Molecular markers and genetic diversity of Plasmodium vivax

Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3α, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.

Combining Legendre's Polynomials and Genetic Algorithm in the Solution of Nonlinear Initial-Value Problems

This work develops a method for solving ordinary differential equations, that is, initial-value problems, with solutions approximated by using Legendre's polynomials. An iterative procedure for the adjustment of the polynomial coefficients is developed, based on the genetic algorithm. This procedure is applied to several examples providing comparisons between its results and the best polynomial fitting when numerical solutions by the traditional Runge-Kutta or Adams methods are available. The resulting algorithm provides reliable solutions even if the numerical solutions are not available, that is, when the mass matrix is singular or the equation produces unstable running processes.

Factors influencing paternity success in Antechinus agilis: last-male sperm precedence, timing of mating and genetic compatibility

We describe the patterns of paternity success from laboratory mating experiments conducted in Antechinus agilis, a small size dimorphic carnivorous marsupial (males are larger than females). A previous study found last-male sperm precedence in this species, but they were unable to sample complete Utters, and did not take male size and relatedness into account. We tested whether last-male sperm precedence regardless of male size still holds for complete litters. We explored the relationship between male mating order, male size, timing of mating and relatedness on paternity success. Females were mated with two males of different size with either the large or the small male first, with 1 day rest between the matings. Matings continued for 6 h. in these controlled conditions male size did not have a strong effect on paternity success, but mating order did. Males mating second sired 69.5% of the offspring. Within first mated males, males that mated closer to ovulation sired more offspring, To a lesser degree, variation appeared also to be caused by differences in genetic compatibility of the female and the male, where high levels of allele-sharing resulted in lower paternity success.

Terminology and knowledge engineering conference. New frontiers in the constructive symbiosis of terminology and knowledge engineering

To meet the increasing demands of the complex inter-organizational processes and the demand for continuous innovation and internationalization, it is evident that new forms of organisation are being adopted, fostering more intensive collaboration processes and sharing of resources, in what can be called collaborative networks (Camarinha-Matos, 2006:03). Information and knowledge are crucial resources in collaborative networks, being their management fundamental processes to optimize. Knowledge organisation and collaboration systems are thus important instruments for the success of collaborative networks of organisations having been researched in the last decade in the areas of computer science, information science, management sciences, terminology and linguistics. Nevertheless, research in this area didn’t give much attention to multilingual contexts of collaboration, which pose specific and challenging problems. It is then clear that access to and representation of knowledge will happen more and more on a multilingual setting which implies the overcoming of difficulties inherent to the presence of multiple languages, through the use of processes like localization of ontologies. Although localization, like other processes that involve multilingualism, is a rather well-developed practice and its methodologies and tools fruitfully employed by the language industry in the development and adaptation of multilingual content, it has not yet been sufficiently explored as an element of support to the development of knowledge representations - in particular ontologies - expressed in more than one language. Multilingual knowledge representation is then an open research area calling for cross-contributions from knowledge engineering, terminology, ontology engineering, cognitive sciences, computational linguistics, natural language processing, and management sciences. This workshop joined researchers interested in multilingual knowledge representation, in a multidisciplinary environment to debate the possibilities of cross-fertilization between knowledge engineering, terminology, ontology engineering, cognitive sciences, computational linguistics, natural language processing, and management sciences applied to contexts where multilingualism continuously creates new and demanding challenges to current knowledge representation methods and techniques. In this workshop six papers dealing with different approaches to multilingual knowledge representation are presented, most of them describing tools, approaches and results obtained in the development of ongoing projects. In the first case, Andrés Domínguez Burgos, Koen Kerremansa and Rita Temmerman present a software module that is part of a workbench for terminological and ontological mining, Termontospider, a wiki crawler that aims at optimally traverse Wikipedia in search of domainspecific texts for extracting terminological and ontological information. The crawler is part of a tool suite for automatically developing multilingual termontological databases, i.e. ontologicallyunderpinned multilingual terminological databases. In this paper the authors describe the basic principles behind the crawler and summarized the research setting in which the tool is currently tested. In the second paper, Fumiko Kano presents a work comparing four feature-based similarity measures derived from cognitive sciences. The purpose of the comparative analysis presented by the author is to verify the potentially most effective model that can be applied for mapping independent ontologies in a culturally influenced domain. For that, datasets based on standardized pre-defined feature dimensions and values, which are obtainable from the UNESCO Institute for Statistics (UIS) have been used for the comparative analysis of the similarity measures. The purpose of the comparison is to verify the similarity measures based on the objectively developed datasets. According to the author the results demonstrate that the Bayesian Model of Generalization provides for the most effective cognitive model for identifying the most similar corresponding concepts existing for a targeted socio-cultural community. In another presentation, Thierry Declerck, Hans-Ulrich Krieger and Dagmar Gromann present an ongoing work and propose an approach to automatic extraction of information from multilingual financial Web resources, to provide candidate terms for building ontology elements or instances of ontology concepts. The authors present a complementary approach to the direct localization/translation of ontology labels, by acquiring terminologies through the access and harvesting of multilingual Web presences of structured information providers in the field of finance, leading to both the detection of candidate terms in various multilingual sources in the financial domain that can be used not only as labels of ontology classes and properties but also for the possible generation of (multilingual) domain ontologies themselves. In the next paper, Manuel Silva, António Lucas Soares and Rute Costa claim that despite the availability of tools, resources and techniques aimed at the construction of ontological artifacts, developing a shared conceptualization of a given reality still raises questions about the principles and methods that support the initial phases of conceptualization. These questions become, according to the authors, more complex when the conceptualization occurs in a multilingual setting. To tackle these issues the authors present a collaborative platform – conceptME - where terminological and knowledge representation processes support domain experts throughout a conceptualization framework, allowing the inclusion of multilingual data as a way to promote knowledge sharing and enhance conceptualization and support a multilingual ontology specification. In another presentation Frieda Steurs and Hendrik J. Kockaert present us TermWise, a large project dealing with legal terminology and phraseology for the Belgian public services, i.e. the translation office of the ministry of justice, a project which aims at developing an advanced tool including expert knowledge in the algorithms that extract specialized language from textual data (legal documents) and whose outcome is a knowledge database including Dutch/French equivalents for legal concepts, enriched with the phraseology related to the terms under discussion. Finally, Deborah Grbac, Luca Losito, Andrea Sada and Paolo Sirito report on the preliminary results of a pilot project currently ongoing at UCSC Central Library, where they propose to adapt to subject librarians, employed in large and multilingual Academic Institutions, the model used by translators working within European Union Institutions. The authors are using User Experience (UX) Analysis in order to provide subject librarians with a visual support, by means of “ontology tables” depicting conceptual linking and connections of words with concepts presented according to their semantic and linguistic meaning. The organizers hope that the selection of papers presented here will be of interest to a broad audience, and will be a starting point for further discussion and cooperation.

Metabolic and morphogenetic engineering of Bacillus subtilis: biotechnology for industry

Dissertation presented to obtain the Ph.D. degree in “Biology” at the Institute of Chemical and Biological Technology of the New University of Lisbon

Antigenic and genetic characterization of the first rabies virus isolated from the bat Eumops perotis in Brazil

Although the main transmitters of rabies in Brazil are dogs and vampire bats, the role of other species such as insectivorous and frugivorous bats deserves special attention, as the rabies virus has been isolated from 36 bat species. This study describes the first isolation of the rabies virus from the insectivorous bat Eumops perotis. The infected animal was found in the city of Ribeirão Preto, São Paulo. The virus was identified by immunofluorescence antibody test (FAT) in central nervous system (CNS) samples, and the isolation was carried out in N2A cell culture and adult mice. The sample was submitted to antigenic typing using a panel of monoclonal antibodies (CDC/Atlanta/USA). The DNA sequence of the nucleoprotein gene located between nucleotides 102 and 1385 was aligned with homologous sequences from GenBank using the CLUSTAL/W method, and the alignment was used to build a neighbor-joining distance-based phylogenetic tree with the K-2-P model. CNS was negative by FAT, and only one mouse died after inoculation with a suspension from the bat's CNS. Antigenic typing gave a result that was not compatible with the patterns defined by the panel. Phylogenetic analysis showed that the virus isolated segregated into the same cluster related to other viruses isolated from insectivorous bats belonging to genus Nyctinomops ssp. (98.8% nucleotide identity with each other).

Molecular markers and genetic diversity of Plasmodium vivax

Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3α, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.

Applying recommendations to aligncompetences, methodology and assessment in Telematics, Computing and Electronic Engineering courses

The alignment between competences, teaching-learning methodologies and assessment is a key element of the European Higher Education Area. This paper presents the efforts carried out by six Telematics, Computer Science and Electronic Engineering Education teachers towards achieving this alignment in their subjects. In a joint work with pedagogues, a set of recommended actions were identified. A selection of these actions were applied and evaluated in the six subjects. The cross-analysis of the results indicate that the actions allow students to better understand the methodologies and assessment planned for the subjects, facilitate (self-) regulation and increase students’ involvement in the subjects.

Dynamics and genetic structure of Argentine ant supercolonies in their native range.

Some introduced ant populations have an extraordinary social organization, called unicoloniality, whereby individuals mix freely within large supercolonies. We investigated whether this mode of social organization also exists in native populations of the Argentine ant Linepithema humile. Behavioral analyses revealed the presence of 11 supercolonies (width 1 to 515 m) over a 3-km transect. As in the introduced range, there was always strong aggression between but never within supercolonies. The genetic data were in perfect agreement with the behavioral tests, all nests being assigned to identical supercolonies with the different methods. There was strong genetic differentiation between supercolonies but no genetic differentiation among nests within supercolonies. We never found more than a single mitochondrial haplotype per supercolony, further supporting the view that supercolonies are closed breeding units. Genetic and chemical distances between supercolonies were positively correlated, but there were no other significant associations between geographic, genetic, chemical, and behavioral distances. A comparison of supercolonies sampled in 1999 and 2005 revealed a very high turnover, with about one-third of the supercolonies being replaced yearly. This dynamic is likely to involve strong competition between supercolonies and thus act as a potent selective force maintaining unicoloniality over evolutionary time.

Diversity and genetic structure of the wood ant Formica lugubris in unmanaged forests

Wood ant species show differences in their social structure, especially in the level of polygyny (number of laying queens per nest) and polydomy (number of nest per colony), both within and between species. We demonstrate here for the first time that Formica lugubris displays two different social forms in close proximity in alpine unmanaged forests of the Swiss National Park. The genetic data (7 microsatellite loci) and field data indicate that one population is mostly monogynous to weakly polygynous (r = 0.438) and monodomous, the second one being polygynous (r = 0.113) and polydomous. Within this latter population new nests are founded by budding, leading to the observed high density of nests. These two different social structures, possibly being two expressions of a same continuum, could be explained by several ecological or environmental factors (e.g. habitat saturation, resource competition) and also historical effects.

Transgene inheritances and genetic similarities of near isogenic lines of genetically modified common beans

The objective of the present work was to determine the inheritance and stability of transgenes of a transgenic bean line expressing the genes rep-trap-ren from Bean golden mosaic virus and the bar gene. Crosses were done between the transgenic line and four commercial bean cultivars, followed by four backcrosses to the commercial cultivars. Progenies from each cross were evaluated for the presence of the transgenes by brushing the leaves with glufosinate ammonium and by polymerase chain reaction using specific oligonucleotides. Advanced generations were rub-inoculated with an isolate of Bean common mosaic necrosis virus (BCMNV). The transgenes were inherited consistently in a Mendelian pattern in the four crosses studied. The analyzed lines recovered close to 80% of the characteristics of the recurrent parent, as determined by the random amplified DNA markers used, besides maintaining important traits such as resistance to BCMNV. The presence of the transgene did not cause any detectable undesirable effect in the evaluated progenies.

Sex-chromosome evolution of Palearctic tree frogs in space and time

Sexual reproduction is nearly universal in eukaryotes and genetic determination of sex prevails among animals. The astonishing diversity of sex-determining systems and sex chromosomes is yet bewildering. Some taxonomic groups possess conserved and dimorphic sex chromosomes, involving a functional copy (e.g. mammals' X, birds' Z) and a degenerated copy (mammals' Y, birds' W), implying that sex- chromosomes are expected to decay. In contrast, others like amphibians, reptiles and fishes yet maintained undifferentiated sex chromosomes. Why such different evolutionary trajectories? In this thesis, we empirically test and characterize the main hypotheses proposed to prevent the genetic decay of sex chromosomes, namely occasional X-Y recombination and frequent sex-chromosome transitions, using the Palearctic radiation of Hyla tree frogs as a model system. We take a phylogeographic and phylogenetic approach to relate sex-chromosome recombination, differentiation, and transitions in a spatial and temporal framework. By reconstructing the recent evolutionary history of the widespread European tree frog H. arborea, we showed that sex chromosomes can recombine in males, preventing their differentiation, a situation that potentially evolves rapidly. At the scale of the entire radiation, X-Y recombination combines with frequent transitions to prevent sex-chromosome degeneration in Hyla: we traced several turnovers of sex-determining system within the last 10My. These rapid changes seem less random than usually assumed: we gathered evidences that one chromosome pair is a sex expert, carrying genes with key role in animal sex determination, and which probably specialized through frequent reuse as a sex chromosome in Hyla and other amphibians. Finally, we took advantage of secondary contact zones between closely-related Hyla lineages to evaluate the consequences of sex chromosome homomorphy on the genetics of speciation. In comparison with other systems, the evolution of sex chromosomes in Hyla emphasized the existence of consistent evolutionary patterns within the chaotic diversity of flexibility of cold-blooded vertebrates' sex-determining systems, and provides insights into the evolution of recombination. Beyond sex-chromosome evolution, this work also significantly contributed to speciation, phylogeography and applied conservation research. -- La reproduction sexuée est quasi-universelle chez les eucaryotes et le sexe est le plus souvent déterminé génétiquement au sein du règne animal. L'incroyable diversité des systèmes de reproduction et des chromosomes sexuels est particulièrement étonnante. Certains groupes taxonomiques possèdent des chromosomes sexuels dimorphiques et très conservés, avec une copie entièrement fonctionnelle (ex : le X des mammifères, le Z des oiseaux) et une copie dégénérée (ex : le Y des mammifères, le W des oiseaux), suggérant que les chromosomes sexuels sont voués à se détériorer. Cependant les chromosomes sexuels d'autres groupes tels que les amphibiens, les reptiles et les poissons sont pour la plupart indifférenciés. Comment expliquer des trajectoires évolutives si différentes? Au cours de cette thèse, nous avons étudié empiriquement les processus évolutifs pouvant maintenir les chromosomes sexuels intacts, à savoir la recombinaison X-Y occasionnel ainsi que les substitutions fréquentes de chromosomes sexuels, en utilisant les rainettes Paléarctiques du genre Hyla comme modèle d'étude. Nous avons adopté une approche phylogéographique et phylogénétique pour appréhender les événements de recombinaison, de différenciation et de transitions de chromosomes sexuels dans un contexte spatio-temporel. En retraçant l'histoire évolutive récente de la rainette verte H. arborea, nous avons mis en évidence que les chromosomes sexuels pouvaient recombiner chez les mâles, empêchant ainsi leur différenciation, et que ce processus avait le potentiel d'évoluer très rapidement. A l'échelle plus globale de la radiation, il apparait que les phénomènes de recombinaison X-Y soient également accompagnés de substitutions de chromosomes sexuels, et participent de concert au maintien de chromosomes sexuels intacts dans les populations: le système de détermination du sexe des rainettes a changé plusieurs fois au cours des 10 derniers millions d'années. Ces transitions fréquentes ne semblent pas aléatoires: nous avons identifié une paire de chromosomes qui présente des caractéristiques présageant d'une spécialisation dans le déterminisme du sexe (notamment car elle possède des gènes importants pour cette fonction), et qui a été réutilisée plusieurs fois comme tel chez les rainettes ainsi que d'autres amphibiens. Enfin, nous avons étudié l'hybridation entre différentes espèces dans leurs zones de contact, afin d'évaluer si l'absence de différenciation entre X et Y jouaient un rôle dans les processus génétiques de spéciation. Outre son intérêt pour la compréhension de l'évolution des chromosomes sexuels, ce travail contribue de manière significative à d'autres domaines de recherche tels que la spéciation, la phylogéographie, ainsi que la biologie de la conservation.

Vitamin D time profile based on the contribution of non-genetic and genetic factors in HIV-infected individuals of European ancestry.

BACKGROUND: Vitamin D deficiency is prevalent in HIV-infected individuals and vitamin D supplementation is proposed according to standard care. This study aimed at characterizing the kinetics of 25(OH)D in a cohort of HIV-infected individuals of European ancestry to better define the influence of genetic and non-genetic factors on 25(OH)D levels. These data were used for the optimization of vitamin D supplementation in order to reach therapeutic targets. METHODS: 1,397 25(OH)D plasma levels and relevant clinical information were collected in 664 participants during medical routine follow-up visits. They were genotyped for 7 SNPs in 4 genes known to be associated with 25(OH)D levels. 25(OH)D concentrations were analysed using a population pharmacokinetic approach. The percentage of individuals with 25(OH)D concentrations within the recommended range of 20-40 ng/ml during 12 months of follow-up and several dosage regimens were evaluated by simulation. RESULTS: A one-compartment model with linear absorption and elimination was used to describe 25(OH)D pharmacokinetics, while integrating endogenous baseline plasma concentrations. Covariate analyses confirmed the effect of seasonality, body mass index, smoking habits, the analytical method, darunavir/ritonavir and the genetic variant in GC (rs2282679) on 25(OH)D concentrations. 11% of the inter-individual variability in 25(OH)D levels was explained by seasonality and other non-genetic covariates, and 1% by genetics. The optimal supplementation for severe vitamin D deficient patients was 300,000 IU two times per year. CONCLUSIONS: This analysis allowed identifying factors associated with 25(OH)D plasma levels in HIV-infected individuals. Improvement of dosage regimen and timing of vitamin D supplementation is proposed based on those results.