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Zemliakova VV Strel'nikov VV Zborovskaia IB Balukova OV Maĭorova OA Vasil'ev EV Zaletaev DV Nemtsova MV 《Molekuliarnaia biologiia》2004,38(6):966-972
Multiplex methylation-sensitive PCR and methylation-specific PCR were employed in studying the methylation of CpG islands in the p16/CDKN2A and p14/ARF promoter and the first exon regions in non-small cell lung cancer (54 samples) and acute B-cell lymphoblastic leukemia (61 samples). Differences in methylation were detected between types of neoplasia as well as between CpG islands studied within the same types of tumors. High level of the p16/CDKN2A first exon CpC island methylation was revealed in non-small cell lung cancer (68%) and in acute B-cell lymphoblastic leukemia (55%) and the CpG island of p14/ARF first exon was nonmethylated in these types of tumors. The methylation of CpG-rich fragments of genes p16/CDKN2A and p14/ARF promoters was analysed. As was found out, CpG islands located in 5' areas of one and the same gene can differ in methylation frequencies. The comparison of sensitivity between methylation-specific PCR and methylation-sensitive PCR used in the methylations studies was carried out. 相似文献
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Aruna Kasoju M Lakshmi Narasu Charuvaka Muvva Bathula VV SubbaRao 《Bioinformation》2012,8(14):684-686
Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse
consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a
protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server.
The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the
backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the
3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer
molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of
inhibition of aflatoxin. 相似文献
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Kuznetsova EB Kekeeva TV Larin SS Zemliakova VV Babenko OV Nemtsova MV Zaletaev DV Strel'nikov VV 《Molekuliarnaia biologiia》2007,41(4):624-633
We have developed a modification of methylation sensitive arbitrarily primed PCR, one of the methods of differentially methylated CpG islands in cancer cells genomes screening. Seven genes undergoing abnormal epigenetic regulation in breast cancer, SEMA6B, BIN1, VCPIP1, LAMC3, KCNH2, CACNG4 and PSMF1, have been identified by this method. Methylation and loss of expression frequencies were evaluated for each of the identified genes on 100 paired (cancer/morphologically intact control) breast tissue samples. Significant frequencies of abnormal methylation were detected for SEMA6B, BIN1, and LAMC3 (38%, 18%, and 8% correspondingly). Methylation of the above genes was not characteristic for morphologically intact breast tissues. Downregulation of SEMA6B, BIN1, VCPIP1, LAMC3, KCNH2, CACNG4 and PSMF1 in breast cancer was as frequent as 44-94% by real-time PCR expression assay. The most pronounced functional alterations were demonstrated for SEMA6B and LAMC3 genes, which allows recommending their inclusion into the panels of carcinogenesis diagnostic panels. Fine methylation mapping was performed for the genes most frequently methylated in breast cancer (SEMA6B, BIN1, LAMC3), providing a fundamental basis for the development of effective methylation tests for these genes. 相似文献
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Visualization of molecular structures aids in the understanding of structural and functional roles of biological macromolecules.
Macromolecular transport between the cell nucleus and cytoplasm is facilitated by the nuclear pore complex (NPC). The ring
structure of the NPC is large and contains several distinct proteins (nucleoporins) which function as a selective gate for the passage
of certain molecules into and out of the nucleus. In this note we demonstrate the utility of a python code that allows direct
mapping of the physiochemical properties of the constituent nucleoporins on the scaffold of the yeast NPC׳s cytoplasmic view. We
expect this tool to be useful for researchers to visualize the NPC based on their physiochemical properties and how it alters when
specific mutations are introduced in one or more of the nucleoporins. The code developed using Python is available freely from the
authors. 相似文献
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Babenko OV Zemliakova VV Saakian SV Brovkina AF Strel'nikov VV Zaletaev DV Nemtsova MV 《Molekuliarnaia biologiia》2002,36(5):777-783
Multiplex methylation-sensitive PCR was employed in studying the methylation of the RB1 and CDKN2A/p16 promoter regions in 52 retinoblastomas. Aberrant methylation inactivating RB1 was detected in 14 (27%) tumors. Methylation of p16 was for the first time observed in retinoblastoma (9 tumors, 17%). Both promoters proved to be methylated in two tumors. In four tumors, aberrant methylation was combined with structural defects of both RB1 alleles. Aberrant methylation of the p16 promoter was the second mutation event in two tumors and was not accompanied by RB1 defects in one tumor. Complex testing for RB1 mutations, loss of heterozygosity, and functional inactivation of the two genes revealed a molecular defect in at least one allele in 51 (98%) tumors. 相似文献
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Drozd OV Strel'nikov VV Babenko OV Zemliakova VV Nemtsova MV Zaletaev DV 《Genetika》2003,39(3):433-438
A PCR-based survey of allelic polymorphism of three microsatellite markers, DXS998, DXS548, and FRAXAC1, mapped to chromosome region Xp27.3, and two microsatellite markers, DXS8091 and DXS1691 located on Xq28 was carried out using a series of DNA samples obtained from 98 unrelated individuals from Russia. The number of alleles detected on electrophregrams for each marker tested was 4, 6, 4, 5, and 3, respectively. The values of heterozygosity index for the markers examined were 0.65, 0.27, 0.38, 0.70, and 0.29, respectively. The observed distribution of the allelic frequencies for each microsatellite marker examined fitted Hardy--Weinberg expectations. The values of individualization potential determined for each marker were 0.24, 0.53, 0.43, 0.12, and 0.52, respectively. In the sample tested the genotype distribution with regard to above loci was determined. The perspectives of using the analyzed allelic polymorphisms for indirect DNA diagnostics of the monogenic diseases located in this chromosome region (X-linked mental retardations, FRAXA and FRAXE) as well as for human population genetics and personal identification is discussed. 相似文献
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Zemliakova VV Zhevlova AI Zborovskaia IB Strel'nikov VV Laktionov KK Zaletaev DV Nemtsova MV 《Molekuliarnaia biologiia》2003,37(6):983-988
Multiplex methylation-sensitive PCR was employed in studying the methylation of CpG islands in the RB1, p16/CDKN2A, p15/CDKN2B, p14/ARF, CDH1, HIC1, and N33 5' regions in non-small cell lung cancer (51 tumors). Methylation was observed for the two suppressor genes involved in controlling the cell cycle through the Cdk-Rb-E2F signaling pathway, RB1 (10/51, 19%) and p16 (20/51, 39%). The highest methylation frequencies were established for CDH1 (72%) and HIC1 (82%). The CpG islands of p14 and p15 proved to be nonmethylated. At least one gene was methylated in 90% (46/51) tumors and no gene, in 10% (5/51) tumors. In addition, the genes were tested for methylation in peripheral blood lymphocytes of healthy subjects. Methylation frequency significantly differed between tumors and normal cells in the case of RB1, p16, CDH1, HIC1, and N33. Gene methylation frequency was tested for association with histological type of the tumor and stage of tumor progression. Methylation index of a panel of tumor suppressor genes was established for groups of tumors varying in clinical and morphological parameters. 相似文献
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Zemliakova VV Zhevlova AI Strel'nikov VV Liubchenko LN Vishnevskaia IaV Tret'iakova VA Zaletaev DV Nemtsova MV 《Molekuliarnaia biologiia》2003,37(4):696-703
Multiplex methylation-sensitive PCR was employed in studying the methylation of CpG islands in the RB1, p16/CDKN2A, p15/CDKN2B, p14/ARF, CDH1, MGMT, HIC1, and N33 promoter regions in breast carcinoma (105 tumors). Methylation was often observed for the two major suppressor genes involved in cell-cycle control through the Cdk-Rb-E2F signaling pathway, RB1 (18/105, 17%) and p16 (59/105, 56%); both genes were methylated in 13 tumors. Methylation involved p15 in two (2%) tumors; CDH1, in 83 (79%) tumors; MGMT, in eight (8%) tumors, and N33, in nine (9%) tumors. The p14 promoter was not methylated in the tumors examined. 相似文献