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Search Results: 1 - 10 of 223509 matches for " Mariana C. Boité "
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New Insights on Taxonomy, Phylogeny and Population Genetics of Leishmania (Viannia) Parasites Based on Multilocus Sequence Analysis
Mariana C. Boité,Isabel L. Mauricio,Michael A. Miles,Elisa Cupolillo
PLOS Neglected Tropical Diseases , 2012, DOI: 10.1371/journal.pntd.0001888
Abstract: The Leishmania genus comprises up to 35 species, some with status still under discussion. The multilocus sequence typing (MLST)—extensively used for bacteria—has been proposed for pathogenic trypanosomatids. For Leishmania, however, a detailed analysis and revision on the taxonomy is still required. We have partially sequenced four housekeeping genes—glucose-6-phosphate dehydrogenase (G6PD), 6-phosphogluconate dehydrogenase (6PGD), mannose phosphate isomerase (MPI) and isocitrate dehydrogenase (ICD)—from 96 Leishmania (Viannia) strains and assessed their discriminatory typing capacity. The fragments had different degrees of diversity, and are thus suitable to be used in combination for intra- and inter-specific inferences. Species-specific single nucleotide polymorphisms were detected, but not for all species; ambiguous sites indicating heterozygosis were observed, as well as the putative homozygous donor. A large number of haplotypes were detected for each marker; for 6PGD a possible ancestral allele for L. (Viannia) was found. Maximum parsimony-based haplotype networks were built. Strains of different species, as identified by multilocus enzyme electrophoresis (MLEE), formed separated clusters in each network, with exceptions. NeighborNet of concatenated sequences confirmed species-specific clusters, suggesting recombination occurring in L. braziliensis and L. guyanensis. Phylogenetic analysis indicates L. lainsoni and L. naiffi as the most divergent species and does not support L. shawi as a distinct species, placing it in the L. guyanensis cluster. BURST analysis resulted in six clonal complexes (CC), corresponding to distinct species. The L. braziliensis strains evaluated correspond to one widely geographically distributed CC and another restricted to one endemic area. This study demonstrates the value of systematic multilocus sequence analysis (MLSA) for determining intra- and inter-species relationships and presents an approach to validate the species status of some entities. Furthermore, it contributes to the phylogeny of L. (Viannia) and might be helpful for epidemiological and population genetics analysis based on haplotype/diplotype determinations and inferences.
Multilocus Sequence Analysis for Leishmania braziliensis Outbreak Investigation
Mariel A. Marlow,Mariana C. Boité,Gabriel Eduardo M. Ferreira,Mario Steindel,Elisa Cupolillo
PLOS Neglected Tropical Diseases , 2014, DOI: 10.1371/journal.pntd.0002695
Abstract: With the emergence of leishmaniasis in new regions around the world, molecular epidemiological methods with adequate discriminatory power, reproducibility, high throughput and inter-laboratory comparability are needed for outbreak investigation of this complex parasitic disease. As multilocus sequence analysis (MLSA) has been projected as the future gold standard technique for Leishmania species characterization, we propose a MLSA panel of six housekeeping gene loci (6pgd, mpi, icd, hsp70, mdhmt, mdhnc) for investigating intraspecific genetic variation of L. (Viannia) braziliensis strains and compare the resulting genetic clusters with several epidemiological factors relevant to outbreak investigation. The recent outbreak of cutaneous leishmaniasis caused by L. (V.) braziliensis in the southern Brazilian state of Santa Catarina is used to demonstrate the applicability of this technique. Sequenced fragments from six genetic markers from 86 L. (V.) braziliensis strains from twelve Brazilian states, including 33 strains from Santa Catarina, were used to determine clonal complexes, genetic structure, and phylogenic networks. Associations between genetic clusters and networks with epidemiological characteristics of patients were investigated. MLSA revealed epidemiological patterns among L. (V.) braziliensis strains, even identifying strains from imported cases among the Santa Catarina strains that presented extensive homogeneity. Evidence presented here has demonstrated MLSA possesses adequate discriminatory power for outbreak investigation, as well as other potential uses in the molecular epidemiology of leishmaniasis.
Distinct Leishmania Species Infecting Wild Caviomorph Rodents (Rodentia: Hystricognathi) from Brazil
Renata Cássia-Pires,Mariana C. Boité,Paulo S. D'Andrea,Heitor M. Herrera,Elisa Cupolillo,Ana Maria Jansen,André Luiz R. Roque
PLOS Neglected Tropical Diseases , 2014, DOI: 10.1371/journal.pntd.0003389
Abstract: Background Caviomorph rodents, some of the oldest Leishmania spp. hosts, are widely dispersed in Brazil. Despite both experimental and field studies having suggested that these rodents are potential reservoirs of Leishmania parasites, not more than 88 specimens were analyzed in the few studies of natural infection. Our hypothesis was that caviomorph rodents are inserted in the transmission cycles of Leishmania in different regions, more so than is currently recognized. Methodology We investigated the Leishmania infection in spleen fragments of 373 caviomorph rodents from 20 different species collected in five Brazilian biomes in a period of 13 years. PCR reactions targeting kDNA of Leishmania sp. were used to diagnose infection, while Leishmania species identification was performed by DNA sequencing of the amplified products obtained in the HSP70 (234) targeting. Serology by IFAT was performed on the available serum of these rodents. Principal findings In 13 caviomorph rodents, DNA sequencing analyses allowed the identification of 4 species of the subgenus L. (Viannia): L. shawi, L. guyanensis, L. naiffi, and L. braziliensis; and 1 species of the subgenus L. (Leishmania): L. infantum. These include the description of parasite species in areas not previously included in their known distribution: L. shawi in Thrichomys inermis from Northeastern Brazil and L. naiffi in T. fosteri from Western Brazil. From the four other positive rodents, two were positive for HSP70 (234) targeting but did not generate sequences that enabled the species identification, and another two were positive only in kDNA targeting. Conclusions/Significance The infection rate demonstrated by the serology (51.3%) points out that the natural Leishmania infection in caviomorph rodents is much higher than that observed in the molecular diagnosis (4.6%), highlighting that, in terms of the host species responsible for maintaining Leishmania species in the wild, our current knowledge represents only the “tip of the iceberg.”
Development and validation of PCR-based assays for diagnosis of American cutaneous leishmaniasis and identificatio nof the parasite species
Gra?a, Grazielle Cardoso da;Volpini, Angela Cristina;Romero, Gustavo Adolfo Sierra;Oliveira Neto, Manoel Paes de;Hueb, Marcia;Porrozzi, Renato;Boité, Mariana C?rtes;Cupolillo, Elisa;
Memórias do Instituto Oswaldo Cruz , 2012, DOI: 10.1590/S0074-02762012000500014
Abstract: in this study, pcr assays targeting different leishmania heat-shock protein 70 gene (hsp70) regions, producing fragments ranging in size from 230-390 bp were developed and evaluated to determine their potential as a tool for the specific molecular diagnosis of cutaneous leishmaniasis (cl). a total of 70 leishmania strains were analysed, including seven reference strains (rs) and 63 previously typed strains. analysis of the rs indicated a specific region of 234 bp in the hsp70 gene as a valid target that was highly sensitive for detection of leishmania species dna with capacity of distinguishing all analyzed species, after polymerase chain reaction-restriction fragment length polymorfism (pcr-rflp). this pcr assay was compared with other pcr targets used for the molecular diagnosis of leishmaniasis: hsp70 (1400-bp region), internal transcribed spacer (its)1 and glucose-6-phosphate dehydrogenase (g6pd). a good agreement among the methods was observed concerning the leishmania species identification. moreover, to evaluate the potential for molecular diagnosis, we compared the pcr targets hsp70-234 bp, its1, g6pd and mkdna using a panel of 99 dna samples from tissue fragments collected from patients with confirmed cl. both pcr-hsp70-234 bp and pcr-its1 detected leishmania dna in more than 70% of the samples. however, using hsp70-234 bp pcr-rflp, identification of all of the leishmania species associated with cl in brazil can be achieved employing a simpler and cheaper electrophoresis protocol.
Population Structure and Evidence for Both Clonality and Recombination among Brazilian Strains of the Subgenus Leishmania (Viannia)
Katrin Kuhls,Elisa Cupolillo,Soraia O. Silva,Carola Schweynoch,Mariana C?rtes Boité,Maria N. Mello,Isabel Mauricio,Michael Miles,Thierry Wirth,Gabriele Sch?nian
PLOS Neglected Tropical Diseases , 2013, DOI: 10.1371/journal.pntd.0002490
Abstract: Background/Objectives: Parasites of the subgenus Leishmania (Viannia) cause varying clinical symptoms ranging from cutaneous leishmaniases (CL) with single or few lesions, disseminated CL (DL) with multiple lesions to disfiguring forms of mucocutaneous leishmaniasis (MCL). In this population genetics study, 37 strains of L. (V.) guyanensis, 63 of L. (V.) braziliensis, four of L. (V.) shawi, six of L. (V.) lainsoni, seven of L. (V.) naiffi, one each of L. (V.) utingensis and L. (V.) lindenbergi, and one L. (V.) lainsoni/L. naiffi hybrid from different endemic foci in Brazil were examined for variation at 15 hyper-variable microsatellite markers. Methodology/Principal findings: The multilocus microsatellite profiles obtained for the 120 strains were analysed using both model- and distance-based methods. Significant genetic diversity was observed for all L. (Viannia) strains studied. The two cluster analysis approaches identified two principal genetic groups or populations, one consisting of strains of L. (V.) guyanensis from the Amazon region and the other of strains of L. (V.) braziliensis isolated along the Atlantic coast of Brazil. A third group comprised a heterogeneous assembly of species, including other strains of L. braziliensis isolated from the north of Brazil, which were extremely polymorphic. The latter strains seemed to be more closely related to those of L. (V.) shawi, L. (V.) naiffi, and L. (V.) lainsoni, also isolated in northern Brazilian foci. The MLMT approach identified an epidemic clone consisting of 13 strains of L. braziliensis from Minas Gerais, but evidence for recombination was obtained for the populations of L. (V.) braziliensis from the Atlantic coast and for L. (V.) guyanensis. Conclusions/Significance: Different levels of recombination versus clonality seem to occur within the subgenus L. (Viannia). Though clearly departing from panmixia, sporadic, but long-term sustained recombination might explain the tremendous genetic diversity and limited population structure found for such L. (Viannia) strains.
Physical IC debug ─ backside approach and nanoscale challenge
C. Boit,R. Schlangen,A. Glowacki,U. Kindereit
Advances in Radio Science : Kleinheubacher Berichte , 2008,
Abstract: Physical analysis for IC functionality in submicron technologies requires access through chip backside. Based upon typical global backside preparation with 50–100 μm moderate silicon thickness remaining, a state of the art of the analysis techniques available for this purpose is presented and evaluated for functional analysis and layout pattern resolution potential. A circuit edit technique valid for nano technology ICs, is also presented that is based upon the formation of local trenches using the bottom of Shallow Trench Isolation (STI) as endpoint for Focused Ion Beam (FIB) milling. As a derivative from this process, a locally ultra thin silicon device can be processed, creating a back surface as work bench for breakthrough applications of nanoscale analysis techniques to a fully functional circuit through chip backside. Several applications demonstrate the power and potential of this new approach.
Power-laws in the dynamic hysteresis of quantum nonlinear photonic resonators
W. Casteels,F. Storme,A. Le Boité,C. Ciuti
Physics , 2015,
Abstract: We explore theoretically the physics of dynamic hysteresis for driven-dissipative nonlinear photon resonators. In the regime where the semiclassical mean-field theory predicts bistability, the exact steady-state density matrix is known to be unique, being a statistical mixture of two states: in particular, no static hysteresis cycle of the excited population occurs as a function of the driving intensity. Here, we predict that in the quantum regime a {\it dynamic} hysteresis with a rich phenomenology does appear when sweeping the driving amplitude in a finite time. The hysteresis area as a function of the sweep time reveals a power-law decay with an universal exponent, with a behavior qualitatively different from the mean-field predictions. The dynamic hysteresis power-law defines a characteristic time, which depends dramatically on the size of the nonlinearity and on the frequency detuning between the driving and the resonator. In the strong nonlinearity regime, the characteristic time oscillates as a function of the intrinsic system parameters due to multiphotonic resonances. We also consider the case of two coupled driven-dissipative nonlinear resonators, showing that dynamic hysteresis and power-law behavior occur also in presence of correlations between the resonators. Our theoretical predictions can be explored in a broad variety of physical systems, e.g., circuit QED superconducting resonators and semiconductor optical microcavities.
Boit? Marius
Studia Universitatis Vasile Goldis Arad, Seria Stiinte Economice , 2011,
Abstract: Availability of food resources was one of the first issues addressed at the global level and isstill a central topic in international debates concerning development. Location on thisposition is determined by several factors, among which a prominent place occupies thepopulation growth, which increases demand for food and the insufficiency of the dailyration for a significant proportion of world population. Thus, the increase of the number ofpeople covered by extreme poverty means a greater malnutrition, given that poor people eatless and are forced to buy cheaper and less nutritious food.
Corner space renormalization method for driven-dissipative 2D correlated systems
S. Finazzi,A. Le Boité,F. Storme,A. Baksic,C. Ciuti
Physics , 2015, DOI: 10.1103/PhysRevLett.115.080604
Abstract: We present a theoretical method to study driven-dissipative correlated systems on lattices with two spatial dimensions (2D). The steady-state density-matrix of the lattice is obtained by solving the master equation in a corner of the Hilbert space. The states spanning the corner space are determined through an iterative procedure, using eigenvectors of the density-matrix of smaller lattice systems, merging in real space two lattices at each iteration and selecting M pairs of states by maximizing their joint probability. Accuracy of the results is then improved by increasing M, the number of states of the corner space, until convergence is reached. We demonstrate the efficiency of such an approach by applying it to the driven-dissipative 2D Bose-Hubbard model, describing, e.g., lattices of coupled cavities with quantum optical nonlinearities.
Benchmarking Successional Progress in a Quantitative Food Web
Alice Boit, Ursula Gaedke
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090404
Abstract: Central to ecology and ecosystem management, succession theory aims to mechanistically explain and predict the assembly and development of ecological communities. Yet processes at lower hierarchical levels, e.g. at the species and functional group level, are rarely mechanistically linked to the under-investigated system-level processes which drive changes in ecosystem properties and functioning and are comparable across ecosystems. As a model system for secondary succession, seasonal plankton succession during the growing season is readily observable and largely driven autogenically. We used a long-term dataset from large, deep Lake Constance comprising biomasses, auto- and heterotrophic production, food quality, functional diversity, and mass-balanced food webs of the energy and nutrient flows between functional guilds of plankton and partly fish. Extracting population- and system-level indices from this dataset, we tested current hypotheses about the directionality of successional progress which are rooted in ecosystem theory, the metabolic theory of ecology, quantitative food web theory, thermodynamics, and information theory. Our results indicate that successional progress in Lake Constance is quantifiable, passing through predictable stages. Mean body mass, functional diversity, predator-prey weight ratios, trophic positions, system residence times of carbon and nutrients, and the complexity of the energy flow patterns increased during succession. In contrast, both the mass-specific metabolic activity and the system export decreased, while the succession rate exhibited a bimodal pattern. The weighted connectance introduced here represents a suitable index for assessing the evenness and interconnectedness of energy flows during succession. Diverging from earlier predictions, ascendency and eco-exergy did not increase during succession. Linking aspects of functional diversity to metabolic theory and food web complexity, we reconcile previously disjoint bodies of ecological theory to form a complete picture of successional progress within a pelagic food web. This comprehensive synthesis may be used as a benchmark for quantifying successional progress in other ecosystems.
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