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1.
BMC Bioinformatics ; 20(Suppl 9): 495, 2019 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-31757210

RESUMO

BACKGROUND: Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. RESULTS: In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. CONCLUSION: We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.


Assuntos
Elementos de DNA Transponíveis/genética , Bases de Dados Genéticas , Linfócitos/metabolismo , Polimorfismo Genético , Locos de Características Quantitativas/genética , Transcrição Genética , Elementos Alu/genética , Animais , Comportamento , Linhagem Celular , Genoma Humano , Humanos , Imunidade/genética , Repetições Minissatélites/genética
2.
BMC Infect Dis ; 19(1): 908, 2019 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-31664926

RESUMO

BACKGROUND: Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan. METHODS: The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed. RESULTS: The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94-32 (n = 145) and 100-32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes. CONCLUSIONS: Beijing clusters 94-32 and 100-32 are the dominant MTB genotypes in Central Asia. The relative size of 100-32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.


Assuntos
Epidemias , Genótipo , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Estudos Transversais , Feminino , Humanos , Quirguistão/epidemiologia , Masculino , Pessoa de Meia-Idade , Repetições Minissatélites/genética , Epidemiologia Molecular , Tipagem Molecular , Mycobacterium tuberculosis/isolamento & purificação , Fenótipo , Tadjiquistão/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Tuberculose Resistente a Múltiplos Medicamentos/prevenção & controle , Uzbequistão/epidemiologia , Adulto Jovem
4.
Res Dev Disabil ; 92: 103430, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31306870

RESUMO

Dopamine active transporter gene (DAT1) is a candidate gene associated with attention-deficit/hyperactivity disorder (ADHD). The DAT1 variable number tandem repeat (VNTR)-3' polymorphism is functional and 9R carriers have been shown to produce more DAT than 10R homozygotes. We used functional magnetic resonance imaging (fMRI) to investigate the effects of this polymorphism on the neural substrates of working memory (WM) in a small but selected population of children with ADHD, naïve of any psychotropic treatment and without comorbidity. MRI and genotype data were obtained for 36 children (mean age: 10,36 +/- 1,49 years) with combined-type ADHD (9R n = 15) and 25 typically developing children (TDC) (mean age: 9,55 +/- 1,25 years) (9R n = 12). WM performance was similar between conditions. We found a cross-over interaction effect between gene (9R vs. 10R) and diagnosis (TDC vs. ADHD) in the orbito-frontal gyrus, cerebellum and inferior temporal lobe. In these areas, WM-related activity was higher for 9R carriers in ADHD subjects and lower in TDC. In ADHD children only, 10R homozygotes exhibited higher WM-related activity than 9R carriers in a network encompassing the parietal and the temporal lobes, the ventral visual cortex, the orbito-frontal gyrus and the head of the caudate nucleus. There was no significant results in TDC group. Our preliminary findings suggest that DAT1 VNTR polymorphism can modulate WM-related brain activity ADHD children.


Assuntos
Transtorno do Deficit de Atenção com Hiperatividade , Encéfalo , Proteínas da Membrana Plasmática de Transporte de Dopamina/genética , Memória de Curto Prazo/fisiologia , Transtorno do Deficit de Atenção com Hiperatividade/genética , Transtorno do Deficit de Atenção com Hiperatividade/psicologia , Encéfalo/diagnóstico por imagem , Encéfalo/fisiopatologia , Criança , Correlação de Dados , Feminino , Humanos , Imagem por Ressonância Magnética/métodos , Masculino , Repetições Minissatélites/genética , Polimorfismo Genético
5.
Zhonghua Liu Xing Bing Xue Za Zhi ; 40(6): 676-681, 2019 Jun 10.
Artigo em Chinês | MEDLINE | ID: mdl-31238618

RESUMO

Objective: To study the molecular-epidemiological characteristics of Brucella species isolated from different countries, using the multiple locus tandem-repeat (MLVA) analysis. Methods: Eleven variable-number tandem-repeat (VNTR) loci were selected. VNTR strains of Brucella isolated from 48 different countries in 1953-2013, were analyzed by using the BioNumerics software. Unweighted Paired Arithmetic Average method was used to cluster and draw phylogenetic tree as well as the minimum spannin. Results: The evolutionary relationship of Brucella phylogenetic tree was consistent with the classical biological typing method. However, the Brucella suis biovar 5 strains were different from the other Brucella suis biovars 1, 2, 3 and 4. Brucella ceti strains were divided into two parts and different from each other. Worldwide epidemics of brucellosis were emerged from 2005 to 2008 under the MLVA11 Orsay analysis. China has been a brucellosis-prone regions, with Brucella melitensis as the main epidemic Brucella species, followed by Brucella abortus. Brucella suis was mainly identified in the southern provinces, but Brucella canis was mainly found in dogs. No human cases were found. Conclusion: Molecular-epidemiological characteristics of the Brucella strains were related to factors as time, region and hosts of isolation, which are important to setting up prevention and control programs on brucellosis.


Assuntos
Brucella/genética , Brucella/isolamento & purificação , Brucelose/epidemiologia , Tipagem de Sequências Multilocus/métodos , Brucella/classificação , Brucelose/diagnóstico , Brucelose/microbiologia , China , DNA Bacteriano/genética , Loci Gênicos , Genótipo , Humanos , Repetições de Microssatélites/genética , Repetições Minissatélites/genética , Epidemiologia Molecular , Filogenia , Sequências de Repetição em Tandem
6.
Hum Immunol ; 80(10): 878-882, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31213370

RESUMO

Mucin 1 is a cell-membrane associated mucin, expressed on epithelial and immune cells that helps protect against pathogenic infections. In humans, MUC1 is highly polymorphic, predominantly due to the presence of a variable number tandem repeat (VNTR) region in the extracellular domain that results in MUC1 molecules of typically either short or long length. A genetic link is known between these MUC1 polymorphisms and inflammation-driven diseases, although the mechanism is not fully understood. We previously showed that MUC1 on murine macrophages specifically restricts activation of the NLRP3 inflammasome, thereby repressing inflammation. This study evaluated the effect of MUC1 VNTR polymorphisms on activity of the NLRP3 inflammasome in human macrophages, finding that long MUC1 alleles correlated with increased IL-1ß production following NLRP3 inflammasome activation. This indicates that the length of MUC1 can influence IL-1ß production, thus providing the first evidence of an immune-modulatory role of MUC1 VNTR polymorphisms in human macrophages.


Assuntos
Inflamassomos/imunologia , Macrófagos/imunologia , Mucina-1/genética , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Polimorfismo Genético/imunologia , Adolescente , Alelos , Criança , Frequência do Gene/genética , Genótipo , Voluntários Saudáveis , Humanos , Inflamassomos/efeitos dos fármacos , Inflamassomos/metabolismo , Interleucina-1beta/genética , Interleucina-1beta/metabolismo , Lipopolissacarídeos/farmacologia , Macrófagos/metabolismo , Masculino , Repetições Minissatélites/genética , Proteína 3 que Contém Domínio de Pirina da Família NLR/genética , Nigericina/farmacologia , Transdução de Sinais/efeitos dos fármacos
7.
Vet Res Commun ; 43(3): 155-164, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31222520

RESUMO

Cattle are the domestic animal reservoir for Mycobacterium bovis (M. bovis) which also affects other domestic animals, several wildlife species and humans leading to tuberculosis. The study area is in a resource-poor community that is surrounded by several game parks, where M. bovis infection has been previously diagnosed in wildlife. A cross-sectional study was carried out to determine the prevalence of M. bovis infection in 659 cattle from a total of 192 traditionally managed herds using the BOVIGAM® interferon gamma assay (IFN-γ). Infection was confirmed by post mortem examination and M. bovis isolation from three test-positive cattle. Genotyping of the M. bovis isolates was done using spoligotyping and VNTR (variable number of tandem repeats typing). The apparent M. bovis prevalence rate in cattle at animal level was 12% with a true population prevalence of 6% (95% Confidence interval (C.I) 3.8 to 8.1) and a herd prevalence of 28%. Spoligotyping analysis revealed that the M. bovis isolates belonged to spoligotype SB0130 and were shared with wildlife. Three VNTR profiles were identified among the SB0130 isolates from cattle, two of which had previously been detected in buffalo in a game reserve adjacent to the study area. The apparent widespread presence of M. bovis in the cattle population raises a serious public health concern and justifies further investigation into the risk factors for M. bovis transmission to cattle and humans. Moreover, there is an urgent need for effective bTB control measures to reduce infection in the communal cattle and prevent its spread to uninfected herds.


Assuntos
Tuberculose Bovina/epidemiologia , Animais , Animais Selvagens/microbiologia , Bovinos , Genótipo , Gado/microbiologia , Repetições Minissatélites/genética , Mycobacterium bovis/genética , Prevalência , Fatores de Risco , África do Sul/epidemiologia
8.
Transbound Emerg Dis ; 66(5): 1840-1854, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31099490

RESUMO

Mycoplasma hyopneumoniae (M. hyopneumoniae) is the aetiologic agent of enzootic pneumonia in swine, a prevalent chronic respiratory disease worldwide. Mycoplasma hyopneumoniae is a small, self-replicating microorganism that possesses several characteristics allowing for limited biosynthetic abilities, resulting in the fastidious, host-specific growth and unique pathogenic properties of this microorganism. Variation across several isolates of M. hyopneumoniae has been described at antigenic, proteomic, transcriptomic, pathogenic and genomic levels. The microorganism possesses a minimal number of genes that regulate the transcription process. Post-translational modifications (PTM) occur frequently in a wide range of functional proteins. The PTM by which M. hyopneumoniae regulates its surface topography could play key roles in cell adhesion, evasion and/or modulation of the host immune system. The clinical outcome of M. hyopneumoniae infections is determined by different factors, such as housing conditions, management practices, co-infections and also by virulence differences among M. hyopneumoniae isolates. Factors contributing to adherence and colonization as well as the capacity to modulate inflammatory and immune responses might be crucial. Different components of the cell membrane (i.e. proteins, glycoproteins and lipoproteins) may serve as adhesins and/or be toxic for the respiratory tract cells. Mechanisms leading to virulence are complex and more research is needed to identify markers for virulence. The utilization of typing methods and complete or partial-gene sequencing for M. hyopneumoniae characterization has increased in diagnostic laboratories as control and elimination strategies for this microorganism are attempted worldwide. A commonly employed molecular typing method for M. hyopneumoniae is Multiple-Locus Variable number tandem repeat Analysis (MLVA). The agreement of a shared terminology and classification for the various techniques, specifically MLVA, has not been described, which makes inferences across the literature unsuitable. Therefore, molecular trends for M. hyopneumoniae have been outlined and a common terminology and classification based on Variable Number Tandem Repeats (VNTR) types has been proposed.


Assuntos
Variação Genética , Genoma Bacteriano/genética , Mycoplasma hyopneumoniae/classificação , Pneumonia Suína Micoplasmática/virologia , Adesinas Bacterianas/genética , Animais , Genômica , Repetições Minissatélites/genética , Mycoplasma hyopneumoniae/genética , Mycoplasma hyopneumoniae/patogenicidade , Proteômica , Suínos , Terminologia como Assunto , Virulência
9.
Taiwan J Obstet Gynecol ; 58(3): 390-395, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31122531

RESUMO

OBJECTIVE: Examine the association of the 4a/4b polymorphism of endothelial nitric oxide synthase (eNOS) with blood pressure in women at late pregnancy. MATERIALS AND METHODS: Blood pressure before pregnancy and at the end of gestation (37-40-week term) was measured in 588 women of the Russian ancestry. The women were divided into groups according to the body mass index and the presence of preeclampsia at late pregnancy. The 4a/4b polymorphism of the eNOS gene was genotyped using PCR with subsequent screening of amplified fragment length polymorphisms. RESULTS: The 4a4a eNOS genotype was associated with higher levels of diastolic blood pressure in pregnant women and with more pronounced dynamics of the diastolic and mean arterial pressure in the development of pregnancy (p = 0.02-0.03). Pregnant women with the 4a4a genotype and increased body mass index had higher systolic, diastolic, and mean arterial pressure (p = 0.001-0.009). In pregnant women with preeclampsia, the 4a4a genotype was associated with higher level of diastolic blood pressure at the end of pregnancy (p = 0.04), whereas in the women without preeclampsia this genotype was associated with more pronounced changes of blood pressure at pregnancy (p = 0.02). CONCLUSION: The results of our study suggest that the genotype 4a4a of the eNOS gene is associated with higher levels of blood pressure in women at the end of pregnancy.


Assuntos
Pressão Sanguínea/genética , Óxido Nítrico Sintase Tipo III/genética , Pré-Eclâmpsia/genética , Adulto , Estudos de Coortes , Feminino , Humanos , Repetições Minissatélites/genética , Polimorfismo de Nucleotídeo Único , Gravidez , Terceiro Trimestre da Gravidez , Adulto Jovem
10.
Infect Genet Evol ; 71: 159-165, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30928606

RESUMO

Tuberculosis among foreign-born patients is a key indicator of country-level epidemiological profiles and, of an increasing concern in Europe given the more intensified migratory waves of refugees. Since Portugal presents a lower immigrant-associated TB incidence rate when compared to other European countries, we sought to characterize the epidemiology and transmission dynamics among the foreign-born population coming from Portuguese-speaking countries that are associated with higher TB incidences. In the present study we analyzed 133 Mycobacterium tuberculosis isolates obtained from foreign-born individuals over a three-year period in Lisbon, Portugal, using molecular epidemiological methods such as spoligotyping and 24-loci MIRU-VNTR. Moreover, all strains were subjected to drug susceptibility testing. The genetic profiles obtained suggest that strain importation from Portuguese speaking countries plays a less important role in TB epidemiology but instead argue in favor of a high degree of penetrance of Portuguese endemic strains to the migrant population, including multidrug resistant strains, which is particularly relevant to active screening programs.


Assuntos
Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/transmissão , Tuberculose/epidemiologia , Tuberculose/transmissão , Doenças Transmissíveis Importadas/epidemiologia , Doenças Transmissíveis Importadas/transmissão , Europa (Continente)/epidemiologia , Feminino , Técnicas de Genotipagem , Nível de Saúde , Humanos , Masculino , Testes de Sensibilidade Microbiana , Repetições Minissatélites/genética , Epidemiologia Molecular/métodos , Filogenia , Vigilância da População , Portugal/epidemiologia , Migrantes , Tuberculose/microbiologia
11.
Expert Rev Med Devices ; 16(5): 413-420, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30957585

RESUMO

OBJECTIVES: Endogenous and exogenous infection of the biliary tract could occur during endoscopic retrograde cholangiopancreatography. METHODS: Bile samples of patients with hepatobiliary diseases, and swab samples of elevator channel samples of duodenoscope and washing instruments were prepared simultaneously and cultured aerobically and anaerobically. Antimicrobial susceptibility of the most common characterized bacterial species was tested, and their genetic relatedness was analyzed by multiple locus variable number of tandem repeats method. RESULTS: Contamination with Pseudomonas aeruginosa was detected in 38.2% of the elevator channels' and 26.6% of the bile samples. Staphylococcus aureus, Enterococcus spp., Staphylococcus epidermidis, Escherichia coli, Enterobacter spp., and Clostridium perfringenes were among other bacterial isolates in the elevator channel swab samples. Highest antimicrobial resistance rate among P. aeruginosa isolates from the bile and swab samples were detected against gentamicin (100% and 73%, respectively), while the lowest one was measured to piperacillin-tazobactam (25% and 0%, respectively). Out of the 27 distinct MLVA profiles, relatedness of P. aeruginosa strains in the bile samples compared with those from the elevators was shown in three series of the samples. CONCLUSION: Identity of P. aeruginosa strains among the bile and elevator channel samples showed possibility of cross-contamination among patients even at distinct time intervals. Expert opinion: Bacterial infection is considered as main complications of ERCP. Entry of bacteria into the biliary tract via contaminated device and its related instruments and their proliferation in this tissue could cause serious infections. To prevent this side effect, reprocessing of medical equipment via standard cleaning and disinfection procedures are needed. Our results showed incompliance of methods used for endoscope cleaning and disinfection procedure. Although host risk factors, such as sphincterotomy, could increase rate of infection with different types of bacteria, their ability for formation of biofilm and spore, which could help them to resist disinfectants and washing procedures seems to be main cause of persistent colonization and transmission among different patients. New standards for disinfection compared with currently used methods and use of materials to eliminate formation of bacterial microcolonies seem to be necessary to prevent cross-contamination.


Assuntos
Bactérias/genética , Colangiopancreatografia Retrógrada Endoscópica , Duodenoscópios , Repetições Minissatélites/genética , Bactérias/classificação , Bactérias/isolamento & purificação , Bile/microbiologia , Desinfecção , Resistência Microbiana a Medicamentos , Feminino , Humanos , Masculino , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Pseudomonas aeruginosa/genética
12.
Biomed Res Int ; 2019: 7168949, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31008110

RESUMO

Background: Mycoplasma pneumoniae is a common cause of community-acquired pneumonia (CAP). This cross-sectional study aimed to determine the prevalence of macrolide-resistant M. pneumoniae strains in a convenience series of 234 adult hospitalised and nonhospitalised subjects with a diagnosis of CAP in January 2013 to April 2015 in South Italy. Methods: Respiratory samples were subjected to real-time PCR. In M. pneumoniae-positive samples, domain V of 23S rRNA was sequenced to detect resistance-conferring point mutations. P1 major adhesion protein typing and multiple loci variable-number tandem repeat analysis (MLVA) were also performed. Results: Of the 234 samples, 15 (6.4%) were positive for M. pneumoniae. Three of these had a macrolide-resistant genotype: two and one had A2063G and A2064G mutations, respectively. Fourteen of the 15 strains were subtyped: half had subtype 1 and half had subtype 2. Eight strains underwent MLVA profiling: one each had the J, A, and Z type. The remainder was unclassifiable. Conclusions: This novel discovery of macrolide-resistant M. pneumoniae strains in adults with CAP in Italy suggests that there may be increasing circulation of these strains in the population. To facilitate rapid optimization of the antibiotic strategy in Italy, macrolide resistance should be monitored by a surveillance system that is based on molecular methods.


Assuntos
Infecções Comunitárias Adquiridas/tratamento farmacológico , Farmacorresistência Bacteriana/genética , Macrolídeos/uso terapêutico , Pneumonia por Mycoplasma/tratamento farmacológico , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/efeitos adversos , Antibacterianos/uso terapêutico , Infecções Comunitárias Adquiridas/epidemiologia , Infecções Comunitárias Adquiridas/genética , Infecções Comunitárias Adquiridas/microbiologia , Feminino , Genótipo , Humanos , Itália/epidemiologia , Macrolídeos/efeitos adversos , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Repetições Minissatélites/genética , Mutação , Mycoplasma pneumoniae/efeitos dos fármacos , Mycoplasma pneumoniae/genética , Mycoplasma pneumoniae/patogenicidade , Pneumonia por Mycoplasma/epidemiologia , Pneumonia por Mycoplasma/genética , Pneumonia por Mycoplasma/microbiologia , Adulto Jovem
13.
Turk J Med Sci ; 49(2): 589-594, 2019 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-30997974

RESUMO

Background/aim: We aimed to investigate the associations between endothelial nitric oxide synthase(eNOS) gene polymorphisms [G894T (rs1799983)], intron 4 (27-bpTR) variable number tandem repeat (VNTR) and T786C (rs2070744), and ischemic stroke in the Anatolian population. Materials and methods: This case-control study included 112 patients with "stroke of undetermined etiology" and 160 controls. Real-time polymerase chain reaction (RT-PCR) analysis was used to analyze these polymorphisms. Between-group frequencies of alleles and genotypes were compared using binary logistic regression analysis. Results: No significant difference was observed between the two groups in terms of the genotype and allele distributions of the eNOS G894T (rs1799983) polymorphism (P > 0.05). The a alleles and the 4b/a and 4a/a genotypes of the intron 4 (27-bpTR) VNTR polymorphism had significantly higher frequencies in the patient group than in the control group (OR: 2.715, P < 0.001; OR: 3.396, P < 0.001; OR: 10.631, P = 0.016, respectively). On the contrary, the TC genotype and C alleles of the T786C (rs2070744) polymorphism had a significantly lower frequency in the patient group than in the control group (OR: 0.244, P < 0.001, OR: 0.605, P = 0.006, respectively) Conclusion: Our findings indicate that the eNOS G894T and T786C [rs2070744] polymorphisms are not associated with the risk of ischemic stroke, whereas the intron 4 [27-bpTR] VNTR may be a risk factor in the Anatolian population.


Assuntos
Isquemia Encefálica/genética , Predisposição Genética para Doença/genética , Íntrons/genética , Óxido Nítrico Sintase Tipo III/genética , Polimorfismo de Nucleotídeo Único , Acidente Vascular Cerebral/genética , Idoso , Idoso de 80 Anos ou mais , Isquemia Encefálica/enzimologia , Isquemia Encefálica/fisiopatologia , Estudos de Casos e Controles , Feminino , Frequência do Gene , Estudos de Associação Genética , Humanos , Masculino , Repetições Minissatélites/genética , Acidente Vascular Cerebral/enzimologia , Acidente Vascular Cerebral/fisiopatologia
14.
Infect Genet Evol ; 71: 211-214, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30974263

RESUMO

Mycobacterium bovis is a notorious infectious agent leading to serious economic losses for cattle farms worldwide. Analysis of the widely spreading genotypes is vital for tracing infections, understanding transmission dynamics, and controlling the cluster growth. This study aimed to evaluate the discrimination ability of 15 mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTR) loci and to assess the extremely efficient loci subset for molecular epidemiological investigations of M.bovis from farms in the Delta area of Egypt. The discriminating ability of MIRU-VNTR genotyping using 15 loci {2 exact tandem repeat (ETR) loci, 6 MIRU loci, 4 Mtub loci, and 3 Queen's University of Belfast (QUB) group loci)} were evaluated on 61 M.bovis isolates from cattle (Holstein Frisian) and buffaloes. The results indicate that there are 48 genotypes: 3 unique genotypes and 45 genotypes with shared similarities. Using the MIRU-VNTRplus database, M.bovis ID 7540/01 and ID 5346/02 were the nearest lineages to both groups. Six loci (MIRU10, QUB11b, QUB26, ETRA, Mtub30, and Mtub39) were highly discriminating, seven other loci (Mtub21, MIRU26, QUB4156, MIRU04 (ETRD), MIRU16, MIRU 40, and ETRC) gave moderate discriminatory power, and the last two loci (Mtub04 and MIRU31) were poorly discriminative. MIRU-VNTR typing generally proved efficacy and high discriminatory power, with a collective allele's diversification of 0.9641. Both the six highly discriminating (DI = 0.9492) and the seven moderately discriminating loci (DI = 0.9269) evidenced to be suitable for M.bovis first-step initial genotyping from cattle herds in Egypt. MIRU-VNTR is rapid and effective in the genotyping of M.bovis from cattle and buffaloes in Egypt.


Assuntos
Técnicas de Tipagem Bacteriana/métodos , Mycobacterium bovis/genética , Tuberculose Bovina/epidemiologia , Tuberculose Bovina/microbiologia , Animais , Bovinos , Egito , Fazendas , Repetições Minissatélites/genética , Epidemiologia Molecular
15.
Neuropsychobiology ; 78(2): 86-94, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30943524

RESUMO

BACKGROUND: The serotonergic and noradrenergic systems have a strong impact on several affective disorders and are key targets for psychopharmacological therapy. With respect to pathogenesis, there is a growing body of evidence showing an influence of a promoter repeat polymorphism (MAOA-uVNTR) altering the expression rate of monoamine oxidase A. However, only a few studies investigate its influence on depression with only 2 of them considering the moderating effects of life stress. For burnout, there are no studies so far investigating the genetic basis. OBJECTIVES: The aim of the present study was to replicate an interaction effect of MAOA-uVNTR and life stress on depression, and extend these possible findings to the burnout syndrome. Especially, the latter one might help in understanding the underlying mechanisms of burnout and its association to depression. METHOD: A total of n = 1,541 participants (n = 1,099 healthy controls, n = 442 inpatients with affective disorders) provided genetic samples and filled in self-report questionnaires measuring depression, burnout, and the extent of experienced stressful life events (SLEs). RESULTS: A life stress x MAOA-uVNTR interaction on depression and burnout was observed in women suggesting that carriers of the high expressing allele (MAO-H) with many SLEs had the highest scores in both burnout and depression. In men, there was only a weak effect of MAOA-uVNTR on depression. CONCLUSIONS: The results suggest a more pronounced reactivity to adverse environmental factors in carriers of the MAO-H allele. Especially the effect of life stress and MAOA-uVNTR on burnout should be independently replicated in the future as this is the first study showing this association.


Assuntos
Esgotamento Psicológico/genética , Depressão/genética , Repetições Minissatélites/genética , Monoaminoxidase/genética , Estresse Psicológico/genética , Adolescente , Adulto , Alelos , Estudos de Casos e Controles , Feminino , Frequência do Gene , Estudos de Associação Genética , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo Genético/genética , Fatores Sexuais , Adulto Jovem
16.
Int J Med Microbiol ; 309(3-4): 189-193, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30879971

RESUMO

Clostridium (Clostridioides) difficile is the main cause of nosocomial diarrhoea. Ribotype 018 (RT018) has been recognized as the predominant strain responsible for C. difficile infection (CDI) in Italy, whereas in most other European countries only sporadic RT018 cases occur. Between August and October 2015, a suspected C. difficile outbreak at two associated hospitals in Southern Germany was investigated by comprehensive molecular typing. Surprisingly, RT018 was detected in 9/82 CDI patients, which has never been described before in a German outbreak. Phenotypic analysis revealed fluoroquinolone and macrolide resistance. Genetic subtyping using multiple-locus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS) was performed and outbreak isolates were directly compared to sporadic German RT018 isolates and to epidemic ones from Milan, Northern Italy. Molecular typing confirmed a hospital outbreak with closely related RT018 isolates. Both, MLVA and WGS revealed high similarity of outbreak strains with epidemic isolates from Italy, but low similarity to other German isolates. Comparison between both typing strategies showed that ribotyping in combination with MLVA was appropriate to identify related isolates and clonal complexes, whereas WGS provided a better discrimination with more detailed information about the phylogenetic relationship of isolates. This is the first hospital outbreak in Germany presumably caused by cross-national transmission of an Italian epidemic RT018 strain.


Assuntos
Infecções por Clostridium/epidemiologia , Infecções por Clostridium/microbiologia , Clostridium difficile/isolamento & purificação , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/microbiologia , Surtos de Doenças , Antibacterianos , Toxinas Bacterianas/genética , Clostridium difficile/classificação , Clostridium difficile/efeitos dos fármacos , Clostridium difficile/genética , DNA Bacteriano/genética , Diarreia/epidemiologia , Diarreia/microbiologia , Farmacorresistência Bacteriana , Genoma Bacteriano/genética , Alemanha/epidemiologia , Humanos , Testes de Sensibilidade Microbiana , Repetições Minissatélites/genética , Tipagem de Sequências Multilocus , Filogenia , Reação em Cadeia da Polimerase , Ribotipagem
17.
Pathog Glob Health ; 113(1): 39-48, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30821646

RESUMO

BACKGROUND: Different strains of Mycobacterium tuberculosis (MTB) are known to have different epidemiological and clinical characteristics. Some of them are widely distributed and associated with drug resistance, whereas others are locally predominated. Molecular epidemiological investigations have always been beneficial in identifying new strains and studying their transmission dynamics. Sahariya a primitive tribe of North Madhya Pradesh, India, has already been reported to have high prevalence of tuberculosis (TB) than their non-tribal neighbours. However, the information about MTB genotypes prevalent in Sahariya tribe and their non-tribal neighbours is not available. METHODS: A total of 214 clinical isolates representing Sahariya tribe and non-tribes were analyzed by spoligotyping and MIRU-VNTR typing. RESULTS: The EAI3_IND/SIT11 genotype was observed as major genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. A 3.04 fold higher risk of getting TB with EAI3_IND/SIT11 genotype was observed in Sahariya as compared to the non-tribal population. The EAI_IND/SIT11 genotype also found to have more number of MDR-TB cases in Sahariya as well as true and possible transmission links. In Sahariya tribe, 3 clusters (6 isolates) reflected true transmission links, whereas 8 clusters consisted of 26 isolates revealed possible transmission links within the same geographical location or nearby houses. CONCLUSION: The present study highlighted the predominance of EAI3_IND/SIT11 genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. Combined approach of MIRU-VNTR typing and spoligotyping was observed more favourable in discrimination of MTB genotypes. Further, longitudinal studies using whole genome sequencing can provide more insights into genetic diversity, drug resistance and transmission dynamics of these prevalent genotypes.


Assuntos
Variação Genética , Mycobacterium tuberculosis/genética , Tuberculose/microbiologia , Técnicas de Tipagem Bacteriana/métodos , Análise por Conglomerados , Farmacorresistência Bacteriana Múltipla/genética , Predisposição Genética para Doença , Genótipo , Humanos , Índia/epidemiologia , Repetições Minissatélites/genética , Mycobacterium tuberculosis/classificação , Mycobacterium tuberculosis/isolamento & purificação , Escarro/microbiologia , Tuberculose/epidemiologia , Tuberculose/etnologia , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/etnologia , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia
18.
Microb Drug Resist ; 25(6): 931-937, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30883259

RESUMO

The Beijing family, the most successful Mycobacterium tuberculosis lineage, is considered hypervirulent, associated with clustering and has a strong association with multidrug-resistant tuberculosis. The Beijing strains have spread worldwide and also to Latin America. Genotyping of a countrywide collection of 380 M. tuberculosis strains from Ecuador, with 24-loci mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR), revealed only six Beijing strains, but four of these were MDR-TB. There was no clustering as all six strains had very distinct MIRU-VNTR profiles that have not been reported in the rest of Latin America. Although active transmission for Beijing has been described for the neighboring countries Peru and Colombia, there is no evidence that Beijing strains in Ecuador are more frequently transmitted than other strains. Moreover, the low prevalence (1.6%) of the Beijing sublineage in Ecuador challenges the concept of hyperadaptability and transmissibility of the Beijing strains in our country.


Assuntos
Variação Genética/genética , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/genética , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Antibacterianos/uso terapêutico , Pequim , Colômbia , DNA Bacteriano/genética , Equador/epidemiologia , Genótipo , Humanos , Repetições Minissatélites/genética , Mycobacterium tuberculosis/efeitos dos fármacos , Peru , Prevalência , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia
19.
Insect Mol Biol ; 28(5): 616-627, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-30793407

RESUMO

A monophyletic group of Drosophila hAT transposable elements, referred to as Herves-like, was characterized and found to be present in 46% of 57 screened Drosophila species. A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (MnRs) in both subterminal extremities of the elements. The copy number of these minisatellites was highly variable between and within populations. Twenty-three strains of Drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5' MnRs, showing a variation from 7 to 20 repeat copies. These MnRs are well conserved among Drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other hAT elements. Miniature inverted repeat transposable elements were found in 27% of species carrying Herves-like elements. Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.


Assuntos
Elementos de DNA Transponíveis/genética , Drosophila/genética , Evolução Molecular , Animais , Variações do Número de Cópias de DNA , Drosophila/classificação , Transferência Genética Horizontal , Repetições Minissatélites/genética , Filogenia
20.
PLoS One ; 14(2): e0211637, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30785899

RESUMO

Molecular typing techniques are useful in understanding tuberculosis epidemiology; yet, they have been under-utilised at the human-animal interface in Nigeria. Sixty-four Mycobacterium tuberculosis complex (MTBC) isolates including 42 M. tuberculosis, 13 M. bovis and nine M. africanum obtained from livestock workers (LW, n = 47) and their cattle (n = 17) in three geographical zones of Nigeria were genotyped to identify and evaluate the genetic diversity of the circulating MTBC using spoligotyping. Distribution into clades of M. tuberculosis revealed; 45.3% Uganda I- [SIT46- cattle: 1; LW: 28], 14.1% Latin American Mediterranean- [SIT61, cattle: 1; LW: 8], and 1.6% T- [SIT53-LW: 1]. The M. bovis strains were 6.3% SB0944 [cattle: 4] and 1.6% each of SB0300, SB1026, SB1027 and SB1439 [cattle: 4]. Seventeen MTBC isolates [cattle: 7; LW: 10] yielded 14 new spoligotype patterns including three M. tuberculosis strains (three isolates), five M. bovis strains (five isolates) and six M. africanum strains (nine isolates), two of which belonged to MAF1. Only few families namely, the not previously described Uganda I-, LAM and SB0944 are predominant among the LW and cattle, with other types in lower prevalences. The strain population structure indicates an intriguing diversity and possible zoonotic linkage with consequences for TB control in the country. The need to employ newer molecular techniques such as Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats and whole genome sequence to decipher circulating MTBC strains in Nigeria is advocated.


Assuntos
Gado/microbiologia , Mycobacterium tuberculosis/genética , Tuberculose Bovina/microbiologia , Animais , Técnicas de Tipagem Bacteriana/métodos , Bovinos , DNA Bacteriano/genética , Genótipo , Repetições Minissatélites/genética , Epidemiologia Molecular/métodos , Tipagem Molecular/métodos , Mycobacterium bovis/genética , Nigéria/epidemiologia , Tuberculose/epidemiologia , Tuberculose/microbiologia , Tuberculose/veterinária , Tuberculose Bovina/epidemiologia , Uganda/epidemiologia
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