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In this paper, we present a systematic approach to building useful time-dependent effective Hamiltonians in molecular quantum electrodynamics. The method is based on considering part of the system as an open quantum system and choosing a convenient unitary transformation based on the evolution operator. We illustrate our formalism by obtaining four Hamiltonians, each suitable to a different class of applications. We show that we may treat several effects of molecular quantum electrodynamics with a direct first-order perturbation theory. In addition, our effective Hamiltonians shed light on interesting physical aspects that are not explicit when employing more standard approaches. As applications, we discuss three examples: two-photon spontaneous emission, resonance energy transfer, and dispersion interactions.
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Innovative strategies to control malaria are urgently needed. Exploring the interplay between Plasmodium sp. parasites and host red blood cells (RBCs) offers opportunities for novel antimalarial interventions. Pyruvate kinase deficiency (PKD), characterized by heightened 2,3-diphosphoglycerate (2,3-DPG) concentration, has been associated with protection against malaria. Elevated levels of 2,3-DPG, a specific mammalian metabolite, may hinder glycolysis, prompting us to hypothesize its potential contribution to PKD-mediated protection. We investigated the impact of the extracellular supplementation of 2,3-DPG on the Plasmodium falciparum intraerythrocytic developmental cycle in vitro. The results showed an inhibition of parasite growth, resulting from significantly fewer progeny from 2,3-DPG-treated parasites. We analyzed differential gene expression and the transcriptomic profile of P. falciparum trophozoites, from in vitro cultures subjected or not subjected to the action of 2,3-DPG, using Nanopore Sequencing Technology. The presence of 2,3-DPG in the culture medium was associated with the significant differential expression of 71 genes, mostly associated with the GO terms nucleic acid binding, transcription or monoatomic anion channel. Further, several genes related to cell cycle control were downregulated in treated parasites. These findings suggest that the presence of this RBC-specific glycolytic metabolite impacts the expression of genes transcribed during the parasite trophozoite stage and the number of merozoites released from individual schizonts, which supports the potential role of 2,3-DPG in the mechanism of protection against malaria by PKD.
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Malaria Falciparum , Parásitos , Animales , 2,3-Difosfoglicerato/metabolismo , Ácidos Difosfoglicéricos/metabolismo , Malaria Falciparum/genética , Malaria Falciparum/metabolismo , Plasmodium falciparum/genética , Glucólisis/genética , Eritrocitos/metabolismo , Expresión Génica , MamíferosRESUMEN
NorA is one of the main native MDR efflux pumps of Staphylococcus aureus, contributing to reduced susceptibility towards fluoroquinolones and biocides, but little is known about its variability within S. aureus or its distribution and conservation among other staphylococci. We screened for sequences homologous to S. aureus norA and found it in 61 out of the 63 Staphylococcus species described. To the best of our knowledge, this is the first study to report the occurrence of norA across the Staphylococcus genus. The norA phylogenetic tree follows the evolutionary relations of staphylococci and the closely related Mammalliicoccus genus. Comparative analyses suggest a conservation of the NorA function in staphylococci. We also analyzed the variability of norA within S. aureus, for which there are several circulating norA alleles, differing up to 10% at the nucleotide level, which may hamper proper norA detection. We demonstrate the applicability of a PCR-based algorithm to detect and differentiate norA alleles in 52 S. aureus representing a wider collection of 89 isolates from different hosts. Our results highlight the prevalence of norAI and norAII in different settings and the association of norA alleles with specific S. aureus clonal lineages. Ultimately, it confirms the applicability of our PCR-based algorithm to rapidly detect and assign the different norA alleles, a trait that may impact antimicrobial efflux capacity and the search for potential NorA inhibitors.
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Staphylococcus aureus , Staphylococcus , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo , Staphylococcus/genética , Staphylococcus/metabolismo , Proteínas Asociadas a Resistencia a Múltiples Medicamentos/genética , Antibacterianos/farmacología , Filogenia , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Pruebas de Sensibilidad MicrobianaRESUMEN
Staphylococcus pseudintermedius is the main bacterial cause of skin and soft tissue infections (SSTIs) in companion animals, particularly dogs. The emergence of methicillin-resistant S. pseudintermedius (MRSP) strains, frequently with multidrug resistance phenotypes is a public health concern. This study aimed to evaluate efflux, a resistance mechanism still poorly characterized in S. pseudintermedius, as a contributor to biocide and fluoroquinolone resistance. Susceptibility to the efflux pump substrates ethidium bromide (EtBr), tetraphenylphosphonium bromide (TPP) and ciprofloxacin (CIP) was evaluated by minimum inhibitory concentration (MIC) determination for 155 SSTIs-related S. pseudintermedius in companion animals. EtBr and TPP MIC distributions were analyzed to estimate cut-off (COWT) values. The effect of the efflux inhibitors (EIs) thioridazine and verapamil was assessed upon MICs and fluorometric EtBr accumulation assays, performed with/without glucose and/or EIs. This approach detected a non-wild type population towards TPP with increased efflux, showed to be strain-specific and glucose-dependent. Resistance to fluoroquinolones was mainly linked to target gene mutations, yet a contribution of efflux on CIP resistance levels could not be ruled out. In sum, this study highlights the relevance of efflux-mediated resistance in clinical S. pseudintermedius, particularly to biocides, and provides a methodological basis for further studies on the efflux activity on this important pathogen of companion animals.
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Staphylococcus pseudintermedius is the main bacterial pathogen of skin and soft-tissue infections (SSTIs) in companion animals. Antimicrobial resistance in this species is a growing public health concern. This study aims to characterize a collection of S. pseudintermedius causing SSTIs in companion animals, establishing the main clonal lineages and antimicrobial resistance traits. The collection corresponded to all S. pseudintermedius (n = 155) causing SSTIs in companion animals (dogs, cats and one rabbit) collected between 2014 and 2018 at two laboratories in Lisbon, Portugal. Susceptibility patterns were established by disk diffusion for 28 antimicrobials (15 classes). For antimicrobials without clinical breakpoints available, a cut-off value (COWT) was estimated, based on the distribution of the zones of inhibition. The blaZ and mecA genes were screened for the entire collection. Other resistance genes (e.g., erm, tet, aadD, vga(C), dfrA(S1)) were searched only for those isolates showing an intermediate/resistance phenotype. For fluoroquinolone resistance, we determined the chromosomal mutations in the target genes grlA and gyrA. All the isolates were typed by PFGE following SmaI macrorestriction and isolates representative of each PFGE type were further typed by MLST. Forty-eight out of the 155 S. pseudintermedius isolates (31.0%) were methicillin-resistant (mecA +, MRSP). Multidrug-resistant (MDR) phenotypes were detected for 95.8% of the MRSP and 22.4% of the methicillin-susceptible (MSSP) isolates. Of particular concern, only 19 isolates (12.3%) were susceptible to all antimicrobials tested. In total, 43 different antimicrobial resistance profiles were detected, mostly associated with the carriage of blaZ, mecA, erm(B), aph3-IIIa, aacA-aphD, cat pC221, tet(M) and dfr(G) genes. The 155 isolates were distributed within 129 PFGE clusters, grouped by MLST in 42 clonal lineages, 25 of which correspond to new sequence types (STs). While ST71 remains the most frequent S. pseudintermedius lineage, other lineages that have been replacing ST71 in other countries were detected, including ST258, described for the first time in Portugal. This study revealed a high frequency of MRSP and MDR profiles among S. pseudintermedius associated with SSTIs in companion animals in our setting. Additionally, several clonal lineages with different resistance profiles were described, evidencing the importance of a correct diagnosis and selection of the therapy.
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Agriculture provides the largest share of food supplies and ensures a critical number of ecosystem services (e.g., food provisioning). Therefore, agriculture is vital for food security and supports the Sustainable Development Goal (SDGs) 2 (SDG 2 - zero hunger) as others SDG's. Several studies have been published in different world areas with different research directions focused on increasing food and nutritional security from an agricultural land system perspective. The heterogeneity of the agricultural research studies calls for an interdisciplinary and comprehensive systematization of the different research directions and the plethora of approaches, scales of analysis, and reference data used. Thus, this work aims to systematically review the contributions of the different agricultural research studies by systematizing the main research fields and present a synthesis of the diversity and scope of research and knowledge. From an initial search of 1151 articles, 260 meet the criteria to be used in the review. Our analysis revealed that most articles were published between 2015 and 2019 (59%), and most of the case studies were carried out in Asia (36%) and Africa (20%). The number of studies carried out in the other continents was lower. In the last 30 years, most of the research was centred in six main research fields: land-use changes (28%), agricultural efficiency (27%), climate change (16%), farmer's motivation (12%), urban and peri-urban agriculture (11%), and land suitability (7%). Overall, the research fields identified are directly or indirectly linked to 11 of the 17 SDGs. There are essential differences in the number of articles among research fields, and future efforts are needed in the ones that are less represented to support food security and the SDGs.
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Ecosistema , Desarrollo Sostenible , Agricultura , Seguridad Alimentaria , Abastecimiento de AlimentosRESUMEN
Coagulase-positive staphylococci (CoPS) account for most bacteria-related pyoderma in companion animals. Emergence of methicillin-resistant strains of Staphylococcus pseudintermedius (MRSP), Staphylococcus aureus (MRSA) or Staphylococcus coagulans (MRSC), often with multidrug-resistant (MDR) phenotypes, is a public health concern. The study collection comprised 237 staphylococci (S. pseudintermedius (n = 155), S. aureus (n = 55) and S. coagulans (n = 27)) collected from companion animals, previously characterized regarding resistance patterns and clonal lineages. Biofilm production was detected for 51.0% (79/155), 94.6% (52/55) and 88.9% (24/27) of the S. pseudintermedius, S. aureus and S. coagulans, respectively, and was a frequent trait of the predominant S. pseudintermedius and S. aureus clonal lineages. The production of biofilm varied with NaCl supplementation of the growth media. All S. pseudintermedius and S. aureus strains carried icaADB. Kaplan-Meier survival analysis of Galleria mellonella infected with different CoPS revealed a higher virulence potential of S. aureus when compared with other CoPS. Our study highlights a high frequency of biofilm production by prevalent antimicrobial-resistant clonal lineages of CoPS associated with animal pyoderma, potentially related with a higher virulence potential and persistent or recurrent infections.
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After the eradication of polio infection, the plan is to phase-out the live-attenuated oral polio vaccine (OPV). Considering the protective non-specific effects (NSE) of OPV on unrelated pathogens, the withdrawal may impact child health negatively. Within a cluster-randomized trial, we carried out 16S rRNA deep sequencing analysis of fecal and nasopharyngeal microbial content of Bissau-Guinean infants aged 4-8 months, before and after 2 months of OPV revaccination (revaccinated infants = 47) vs. no OPV revaccination (control infants = 47). The aim was to address changes in the gut and upper respiratory bacterial microbiotas due to revaccination. Alpha-diversity for both microbiotas increased similarly over time in OPV-revaccinated infants and controls, whereas greater changes over time in the bacterial composition of gut (p adjusted < 0.001) and upper respiratory microbiotas (p adjusted = 0.018) were observed in the former. Taxonomic analysis of gut bacterial microbiota revealed a decrease over time in the median proportion of Bifidobacterium longum for all infants (25-14.3%, p = 0.0006 in OPV-revaccinated infants and 25.3-11.6%, p = 0.01 in controls), compatible with the reported weaning. Also, it showed a restricted increase in the median proportion of Prevotella_9 genus in controls (1.4-7.1%, p = 0.02), whereas in OPV revaccinated infants an increase over time in Prevotellaceae family (7.2-17.4%, p = 0.005) together with a reduction in median proportion of potentially pathogenic/opportunistic genera such as Escherichia/Shigella (5.8-3.4%, p = 0.01) were observed. Taxonomic analysis of upper respiratory bacterial microbiota revealed an increase over time in median proportions of potentially pathogenic/opportunistic genera in controls, such as Streptococcus (2.9-11.8%, p = 0.001 and Hemophilus (11.3-20.5%, p = 0.03), not observed in OPV revaccinated infants. In conclusion, OPV revaccination was associated with a healthier microbiome composition 2 months after revaccination, based on a more abundant and diversified bacterial community of Prevotellaceae and fewer pathogenic/opportunistic organisms. Further information on species-level differentiation and functional analysis of microbiome content are warranted to elucidate the impact of OPV-associated changes in bacterial microbiota on child health.
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Apramycin and florfenicol are two antimicrobial agents exclusively used in veterinary medicine. Resistance determinants to these antimicrobial agents have been described in several staphylococci, yet no inhibition zone-based epidemiological cutoff (ECOFF) values are available to detect populations harboring resistance mechanisms. In this study, we propose disk diffusion inhibition zone ECOFF values of Staphylococcus aureus for apramycin and florfenicol. The susceptibility to apramycin and florfenicol was evaluated by disk diffusion of five S. aureus collections, comprising 352 isolates of animal (n = 265) and human (n = 87) origin. The aggregated distributions of inhibition zone diameters were analyzed by the normalized resistance interpretation method to obtain normalized wild-type (WT) population distributions and corresponding ECOFF values. The putative WT populations of S. aureus were characterized by an inhibition zone ≥15 mm (ECOFF = 15 mm) for apramycin and ≥21 mm for florfenicol (ECOFF = 21 mm). Five nonwild-type (NWT) isolates were detected for apramycin, all without inhibition zone and harboring the apmA gene, whereas five NWT isolates were identified for florfenicol, all carrying the fexA gene. The proposed ECOFF values for apramycin and florfenicol may be a valuable tool in future antimicrobial resistance monitoring and surveillance studies to identify S. aureus NWT populations toward these antimicrobial agents.
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Antibacterianos/farmacología , Pruebas de Sensibilidad Microbiana/normas , Nebramicina/análogos & derivados , Staphylococcus aureus/efectos de los fármacos , Tianfenicol/análogos & derivados , Farmacorresistencia Bacteriana , Nebramicina/farmacología , Tianfenicol/farmacología , Medicina VeterinariaRESUMEN
Future land use/cover change (LUCC) analysis has been increasingly applied to spatial planning instruments in the last few years. Nevertheless, stakeholder participation in the land use modelling process and analysis is still low. This paper describes a methodology engaging stakeholders (from the land use planning, agriculture, and forest sectors) in the building and assessment of future LUCC scenarios. We selected as case study the Torres Vedras Municipality (Portugal), a peri-urban region near Lisbon. Our analysis encompasses a participatory workshop to analyse LUCC model outcomes, based on farmer LUCC intentions, for the following scenarios: A0 - current social and economic trend (Business as Usual); A1 - regional food security; A2 - climate change; and B0 - farming under urban pressure. This analysis allowed local stakeholders to develop and discuss their own views on the most plausible future LUCC for the following land use classes: artificial surfaces, non-irrigated arable land, permanently irrigated land, permanent crops and heterogeneous agricultural land, pastures, forest and semi-natural areas, and water bodies and wetlands. Subsequently, we spatialized these LUCC views into a hybrid model (Cellular Automata - Geographic Information Systems), identifying the most suitable land conversion areas. We refer to this model, implemented in NetLogo, as the stakeholder-LUCC model. The results presented in this paper model where, when, why, and what conversions may occur in the future in regard to stakeholders' points of view. These outcomes can better enable decision-makers to perform land use planning more efficiently and develop measures to prevent undesirable futures, particularly in extreme events such as scenarios of food security, climate change, and/or farming under pressure.
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This study identified patterns of sexual risk behavior among a sub-Saharan African migrant (SAM) population in Portugal and examined its associations with human immunodeficiency virus (HIV) prevalence, sociodemographics, use of sexual health services, and HIV testing. A cross-sectional biobehavioral survey was conducted with a venue-based sample of 790 SAMs. Data were collected using questionnaires and rapid HIV tests. Cluster analysis identified five subgroups with differing levels of HIV infection (2.5% to 11.3%). In Cluster 1, most participants reported sexual abstinence over the past year and the remaining used condoms consistently; this cluster had the highest HIV prevalence (11.3%). In Cluster 2, most reported one sexual partner and all reported unprotected sex; all HIV-positive participants in this cluster were unaware of their HIV-positive status. In Clusters 3 and 4, most had four or more partners, yet all used condoms. In Cluster 3, 56.5% reported both regular and occasional partners. In Cluster 4, 74% had only occasional partners; all engaged in commercial sex. In Cluster 5, all reported four or more partners and condomless sex. In all subgroups we found low rates of HIV testing and high unawareness of HIV serostatus. Targeted prevention interventions are needed to reduce unprotected sexual relations and undiagnosed infection, as well as improve linkage to sexual health services.
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Infecciones por VIH , Migrantes , África del Sur del Sahara/epidemiología , Condones , Estudios Transversales , Infecciones por VIH/epidemiología , Servicios de Salud , Humanos , Portugal/epidemiología , Asunción de Riesgos , Trabajo Sexual , Conducta Sexual , Parejas SexualesRESUMEN
BACKGROUND: Elimination of malaria depends on mastering transmission and understanding the biological basis of Plasmodium infection in the vector. The first mosquito organ to interact with the parasite is the midgut and its transcriptomic characterization during infection can reveal effective antiplasmodial responses able to limit the survival of the parasite. The vector response to Plasmodium vivax is not fully characterized, and its specificities when compared with other malaria parasites can be of fundamental interest for specific control measures. METHODS: Experimental infections were performed using a membrane-feeding device. Three groups were used: P. vivax-blood-fed, blood-fed on inactivated gametocytes, and unfed mosquitoes. Twenty-four hours after feeding, the mosquitoes were dissected and the midgut collected for transcriptomic analysis using RNAseq. Nine cDNA libraries were generated and sequenced on an Illumina HiSeq2500. Readings were checked for quality control and analysed using the Trinity platform for de novo transcriptome assembly. Transcript quantification was performed and the transcriptome was functionally annotated. Differential expression gene analysis was carried out. The role of the identified mechanisms was further explored using functional approaches. RESULTS: Forty-nine genes were identified as being differentially expressed with P. vivax infection: 34 were upregulated and 15 were downregulated. Half of the P. vivax-related differentially expressed genes could be related to autophagy; therefore, the effect of the known inhibitor (wortmannin) and activator (spermidine) was tested on the infection outcome. Autophagic activation significantly reduced the intensity and prevalence of infection. This was associated with transcription alterations of the autophagy regulating genes Beclin, DRAM and Apg8. CONCLUSIONS: Our data indicate that P. vivax invasion of An. aquasalis midgut epithelium triggers an autophagic response and its activation reduces infection. This suggests a novel mechanism that mosquitoes can use to fight Plasmodium infection.
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Anopheles/genética , Autofagia , Sistema Digestivo/parasitología , Interacciones Huésped-Parásitos/genética , Plasmodium vivax/patogenicidad , Transcriptoma , Animales , Anopheles/parasitología , Femenino , Perfilación de la Expresión Génica , Biblioteca de Genes , Malaria Vivax/transmisión , Mosquitos Vectores/genética , Mosquitos Vectores/parasitologíaRESUMEN
This study investigates the use of antibiotics and prescribing patterns and identifies the antibiotics most frequently prescribed in public health units of Belo Horizonte, MG. The methods used were observational, cross-sectional study aimed at analyzing the consistency between a sample of medical records and antibiotic prescriptions dispensed during March 2002 in eleven public health units in Belo Horizonte, Minas Gerais, Brazil. Pediatrics showed the highest proportion of antibiotic prescribing among four specialties; amoxicillin was the most frequently prescribed antibiotic, followed by benzathine penicillin G, sulfamethoxazole/trimethoprim, and erythromycin. Upper respiratory tract infections, tonsillitis, acute otitis media and urinary tract infections were the diagnostic hypotheses most frequently recorded. Overall consistency between the recorded diagnostic hypotheses and the prescribed antibiotic was lower than 75%. The duration of the therapy prescribed varied largely and in approximately 10% of the prescriptions this information was lacking. Moreover, data on the patient such as age, body weight, co-morbidity, diagnostic hypotheses and adverse reactions, were systematically absent in the medical records. This study demonstrates the need for interventions in order to promote a more rational use of antibiotics.
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Antibacterianos , Prescripciones de Medicamentos/normas , Brasil , Estudios Transversales , Prescripciones de Medicamentos/estadística & datos numéricos , Humanos , Salud PúblicaRESUMEN
BACKGROUND: The anti-malarial chloroquine can modulate the outcome of infection during the Plasmodium sporogonic development, interfering with Plasmodium gene expression and subsequently, with transmission. The present study sets to identify Plasmodium genes that might be regulated by chloroquine in the mosquito vector. METHODS: Differential display RT-PCR (DDRT-PCR) was used to identify genes expressed during the sporogonic cycle that are regulated by exposure to chloroquine. Anopheles stephensi mosquitoes were fed on Plasmodium yoelii nigeriensis-infected mice. Three days post-infection, mosquitoes were fed a non-infectious blood meal from mice treated orally with 50 mg/kg chloroquine. Two differentially expressed Plasmodium transcripts (Pyn_chl091 and Pyn_chl055) were further characterized by DNA sequencing and real-time PCR analysis. RESULTS: Both transcripts were represented in Plasmodium EST databases, but displayed no homology with any known genes. Pyn_chl091 was upregulated by day 18 post infection when the mosquito had a second blood meal. However, when the effect of chloroquine on that transcript was investigated during the erythrocytic cycle, no significant differences were observed. Although slightly upregulated by chloroquine exposure the expression of Pyn_chl055 was more affected by development, increasing towards the end of the sporogonic cycle. Transcript abundance of Pyn_chl055 was reduced when erythrocytic stages were treated with chloroquine. CONCLUSION: Chloroquine increased parasite load in mosquito salivary glands and interferes with the expression of at least two Plasmodium genes. The transcripts identified contain putative signal peptides and transmembrane domains suggesting that these proteins, due to their location, are targets of chloroquine (not as an antimalarial) probably through cell trafficking and recycling.
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Cloroquina/farmacología , Culicidae/parasitología , Expresión Génica/efectos de los fármacos , Plasmodium yoelii/genética , Secuencia de Aminoácidos , Animales , Antimaláricos/farmacología , Antimaláricos/uso terapéutico , Cloroquina/uso terapéutico , Femenino , Perfilación de la Expresión Génica , Regulación del Desarrollo de la Expresión Génica/efectos de los fármacos , Insectos Vectores/parasitología , Malaria/tratamiento farmacológico , Malaria/parasitología , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Datos de Secuencia Molecular , Parasitemia/tratamiento farmacológico , Parasitemia/parasitología , Plasmodium yoelii/efectos de los fármacos , Plasmodium yoelii/crecimiento & desarrollo , Proteínas Protozoarias/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Factores de TiempoRESUMEN
Overuse of antibiotics is a public health problem and has raised discussions concerning their rational use. This cross-sectional study focuses on the use of systemic antibiotics under the Belo Horizonte Municipal Health Department, Minas Gerais, Brazil, evaluating prescriptions dispensed in March 2002, based on WHO indicators for antibiotic use. On average, 20% of prescriptions dispensed involved at least one systemic antibiotic, among which approximately 46% originated from health care facilities not belonging to the municipal system itself. Amoxicillin was the most frequently prescribed antibiotic, followed by benzathine penicillin. Recording of technical data (dose, intervals between doses, administration, and treatment period) varied from 23.6 to 99.6%. Some 10% of prescriptions failed to specify the treatment period. The study showed the need for rules to allow quality improvement of antibiotic prescriptions, assuring the rational use of such medication by municipal health services.
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Instituciones de Atención Ambulatoria/normas , Antibacterianos/uso terapéutico , Prescripciones de Medicamentos/normas , Revisión de la Utilización de Medicamentos/normas , Instituciones de Atención Ambulatoria/estadística & datos numéricos , Amoxicilina/uso terapéutico , Brasil , Estudios Transversales , Prescripciones de Medicamentos/estadística & datos numéricos , Humanos , Programas Nacionales de Salud/normas , Penicilina G Benzatina/uso terapéutico , Pautas de la Práctica en Medicina/estadística & datos numéricos , Atención Primaria de SaludRESUMEN
AIM: To explain the missing heritability after the genome-wide association studies era, sequencing studies allow the identification of low-frequency variants with a stronger effect on disease risk. Common variants in the interleukin 10 gene (IL10) have been consistently associated with Behçet's disease (BD) and the goal of this study is to investigate the role of low-frequency IL10 variants in BD susceptibility. METHODS: To identify IL10 low-frequency variants, a discovery group of 50 Portuguese BD patients were Sanger-sequenced in a 7.7 kb genomic region encompassing the complete IL10 gene, 0.9 kb upstream and 2 kb downstream, and two conserved regions in the putative promoter. To assess if the novel variants are BD- and/or Portuguese-specific, they were assayed in an additional group of BD patients (26 Portuguese and 964 Iranian) and controls (104 Portuguese and 823 Iranian). RESULTS: Rare IL10 coding variants were not detected in BD patients, but we identified 28 known single nucleotide polymorphisms with minor allele frequencies ranging from 0.010 to 0.390, and five novel non-coding variants in five heterozygous cases. ss836185595, located in the IL10 3' untranslated region, was also detected in one Iranian control individual and therefore is not specific to BD. The remaining novel IL10 variants (ss836185596 and ss836185602 in intron 3, ss836185598 and ss836185604 in the putative promoter region) were not found in the replication dataset. CONCLUSION: This study highlights the importance of screening the whole gene and regulatory regions when searching for novel variants associated with complex diseases, and the need to develop bioinformatics tools to predict the functional impact of non-coding variants and statistical tests which incorporate these predictions.
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Síndrome de Behçet/genética , Interleucina-10/genética , Mutación , Polimorfismo de Nucleótido Simple , Adulto , Síndrome de Behçet/diagnóstico , Síndrome de Behçet/inmunología , Estudios de Casos y Controles , Análisis Mutacional de ADN , Femenino , Frecuencia de los Genes , Estudios de Asociación Genética , Marcadores Genéticos , Predisposición Genética a la Enfermedad , Humanos , Irán , Masculino , Persona de Mediana Edad , Tasa de Mutación , Fenotipo , Reacción en Cadena de la Polimerasa , Portugal , Factores de Riesgo , Adulto JovenRESUMEN
BACKGROUND AND AIMS: Peripheral arterial disease (PAD) and venous thromboembolism (VTE) are vascular traits sharing common modifiable and non-modifiable risk factors. These vascular pathologies have known nuclear-encoded genetic risk factors and the mitochondrial DNA may account for part of the missing heritability. To determine if PAD and VTE have a dual genetic control (mitochondrial and nuclear), we hereby investigated the association of mitochondrial DNA polymorphisms and haplogroups with these vascular traits. METHODS: The association of mitochondrial single nucleotide polymorphisms (mtSNPs) and haplogroups was tested in 1652 PAD cases and 1629 controls from the eMERGE PAD genome-wide association study (GWAS), and 1241 VTE cases and 1278 controls from the GENEVA GWAS of venous thrombosis (dbGaP accession numbers phs000203.v1.p1 and phs000289.v2.p1, respectively). RESULTS: 66 and 72 mtSNPs passed quality control filters and were tested for association with PAD and VTE, respectively. Significant evidence of population stratification could not be detected in both datasets. Three mtSNPs (m.477T > C, m.9667A > G, and m.10915T > C) were nominally associated (3.01 × 10(-3) ≤ pa ≤ 3.96 × 10(-2)) with PAD in the logistic regression adjusted for confounding factors, and m.11914G > A was nominally associated (pa = 4.14 × 10(-2)) with VTE. None of the nine major mitochondrial haplogroups were associated with either PAD or VTE. CONCLUSION: Unlike other vascular diseases such as stroke and diabetes, these results suggest that common mitochondrial variants individually or in combination do not play a major role in PAD and VTE susceptibility.
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Genoma Mitocondrial , Enfermedad Arterial Periférica/genética , Polimorfismo de Nucleótido Simple , Tromboembolia Venosa/genética , Adulto , Anciano , Anciano de 80 o más Años , Índice Tobillo Braquial , Bases de Datos Factuales , Femenino , Predisposición Genética a la Enfermedad , Variación Genética , Genotipo , Haplotipos , Humanos , Modelos Logísticos , Masculino , Persona de Mediana Edad , Fenotipo , Factores de RiesgoRESUMEN
BACKGROUND: Cellular oxidative stress and genetic susceptibility have been implicated in the multifactorial etiology of ulcerative colitis (UC). The nuclear genome association with UC has been intensely investigated, but the role of the mitochondrial DNA (mtDNA) has received far less attention and may account for part of the missing heritability. This study is a comprehensive analysis of the mtDNA contribution to UC susceptibility. METHODS: The association of mitochondrial single-nucleotide polymorphisms (mtSNPs) and haplogroups with UC was tested in 488 cases and 833 controls of European ancestry from the NIDDK IBD Genetics Consortium Ulcerative Colitis Genome-Wide Association Study available through dbGaP and from the Illumina Genotype Control Database (studies 64 and 65). RESULTS: No evidence of population stratification could be detected using 218 ancestry informative markers for European Americans. Seven of the 58 tested mtSNPs were nominally associated with UC, and A10550G in MT-ND4L withstands the Bonferroni correction (P = 1.29E-06, odds ratio [ORG] [95% confidence interval (CI)] = 4.80 [2.54-9.05], 10550G allele: 8.1% of patients and 1.9% of controls). A10550G remains equally associated after conditional analyses on the 11 UC genome-wide association studies (GWAS) top SNPs (6.35E-07 < Pcond < 4.58E-06), which suggests that it constitutes an independent risk factor from nuclear-encoded susceptibility loci. We detected additive (but not multiplicative) epistatic interactions between A10550G and all 11 top GWAS hits. Subhaplogroup K1 (P = 0.021, OR [95% CI] = 1.71 [1.08-2.69]) increased the risk for UC, whereas the U5b lineage conferred protection (P = 0.016, OR [95% CI] = 0.34 [0.14-0.82]). CONCLUSIONS: These results suggest that UC has a dual mitochondrial and nuclear genetic control that warrants further replication in independent data sets and reinforces its etiopathogenic complexity.
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Colitis Ulcerosa/genética , Regulación de la Expresión Génica , Genes Mitocondriales/genética , Proteínas Nucleares/genética , Polimorfismo de Nucleótido Simple/genética , Estudios de Casos y Controles , Bases de Datos Factuales , Femenino , Estudios de Seguimiento , Sitios Genéticos , Predisposición Genética a la Enfermedad , Genoma Mitocondrial , Estudio de Asociación del Genoma Completo , Humanos , Masculino , Persona de Mediana Edad , Factores de RiesgoRESUMEN
Despite elevated incidence and recurrence rates for Primary Spontaneous Pneumothorax (PSP), little is known about its etiology, and the genetics of idiopathic PSP remains unexplored. To identify genetic variants contributing to sporadic PSP risk, we conducted the first PSP genome-wide association study. Two replicate pools of 92 Portuguese PSP cases and of 129 age- and sex-matched controls were allelotyped in triplicate on the Affymetrix Human SNP Array 6.0 arrays. Markers passing quality control were ranked by relative allele score difference between cases and controls (|RASdiff|), by a novel cluster method and by a combined Z-test. 101 single nucleotide polymorphisms (SNPs) were selected using these three approaches for technical validation by individual genotyping in the discovery dataset. 87 out of 94 successfully tested SNPs were nominally associated in the discovery dataset. Replication of the 87 technically validated SNPs was then carried out in an independent replication dataset of 100 Portuguese cases and 425 controls. The intergenic rs4733649 SNP in chromosome 8 (between LINC00824 and LINC00977) was associated with PSP in the discovery (P = 4.07E-03, ORC[95% CI] = 1.88[1.22-2.89]), replication (P = 1.50E-02, ORC[95% CI] = 1.50[1.08-2.09]) and combined datasets (P = 8.61E-05, ORC[95% CI] = 1.65[1.29-2.13]). This study identified for the first time one genetic risk factor for sporadic PSP, but future studies are warranted to further confirm this finding in other populations and uncover its functional role in PSP pathogenesis.
Asunto(s)
Estudio de Asociación del Genoma Completo/métodos , Neumotórax/genética , Cromosomas Humanos Par 8/genética , Femenino , Predisposición Genética a la Enfermedad/genética , Genotipo , Humanos , Masculino , Polimorfismo de Nucleótido Simple/genética , Factores de RiesgoRESUMEN
OBJECTIVE: To investigate the influence of common and low-frequency genetic variants on the risk of ischemic stroke (all IS) and etiologic stroke subtypes. METHODS: We meta-analyzed 12 individual genome-wide association studies comprising 10,307 cases and 19,326 controls imputed to the 1000 Genomes (1 KG) phase I reference panel. We selected variants showing the highest degree of association (p < 1E-5) in the discovery phase for replication in Caucasian (13,435 cases and 29,269 controls) and South Asian (2,385 cases and 5,193 controls) samples followed by a transethnic meta-analysis. We further investigated the p value distribution for different bins of allele frequencies for all IS and stroke subtypes. RESULTS: We showed genome-wide significance for 4 loci: ABO for all IS, HDAC9 for large vessel disease (LVD), and both PITX2 and ZFHX3 for cardioembolic stroke (CE). We further refined the association peaks for ABO and PITX2. Analyzing different allele frequency bins, we showed significant enrichment in low-frequency variants (allele frequency <5%) for both LVD and small vessel disease, and an enrichment of higher frequency variants (allele frequency 10% and 30%) for CE (all p < 1E-5). CONCLUSIONS: Our findings suggest that the missing heritability in IS subtypes can in part be attributed to low-frequency and rare variants. Larger sample sizes are needed to identify the variants associated with all IS and stroke subtypes.