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1.
An Bras Dermatol ; 94(6): 658-663, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31789248

RESUMO

BACKGROUND: Palmoplantar pustulosis is considered to be a localized pustular psoriasis confined to the palms and soles. Mutation of the IL36RN gene, encoding interleukin-36 receptor antagonist (IL-36Ra), is associated with generalized pustular psoriasis, but IL36RN mutations in Chinese palmoplantar pustulosis patients have not previously been investigated. OBJECTIVE: The aim of this study was to evaluate the mutation of IL36RN in Chinese patients with palmoplantar pustulosis. METHODS: Fifty-one Han Chinese patients with palmoplantar pustulosis were recruited. All exons and exon-intron boundary sequences of IL36RN were amplified in polymerase chain reactions, and Sanger sequencing of the amplicons was performed. RESULTS: Among the 51 palmoplantar pustulosis patients, four different single-base substitutions were identified in nine patients. The mutations were c.140A>G/p.Asn47Ser in five patients, c.258G>A/p.Met86IIe in two patients, and c.115+6T>C and c.169G>A/p.Val57IIe in one patient each. All mutations were heterozygous. Comparison with the human genome database and reported literature suggested that these variants may not be pathogenic mutations causing palmoplantar pustulosis. Furthermore, there was no difference in disease severity, onset age, or disease duration between patients with these heterozygous IL36RN variants and those without (p>0.1). STUDY LIMITATION: Lack of the further evaluation of IL36Ra protein in palmoplantar pustulosis lesions. CONCLUSIONS: The four variants of IL36RN identified did not appear to be associated with the specific phenotypes of palmoplantar pustulosis.


Assuntos
Interleucinas/genética , Mutação , Psoríase/genética , Adulto , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Grupo com Ancestrais do Continente Asiático/genética , China , Feminino , Dermatoses do Pé/genética , Dermatoses do Pé/patologia , Estudos de Associação Genética , Dermatoses da Mão/genética , Dermatoses da Mão/patologia , Heterozigoto , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo , Psoríase/patologia , Análise de Sequência de DNA , Estatísticas não Paramétricas
2.
BMC Plant Biol ; 19(1): 588, 2019 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-31881840

RESUMO

BACKGROUND: Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. RESULTS: The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. CONCLUSIONS: This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.


Assuntos
Cromossomos de Plantas , Sesamum/genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Mapeamento Cromossômico/métodos , Marcadores Genéticos , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Sementes/genética , Sesamum/crescimento & desenvolvimento
3.
Environ Pollut ; 255(Pt 1): 113238, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31655460

RESUMO

The effects of exposure to different levels of ionising radiation were assessed on the genetic, epigenetic and microbiome characteristics of the "hologenome" of earthworms collected at sites within the Chernobyl exclusion zone (CEZ). The earthworms Aporrectodea caliginosa (Savigny, 1826) and Octolasion lacteum (Örley, 1881) were the two species that were most frequently found at visited sites, however, only O. lacteum was present at sufficient number across different exposure levels to enable comparative hologenome analysis. The identification of morphotype O. lacteum as a probable single clade was established using a combination of mitochondrial (cytochrome oxidase I) and nuclear genome (Amplified Fragment Length Polymorphism (AFLP) using MspI loci). No clear site associated differences in population genetic structure was found between populations using the AFLP marker loci. Further, no relationship between ionising radiation exposure levels and the percentage of methylated loci or pattern of distribution of DNA methylation marks was found. Microbiome structure was clearly site dependent, with gut microbiome community structure and diversity being systematically associated with calculated site-specific earthworm dose rates. There was, however, also co-correlation between earthworm dose rates and other soil properties, notably soil pH; a property known to affect soil bacterial community structure. Such co-correlation means that it is not possible to attribute microbiome changes unequivocally to radionuclide exposure. A better understanding of the relationship between radionuclide exposure soil properties and their interactions on bacterial microbiome community response is, therefore, needed to establish whether these the observed microbiome changes are attributed directly to radiation exposure, other soil properties or to an interaction between multiple variables at sites within the CEZ.


Assuntos
Acidente Nuclear de Chernobyl , Microbiota/efeitos da radiação , Oligoquetos/fisiologia , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Animais , Bactérias/efeitos dos fármacos , Epigênese Genética , Microbioma Gastrointestinal , Oligoquetos/efeitos dos fármacos , Oligoquetos/microbiologia , Oligoquetos/efeitos da radiação , Exposição à Radiação , Monitoramento de Radiação , Radioisótopos , Solo/química
4.
Zhonghua Gan Zang Bing Za Zhi ; 27(8): 638-642, 2019 Aug 20.
Artigo em Chinês | MEDLINE | ID: mdl-31594083

RESUMO

Objective: To investigate the changes in clinical characteristics and laboratory indexes before and after the termination of pregnancy in patients with acute fatty liver of pregnancy (AFLP). Methods: Patients with acute fatty liver of pregnancy who had been admitted to the Department of Obstetrics and Gynecology at the Second Affiliated Hospital of Chongqing Medical University and Chongqing Municipal People's Hospital of Jiangbei District between 2007 and 2018 were selected. Clinical characteristics and complications during diagnosis and treatment, changes in blood coagulation, liver and kidney function, and postpartum recovery were collected for retrospectively analysis. Results: 54 cases with average gestational age of 35.0±1.7 weeks at third trimester of pregnancy with AFLP were treated. The most common gastrointestinal symptoms were yellow urine, nausea and vomiting. All patients had elevated bilirubin. 90.7% patients had changes in blood coagulation function and 68.5% had elevated serum creatinine. Transaminase levels were dropped rapidly within 1-2 days after the termination of pregnancy. Total bilirubin recovery was slow and partially recovered after 6-8 days. Serum creatinine and BUN increased slightly after delivery, reaching a peak at 3-4 days and then began to deplete. There was slight change in prothrombin time and fibrinogen after delivery, but returned to normal level after 5-6 days. The most common complications were AKI (74.1%), LF (42.6%), PPH (40.7%) and DIC (33.3%). Twenty-three of the 54 cases (42.6%) progressed to acute liver failure. AFLP complicated with ALF course was significantly longer than healthy controls, and the disease severity was significantly increased, with a mortality rate of 17.4% (4/23), and 0 in healthy controls. The difference was statistically significant. Conclusion: Early diagnosis and termination of pregnancy are the key factors to determine the prognosis of pregnant patients with acute fatty liver. Blood coagulation function does not deteriorate after termination of pregnancy and renal function begins to recover after 4 days with slight restoration of liver function. The control of complications is an important factor to determine the prognosis of patients.


Assuntos
Fígado Gorduroso/diagnóstico , Complicações na Gravidez/diagnóstico , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Estudos de Casos e Controles , Feminino , Humanos , Período Pós-Parto , Gravidez , Estudos Retrospectivos
5.
Medicine (Baltimore) ; 98(40): e17313, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31577725

RESUMO

To investigate the impact of carriage of single nucleotide polymorphisms (SNPs) of the Toll-like receptor-4 (TLR4) and of autophagy-related gene 16-like-1 (ATG16L1) in preterm delivery (PTD).A prospective cohort of 145 pregnant women was studied. Women were prospectively followed-up until delivery. Genotyping for rs4986790 (Asp299Gly transition) and rs4986791 (Thr399Ile transition) of TLR4 and for rs2241880 of ATG16L1 was done by PCR-restriction fragment length polymorphism. The primary study endpoint was the impact of carriage of minor alleles of TLR4 on early PTD before gestational week 32. Associations with human chorionic gonadotrophin (hCG) were also analyzed. Peripheral blood mononuclear cells were isolated from 15 healthy women and stimulated for cytokine production.No difference in clinical characteristics was observed between women delivering full term and preterm. The frequency of early PTD was 25% among women carrying minor alleles of TLR4 and 6.8% among women carrying major alleles (P: .032). Odds ratios for PTD were 3.85 among women carrying the GG genotype of rs2241880 and major alleles of TLR4 and 0.26 among carriers of GG genotype and minor alleles of TLR4 (P: .030). The co-presence of GG genotype of rs2241880 and hCG above 70 U/L was an independent variable for PTD. Stimulated production of interleukin-6 was greater among women with GG genotypes of rs2241880.Minor alleles of SNPs of TLR4 predispose to early PTD. The GG genotype of rs2241880 of ATG16L1 is associated with PTD when hCG is supra-elevated.


Assuntos
Proteínas Relacionadas à Autofagia/genética , Nascimento Prematuro/genética , Receptor 4 Toll-Like/genética , Adulto , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Autofagia/fisiologia , Gonadotropina Coriônica/sangue , Citocinas/biossíntese , Feminino , Frequência do Gene , Predisposição Genética para Doença , Genótipo , Idade Gestacional , Humanos , Polimorfismo de Nucleotídeo Único , Gravidez , Estudos Prospectivos
6.
Acta Biochim Pol ; 66(3): 315-319, 2019 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-31518089

RESUMO

The epidermal growth factor receptor (EGFR) is a tyrosine kinase cell surface protein that plays a role in the process of carcinogenesis. In this study, we investigated the association between EGFR rs2233947 and rs884225 SNPs and the risk of lung cancer. A total of 258 participants (129 lung cancer patients and 129 healthy controls) took part in the study. Restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) technique was used to genotype EGFR SNPs. A strong association was detected between rs2233947 and lung cancer (P<0.01). Compared with the rs2293347 GG genotype, the AA/AG genotypes were associated with a significantly decreased risk of lung cancer (adjusted OR = 0.28, 95% confidence interval [CI]=0.13-0.61, P<0.01). EGFR rs2233947 correlated with lung cancer in males, smokers, and in the squamous cell carcinoma lung cancer subtype (P<0.01). Haplotype analysis of rs2233947 and rs884225 showed that the AA haplotype was associated with a significantly decreased risk of lung cancer (P<0.01). The data presented in the current study support a protective role for the rs2233947 A allele against the development of lung cancer. This result, however, requires further validation in a larger population.


Assuntos
Carcinoma de Células Escamosas/genética , Neoplasias Pulmonares/genética , Polimorfismo de Fragmento de Restrição/genética , Polimorfismo de Nucleotídeo Único/genética , Idoso , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Estudos de Casos e Controles , Receptores ErbB/genética , Feminino , Frequência do Gene/genética , Predisposição Genética para Doença , Genótipo , Haplótipos , Humanos , Jordânia , Masculino , Pessoa de Meia-Idade , Fatores Sexuais , Fumar/efeitos adversos
7.
Braz J Infect Dis ; 23(5): 322-330, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31539511

RESUMO

At present, there is no standardized marker that is routinely used in clinical laboratories to diagnose coccidioidomycosis. Thus, the goals of this study were to obtain a sequence characterized amplified region (SCAR) marker for the identification of Coccidioides spp., evaluate its specificity and sensitivity in fungal DNA-spiked blood and sputum samples, and compare it with previously described molecular markers. Specific amplified fragment length polymorphism (AFLP) amplicons for Coccidioides immitis and Coccidioides posadasii were cloned into the vector pGEM® -T Easy vector and sequenced to develop a SCAR marker. Oligonucleotides were designed to identify Coccidioides spp. by polymerase chain reaction (PCR), and the specificity and sensitivity of these oligonucleotides were tested with the DNA from related pathogens. The specificity and sensitivity of the SCAR marker was evaluated with blood and sputum samples spiked with Coccidioides DNA and compared with other previously described markers (621, GAC2, and Ag2/PRA). In addition, the conditions for its use were established using biological samples. A specific marker named SCAR300 was obtained to identify Coccidioides spp. that exhibited good sensitivity and specificity. The results showed that all of the markers tested in this study can identify Coccidioides spp. However, the SCAR300 and 621 markers were the most sensitive, whereas the SCAR300 marker was the most specific. Thus, the SCAR300 marker is a useful tool to identify Coccidioides spp.


Assuntos
Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Coccidioides/genética , Coccidioidomicose/diagnóstico , DNA Fúngico/genética , Sequência de Bases , Coccidioides/classificação , Coccidioides/isolamento & purificação , Coccidioidomicose/microbiologia , Humanos , Reação em Cadeia da Polimerase , Polimorfismo Genético , Sensibilidade e Especificidade
8.
Plant Physiol Biochem ; 143: 299-307, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31539759

RESUMO

The genetic and epigenetic stability (analysis of DNA methylation using MSAP markers) of mint (Mentha x piperita L.) apices was studied after each step of a cryopreservation protocol, by encapsulation-dehydration. The effect of the addition of an antioxidant (ascorbic acid) during one of the protocol steps was also evaluated. Eight-week old in vitro recovered shoots from apices after each step of the protocol were genetically stable when compared to control in vitro shoots, using RAPD and AFLP markers. The addition of ascorbic acid in the medium with the highest sucrose concentration did not improve recovery and did not have any effect on stability. Apices sampled immediately after each step showed increased epigenetic differences as the protocol advanced, compared to in vitro control apices, in particular related to de novo methylation events. However, after one-day in vitro recovery, methylation status was similar to control apices. To improve the quality of methylation data interpretation, a simple and fast method for MSAP markers analysis, based on R programming, has been developed which allows the statistical comparison of treatments to control samples and its graphical representation.


Assuntos
DNA de Plantas/genética , Mentha/metabolismo , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Antioxidantes/metabolismo , Criopreservação , Metilação de DNA/genética , Metilação de DNA/fisiologia , Desidratação , Epigênese Genética/genética , Mentha/genética , Brotos de Planta/genética , Brotos de Planta/metabolismo
9.
Zhonghua Liu Xing Bing Xue Za Zhi ; 40(8): 982-987, 2019 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-31484265

RESUMO

Objective: To understand the distribution of HIV-1 genotypes and the status of drug resistance among people living with HIV who had prepared to initiate antiretroviral therapy (ART) in Dehong Dai and Jingpo autonomous prefecture (Dehong). Methods: A total of 170 adults with HIV were recruited in Dehong from January to June 2017, before initiating ART. HIV-1 pol genes were amplified and used to analyze the HIV-1 genotypes and drug resistance. Results: A total of 147 samples were successfully sequenced. Based on the phylogenetic analysis, 12 HIV-1 genotypes were found among the subjects, including three predominant genotypes such as subtype C (29.9%, 44/147), unique recombinant forms (URFs) (27.2%, 40/147) and CRF01_AE (19.7%, 29/147). Circulating recombinant forms (CRFs) which were newly identified in this area in recent years were also found among these subjects, including CRF62_BC, CRF64_BC, CRF86_BC and CRF96_cpx. The distribution of HIV-1 genotypes between heterosexual transmission or intravenous drug use, showed statistical difference. Surveillance drug resistance mutations (SDRMs) were found among 8.8% (13/147) of the subjects. Proportion of drug resistant strains among injecting drug users (25.0%, 8/32) was higher than that among those heterosexual transmitted individuals (4.6%, 5/109, χ(2)=10.166, P=0.002). Conclusions: Among people living with HIV-1 who had prepared to initiate ART, their HIV-1 genetics were highly complicated, with moderate prevalence rate of HIV-1 drug-resistant strains.


Assuntos
Fármacos Anti-HIV/uso terapêutico , Farmacorresistência Viral/genética , Infecções por HIV/tratamento farmacológico , Infecções por HIV/virologia , HIV-1/genética , Adulto , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Fármacos Anti-HIV/farmacologia , Terapia Antirretroviral de Alta Atividade , China/epidemiologia , Genes pol , Genótipo , Infecções por HIV/epidemiologia , HIV-1/efeitos dos fármacos , Humanos , Filogenia
10.
Genes (Basel) ; 10(8)2019 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-31370324

RESUMO

A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht's larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.


Assuntos
Cromossomos de Plantas/genética , Larix/genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados/métodos , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados/normas , Ligação Genética , Genoma de Planta , Polimorfismo de Nucleotídeo Único
11.
Plant Dis ; 103(9): 2252-2262, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31298990

RESUMO

Spot blotch, caused by the fungal pathogen Cochliobolus sativus, is a limiting factor for barley (Hordeum vulgare) production in northeast China, which causes significant grain yield losses and kernel quality degradation. It is critical to determine the virulence diversity of C. sativus populations for barley resistance breeding and the judicious grouping of available resistance varieties according to the predominant pathotypes in disease epidemic regions. With little information on the barley pathogen in China, this study selected 12 typical barley genotypes to differentiate the pathotypes of C. sativus isolates collected in China. Seventy-one isolates were grouped into 19 Chinese pathotypes based on infection responses. Seventeen isolates were classified as pathotype 3, which has only been identified in China, whereas most (52 of 71) were classified as pathotype 1. All of the tested isolates had low virulence on the North Dakota (ND) durable, resistant line ND B112. Using 22 selected amplified fragment-length polymorphism (AFLP) primer combinations, genetic polymorphism was used to analyze 68 isolates, which clustered into three distinct groups using the unweighted pair group method average with the genetic distance coefficient. No relationship was found between the virulence of isolates and their origins. Isolates of the same pathotype or those collected from the same location did not group into clusters based on the AFLP analysis.


Assuntos
Ascomicetos , Variação Genética , Hordeum , Virulência , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Ascomicetos/classificação , Ascomicetos/genética , China , Hordeum/microbiologia , Doenças das Plantas/microbiologia , Polimorfismo Genético , Virulência/genética
12.
Int J Mol Sci ; 20(13)2019 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-31261867

RESUMO

Most methods developed for detecting known single nucleotide polymorphisms (SNP) and deletion-insertion polymorphisms (DIP) are dependent on sequence conservation around the SNP/DIP and are therefore not suitable for application to heterogeneous organisms. Here we describe a novel, versatile and simple PCR-RFLP procedure baptised 'derived Polymorphic Amplified Cleaved Sequence' (dPACS) for genotyping individual samples. The notable advantage of the method is that it employs a pair of primers that cover the entire fragment to be amplified except for one or few diagnostic bases around the SNP/DIP being investigated. As such, it provides greater opportunities to introduce mismatches in one or both of the 35-55 bp primers for creating a restriction site that unambiguously differentiates wild from mutant sequences following PCR-RFLP and horizontal MetaPhorTM gel electrophoresis. Selection of effective restriction enzymes and primers is aided by the newly developed dPACS 1.0 software. The highly transferable dPACS procedure is exemplified here with the positive detection (in up to 24 grass and broadleaf species tested) of wild type proline106 of 5-enolpyruvylshikimate-3-phosphate synthase and its serine, threonine and alanine variants that confer resistance to glyphosate, and serine264 and isoleucine2041 which are key target-site determinants for weed sensitivities to some photosystem II and acetyl-CoA carboxylase inhibiting herbicides, respectively.


Assuntos
Análise do Polimorfismo de Comprimento de Fragmentos Amplificados/métodos , Técnicas de Genotipagem/métodos , Mutação INDEL , Polimorfismo de Nucleotídeo Único , 3-Fosfoshikimato 1-Carboxiviniltransferase/genética , Amaranthus/genética , Estudo de Associação Genômica Ampla/métodos , Lolium/genética , Proteínas de Plantas/genética
13.
J Dairy Sci ; 102(9): 7765-7772, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31301828

RESUMO

The expression of genes associated with aflatoxin biosynthesis by different Aspergillus flavus strains growing on a cheese model system has not been studied. To control aflatoxin biosynthesis, it would be useful to understand the changes in gene expression during cheesemaking and relate those changes to toxin production. The objective of this study was to evaluate the effects of pH, water activity, and temperature on the expression of 2 regulatory genes (aflR and aflS) and 1 structural gene (aflP) involved in aflatoxin biosynthesis, using 3 aflatoxigenic A. flavus strains growing on a cheese-based medium and reverse-transcription real-time PCR. The gene expression patterns were influenced by A. flavus strain and environmental conditions. The structural gene aflP and the regulatory genes aflR and aflS showed similar expression patterns in each A. flavus strain, but we also observed inter-strain differences. We observed the highest expression levels at 6 and 9 d of incubation by A. flavus strains CQ8 and CQ103, and saw a decrease in the days following. Strain CQ7 showed the lowest expression of these genes. We observed the highest expression levels of these genes at pH 5.5, water activity 0.95, and 20 to 25°C; strain CQ103 showed a different pattern for the aflS gene, with maximum expression at pH 6.0 on d 6 of incubation. For the 3 strains, we found a strong correlation between the relative expression of the aflR and aflS genes and the concentration of aflatoxins under conditions that simulated cheese ripening. Control strategies to avoid aflatoxin contamination during cheesemaking could use the detection of regulatory gene expression.


Assuntos
Aflatoxinas/biossíntese , Aspergillus flavus/metabolismo , Queijo/microbiologia , Microbiologia de Alimentos , Regulação Fúngica da Expressão Gênica , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados
14.
J Genet ; 98(2)2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31204696

RESUMO

Evaluation of sequence variations in the internal transcribed spacer (ITS) region of 19 accessions, comprising of 11 accessions of Chenopodium quinoa, eight accessions of Chenopodium album and 165 retrieved sequences of different species of Chenopodium belonging to subfamily Chenopodioideae revealed a higher intraspecific genetic diversity in Himalayan C. album than that in C. quinoa. ITS and amplified fragment-length profiles of the accessions suggest the existence of accessions of Himalayan C. album as heteromorphs of the same species rather than a heterogenous assemblage of taxa. While the evolutionary relationship reconstructed from variations in 184 sequences of ITS region from species belonging to Chenopodiaceae, Amaranthaceae, Polygonaceae and Nelumbonaceae established a paraphyletic evolution of family Chenopodiaceae, it also revealed a monophyletic evolution of Chenopodieae I. The reconstruction also established five independent lineages of the subfamily Chenopodioideae with C. album as a sister clade of C. quinoa within the tribe Chenopodieae I. The results also indicate a much younger age for Himalayan chenopods (C. album) than the reported crown age of Chenopodieae I.


Assuntos
Chenopodium/classificação , Chenopodium/genética , DNA Espaçador Ribossômico/genética , Evolução Molecular , Variação Genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Biologia Computacional/métodos , Conformação de Ácido Nucleico , Filogenia , Reação em Cadeia da Polimerase , Análise de Sequência de DNA
15.
PLoS One ; 14(6): e0218562, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31251752

RESUMO

The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.


Assuntos
Variação Genética , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo Único , Triticum/classificação , Triticum/genética , Alelos , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Frequência do Gene , Marcadores Genéticos , Genética Populacional , Genótipo , Filogenia , Reação em Cadeia da Polimerase
16.
Afr Health Sci ; 19(1): 1346-1352, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31148960

RESUMO

Introduction: Hymenolepis nana is a zoonotic tapeworm with widespread distribution. The goal of the present study was to identify the parasite in the specimens collected from NorthWestern regions of Iran using PCR-sequencing method. Methods: A total of 1521 stool samples were collected from the study individuals. Initially, the identification of hymenolepis nana was confirmed by parasitological method including direct wet-mount and formalin-ethyl acetate concentration methods. Afterward, PCR-sequencing analysis of ribosomal ITS2 fragment was targeted to investigate the molecular identification of the parasite. Results: Overall, 0.65% (10/1521) of the isolates were contaminated with H. nana in formalin-ethyl acetate concentration. All ten isolates were succefully amplified by PCR and further sequenced. The determined sequences were deposited in GenBank under the accession numbers MH337810 -MH337819. Conclusion: Our results clarified the presence of H. nana among the patients in the study areas. In addition, the molecular technique could be accessible when the human eggs are the only sources available to identify and diagnose the parasite.


Assuntos
DNA Ribossômico/genética , Himenolepíase/parasitologia , Hymenolepis nana/genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Animais , Fezes/parasitologia , Marcadores Genéticos/genética , Humanos , Himenolepíase/diagnóstico , Hymenolepis nana/isolamento & purificação , Irã (Geográfico) , Filogenia , Reação em Cadeia da Polimerase
17.
Pediatr Int ; 61(8): 759-767, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31211452

RESUMO

BACKGROUND: While leukocyte telomere length has been linked with altered risk in adult cancer, limited information is available on its association with risk in pediatric solid tumors. We investigated the association of telomeric alterations with risk of pediatric solid tumors. We also investigated whether altered telomeres cooperated with the TP53 rs1042522, MDM2 rs2279744 and CDKN1A (p21cip1 ) rs1059234 single-nucleotide polymorphisms to modify cancer risk. METHODS: A total of 101 tumor patients and 202 controls were recruited for this age- and gender-matched case-control study. Relative telomere length (RTL) was determined in peripheral blood leukocytes using quantitative real-time polymerase chain reaction (PCR), and the polymorphisms were genotyped using PCR-restriction fragment length polymorphism. RESULTS: Using median RTL in the healthy controls as a cut-off, children with longer telomeres were at an increased risk of developing a solid tumor (OR, 2.70; P < 0.01). When participants were categorized according to control RTL quartiles, a significant dose-response relationship was observed (χ2  = 10.95; P < 0.001). The risk for tumors increased nearly threefold (P = 0.001) for the triple interaction RTL × TP53 rs1042522 × p21cip1 rs1059234 compared with the maximum effect of any single factor, although the interaction effect was less than additive. The MDM2 rs2279744 GG genotype reduced pediatric solid tumor risk significantly (OR, 0.51). CONCLUSION: Combined analysis of telomeres and genetic polymorphisms in the TP53 pathway can provide important clues to understanding pediatric solid tumor etiology.


Assuntos
Biomarcadores Tumorais/genética , Inibidor de Quinase Dependente de Ciclina p21/genética , Genes p53/genética , Neoplasias/genética , Polimorfismo de Nucleotídeo Único , Proteínas Proto-Oncogênicas c-mdm2/genética , Homeostase do Telômero , Adolescente , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Estudos de Casos e Controles , Criança , Pré-Escolar , Feminino , Predisposição Genética para Doença , Humanos , Lactente , Recém-Nascido , Masculino , Neoplasias/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real , Medição de Risco , Sensibilidade e Especificidade
18.
Ideggyogy Sz ; 72(5-6): 181-186, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-31241262

RESUMO

Background and purpose: Methylation is a key epigenetic modification of DNA and regarding its impact on epilepsy, it is argued that "DNA methylation may play an important role in seizure susceptibility and maintenance of the disorder". DNA methylation status of KCC2 (SCL12A5) and NKCC1 (SCL12A2) associated with refractory temporal lobe epilepsy was investigated in our study. Methods: Thirty-eight patients with temporal lobe epilepsy (TLE) who were diagnosed by video EEG monitoring and 32 healthy control subjects were included in the study. Twenty-three patients in TLE group were men and the remaining 15 were women. Among them, 27 had unilateral temporal focus (9 with right; 18 with left) and 11 patients had bilateral TLE. We analyzed promoter region methylation status of the KCC2 (SCL12A5) and NKCC1 (SCL12A2) genes in the case and control groups. Gene regions of interest were amplified through PCR and sequencing was accomplished with pyro-sequencing. Results: We found a significant relationship between TLE and methylation on the NKCC1. However, there was no association between TLE and methylation on the KCC2 gene. Also, we found no association between right or left and unilateral or bilateral foci of TLE. There was no relationship between TLE and methylation on the NKCC1and KCC2 genes in terms of mesial temporal sclerosis in cranial MRI, head trauma or febrile convulsions. Conclusion: The methylation of NKCC1 can be a mecha-nism of refractory temporal lobe epilepsy. There are limited findings about DNA methylation in TLE. Therefore, further studies with large sample sizes are necessary.


Assuntos
Metilação de DNA , Epilepsia do Lobo Temporal/metabolismo , Membro 2 da Família 12 de Carreador de Soluto/metabolismo , Simportadores/metabolismo , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Estudos de Casos e Controles , Eletroencefalografia , Epilepsia do Lobo Temporal/diagnóstico , Epilepsia do Lobo Temporal/genética , Feminino , Humanos , Imagem por Ressonância Magnética , Masculino , Regiões Promotoras Genéticas , Membro 2 da Família 12 de Carreador de Soluto/genética , Simportadores/genética
19.
Plant Dis ; 103(7): 1728-1737, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31107642

RESUMO

Curvularia leaf spot (CuLS), caused by Curvularia lunata, is a devasting foliar disease in the maize-growing regions of China. Resistant varieties were widely planted in these regions in response to CuLS. However, over time, C. lunata has gradually adapted to the selective pressure and, in recent years, the incidence of CuLS has increased. To assess the correlation between virulence and genetic diversity, a total of 111 isolates was collected from 15 maize-growing regions located in nine provinces in China. These isolates were evaluated for virulence on maize using nine differential hosts: Shen135, CN165, Mo17, Luyuan92, 78599, Ye478, B73, E28, and Huangzaosi. To evaluate the genetic diversity, 657 polymorphic amplified fragment length polymorphism markers were generated. Results showed that the isolates could be grouped into three pathotypes according to the phenotypic expression of the differential inbred lines. Isolates were clustered into two genetic diversity groups and further divided into subgroups. However, the correlation between virulence and genetic diversity grouping was low. Also, there was a low correlation observed between pathotype and geographic distribution. The ratio of mating type I to mating type II for all isolates was close to 3:4.


Assuntos
Ascomicetos , Doenças das Plantas , Virulência , Zea mays , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Ascomicetos/genética , Ascomicetos/patogenicidade , China , Doenças das Plantas/microbiologia , Virulência/genética , Zea mays/microbiologia
20.
PLoS One ; 14(5): e0216717, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31095626

RESUMO

Plant in vitro vegetative propagation using classical semi-solid culture medium is limited due to the low degree of automation, suboptimal nutrient availability and induced physiological stress which often reduce its efficiency. Temporary Immersion System (TIS) emerged as an innovative approach to optimize and eliminate the drawbacks associated with the conventional system of micropropagation. In this study, both Dioscorea and Musa spp. were subjected to conventional semi-solid culture media, complete immersion in shaking liquid culture media and TIS using RITA bioreactor. In vitro grown plantlets were screened for possible vegetative changes using agro-morphological descriptors while genetic and methylation differences were assessed using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP). In vitro results showed that the number of shoots produced in Musa spp. varied significantly (P≤0.001) with the type of culture system. The highest mean shoot produced was observed with TIS (28.40) and the least using semi-solid culture medium (1.13). For Dioscorea spp., there was no significant interaction between the hormone combination and the culture system. However, the lowest mean shoot value (1.55) was observed in the semi-solid culture medium. Genetic analysis via AFLP using 15 primer pair combinations revealed that the 3 culture systems maintained genetic variation for Musa and Dioscorea spp. under in vitro and field conditions. Results showed 99% and 91% of the total bands were polymorphic under in vitro and field conditions respectively for Musa and 100% polymorphism for Dioscorea under in vitro and field conditions. Methylation investigation via MSAP using 12 primer pair combinations showed 25% and 46% polymorphic methylated-sensitive loci, 100% and 78% of non-methylated loci of the total bands generated under in vitro and field conditions respectively. Unmethylated (HPA+/MSP+) levels were highest in TIS (0.0842) as compared to CI (0.0227) and SS (0.0161) while full methylation or absence of target (HPA-/MSP-) was lowest in TIS (0.5890) and highest in SS (0.7138). For Dioscorea, 52% and 53% methylated sensitive loci and 100% non-methylated loci were polymorphic under in vitro and field conditions respectively. Although in vitro plant tissue culture techniques led to methylation at some loci of both species, there were no observable changes in the phenotype of both crops under field conditions. This also confirmed that not all methylation events lead to phenotypic changes.


Assuntos
Metilação de DNA , Dioscorea/crescimento & desenvolvimento , Dioscorea/genética , Musa/crescimento & desenvolvimento , Musa/genética , Aclimatação/genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Dioscorea/fisiologia , Marcadores Genéticos/genética , Genótipo , Musa/fisiologia
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