scholarly journals Comparability of Microarray Data between Amplified and Non Amplified RNA in Colorectal Carcinoma

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Roland S. Croner ◽  
Berthold Lausen ◽  
Vera Schellerer ◽  
Isabel Zeittraeger ◽  
Axel Wein ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Colorectal Carcinoma ◽  
Differentially Expressed Genes ◽  
Microarray Data ◽  
Gene Clusters ◽  
The Other ◽  
Research Groups ◽  
Amplification Bias ◽  
Microarray Hybridisation ◽  
Pre Treatment

Microarray analysis reaches increasing popularity during the investigation of prognostic gene clusters in oncology. The standardisation of technical procedures will be essential to compare various datasets produced by different research groups. In several projects the amount of available tissue is limited. In such cases the preamplification of RNA might be necessary prior to microarray hybridisation. To evaluate the comparability of microarray results generated either by amplified or non amplified RNA we isolated RNA from colorectal cancer samples (stage UICC IV) following tumour tissue enrichment by macroscopic manual dissection (CMD). One part of the RNA was directly labelled and hybridised to GeneChips (HG-U133A, Affymetrix), the other part of the RNA was amplified according to the “Eberwine” protocol and was then hybridised to the microarrays. During unsupervised hierarchical clustering the samples were divided in groups regarding the RNA pre-treatment and 5.726 differentially expressed genes were identified. Using independent microarray data of 31 amplified vs. 24 non amplified RNA samples from colon carcinomas (stage UICC III) in a set of 50 predictive genes we validated the amplification bias. In conclusion microarray data resulting from different pre-processing regarding RNA pre-amplification can not be compared within one analysis.

scholarly journals Screening and identification of muscle-specific candidate genes via mouse microarray data analysis

2021 ◽  
Author(s):  
Sayed Haidar Abbas Raza ◽  
Chengcheng Liang ◽  
Wang Guohua ◽  
Linsen Zan
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Muscle Tissue ◽  
Microarray Data ◽  
Muscle Development ◽  
The Other ◽  
Differentially Expressed ◽  
Regulatory Mechanisms ◽  
Potential Candidate ◽  
Differential Genes

Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 17 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 16 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 16 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.

scholarly journals Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis

2021 ◽  
Vol 8 ◽  
Author(s):  
Sayed Haidar Abbas Raza ◽  
Chengcheng Liang ◽  
Wang Guohua ◽  
Sameer D. Pant ◽  
Zuhair M. Mohammedsaleh ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Muscle Tissue ◽  
Microarray Data ◽  
Muscle Development ◽  
The Other ◽  
Differentially Expressed ◽  
Regulatory Mechanisms ◽  
Potential Candidate ◽  
Differential Genes

Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.

The Structure of Wiggins' Interpersonal Circumplex: Cross-Cultural Studies

1999 ◽  
Vol 15 (3) ◽  
pp. 196-205 ◽  
Author(s):  
Rosario Martínez-Arias ◽  
Fernando Silva ◽  
Ma Teresa Díaz-Hidalgo ◽  
Generós Ortet ◽  
Micaela Moro
Keyword(s):  
Cultural Studies ◽  
Cross Cultural ◽  
The Other ◽  
Spanish Version ◽  
Interpersonal Circumplex ◽  
Research Groups ◽  
Independent Research ◽  
Research Results ◽  
Cross Cultural Studies

Summary: This paper presents the results obtained in Spain with The Interpersonal Adjective Scales of J.S. Wiggins (1995) concerning the variables' structure. There are two Spanish versions of IAS, developed by two independent research groups who were not aware of each other's work. One of these versions was published as an assessment test in 1996. Results from the other group have remained unpublished to date. The set of results presented here compares three sources of data: the original American manual (from Wiggins and collaborators), the Spanish manual (already published), and the new IAS (our own research). Results can be considered satisfactory since, broadly speaking, the inner structure of the original instrument is well replicated in the Spanish version.

Fatty Acid Profile and In Vitro Anticancer Activity of Two Marine Sponge- Associated Bacteria

2020 ◽  
Vol 16 (9) ◽  
pp. 1273-1280
Author(s):  
Giuseppina Tommonaro ◽  
Ali M. El-Hagrassi ◽  
Walid Fayad ◽  
Carmine Iodice ◽  
Kamel H. Shaker ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Fatty Acids ◽  
Fatty Acid ◽  
Colorectal Carcinoma ◽  
Cell Line ◽  
Marine Sponge ◽  
Hct116 Cell ◽  
Associated Bacteria ◽  
Sponge Associated Bacteria ◽  
Human Colorectal Carcinoma

Background: Colorectal cancer represents one of the prominent causes of mortality worldwide in men and women. The objective of this study was to search for new potential anticancer compounds, both in prevention and treatment of colorectal cancer. The anticancer potential of marine bacterial extracts against Human colorectal carcinoma cell line (HCT116) was evaluated as well as the partial identification of bioactive metabolites. Methods: All bacterial extracts were tested for their cytotoxicity against HCT116 cell line by means of MTT assay. The highly cytotoxic dichloromethane extracts of marine sponge-associated bacteria Vibrio sp. and Bacillus sp. were analyzed by GC-MS. Results: Two fractions, Vib3 and Bac3, exhibited a very interesting cytotoxicity against human colorectal carcinoma (HCT116) cell line, with a percentage of cytotoxicity of 96.04 % and 29.48 %, respectively. Discussion: The GC-MS analysis revealed the presence of two major fatty acids, palmitic and oleic acids, in Vib3 fraction and fatty acid esters and phenolic compounds in Bac3 fraction. Conclusion: Based on previous literature, it may be hypothesized that the anticancer activity of bacterial extracts could be, at least partially, to the fatty acids fraction.

scholarly journals A Study on the Impact of R&D Intensity on Business Performance: Evidence from South Korea

2021 ◽  
Vol 7 (2) ◽  
pp. 135
Author(s):  
Hun Park ◽  
Jun-Hwan Park ◽  
Sujin Lee ◽  
Hyuk Hahn
Keyword(s):  
South Korea ◽  
Research And Development ◽  
Business Performance ◽  
Decision Makers ◽  
The Other ◽  
Research Groups ◽  
Innovative Firms ◽  
The Impact ◽  
Knowledge Services

The role of R&D (research and development) intensity on the effect of knowledge services on the business performance of firms has been discussed by using PLS-SEM and PLS-MGA methods. Research groups were divided into two groups, innovative and non-innovative. Respondents were classified into innovative firms if their R&D intensity was over 3% and vice versa. PLS-SEM and PLS-MGA results were compared for two groups and valuable insights were extracted. For innovative firms, knowledge services seemed to be verified and processed by the decision makers and utilized to achieve their business performance. On the other hand, a large number of non-innovative firms seemed to have a stronger tendency to utilize knowledge services directly for their business without sufficient verification by the decision makers.

scholarly journals Measurement of δ18O and δ2H of water and ethanol in wine by Off-Axis Integrated Cavity Output Spectroscopy and Isotope Ratio Mass Spectrometry

2021 ◽  
Author(s):  
Xing Wang ◽  
Henk G. Jansen ◽  
Haico Duin ◽  
Harro A. J. Meijer
Keyword(s):  
Mass Spectrometry ◽  
Isotope Ratio ◽  
Isotope Analysis ◽  
Isotope Ratio Mass Spectrometry ◽  
Growth Conditions ◽  
The Other ◽  
H Nmr ◽  
Cavity Output ◽  
Pre Treatment ◽  
Output Laser

AbstractThere are two officially approved methods for stable isotope analysis for wine authentication. One describes δ18O measurements of the wine water using Isotope Ratio Mass Spectrometry (IRMS), and the other one uses Deuterium-Nuclear Magnetic Resonance (2H-NMR) to measure the deuterium of the wine ethanol. Recently, off-axis integrated cavity output (laser) spectroscopy (OA-ICOS) has become an easier alternative to quantify wine water isotopes, thanks to the spectral contaminant identifier (SCI). We utilized an OA-ICOS analyser with SCI to measure the δ18O and δ2H of water in 27 wine samples without any pre-treatment. The OA-ICOS results reveal a wealth of information about the growth conditions of the wines, which shows the advantages to extend the official δ18O wine water method by δ2H that is obtained easily from OA-ICOS. We also performed high-temperature pyrolysis and chromium reduction combined with IRMS measurements to illustrate the “whole wine” isotope ratios. The δ18O results of OA-ICOS and IRMS show non-significant differences, but the δ2H results of both methods differ much more. As the δ2H difference between these two methods is mainly caused by ethanol, we investigated the possibility to deduce deuterium of wine ethanol from this difference. The results present large uncertainties and deviate from the obtained 2H-NMR results. The deviation is caused by the other constituents in the wine, and the uncertainty is due to the limited precision of the SCI-based correction, which need to improve to obtain the 2H values of ethanol as alternative for the 2H-NMR method.

scholarly journals EZH2 Expression and its Correlation with Clinicopathological Features in Patients with Colorectal Carcinoma

2016 ◽  
Vol 11 (1) ◽  
pp. 287-292
Author(s):  
Xiao-yang Liu ◽  
Hua Liu ◽  
Lin Gu ◽  
Hai-lun Zheng
Keyword(s):  
Colorectal Cancer ◽  
Colorectal Carcinoma ◽  
Disease Progression ◽  
Western Blotting ◽  
Progression Free Survival ◽  
Clinicopathological Features ◽  
Tumor Biomarker ◽  
Ezh2 Expression ◽  
Significant Difference ◽  
Colorectal Cancer Patients

AbstractObjectiveTo explore the correlation between the enhancer of zeste homolog 2 (EZH2) expression and clinicopathological features in colorectal cancer patients.MethodsA total of sixty-six patients with colorectal carcinoma were admitted to our general surgery department from January 2011 to December 2014. The EZH2 expression levels in the cancer tissues (CTs) from the 66 patients with colorectal cancer and those in distant normal colorectal tissues from 30 cases were examined through immunohistochemistry and western blotting assays. The relationship between the expression of EZH2 and the clinicopathological features and prognosis of the patients was analyzed.ResultsEZH2 in colorectal carcinoma tissues is granularly brown, predominantly expressed and diffused in the nuclei of tumor cells. Positive rates of EZH2 in intestinal CTs and in distant normal intestinal tissues are 62.12% (41/66) and 6.67% (2/30), respectively with significant difference (P < 0.05). Western blotting also confirmed its elevated expression in colorectal CTs. EZH2-positive expression in CTs was related to degree of differentiation, Duke staging, and tumor size (P < 0.05) but was unrelated to the patient’s gender, age or tumor site (P = 0.05). The 3-year progression-free survival (PFS) rates of the EZH2-positive group and the EZH2-negative group were 43.8% and 67.5%, respectively. The risk of disease progression of the EZH2-positive patients in the follow-up period was significantly higher than that of the EZH2-negative patients (HR = 2.49, 95% CI = 1.04–4.80, P < 0.05).ConclusionEZH2 is closely related to colorectal carcinoma development and disease progression, and thus could be used as a tumor biomarker that may indicate prognosis.

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