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Prognostic value of TP53 Pro47Ser and Arg72Pro single nucleotide polymorphisms and the susceptibility to gliomas in individuals from Southeast Brazil

PINTO, G. R.; YOSHIOKA, F. K. N.; SILVA, R. L. L.; CLARA, C. A.; SANTOS, M. J.; ALMEIDA, J. R. W.; BURBANO, R. R.; REY, J. A.; CASARTELLI, C.
Fonte: FUNPEC-EDITORA Publicador: FUNPEC-EDITORA
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
76.03%
The TP53 tumor suppressor gene codifies a protein responsible for preventing cells with genetic damage from growing and dividing by blocking cell growth or apoptosis pathways. A common single nucleotide polymorphism (SNP) in TP53 codon 72 (Arg72Pro) induces a 15-fold decrease of apoptosis-inducing ability and has been associated with susceptibility to human cancers. Recently, another TP53 SNP at codon 47 (Pro47Ser) was reported to have a low apoptosis-inducing ability; however, there are no association studies between this SNP and cancer. Aiming to study the role of TP53 Pro47Ser and Arg72Pro on glioma susceptibility and oncologic prognosis of patients, we investigated the genotype distribution of these SNPs in 94 gliomas (81 astrocytomas, 8 ependymomas and 5 oligodendrogliomas) and in 100 healthy subjects by the polymerase chain reaction-restriction fragment length polymorphism approach. Chi-square and Fisher exact test comparisons for genotype distributions and allele frequencies did not reveal any significant difference between patients and control groups. Overall and disease-free survivals were calculated by the Kaplan-Meier method, and the log-rank test was used for comparisons, but no significant statistical difference was observed between the two groups. Our data suggest that TP53 Pro47Ser and Arg72Pro SNPs are not involved either in susceptibility to developing gliomas or in patient survival...

Single nucleotide polymorphism C/T-13910, located upstream of the lactase gene, associated with adult-type hypolactasia: Validation for clinical practice

MATTAR, Rejane; MONTEIRO, Maria do Socorro; VILLARES, Cibele Aparecida; SANTOS, Anibal Ferreira dos; CARRILHO, Flair Jose
Fonte: PERGAMON-ELSEVIER SCIENCE LTD Publicador: PERGAMON-ELSEVIER SCIENCE LTD
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
76.01%
Objectives: To validate C/T-13910 polymorphism associated with primary hypolactasia for clinical practice. Design and methods: Lactose breath test and PCR-RFLP for the C/T-13910 polymorphism were performed. Results: Twenty-seven of 28 patients with genotype CC had positive breath tests, all twenty-two patients with genotypes CT or TT had negative breath tests. Agreement of tests was high (p<0.0001; Kappa Index 0.96). Conclusion: C/T-13910 polymorphism detection may be a new tool for primary hypolactasia diagnosis. (C) 2008 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

The broad effects of the functional IL-10 promoter-592 polymorphism: modulation of IL-10, TIMP-3, and OPG expression and their association with periodontal disease outcome

CLAUDINO, Marcela; TROMBONE, Ana Paula F.; CARDOSO, Cristina R.; FERREIRA JR., Samuel B.; MARTINS JR., Walter; ASSIS, Gerson F.; SANTOS, Carlos F.; TREVILATTO, Paula C.; CAMPANELLI, Ana Paula; SILVA, Joao S.; GARLET, Gustavo P.
Fonte: FEDERATION AMER SOC EXP BIOL Publicador: FEDERATION AMER SOC EXP BIOL
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
75.99%
Periodontal diseases are infectious diseases, in which periodontopathogens trigger chronic inflammatory and immune responses that lead to tissue destruction. It occurs through the generation of metalloproteinases and the activation of bone resorption mechanisms. Anti-inflammatory cytokines such as IL-10 seem to attenuate periodontal tissue destruction through the induction of tissue inhibitors of metalloproteinases (TIMPs) and the inhibitor of osteoclastogenesis osteoprotegerin (OPG). A high individual variation in levels of IL-10 mRNA is verified in periodontitis patients, which is possibly determined by genetic polymorphisms. In this study, the IL-10 promoter -592C/A single nucleotide polymorphism ( SNP), which is associated with a decrease in IL-10 production, was analyzed by RFLP in 116 chronic periodontitis (CP) patients and 173 control (C) subjects, and the IL-10, TIMPs, and OPG mRNA expression levels in diseased gingival tissues were determined by real-time-PCR. The IL-10-592 SNP CA (P=0.0012/OR=2.4/CI:1.4-4.1), AA (P=0.0458/OR=2.3/CI:1.1-4.9), and CA+AA (P=0.0006/OR=2.4/CI: 1.4-3.4) genotypes and the allele A (P=0.0036/OR=1.7/CI:1.2-2.4) were found to be significantly more prevalent in the CP group when compared with control subjects. Both CA and AA genotypes were associated with lower levels of IL-10...

Tumor necrosis factor-alpha-308G/A single nucleotide polymorphism and red-complex periodontopathogens are independently associated with increased levels of tumor necrosis factor-alpha in diseased periodontal tissues

TROMBONE, A. P. F.; CARDOSO, C. R.; REPEKE, C. E.; FERREIRA JR., S. B.; MARTINS JR., W.; CAMPANELLI, A. P.; AVILA-CAMPOS, M. J.; TREVILATTO, P. C.; SILVA, J. S.; GARLET, G. P.
Fonte: WILEY-BLACKWELL PUBLISHING, INC Publicador: WILEY-BLACKWELL PUBLISHING, INC
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
76.12%
Background and Objective: Inflammatory cytokines such as tumor necrosis factor-alpha are involved in the pathogenesis of periodontal diseases. A high between-subject variation in the level of tumor necrosis factor-alpha mRNA has been verified, which may be a result of genetic polymorphisms and/or the presence of periodontopathogens such as Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola (called the red complex) and Aggregatibacter actinomycetemcomitans. In this study, we investigated the effect of the tumor necrosis factor-alpha (TNFA) -308G/A gene polymorphism and of periodontopathogens on the tumor necrosis factor-alpha levels in the periodontal tissues of nonsmoking patients with chronic periodontitis (n = 127) and in control subjects (n = 177). Material and Methods: The TNFA-308G/A single nucleotide polymorphism was investigated using polymerase chain reaction-restriction fragment length polymorphism analysis, whereas the tumor necrosis factor-alpha levels and the periodontopathogen load were determined using real-time polymerase chain reaction. Results: No statistically significant differences were found in the frequency of the TNFA-308 single nucleotide polymorphism in control and chronic periodontitis groups...

Detection of the single nucleotide polymorphism (rs2227307) in the human interleukin 8 gene using a pcr-rflp assay

Kim, Yeon Jung; Viana, Aline Cavalcanti; Tfaile Corbi, Samia Cruz; de Carvalho Curtis, Karen Maria; Renzi, Rivelto; Perez Orrico, Silvana Regina; Cirelli, Joni Augusto; Scarel-Caminaga, Raquel Mantuaneli
Fonte: Universidade Federal de Uberlândia (UFU) Publicador: Universidade Federal de Uberlândia (UFU)
Tipo: Artigo de Revista Científica Formato: 136-142
ENG
Relevância na Pesquisa
86.03%
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Processo FAPESP: 03/10424-0; Processo FAPESP: 05/03231-7; Processo FAPESP: 05/04553-8; Processo FAPESP: 06/04492-1; Interleukin 8 (IL-8) is a chemokine that acts as a potent chemoattractant for neutrophils. Single nucleotide polymorphisms ( SNPs) in the human IL8 gene have been investigated in many disease association studies. We have developed a different PCR-RFLP (Polymerase Chain Reaction - Restriction Fragment of Length Polymorphism) assay for genotyping the SNP (rs2227307) in the IL8 gene. This method was used for typing 147 white healthy Brazilian individuals, whose DNA was obtained from buccal epithelial cells and extracted with phenol: chloroform: isoamyl alcohol. Genomic DNA was amplified by PCR using a conventional thermal cycler. The PCR products ( 573 bp) were submitted to RFLP reactions. The RFLP fragments were analyzed in a 4% agarose gel stained with ethidium bromide. The genotype distribution observed in this study was consistent with the assumption of Hardy-Weinberg equilibrium and was similar (p=0.30) to those reported for other white populations in the SNP Database of the National Center for Biotechnology Information (NCBI). Because the PCR-RFLP method presented here was efficient...

Characterization of eight single nucleotide polymorphism markers in Aedes aegypti

Paduan, K. S.; Ribolla, Pem
Fonte: Wiley-Blackwell Publishing, Inc Publicador: Wiley-Blackwell Publishing, Inc
Tipo: Artigo de Revista Científica Formato: 114-116
ENG
Relevância na Pesquisa
85.98%
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Processo FAPESP: 01/06647-9; Sequencing of part of seven genes from Aedes aegypti collected in 16 Brazilian cities revealed the existence of 53 single nucleotide polymorphisms (SNPs), representing one SNP every 52 base pairs. From these 53 SNPs, we selected eight that are independent and highly polymorphic. We describe the use of these markers for differentiation of Brazilian populations of A. aegypti. These are the first SNPs developed for delineating population structure in A. aegypti, and will be a useful complement to epidemiological studies.

Effects of a single nucleotide polymorphism in the leptin gene on the productive traits of dairy buffaloes (Bubalus bubalis)

Zetouni, Larissa; De Camargo, Gregório Miguel Ferreira; Da Silva Fonseca, Patrícia Dias; Gil, Fernanda Maria Monsalves; Lugo, Naudin Alejandro Hurtado; Aspilcueta-Borquis, Rusbel Raul; Cervini, Marcelo; Tonhati, Humberto
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 5159-5163
ENG
Relevância na Pesquisa
76.06%
The gene responsible for coding the leptin hormone has been associated with productive and reproductive traits in cattle. In dairy cattle, different polymorphisms found in the leptin gene have been associated with several traits of economic interest, such as energy balance, milk yield and composition, live weight, fertility and dry matter consumption. The aim of this study was to detect genetic variability in the leptin gene of buffaloes and to test possible associations with milk yield, fat and protein percentages, age at first calving and first calving interval. Three genotypes (AA, AG and GG) were identified by polymerase chain reaction-restriction fragment length polymorphism, which presented genotypic frequencies of 0.30, 0.54 and 0.16, respectively. The allele frequencies were 0.57 for the A allele and 0.43 for the G allele. No significant effects were found in the present study, but there is an indicative that leptin gene affects lipid metabolism. © 2013 Springer Science+Business Media Dordrecht.

Development and characterization of 35 single nucleotide polymorphism markers for the brown alga Fucus vesiculosus

Cánovas, Fernando G.; Mota, Catarina F.; Ferreira Costa, J.; Serrão, Ester; Coyer, J. A.; Olsen, J. L.; Pearson, G. A.
Fonte: Taylor & Francis Group Publicador: Taylor & Francis Group
Tipo: Artigo de Revista Científica
Publicado em 18/10/2011 ENG
Relevância na Pesquisa
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We characterized 35 single nucleotide polymorphism (SNP) markers for the brown alga Fucus vesiculosus. Based on existing Fucus Expressed Sequence Tag libraries for heat and desiccation-stressed tissue, SNPs were developed and confirmed by re-sequencing cDNA from a diverse panel of individuals. SNP loci were genotyped using the SEQUENOM single base extension iPLEXTM system for multiplex assays on the MassARRAY platform, which uses matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS) to discriminate allele-specific products. The SNP markers showed a wide range of variability among 16 populations from the south-west of the UK, northern Portugal and Morocco. The analysis of the information provided by these markers will be useful for studying population structure, historical demography and phylogeography of F. vesiculosus. They can also be used for the identification of genes and/or linked genomic regions potentially subject to selection in response to abiotic stressors like temperature extremes and desiccation intensity that vary across habitats and geographical range.

Association of the rs7903146 single nucleotide polymorphism at the Transcription Factor 7-like 2 (TCF7L2) locus with type 2 diabetes in Brazilian subjects

Barra,Gustavo Barcelos; Dutra,Ludmila Alves Sanches; Watanabe,Sílvia Conde; Costa,Patrícia Godoy Garcia; Cruz,Patrícia Sales Marques da; Azevedo,Monalisa Ferreira; Amato,Angélica Amorim
Fonte: Sociedade Brasileira de Endocrinologia e Metabologia Publicador: Sociedade Brasileira de Endocrinologia e Metabologia
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/11/2012 EN
Relevância na Pesquisa
96.03%
OBJECTIVE:To investigate the association of the T allele of the single nucleotide polymorphism (SNP) rs7903146 of TCF7L2 with the occurrence of T2D in a sample of subjects followed up at the Brasilia University Hospital. SUBJECTS AND METHODS: The SNP rs7903146 of TCF7L2 was genotyped by allele-specific PCR in 113 patients with known T2D and in 139 non-diabetic controls in Brasilia, Brazil. RESULTS:We found that the T allele of the SNP rs7903146 of TCF7L2 was significantly associated with T2D risk (odds ratio of 3.92 for genotype TT in the recessive genetic model, p = 0.004 and 1.5 for T allele, p = 0.032). CONCLUSION:These results reinforce previous findings on the consistent association of this genetic factor and the risk of T2D in populations of diverse ethnic backgrounds. Arq Bras Endocrinol Metab. 2012;56(8):479-84

Diagnosis of adult-type hypolactasia/lactase persistence: genotyping of single nucleotide polymorphism (SNP C/T-13910) is not consistent with breath test in Colombian Caribbean population

Mendoza Torres,Evelyn; Varela Prieto,Lourdes Luz; Villarreal Camacho,José Luis; Villanueva Torregroza,Daniel Antonio
Fonte: Instituto Brasileiro de Estudos e Pesquisas de Gastroenterologia - IBEPEGE ; Colégio Brasileiro de Cirurgia Digestiva - CBCD ; Sociedade Brasileira de Motilidade Digestiva - SBMD ; Federação Brasileira de Gastroenterologia - FBG; Sociedade Brasileira de Hepatologia - SBH; Sociedade Brasileira de Endoscopia Digestiva - SOBED Publicador: Instituto Brasileiro de Estudos e Pesquisas de Gastroenterologia - IBEPEGE ; Colégio Brasileiro de Cirurgia Digestiva - CBCD ; Sociedade Brasileira de Motilidade Digestiva - SBMD ; Federação Brasileira de Gastroenterologia - FBG; Sociedade Brasileira de Hepatologia - SBH; Sociedade Brasileira de Endoscopia Digestiva - SOBED
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/03/2012 EN
Relevância na Pesquisa
86.09%
CONTEXT: Genotyping of single nucleotide polymorphism (SNP C/T-13910) located upstream of the lactase gene is used to determine adult-type hypolactasia/lactase persistence in North-European Caucasian subjects. The applicability of this polymorphism has been studied by comparing it with the standard diagnostic methods in different populations. OBJECTIVE: To compare the lactose hydrogen breath test with the genetic test in a sample of the Colombian Caribbean population. METHODS: Lactose hydrogen breath test and genotyping of SNP C/T-13910 were applied to 128 healthy individuals (mean age 35 ± 1). A positive lactose hydrogen breath test was indicative of hypolactasia. Genotyping was done using polymerase chain reaction/restriction fragment length polymorphism. The kappa index was used to establish agreement between the two methods. RESULTS: Seventy-six subjects (59%) were lactose-maldigesters (hypolactasia) and 52 subjects (41%) were lactose-digesters (lactase persistence). The frequencies of the CC, CT and TT genotypes were 80%, 20% and 0%, respectively. Genotyping had 97% sensitivity and 46% specificity. The kappa index = 0.473 indicates moderate agreement between the genotyping of SNP C/T-13910 and the lactose hydrogen breath test. CONCLUSION: The moderate agreement indicates that the genotyping of the SNP C/T-13910 is not applicable to determine adult-type hypolactasia/lactase persistence in the population participating in this study.

Glucokinase gene promoter -30G>A polymorphism: a cross-sectional association study with obesity, diabetes Mellitus, hyperlipidemia, hypertension and metabolic syndrome in an Iranian hospital

Oladi,Mohammad Reza; Behravan,Javad; Hassani,Mitra; Kassaeian,Jamal; Sahebkar,Amirhossein; Tavallaie,Shima; Paydar,Roghayeh; Saber,Hamidreza; Esmaeili,Habib Allah; Azimi-Nezhad,Mohsen; Ferns,Gordon; Ghayour-Mobarhan,Majid
Fonte: Pontifícia Universidade Católica de Campinas Publicador: Pontifícia Universidade Católica de Campinas
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/08/2012 EN
Relevância na Pesquisa
76.04%
OBJECTIVE: A -30G>A single nucleotide polymorphism in the promoter region of the glucokinase gene has been previously associated with obesity, insulin resistance and diabetes. The present study aimed to evaluate the association of this polymorphism with obesity and its comorbidities in a population from Northeast Iran. METHODS: Five hundred and forty-two subjects aged 18 to 65 years were included in the study and divided into normal (BMI<25, n=220), overweight (25

Identifying the similarities and differences between single nucleotide polymorphism array (SNPa) analysis and karyotyping in acute myeloid leukemia and myelodysplastic syndromes

Noronha,Thiago Rodrigo de; Rohr,Sandra Serson; Chauffaille,Maria de Lourdes Lopes Ferrari
Fonte: Associação Brasileira de Hematologia e Hemoterapia e Terapia Celular Publicador: Associação Brasileira de Hematologia e Hemoterapia e Terapia Celular
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/02/2015 EN
Relevância na Pesquisa
96.26%
Objective: To standardize the single nucleotide polymorphism array (SNPa) method in acute myeloid leukemia/myelodysplastic syndromes, and to identify the similarities and differ- ences between the results of this method and karyotyping. Methods: Twenty-two patients diagnosed with acute myeloid leukemia and three with myelodysplastic syndromes were studied. The G-banding karyotyping and single nucleotide polymorphism array analysis (CytoScan(r) HD) were performed using cells from bone marrow, DNA extracted from mononuclear cells from bone marrow and buccal cells (BC). Results: The mean age of the patients studied was 54 years old, and the median age was 55 years (range: 28-93). Twelve (48%) were male and 13 (52%) female. Ten patients showed abnormal karyotypes (40.0%), 11 normal (44.0%) and four had no mitosis (16.0%). Regarding the results of bone marrow single nucleotide polymorphism array analysis: 17 were abnor- mal (68.0%) and eight were normal (32.0%). Comparing the two methods, karyotyping identified a total of 17 alterations (8 deletions/losses, 7 trissomies/gains, and 2 translocations) and single nucleotide polymorphism array analysis identified a total of 42 alterations (17 losses, 16 gains and 9 copy-neutral loss of heterozygosity). Conclusion: It is possible to standardize single nucleotide polymorphism array analysis in acute myeloid leukemia/myelodysplastic syndromes and compare the results with the abnormalities detected by karyotyping. Single nucleotide polymorphism array analysis increased the detection rate of abnormalities compared to karyotyping and also identified a new set of abnormalities that deserve further investigation in future studies.

Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis

Bunyavanich, Supinda; Schadt, Eric E; Himes, Blanca E; Lasky-Su, Jessica; Qiu, Weiliang; Lazarus, Ross; Ziniti, John P; Cohain, Ariella; Linderman, Michael; Torgerson, Dara G; Eng, Celeste S; Pino-Yanes, Maria; Padhukasahasram, Badri; Yang, James J; Mathi
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
85.98%
Background: Allergic rhinitis is a common disease whose genetic basis is incompletely explained. We report an integrated genomic analysis of allergic rhinitis. Methods: We performed genome wide association studies (GWAS) of allergic rhinitis in 5633 ethnically diverse North American subjects. Next, we profiled gene expression in disease-relevant tissue (peripheral blood CD4+ lymphocytes) collected from subjects who had been genotyped. We then integrated the GWAS and gene expression data using expression single nucleotide (eSNP), coexpression network, and pathway approaches to identify the biologic relevance of our GWAS. Results: GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups. To identify biologic context for these results, we constructed a coexpression network to define modules of genes with similar patterns of CD4+ gene expression (coexpression modules) that could serve as constructs of broader gene expression. 6 of the 22 GWAS loci with P-value ≤ 1x10−6 tagged one particular coexpression module (4.0-fold enrichment, P-value 0.0029), and this module also had the greatest enrichment (3.4-fold enrichment...

Genome-wide copy number analysis in esophageal adenocarcinoma using high-density single-nucleotide polymorphism arrays

Nancarrow, D.; Handoko, H.; Smithers, B.; Gotley, D.; Drew, P.; Watson, D.; Clouston, A.; Hayward, N.; Whiteman, D.
Fonte: Amer Assoc Cancer Research Publicador: Amer Assoc Cancer Research
Tipo: Artigo de Revista Científica
Publicado em //2008 EN
Relevância na Pesquisa
86.03%
We applied whole-genome single-nucleotide polymorphism arrays to define a comprehensive genetic profile of 23 esophageal adenocarcinoma (EAC) primary tumor biopsies based on loss of heterozygosity (LOH) and DNA copy number changes. Alterations were common, averaging 97 (range, 23–208) per tumor. LOH and gains averaged 33 (range, 3–83) and 31 (range, 11–73) per tumor, respectively. Copy neutral LOH events averaged 27 (range, 7–57) per EAC. We noted 126 homozygous deletions (HD) across the EAC panel (range, 0–11 in individual tumors). Frequent HDs within FHIT (17 of 23), WWOX (8 of 23), and DMD (6 of 23) suggest a role for common fragile sites or genomic instability in EAC etiology. HDs were also noted for known tumor suppressor genes (TSG), including CDKN2A, CDKN2B, SMAD4, and GALR1, and identified PDE4D and MGC48628 as potentially novel TSGs. All tumors showed LOH for most of chromosome 17p, suggesting that TSGs other than TP53 may be targeted. Frequent gains were noted around MYC (13 of 23), BCL9 (12 of 23), CTAGE1 (14 of 23), and ZNF217 (12 of 23). Thus, we have confirmed previous reports indicating frequent changes to FHIT, CDKN2A, TP53, and MYC in EAC and identified additional genes of interest. Meta-analysis of previous genome-wide EAC studies together with the data presented here highlighted consistent regions of gain on 8q...

Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method

Kenta, T.; Gratten, J.; Watson-Haigh, N.S.; Hinten, G.N.; Slate, J.; Butlin, R.K.; Burke, T.
Fonte: Blackwell Publishing Publicador: Blackwell Publishing
Tipo: Artigo de Revista Científica
Publicado em //2008 EN
Relevância na Pesquisa
96.03%
We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous amplification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-µL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.; T. Kenta, J. Gratten, N. S. Haigh, G. N. Hinten, J. Slate, R. K. Butlin, and T. Burke

Genotyping single nucleotide polymorphisms for selection of barley b-amylase alleles

Paris, M.; Jones, M.; Eglinton, J.
Fonte: Kluwer Academic Publ Publicador: Kluwer Academic Publ
Tipo: Artigo de Revista Científica
Publicado em //2002 EN
Relevância na Pesquisa
86.07%
A high-throughput single nucleotide polymorphism (SNP) genotyping system was developed and used to select barley seedlings carrying superior alleles of beta-amylase. In the malting process, beta-amylase is a key enzyme involved in the degradation of starch. Four allelic forms of the enzyme are found in barley, each exhibiting a different rate of thermal inactivation, or thermostability. The level of thermostability influences starch degradation, which determines the yield of fermentable sugars for alcohol production during brewing. Control of the fermentability level is important for barley breeding programs to allow targeting quality profiles of new varieties to suit end-user requirements. Alignment of the cDNA sequences encoding the 4 enzyme forms revealed 6 SNPs (cSNPs). The 4 alleles could be identified unambiguously by codominantly genotyping 2 of the cSNPs using a duplex single nucleotide primer extension (SNuPE) assay. Two genotyping primers with their 3' ends directly flanking the selected SNPs were annealed to the amplified target sequences and extended by single dideoxynucleotides complementary to the polymorphic nucleotides. Extended primers were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). Making use of the inherent molecular weight difference between DNA bases...

Single-nucleotide polymorphism associations with preterm delivery: a case-control replication study and meta-analysis

O'Callaghan, M.; MacLennan, A.; McMichael, G.; Haan, E.; Dekker, G.
Fonte: Int Pediatric Research Foundation Inc Publicador: Int Pediatric Research Foundation Inc
Tipo: Artigo de Revista Científica
Publicado em //2013 EN
Relevância na Pesquisa
86.03%
BACKGROUND: The aim of this study was to replicate single-nucleotide polymorphism (SNP) associations with preterm birth (PTB; birth at <37 completed weeks of gestation) and synthesize currently available evidence using meta-analysis. METHODS: Spontaneous PTB cases and controls were selected from an existing cohort. Candidate SNPs were taken from an existing genotype panel. A systematic review was conducted for each SNP in the panel to determine suitability as a PTB candidate. Those with significant associations previously reported in Caucasians were selected for replication. Candidate SNPs were already genotyped in cases and controls and clinical data were accessed from state perinatal and cerebral palsy databases. Association analysis was conducted between each SNP and PTB, and meta-analysis was conducted if there were ≥ 3 studies in the literature. Maternal and fetal SNPs were considered as separate candidates. RESULTS: A cohort of 170 cases and 583 controls was formed. Eight SNPs from the original panel of genotyped SNPs were selected as PTB candidates and for replication on the basis of systematic literature review results. In our cohort, fetal factor V Leiden (FVL) was significantly associated with PTB (odds ratio (OR): 2.6...

A single-nucleotide-polymorphism real-time PCR assay for genotyping of Mycobacterium tuberculosis complex in peri-urban Kampala

Wampande, Eddie M.; Hatzios, Stavroula K.; Achan, Beatrice; Mupere, Ezekiel; Nsereko, Mary; Mayanja, Harriet K.; Eisenach, Kathleen; Boom, W Henry; Gagneux, Sebastien; Joloba, Moses L.
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
96.13%
Background: Accurate and high-throughput genotyping of Mycobacterium tuberculosis complex (MTBC) may be important for understanding the epidemiology and pathogenesis of tuberculosis (TB). In this study, we report the development of a LightCycler® real-time PCR single-nucleotide-polymorphism (LRPS) assay for the rapid determination of MTBC lineages/sublineages in minimally processed sputum samples from TB patients. Method Genotyping analysis of 70 MTBC strains was performed using the Long Sequence Polymorphism-PCR (LSP-PCR) technique and the LRPS assay in parallel. For targeted sequencing, 9 MTBC isolates (three isolates per MTBC lineage) were analyzed for lineage-specific single nucleotide polymorphisms (SNPs) in the following three genes to verify LRPS results: Rv004c for MTB Uganda family, Rv2962 for MTB lineage 4, and Rv0129c for MTB lineage 3. The MTBC lineages present in 300 smear-positive sputum samples were then determined by the validated LRPS method without prior culturing. Results: The LSP-PCR and LRPS assays produced consistent genotyping data for all 70 MTBC strains; however, the LSP-PCR assay was 10-fold less sensitive than the LRPS method and required higher DNA concentrations to successfully characterize the MTBC lineage of certain samples. Targeted sequencing of genes containing lineage-specific SNPs was 100 % concordant with the genotyping results and provided further validation of the LRPS assay. Of the 300 sputum samples analyzed...

Development and use of single nucleotide polymorphism markers for candidate resistance genes in wild peanuts (Arachis spp)

Alves, Dione Mendes Teixeira; Pereira, Rinaldo Wellerson; Leal-Bertioli, Soraya Cristina de Macedo; Moretzsohn, Márcio de Carvalho; Guimarães, Patrícia M.; Bertioli, David John
Fonte: Universidade Católica de Brasília Publicador: Universidade Católica de Brasília
Tipo: Artigo de Revista Científica Formato: Texto
EN
Relevância na Pesquisa
86.05%
The cultivated peanut (Arachis hypogaea L.) is an al¬lotetraploid of recent origin, with an AABB genome and low genetic diversity. Perhaps because of its limited genetic diversity, this spe¬cies lacks resistance to a number of important pests and diseases. In contrast, wild species of Arachis are genetically diverse and are rich sources of disease resistance genes. Consequently, a study of wild peanut relatives is attractive from two points of view: to help un¬derstand peanut genetics and to characterize wild alleles that could confer disease resistance. With this in mind, a diploid population from a cross between two wild peanut relatives was developed, in order to make a dense genetic map that could serve as a reference for pea-nut genetics and in order to characterize the regions of the Arachis genome that code for disease resistance. We tested two methods for developing and genotyping single nucleotide polymorphisms in can¬didate genes for disease resistance; one is based on single-base primer extension methods and the other is based on amplification refractory mutation system-polymerase chain reaction. We found single-base pair extension to be an efficient method, suitable for high-throughput, single-nucleotide polymorphism mapping; it allowed us to locate five candidate genes for resistance on our genetic map.

Association of polymorphism in Exon 3 of toll-like receptor 4 gene with somatic cell score and milk production traits in Holstein dairy cows of Iran

Noori,R.; Mahdavi,A.H.; Edriss,M.A.; Rahmani,H.R.; Talebi,M.; Soltani-Ghombavani,M.
Fonte: South African Journal of Animal Science Publicador: South African Journal of Animal Science
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/40/2013 EN
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Mastitis is a complex inflammatory disease of the mammary gland that is caused by the invasion of pathogens. This leads to reduced synthetic capacity, compositional changes and increased somatic cell counts (SCC) in milk. Toll-like receptor 4 (TLR4) is a cell surface receptor that recognizes lipopolysaccharides (LPS) of gram-negative bacteria. Its role in pathogen recognition and the subsequent immune response and differential expression of the gene during mastitis have prompted the investigation of TLR4 gene as a candidate to improve mastitis resistance in dairy cattle. The aim of this study was to analyse the possible association of a single nucleotide polymorphism (SNP) in putative co-receptor-binding region 2 (T4CRBR2) of the TLR4 gene with somatic cell score (SCS) and milk-related traits in 408 Iranian Holstein cows. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was performed for genotyping. The effect of the genotype on the traits of interest was analysed using the general linear model (GLM) procedure of SAS software. The B allele frequency was 0.634 and the distribution of genotypes was not in Hardy-Weinberg equilibrium in the overall population. The B allele of the SNP was associated with higher 305-day milk yield and breeding value for milk yield...