Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.

MOTIVATION: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species. RESULTS: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee. AVAILABILITY: download section of the Bgee website http://bgee.unil.ch/

Batflies Parasitic on Some Phyllostomid Bats in Southeastern Brazil: Parasitism Rates and Host-parasite Relationships

Ectoparasitic batflies were studied on 12 species of phyllostomid bats, by making 35 nightly collections of bats using mist nets at the "Panga" Ecological Reservation near Uberlândia, State of Minas Gerais, southeastern Brazil, from August 1989 to July 1990. Eleven species of Streblidae and one of Nycteribiidae were collected on 12 species of bats. Prevalence of ectoparasitic flies was lower than those reported by other authors for the New World and may be the result of the lack of caves in the study area, causing bats to roost in less favorable locations, forming smaller colonies. The fly, Trichobius joblingi Wenzel, was found on Carollia perspicillata (Linnaeus), showing preference for adult male bats. This could be explained by the predominance of males in the bat colonies, and by the fact that females rest in isolation during the reproductive period making them less exposed to the parasites. The streblid flies, Aspidoptera falcata Wenzel and Megistopoda proxima (Séguy), were found on Sturnira lilium (Geoffroy). A. falcata occurred mainly on young and adult females, whereas M. proxima did not show any preferences relative to the reproductive condition of the host. Ecological factors are important in determining differential numbers of parasites occurring on the different sexes, ages and reproductive state of the hosts.

A Mitochondrial DNA Phylogeny Indicates Close Relationships between Populations of Lutzomyia whitmani (Diptera: Psychodidae, Phlebotominae) from the Rain-forest Regions of Amazônia and Northeast Brazil

Phylogenetic analysis of all 31 described mitochondrial (cytochrome b) haplotypes of Lutzomyia whitmani demonstrated that new material from the State of Rondônia, in southwest Amazônia, forms a clade within a lineage found only in the rain-forest regions of Brazil. This rain-forest lineage also contains two other clades of haplotypes, one from eastern Amazônia and one from the Atlantic forest zone of northeast Brazil (including the type locality of the species in Ilhéus, State of Bahia). These findings do not favour recognizing two allopatric cryptic species of L. whitmani, one associated with the silvatic transmission of Leishmania shawi in southeast Amazônia and the other with the peridomestic transmission of Le. braziliensis in northeast Brazil. Instead, they suggest that there is (or has been in the recent past) a continuum of inter-breeding populations of L. whitmani in the rain-forest regions of Brazil.

Closeness in relationships as a mediator between sexual abuse in childhood or adolescence and psychopathological outcome in adulthood.

The risk of adverse psychological outcomes in adult victims of childhood and adolescent sexual abuse (CSA) has been documented; however, research on possible mediating variables is still required, namely with a clinical perspective. The attachment literature suggests that secure interpersonal relationships may represent such a variable. Twenty-eight women who had experienced episodes of CSA, and 16 control women, were interviewed using Bremner's Early Trauma Inventory and the DSM-IV Global Assessment of Functioning; they also responded to Collins' Relationship Scales Questionnaire, evaluating adult attachment representations in terms of Closeness, Dependence and Anxiety. Subjects with an experience of severe abuse reported significantly more interpersonal distance in relationships (low index of Closeness) than other subjects. The index of psychopathological functioning was correlated with both the severity of abuse and attachment (low index of Closeness). Regression analysis on the sample of abused women revealed that attachment predicted psychopathology when abuse was controlled for, whereas abuse did not predict psychopathology when attachment was controlled for. Therefore, preserving a capacity for closeness with attachment figures in adulthood appears to mediate the consequences of CSA on subsequent psychopathological outcome.

Noves tecnologies per l'estudi de l'arqueologia de Patagònia (Amèrica del Sud)

The goal of this project was the historical study of Patagonia, the southernmost human settled area of the world. Our aim has been the anlysis of those societies to understand how they maintained their socioeconomic system, that is to say, how social reproduction allowed resolving the basic contradiction between production and reproduction, which is characteristic of all hunter-gatherer societies. New computational technologies have allowed a bettwer integration of the big amount and diversity of data needed. We have analyzed the historical evolution of inter-group and intra-group social relationships among nomad patagonian societies. We have compared different social answers in front of the radical change of their immediate reality produced by european colonization. We have exhaustively analyzed the results of archaeological excavations from diferent regions. We have also integrated information from anthropology, ethnohistory and geography. We are developing computing programs to integrate geographical actual data with paleoenvironmental data about the dynamic nature of soil formation, vegetation, hidrography, etc., with information about the history of productive action and how products were distributed among different human groups.

Natural Arabidopsis brx loss-of-function alleles confer root adaptation to acidic soil.

Soil acidification is a major agricultural problem that negatively affects crop yield. Root systems counteract detrimental passive proton influx from acidic soil through increased proton pumping into the apoplast, which is presumably also required for cell elongation and stimulated by auxin. Here, we found an unexpected impact of extracellular pH on auxin activity and cell proliferation rate in the root meristem of two Arabidopsis mutants with impaired auxin perception, axr3 and brx. Surprisingly, neutral to slightly alkaline media rescued their severely reduced root (meristem) growth by stimulating auxin signaling, independent of auxin uptake. The finding that proton pumps are hyperactive in brx roots could explain this phenomenon and is consistent with more robust growth and increased fitness of brx mutants on overly acidic media or soil. Interestingly, the original brx allele was isolated from a natural stock center accession collected from acidic soil. Our discovery of a novel brx allele in accessions recently collected from another acidic sampling site demonstrates the existence of independently maintained brx loss-of-function alleles in nature and supports the notion that they are advantageous in acidic soil pH conditions, a finding that might be exploited for crop breeding.

Paleoparasitology and the antiquity of human host-parasite relationships

Paleoparasitology may be developed as a new tool to parasite evolution studies. DNA sequences dated thousand years ago, recovered from archaeological material, means the possibility to study parasite-host relationship coevolution through time. Together with tracing parasite-host dispersion throughout the continents, paleoparasitology points to the interesting field of evolution at the molecular level. In this paper a brief history of paleoparasitology is traced, pointing to the new perspectives opened by the recent techniques introduced.

Estràtegies de gestió per al manteniment de la biodiversitat a la sabana brasilera: control d'especies exòtiques amb foc

Report for the scientific sojourn at the Instituto de Biociências, of the Universidade de Sao Paulo, Brazil, from 2007 to 2009. African exotic grasses, used as forage crops for cattle, found optimal conditions in Brazilian savannas for their spread. They established as invasive grasses in almost all conservation units, becoming a serius threat to native biote and to most ecological processes. Fire is a cyclical event in Brazilian savannas and can be used as a management tool for enhancing competitivity of native grasses and controlling exotic grasses. Seeking for alternatives for the management of these grasses, this study investigates the effect of recurrent burnings in different periods of the year (fire regimes) on: distribution patterns of exotic grasses and their associations wotih native grasses, the local edaphic characteristics, the nutrient pool of the aerial biomass of both native and exotic grasses, and soil seed banks. This project is held on the IBGE Ecological Reserve, in Brasília (Brazil), in an area destined specifically for research of fire effects on brazilian savannas. The project quantifies: aerial biomass of native and exotic grasses, soil seed bank of exotic grasses, nutrient pool in soil and also in grasses tissues. Spatial relationships for any association between species, as well as for nutrient pools in soil and in plant tissues will be established. A better understanding of these processes will provide useful tools for adopting specific policies on the management of exotic grasses in Brazilian savanna.

A soil emergence trap for collections of phlebotomine sand flies

The identification of breeding sites of sand flies is of great epidemiological interest. A soil emergence trap for investigating potential sand fly breeding sites is described. The trap was tested in two rural areas in the Mogi Guaçu River Valley where the American cutaneous leishmaniasis is an endemic disease. Seventy-three sand fly individuals of three species, Lutzomyia intermedia s. l., L. whitmani and L. pessoai, were collected on the forest floor and peridomicile.

Treeline and climate change : analyzing and modeling patterns and shifts in the Swiss Alps

Summary: Global warming has led to an average earth surface temperature increase of about 0.7 °C in the 20th century, according to the 2007 IPCC report. In Switzerland, the temperature increase in the same period was even higher: 1.3 °C in the Northern Alps anal 1.7 °C in the Southern Alps. The impacts of this warming on ecosystems aspecially on climatically sensitive systems like the treeline ecotone -are already visible today. Alpine treeline species show increased growth rates, more establishment of young trees in forest gaps is observed in many locations and treelines are migrating upwards. With the forecasted warming, this globally visible phenomenon is expected to continue. This PhD thesis aimed to develop a set of methods and models to investigate current and future climatic treeline positions and treeline shifts in the Swiss Alps in a spatial context. The focus was therefore on: 1) the quantification of current treeline dynamics and its potential causes, 2) the evaluation and improvement of temperaturebased treeline indicators and 3) the spatial analysis and projection of past, current and future climatic treeline positions and their respective elevational shifts. The methods used involved a combination of field temperature measurements, statistical modeling and spatial modeling in a geographical information system. To determine treeline shifts and assign the respective drivers, neighborhood relationships between forest patches were analyzed using moving window algorithms. Time series regression modeling was used in the development of an air-to-soil temperature transfer model to calculate thermal treeline indicators. The indicators were then applied spatially to delineate the climatic treeline, based on interpolated temperature data. Observation of recent forest dynamics in the Swiss treeline ecotone showed that changes were mainly due to forest in-growth, but also partly to upward attitudinal shifts. The recent reduction in agricultural land-use was found to be the dominant driver of these changes. Climate-driven changes were identified only at the uppermost limits of the treeline ecotone. Seasonal mean temperature indicators were found to be the best for predicting climatic treelines. Applying dynamic seasonal delimitations and the air-to-soil temperature transfer model improved the indicators' applicability for spatial modeling. Reproducing the climatic treelines of the past 45 years revealed regionally different attitudinal shifts, the largest being located near the highest mountain mass. Modeling climatic treelines based on two IPCC climate warming scenarios predicted major shifts in treeline altitude. However, the currently-observed treeline is not expected to reach this limit easily, due to lagged reaction, possible climate feedback effects and other limiting factors. Résumé: Selon le rapport 2007 de l'IPCC, le réchauffement global a induit une augmentation de la température terrestre de 0.7 °C en moyenne au cours du 20e siècle. En Suisse, l'augmentation durant la même période a été plus importante: 1.3 °C dans les Alpes du nord et 1.7 °C dans les Alpes du sud. Les impacts de ce réchauffement sur les écosystèmes - en particuliers les systèmes sensibles comme l'écotone de la limite des arbres - sont déjà visibles aujourd'hui. Les espèces de la limite alpine des forêts ont des taux de croissance plus forts, on observe en de nombreux endroits un accroissement du nombre de jeunes arbres s'établissant dans les trouées et la limite des arbres migre vers le haut. Compte tenu du réchauffement prévu, on s'attend à ce que ce phénomène, visible globalement, persiste. Cette thèse de doctorat visait à développer un jeu de méthodes et de modèles pour étudier dans un contexte spatial la position présente et future de la limite climatique des arbres, ainsi que ses déplacements, au sein des Alpes suisses. L'étude s'est donc focalisée sur: 1) la quantification de la dynamique actuelle de la limite des arbres et ses causes potentielles, 2) l'évaluation et l'amélioration des indicateurs, basés sur la température, pour la limite des arbres et 3) l'analyse spatiale et la projection de la position climatique passée, présente et future de la limite des arbres et des déplacements altitudinaux de cette position. Les méthodes utilisées sont une combinaison de mesures de température sur le terrain, de modélisation statistique et de la modélisation spatiale à l'aide d'un système d'information géographique. Les relations de voisinage entre parcelles de forêt ont été analysées à l'aide d'algorithmes utilisant des fenêtres mobiles, afin de mesurer les déplacements de la limite des arbres et déterminer leurs causes. Un modèle de transfert de température air-sol, basé sur les modèles de régression sur séries temporelles, a été développé pour calculer des indicateurs thermiques de la limite des arbres. Les indicateurs ont ensuite été appliqués spatialement pour délimiter la limite climatique des arbres, sur la base de données de températures interpolées. L'observation de la dynamique forestière récente dans l'écotone de la limite des arbres en Suisse a montré que les changements étaient principalement dus à la fermeture des trouées, mais aussi en partie à des déplacements vers des altitudes plus élevées. Il a été montré que la récente déprise agricole était la cause principale de ces changements. Des changements dus au climat n'ont été identifiés qu'aux limites supérieures de l'écotone de la limite des arbres. Les indicateurs de température moyenne saisonnière se sont avérés le mieux convenir pour prédire la limite climatique des arbres. L'application de limites dynamiques saisonnières et du modèle de transfert de température air-sol a amélioré l'applicabilité des indicateurs pour la modélisation spatiale. La reproduction des limites climatiques des arbres durant ces 45 dernières années a mis en évidence des changements d'altitude différents selon les régions, les plus importants étant situés près du plus haut massif montagneux. La modélisation des limites climatiques des arbres d'après deux scénarios de réchauffement climatique de l'IPCC a prédit des changements majeurs de l'altitude de la limite des arbres. Toutefois, l'on ne s'attend pas à ce que la limite des arbres actuellement observée atteigne cette limite facilement, en raison du délai de réaction, d'effets rétroactifs du climat et d'autres facteurs limitants.

Coevolutionary networks: a novel approach to understanding the relationships of humans with the infectious agents

Human organism is interpenetrated by the world of microorganisms, from the conception until the death. This interpenetration involves different levels of interactions between the partners including trophic exchanges, bi-directional cell signaling and gene activation, besides genetic and epigenetic phenomena, and tends towards mutual adaptation and coevolution. Since these processes are critical for the survival of individuals and species, they rely on the existence of a complex organization of adaptive systems aiming at two apparently conflicting purposes: the maintenance of the internal coherence of each partner, and a mutually advantageous coexistence and progressive adaptation between them. Humans possess three adaptive systems: the nervous, the endocrine and the immune system, each internally organized into subsystems functionally connected by intraconnections, to maintain the internal coherence of the system. The three adaptive systems aim at the maintenance of the internal coherence of the organism and are functionally linked by interconnections, in such way that what happens to one is immediately sensed by the others. The different communities of infectious agents that live within the organism are also organized into functional networks. The members of each community are linked by intraconnections, represented by the mutual trophic, metabolic and other influences, while the different infectious communities affect each other through interconnections. Furthermore, by means of its adaptive systems, the organism influences and is influenced by the microbial communities through the existence of transconnections. It is proposed that these highly complex and dynamic networks, involving gene exchange and epigenetic phenomena, represent major coevolutionary forces for humans and microorganisms.

Oxygen-sensing reporter strain of Pseudomonas fluorescens for monitoring the distribution of low-oxygen habitats in soil.

The root-colonizing bacterium Pseudomonas fluorescens CHA0 was used to construct an oxygen-responsive biosensor. An anaerobically inducible promoter of Pseudomonas aeruginosa, which depends on the FNR (fumarate and nitrate reductase regulation)-like transcriptional regulator ANR (anaerobic regulation of arginine deiminase and nitrate reductase pathways), was fused to the structural lacZ gene of Escherichia coli. By inserting the reporter fusion into the chromosomal attTn7 site of P. fluorescens CHA0 by using a mini-Tn7 transposon, the reporter strain, CHA900, was obtained. Grown in glutamate-yeast extract medium in an oxystat at defined oxygen levels, the biosensor CHA900 responded to a decrease in oxygen concentration from 210 x 10(2) Pa to 2 x 10(2) Pa of O(2) by a nearly 100-fold increase in beta-galactosidase activity. Half-maximal induction of the reporter occurred at about 5 x 10(2) Pa. This dose response closely resembles that found for E. coli promoters which are activated by the FNR protein. In a carbon-free buffer or in bulk soil, the biosensor CHA900 still responded to a decrease in oxygen concentration, although here induction was about 10 times lower and the low oxygen response was gradually lost within 3 days. Introduced into a barley-soil microcosm, the biosensor could report decreasing oxygen concentrations in the rhizosphere for a 6-day period. When the water content in the microcosm was raised from 60% to 85% of field capacity, expression of the reporter gene was elevated about twofold above a basal level after 2 days of incubation, suggesting that a water content of 85% caused mild anoxia. Increased compaction of the soil was shown to have a faster and more dramatic effect on the expression of the oxygen reporter than soil water content alone, indicating that factors other than the water-filled pore space influenced the oxygen status of the soil. These experiments illustrate the utility of the biosensor for detecting low oxygen concentrations in the rhizosphere and other soil habitats.

Environmental pollution with soil-transmitted helminths in Sanliurfa, Turkey

Soil transmitted helminth (STH) infection are endemic in developing countries. A study was carried out of sewage farms, streams and vegetables to determine the sources and routes of STH infection in Sanliurfa, Turkey. Stool samples from farmhouse inhabitants as well as soil and vegetable samples from the gardens were collected and examined. In addition, water samples from streams and vegetable samples from the city market were collected and examined. One hundred and eighty-seven (59.5%) of a total of 314 samples, including 88.4% of the stool samples, 60.8% of the water samples, 84.4% of the soil samples and 14% of the vegetable samples, were found to be positive for STH eggs. These results indicate that the water, soil and vegetables are heavily contaminated, and suggest a vicious circle between humans and the environment. Improving environmental sanitation is imperative for the control of soil-transmitted helminthiasis in Sanliurfa.