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Navegando por Autor "SCHNEIDER, Maria Paula Cruz"

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    Biochemical polymorphisms and genetic relationships between Brazilian and foreign breeds of pigs reared in Brazil
    (1999-06) TAGLIARO, Claudia Helena; FRANCO, Maria Helena Lartigau Pereira; SCHNEIDER, Maria Paula Cruz; BRITO, Benito Guimarães de; BARBOSA, Antonio Stockler; Centro de Ciências Rurais
    The genetic variability of 14 protein systems encoded by 15 structural loci was investigated in blood samples of Piau and Caruncho pig breeds. The results were compared with those obtained previously for samples of Landrace, Large White, Duroc and Mouro. The degree of genetic variability obtained for Piau (He=0.114) was similar to that estimated for other breeds reared in Brazil (Landrace, He=0.116; Large White, He=0.119; Duroc, 0.095; Mouro, He= 0.130). Caruncho showed the lowest variability (He= 0.056). The gene frequencies at the polymorphic loci were used to evaluate the usefulness of these systems for paternity testing and the combined probabilities of paternity exclusion were estimated at 58% for the Piau and 36% for the Caruncho breed. Analysis of genetic distances revealed that the greatest similarity observed was between Piau and Landrace (D=0.042). Caruncho showed the greatest divergence among all breeds compared and the distances between this breed and others range from 0.107 (with Landrace) to 0.176 (with Duroc). The tree constructed by UPGMA and Rogers Distance gave a topology in which Piau and Mouro joined with the European breeds (Landrace and Large White) whereas Caruncho was separated from all the other breeds. The results of the analysis of the Caruncho samples should be interpreted with caution since the number of animals studied was small.
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    A comparative study of eleven protein systems in tamarins, genus Saguinus (Platyrrhini, Callitrichinae)
    (1997-03) MEIRELES, Carla Maria Marques; SAMPAIO, Maria Iracilda da Cunha; SCHNEIDER, Horacio; FERRARI, Stephen Francis; COIMBRA-FILHO, Adelmar Faria; PISSINATTI, Alcides; SCHNEIDER, Maria Paula Cruz
    The genetic variability of six tamarin taxa, genus Saguinus, was analyzed comparatively using protein data from eleven systems coded by 15 loci. S. fuscicollis weddelli and S. midas midas were the most polymorphic taxa, and S. bicolor the least. The results of the phylogenetic analyses (UPGMA and neighbor-joining) and the genetic distances between taxa were generally consistent with their geographic and probable phylogenetic relationships. Analyses of the S. bicolor and S. midas populations suggested that they represent no more than three subspecies of a single species, S. midas, with the bicolor forms belonging to a single subspecies, S. midas bicolor. If supported by additional studies, this would have important implications for the conservation of the bicolor form, which is endangered with extinction. The genetic similarity of S. fuscicollis and S. mystax was also consistent with their geographical and morphological proximity, although more data from a larger number of taxa will be required before the taxonomic relationships within the genus can be defined.
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    Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation sequencing technology
    (BioMed Central, 2012) HASSAN, Syed Shah; GUIMARÃES, Luís Carlos; PEREIRA, Ulisses de Pádua; ISLAM, Arshad; ALI, Amjad; BAKHTIAR, Syeda Marriam; RIBEIRO, Dayana; SANTOS, Anderson Rodrigues dos; SOARES, Siomar de Castro; DORELLA, Fernanda Alves; GOMIDE, Anne Cybelle Pinto; SCHNEIDER, Maria Paula Cruz; BARBOSA, Maria Silvanira Ribeiro; ALMEIDA, Sintia Silva de; ABREU, Vinicius Augusto Carvalho de; ABURJAILE, Flavia Figueira; CARNEIRO, Adriana Ribeiro; CERDEIRA, Louise Teixeira; NASCIMENTO, Karina Kelly Fiaux do; BARBOSA, Eudes Guilherme Vieira; DINIZ, Carlos Augusto Almeida; ROCHA, Flávia de Souza; RAMOS, Rommel Thiago Juca; JAIN, Neha; TIWARI, Sandeep; BARH, Debmalya; MIYOSHI, Anderson; MÜLLER, Borna; SILVA, Artur Luiz da Costa da; AZEVEDO, Vasco Ariston de Carvalho
    The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile, non sporulating and a mesophile bacterium, was isolated from liver, lung and mediastinal lymph node lesions in an antelope from South Africa. This strain is interesting in the sense that it has been found together with non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the lesion formation. In this work, we describe a set of features of C. pseudotuberculosis P54B96, together with the details of the complete genome sequence and annotation. The genome comprises of 2.34 Mbp long, single circular genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a G+C content of 52.19%. The analysis of the genome se quence provides means to better understanding the molecular and genetic basis of virulence of this bacterium, enabling a detailed investigation of its pathogenesis.
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    Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis
    (American Society for Microbiology, 2011-01) SILVA, Artur Luiz da Costa da; SCHNEIDER, Maria Paula Cruz; CERDEIRA, Louise Teixeira; BARBOSA, Maria Silvanira Ribeiro; RAMOS, Rommel Thiago Juca; CARNEIRO, Adriana Ribeiro; OLIVEIRA, Rodrigo Santos de; LIMA, Margarida Maria Celeira de; CONCEIÇÃO, Marília Lima da; FERREIRA, Vívian D'Afonseca da Silva; ALMEIDA, Sintia Silva de; SANTOS, Anderson Rodrigues dos; SOARES, Siomar de Castro; GOMIDE, Anne Cybelle Pinto; ALI, Amjad; DORELLA, Fernanda Alves; ROCHA, Flávia de Souza; ABREU, Vinicius Augusto Carvalho de; TROST, Eva; TAUCH, Andreas; SHPIGEL, Nahum; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho
    This work reports the completion and annotation of the genome sequence of Corynebacterium pseudotuberculosis I19, isolated from an Israeli dairy cow with severe clinical mastitis. To present the whole-genome sequence, a de novo assembly approach using 33 million short (25-bp) mate-paired SOLiD reads only was applied. Furthermore, the automatic, functional, and manual annotations were attained with the use of several algorithms in a multistep process.
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    Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 1/06-A, Isolated from a Horse in North America
    (American Society for Microbiology, 2012-08) PETHICK, Florence E.; LAINSON, Alex F.; YAGA, Raja; FLOCKHART, Allen; SMITH, David G. E.; DONACHIE, Willie; CERDEIRA, Louise Teixeira; SILVA, Artur Luiz da Costa da; BOL, Erick Johny Maciel; LOPES, Thiago Souza; BARBOSA, Maria Silvanira Ribeiro; GOMIDE, Anne Cybelle Pinto; SANTOS, Anderson Rodrigues dos; SOARES, Siomar de Castro; ALMEIDA, Sintia Silva de; GUIMARÃES, Luís Carlos; ABURJAILE, Flavia Figueira; ABREU, Vinicius Augusto Carvalho de; RIBEIRO, Dayana; NASCIMENTO, Karina Kelly Fiaux do; DINIZ, Carlos Augusto Almeida; BARBOSA, Eudes Guilherme Vieira; PEREIRA, Ulisses de Pádua; HASSAN, Syed Shah; ALI, Amjad; BAKHTIAR, Syeda Marriam; DORELLA, Fernanda Alves; CARNEIRO, Adriana Ribeiro; RAMOS, Rommel Thiago Juca; ROCHA, Flávia de Souza; SCHNEIDER, Maria Paula Cruz; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho; FONTAINE, Michael C.
    Corynebacterium pseudotuberculosis causes disease in several animal species, although distinct biovars exist that appear to be restricted to specific hosts. In order to facilitate a better understanding of the differences between biovars, we report here the complete genome sequence of the equine pathogen Corynebacterium pseudotuberculosis strain 1/06-A.
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    Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama
    (American Society for Microbiology, 2012-07) LOPES, Thiago Souza; SILVA, Artur Luiz da Costa da; RAMOS, Rommel Thiago Juca; CARNEIRO, Adriana Ribeiro; DORELLA, Fernanda Alves; ROCHA, Flávia de Souza; SANTOS, Anderson Rodrigues dos; LIMA, Alex Ranieri Jerônimo; GUIMARÃES, Luís Carlos; BARBOSA, Eudes Guilherme Vieira; RIBEIRO, Dayana; NASCIMENTO, Karina Kelly Fiaux do; DINIZ, Carlos Augusto Almeida; ABREU, Vinicius Augusto Carvalho de; ALMEIDA, Sintia Silva de; HASSAN, Syed Shah; ALI, Amjad; BAKHTIAR, Syeda Marriam; ABURJAILE, Flavia Figueira; GOMIDE, Anne Cybelle Pinto; SOARES, Siomar de Castro; PEREIRA, Ulisses de Pádua; SCHNEIDER, Maria Paula Cruz; MIYOSHI, Anderson; EDMAN, Judy; SPIER, Sharon; AZEVEDO, Vasco Ariston de Carvalho
    In this work we report the genome of Corynebacterium pseudotuberculosis strain 267, isolated from a llama. This pathogen is of great veterinary and economic importance, as it is the cause of caseous lymphadenitis in several livestock species around the world and causes significant losses due to the high cost of treatment.
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    Complete genome sequences of Corynebacterium pseudotuberculosis Strains 3/99-5 and 42/02-A, isolated from sheep in Scotland and Australia, respectively
    (American Society for Microbiology, 2012-09) PETHICK, Florence E.; LAINSON, Alex F.; YAGA, Raja; FLOCKHART, Allen; SMITH, David G. E.; DONACHIE, Willie; CERDEIRA, Louise Teixeira; SILVA, Artur Luiz da Costa da; BOL, Erick Johny Maciel; LOPES, Thiago Souza; BARBOSA, Maria Silvanira Ribeiro; GOMIDE, Anne Cybelle Pinto; SANTOS, Anderson Rodrigues dos; SOARES, Siomar de Castro; ALMEIDA, Sintia Silva de; GUIMARÃES, Luís Carlos; ABURJAILE, Flavia Figueira; ABREU, Vinicius Augusto Carvalho de; RIBEIRO, Dayana; NASCIMENTO, Karina Kelly Fiaux do; DINIZ, Carlos Augusto Almeida; BARBOSA, Eudes Guilherme Vieira; PEREIRA, Ulisses de Pádua; HASSAN, Syed Shah; ALI, Amjad; BAKHTIAR, Syeda Marriam; DORELLA, Fernanda Alves; CARNEIRO, Adriana Ribeiro; RAMOS, Rommel Thiago Juca; ROCHA, Flávia de Souza; SCHNEIDER, Maria Paula Cruz; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho; FONTAINE, Michael C.
    Here, we report the whole-genome sequences of two ovine-pathogenic Corynebacterium pseudotuberculosisisolates: strain 3/99-5, which represents the first C. pseudotuberculosis genome originating from the United Kingdom, and 42/02-A, the second from Austra lia. These genome sequences will contribute to the objective of determining the global pan-genome of this bacterium.
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    Diversidade genética e eficiência de DNA microssatélites para o controle genealógico da raça Nelore
    (2007-10) CARNEIRO, Thomaz Xavier; GONÇALVES, Evonnildo Costa; SCHNEIDER, Maria Paula Cruz; SILVA, Artur Luiz da Costa da
    The genetic variability and paternity testing values in Nelore breed were estimated using 11 ISAG/FAO microsatellites. The markers were organized into 4 amplification groups for semi-automated fluorescence genotyping. All markers were highly polymorphic, with an average of 8.2 alleles per locus. With a mean value of 0.48, the observed heterozygosity was lower than the expected for 10 of the loci. A significant deficit of heterozygotes was observed for 9 loci, resulting in a lack of Hardy-Weinberg equilibrium in the studied population. Polymorphism information content values exceeded 0.5 for 10 loci. The power of discrimination was >0.999 and paternity exclusion probabilities when a mother, her offspring and a putative sire are compared or when one or other parental genotype is unavailable for the combined set of markers were, respectively, >0.999 and >0.989. The set of 11 microsatellite markers proved to be an efficient tool for paternity testing in Nelore cattle.
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    Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia
    (2012-01) SANTANA, Priscila di Paula Bessa; GHILARDI JUNIOR, Rubens; ALVES, Claudio Nahum; SILVA, Jeronimo Lameira; MCCULLOCH, John Anthony; SCHNEIDER, Maria Paula Cruz; SILVA, Artur Luiz da Costa da
    Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the a subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95% similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified -the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.
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    Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains
    (Public Library of Science, 2011-04) RUIZ, Jeronimo Conceição; FERREIRA, Vívian D'Afonseca da Silva; SILVA, Artur Luiz da Costa da; ALI, Amjad; GOMIDE, Anne Cybelle Pinto; SANTOS, Anderson Rodrigues dos; ROCHA, Aryane Aparecida Magalhães Cassiano; DORELLA, Fernanda Alves; PACHECO, Luis Gustavo Carvalho; COSTA, Marcilia Pinheiro da; TURK, Meritxell Zurita; SEYFFERT, Núbia; MORAES, Pablo Matias Ribeiro de Oliveira; SOARES, Siomar de Castro; ALMEIDA, Sintia Silva de; CASTRO, Thiago Luiz de Paula; ABREU, Vinicius Augusto Carvalho de; TROST, Eva; BAUMBACH, Jan; TAUCH, Andreas; SCHNEIDER, Maria Paula Cruz; MCCULLOCH, John Anthony; CERDEIRA, Louise Teixeira; RAMOS, Rommel Thiago Juca; ZERLOTINI NETO, Adhemar; DOMINITINI, Anderson Joaquim; RESENDE, Daniela de Melo; COSER, Elisângela Monteiro; OLIVEIRA, Luciana Márcia de; PEDROSA, André Luiz; VIEIRA, Carlos Ueira; GUIMARÃES, Claudia Teixeira; BARTHOLOMEU, Daniela C.; OLIVEIRA, Diana Magalhães de; SANTOS, Fabrício Rodrigues dos; RABELO, Elida Mara Leite; LOBO, Francisco Pereira; FRANCO, Gloria Regina; COSTA, Ana Flávia Dias Vieira da
    Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity.
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    Exposure to an extremely low-frequency electromagnetic field only slightly modifies the proteome of Chromobacterium violaceum ATCC 12472
    (2015-06) BARAÚNA, Rafael Azevedo; SANTOS, Agenor Valadares; GRAÇAS, Diego Assis das; SANTOS, Daniel Moreira dos; GHILARDI JUNIOR, Rubens; PIMENTA, Adriano Monteiro de Castro; CAREPO, Marta Sofia Peixe; SCHNEIDER, Maria Paula Cruz; SILVA, Artur Luiz da Costa da
    Several studies of the physiological responses of different organisms exposed to extremely low-frequency electromagnetic fields (ELF-EMF) have been described. In this work, we report the minimal effects of in situ exposure to ELF-EMF on the global protein expression of Chromobacterium violaceum using a gel-based proteomic approach. The protein expression profile was only slightly altered, with five differentially expressed proteins detected in the exposed cultures; two of these proteins (DNA-binding stress protein, Dps, and alcohol dehydrogenase) were identified by MS/MS. The enhanced expression of Dps possibly helped to prevent physical damage to DNA. Although small, the changes in protein expression observed here were probably beneficial in helping the bacteria to adapt to the stress generated by the electromagnetic field.
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    Genetic structure of red-handed howler monkey populations in the fragmented landscape of Eastern Brazilian Amazonia
    (2010) BASTOS, Heitor Burlamaqui; GONÇALVES, Evonnildo Costa; FERRARI, Stephen Francis; SILVA, Artur Luiz da Costa da; SCHNEIDER, Maria Paula Cruz
    We genotyped 15 microsatellite loci in order to evaluate the effects of habitat fragmentation, caused by flooding of the Tucuruí reservoir, on the genetic structure of Alouatta belzebul in eastern Amazonia. The analysis included two populations sampled in 1984, representing both margins of the Tocantins river, and three populations sampled 18 years later. Minimal differences in the diversity levels between present-day (Ho = 0.62-0.69 and AR = 6.07-7.21) and pre-flooding (Ho = 0.60-0.62 and AR = 6.27-6.77) populations indicated there was no significant loss of genetic variability, possibly because of successful management strategies applied during the flooding. The changes observed were limited to shifts in the composition of alleles, which presumably reflect the admixture of subpopulations during flooding. Given this, there were significant differences in the Rst values (p = 0.05) in all but one between-site comparison. Both present-day and original populations showed a deficit of heterozygotes, which suggests that this may be typical of the species, at least at a local level, perhaps because of specific ecological characteristics. The relatively large number of private alleles recorded in all populations may be a consequence of the Wahlund effect resulting from population admixture or a process of expansion rather than the loss of rare alleles through genetic drift. Additionally, the levels of genetic variability observed in this study were higher than those reported for other species of Neotropical primates, suggesting good fitness levels in these A. belzebul populations. Regular genetic monitoring of remnant populations, especially on islands, should nevertheless be an integral component of long-term management strategies.
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    Genetic variability and efficiency of DNA microsatellite markers for paternity testing in horse breeds from the Brazilian Marajó archipelago
    (2008) REIS, Sávio Pinho dos; GONÇALVES, Evonnildo Costa; SILVA, Artur Luiz da Costa da; SCHNEIDER, Maria Paula Cruz
    In this study, 15 microsatellite DNA loci used in comparative tests by the International Society for Animal Genetics were applied to the evaluation of genetic diversity and management, and the efficiency of paternity testing in Marajoara horses and Puruca ponies from the Marajó Archipelago. Based on the genotyping of 93 animals, mean allelic diversity was estimated as 9.14 and 7.00 for the Marajoara and Puruca breeds, respectively. While these values are similar to those recorded in most European breeds, mean levels of heterozygosity were much lower (Marajoara 49%, Puruca 40%), probably as a result of high levels of inbreeding in the Marajó populations. The mean informative polymorphic content of this 15-marker system was over 50% in both breeds, and was slightly higher in the Marajoara horses. The discriminative power and exclusion probabilities derived from this system were over 99% for both populations, emphasizing the efficacy of these markers for paternity testing and genetic management in the two breeds.
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    Mitochondrial DNA-like sequence in the nuclear genome of Saguinus (Callitrichinae, Primates): transfer estimation
    (2000-03) SOUZA, Marcelo Nazareno Vallinoto de; SENA, Leonardo dos Santos; SAMPAIO, Maria Iracilda da Cunha; SCHNEIDER, Horacio; SCHNEIDER, Maria Paula Cruz
    Mitochondrial DNA-like sequences have been found in the nuclei of a variety of organisms. These nuclear pseudogenes can be used to estimate relative evolutionary rates of mitochondrial genes, and can be used as outgroups in phylogenetic analyses. In this study, mitochondrial sequences with pseudogene-like characteristics, including deletions and/or insertions and stop codons, were found in tamarins (Saguinus spp., Callitrichinae, Primates). Phylogenetic analysis allowed estimation of the timing of the migration of these sequences to the nuclear genome, and also permitted inferences on the phylogeny of the genus. The choice of an inadequate outgroup (Aotus infulatus) prevented a good phylogenetic resolution of the subfamily Callitrichinae. The relatively ancient divergence of the Cebidae (Callitrichinae, Aotinae and Cebinae) may have favored confounding homoplasies.
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    Molecular phylogeny of the genus Saguinus (Platyrrhini, Primates) based on the ND1 mitochondrial gene and implications for conservation
    (2005-03) TAGLIARO, Claudia Helena; SCHNEIDER, Horacio; SAMPAIO, Maria Iracilda da Cunha; SCHNEIDER, Maria Paula Cruz; SOUZA, Marcelo Nazareno Vallinoto de; STANHOPE, Michael
    The systematics of the subfamily Callitrichinae (Platyrrhini, Primates), a group of small monkeys from South America and Panama, remains an area of considerable discussion despite many investigations, there being continuing controversy over subgeneric taxonomic classifications based on morphological characters. The purpose of our research was to help elucidate the phylogenetic relationships within the monkey genus Saguinus (Callitrichinae) using a molecular approach to discover whether or not the two different sections containing hairy-faced and bare-faced species are monophyletic, whether Saguinus midas midas and Saguinus bicolor are more closely related than are S. midas midas and Saguinus midas niger, and if Saguinus fuscicollis melanoleucus and Saguinus fuscicollis weddelli really are different species. We sequenced the 957 bp ND1 mitochondrial gene of 21 Saguinus monkeys (belonging to six species and nine morphotypes) and one Cebus monkey (the outgroup) and constructed phylogenetic trees using maximum parsimony, neighbor joining, and maximum likelihood methods. The phylogenetic trees obtained divided the genus Saguinus into two groups, one containing the small-bodied species S. fuscicollis and the other, the large-bodied species S. mystax, S. leucopus, S. oedipus, S. midas, S. bicolor. The most derived taxa, S. midas and S. bicolor, grouped together, while S. fuscicollis melanoleucus and S. f. weddelli showed divergence values that did not support the division of these morphotypes into subspecies. On the other hand, S. midas individuals showed divergence compatible with the existence of three subspecies, two of them with the same morphotype as the subspecies S. midas niger. The results of our study suggest that there is at least one Saguinus subspecies that has not yet been described and that the conservation status of Saguinus species and subspecies should be carefully revised using modern molecular approaches.
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    Molecular studies of Callithrix pygmaea (Primates, Platyrrhini) based on transferrin intronic and ND1 regions: implications for taxonomy and conservation
    (2000-12) TAGLIARO, Claudia Helena; SCHNEIDER, Maria Paula Cruz; SCHNEIDER, Horacio; SAMPAIO, Maria Iracilda da Cunha; STANHOPE, Michael
    Traditional classifications of Platyrrhini monkeys, based mainly on morphological features, are being contested by recent molecular data. The subfamily Callitrichinae (Platyrrhini, Primates) consists of a diverse group of species, many of them considered endangered. Our analysis of two DNA regions, a mtDNA gene (ND1) and a nuclear gene (intronic regions of the transferrin gene), suggests that Callithrix pygmaea may have sufficient variability to justify the existence of subspecies or even separate species. Phylogenetic dendrograms based on the ND1 region show that this species is more closely related to Amazonian than to Atlantic forest marmosets. These results reopen the discussion about diversity and conservation programs based exclusively on traditional classifications.
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    Phylogenetic relationships among Brazilian howler monkeys, genus Alouatta (Platyrrhini, Atelidae), based on γ¹-globin pseudogene sequences
    (1999-09) MEIRELES, Carla Maria Marques; CZELUSNIAK, John; FERRARI, Stephen Francis; SCHNEIDER, Maria Paula Cruz; GOODMAN, Morris
    The genus Alouatta (howler monkeys) is the most widely distributed of New World primates, and has been arranged in three species groups: the Central American Alouatta palliata group and the South American Alouatta seniculus and Alouatta caraya groups. While the latter is monotypic, the A. seniculus group encompasses at least three species (A. seniculus, A. belzebul and A. fusca). In the present study, approximately 600 base pairs of the g1-globin pseudogene were sequenced in the four Brazilian species (A. seniculus, A. belzebul, A. fusca and A. caraya). Maximum parsimony and maximum likelihood methods yielded phylogenetic trees with the same arrangement: {A. caraya [A. seniculus (A. fusca, A. belzebul)]}. The most parsimonious tree had bootstrap values greater than 82% for all groupings, and strength of grouping values of at least 2, supporting the sister clade of A. fusca and A. belzebul. The study also confirmed the presence of a 150-base pair Alu insertion element and a 1.8-kb deletion in the g1-globin pseudogene in A. fusca, features found previously in the remaining three species. The cladistic classification based on molecular data agrees with those of morphological studies, with the monospecific A. caraya group being clearly differentiated from the A. seniculus group.
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    A putative RA-like region in the brain of the scale-backed antbird, Willisornis poecilinotus (Furnariides, Suboscines, Passeriformes, Thamnophilidae)
    (Universidade Federal do Pará, 2015-09) LIMA, Jamily Lorena Ramos de; SOARES, Luiz Fabrício Angioletti; REMÉDIOS, Ana Cláudia Santana dos; SILVA, Gregory Thom e; WIRTHLIN, Morgan; ALEIXO, Alexandre Luis Padovan; SCHNEIDER, Maria Paula Cruz; MELLO, Claudio Vianna de; SCHNEIDER, Patrícia Neiva Coelho
    The memorization and production of song in songbirds share important parallels with the process of speech acquisition in humans. In songbirds, these processes are dependent on a group of specialized telencephalic nuclei known as the song system: HVC (used as a proper name), RA (robust nucleus of arcopallium), LMAN (lateral magnocellular nucleus of the nidopallium) and striatal Area X. A recent study suggested that the arcopallium of the Sayornis phoebe, a non vocal learner suboscine species, contains a nucleus with some properties similar to those of songbird RA, suggesting that the song system may have been present in the last common ancestor of these groups. Here we report morphological and gene expression evidence that a region with some properties similar to RA is present in another suboscine, the Amazonian endemic Willisornis poecilinotus. Specifically, a discrete domain with a distinct Nissl staining pattern and that expresses the RA marker RGS4 was found in the arcopallium where the oscine RA is localized. Our findings, combined with the previous report on the S. phoebe, suggest that an arcopallial region with some RA-like properties was present in the ancestor of both Suboscines infraorders Tyranni and Furnarii, and is possibly an ancestral feature of Passeriformes.
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    Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
    (Dove Medical Press, 2012-02) FERREIRA, Vívian D'Afonseca da Silva; SOARES, Siomar de Castro; ALI, Amjad; SANTOS, Anderson Rodrigues dos; GOMIDE, Anne Cybelle Pinto; ROCHA, Aryane Aparecida Magalhães Cassiano; FARIA, Cássio de Jesus; BARBOSA, Eudes Guilherme Vieira; GUIMARÃES, Luís Carlos; ESLABÃO, Marcus Redü; ALMEIDA, Sintia Silva de; ABREU, Vinicius Augusto Carvalho de; ZERLOTINI NETO, Adhemar; CARNEIRO, Adriana Ribeiro; CERDEIRA, Louise Teixeira; RAMOS, Rommel Thiago Juca; HIRATA JÚNIOR, Raphael; GUARALDI, Ana Luiza de Mattos; TROST, Eva; TAUCH, Andreas; SILVA, Artur Luiz da Costa da; SCHNEIDER, Maria Paula Cruz; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho
    Background: The reannotation of genomes already on file is a new approach to discovering new genetic elements and to make the genomes more descriptive and current with relevant features regarding the organism’s lifestyle. Within this approach, the present study aimed to reannotate the genome of the Gram-positive human pathogen Corynebacterium diphtheriae, which causes diphtheria. The deposit of massive amounts of information linked to other spe cies of the genus Corynebacterium has facilitated the updating of the genomic interpretation of this microorganism. Additionally, the emergence of invasive disease by nontoxigenic strains of C. diphtheriae and the reemergence of diphtheria in partially immunized populations have given impetus to new studies in relation to its structural and functional genome. Results: In relation to structural genomics, 23 coding regions (coding sequences) were deleted and 71 new genes were added to the genome annotation. Nevertheless, all the pseudogenes were validated and ten new pseudogenes were created. In relation to functional genomics, about 57% of the genome annotation was updated and became functionally more informative. The product descriptions of 41% (973 proteins) were updated. Among them, 370 that were previously annotated as “hypothetical proteins,” now have more informative descriptions. With the new annotation, the plasticity of the genome became evident, which shows improvements in the annotation of 13 pathogenicity islands already described in the literature. In addition, the large number of transposases and the presence of structural genes of bacteriophages make their genomic versatility evident. Contrasting with this reality, it also allowed the clarification of some aspects concerned with mechanisms used by C. diphtheriae to stop the invasion of the genome by bacteriophages, mediated by the clustered regularly interspaced short palindromic repeats region. Conclusion: The reannotation of the C. diphtheriae genome provided an improvement in annotation of the C. diphtheriae genome in several aspects, such as virulence characteristics and plasticity events. Moreover, the protocol used here can be extended to various other pathogens in order to improve the genomic information already on file in public databases and to minimize propagating errors. The reannotated archive and updated archive are available at: http://lgcm. icb.ufmg.br/pub/C_diphtheriae_reannotation.embl.
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    ItemAcesso aberto (Open Access)
    The Pan-Genome of the Animal Pathogen Corynebacterium pseudotuberculosis Reveals Differences in Genome Plasticity between the Biovar ovis and equi Strains
    (Public Library of Science, 2013-01) SOARES, Siomar de Castro; SILVA, Artur Luiz da Costa da; TROST, Eva; BLOM, Jochen; RAMOS, Rommel Thiago Juca; CARNEIRO, Adriana Ribeiro; ALI, Amjad; SANTOS, Anderson Rodrigues dos; GOMIDE, Anne Cybelle Pinto; DINIZ, Carlos Augusto Almeida; BARBOSA, Eudes Guilherme Vieira; DORELLA, Fernanda Alves; ABURJAILE, Flavia Figueira; ROCHA, Flávia de Souza; NASCIMENTO, Karina Kelly Fiaux do; GUIMARÃES, Luís Carlos; ALMEIDA, Sintia Silva de; HASSAN, Syed Shah; BAKHTIAR, Syeda Marriam; PEREIRA, Ulisses de Pádua; ABREU, Vinicius Augusto Carvalho de; SCHNEIDER, Maria Paula Cruz; MIYOSHI, Anderson; TAUCH, Andreas; AZEVEDO, Vasco Ariston de Carvalho
    Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.
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