This paper reports an approach to detection of single nucleotide polymorphism based on special amplification assay and surface plasmon resonance biosensor technology. In this assay, a part of the target DNA is recognized by a probe (probe A) coupled with streptavidin-oligonucleotide (SON) complexes ex situ, and when the mixture is injected in the sensor, another part of the target DNA is recognized by a DNA probe (probe B) immobilized on the sensor surface. To achieve high sensitivity and specificity, the assay is optimized in terms of composition of SON complexes, probe design, and assay temperature. It is demonstrated that this approach provides high specificity (no response to targets containing single-mismatched bases) and sensitivity (improves sensor response to perfectly matched oligonucleotides by one order of magnitude compared to the direct detection method). The assay is applied to detection of a short synthetic analogue of TP53 containing a "hot spot"-single nucleotide mismatch frequently mutated in germ line cancer-at levels down to 40 pM.
- MeSH
- Biosensing Techniques methods MeSH
- Molecular Diagnostic Techniques methods MeSH
- DNA Probes genetics MeSH
- DNA genetics MeSH
- Genes, p53 genetics MeSH
- Polymorphism, Single Nucleotide genetics MeSH
- Humans MeSH
- Oligonucleotides genetics MeSH
- Surface Plasmon Resonance instrumentation methods MeSH
- Sensitivity and Specificity MeSH
- Streptavidin chemistry MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Klasifikace nádorových onemocnění a identifikace terapeutických cílů pro jejich léčbu vyžaduje důkladnou znalost a popis genetických změn. Analýza single nukleotidových polymorfi zmů je cenným nástrojem pro detekci a charakterizaci genetických variací u nádorových onemocnění. Účelem této práce je podat souhrnný přehled o metodách detekce SNP aplikovatelných na výzkum MM.
Tumor classification and identifi cation of targets for therapeutic applications requires very good knowledge and description of genetic changes connected to an illness. SNP analysis seems to be a valuable tool for detection and characterisation of genetic variations in cancer. The aim of this review is to summarise methods usable for SNP detection and its applicabillity for MM research.
Studium polymorfizmů v genech asociovaných s mnohočetným myelomem (MM) je atraktivní oblastí výzkumu, který může přispět k celkovému pochopení této nemoci. Výzkumy v oblasti polymorfi zmů u MM jsou zatím na experimentální úrovní. Cílem této práce je demonstrovat na vybraných zahraničních prácích možnost klinického využití polymorfi zmů v oblasti MM.
Study of polymorphisms in genes associated with multiple myeloma (MM) is promising fi eld of research. Study of this field could bring important piece to a global understanding of this illness. Research of polymorphisms associated with MM still remain at experimental stage. The aim of this work is to demonstrate a possible clinical utilization of polymorphisms in MM field.
- MeSH
- Polymorphism, Single Nucleotide * genetics MeSH
- Humans MeSH
- Multiple Myeloma genetics MeSH
- Molecular Biology MeSH
- DNA Repair MeSH
- Research Design MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- MeSH
- Adult MeSH
- Polymorphism, Single Nucleotide MeSH
- Colorectal Neoplasms genetics MeSH
- Middle Aged MeSH
- Humans MeSH
- Matrix Metalloproteinase 1 genetics metabolism MeSH
- Aged MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged MeSH
- Female MeSH
- Geographicals
- Czech Republic MeSH
Monocyte chemoattractant protein (MCP)-1 is the key chemokine in the process of atheroslerotic vascular inflammation. Examining already reported association between coronary artery disease (CAD) and the SNP A/G in the MCP-1 gene (position -2518), 139 Czech patients with CAD manifested as myocardial infarction (MI) and 359 unrelated healthy control (C) subjects were genotyped by PCR-SSP. Genotype and allele frequencies were not different in MI and C groups (allele G: MI, 20.5%; C, 23.8%, OR = 0.8, P > 0.05). No differences were detected when the patients were subdivided based on sex or the age of MI first occurrence. Further, no relationship was observed between circulating MCP-1 levels and carriage of the G allele. The data do not support a role for the MCP-1 -2518 single nucleotide polymorphism in susceptibility to CAD manifested by myocardial infarction.
- MeSH
- Alleles MeSH
- Chemokine CCL2 genetics immunology MeSH
- Financing, Organized MeSH
- Genetic Predisposition to Disease genetics MeSH
- Myocardial Infarction genetics immunology MeSH
- Polymorphism, Single Nucleotide genetics immunology MeSH
- Coronary Disease genetics immunology MeSH
- Middle Aged MeSH
- Humans MeSH
- Predictive Value of Tests MeSH
- Check Tag
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Female MeSH
Cíl: Stanovení alelové frekvence polymorfizmu p.Val66Met (rs6265) v genu pro mozkový neurotrofní faktor (brain-derived neurotrophic factor; BDNF) v české populaci. Přítomnost polymorfizmu p.Val66Met v genu BDNF je spojována s porušeným intracelulárním transportem a sekrecí BDNF. Změny v expresi a funkci BDNF jsou spojeny s různými onemocněními mozku a představují jeden z mechanizmů odpovědi na stres. Soubor a metodika: Retrospektivně bylo v kontrolní skupině vyšetřeno 317 vzorků DNA jedinců z české populace (173 mužů a 144 žen) ve věku 45–81 let. Polymorfizmus p.Val66Met v genu BDNF byl vyšetřen analýzou křivek tání. Výsledky: Frekvence mutantní alely (A) v kontrolní skupině činila 16,3 %; frekvence standardní alely (G) činila 83,7 %. Závěr: Byla stanovena frekvence polymorfizmu p.Val66Met v genu BDNF, která je srovnatelná s frekvencemi v okolních zemích.
Aim: To determine the allele frequency of the p.Val66Met (rs6265) polymorphism in BDNF gene (brain-derived neurotrophic factor, BDNF) in the Czech population. The p.Val66Met (rs6265) polymorphism in the BDNF gene is associated with impaired intracellular trafficking and secretion of BDNF. Alterations in BDNF expression and function are involved in different brain disorders and represent a major downstream mechanism for stress response. Material and methods: Retrospectively, 317 DNA control samples of Czech individuals aged between 45 and 81 years (173 men and 144 women), were examined for p.Val66Met polymorphism in the BDNF gene using the melting analysis. Results: Frequency of the mutant allele (A) was 16.3% and it was 83.7% for the wild type allele (G). Conclusion: The requency of the p.Val66Met polymorphism in the BDNF gene in the Czech population was determined.
- MeSH
- Adult MeSH
- Genotype MeSH
- Polymorphism, Single Nucleotide * MeSH
- Clinical Studies as Topic MeSH
- Middle Aged MeSH
- Humans MeSH
- Brain-Derived Neurotrophic Factor * genetics MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Female MeSH
- Geographicals
- Czech Republic MeSH
Cíl: Gen pro adiponektin bývá označován jako kandidátní gen inzulinové rezistence (IR). V naší práci byl sledován možný vztah mezi jednonukleotidovým polymorfi smem (SNP) +276 G > T a markery inzulinové rezistence včetně lipidového a lipoproteinového profi lu u 355 dyslipidemických pacientů lipidové ambulance III. interní kliniky Fakultní nemocnice Olomouc a jejich prvostupňových příbuzných. Metody: SNP genu pro adiponektin byl detekován metodou polymerázové řetězové reakce v reálném čase s hybridizačními fl uorescenčními sondami. Rozdíly mezi genotypy ve spojitých proměnných byly analyzovány metodou ANOVA (upraveno na věk, pohlaví a obvod pasu). Výsledky: Nosiči genotypu GG měli významně vyšší hladiny celkového cholesterolu (GG: 6,54 ± 1,74 mmol/l, GT: 6,18 ± 1,45 mmol/l, TT: 6,25 ± 1,64 mmol/l, p < 0,05) a LDL cholesterolu (GG: 4,12 ± 1,49 mmol/l, GT: 3,78 ± 1,31 mmol/l, TT: 3,70 ± 1,34 mmol/l, p < 0,05) než jedinci s alelou T. Přítomnost alely T na pozici 276 byla u heterozygotů naopak spojena s vyšší koncentrací inhibitoru aktivátoru plasminogenu 1 (PAI-1) (GG: 71,50 ± 41,0 μg/l, GT: 81,0 ± 38,7 μg/l, TT: 70,14 ± 44,4 μg/l, p < 0,05). Závěr: Ve studii byla zjištěna slabá asociace heterozygotů-nosičů T alely polymorfi smu +276 G > T genu pro adiponektin a jedním markerem inzulinové rezistence, avšak nebyl nalezen vztah k sérovému adiponektinu, inzulinu, body mass indexu a dyslipidemickým fenotypům.
Aim: The adiponectin gene has been proposed as a potential candidate gene for IR. We analysed possible relationship between +276 G > T SNP and IR markers together with lipid and lipoprotein profi les in 355 Czech dyslipidemic patients of Lipid Center, University Hospital Olomouc, and their fi rst degree relatives. Methods: The +276 G > T SNP of adiponectin gene was detected by real time PCR method with hybridization fl uorescence probes in LightCycler. Between-genotype differences in continuous variables were analyzed by ANOVA after adjustment for age, sex and waist circumference. Results: Subjects with GG genotype were associated with higher total cholesterol (GG: 6.54 ± 1.74 mmol/l, GT: 6.18 ± 1.45 mmol/l, TT: 6.25 ± 1.64 mmol/l, p < 0.05) and LDL cholesterol (GG: 4.12 ± 1.49 mmol/l, GT: 3.78 ± 1.31 mmol/l, TT: 3.70 ± 1.34 mmol/l, p < 0.05) in comparison with T allele carriers. On the contrary, the presence of T allele in position 276 in heterozygotes was associated with higher levels of plasma inhibitor of activator of plasminogen 1 (PAI-1) (GG: 71.50 ± 41.0 μg/l, GT: 81.0 ± 38.7 μg/l, TT: 70.14 ± 44.4 μg/l, p < 0.05). Conclusion: In this study, the poor association between carriers- heterozygotes of T alelle of +276 G > T polymorphism of gene for adiponectin and one marker of insulin resistance was found. However, no relationship was detected with plasma adiponectin, insulin, body mass index and dyslipidemic phenotypes.
During a survey on grapevine yellows disease complex in vineyards of Lombardy region (northern Italy), phytoplasmas associated with Flavescence dorée disease were identified in symptomatic grapevines. Polymerase chain reaction and restriction fragment length polymorphism (RFLP) analyses of 16S rDNA revealed the prevalence of phytoplasmal subgroup 16SrV-D. Bioinformatic analyses of nucleotide sequences of rplV and rpsC genes, amplified from 16SrV-D phytoplasma infected grapevines and cloned, underscored the presence of five confirmed rpsC single nucleotide polymorphism (SNP) lineages, determined by different combination of SNPs at nucleotide positions 29, 365, 680, and 720 of rpsC gene. Virtual and actual RFLP analyses with the enzyme TaqI validated the presence of these SNPs. Co-infections by up to four distinct rpsC SNP lineages of 16SrV-D phytoplasma were found in grapevines. These results could open new perspectives for the study of the ecology and the epidemiology of Flavescence dorée.
- MeSH
- Bacterial Proteins genetics MeSH
- DNA, Bacterial genetics chemistry MeSH
- DNA Fingerprinting MeSH
- Financing, Organized MeSH
- Phylogeny MeSH
- Polymorphism, Single Nucleotide MeSH
- Molecular Sequence Data MeSH
- Plant Diseases microbiology MeSH
- Phytoplasma genetics isolation & purification classification MeSH
- Polymerase Chain Reaction MeSH
- Polymorphism, Restriction Fragment Length MeSH
- DNA, Ribosomal genetics MeSH
- Ribosomal Proteins genetics MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Sequence Analysis, DNA MeSH
- Sequence Homology MeSH
- Cluster Analysis MeSH
- Vitis microbiology MeSH
- Geographicals
- Italy MeSH
