Navegando por Autor "SILVA, Artur Luiz da Costa da"

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Acesso aberto (Open Access)
CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS)
(Universidade Federal do Pará, 2016-06) EL HUSNY, Antonette Souto; MORAES, Milene Raiol de; AMADOR, Marcos Antônio Trindade; SANTOS, André Maurício Ribeiro dos; MONTAGNINI, Andre Luis; BARBOSA, Maria Silvanira Ribeiro; SILVA, Artur Luiz da Costa da; ASSUMPÇÃO, Paulo Pimentel de; ISHAK, Geraldo; SANTOS, Sidney Emanuel Batista dos; PINTO, Pablo Diego do Carmo; CRUZ, Aline Maria Pereira; SANTOS, Ândrea Kely Campos Ribeiro dos
Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline mutations in two cases (40%). The mutation c.1023T > G was found in a HDGC family and the mutation c.1849G > A, which is nearly exclusive to African populations, was found in an early-onset case of gastric adenocarcinoma. The mutations described highlight the existence of gastric cancer cases caused by CDH1 germline mutations in northern Brazil, although such information is frequently ignored due to the existence of a large number of environmental factors locally. Our report represent the first CDH1 mutations in HDGC described from Brazil by an NGS platform.
Acesso aberto (Open Access)
CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks
(BioMed Central Ltd, 2015-06) ABREU, Vinicius Augusto Carvalho de; ALMEIDA, Sintia Silva de; TIWARI, Sandeep; HASSAN, Syed Shah; MARIANO, Diego César Batista; SILVA, Artur Luiz da Costa da; BAUMBACH, Jan; AZEVEDO, Vasco Ariston de Carvalho; RÖTTGER, Richard
Background: Organisms utilize a multitude of mechanisms for responding to changing environmental conditions, maintaining their functional homeostasis and to overcome stress situations. One of the most important mechanisms is transcriptional gene regulation. In-depth study of the transcriptional gene regulatory network can lead to various practical applications, creating a greater understanding of how organisms control their cellular behavior. Description: In this work, we present a new database, CMRegNet for the gene regulatory networks of Corynebacterium glutamicum ATCC 13032 and Mycobacterium tuberculosis H37Rv. We furthermore transferred the known networks of these model organisms to 18 other non-model but phylogenetically close species (target organisms) of the CMNR group. In comparison to other network transfers, for the first time we utilized two model organisms resulting into a more diverse and complete network of the target organisms. Conclusion: CMRegNet provides easy access to a total of 3,103 known regulations in C. glutamicum ATCC 13032 and M. tuberculosis H37Rv and to 38,940 evolutionary conserved interactions for 18 non-model species of the CMNR group. This makes CMRegNet to date the most comprehensive database of regulatory interactions of CMNR bacteria. The content of CMRegNet is publicly available online via a web interface found at http://lgcm.icb.ufmg.br/cmregnet.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
Complete Genome Sequence of Type Strain Campylobacter fetus subsp. venerealis NCTC 10354
(American Society for Microbiology, 2011-10) STYNEN, Ana Paula Reinato; LAGE, Andrey Pereira; MOORE, Robert J.; REZENDE, Antonio Mauro; FERREIRA, Vívian D'Afonseca da Silva; RUY, Patrícia de Cássia; OLIVEIRA, Nesley Jesus Daher de; RESENDE, Daniela de Melo; ALMEIDA, Sintia Silva de; SOARES, Siomar de Castro; ABREU, Vinicius Augusto Carvalho de; ROCHA, Aryane Aparecida Magalhães Cassiano; SANTOS, Anderson Rodrigues dos; BARBOSA, Eudes Guilherme Vieira; COUTO, Danielle Costa Carrara; DORELLA, Fernanda Alves; MIYOSHI, Anderson; LIMA, Alex Ranieri Jerônimo; CAMPOS, Frederico Davi da Silva; SÁ, Pablo Henrique Caracciolo Gomes de; LOPES, Thiago Souza; RODRIGUES, Ryan Maurício Araújo; CARNEIRO, Adriana Ribeiro; LEÃO, Tiago Ferreira; CERDEIRA, Louise Teixeira; RAMOS, Rommel Thiago Juca; SILVA, Artur Luiz da Costa da; AZEVEDO, Vasco Ariston de Carvalho; RUIZ, Jeronimo Conceição
Campylobacter fetus subsp. venerealis is the etiologic agent of bovine genital campylobacteriosis, a sexually transmitted disease of cattle that is of worldwide importance. The complete sequencing and annotation of the genome of the type strain C. fetus subsp. venerealis NCTC 10354T are reported.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
Draft genome sequences of two species of “difficult-to-identify” human-pathogenic corynebacteria: implications for better identification tests.
(Ivyspring International Publisher, 2015) PACHECO, Luis Gustavo Carvalho; GUARALDI, Ana Luiza de Mattos; SANTOS, Carolina Silva; VERAS, Adonney Allan de Oliveira; GUIMARÃES, Luís Carlos; ABREU, Vinicius Augusto Carvalho de; PEREIRA, Felipe Luiz; SOARES, Siomar de Castro; DORELLA, Fernanda Alves; CARVALHO, Alex Fiorini de; LEAL, Carlos Augusto Gomes; FIGUEIREDO, Henrique Cesar Pereira; RAMOS, Juliana Nunes; VIEIRA, Verônica Viana; FARFOUR, Eric; GUISO, Nicole; HIRATA JÚNIOR, Raphael; AZEVEDO, Vasco Ariston de Carvalho; SILVA, Artur Luiz da Costa da; RAMOS, Rommel Thiago Juca
Non-diphtheriae Corynebacterium species have been increasingly recognized as the causative agents of infections in humans. Differential identification of these bacteria in the clinical microbiology laboratory by the most commonly used biochemical tests is challenging, and normally requires additional molecular methods. Herein, we present the annotated draft genome sequences of two isolates of “difficult-to-identify” human-pathogenic corynebacterial species: C. xerosis and C. minutissimum. The genome sequences of ca. 2.7 Mbp, with a mean number of 2,580 protein en coding genes, were also compared with the publicly available genome sequences of strains of C. amycolatum and C. striatum. These results will aid the exploration of novel biochemical reactions to improve existing identification tests as well as the development of more accurate molecular identification methods through detection of species-specific target genes for isolate’s identification or drug susceptibility profiling.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds
(Public Library of Science, 2013-01) BARH, Debmalya; SHARMA, Neha Barve; GUPTA, Krishnakant; CHANDRA, Sudha; JAIN, Neha; TIWARI, Sandeep; LEON-SICAIROS, Nidia; CANIZALEZ-ROMAN, Adrian; SANTOS, Anderson Rodrigues dos; HASSAN, Syed Shah; ALMEIDA, Sintia Silva de; RAMOS, Rommel Thiago Juca; ABREU, Vinicius Augusto Carvalho de; CARNEIRO, Adriana Ribeiro; SOARES, Siomar de Castro; CASTRO, Thiago Luiz de Paula; MIYOSHI, Anderson; SILVA, Artur Luiz da Costa da; KUMAR, Anil; NARAYAN MISRA, Amarendra; BLUM, Kenneth; BRAVERMAN, Eric R.; AZEVEDO, Vasco Ariston de Carvalho
Vibrio cholerae is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also alarming. Because of the emergence of new drug resistant strains, even though several generic drugs and vaccines have been developed over time, Vibrio infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (ompU, uppP and yajC) for most of the pathogenic Vibrio strains. Two targets (uppP and yajC) are novel to Vibrio, and two targets (uppP and ompU) can be used to develop both drugs and vaccines (dual targets) against broad spectrum Vibrio serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from Piper betel. Seven compounds were identified first time from Piper betel to be highly effective to render the function of these targets to identify them as emerging potential drugs against Vibrio. Our preliminary validation suggests that these identified peptide vaccines and betel compounds are highly effective against Vibrio cholerae. Currently we are exhaustively validating these targets, candidate peptide vaccines, and betel derived lead compounds against a number of Vibrio species.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
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.
Acesso aberto (Open Access)
Genome sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA - producing strain
(American Society for Microbiology, 2014-10) SARAIVA, Tessália Diniz Luerce; SOARES, Siomar de Castro; RAMOS, Rommel Thiago Juca; SÁ, Pablo Henrique Caracciolo Gomes de; CARNEIRO, Adriana Ribeiro; MIRANDA, Fábio Malcher; FREIRA, Matheus; RENAN, Wendal; OLIVEIRA JÚNIOR, Alberto Fernandes de; SANTOS, Anderson Rodrigues dos; GOMIDE, Anne Cybelle Pinto; SOUZA, Bianca Mendes; CASTRO, Camila Prósperi de; DINIZ, Carlos Augusto Almeida; ROCHA, Clarissa Santos; MARIANO, Diego César Batista; AGUIAR, Edgar Lacerda de; FOLADOR, Edson Luiz; BARBOSA, Eudes Guilherme Vieira; ABURJAILE, Flavia Figueira; GONÇALVES, Lucas Amorim; GUIMARÃES, Luís Carlos; AZEVEDO, Marcela; AGRESTI, Pamela Mancha; SOUZA, Renata de Faria Silva; TIWARI, Sandeep; ALMEIDA, Sintia Silva de; HASSAN, Syed Shah; PEREIRA, Vanessa Bastos; ABREU, Vinicius Augusto Carvalho de; PEREIRA, Ulisses de Pádua; DORELLA, Fernanda Alves; CARVALHO, Alex Fiorini de; PEREIRA, Felipe Luiz; LEAL, Carlos Augusto Gomes; FIGUEIREDO, Henrique Cesar Pereira; SILVA, Artur Luiz da Costa da; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho
Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118, a strain with probiotic potential activity.
Acesso aberto (Open Access)
Lack of evidence for human infection with Xenotropic murine leukemia virus-related virus in the Brazilian Amazon basin
(2014-06) GOMES, Samara Tatielle Monteiro; IMBIRIBA, Luciana; BURBANO, Rommel Mario Rodriguéz; SILVA, Artur Luiz da Costa da; FEITOSA, Rosimar Neris Martins; VALLINOTO, Izaura Maria Vieira Cayres; ISHAK, Marluísa de Oliveira Guimarães; ISHAK, Ricardo; VALLINOTO, Antonio Carlos Rosário
Introduction: This study confirmed the absence of natural infection with Xenotropic murine leukemia virus-related virus (XMRV) or XMRV-related disease in human populations of the Brazilian Amazon basin. We demonstrated that 803 individuals of both sexes, who were residents of Belem in the Brazilian State of Pará, were not infected with XMRV. Methods: Individuals were divided into 4 subgroups: healthy individuals, individuals infected with human immunodeficiency virus, type 1 (HIV-1), individuals infected with human T-lymphotrophic virus, types 1 or 2 (HTLV-1/2), and individuals with prostate cancer. XMRV infection was investigated by nested PCR to detect the viral gag gene and by quantitative PCR to detect pol. Results: There was no amplification of either gag or pol segments from XRMV in any of the samples examined. Conclusions: This study supports the conclusions of the studies that eventually led to the retraction of the original study reporting the association between XMRV and human diseases.
Acesso aberto (Open Access)
PIPS: Pathogenicity Island Prediction Software
(Public Library of Science, 2012-02) SOARES, Siomar de Castro; ABREU, Vinicius Augusto Carvalho de; RAMOS, Rommel Thiago Juca; CERDEIRA, Louise Teixeira; SILVA, Artur Luiz da Costa da; BAUMBACH, Jan; TROST, Eva; TAUCH, Andreas; HIRATA JÚNIOR, Raphael; GUARALDI, Ana Luiza de Mattos; MIYOSHI, Anderson; AZEVEDO, Vasco Ariston de Carvalho
The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands.
Acesso aberto (Open Access)
Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis
(BioMed Central Ltd, 2014) HASSAN, Syed Shah; TIWARI, Sandeep; GUIMARÃES, Luís Carlos; BACHA, Syed Babar Jamal; FOLADOR, Edson Luiz; SHARMA, Neha Barve; SOARES, Siomar de Castro; ALMEIDA, Sintia Silva de; ALI, Amjad; ISLAM, Arshad; PÓVOA, Fabiana Dias; ABREU, Vinicius Augusto Carvalho de; JAIN, Neha; FERREIRA, Rafaela Salgado; BHATTACHARYA, Antaripa; JUNEJA, Lucky; MIYOSHI, Anderson; SILVA, Artur Luiz da Costa da; BARH, Debmalya; TURJANSKI, Adrian Gustavo; AZEVEDO, Vasco Ariston de Carvalho
Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.