Detection of Leishmania RNA virus in Leishmania parasites.

BACKGROUND: Patients suffering from cutaneous leishmaniasis (CL) caused by New World Leishmania (Viannia) species are at high risk of developing mucosal (ML) or disseminated cutaneous leishmaniasis (DCL). After the formation of a primary skin lesion at the site of the bite by a Leishmania-infected sand fly, the infection can disseminate to form secondary lesions. This metastatic phenotype causes significant morbidity and is often associated with a hyper-inflammatory immune response leading to the destruction of nasopharyngeal tissues in ML, and appearance of nodules or numerous ulcerated skin lesions in DCL. Recently, we connected this aggressive phenotype to the presence of Leishmania RNA virus (LRV) in strains of L. guyanensis, showing that LRV is responsible for elevated parasitaemia, destructive hyper-inflammation and an overall exacerbation of the disease. Further studies of this relationship and the distribution of LRVs in other Leishmania strains and species would benefit from improved methods of viral detection and quantitation, especially ones not dependent on prior knowledge of the viral sequence as LRVs show significant evolutionary divergence. METHODOLOGY/PRINCIPAL FINDINGS: This study reports various techniques, among which, the use of an anti-dsRNA monoclonal antibody (J2) stands out for its specific and quantitative recognition of dsRNA in a sequence-independent fashion. Applications of J2 include immunofluorescence, ELISA and dot blot: techniques complementing an arsenal of other detection tools, such as nucleic acid purification and quantitative real-time-PCR. We evaluate each method as well as demonstrate a successful LRV detection by the J2 antibody in several parasite strains, a freshly isolated patient sample and lesion biopsies of infected mice. CONCLUSIONS/SIGNIFICANCE: We propose that refinements of these methods could be transferred to the field for use as a diagnostic tool in detecting the presence of LRV, and potentially assessing the LRV-related risk of complications in cutaneous leishmaniasis.

Investigation into Freezing-Thawing Durability of Low-Permeability Concrete with and without Air Entraining Agent, 2009

The aim of the present study is to investigate the effect of low-permeability concrete, made with reduced water‐to‐binder ratios (w/b) and/or supplementary cementitious materials (SCMs), on the need for air entrainment to achieve freezing‐thawing (F‐T) durability. In the present study, concrete mixes were made with different types of cement (Types I and IP), with or without fly ash replacement (15%), with different water‐to‐binder ratios (w/b =0.25, 0.35, 0.45 and 0.55), and with or without air entraining agent (AEA). All concrete mixtures were controlled to have a similar slump by using different dosages of superplasticizer. The rapid chloride permeability and F-T durability of the concrete samples were determined according to ASTM C1202 and ASTM C666A, respectively. The air void structure of the concrete was studied using the Air Void Analyzer, RapidAir, and porosity tests (ASTM C642). In addition, the general concrete properties, such as slump, air content, unit weight, and 28‐day compressive strength, were evaluated. The results indicate that all concrete mixes with proper air entrainment (ASTM C231 air content ≥ 6%) showed good F‐T resistance (durability factor ≥85%). All concrete mixes without AEA showed poor F‐T resistance (durability factor < 40%), except for one mix that had very low permeability and high strength. This was the concrete made with Type IP cement and with a w/b of 0.25, which had a permeability of 520 coulombs and a compressive strength of 12,760 psi (88 MPa). There were clear relationships between the F‐T durability and hardened concrete properties of non–air entrained concrete. However, such relationships did not exist in concrete with AEA. For concrete with AEA, good F‐T durability was associated with an air void spacing factor ≤ 0.28 mm (by AVA) or ≤ 0.22 mm (by RapidAir).

Evolution and functional characterisation of the IR chemosensory receptors in the Drosophila larval gustatory system

Chemosensory receptor gene families encode divergent proteins capable of detecting a huge diversity of environmental stimuli that are constantly changing over evolutionary time as organisms adapt to distinct ecological niches. While olfaction is dedicated to the detection of volatile compounds, taste is key to assess food quality for nutritional value and presence of toxic substances. The sense of taste also provides initial signals to mediate endocrine regulation of appetite and food metabolism and plays a role in kin recognition. The fruit fly Drosophila melanogaster is a very good model for studying smell and taste because these senses are very important in insects and because a broad variety of genetic tools are available in Drosophila. Recently, a family of 66 chemosensory receptors, the Ionotropic Receptors (IRs) was described in fruit flies. IRs are distantly related to ionotropic glutamate receptors (iGluRs), but their evolutionary origin from these synaptic receptors is unclear. While 16 IRs are expressed in the olfactory system, nothing is known about the other members of this repertoire. In this thesis, I describe bioinformatic, expression and functional analyses of the IRs aimed at understanding how these receptors have evolved, and at characterising the role of the non-olfactory IRs. I show that these have emerged at the basis of the protostome lineage and probably have acquired their sensory function very early. Moreover, although several IRs are conserved across insects, there are rapid and dramatic changes in the size and divergence of IR repertoires across species. I then performed a comprehensive analysis of IR expression in the larva of Drosophila melanogaster, which is a good model to study taste and feeding mechanisms as it spends most of its time eating or foraging. I found that most of the divergent members of the IR repertoire are expressed in both peripheral and internal gustatory neurons, suggesting that these are involved in taste perception. Finally, through the establishment of a new neurophysiological assay in larvae, I identified for the first time subsets of IR neurons that preferentially detect sugars and amino acids, indicating that IRs might be involved in sensing these compounds. Together, my results indicate that IRs are an evolutionarily dynamic and functionally versatile family of receptors. In contrast to the olfactory IRs that are well-conserved, gustatory IRs are rapidly evolving species-specific receptors that are likely to be involved in detecting a wide variety of tastants. - La plupart des animaux possèdent de grandes familles de récepteurs chimiosensoriels dont la fonction est de détecter l'immense diversité de composés chimiques présents dans l'environnement. Ces récepteurs évoluent en même temps que les organismes s'adaptent à leur écosystème. Il existe deux manières de percevoir ces signaux chimiques : l'olfaction et le goût. Alors que le système olfactif perçoit les composés volatiles, le sens du goût permet d'évaluer, par contact, la qualité de la nourriture, de détecter des substances toxiques et de réguler l'appétit et le métabolisme. L'un des organismes modèles les plus pertinents pour étudier le sens du goût est le stade larvaire de la mouche du vinaigre Drosophila melanogaster. En effet, la principale fonction du stade larvaire est de trouver de la nourriture et de manger. De plus, il est possible d'utiliser tous les outils génétiques développés chez la drosophile. Récemment, une nouvelle famille de 66 récepteurs chimiosensoriels appelés Récepteurs Ionotropiques (IRs) a été découverte chez la drosophile. Bien que leur orogine soit peu claire, ces récepteurs sont similaires aux récepteurs ionotropiques glutamatergiques impliqués dans la transmission synaptique. 16 IRs sont exprimés dans le système olfactif de la mouche adulte, mais pour l'instant on ne connaît rien des autres membres de cette famille. Durant ma thèse, j'ai effectué des recherches sur l'évolution de ces récepteurs ainsi que sur l'expression et la fonction des IRs non olfactifs. Je démontre que les IRs sont apparus chez l'ancêtre commun des protostomiens et ont probablement acquis leur fonction sensorielle très rapidement. De plus, bien qu'un certain nombre d'IRs olfactifs soient conservés chez les insectes, d'importantes variations dans la taille et la divergence des répertoires d'IRs entre les espèces ont été constatées. J'ai également découvert qu'un grand nombre d'IRs non olfactifs sont exprimés dans différents organes gustatifs, ce qui leur confère probablement une fonction dans la perception des goûts. Finalement, pour la première fois, des neurones exprimant des IRs ont été identifiés pour leur fonction dans la perception de sucres et d'acides aminés chez la larve. Mes résultats présentent les IRs comme une famille très dynamique, aux fonctions très variées, qui joue un rôle tant dans l'odorat que dans le goût, et dont la fonction est restée importante tout au long de l'évolution. De plus, l'identification de neurones spécialisés dans la perception de certains composés permettra l'étude des circuits neuronaux impliqués dans le traitement de ces informations.

Feasibility of Visualization and Simulation Applications to Improve Work Zone Safety and Mobility

Visualization is a relatively recent tool available to engineers for enhancing transportation project design through improved communication, decision making, and stakeholder feedback. Current visualization techniques include image composites, video composites, 2D drawings, drive-through or fly-through animations, 3D rendering models, virtual reality, and 4D CAD. These methods are used mainly to communicate within the design and construction team and between the team and external stakeholders. Use of visualization improves understanding of design intent and project concepts and facilitates effective decision making. However, visualization tools are typically used for presentation only in large-scale urban projects. Visualization is not widely accepted due to a lack of demonstrated engineering benefits for typical agency projects, such as small- and medium-sized projects, rural projects, and projects where external stakeholder communication is not a major issue. Furthermore, there is a perceived high cost of investment of both financial and human capital in adopting visualization tools. The most advanced visualization technique of virtual reality has only been used in academic research settings, and 4D CAD has been used on a very limited basis for highly complicated specialty projects. However, there are a number of less intensive visualization methods available which may provide some benefit to many agency projects. In this paper, we present the results of a feasibility study examining the use of visualization and simulation applications for improving highway planning, design, construction, and safety and mobility.

Feasibility of Visualization and Simulation Applications, Tech Transfer Summary, 2008

Visualization is a relatively recent tool available to engineers for enhancing transportation project design through improved communication, decision making, and stakeholder feedback. Current visualization techniques include image composites, video composites, 2D drawings, drive-through or fly-through animations, 3D rendering models, virtual reality, and 4D CAD. These methods are used mainly to communicate within the design and construction team and between the team and external stakeholders. Use of visualization improves understanding of design intent and project concepts and facilitates effective decision making. However, visualization tools are typically used for presentation only in large-scale urban projects. Visualization is not widely accepted due to a lack of demonstrated engineering benefits for typical agency projects, such as small- and medium-sized projects, rural projects, and projects where external stakeholder communication is not a major issue. Furthermore, there is a perceived high cost of investment of both financial and human capital in adopting visualization tools. The most advanced visualization technique of virtual reality has only been used in academic research settings, and 4D CAD has been used on a very limited basis for highly complicated specialty projects. However, there are a number of less intensive visualization methods available which may provide some benefit to many agency projects. In this paper, we present the results of a feasibility study examining the use of visualization and simulation applications for improving highway planning, design, construction, and safety and mobility.

Weaker ligands can dominate an odor blend due to syntopic interactions.

Most odors in natural environments are mixtures of several compounds. Perceptually, these can blend into a new "perfume," or some components may dominate as elements of the mixture. In order to understand such mixture interactions, it is necessary to study the events at the olfactory periphery, down to the level of single-odorant receptor cells. Does a strong ligand present at a low concentration outweigh the effect of weak ligands present at high concentrations? We used the fruit fly receptor dOr22a and a banana-like odor mixture as a model system. We show that an intermediate ligand at an intermediate concentration alone elicits the neuron's blend response, despite the presence of both weaker ligands at higher concentration, and of better ligands at lower concentration in the mixture. Because all of these components, when given alone, elicited significant responses, this reveals specific mixture processing already at the periphery. By measuring complete dose-response curves we show that these mixture effects can be fully explained by a model of syntopic interaction at a single-receptor binding site. Our data have important implications for how odor mixtures are processed in general, and what preprocessing occurs before the information reaches the brain.

Biology and parasitic potential of Doryctobracon areolatuson Anastrepha fraterculus larvae

The objective of this work was to study the biology and parasitic potential of Doryctobracon areolatus on larvae of Anastrepha fraterculus. The egg-adult period, the sex ratio, the longevity, the pupal viability, and the parasitism rate of D. areolatus were determined in laboratory, using A. fraterculus as host. The parasitoid development from oviposition to adult emergence required 25.00±1.70 days, the sex ratio was 0.62±0.09, and the mean longevity was 16.36±3.62 days for males and 10.24±1.71 days for females. The mean parasitism rate was 53.50±8.93%, varying from 41.60 to 68.60%, which shows the potential of this parasitoid for biological control of A. fraterculus.

Mate availability and male dispersal in the Argentine ant Linepithema humile (Mayr) (=Iridomyrmex humilis)

In the Argentine ant Linepithema humile (=Iridomyrmex humilis) only males disperse whereas female sexuals (unmated winged queens) stay in their mother nest where they mate. This study investigated (1) whether dispersing males are accepted into foreign colonies, (2) whether they can mate with resident female sexuals, and (3) whether the propensity of males to disperse is affected by the expectation of mating in their mother nest. Field experiments demonstrated that males were accepted into foreign colonies only when these colonies contained female sexuals or queen pupae. Before and after the time of (sic) female sexuals, workers attacked and killed most of the foreign males. Laboratory experiments snowed that males that successfully enter foreign colonies can mate with resident female sexuals. The propensity of males to disperse was significantly influenced by the presence of female sexuals in their nest. Males were more likely to fly out from colonies containing no female sexuals than from those with them. These results are consistent with males preferentially dispersing when there is little or no opportunity to mate in their mother nest. Thus there are two mating strategies available for males: staying in their mother nest when an opportunity to mate arises or dispersing and attempting to mate in a foreign nest when there are no female sexuals in their mother nest. This latter behaviour could mediate gene flow between colonies and account for the lack of significant inbreeding previously documented in this species.

Managing FOSS during development: preventive and curative approaches

Today, most software development teams use free and open source software (FOSS) components, because it increases the speed and the quality of the development. Many open source components are the de facto standard of their category. However, FOSS has licensing restrictions, and corporate organizations usually maintain a list of allowed and forbidden licenses. But how do you enforce this policy? How can you make sure that ALL files in your source depot, either belong to you, or fit your licensing policy? A first, preventive approach is to train and increase the awareness of the development team to these licensing issues. Depending on the size of the team, it may be costly but necessary. However, this does not ensure that a single individual will not commit a forbidden icon or library, and jeopardize the legal status of the whole release... if not the company, since software is becoming more and more a critical asset. Another approach is to verify what is included in the source repository, and check whether it belongs to the open-source world. This can be done on-the-fly, whenever a new file is added into the source depot. It can also be part of the release process, as a verification step before publishing the release. In both cases, there are some tools and databases to automate the detection process. We will present the various options regarding FOSS detection, how this process can be integrated in the "software factory", and how the results can be displayed in a usable and efficient way.

Investigating the relationship between pollination strategies and the size-advantage model in zoophilous plants using the reproductive biology of Arum cylindraceum and other European Arum species as case studies

The size-advantage model (SAM) explains the temporal variation of energetic investment on reproductive structures (i.e. male and female gametes and reproductive organs) in long-lived hermaphroditic plants and animals. It proposes that an increase in the resources available to an organism induces a higher relative investment on the most energetically costly sexual structures. In plants, pollination interactions are known to play an important role in the evolution of floral features. Because the SAM directly concerns flower characters, pollinators are expected to have a strong influence on the application of the model. This hypothesis, however, has never been tested. Here, we investigate whether the identity and diversity of pollinators can be used as a proxy to predict the application of the SAM in exclusive zoophilous plants. We present a new approach to unravel the dynamics of the model and test it on several widespread Arum (Araceae) species. By identifying the species composition, abundance and spatial variation of arthropods trapped in inflorescences, we show that some species (i.e. A. cylindraceum and A. italicum) display a generalist reproductive strategy, relying on the exploitation of a low number of dipterans, in contrast to the pattern seen in the specialist A. maculatum (pollinated specifically by two fly species only). Based on the model presented here, the application of the SAM is predicted for the first two and not expected in the latter species, those predictions being further confirmed by allometric measures. We here demonstrate that while an increase in the female zone occurs in larger inflorescences of generalist species, this does not happen in species demonstrating specific pollinators. This is the first time that this theory is both proposed and empirically tested in zoophilous plants. Its overall biological importance is discussed through its application in other non-Arum systems.

Entomopathogenic nematodes for the control of phorid and sciarid flies in mushroom crops

The objective of this work was to evaluate the efficacy of two nematodes, Steinernema feltiae and S. carpocapsae, to control mushroom flies and to evaluate the effect of these treatments on Agaricus bisporus production. Two mushroom cultivation trials were carried out in controlled conditions, in substrate previously infested with the diptera Megaselia halterata and Lycoriella auripila, with two treatments: 106infective juveniles (IJ) per square meter of S. feltiae and 0.5x106IJ m-2S. feltiae + 0.5x106IJ m-2S. carpocapsae. Another experiment was carried out using the same treatments to evaluate the possible nematode effect on mushroom yield. The number of adults emerging from the substrate was evaluated for each fly species. No decrease in the population of M. halterata was detected with nematode application, whereas the number of L. auripila was reduced in both treatments, particularly in the individual treatment with S. feltiae. The application of entomopathogenic nematodes has no adverse effect on mushroom production.

Comparative transcriptomics of early dipteran development

BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).

Jätteenpolton tuhkien käsittelytekniikoiden ympäristövaikutukset

Jätteenpoltossa syntyvät tuhkat sisältävät paljon haitta-aineita, joiden vuoksi niitä ei yleensä voida suoraan sijoittaa kaatopaikoille. Käsittelyllä pyritään parantamaan tuhkien ominaisuuksia ja vähentämään haitta-aineiden liukoisuutta. Samalla kuitenkin käsittely kuluttaa raaka-aineita ja energiaa sekä aiheuttaa päästöjä. Tuhkien käsittelyn kokonaishyötyjä ja -haittoja ympäristön kannalta arvioitaessa tulisikin ottaa huomioon sekä käsiteltävän tuhkan parantuneet ominaisuudet että käsittelystä aiheutuneet ympäristökuormitukset. Tämän diplomityön tavoitteena oliselvittää jätteenpolton tuhkien käsittelystä aiheutuvia ympäristövaikutuksia tarkastelemalla esimerkinomaisesti neljää erilaista käsittelytekniikkaa (pesua, sementtikiinteytystä, Ferrox-prosessia ja vitrifiointia) sekä kahta muuta loppusijoitusvaihtoehtoa (mahdollisuutta sijoittaa tuhkat kaatopaikalle ilman käsittelyä ja kuljettamista Norjassa sijaitsevalle käsittely- ja loppusijoituslaitokselle). Tarkastelussa keskityttiin jätteenpolton ongelmallisimpiin tuhkajakeisiin, lentotuhkaan ja savukaasujen puhdistusjätteisiin eli APC-jätteisiin. Tavoitteena oli selvittää käsittelyvaihtoehdoista syntyvät ympäristökuormitukset ns. koko niiden elinkaaren ajalta, eli huomioiden käsittelyyn tarvittavien lisäaineiden valmistuksesta, itse käsittelyprosessista sekä loppusijoituksesta aiheutuvat kuormitukset. Tarkastelun perusteella eri käsittelyvaihtoehdot aiheuttavat hyvin erilaisia ja erisuuruisia ympäristökuormituksia. Lisäksi käsitellyn materiaalin ominaisuudet vaihtelevat huomattavasti käsittelytavasta riippuen. Tarkastelluista käsittelyvaihtoehdoista suurimmat ympäristökuormitukset ilmapäästöjen osalta aiheutuivat tyypillisesti joko käsittelyyn tarvittavien raaka-aineiden valmistuksesta tai itse käsittelyprosessin energiankulutuksesta. Loppusijoituksesta sen sijaan aiheutui ympäristöhaittoja kaatopaikkarakenteiden muodostamisesta sekä maaperään vapautuvista haitta-aineista, joiden määrä riippuu tuhkan käsittelyn tehokkuudesta.

Estratègies en la presa de decisió d’una jugadora i el seu entrenador en el rugbi femení d’alt nivell = Estrategias en la toma de decisión de una jugadora y su entrenador en el rugby femenino de alto nivel

This research compared knowledge representation of a female rugby player and her coach concerning decision-making of the fly half in attack from second phase play. The current female England fly half and the England Women’s Rugby head coach analysed, from the fly half perspective, 15 sequences of the England v Spain match played during the 2002 Women’s Rugby World Cup in Barcelona. Protocol analysis of subjects’ verbal reports revealed that the player generated more overall concepts than the coach. The player’s analysis was based on condition-action statements related to goals. In contrast, the knowledge representation of the coach centred on conditions related to actions. Both subjects generated regulatory and do concepts in a similar way, with a majority of positive feedbacks. Knowledge structure of the player appeared to be more complex, but sophistication of concepts was similar for both subjects. Critical analysis of complete sequences viewed revealed a more severe self-assessment of the player compared with that of her coach. In conclusion, and despite the differences found between subjects, the player and her coach demonstrated possession of a similar pattern of decision-making strategies that could be due to a successful transmission of knowledge from the coach to his player

Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.