M3i

@article{,

title = {Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal liver cells},

author = { A. Costa and J. P. Pais de Barros and G. Keith and W. Baranowski and J. Desgres},

year  = {2004},

date = {2004-01-01},

journal = {J Chromatogr B Analyt Technol Biomed Life Sci},

volume = {801},

number = {2},

pages = {237-47},

abstract = {Three queuosine derivatives (Q-derivatives) have been found at position 34 of four mammalian so-called Q-tRNAs: queuosine (Q) in tRNA(Asn) and tRNA(His), mannosyl-queuosine (manQ) in tRNA(Asp), and galactosyl-queuosine (galQ) in tRNA(Tyr). An analytical procedure based on the combined means of purified tRNA isolation from liver cells and ribonucleoside analysis by reverse-phase high performance liquid chromatography coupled with real-time UV-spectrometry (RPLC-UV) was developed for the quantitative analysis of the three Q-derivatives present in total tRNA from liver tissues and liver cell cultures. Using this analytical procedure, the rates of Q-tRNA modification were studied in total tRNAs from various mammalian hepatic cells. Our results show that the four Q-tRNAs are fully modified in liver tissues from adult mammals, regardless of the mammal species. However, a lack in the Q-modification level was observed in Q-tRNAs from newborn rat liver, as well in Q-tRNAs from normal rat liver cell cultures growing in a low queuine content medium, and from a rat hepatoma cell line. It is noteworthy that in all cases of Q-tRNA hypomodification, our analytical procedure showed that tRNA(Asp) is always the least affected by the hypomodification. The biological significance of this phenomenon is discussed.},

note = {1570-0232 

Journal Article},

keywords = {*Chromatography, &, Acyl/chemistry, Amino, Animals, Asn/chemistry, Cells, Chickens, Cultured, derivatives/*analysis, Experimental, Gov't, Hepatocytes/chemistry, high, KEITH, liquid, Liver, Liver/*chemistry, Neoplasms, Non-U.S., Nucleoside, Pressure, purification, Q/*analogs, Rats, RNA, Support, Transfer, Transfer/*chemistry/isolation, tumor},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Microdissection, mRNA amplification and microarray: a study of pleural mesothelial and malignant mesothelioma cells},

author = { S. Mohr and M.C. Bottin and B. Lannes and A. Neuville and J.P. Bellocq and G. Keith and B.H. Rihn},

year  = {2004},

date = {2004-01-01},

journal = {Biochimie},

volume = {86},

number = {1},

pages = {13-9},

abstract = {The studies of molecular alterations in tumor cells with microarrays are often hampered by inherent tissue heterogeneity. The emergence of Laser Capture Microdissection (LCM) allowed us to overcome this challenge since it gives selective access to cancer cells that are isolated from their native tissue environment. In this report, we microdissected mesothelial cells and malignant mesothelioma cells of ex vivo resected specimens using LCM. Amplified RNA from mesothelial and mesothelioma microdissected cells allowed us to measure global gene expression with 10 K-microarrays in four independent experiments. We screened 9850 annotated human genes, 1275 of which have satisfied our data analysis requirements. They included 302 overexpressed genes and 160 downregulated genes in mesothelioma microdissected cells as compared to mesothelial microdissected cells. Among them, the expression levels of eight genes, namely BF, FTL, IGFBP7, RARRES1, RARRES2, RBP1, SAT, and TXN according to HUGO nomenclature, were increased, whereas six: ALOX5AP, CLNS1A, EIF4A2, ELK3, REQ and SYPL, were found to be underexpressed in mesothelioma microdissected cells. The ferritin light polypeptide (FTL) gene overexpression was confirmed by real time quantitative PCR. Our approach allowed a comprehensive in situ examination of mesothelioma and provided an accurate way to find new marker genes that may be useful for diagnosis and treatment of malignant pleural mesothelioma.},

note = {0300-9084 

Journal Article},

keywords = {Analysis, Array, Chain, Epithelium/*metabolism, Expression, Female, Gene, Genetic, Human, KEITH, Lasers, Male, Markers, Mesothelioma/*genetics/metabolism, messenger, Microdissection, Neoplasms/*genetics/metabolism, Neoplastic/*genetics, Oligonucleotide, Pleura/*cytology/*metabolism, Pleural, Polymerase, Profiling, Reaction, Regulation, Reverse, RNA, Sequence, Transcriptase},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray},

author = { S. Mohr and G. Keith and F. Galateau-Salle and P. Icard and B. H. Rihn},

year  = {2004},

date = {2004-01-01},

journal = {Biochim Biophys Acta-Mol Basis Dis},

volume = {1688},

number = {1},

pages = {43-60},

abstract = {Malignant pleural mesothelioma (MPM) is an aggressive serosal tumor, strongly associated with former exposure to asbestos fibers and for which there is currently no effective treatment available. In human, MPM is characterized by a high local invasiveness, poor prognosis and therapeutic outcomes. In order to assess molecular changes that specify this phenotype, we performed a global gene expression profiling of human MPM. Using a 10,000-element microarray, we analyzed mRNA relative gene expression levels by comparing a mesothelioma cell line to either a pleural cell line or tumor specimens. To analyze these gene expression data, we used various bioinformatics softwares. Hierarchical clustering methods were used to group genes and samples with similar expression in an unsupervised mode. Genes of known function were further sorted by enzyme, function and pathway clusters using a supervised software (IncyteGenomics). Taken together, these data defined a molecular fingerprint of human MPM with more than 700 up- or down-regulated genes related to several traits of the malignant phenotype, specially associated with MPM invasiveness, protection and resistance to anticancer defenses. This portrait is meaningful in disease classification and management, and relevant in finding new specific markers of MPM. These molecular markers should improve the accuracy of mesothelioma diagnosis, prognosis and therapy.},

note = {0006-3002 

Journal Article},

keywords = {Analysis, Array, Biological/genetics, Cell, Expression, Family, Gene, Human, KEITH, Line, Markers, Mesothelioma/etiology/genetics/*pathology, Messenger/analysis, Multigene, Neoplasms/etiology/genetics/*pathology, Neoplastic, Pleural, Profiling, Protein, Regulation, RNA, tumor},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The meaning of the methylation of genomic DNA in the regulation of gene expression levels},

author = { A. Popiela and G. Keith and A. Borzecki and G. Popiela and M. Manowiec and M. Gabrys},

year  = {2004},

date = {2004-01-01},

journal = {Eur J Gynaecol Oncol},

volume = {25},

number = {2},

pages = {145-9},

abstract = {INTRODUCTION: Methylation of genomic DNA is one of the major mechanisms that deactivates genes and regulates their tissue-specific transcription levels. Its patterns are based on clonal inheritance that occurs in the early stages of embryogenesis. All changes in the DNA methylation levels occurring especially in the promoter region of the genes, which involve hypo- as well as hyper-methylation, lead to cell differentiation and growth disorders. Therefore it can become an impulse that initiates different pathological processes including carcinogenesis. MATERIAL AND METHODS: The purpose of this review was to present the recent knowledge concerning methylation of genomic DNA based on recent references and authors' experience. RESULTS AND CONCLUSION: Genome stability disorders could be caused either by mutations, which damage the structure of the genes and have not been formerly removed, or as the consequence of an epigenetic mechanism. Methylation plays a decisive role in the activity of many genes and could be a natural weapon of an organism against the expression of foreign genetic material that degrades the original genome structure.},

note = {0392-2936 

Journal Article 

Review 

Review, Tutorial},

keywords = {*DNA, *Gene, Expression, Human, KEITH, Methylation, Neoplasms/*genetics, Neoplastic, Regulation},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Wheat (Triticum vulgare) chloroplast nuclease ChSI exhibits 5' flap structure-specific endonuclease activity},

author = { A. Przykorska and K. Solecka and K. Olszak and G. Keith and B. Nawrot and E. Kuligowska},

year  = {2004},

date = {2004-01-01},

journal = {Biochemistry},

volume = {43},

number = {35},

pages = {11283-94},

abstract = {The structure-specific ChSI nuclease from wheat (Triticum vulgare) chloroplast stroma has been previously purified and characterized in our laboratory. It is a single-strand-specific DNA and RNA endonuclease. Although the enzyme has been initially characterized and used as a structural probe, its biological function is still unknown. Localization of the ChSI enzyme inside chloroplasts, possessing their own DNA that is generally highly exposed to UV light and often affected by numerous redox reactions and electron transfer processes, might suggest, however, that this enzyme could be involved in DNA repair. The repair of some types of DNA damage has been shown to proceed through branched DNA intermediates which are substrates for the structure-specific DNA endonucleases. Thus we tested the substrate specificity of ChSI endonuclease toward various branched DNAs containing 5' flap, 5' pseudoflap, 3' pseudoflap, or single-stranded bulged structural motifs. It appears that ChSI has a high 5' flap structure-specific endonucleolytic activity. The catalytic efficiency (k(cat)/K(M)) of the enzyme is significantly higher for the 5' flap substrate than for single-stranded DNA. The ChSI 5' flap activity was inhibited by high concentrations of Mg(2+), Mn(2+), Zn(2+), or Ca(2+). However, low concentrations of divalent cations could restore the loss of ChSI activity as a consequence of EDTA pretreatment. In contrast to other known 5' flap nucleases, the chloroplast enzyme ChSI does not possess any 5'-->3' exonuclease activity on double-stranded DNA. Therefore, we conclude that ChSI is a 5' flap structure-specific endonuclease with nucleolytic activity toward single-stranded substrates.},

note = {0006-2960 

Journal Article},

keywords = {&, Acid, Catalysis, Chloroplasts/*enzymology, Conformation, Desorption-Ionization, DNA, Endonucleases/*chemistry/isolation, Exonucleases/chemistry/metabolism, Flap, Gov't, Hydrolysis, KEITH, Kinetics, Laser, Mass, Matrix-Assisted, Non-U.S., Nucleic, Oligonucleotides/chemical, Plant/chemistry/metabolism, purification/*metabolism, Relationship, Single-Stranded/chemistry/metabolism, Specificity, Spectrometry, Structure-Activity, Substrate, Support, synthesis/metabolism, Thermodynamics, Triticum/*enzymology},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A simple epigenetic method for the diagnosis and classification of brain tumors},

author = { R. Zukiel and S. Nowak and A. M. Barciszewska and I. Gawronska and G. Keith and M. Z. Barciszewska},

year  = {2004},

date = {2004-01-01},

journal = {Mol Cancer Res},

volume = {2},

number = {3},

pages = {196-202},

abstract = {The new, simple, and reliable method for the diagnosis of brain tumors is described. It is based on a TLC quantitative determination of 5-methylcytosine (m(5)C) in relation to its damage products of DNA from tumor tissue. Currently, there is evidence that oxidative stress through reactive oxygen species (ROS) plays an important role in the etiology and progression of several human diseases. Oxidative damage of DNA, lipids, and proteins is deleterious for the cell. m(5)C, along with other basic components of DNA, is the target for ROS, which results in the appearance of new modified nucleic acid bases. If so, m(5)C residue constitutes a mutational hotspot position, whether it occurs within a nucleotide sequence of a structural gene or a regulatory region. Here, we show the results of the analysis of 82 DNA samples taken from brain tumor tissues. DNA was isolated and hydrolyzed into nucleotides, which, after labeling with [gamma-(32)P]ATP, were separated on TLC. Chromatograms were evaluated using PhosphorImager and the amounts of 5-methyldeoxycytosine (m(5)dC) were calculated as a ratio (R) of m(5)dC to m(5)dC + deoxycytosine + deoxythymidine spot intensities. The R value could not only be a good diagnostic marker for brain tumors but also a factor differentiating low-grade and high-grade gliomas. Therefore, DNA methylation pattern might be a useful tool to give a primary diagnosis of a brain tumor or as a marker for the early detection of the relapse of the disease. This method has several advantages over those existing nowadays.},

note = {1541-7786 

Journal Article},

keywords = {*DNA, *Epigenesis, 5-Methylcytosine/*analysis, Adult, Aged, and, Brain, Chromatography, DNA, Female, Genetic, Gov't, Human, KEITH, Layer, Male, Methylation, Middle, Neoplasm/*chemistry/*metabolism, Neoplasms/*classification/*diagnosis/genetics/pathology, Non-U.S., Oxidative, oxygen, Reactive, Sensitivity, Species/metabolism, Specificity, Stress, Support, Thin},

pubstate = {published},

tppubtype = {article}

}