Effect of urban vs. rural residence on the association between atopy and wheeze in Latin America: findings from a case-control analysis.

BACKGROUND: The association between atopy and asthma is attenuated in non-affluent populations, an effect that may be explained by childhood infections such as geohelminths. OBJECTIVE: To investigate the association between atopy and wheeze in schoolchildren living in urban and rural areas of Ecuador and examine the effects of geohelminths on this association. METHODS: We performed nested case-control studies among comparable populations of schoolchildren living in rural communities and urban neighbourhoods in the Province of Esmeraldas, Ecuador. We detected geohelminths in stool samples, measured recent wheeze and environmental exposures by parental questionnaire, and atopy by specific IgE (sIgE) and skin prick test (SPT) reactivity to aeroallergens. RESULTS: Atopy, particularly sIgE to house dust mite (HDM), was more strongly associated with recent wheeze in urban than rural schoolchildren: (urban, adj. OR 5.19, 95% CI 3.37-8.00, P < 0.0001; rural, adj. OR 1.81, 95%CI 1.09-2.99, P = 0.02; interaction, P < 0.001). The population fractions of wheeze attributable to atopy were approximately two-fold greater in urban schoolchildren: SPT to any allergen (urban 23.5% vs. rural 10.1%), SPT to HDM (urban 18.5% vs. rural 9.6%), and anti-HDM IgE (urban 26.5% vs. rural 10.5%), while anti-Ascaris IgE was related to wheeze in a high proportion of rural (49.7%) and urban (35.4%) children. The association between atopy and recent wheeze was attenuated by markers of geohelminth infections. CONCLUSIONS: Our data suggest that urban residence modifies the association between HDM atopy and recent wheeze, and this effect is explained partly by geohelminth infections

Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota

Background: The soil-transmitted helminth (STH), Trichuris trichiura colonises the human large intestine where it may modify inflammatory responses, an effect possibly mediated through alterations in the intestinal microbiota. We hypothesised that patent T. trichiura infections would be associated with altered faecal microbiota and that anthelmintic treatment would induce a microbiota resembling more closely that observed in uninfected individuals. Materials and Methods: School children in Ecuador were screened for STH infections and allocated to 3 groups: uninfected, T. trichiura only, and mixed infections with T. trichiura and Ascaris lumbricoides. A sample of uninfected children and those with T. trichiura infections only were given anthelmintic treatment. Bacterial community profiles in faecal samples were studied by 454 pyrosequencing of 16 S rRNA genes. Results: Microbiota analyses of faeces were done for 97 children: 30 were uninfected, 17 were infected with T. trichiura, and 50 with T. trichiura and A. lumbricoides. Post-treatment samples were analyzed for 14 children initially infected with T. trichiura alone and for 21 uninfected children. Treatment resulted in 100% cure of STH infections. Comparisons of the microbiota at different taxonomic levels showed no statistically significant differences in composition between uninfected children and those with T. trichiura infections. We observed a decreased proportional abundance of a few bacterial genera from the Clostridia class of Firmicutes and a reduced bacterial diversity among children with mixed infections compared to the other two groups, indicating a possible specific effect of A. lumbricoides infection. Anthelmintic treatment of children with T. trichiura did not alter faecal microbiota composition. Discussion: Our data indicate that patent human infections with T. trichiura may have no effect on faecal microbiota but that A. lumbricoides colonisation might be associated with a disturbed microbiota. Our results also catalogue the microbiota of rural Ecuadorians and indicate differences with individuals from more urban industrialised societies

A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a focus on flagellate plants

Assembling large-scale phenotypic datasets for evolutionary and biodiversity studies of plants can be extremely difficult and time consuming. New semi-automated Natural Language Processing (NLP) pipelines can extract phenotypic data from taxonomic descriptions, and their performance can be enhanced by incorporating information from ontologies, like the Plant Ontology (PO) and the Plant Trait Ontology (TO). These ontologies are powerful tools for comparing phenotypes across taxa for large-scale evolutionary and ecological analyses, but they are largely focused on terms associated with flowering plants. We describe a bottom-up approach to identify terms from flagellate plants (including bryophytes, lycophytes, ferns, and gymnosperms) that can be added to existing plant ontologies. We first parsed a large corpus of electronic taxonomic descriptions using the Explorer of Taxon Concepts tool (http://taxonconceptexplorer.org/) and identified flagellate plant specific terms that were missing from the existing ontologies. We extracted new structure and trait terms, and we are currently incorporating the missing structure terms to the PO and modifying the definitions of existing terms to expand their coverage to flagellate plants. We will incorporate trait terms to the TO in the near future

Impact of early life exposures to geohelminth infections on the development of vaccine immunity, allergic sensitization, and allergic inflammatory diseases in children living in tropical Ecuador: the ECUAVIDA birth cohort study.

Background Geohelminth infections are highly prevalent infectious diseases of childhood in many regions of the Tropics, and are associated with significant morbidity especially among pre-school and school-age children. There is growing concern that geohelminth infections, particularly exposures occurring during early life in utero through maternal infections or during infancy, may affect vaccine immunogenicity in populations among whom these infections are endemic. Further, the low prevalence of allergic disease in the rural Tropics has been attributed to the immune modulatory effects of these infections and there is concern that widespread use of anthelmintic treatment in high-risk groups may be associated with an increase in the prevalence of allergic diseases. Because the most widely used vaccines are administered during the first year of life and the antecedents of allergic disease are considered to occur in early childhood, the present study has been designed to investigate the impact of early exposures to geohelminths on the development of protective immunity to vaccines, allergic sensitization, and allergic disease. Methods/Design A cohort of 2,403 neonates followed up to 8 years of age. Primary exposures are infections with geohelminth parasites during the last trimester of pregnancy and the first 2 years of life. Primary study outcomes are the development of protective immunity to common childhood vaccines (i.e. rotavirus, Haemophilus influenzae type B, Hepatitis B, tetanus toxoid, and oral poliovirus type 3) during the first 5 years of life, the development of eczema by 3 years of age, the development of allergen skin test reactivity at 5 years of age, and the development of asthma at 5 and 8 years of age. Potential immunological mechanisms by which geohelminth infections may affect the study outcomes will be investigated also. Discussion The study will provide information on the potential effects of early exposures to geohelminths (during pregnancy and the first 2 years of life) on the development of vaccine immunity and allergy. The data will inform an ongoing debate of potential effects of geohelminths on child health and will contribute to policy decisions on new interventions designed to improve vaccine immunogenicity and protect against the development of allergic diseases

Continuous colonization of the Atlantic coastal rain forests of South America from Amazônia

The two main extensions of rain forest in South America are the Amazon (Amazônia) and the Atlantic rain forest (Mata Atlântica), which are separated by a wide ‘dry diagonal’ of seasonal vegetation. We used the species-rich tree genus $Inga$ to test if Amazônia—Mata Atlântica dispersals have been clustered during specific time periods corresponding to past, humid climates. We performed hybrid capture DNA sequencing of 810 nuclear loci for 453 accessions representing 164 species that included 62% of Mata Atlântica species and estimated a dated phylogeny for all accessions using maximum likelihood, and a species-level tree using coalescent methods. There have been 16–20 dispersal events to the Mata Atlântica from Amazônia with only one or two dispersals in the reverse direction. These events have occurred over the evolutionary history of $Inga$, with no evidence for temporal clustering, and model comparisons of alternative biogeographic histories and null simulations showing the timing of dispersal events matches a random expectation. Time-specific biogeographic corridors are not required to explain dispersal between Amazônia and the Mata Atlântica for rain forest trees such as $Inga$, which are likely to have used a dendritic net of gallery forests to cross the dry diagonal

Preliminary molecular phylogenetics of Sobralia and relatives (Orchidaceae: Sobralieae)

With over 200 species, the orchid tribe Sobralieae is a major constituent of the Neotropical flora. As currently circumscribed, the tribe includes four genera: Elleanthus, Epilyna, Sertifera, and Sobralia. Most species of these four genera typically produce long, cane-like stems but differ drastically in flower size and inflorescence structure. DNA sequence data support the monophyly of Elleanthus, Epilyna, and Sertifera but not Sobralia, which is a polyphyletic assemblage traditionally placed together due to relatively large flower size. Details of inflorescence structure provide characters that can easily distinguish the different clades of Sobralia. The misleading characteristic of flower size is probably due to at least several shifts in pollination syndrome within the tribe. With few exceptions, species of Sobralia predominantly offer no reward and are pollinated by bees. Elleanthus and Sertifera are small-flowered and mostly pollinated by hummingbirds with legitimate rewards. Nothing is known of pollination in Epilyna. Understanding the evolution of shifts in pollination syndrome will require more empirical observations of pollination within Sobralieae. In addition, increased taxon sampling and improved phylogenetic resolution are needed before generic realignments are made.Con más de 200 especies, la tribu de orquídeas Sobralieae es un componente importante de la riqueza florística de los neotrópicos. Actualmente esta tribu está constituída por cuatro géneros: Elleanthus, Epilyna, Sertifera, y Sobralia. Las plantas de éstos cuatro géneros generalmente producen tallos largos como cañas, pero difieren en forma drástica en el tamaño de la flor y la estructura de las inflorescencias. Datos de ADN apoyan la monofilia de Elleanthus, Epilyna, y Sertifera, pero no de Sobralia. Sobralia es un ensamblaje polifilético, tradicionalmente circunscrito por el gran tamaño de sus flores. Los detalles de la morfología floral y la posición de la inflorescencia proporcionan caracteres que fácilmente permiten distinguir los diferentes clados de Sobralia. El tamaño de la flor y ciertas otras características superficiales probablemente han sufrido cambios evolutivos en respuesta a cambios en el síndrome de polinización dentro de la tribu. La mayoría de las especies de Sobralia no ofrecen ninguna recompensa y son polinizadas por abejas en busca de néctar. Elleanthus y Sertifera tienen flores pequeñas que aparentemente son polinizadas por colibríes, en estos dos géneros las flores ofrecen néctar. No se conoce nada sobre la polinización de Epilyna. Mas observaciones empíricas de los polinizadores de Sobralieae son necesarias para entender la evolución de los síndromes de polinización, y requerirá un mayor muestreo de especies y una mejor resolución filogenética antes de realizar recircumscripciones genéricas.National Science Foundation/[DEB-234064]/NSF/Estados UnidosUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL