RESUMO
Introduction: The hygiene hypothesis identified a relationship between living in rural areas and acquiring protective environmental factors against the development of asthma and atopy. In our previous study, we found a correlation between particular bacterial species and early-onset wheezing in infants from the rural tropics of Ecuador who were corticosteroid-naïve and had limited antibiotic exposure. We now describe a longitudinal study of infants conducted to determine the age-related changes of the microbiome and its relationship with wheezing. Methods: We performed an amplicon sequencing of the 16S rRNA bacterial gene from the oropharyngeal samples obtained from 110 infants who had a history of recurrent episodic wheezing sampled at different ages (7, 12, and 24 months) and compared it to the sequencing of the oropharyngeal samples from 150 healthy infants sampled at the same time points. Bioinformatic analyses were conducted using QIIME and R. Results: As expected, the microbiota diversity consistently increased as the infants grew older. Considering age-based microbiota changes, we found that infants with wheeze had significantly lower species richness than the healthy infants at 7 months, but not at 12 or 24 months. Most of the core and accessory organisms increased in abundance and prevalence with age, except for a few which decreased. At 7 months of age, infants with wheeze had notably higher levels of a single Streptococcus operational taxonomic unit and core microbiota member than controls. Conclusions: In a cohort with limited antibiotic and corticosteroid use, a progressively more complex and diverse respiratory microbial community develops with age. The respiratory microbiota in early life is altered in infants with wheeze, but this does not hold true in older infants.
RESUMO
Metareasoning suffers from the heterogeneity problem, in which different researchers build diverse metareasoning models for intelligent systems with comparable functionality but differing contexts, ambiguous terminology, and occasionally contradicting features and descriptions. This article presents an ontology-driven knowledge representation for metareasoning in intelligent systems. The proposed ontology, called IM-Onto, provides a visual means of sharing a common understanding of the structure and relationships between terms and concepts. A rigorous research method was followed to ensure that the two main requirements of the ontology (integrity based on relevant knowledge and acceptance by researchers and practitioners) were met. The high accuracy rate indicates that most of the knowledge elements in the ontology are useful information for the integration of multiple types of metareasoning problems in intelligent systems.
RESUMO
The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.
Assuntos
Herbaspirillum/enzimologia , Recombinases Rec A/química , Recombinases Rec A/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Domínio Catalítico , DNA/genética , DNA/metabolismo , Ativação Enzimática , Modelos Moleculares , Nucleoproteínas/química , Nucleoproteínas/metabolismo , Ligação Proteica , Conformação Proteica , Multimerização Proteica , Proteínas Recombinantes , Eletricidade Estática , Relação Estrutura-AtividadeRESUMO
Like many small-scale fishing communities around the world, the community of Buen Hombre in the Dominican Republic is dealing with a set of challenges to reconcile its fishing activities with the ecology on which it depends. Also like many such communities, this case has been examined at a particular period in time by a group of social scientists, but not over substantial lengths of time in order to examine the longitudinal validity of the conclusions made during this period. In this paper we combine data from previous anthropological work with our own primary social and ecological data to conduct a longitudinal case study of the Buen Hombre fishery. Our over-time comparison focuses on a suite of mostly social and institutional variables to explain what we find to be a continued degradation of the fishery, and we conclude the analysis by presenting a causal-loop diagram, summarizing our inferences regarding the complex interactions among these variables. We find that a mix of factors, notably changes in gear and fishing sites used, the number of fishermen and their livelihood diversity, as well as an increased connectivity between Buen Hombre and its external environment, have contributed to the decline of the condition of Buen Hombre coral reef fishery. We conclude with a discussion of what may lie ahead for this particular case and others like it.
Assuntos
Conservação dos Recursos Naturais , Pesqueiros , Recifes de Corais , República Dominicana , Estudos LongitudinaisRESUMO
BACKGROUND: Observations that the airway microbiome is disturbed in asthma may be confounded by the widespread use of antibiotics and inhaled steroids. We have therefore examined the oropharyngeal microbiome in early onset wheezing infants from a rural area of tropical Ecuador where antibiotic usage is minimal and glucocorticoid usage is absent. MATERIALS AND METHODS: We performed pyrosequencing of amplicons of the polymorphic bacterial 16S rRNA gene from oropharyngeal samples from 24 infants with non-infectious early onset wheezing and 24 healthy controls (average age 10.2 months). We analyzed microbial community structure and differences between cases and controls by QIIME software. RESULTS: We obtained 76,627 high quality sequences classified into 182 operational taxonomic units (OTUs). Firmicutes was the most common and diverse phylum (71.22% of sequences) with Streptococcus being the most common genus (49.72%). Known pathogens were found significantly more often in cases of infantile wheeze compared to controls, exemplified by Haemophilus spp. (OR=2.12, 95% Confidence Interval (CI) 1.82-2.47; P=5.46×10(-23)) and Staphylococcus spp. (OR=124.1, 95%CI 59.0-261.2; P=1.87×10(-241)). Other OTUs were less common in cases than controls, notably Veillonella spp. (OR=0.59, 95%CI=0.56-0.62; P=8.06×10(-86)). DISCUSSION: The airway microbiota appeared to contain many more Streptococci than found in Western Europe and the USA. Comparisons between healthy and wheezing infants revealed a significant difference in several bacterial phylotypes that were not confounded by antibiotics or use of inhaled steroids. The increased prevalence of pathogens such as Haemophilus and Staphylococcus spp. in cases may contribute to wheezing illnesses in this age group.