OBJECTIVE: In systemic sclerosis (SSc), constitutive expression of the proinflammatory and fibrogenic cytokine interleukin 1alpha (IL-1alpha) by dermal fibroblasts from the affected skin has been observed. We investigated the association of a single-nucleotide polymorphism at position -889 in the IL-1alpha gene in patients with SSc. METHODS: Genotyping of IL-1alpha-889 polymorphism was performed in 46 patients with SSc and in 150 healthy controls by polymerase chain reaction with sequence-specific primers. All subjects were unrelated Slovak Caucasians. RESULTS: In SSc patients, carriers of the IL-1alpha-889 T allele were significantly overrepresented in comparison with controls (63.0% vs 42.0%; p = 0.01, OR 2.3, 95% CI 1.2-4.6). The frequency of the IL-1alpha-889 T allele was increased in SSc patients (38.0%) in comparison with controls (25.7%; p = 0.02). CONCLUSION: The IL-1alpha-889 polymorphism, previously shown to predispose to increased IL-1 protein expression, may be involved in susceptibility to SSc.

• MeSH
• genetická predispozice k nemoci MeSH
• genotyp MeSH
• interleukin-1 genetika   MeSH
• jednonukleotidový polymorfismus * MeSH
• lidé MeSH
• studie případů a kontrol MeSH
• systémová sklerodermie genetika   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• interleukin-1 MeSH

Here, we report the electrochemical detection of single-point mutations using solid-phase isothermal primer elongation with redox-labeled oligonucleotides. A single-base mutation associated with resistance to rifampicin, an antibiotic commonly used for the treatment of Mycobacterium tuberculosis, was used as a model system to demonstrate a proof-of-concept of the approach. Four 5'-thiolated primers, designed to be complementary with the same fragment of the target sequence and differing only in the last base, addressing the polymorphic site, were self-assembled via chemisorption on individual gold electrodes of an array. Following hybridization with single-stranded DNA, Klenow (exo-) DNA polymerase-mediated primer extension with ferrocene-labeled 2'-deoxyribonucleoside triphosphates (dNFcTPs) was only observed to proceed at the electrode where there was full complementarity between the surface-tethered probe and the target DNA being interrogated. We tested all four ferrocenylethynyl-linked dNTPs and optimized the ratio of labeled/natural nucleotides to achieve maximum sensitivity. Following a 20 min hybridization step, Klenow (exo-) DNA polymerase-mediated primer elongation at 37 °C for 5 min was optimal for the enzymatic incorporation of a ferrocene-labeled nucleotide, achieving unequivocal electrochemical detection of a single-point mutation in 14 samples of genomic DNA extracted from Mycobacterium tuberculosis strains. The approach is rapid, cost-effective, facile, and can be extended to multiplexed electrochemical single-point mutation genotyping.

• Klíčová slova
• Klenow (exo-) DNA polymerase, ferrocene-labeled nucleotides, nucleoside triphosphates, single-nucleotide polymorphism (SNP), single-point mutation, solid-phase primer elongation,
• MeSH
• jednonukleotidový polymorfismus MeSH
• metaloceny MeSH
• Mycobacterium tuberculosis * genetika   MeSH
• oxidace-redukce MeSH
• rifampin farmakologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• metaloceny MeSH
• rifampin MeSH

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
• biosenzitivní techniky metody   MeSH
• diagnostické techniky molekulární metody   MeSH
• DNA sondy genetika   MeSH
• DNA genetika   MeSH
• geny p53 genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lidé MeSH
• oligonukleotidy genetika   MeSH
• povrchová plasmonová rezonance přístrojové vybavení   metody   MeSH
• senzitivita a specificita MeSH
• streptavidin chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA sondy MeSH
• DNA MeSH
• oligonukleotidy MeSH
• streptavidin MeSH

Matrix metalloproteinase-1 (MMP-1) is a member of the matrix metalloproteinase enzyme family that degrades components of the extracellular matrix. Recent studies have demonstrated several polymorphic sites in the promoter of the MMP-1 gene. A newly identified single nucleotide polymorphism (SNP) at position -519 in the promoter region of the MMP-1 gene is reported. This polymorphism consists in a guanine to adenine substitution. A linkage between polymorphisms -519A/G and -1607 1G/2G was also studied.

• MeSH
• běloši MeSH
• dospělí MeSH
• frekvence genu MeSH
• jednonukleotidový polymorfismus * MeSH
• kolorektální nádory genetika   MeSH
• lidé středního věku MeSH
• lidé MeSH
• matrixová metaloproteinasa 1 genetika   metabolismus   MeSH
• promotorové oblasti (genetika) MeSH
• senioři MeSH
• vazebná místa MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• matrixová metaloproteinasa 1 MeSH

BACKGROUND: Single nucleotide polymorphisms can create a genetic microenvironment in some tumors that affects the course of treatment, resistance, etc. Whether single nucleotide polymorphisms have an impact on gastrointestinal stromal tumor (GIST) development and disease progression is not yet accurately verified. KIT SNPM541L in exon 10 correlates with a worse prognosis of many cancers. The impact of KIT SNPM541L in GISTs is relatively unknown and, therefore, its analyses could have potential in patient therapy and could provide more detailed information on tumor character, clinical presentation, or tumor behavior in treatment. AIM: The aim of the study was the analysis of the biological and clinical significance of the KIT SNPM541L polymorphism in exon 10. MATERIALS AND METHODS: Paraffin sample tissues were obtained from the National GIST Register in Martin. Retrospective samples from 177 GIST patients were divided into several groups. Detection of SNPM541L was performed by Sanger sequencing. Statisitical analyses were performed to determine the prevalence of KIT SNPM541L in the Slovak GIST cohort, to search for correlation between c-KIT status and clinicopathological, molecular and biological data. RESULTS: Overall, 29 samples out of 177 showed KIT SNPM541L polymorphism. CONCLUSION: Our results do not support the association between KIT SNPM541L and increased risk of relapse in localized primary GISTs. Additionally, we found a positive correlation between KIT SNPM541L occurrence and earlier onset of relapse in PDGFRa and WT subgroup of GISTs.

• Klíčová slova
• Gastrointestinal stromal tumors, M541L, Single nucleotide polymorphism, c-KIT, c.1621 A > C,
• MeSH
• dospělí MeSH
• gastrointestinální nádory epidemiologie   genetika   patologie   MeSH
• gastrointestinální stromální tumory epidemiologie   genetika   patologie   MeSH
• jednonukleotidový polymorfismus * MeSH
• lidé středního věku MeSH
• lidé MeSH
• míra přežití MeSH
• mladiství MeSH
• mladý dospělý MeSH
• nádorové biomarkery genetika   MeSH
• následné studie MeSH
• prognóza MeSH
• protoonkogenní proteiny c-kit genetika   MeSH
• retrospektivní studie MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa epidemiologie   MeSH
• Názvy látek
• KIT protein, human MeSH Prohlížeč
• nádorové biomarkery MeSH
• protoonkogenní proteiny c-kit MeSH

Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment. One such species is the nuisance microalga Gonyostomum semen (Raphidophyceae), which has increased in occurrence in northern Europe in recent decades. The question of whether the species has expanded its habitat range or if it was already present in the lakes but was too rare to be detected remains unanswered. The aim of the present study was to determine the genetic structure and dispersal pathways of G. semen using RAD (restriction-site-associated DNA) tag sequencing. For G. semen, which has a huge genome (32 Gbp), we faced particular challenges, but were nevertheless able to recover over 1000 single nucleotide polymorphisms at high coverage. Our data revealed a distinct population genetic structure, demonstrating a divide of western and eastern populations that probably represent different lineages. Despite significant genetic differentiation among lakes, we found only limited isolation-by-distance. While we had expected a pattern of recent expansion northwards, the data demonstrated gene flow from the northeast/east towards the southwest/west. This genetic signature suggests that the observed gene flow may be due to dispersal by autumn migratory birds, which act as dispersal vectors of resistant resting propagules that form at the end of the G. semen blooms.

• Klíčová slova
• Gonyostomum semen, RAD-seq, SNPs, algal blooms, invasive species, population structure,
• MeSH
• Heterokontophyta * MeSH
• jednonukleotidový polymorfismus * genetika   MeSH
• škodlivý vodní květ MeSH
• tok genů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29,233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations. The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3-7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.

• Klíčová slova
• Populus, association genetics, cellulose, lignin, single nucleotide polymorphism (SNP), wood traits, wood ultrastructure,
• MeSH
• alely MeSH
• buněčná stěna MeSH
• dřevo * růst a vývoj   metabolismus   ultrastruktura   MeSH
• fenotyp * MeSH
• genetické asociační studie MeSH
• genom rostlinný * MeSH
• genotyp * MeSH
• jednonukleotidový polymorfismus * MeSH
• Populus genetika   růst a vývoj   metabolismus   ultrastruktura   MeSH
• rostlinné geny * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

Barley alpha-amylase variability influences the quality of barley grain in the brewing, feed and food industries. alpha-Amylase proteins are encoded by multigene families in cereals, and this study focused on the barley Amy32b gene. We identified coding region single nucleotide polymorphism (cSNP) and insertion/deletion variation in DNA sequences, which resulted in amino acid substitution and stop codon formation, respectively. The substitution affected the beta1 strand in domain C, whereas the stop codon removed the beta5 strand. Possible effects of these changes on the protein are discussed. A cSNP in the coding region of the Amy32b gene was used as a specific marker to map Amy32b loci on chromosome 7H.

• MeSH
• alfa-amylasy genetika   MeSH
• DNA primery MeSH
• genetická variace * MeSH
• genotyp MeSH
• ječmen (rod) genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• mapování chromozomů * MeSH
• molekulární sekvence - údaje MeSH
• rostlinné geny genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sekvenční seřazení MeSH
• substituce aminokyselin genetika   MeSH
• terminační kodon genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• alfa-amylasy MeSH
• DNA primery MeSH
• terminační kodon 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
• alely * MeSH
• chemokin CCL2 genetika   imunologie   MeSH
• genetická predispozice k nemoci genetika   MeSH
• infarkt myokardu genetika   imunologie   MeSH
• jednonukleotidový polymorfismus genetika   imunologie   MeSH
• koronární nemoc genetika   imunologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• prediktivní hodnota testů MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• CCL2 protein, human MeSH Prohlížeč
• chemokin CCL2 MeSH

Clusterin (CLU; also known as apolipoprotein J, ApoJ) is a protein of inconstant structure known to be involved in diverse processes inside and outside of brain cells. CLU can act as a protein chaperon or protein solubilizer, lipid transporter as well as redox sensor and be anti- or proapoptotic, depending on context. Primary structure of CLU is encoded by CLU gene which contains single nucleotide polymorphisms (SNP's) associated with the risk of late-onset Alzheimer's disease (LOAD). Studying a sample of Czech population and using the case-control association approach we identified C allele of the SNP rs11136000 as conferring a reduced risk of LOAD, more so in females than in males. Additionally, data from two smaller subsets of the population sample suggested a possible association of rs11136000 with diabetes mellitus. In a parallel study, we found no association between rs11136000 and mild cognitive impairment (MCI). Our findings on rs11136000 and LOAD contradict those of some previous studies done elsewhere. We discuss the multiple roles of CLU in a broad range of molecular mechanisms that may contribute to the variability of genetic studies of CLU in various ethnic groups. The above discordance notwithstanding, our conclusions support the association of rs1113600 with the risk of LOAD.

• Klíčová slova
• Clusterin, Genetic risk, Late-onset Alzheimer’s disease, Mild cognitive impairment, Neurodegeneration, Neuroprotection, Single nucleotide polymorphism,
• MeSH
• Alzheimerova nemoc etiologie   genetika   MeSH
• genetická predispozice k nemoci MeSH
• jednonukleotidový polymorfismus MeSH
• klusterin genetika   MeSH
• kognitivní dysfunkce etiologie   genetika   MeSH
• lidé MeSH
• rizikové faktory MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• CLU protein, human MeSH Prohlížeč
• klusterin MeSH