Identification of Novel Reference Genes Based on MeSH Categories

Cataloged from PDF version of article.Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds. © 2014 Ersahin et al

Identification of genes induced by BRCA1 in breast cancer cells

Cataloged from PDF version of article.Inherited mutations of the BRCA1 gene predispose to breast, ovarian, and other cancers. The role of the BRCA1 gene in the maintenance of chromosomal integrity is linked to a number of biological properties of its protein product, including transcriptional regulation. In the present study, we have used suppression subtractive hybridisation (SSH) to identify genes induced by BRCA1 by comparing control MCF7 breast carcinoma cells (driver) with MCF7 cells ectopically expressing BRCA1 (tester) and generated a forward subtracted cDNA library. We screened 500 putative positive clones from this library. Two hundred and ten of these clones were positive by differential screening with forward and reverse subtracted probes and the 65 cDNA clones which showed more than fivefold increase were selected for sequencing analysis. We clustered 46 different genes that share high homology with sequences in the GenBank/EMBL databases. Among these, 30 were genes whose function had been previously identified while the remaining 16 clones were genes with,unknown functions. Of particular interest, BRCA1 gene induces the expression of genes encoding DNA repair proteins RAD21 and MSH2, ERBB2/HER2 interacting protein ERBIN, meningioma-associated protein MAC30, and a candidate ovarian tumour-suppressor OVCA1. Northern and Western blot analyses confirmed that the expression of these five genes are up-regulated following BRCA1 overexpression in MCF7 and UBR60-bcl2 cells. This is the first study reporting a set of BRCA1-induced genes in breast carcinoma cells by the SSH technique. We suggest that some known genes identified in this study may provide new insights into the tumour-suppressor function of BRCA1. (C) 2002 Elsevier Science (USA). All rights reserved

Attributed relational graphs for cell nucleus segmentation in fluorescence microscopy Images

Cataloged from PDF version of article.More rapid and accurate high-throughput screening in molecular cellular biology research has become possible with the development of automated microscopy imaging, for which cell nucleus segmentation commonly constitutes the core step. Although several promising methods exist for segmenting the nuclei of monolayer isolated and less-confluent cells, it still remains an open problem to segment the nuclei of more-confluent cells, which tend to grow in overlayers. To address this problem, we propose a new model-based nucleus segmentation algorithm. This algorithm models how a human locates a nucleus by identifying the nucleus boundaries and piecing them together. In this algorithm, we define four types of primitives to represent nucleus boundaries at different orientations and construct an attributed relational graph on the primitives to represent their spatial relations. Then, we reduce the nucleus identification problem to finding predefined structural patterns in the constructed graph and also use the primitives in region growing to delineate the nucleus borders. Working with fluorescence microscopy images, our experiments demonstrate that the proposed algorithm identifies nuclei better than previous nucleus segmentation algorithms

Synthesis of Novel 6-(4-Substituted piperazine-1-yl)-9(b-D-ribofuranosyl) purine Derivatives, Which Lead to Senescence-Induced Cell Death in liver Cancer Cells

Cataloged from PDF version of article.Novel purine ribonucleoside analogues (9-13) containing a 4-substituted piperazine in the substituent at N-6 were synthesized and evaluated for their cytotoxicity on Huh7, HepG2, FOCUS, Mahlavu liver, MCF7 breast, and HCT116 colon carcinoma cell lines. The purine nucleoside analogues were analyzed initially by an anticancer drug-screening method based on a sulforhodamine B assay. Two nucleoside derivatives with promising cytotoxic activities (11 and 12) were further analyzed on the hepatoma cells. The N-6-(4-Trifluoromethylphenyl)piperazine analogue 11 displayed the best antitumor activity, with IC50 values between 5.2 and 9.2 mu M. Similar to previously described nucleoside analogues, compound 11 also interferes with cellular ATP reserves, possibly through influencing cellular kinase activities. Furthermore, the novel nucleoside analogue 11 was shown to induce senescence-associated cell death, as demonstrated by the SA beta-gal assay. The senescence-dependent cytotoxic effect of 11 was also confirmed through phosphorylation of the Rb protein by p15(INK4b) overexpression in the presence of this compound

Risk Factors for Trabeculotomy Failure in Primary Congenital Glaucoma

Précis: This study demonstrates that a baseline corneal diameter >12.25, initial age [removed]12.25 mm did by 4.2 times, younger age than 4 months did by 2.5 times, bilaterality did by 1.5 times. Conclusions: A higher baseline IOP, younger age, larger corneal diameter, and bilaterality were identified as risk factors for trabeculotomy failure in congenital glaucoma. The presence of one or more of these should be considered in the decision-making process when considering surgical options to manage glaucoma in these patients. © 2022 Wolters Kluwer Health, Inc. All rights reserved

Bi-k-bi clustering: Mining large scale gene expression data using two-level biclustering

Due to the increase in gene expression data sets in recent years, various data mining techniques have been proposed for mining gene expression profiles. However, most of these methods target single gene expression data sets and cannot handle all the available gene expression data in public databases in reasonable amount of time and space. In this paper, we propose a novel framework, bi-k-bi clustering, for finding association rules of gene pairs that can easily operate on large scale and multiple heterogeneous data sets. We applied our proposed framework on the available NCBI GEO Homo sapiens data sets. Our results show consistency and relatedness with the available literature and also provides novel associations. Copyright © 2010 Inderscience Enterprises Ltd

Protection of specific maternal messenger RNAs by the P body protein CGH-1 (Dhh1/RCK) during Caenorhabditis elegans oogenesis

During oogenesis, numerous messenger RNAs (mRNAs) are maintained in a translationally silenced state. In eukaryotic cells, various translation inhibition and mRNA degradation mechanisms congregate in cytoplasmic processing bodies (P bodies). The P body protein Dhh1 inhibits translation and promotes decapping-mediated mRNA decay together with Pat1 in yeast, and has been implicated in mRNA storage in metazoan oocytes. Here, we have investigated in Caenorhabditis elegans whether Dhh1 and Pat1 generally function together, and how they influence mRNA sequestration during oogenesis. We show that in somatic tissues, the Dhh1 orthologue (CGH-1) forms Pat1 (patr-1)-dependent P bodies that are involved in mRNA decapping. In contrast, during oogenesis, CGH-1 forms patr-1–independent mRNA storage bodies. CGH-1 then associates with translational regulators and a specific set of maternal mRNAs, and prevents those mRNAs from being degraded. Our results identify somatic and germ cell CGH-1 functions that are distinguished by the involvement of PATR-1, and reveal that during oogenesis, numerous translationally regulated mRNAs are specifically protected by a CGH-1–dependent mechanism

Nanowires of Lead-Free Solder Alloy SnCuAg

Ternary Sn88Ag5Cu7, Sn93Ag4Cu3, Sn58Ag18Cu24, Sn78Ag16Cu6, Sn90Ag4Cu6, Sn87Ag4Cu9 alloy nanowires were produced at various values of deposition potential by dc electrodeposition on highly ordered porous anodic alumina oxide (AAO) templates. During the deposition process some parameters, such as ion content, deposition time, pH, and temperature of the solution, were kept constant. The diameter and length of regular Sn93Ag4Cu3 nanowires electrodeposited at −1 V were determined by scanning electron microscopy (SEM) to be approximately 200–250 nm and 7-8 μm, respectively. Differential scanning calorimetry (DSC) results indicate that the melting onset temperature of Sn93Ag4Cu3 nanowires is about 204°C

Systematic evaluation of psychometric characteristics of the michigan alcoholism screening test 13-Item short (SMAST) and 10-Item brief (BMAST) versions

The psychometric properties of the Michigan Alcohol Screening Test (MAST) 13-item short (SMAST) and 10-item brief (BMAST) versions were aggregated and synthesized across 40 and 21 studies, respectively. Results for reliability, validity, and nonclinical descriptive statistics were reported separately for the SMAST and BMAST, and implications for counseling practice and research were discussed.WOS:000455237000002Scopus - Affiliation ID: 60105072Social Sciences Citation IndexQ3 - Q4ArticleUluslararası işbirliği ile yapılan - EVETOcak2019YÖK - 2018-1

Identification of genes induced by BRCA1 in breast cancer cells

Inherited mutations of the BRCA1 gene predispose to breast, ovarian, and other cancers. The role of the BRCA1 gene in the maintenance of chromosomal integrity is linked to a number of biological properties of its protein product, including transcriptional regulation. In the present study, we have used suppression subtractive hybridisation (SSH) to identify genes induced by BRCA1 by comparing control MCF7 breast carcinoma cells (driver) with MCF7 cells ectopically expressing BRCA1 (tester) and generated a forward subtracted cDNA library. We screened 500 putative positive clones from this library. Two hundred and ten of these clones were positive by differential screening with forward and reverse subtracted probes and the 65 cDNA clones which showed more than fivefold increase were selected for sequencing analysis. We clustered 46 different genes that share high homology with sequences in the GenBank/EMBL databases. Among these, 30 were genes whose function had been previously identified while the remaining 16 clones were genes with unknown functions. Of particular interest, BRCA1 gene induces the expression of genes encoding DNA repair proteins RAD21 and MSH2, ERBB2/HER2 interacting protein ERBIN, meningioma-associated protein MAC30, and a candidate ovarian tumour-suppressor OVCA1. Northern and Western blot analyses confirmed that the expression of these five genes are up-regulated following BRCA1 overexpression in MCF7 and UBR60-bcl2 cells. This is the first study reporting a set of BRCA1-induced genes in breast carcinoma cells by the SSH technique. We suggest that some known genes identified in this study may provide new insights into the tumour-suppressor function of BRCA1. © 2002 Elsevier Science (USA). All rights reserved