A theoretical study on cytosine tautomers in aqueous media by using continuum models

B3LYP/6-31 + + G** and MP2/6-31 + + G** calculations have been carried out to study six tautomers of the nucleic acid base cytosine in aqueous media. Solvent effects have been analyzed using the self-consistent reaction field theory with two continuum methods. Relative stabilities and optimized geometries have been calculated for the tautomers and compared with experimental data. The present results show the importance of electrostatic solvent effects in determining observable properties of the cytosine tautomers. The amino-oxo form (C1) is the most abundant tautomer in aqueous media while the other amino-oxo form (C4) is the most energetically favored when solvent effects are included. These results can be justified by the larger values of the dipole moments for both C1 and C4 tautomers. Theoretical and experimental results of the harmonic vibrational frequencies and rotational constants show good agreement. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Chromosome damage induced by 5-azacytidine under the influence of caffeine or cytosine arabinoside in CHO-K1 (wild-type) and XRS-5 (mutant) cell lines

5-azacytidine (5-azaC) treatment combined with cytosine arabinoside (ara-C) or caffeine were performed in vitro in Chinese hamster cells, CHO-K1 (wild-type) and xrs-5 (mutant) cell lines, in order to compare the cell response to the induction of chromosomal aberrations. Exponentially growing cells were treated with 5-azaC (4-16 uM) for 1 h, the cells were washed and incubated for 7 h, and 500 uM caffeine or 5 uM ara-C were added to the cultures for the last 2 h. In both cell lines, 5-azaC induced a significantly increase (P<0.01) in the frequencies of aberrations; in the combined treatments (5-azaC + Ara-C), a significant reduction (P<0.05) was observed for the aberrations which were randomly distributed. Caffeine had no influence at the same conditions. 5-azaC induced-DNA lesions were probably processed at S/G2 phase in a common pathway in both cell lines, but alternatively, 5-azaC may cause xrs-5 cells to revert to the wild-type.

Characterization and polymorphism screening of IGF-I and prolactin genes in Nelore heifers

Insulin growth factor I (IGF-I) and prolactin (PRL) are peptide hormones that exert complementary effects on reproductive traits by acting on folliculogenesis. In view of the lack of information about the IGF-I and PRL genes in Bos indicus, the objective of this study was to partially characterize the promoter regions of these genes and to screen animals of different ages at first pregnancy for the presence of polymorphisms in these regions. In addition, we determined whether polymorphisms influence the regulation of the two hormone genes, evaluating their association with sexual precocity.The animals were divided into three groups according to age at first pregnancy: 1) 100 heifers considered to be sexually precocious that became pregnant at 15-16 months of age, 2) 100 heifers that became pregnant during the normal breeding season at 24 months of age, and 3) 100 heifers that did not become pregnant until 24 months of age. For the IGF-I gene, PCR-RFLP-SnaBI analysis showed the presence of genotypes AB and BB at frequencies of 0.02 and 0.98, respectively. Sequencing of the IGF-I gene fragment revealed a single nitrogen base change from cytosine to thymine, corresponding to the restriction site of SnaBI. The polymorphisms identified in the 5'-flanking region of the IGF-I gene may serve as a basis for future studies of molecular markers in cattle. For the PRL gene, PCR-RFLP-HaeIII analysis showed the presence of only one migration pattern, a finding characterizing the region studied as monomorphic. The study of other regions in the IGF-I and PRL genes might provide molecular data that can be used in the future for the selection of sexually precocious animals.

Anti-clastogenic effect of beta-glucan extracted from barley towards chemically induced DNA damage in rodent cells

beta-Glucan (BG) was tested in vitro to determine its potential clastogenic and/or anti-clastogenic activity, and attempts were made to elucidate its possible mechanism of action by using combinations with an inhibitor of DNA polymerase. The study was carried out on cells deficient (CHO-k1) and cells proficient (HTC) in phases I and II enzymes, and the DNA damage was assessed by the chromosomal aberration assay. BG did not show a clastogenic effect, but was anti-clastogenic in both cell lines used, and at all concentrations tested (2.5, 5 and 10 mg/mL) in combination with damage inducing agents (methylmethane sulfonate in cell line CHO-k1, and methylmethane sulfonate or 2-aminoanthracene in cell line HTC). BG also showed a protective effect in the presence of a DNA polymerase beta inhibitor (cytosine arabinoside-3-phosphate, Ara-C), demonstrating that BG does not act through an anti-mutagenic mechanism of action involving DNA polymerase beta.

A single nucleotide deletion at the C1 inhibitor gene as the cause of hereditary angioedema: insights from a Brazilian family

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

LHX6 is a sensitive methylation marker in head and neck carcinomas

Head and neck cancer remains a morbid and often fatal disease and at the present time few effective molecular markers have been identified. The purpose of the present work was to identify new molecular markers for head and neck squamous cell carcinoma (HNSCC). We applied methylation-sensitive arbitrarily primed PCR (MS/APPCR) to isolate sequences differentially methylated in HNSCC. The most frequently hypermethylated fragment we found maps close to a cytosine guanine dinucleotide (CpG) island on chromosome 9q33.2, and hypermethylation of this CpG island was associated with transcriptional silencing of an alternative transcript of the LHX6 gene. Using combined bisulfite restriction analysis (COBRA), hypermethylation of this fragment was detected in 13 of 14 (92.8%) HNSCC cell lines studied and 21 of 32 (65.6%) primary tumors, whereas little or no methylation was seen in 10 normal oral mucosa samples. We extended this investigation to other cancer cell lines and methylation was found in those derived from colon, breast, leukemia and lung, and methylation was also found in 12/14 primary colon tumors. These findings suggest that differentially methylated (DIME)-6 hypermethylation is a good cancer marker in HNSCC as well as in other kinds of neoplasias and confirm the importance of searching for markers of epigenetic dysregulation in cancer.

Adsorptive potentiometric stripping analysis of nucleic acids at mercury electrodes

The application of adsorptive stripping potentiometry to the reductive detection of nucleic acids at mercury electrodes is reported. Compared to analogous voltammetric stripping modes, constant current potentiometric stripping analysis (PSA) effectively addresses the hydrogen discharge background problem, and hence greatly improves the characteristics of the superimposed cytosine/adenine (CA) reduction peak. Compared to earlier schemes for trace measurements of nucleic acids at mercury or carbon electrodes that rely on anodic signals arising from the guanine residue, convenient quantitation can now be carried out in connection with the cytosine and adenine residues. Variables influencing the adsorptive PSA response are explored and optimized. With five minute accumulation, the detection limits for tRNA, ssDNA and dsDNA are 30 mu g l(-1), 60 mu g l(-1) and 2 mg l(-1), respectively. Such different values reflect the strong dependence of the PSA CA signal upon the nucleic-acid structure. This allows the quantitation of ssDNA or tRNA in the presence of dsDNA, and offers new possibilities for electrochemical studies of DNA structure and interactions.

Fractionation and identification of the nucleic acid-related substances secreted by Streptomyces aureofaciens

S. aureofaciens growth in a chemically defined medium was associated with the active secretion of nucleic acid-related substances in the medium. High secretion depended on low availability of phosphate, and fractionation showed 7 anionic substances were secreted as major components. When compared to 76 known purine and pyrimidine derivatives only erotic acid was identified. Cationic components are among the minor concentration components secreted which have been identified as cytosine, inosine, cytidine, adenine, guanine and, probably, 1-methyl-adenine.

The effect of CpG-ODN on antigen presenting cells of the foal

Background: Cytosine-phosphate-guanosine oligodeoxynucleotide (CpG-ODN) has been used successfully to induce immune responses against viral and intracellular organisms in mammals. The main objective of this study was to test the effect of CpG-ODN on antigen presenting cells of young foals. Methods: Peripheral blood monocytes of foals (n = 7) were isolated in the first day of life and monthly thereafter up to 3 months of life. Adult horse (n = 7) monocytes were isolated and tested once for comparison. Isolated monocytes were stimulated with IL-4 and GM-CSF (to obtain dendritic cells, DC) or not stimulated (to obtain macrophages). Macrophages and DCs were stimulated for 14-16 hours with either CpG-ODN, LPS or not stimulated. The stimulated and non-stimulated cells were tested for cell surface markers (CD86 and MHC class II) using flow cytometry, mRNA expression of cytokines (IL-12, IFNα, IL-10) and TLR-9 using real time quantitative RT-PCR, and for the activation of the transcription factor NF-κB p65 using a chemiluminescence assay. Results: The median fluorescence of the MHC class II molecule in non-stimulated foal macrophages and DCs at birth were 12.5 times and 11.2 times inferior, respectively, than adult horse cells (p = 0.009). That difference subsided at 3 months of life (p = 0.3). The expression of the CD86 co-stimulatory molecule was comparable in adult horse and foal macrophages and DCs, independent of treatment. CpG-ODN stimulation induced IL-12p40 (53 times) and IFNα (23 times) mRNA expression in CpG-ODN-treated adult horse DCs (p = 0.078), but not macrophages, in comparison to non-stimulated cells. In contrast, foal APCs did not respond to CpG-ODN stimulation with increased cytokine mRNA expression up to 3 months of age. TLR-9 mRNA expression and NF-kB activation (NF-kB p65) in foal DCs and macrophages were comparable (p > 0.05) to adult horse cells. Conclusion: CpG-ODN treatment did not induce specific maturation and cytokine expression in foal macrophages and DCs. Nevertheless, adult horse DCs, but not macrophages, increased their expression of IL-12 and IFNα cytokines upon CpG-ODN stimulation. Importantly, foals presented an age-dependent limitation in the expression of MHC class II in macrophages and DCs, independent of treatment. © 2007 Flaminio et al; licensee BioMed Central Ltd.

The electrochemical reduction of the purines guanine and adenine at platinum electrodes in several room temperature ionic liquids

The reduction of guanine was studied by microelectrode voltammetry in the room temperature ionic liquids (RTILs) N-hexyltriethylammonium bis (trifluoromethanesulfonyl) imide [N6,2,2,2][N(Tf)2], 1-butyl-3-methylimidazolium hexafluorosphosphate [C4mim][PF6], N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide [C4mpyrr][N(Tf)2], 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C4mim][N(Tf)2], N-butyl-N-methyl-pyrrolidinium dicyanamide [C4mpyrr][N(NC)2] and tris(P-hexyl)-tetradecylphosphonium trifluorotris(pentafluoroethyl)phosphate [P14,6,6,6][FAP] on a platinum microelectrode. In [N6,2,2,2][NTf2] and [P14,6,6,6][FAP], but not in the other ionic liquids studied, guanine reduction involves a one-electron, diffusion-controlled process at very negative potential to produce an unstable radical anion, which is thought to undergo a dimerization reaction, probably after proton abstraction from the cation of the ionic liquid. The rate of this subsequent reaction depends on the nature of the ionic liquid, and it is faster in the ionic liquid [P14,6,6,6][FAP], in which the formation of the resulting dimer can be voltammetrically monitored at less negative potentials than required for the reduction of the parent molecule. Adenine showed similar behaviour to guanine but the pyrimidines thymine and cytosine did not; thymine was not reduced at potentials less negative than required for solvent (RTIL) decomposition while only a poorly defined wave was seen for cytosine. The possibility for proton abstraction from the cation in [N6,2,2,2][NTf2] and [P14,6,6,6][FAP] is noted and this is thought to aid the electrochemical dimerization process. The resulting rapid reaction is thought to shift the reduction potentials for guanine and adenine to lower values than observed in RTILs where the scope for proton abstraction is not present. Such shifts are characteristic of so-called EC processes where reversible electron transfer is followed by a chemical reaction. © 2009 Elsevier B.V.

Epigenetic mechanisms in penile carcinoma

Penile carcinoma (PeCa) represents an important public health problem in poor and developing countries. Despite its unpredictable behavior and aggressive treatment, there have only been a few reports regarding its molecular data, especially epigenetic mechanisms. The functional diversity in different cell types is acquired by chromatin modifications, which are established by epigenetic regulatory mechanisms involving DNA methylation, histone acetylation, and miRNAs. Recent evidence indicates that the dysregulation in these processes can result in the development of several diseases, including cancer. Epigenetic alterations, such as the methylation of CpGs islands, may reveal candidates for the development of specific markers for cancer detection, diagnosis and prognosis. There are a few reports on the epigenetic alterations in PeCa, and most of these studies have only focused on alterations in specific genes in a limited number of cases. This review aims to provide an overview of the current knowledge of the epigenetic alterations in PeCa and the promising results in this field. The identification of epigenetically altered genes in PeCa is an important step in understanding the mechanisms involved in this unexplored disease. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Search for methylation-sensitive amplification polymorphisms in mutant figs

Fig (Ficus carica) breeding programs that use conventional approaches to develop new cultivars are rare, owing to limited genetic variability and the difficulty in obtaining plants via gamete fusion. Cytosine methylation in plants leads to gene repression, thereby affecting transcription without changing the DNA sequence. Previous studies using random amplification of polymorphic DNA and amplified fragment length polymorphism markers revealed no polymorphisms among select fig mutants that originated from gamma-irradiated buds. Therefore, we conducted methylation-sensitive amplified polymorphism analysis to verify the existence of variability due to epigenetic DNA methylation among these mutant selections compared to the main cultivar 'Roxo-de-Valinhos'. Samples of genomic DNA were double-digested with either HpaII (methylation sensitive) or MspI (methylation insensitive) and with EcoRI. Fourteen primer combinations were tested, and on an average, non-methylated CCGG, symmetrically methylated CmCGG, and hemimethylated hmCCGG sites accounted for 87.9, 10.1, and 2.0%, respectively. MSAP analysis was effective in detecting differentially methylated sites in the genomic DNA of fig mutants, and methylation may be responsible for the phenotypic variation between treatments. Further analyses such as polymorphic DNA sequencing are necessary to validate these differences, standardize the regions of methylation, and analyze reads using bioinformatic tools. © FUNPEC-RP.

Análise prospectiva do padrão de metilação nos genes associados a doenças cardíacas SCN5A e MTR para aplicação na genética forense

Pós-graduação em Biotecnologia - IQ

Investigação da condução elétrica em fitas duplas de dna imobilizadas em eletrodos de ouro por medidas eletroquímicas

Pós-graduação em Química - IQ

Análise de metilação do gene FOXE1 em carcinoma de células escamosas em cães: padronização metodológica

It is believed that epigenetic mechanisms such as DNA methylation are important for the tumorigenesis and maintenance of the altered state of tumor cells. DNA methylation occurs by the addition of a methyl group to carbon 5 of cytosine, catalyzed by the enzyme DNA methyl-transferase, which can change the expression of a gene, including the tumor suppressor genes. In human squamous cell carcinoma, several features have shown the etiological role of genes in tumor development. Among them, FOXE1 gene (forkhead box E1 - thyroid transcription factor) is presented with an important role in susceptibility to disease. Similarly the FOXE1 methylation pattern could alter the expression of this gene in dogs and predisposed to tumor on. Therefore, this study aims to investigate in dogs, the validity of the strategy employed in humans to analyze the FOXE1 methylation status. DNA extraction from fresh frozen tumoral samples was performed by Wizard Genomic® DNA Purification Kit. The methylation status was determined by MSP-PCR (methylation-specific polymerase chain reaction), using 2.0 ng of DNA treated with sodium bisulphate. One hundred micrograms of bisulphite-modified DNA was amplified using primers specific for either methylated or unmethylated DNA (primers sequences are available at http://pathology2.jhu.edu/pancreas/primer.pdf). The analysis of fragments was loaded on to 7% polyacrylamide gels and silver nitrate staining. In this stage of technical approach, 60% were FOXE1 hypermethylated. In conclusion, it was observed that the standard technique for assessing the methylation pattern of gene FOXE1 in humans can be used for the same evaluation in dogs. The correlation of these molecular data with clinical and histopathological parameters may have diagnostic and prognostic value and still be used as a tumor marker for therapeutic decision and surgical approach