododendron simsii(Ericaeae:Rhododendron) has high ornamental value and ecological value.In this study,7 pairs of novel EST-SSR markers were developed from the genomic sequence of R.simsii,and they were used to investigate the genetic diversity of 32 natural R.simsii samples from Guifeng Mountain,Hubei Province.Results showed that a total of 31 polymorphic bands were amplified with allele number per locus of 4.43.Mean values of heterozygosity(Ho) and expected heterozygosity(He) were 0.679 58 and 0.723 14,respectively.This research will not only enrich the existing SSR database,but also lay a foundation for subsequent studies about molecular marker-assisted breeding,genetic diversity analysis,genetic structure analysis and phylogenetic analysis.展开更多
Objective: To investigate the expression of angiopoietin-2 (Ang-2) and vascular endothelialcell growth factor (VEGF) in oral squamous cell carcinoma (OSCC) and their correlations with clinicopathologic paramete...Objective: To investigate the expression of angiopoietin-2 (Ang-2) and vascular endothelialcell growth factor (VEGF) in oral squamous cell carcinoma (OSCC) and their correlations with clinicopathologic parameters, angiogenesis and vessel maturation of OSCC. Methods: The expression of Ang-2 and VEGF was detected in 41 speciments of human OSCC, 30 adjacent noncancerous oral tissues and 10 specimens of normal oral mucosa by conventional immumohistochemistry. Microvessel density (MVD) and vessel maturation index (VMI) were also assessed by double-labelling immumohistochemistry staining against CD34, a marker of pan-endothelial cells, and that against alpha-smooth muscle actin (α-SMA), a marker of mural cells (pericytes/smooth muscle cells). Results: The positive expression rate of Ang-2 and VEGF in 41 OSCC tissues was 51.22% and 63.42%, respectively. The expression of Ang-2 and VEGF was significantly higher in OSCC than in adjacent noncancerous oral tissues (all P〈0.05) and normal oral mucosa (all P〈0.05). In the clinicopathologic parameters, the Ang-2 expression was closely correlated with tumor lymph node metastasis (P〈0.01) and the VEGF expression was correlated with tumor differentiated degree (P〈0.05), but there was no significant correlation among the Ang-2 and VEGF expression and patients' sex, age and TNM stages (all P〉0.05). The MVD of OSCC positive for both Ang-2 and VEGF was significantly higher than that of OSCC negative for both Ang-2 and VEGF (P〈0.05). The VMI of OSCC positive for Ang-2 was significantly lower than that of OSCC negative for Ang-2 (P〈0.05). When Ang-2 expression was combined with the staus of VEGF expression, MVD of OSCC positive for both Ang-2 and VEGF was the highest (51.08±2.99) as compared with that of other status in patient with OSCC (all P〈0.05). Conclusion: The overexpression of Ang-2 and VEGF may play a crucial role in the development of OSCC. They are closely associated with angiogenesis and vessel maturation of tumor.展开更多
To better understand the toxicity of an antifouling booster biocide Irgarol-1051 degradation product M2 3-4-tert-butylamino-6-methylthiol-s-triazin-2-ylamino pro-pionaldehyde this study utilized a DNA microarray techn...To better understand the toxicity of an antifouling booster biocide Irgarol-1051 degradation product M2 3-4-tert-butylamino-6-methylthiol-s-triazin-2-ylamino pro-pionaldehyde this study utilized a DNA microarray technique to explore the genotoxicity of M2. The Affymetrix Inc. rat genome 230 2.0 GeneChip was employed to examine alterations in gene regulation in rat hepatoma cells exposed to 30 μmol/L of M2 for 96 h.The results showed that 38 genes were significantly p<0.002 5 altered by M2 at two-fold changes in all the four possible control/exposure comparisons. Accn5 was the only well described gene consistently being suppressed which likely altered the epithelial sodium channel ENaC .10 and 82 annotated genes were up-and down-regulated in at least one of the control/exposure comparisons respectively. The induced genes were mainly involved in the nucleus belonging to the cellular component. The largest categories of suppression concerned G-protein coupled receptor protein signaling pathways belonging to the biological process and integral to membranes belonging to the cellular component.展开更多
Objctive The aim was to make better use of the EST-SSR resources of kiwifruit for further molecular biological studies and new EST-SSR marker development by screening and mining the SSR repeats in the EST database of ...Objctive The aim was to make better use of the EST-SSR resources of kiwifruit for further molecular biological studies and new EST-SSR marker development by screening and mining the SSR repeats in the EST database of kiwifruit (Actinidia spp. ) [ Method] 56 400 of EST sequences were randomly selected from EST( Expressed Sequence Tag)sequences of kiwifruit in the database of NCBI. EST sequences were analyzed and the SSR(Microsatellite) was screened by using the SSRHunter software. [ Result] 7 939 SSRs were identified from the ran- domly selected kiwifruit EST resources, among which there were 5 131 (64.63%) dinucleotide, 1 237 ( 15.58% ) trinucleotide, 284 ( 3.58% ) tetra nucleotide, 397 (5.00%) pentanucleotide and 890 ( 11.21% ) hexanucleotide SSRs. Among the dinucleotide sequences, AG/CT repeat motif was accounted for 4 654(90.70% ). The frequency of SSRs was approximately 1/2.48 kb, which could exist to 1 SSR in 7 unigenes. [ Conclusion] The dinucleotide repeats appeared to be the most abundant SSRs, followed by the trinucleotide and hexanucleotide repeats. Among them the repeat motif such as AG/CT was predominant in each type of SSRs.展开更多
To study the relationship between the expression of E-cadherin andmicrovessel density (MVD) in lung cancer. Methods: The expression of E-cadherin and factor VIII wasdetected in 104 lung cancer tissues by an immunohist...To study the relationship between the expression of E-cadherin andmicrovessel density (MVD) in lung cancer. Methods: The expression of E-cadherin and factor VIII wasdetected in 104 lung cancer tissues by an immunohistochemical method, and MVD was calculated by animage-analysis system. Results: The expression of E-cadherin was significantly related to thedifferentiation of lung cancers (P 【 0.05). A negative correlation was found between E-cadherinexpression and MVD in lung cancer tissues (P=0.047). Conclusion: Down-expression of E-cadherin andan increase of MVD may play an important role in the invasion and metastasis of lung cancer, and mayalso be used as a useful marker for tumor prognosis.展开更多
From the NCBI database, 81,518 Lactuca sativa EST sequences were downloaded, from which 61,757 non-redundant sequences were obtained. In total, 2040 SSR loci were identified, with the frequency of 3.3%. Trinucleotide ...From the NCBI database, 81,518 Lactuca sativa EST sequences were downloaded, from which 61,757 non-redundant sequences were obtained. In total, 2040 SSR loci were identified, with the frequency of 3.3%. Trinucleotide repeat was dominant, followed by dinucieotide and hexanucleotide repeats. Among 181 types of repeat motifs, (AGA)n and (ATG)n were the dominant repeat motif types, taking up 12.01% and 3.53%, respectively. Totally, four material-special EST-SSR markers were characterized. This study enriches molecular markers of L. sativa, and also lays a theoretical foundation for following germplasm identification, molecular marker assisted breeding and genetic map construction.展开更多
Objective: To investigate the correlation between the microsatellite instability (MSI) and the expression of vascular endothelial growth factor (VEGF) in gastric adenocarcinoma. Methods: PCR SSCP method was used to d...Objective: To investigate the correlation between the microsatellite instability (MSI) and the expression of vascular endothelial growth factor (VEGF) in gastric adenocarcinoma. Methods: PCR SSCP method was used to detect MSI of thirty cases with gastric adenocarcinoma at five loci in each patient. Expression of VEGF was examined by the method of immunohistochemistry. Results: The positive of MSI was in 13 patients out of 30 patients (43.4%) in our study. Positive VEGF Immunostaining was detected in 18 patients (60.0%). VEGF was decreased in microsatellite instability high (MSI H) gastric adenocarcinoma. Conclusion: MSI H and microsatellite stable (MSS) gastric adenocarcinoma may follow a different pathway of angiogenesis. The low frequency of VEGF expression among MSI H cancer may partially explain why these cancers are less aggressive.展开更多
AIM: To investigate the mRNA expressions of bFGF and MMP-9 in gastric carcinomas so as to reveal their correlations with tumor microvascular density (MVD), invasion, metastasis, and prognosis.METHODS: In situ hybridiz...AIM: To investigate the mRNA expressions of bFGF and MMP-9 in gastric carcinomas so as to reveal their correlations with tumor microvascular density (MVD), invasion, metastasis, and prognosis.METHODS: In situ hybridization and immunohistochemical techniques were used to detect the expressions of bFGFmRNA and MMP-9mRNA and the proteins of CD34 in 105 specimens of gastric carcinomas.RESULTS: In situ hybridization study showed that positive rates of bFGF mRNA and MMP-9mRNA expressions were 60.95% and 59.19%; the mean MVD was 46.09±11.52 and 43.75±13.41, respectively in piece/0.72 mm2 in tumors with bFGFmRNA and MMP-9mRNA positive expressions,which were significantly higher than those with negative expression (29.41±12.47; 33.45±13.92 piece/0.72 mm2,respectively). The positive expression rates of bFGFmRNA and MMP-9mRNA were correlated to the tumor invasion depth (rs = 0.211, P= 0.031; rs = 0.335, P= 0.001), growing pattern (rs= 0.324, P= 0.001; rs= 0.267, P= 0.006), vessel invasion (rs = 0.579, P = 0.001; rs = 0.209, P = 0.032),lymph node metastasis (rs = 0.405, P = 0.001; rs= 0.343,P = 0.001) and distant metastasis (rs= 0.474, P = 0.001;rs = 0.468, P = 0.001), but not correlated to tumortype (rs= 0.134, P= 0.173; rs= 0.103, P= 0.145) anddifferentiations (rs = 0.096, P= 0.332; rs = 0.102, P= 0.298).The mean MVD was much higher in the tumors withinfiltrating growth at stage T3-T4, with vessel invasion, lymph node metastasis and distant metastasis than those with expanding growth type (t = 10.105, P= 0.001) at stage T1-T2 (t = 5.961, P = 0.001), with non-vessel invasion (t= 7.394, P= 0.001), non-lymph node metastasis (t= 3.819, P= 0.01) and non-distant metastasis (t= 10.578, P = 0.001). Positive correlation was observed between MVD and the expressions of bFGFmRNA and MMP-9mRNA(t= 3.207, P= 0.002; t= 7.035, P= 0.001, respectively). The mean survival time and 5-year survival rate werelower in cases with MVD over 39.5 and the positive expressions of bFGFmRNA and MMP-9mRNA than those with MVD less than 39.5 and the negative expressions of bFGFmRNA and MMP-9mRNA.CONCLUSION: bFGF and MMP-9 promote the angiogenesis of the gastric cancers. Detection of the expressions of bF-GF and MMP-9 can serve as a useful index to determine the angiogenesis, invasion, metastasis, and prognosis of gastric cancers.展开更多
Objective: To identify differentially expressed long non-coding RNAs (lncRNAs) involved in the metastasis of epithelial ovarian cancer. Methods: An in vitro invasion assay was performed to validate the invasive ca...Objective: To identify differentially expressed long non-coding RNAs (lncRNAs) involved in the metastasis of epithelial ovarian cancer. Methods: An in vitro invasion assay was performed to validate the invasive capability of SKOV3 and SKOV3.ip1 cell lines. Total R.NA was then extracted, and microarray analysis was performed. Moreover, nine lncRNAs were selected for validation using RT-qPCR. Results: Compared with the SKOV3 cells, the SKOV3.ip1 cells significantly improved in the in vitro invasive activity. Of the 4,956 lncRNAs detected in the microarra~ 583 and 578 lncRNAs were upregulated and downregulated, respectivel~ in SKOV3.ip1 cells, compared with the parental SKOV3 cells. Seven of the analyzed lncRNAs (MALAT1, H19, UCA1, CCAT1, LOC645249, LOC100128881, and LOC100292680) confirmed the deregulation found by microarray analysis. Conclusion: LncRNAs clusters were differentially expressed in ovarian cancer cells with varying metastatic potentials. This result indicates that some lncRNAs might exert a partial or key role in epithelial ovarian cancer metastasis. Further studies should be conducted to determine the roles of these lncRNAs in ovarian cancer metastasis.展开更多
AIM: To find out key genes responsible for hepatocarc inogenesis and to further understand the underlying molecular mechanism through investigating the differential gene expression between human normal liver tissue an...AIM: To find out key genes responsible for hepatocarc inogenesis and to further understand the underlying molecular mechanism through investigating the differential gene expression between human normal liver tissue and hepatocellular carcinoma (HCC).METHODS: DNA microarray was prepared by spotting PCR products of 1 000 human genes including 445 novel genes, 540 known genes as well as 12 positive (housekeeping) and 3 negative controls (plant gene) onto treated glass slides. cDNA probes were prepared by labeling normal liver tissue mRNA and cancer liver tissue mRNA with Cy3-dUTP and Cy5-dUTP separately through reverse transcription. The arrays were hybridized against the cDNA probe and the fluorescent signals were scanned. The dataobtained from repeated experiments were analyzed. RESULTS: Among the 20 couple samples investigated (from cancerous liver tissue and normal liver tissue), 38 genes including 21 novel genes and 17 known genes exhibited different expressions. CONCLUSION: cDNA microarray technique is powerful to identify candidate target genes that may play important roles in human carcinogenesis. Further analysis of the obtained genes is helpful to understand the molecular changes in HCC progression and ultimately may lead to the identification of new targets for HCC diagnosis and intervention.展开更多
AIM:To globally compare the gene expression profiles during the capillary morphogenesis of human microvascular endothelial cells (HMVECs) in an in vitro angiogeness system with affymetrix oligonucleotide array. METHOD...AIM:To globally compare the gene expression profiles during the capillary morphogenesis of human microvascular endothelial cells (HMVECs) in an in vitro angiogeness system with affymetrix oligonucleotide array. METHODS: A microcarrier-based in vitro angiogenesis system was developed, in which ECs migrated into the matrix, proliferated, and formed capillary sprouts. The sprouts elongated, branched and formed networks. The total RNA samples from the HMVECs at the selected time points (0.5, 24, and 72 h) during the capillary morphogenesis were used for microarray analyses, and the data were processed with the softwares provided by the manufacturers. The expression patterns of some genes were validated and confirmed by semi-quantitative RT-PCR. The regulated genes were grouped based on their molecular functions and expression patterns, and among them the expression of chemokines and chemokine receptors was specially examined and their functional implications were analyzed. RESULTS: A total of 1 961 genes were up- or downreg-ulated two-folds or above, and among them, 468 genes were up- or down-regulated three-folds or above. The regulated genes could be grouped into categories based on their molecular functions, and were also clustered into six groups based on their patterns of expression. As for chemokines and chemokine receptors, CXCL1/GRO-α, CXCL2/GRO-β, CXCL5/ENA-78, CXCL6/GCP2, IL-8/CXCL8, CXCL12/SDF-1, CXCL9/Mig, CXC11/ITAC, OOCL1/fractalkine, CCL2/MCP-1, CCL3, CCL5/RANTES, CCL7, CCL15, CCL21, CCL23, CCL28, and CCR1, CCR9, CXCR4 were identified. Moreover, these genes demonstrated different changing patterns during the capillary morphogenesis, which implied that they might have different roles in the sequential process. Among the chemokines identified, CCL2/MCP-1, CCL5/RANTES and CX3CL1 were specially up-regulated at the 24-h time point when the sprouting characterized the morphological change. It was thus suggested that they might exert crucial roles at the early stage of angiogenesis. CONCLUSION: The present study demonstrates a global profile of gene expression during endothelial capillary morphogenesis, and the results provide us much information about the molecular mechanisms of angiogenesis, with which further evaluation of individual genes can be conducted.展开更多
AIM: To identify alterations in genes and molecular functional pathways in esophageal cancer in a high incidence region of India where there is a widespread use of tobacco and betel quid with fermented areca nuts. ME...AIM: To identify alterations in genes and molecular functional pathways in esophageal cancer in a high incidence region of India where there is a widespread use of tobacco and betel quid with fermented areca nuts. METHODS: Total RNA was isolated from tumor and matched normal tissue of 16 patients with esophageal squamous cell carcinoma. Pooled tumor tissue RNA was labeled with Cy3-dUTP and pooled normal tissue RNA was labeled with Cy5-dUTP by direct labeling method. The labeled probes were hybridized with human 10K cDNA chip and expression profiles were analyzed by Genespring GX V 7.3 (Silicon Genetics). RESULTS: Nine hundred twenty three genes were differentially expressed. Of these, 611 genes were upregulated and 312 genes were downregulated. Using stringent criteria (P ≤ 0.05 and ≥ 1.5 fold change), 127 differentially expressed genes (87 upregulated and 40 downregulated) were identified in tumor tissue. On the basis of Gene Ontology, four different molecular functional pathways (HAPK pathway, G-protein coupled receptor family, ion transport activity, and serine or threonine kinase activity)were most significantly upregulated and six different molecular functional pathways (structural constituent of ribosome, endopeptidase inhibitor activity, structural constituent of cytoskeleton, antioxidant activity, acyl group transferase activity, eukaryotic translation elongation factor activity)were most significantly downregulated. CONCLUSION: Several genes that showed alterations in our study have also been reported from a high incidence area of esophageal cancer in China. This indicates that molecular profiles of esophageal cancer in these two different geographic locations are highly consistent.展开更多
Over the past 5 years there has been a rapid increase in the use of microarray technology in the field of cancer research, The majority of studies use microarray analysis of tumor biopsies for profiling of molecular c...Over the past 5 years there has been a rapid increase in the use of microarray technology in the field of cancer research, The majority of studies use microarray analysis of tumor biopsies for profiling of molecular characteristics in an attempt to produce robust classifiers for prognosis. There are now several published gene sets that have been shown to predict for aggressive forms of breast cancer, where patients are most likely to benefit from adjuvant chemotherapy and tumors most likely to develop distant metastases, or be resistant to treatment. The number of publications relating to the use of microarrays for analysis of normal tissue damage, after cancer treatment or genotoxic exposure, is much more limited. A PublVled literature search was conducted using the following keywords and combination of terms: radiation, normal tissue, microarray, gene expression profiling, prediction. With respect to normal tissue radiation injury, microarrays have been used in three ways: (1) to generate gene signatures to identify sensitive and resistant populations (prognosis); (2) to identify sets of biomarker genes for estimating radiation exposure, either accidental or as a result of terrorist attack (diagnosis); (3) to identify genes and pathways involved in tissue response to injury (mechanistic). In this article we will review all (relevant) papers that covered our literature search criteria on microarray technology as it has been applied to normal tissue radiation biology and discuss how successful this has been in defining predisposition markers for radiation sensitivity or how it has helped us to unravel molecular mechanisms leading to acute and late tissue toxicity. We also discuss some of the problems and limitations in application and interpretation of such data.展开更多
文摘Rhododendron simsii(Ericaeae:Rhododendron) has high ornamental value and ecological value.In this study,7 pairs of novel EST-SSR markers were developed from the genomic sequence of R.simsii,and they were used to investigate the genetic diversity of 32 natural R.simsii samples from Guifeng Mountain,Hubei Province.Results showed that a total of 31 polymorphic bands were amplified with allele number per locus of 4.43.Mean values of heterozygosity(Ho) and expected heterozygosity(He) were 0.679 58 and 0.723 14,respectively.This research will not only enrich the existing SSR database,but also lay a foundation for subsequent studies about molecular marker-assisted breeding,genetic diversity analysis,genetic structure analysis and phylogenetic analysis.
文摘Objective: To investigate the expression of angiopoietin-2 (Ang-2) and vascular endothelialcell growth factor (VEGF) in oral squamous cell carcinoma (OSCC) and their correlations with clinicopathologic parameters, angiogenesis and vessel maturation of OSCC. Methods: The expression of Ang-2 and VEGF was detected in 41 speciments of human OSCC, 30 adjacent noncancerous oral tissues and 10 specimens of normal oral mucosa by conventional immumohistochemistry. Microvessel density (MVD) and vessel maturation index (VMI) were also assessed by double-labelling immumohistochemistry staining against CD34, a marker of pan-endothelial cells, and that against alpha-smooth muscle actin (α-SMA), a marker of mural cells (pericytes/smooth muscle cells). Results: The positive expression rate of Ang-2 and VEGF in 41 OSCC tissues was 51.22% and 63.42%, respectively. The expression of Ang-2 and VEGF was significantly higher in OSCC than in adjacent noncancerous oral tissues (all P〈0.05) and normal oral mucosa (all P〈0.05). In the clinicopathologic parameters, the Ang-2 expression was closely correlated with tumor lymph node metastasis (P〈0.01) and the VEGF expression was correlated with tumor differentiated degree (P〈0.05), but there was no significant correlation among the Ang-2 and VEGF expression and patients' sex, age and TNM stages (all P〉0.05). The MVD of OSCC positive for both Ang-2 and VEGF was significantly higher than that of OSCC negative for both Ang-2 and VEGF (P〈0.05). The VMI of OSCC positive for Ang-2 was significantly lower than that of OSCC negative for Ang-2 (P〈0.05). When Ang-2 expression was combined with the staus of VEGF expression, MVD of OSCC positive for both Ang-2 and VEGF was the highest (51.08±2.99) as compared with that of other status in patient with OSCC (all P〈0.05). Conclusion: The overexpression of Ang-2 and VEGF may play a crucial role in the development of OSCC. They are closely associated with angiogenesis and vessel maturation of tumor.
基金The Research Grants Council of Hong Kong SAR,China(No.City U,1445/05M)the National Natural Science Foundation of China(No.41301546)
文摘To better understand the toxicity of an antifouling booster biocide Irgarol-1051 degradation product M2 3-4-tert-butylamino-6-methylthiol-s-triazin-2-ylamino pro-pionaldehyde this study utilized a DNA microarray technique to explore the genotoxicity of M2. The Affymetrix Inc. rat genome 230 2.0 GeneChip was employed to examine alterations in gene regulation in rat hepatoma cells exposed to 30 μmol/L of M2 for 96 h.The results showed that 38 genes were significantly p<0.002 5 altered by M2 at two-fold changes in all the four possible control/exposure comparisons. Accn5 was the only well described gene consistently being suppressed which likely altered the epithelial sodium channel ENaC .10 and 82 annotated genes were up-and down-regulated in at least one of the control/exposure comparisons respectively. The induced genes were mainly involved in the nucleus belonging to the cellular component. The largest categories of suppression concerned G-protein coupled receptor protein signaling pathways belonging to the biological process and integral to membranes belonging to the cellular component.
基金Supported by the National Natural Science Foundation of China(30660113,30860167)~~
文摘Objctive The aim was to make better use of the EST-SSR resources of kiwifruit for further molecular biological studies and new EST-SSR marker development by screening and mining the SSR repeats in the EST database of kiwifruit (Actinidia spp. ) [ Method] 56 400 of EST sequences were randomly selected from EST( Expressed Sequence Tag)sequences of kiwifruit in the database of NCBI. EST sequences were analyzed and the SSR(Microsatellite) was screened by using the SSRHunter software. [ Result] 7 939 SSRs were identified from the ran- domly selected kiwifruit EST resources, among which there were 5 131 (64.63%) dinucleotide, 1 237 ( 15.58% ) trinucleotide, 284 ( 3.58% ) tetra nucleotide, 397 (5.00%) pentanucleotide and 890 ( 11.21% ) hexanucleotide SSRs. Among the dinucleotide sequences, AG/CT repeat motif was accounted for 4 654(90.70% ). The frequency of SSRs was approximately 1/2.48 kb, which could exist to 1 SSR in 7 unigenes. [ Conclusion] The dinucleotide repeats appeared to be the most abundant SSRs, followed by the trinucleotide and hexanucleotide repeats. Among them the repeat motif such as AG/CT was predominant in each type of SSRs.
基金This study is a key project of Tianjin Scientific Committee (No. 033804211).
文摘To study the relationship between the expression of E-cadherin andmicrovessel density (MVD) in lung cancer. Methods: The expression of E-cadherin and factor VIII wasdetected in 104 lung cancer tissues by an immunohistochemical method, and MVD was calculated by animage-analysis system. Results: The expression of E-cadherin was significantly related to thedifferentiation of lung cancers (P 【 0.05). A negative correlation was found between E-cadherinexpression and MVD in lung cancer tissues (P=0.047). Conclusion: Down-expression of E-cadherin andan increase of MVD may play an important role in the invasion and metastasis of lung cancer, and mayalso be used as a useful marker for tumor prognosis.
基金Supported by General Project of Natural Science Foundation of Hubei Province(2015CFC816)~~
文摘From the NCBI database, 81,518 Lactuca sativa EST sequences were downloaded, from which 61,757 non-redundant sequences were obtained. In total, 2040 SSR loci were identified, with the frequency of 3.3%. Trinucleotide repeat was dominant, followed by dinucieotide and hexanucleotide repeats. Among 181 types of repeat motifs, (AGA)n and (ATG)n were the dominant repeat motif types, taking up 12.01% and 3.53%, respectively. Totally, four material-special EST-SSR markers were characterized. This study enriches molecular markers of L. sativa, and also lays a theoretical foundation for following germplasm identification, molecular marker assisted breeding and genetic map construction.
文摘Objective: To investigate the correlation between the microsatellite instability (MSI) and the expression of vascular endothelial growth factor (VEGF) in gastric adenocarcinoma. Methods: PCR SSCP method was used to detect MSI of thirty cases with gastric adenocarcinoma at five loci in each patient. Expression of VEGF was examined by the method of immunohistochemistry. Results: The positive of MSI was in 13 patients out of 30 patients (43.4%) in our study. Positive VEGF Immunostaining was detected in 18 patients (60.0%). VEGF was decreased in microsatellite instability high (MSI H) gastric adenocarcinoma. Conclusion: MSI H and microsatellite stable (MSS) gastric adenocarcinoma may follow a different pathway of angiogenesis. The low frequency of VEGF expression among MSI H cancer may partially explain why these cancers are less aggressive.
文摘AIM: To investigate the mRNA expressions of bFGF and MMP-9 in gastric carcinomas so as to reveal their correlations with tumor microvascular density (MVD), invasion, metastasis, and prognosis.METHODS: In situ hybridization and immunohistochemical techniques were used to detect the expressions of bFGFmRNA and MMP-9mRNA and the proteins of CD34 in 105 specimens of gastric carcinomas.RESULTS: In situ hybridization study showed that positive rates of bFGF mRNA and MMP-9mRNA expressions were 60.95% and 59.19%; the mean MVD was 46.09±11.52 and 43.75±13.41, respectively in piece/0.72 mm2 in tumors with bFGFmRNA and MMP-9mRNA positive expressions,which were significantly higher than those with negative expression (29.41±12.47; 33.45±13.92 piece/0.72 mm2,respectively). The positive expression rates of bFGFmRNA and MMP-9mRNA were correlated to the tumor invasion depth (rs = 0.211, P= 0.031; rs = 0.335, P= 0.001), growing pattern (rs= 0.324, P= 0.001; rs= 0.267, P= 0.006), vessel invasion (rs = 0.579, P = 0.001; rs = 0.209, P = 0.032),lymph node metastasis (rs = 0.405, P = 0.001; rs= 0.343,P = 0.001) and distant metastasis (rs= 0.474, P = 0.001;rs = 0.468, P = 0.001), but not correlated to tumortype (rs= 0.134, P= 0.173; rs= 0.103, P= 0.145) anddifferentiations (rs = 0.096, P= 0.332; rs = 0.102, P= 0.298).The mean MVD was much higher in the tumors withinfiltrating growth at stage T3-T4, with vessel invasion, lymph node metastasis and distant metastasis than those with expanding growth type (t = 10.105, P= 0.001) at stage T1-T2 (t = 5.961, P = 0.001), with non-vessel invasion (t= 7.394, P= 0.001), non-lymph node metastasis (t= 3.819, P= 0.01) and non-distant metastasis (t= 10.578, P = 0.001). Positive correlation was observed between MVD and the expressions of bFGFmRNA and MMP-9mRNA(t= 3.207, P= 0.002; t= 7.035, P= 0.001, respectively). The mean survival time and 5-year survival rate werelower in cases with MVD over 39.5 and the positive expressions of bFGFmRNA and MMP-9mRNA than those with MVD less than 39.5 and the negative expressions of bFGFmRNA and MMP-9mRNA.CONCLUSION: bFGF and MMP-9 promote the angiogenesis of the gastric cancers. Detection of the expressions of bF-GF and MMP-9 can serve as a useful index to determine the angiogenesis, invasion, metastasis, and prognosis of gastric cancers.
文摘Objective: To identify differentially expressed long non-coding RNAs (lncRNAs) involved in the metastasis of epithelial ovarian cancer. Methods: An in vitro invasion assay was performed to validate the invasive capability of SKOV3 and SKOV3.ip1 cell lines. Total R.NA was then extracted, and microarray analysis was performed. Moreover, nine lncRNAs were selected for validation using RT-qPCR. Results: Compared with the SKOV3 cells, the SKOV3.ip1 cells significantly improved in the in vitro invasive activity. Of the 4,956 lncRNAs detected in the microarra~ 583 and 578 lncRNAs were upregulated and downregulated, respectivel~ in SKOV3.ip1 cells, compared with the parental SKOV3 cells. Seven of the analyzed lncRNAs (MALAT1, H19, UCA1, CCAT1, LOC645249, LOC100128881, and LOC100292680) confirmed the deregulation found by microarray analysis. Conclusion: LncRNAs clusters were differentially expressed in ovarian cancer cells with varying metastatic potentials. This result indicates that some lncRNAs might exert a partial or key role in epithelial ovarian cancer metastasis. Further studies should be conducted to determine the roles of these lncRNAs in ovarian cancer metastasis.
基金Supported by the Special Fund of Chinese Academy of Sciences, No. KSCX1-06
文摘AIM: To find out key genes responsible for hepatocarc inogenesis and to further understand the underlying molecular mechanism through investigating the differential gene expression between human normal liver tissue and hepatocellular carcinoma (HCC).METHODS: DNA microarray was prepared by spotting PCR products of 1 000 human genes including 445 novel genes, 540 known genes as well as 12 positive (housekeeping) and 3 negative controls (plant gene) onto treated glass slides. cDNA probes were prepared by labeling normal liver tissue mRNA and cancer liver tissue mRNA with Cy3-dUTP and Cy5-dUTP separately through reverse transcription. The arrays were hybridized against the cDNA probe and the fluorescent signals were scanned. The dataobtained from repeated experiments were analyzed. RESULTS: Among the 20 couple samples investigated (from cancerous liver tissue and normal liver tissue), 38 genes including 21 novel genes and 17 known genes exhibited different expressions. CONCLUSION: cDNA microarray technique is powerful to identify candidate target genes that may play important roles in human carcinogenesis. Further analysis of the obtained genes is helpful to understand the molecular changes in HCC progression and ultimately may lead to the identification of new targets for HCC diagnosis and intervention.
文摘AIM:To globally compare the gene expression profiles during the capillary morphogenesis of human microvascular endothelial cells (HMVECs) in an in vitro angiogeness system with affymetrix oligonucleotide array. METHODS: A microcarrier-based in vitro angiogenesis system was developed, in which ECs migrated into the matrix, proliferated, and formed capillary sprouts. The sprouts elongated, branched and formed networks. The total RNA samples from the HMVECs at the selected time points (0.5, 24, and 72 h) during the capillary morphogenesis were used for microarray analyses, and the data were processed with the softwares provided by the manufacturers. The expression patterns of some genes were validated and confirmed by semi-quantitative RT-PCR. The regulated genes were grouped based on their molecular functions and expression patterns, and among them the expression of chemokines and chemokine receptors was specially examined and their functional implications were analyzed. RESULTS: A total of 1 961 genes were up- or downreg-ulated two-folds or above, and among them, 468 genes were up- or down-regulated three-folds or above. The regulated genes could be grouped into categories based on their molecular functions, and were also clustered into six groups based on their patterns of expression. As for chemokines and chemokine receptors, CXCL1/GRO-α, CXCL2/GRO-β, CXCL5/ENA-78, CXCL6/GCP2, IL-8/CXCL8, CXCL12/SDF-1, CXCL9/Mig, CXC11/ITAC, OOCL1/fractalkine, CCL2/MCP-1, CCL3, CCL5/RANTES, CCL7, CCL15, CCL21, CCL23, CCL28, and CCR1, CCR9, CXCR4 were identified. Moreover, these genes demonstrated different changing patterns during the capillary morphogenesis, which implied that they might have different roles in the sequential process. Among the chemokines identified, CCL2/MCP-1, CCL5/RANTES and CX3CL1 were specially up-regulated at the 24-h time point when the sprouting characterized the morphological change. It was thus suggested that they might exert crucial roles at the early stage of angiogenesis. CONCLUSION: The present study demonstrates a global profile of gene expression during endothelial capillary morphogenesis, and the results provide us much information about the molecular mechanisms of angiogenesis, with which further evaluation of individual genes can be conducted.
基金Supported by Non Communicable Disease Division,Indian Council of Medical Research
文摘AIM: To identify alterations in genes and molecular functional pathways in esophageal cancer in a high incidence region of India where there is a widespread use of tobacco and betel quid with fermented areca nuts. METHODS: Total RNA was isolated from tumor and matched normal tissue of 16 patients with esophageal squamous cell carcinoma. Pooled tumor tissue RNA was labeled with Cy3-dUTP and pooled normal tissue RNA was labeled with Cy5-dUTP by direct labeling method. The labeled probes were hybridized with human 10K cDNA chip and expression profiles were analyzed by Genespring GX V 7.3 (Silicon Genetics). RESULTS: Nine hundred twenty three genes were differentially expressed. Of these, 611 genes were upregulated and 312 genes were downregulated. Using stringent criteria (P ≤ 0.05 and ≥ 1.5 fold change), 127 differentially expressed genes (87 upregulated and 40 downregulated) were identified in tumor tissue. On the basis of Gene Ontology, four different molecular functional pathways (HAPK pathway, G-protein coupled receptor family, ion transport activity, and serine or threonine kinase activity)were most significantly upregulated and six different molecular functional pathways (structural constituent of ribosome, endopeptidase inhibitor activity, structural constituent of cytoskeleton, antioxidant activity, acyl group transferase activity, eukaryotic translation elongation factor activity)were most significantly downregulated. CONCLUSION: Several genes that showed alterations in our study have also been reported from a high incidence area of esophageal cancer in China. This indicates that molecular profiles of esophageal cancer in these two different geographic locations are highly consistent.
文摘Over the past 5 years there has been a rapid increase in the use of microarray technology in the field of cancer research, The majority of studies use microarray analysis of tumor biopsies for profiling of molecular characteristics in an attempt to produce robust classifiers for prognosis. There are now several published gene sets that have been shown to predict for aggressive forms of breast cancer, where patients are most likely to benefit from adjuvant chemotherapy and tumors most likely to develop distant metastases, or be resistant to treatment. The number of publications relating to the use of microarrays for analysis of normal tissue damage, after cancer treatment or genotoxic exposure, is much more limited. A PublVled literature search was conducted using the following keywords and combination of terms: radiation, normal tissue, microarray, gene expression profiling, prediction. With respect to normal tissue radiation injury, microarrays have been used in three ways: (1) to generate gene signatures to identify sensitive and resistant populations (prognosis); (2) to identify sets of biomarker genes for estimating radiation exposure, either accidental or as a result of terrorist attack (diagnosis); (3) to identify genes and pathways involved in tissue response to injury (mechanistic). In this article we will review all (relevant) papers that covered our literature search criteria on microarray technology as it has been applied to normal tissue radiation biology and discuss how successful this has been in defining predisposition markers for radiation sensitivity or how it has helped us to unravel molecular mechanisms leading to acute and late tissue toxicity. We also discuss some of the problems and limitations in application and interpretation of such data.