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Número mínimo de indivíduos e diversidade genética de Onça-parda (Puma concolor) no Núcleo Santa Virgínia, Parque Estadual da Serra do Mar, São Paulo
(Universidade Federal de São Carlos, 2011-05-27) Martins, Niara; Galetti Júnior, Pedro Manoel; https://lattes.cnpq.br/8227849982052024
ABSTRACT The cougar (Puma concolor) is the second largest feline species in Brazil. It has a wide distribution across the Americas, occurring from southwestern Canada to the Strait of Magellan, in the extreme south of Argentina and Chile, throughout the Brazilian territory. In this study we estimated the minimum number of individuals and genetic diversity of cougars in the Santa Virginia Unit, Serra do Mar State Park (PESM), São Paulo, based on fecal DNA analysis. Hair snares were also used to an attempt to obtain more samples. For the diagnosis of the species, we amplified a 146bp fragment of the cytochrome b gene of mitochondrial DNA. We used six microsatellite loci for the fecal samples individualization, to estimate the minimum number of individuals and genetic characterization of the population. No hair sample was obtained during the study. Among the 40 fecal samples obtained, 34 were successfully diagnosed, and we found 25 samples of P. concolor, eight of Leopardus tigrinus and one of Leopardus pardalis. The multiloci genotypes were obtained for only 15 samples belonging to 12 different puma individuals. The allelic dropout average rate was 10.43%. The mean observed heterozygosity was 0.6202, lower than that found for the species in fragmented areas of Cerrado, in the northeastern São Paulo. There were deviations in Hardy-Weinberg equilibrium (HWE) for one locus and a deficit of heterozygous for the set loci used. However, there was no evidence of recent population bottleneck. Therefore, the deviation in HWE could be caused by the presence of null alleles or the low number of samples. Little relationship was found between individuals (6.1% Half-Sibs), indicating a possible continuous stream of cougars in the region. Thus, the PESM deserves special attention for being the largest continuous remnant of Brazilian Atlantic Forest and, therefore, similar studies are needed in the others Units of this Park so that together they can provide a more comprehensive view of the P. concolor situation in this biome.
O problema de Cauchy para a equação da onda cúbica
(Universidade Federal de São Carlos, 2011-05-27) Farias, Marcos Alves de; Santos Filho, José Ruidival Soares dos; https://lattes.cnpq.br/6112529384454347
In this work, we study the result of global well-Posedness for the cubic wave equation @2 t u��_u+u3 = 0 in R_R3, where the Cauchy data is in the Sobolev space Hs(R3)_ Hs��1(R3) with 13 18 < s < 1. The proof is based on the work of T. Roy, [23], in this paper Roy propose a almost conservation law for the energy and from this he get a inequality that together with the local well-posedness theory proved by Lindbald and Sogge in [18] guarantee the global well-posedness for the problem.
Espécies de Eiphosoma Cresson, 1865 (Hymenoptera, Ichneumonidae, Cremastinae) em áreas de mata e cerrado da bacia hidrográfica do rio Mogi-Guaçu
(Universidade Federal de São Carlos, 2011-05-27) Melo, Ivy Frizo de; Dias, Angélica Maria Penteado Martins; https://lattes.cnpq.br/8637344058859147
This work is a study of Eiphosoma s species. The sampling was done in areas of seasonal semidecidual forest and savanna in Mogi-Guaçu River Basin, aiming to increase knowledge about the taxonomy, geographical distribution, population structure, and the influence of seasonality in the occurrence of the species of this genre. Malaise traps were installed in ten fragments along the entire basin. We studied 217 specimens of Eiphosoma distributed in 25 species, among them we found five new records for Brazil - E. strontorium Gauld, 2000; E. kelpanum Gauld, 2000; E. macrum (Enderlein, 1921), E. henorum Gauld, 2000; E. cerfen Gauld, 2000, and also 11 possible new species. The most abundant species was E. macrum with 52% of total individuals, followed by E. laphygmae (13.8%) and Eiphosoma sp. n. 2 (14.2%) which have strong dominance in the places they occurred. In Minas Gerais the two most abundant and richest areas were Jacutinga with 31.8%, and Andradas with 30,6 % of total individuals, richness index was similar at both points, which showed 55.5% of all species (S=5).The municipality of Jacutinga also had the highest diversity index (H =1.21), but the highest equitability index was observed in Damázio district of Bom Repouso (J =0.91). In São Paulo, the fragment with highest abundance was the riparian area in the city of Luiz Antônio (E.E. Jataí) with 40.3% of total individuals. The highest richness index was observed in the fragment of Pontal with 65% of species collected throughout the state (S=13).The areas with highest diversity indexes were the legal reserve area of Usina Bela Vista in Pontal (H =1.73) and a fragment of cerrado on the Luiz Antônio (E.E. Jataí) (H =1.83), which also demonstrated the highest equitability index (J =0.88). We verified no significant correlation between total abundance and seasonality (Fr= 10,3 ; p = 0.32). Amongst main results we point out the description of eleven new species, an increase of information about the distribution of genus with the record of five species in Brazil and the better knowledge of patterns of species richness, diversity and equitability.
Avaliação do status taxonômico e análise populacional de Clyomys bishopi, um roedor endêmico dos Cerrados do estado de São Paulo
(Universidade Federal de São Carlos, 2011-05-27) Arantes, Ana Carolina Ramos; Rodrigues, Fernando Pacheco; https://lattes.cnpq.br/1351286774058975; https://lattes.cnpq.br/0108120233415752
Cerrado is one of the brazilian biomes with the highest concentration of species and endemism, and is considered a hotspot of global biodiversity. Only 20% of its original area remains intact in the country and has been permanently transformed by human actions, which makes this biome a priority area for conservation. Due to the great loss of habitat and biodiversity, it is necessary to increase knowledge of basic characteristics of the existing species. Conservation genetics makes use of the genetic variation to infer the taxonomic status and life history of a species, making possible the study of characteristics such as the pattern of social structure and dispersion. Thus, basic data from species to which we have difficult assess can be accessed and better conservation strategies can be adopted. Mitochondrial and nuclear markers are important tools for studies of genetic and social structure in animals. In this study we assessed the taxonomic status of Clyomys bishopi, a colonial and semi-fossorial rodent inhabiting the Cerrado of São Paulo, and also the social and spatial genetic structure of individuals collected in the Estação Ecológica de Itirapina- SP. To evaluate C. bishopi taxonomic status we analyzed the cytochrome b gene of 21 individuals belonging to the genus and from various localities of its distribution. Phylogenetic methods based on Bayesian Inference, Maximum Parsimony and Neighbor-Joining showed high values of branch support separating individuals from São Paulo with respect to the rest of the samples, and genetic distance of about 4% between these groups, suggesting a significant genetic separation between them. For population analysis, ten microsatellite loci were isolated and characterized within C. bishopi. Through the analysis of 40 individuals sampled at three areas within EE de Itirapina, we verified high levels of genetic diversity (NA = 10, average HO = 0,76 and averaged HE = 0,90). Nine microsatellite loci and the control region of the mitochondrial DNA were used to assess the spatial and social genetic structure of the EE de Itirapina population. The Bayesian clustering analysis indicated no genetic structure, suggesting the occurrence of gene flow between sampled areas. Relatedness analyses indicated, in general, low relatedness indices between analyzed individuals (0.05), with slightly larger values when only individuals in a small geographic scale are considered. The average relatedness by sex indicated no significant differences, suggesting similar dispersion between males and females. Results suggest that colonies of Clyomys bishopi are composed largely by unrelated individuals, and present genetic structure compatible to that showed by species with solitary habits.
Anotação genômica e caracterização de locos microssatélites em sequências expressas do genoma do camarão marinho Litopenaeus vannamei
(Universidade Federal de São Carlos, 2011-05-27) Santos, Camilla Alves; Freitas, Patrícia Domingues de; https://lattes.cnpq.br/6905869491807202
Litopenaeus vannamei is known as Pacific white shrimp and is the main species marketed worldwide. Its geographical distribution includes the Pacific coast, ranging from Mexico to Peru. Due to its outstanding economic importance, this species has been farmed and showing great adapting levels to captivity, having been introduced in several countries, including Brazil. However, despite all the concern to properly manage the farming populations, many countries have not had a renewal of their breeding herds because of the risk of introduction of exogenous pathogens, which has increased the degree of inbreeding of these stocks and decreased levels of genetic diversity. To monitor this loss, microsatellite markers or SSRs (Simple Sequence Repeats), from genome arbitrary and expressed regions have been used. In the specific case of SSRs present in expressed regions of the genome (ESTs, Expressed Sequence Tags) or SSRs-ESTs, they allow the access to the genetic variability of populations, and the ESTs markers devoid of SSRs may be related to genes of interest, subsidizing the development of breeding programs based on Marker Assisted Selection (MAS). Moreover, EST-SSRs loci may show an excellent rate of transferability in taxonomically related species, since they are in more conserved regions of the genome. Within this context, this study aimed (i) the validation population of EST-SSR loci isolated through dataming from L. vannamei ESTs database (www.shrimp.ufscar.br), (ii) the genomic annotation of ESTs and EST-SSRs markers (iii) the determination of EC numbers (Enzyme Codes), aiming respectively, (i) the characterization of polymorphic markers (ii) the description of genes and their protein products and (iii) the establishment of information to describe the possible pathways for the penaeid group. Therefore, we tested 32 EST-SSRs loci in PCR reactions. After establishing the best pattern of reaction and subsequent loci genotyping, nine SSRs-ESTs were polymorphic, with allele number ranging from two to 20, levels of observed heterozygosity from 0.32 to 0.86 and average PIC (Polymorphism Information Content) of 0.78. No pair of loci presented in linkage disequilibrium. However, after Bonferroni correction, we found that one of these showed a significant deficit of heterozygotes. The nine polymorphic loci from L.vannamei showed satisfactory amplification in at least one of the seven native species tested: the marine ones Xiphopenaeus kroyeri, Farfantepenaeus brasiliensis, Farfantepenaeus paulensis, Rimapenaeus constrictus and Litopenaeus schmitti and the freshwater ones Macrobrachium amazonicum and Macrobrachium jeskii, being useful also for genetic studies of these species. The genome annotation performed by access in ShEST website (Litopenaeus vannamei EST Genome Project) showed that only three of nine loci 4 have the gene and its protein product described. The other loci showed no matches with any other genomic database available for research. In this work, gene product could be elucidated for 99% of ESTs, being possible to establish 209 EC numbers, highlighting enzymes responsible for xenobiotics metabolism, immunity, energy production, reproduction, oxidative stress, among others. These codes were used for construction of some metabolic pathways present in the penaeid group, contributing for building a wide database of the genome of this important animal group. These data may be applied in genetic improvement programs as well as gene expression studies, such as realtime PCR and microarrays.
Recuperação de modelos de classes orientados a aspectos a partir de sistemas orientados a objetos usando refatorações de modelos
(Universidade Federal de São Carlos, 2011-05-27) Parreira Júnior, Paulo Afonso; Penteado, Rosângela Aparecida Dellosso; https://lattes.cnpq.br/4061946080136286; https://lattes.cnpq.br/4567261968633725
Aspect-Oriented Programming allows encapsulating the so-called "Crosscutting Concerns (CCC) - software requirements whose implementation is tangled and scattered throughout the functional modules - into new abstractions, such as Aspects, Pointcuts, Advices and Inter-type Declarations. The reengineering of an OO software to an AO is not an easy task due to the existence of different abstractions in these technologies. We develop a set of nine refactorings of annotated OO class models to AO class models. In the context of this work, "annotated class models" are UML class diagrams whose elements (classes, interfaces, attributes and methods) are annotated with stereotypes representing the existing CCC in the application source code. The set of refactorings developed is divided into: i) generic refactorings; and ii) specific refactorings. Three generic refactorings and six specific refactorings to the persistence (which is divided into management and connections, transaction and synchronization) and logging concerns and to the Singleton and Observer design patterns were created. The generic refactorings are responsible for transforming an annotated OO model with indications of CCC into a partial AO model. This model is called partial because it is usually not fully modularized, i.e., there are remaining software elements stereotyped with indications of particular concerns. These refactorings are applicable to any kind of CCC; this is possible, because what is taken into consideration is the scenario in which these concerns appear in the class model. The specific refactorings are responsible for transforming partial AO models into final ones, whose CCC have been fully modularized in aspects. For that, each refactoring has a set of specific steps for modularization of a particular kind of concern. An Eclipse plug-in, called MoBRe was developed to assist the software engineer in the tasks of refactoring application. As a major contribution, the refactorings proposed in this paper allow obtaining well designed AO models. This is so because: i) they provide a step-by-step guide to the modularization of certain CCC and can avoid that software engineers choose inappropriate strategies for modularization of these CCC; and ii) they were prepared based on good design practices recommended by the scientific community. Thus, besides, the models the use of refactorings can lead to generation of better-quality code, for example, free of bad smells. A case study was conducted to assess the applicability of the proposed refactorings in order to compare an AO model generated by them with an AO model obtained from the literature.