Rodrigo Barban Zucoloto | UFBA - Federal University of Bahia (original) (raw)

Papers by Rodrigo Barban Zucoloto

Microsatellite DNA markers have been used to assess genetic diversity and to study ecological beh... more Microsatellite DNA markers have been used to assess genetic diversity and to study ecological behavioral characteristics in animals. Although these markers are powerful tools, their development is labor intensive and costly. Thus, before new markers are developed it is important to prospect the use of markers from related species. In the present study we investigated the possibility of using microsatellite markers developed for Alligator mississipiensis and Caiman latirostris in South American crocodilians. Our results demonstrate the use of microsatellite markers for Paleosuchus palpebrosus, Caiman crocodilus and Caiman yacare.

PCR-Polymerase Chain Reaction (Reação em cadeia da polimerase). RAPD-Randon Amplified Polymorphic... more PCR-Polymerase Chain Reaction (Reação em cadeia da polimerase). RAPD-Randon Amplified Polymorphic DNA (Polimorfismo de DNA amplificado ao acaso). AFLP-Amplified Fragment Lenght Polymorphism (Polimorfismo de comprimento de fragmento amplificado). RWR-Rockfeller Wild Refuge.

Journal of Experimental Zoology, 2002

Journal of Experimental Zoology, 2002

2014 IEEE International Conference on Cluster Computing (CLUSTER), 2014

ABSTRACT Many e-science applications can benefit from the elasticity of resources provided by vol... more ABSTRACT Many e-science applications can benefit from the elasticity of resources provided by volunteer and distributed platforms. While the former is based on resources assigned voluntarily by its owners, the second is based on resources specially configured for this purpose. In this paper, we present the integration of BOINC and Hadoop, two of the most popular middlewares available today, at the infrastructure level of mc2 , a platform designed to support scientific applications. We discuss some case studies related to DNA sequencing running in CloudBurst, model selection running in the MEGA Computational Core and similarity searches running in BLAST. Our results show scientific users can run their experiments in our platform with a high level of abstraction and, in some cases, with very good performance.

ABSTRACT Dissertação (Mestrado)--Centro de Energia Nuclear na Agricultura.

Genetics and Molecular Biology, 2009

Global Ecology and Conservation

Conservation Genetics of New World Crocodilians

The chapter gives an introductory overview on the biology of the 11 species of crocodilians inhab... more The chapter gives an introductory overview on the biology of the 11 species of crocodilians inhabiting the Americas. Geographical distribution is broadly discussed in the light of biogeographical and evolutionary origins. As a broad generalization, crocodilians are morphologically, genetically, and ecologically conservative and show a high dispersal ability, which together complicate the delimitation of species boundaries. Furthermore, distinct clades of crocodilians are a result of environmental selection for different adaptive characteristics. Gene flow occurs between clades, but distinct morphological varieties are sometimes a result of environmental filters. Thus, many taxa of crocodilians can be considered ecological species. Reproductive characteristics, such as nest-site choice and female reproductive output, influence reproductive success and thus population trends, so we discuss reproductive and habitat characteristics in the light of conservation genetics. Finally, the status of crocodilians is discussed both in terms of past hunting pressure and current conservation and management initiatives. In general, crocodilians can look after themselves if they have sufficient habitat, but some species are critically endangered by hunting, even though much of their original habitat remains intact. Conservation actions must be applied locally, taking into account threats and dispersal between source and sink populations. Given the difficulty of studying the F. Villamarín (*) Grupo de Biogeografía y Ecología Espacial (BioGeoE2). Universidad Regional Amazónica Ikiam, Km 7 vía Muyuna., Tena, Ecuador A. H. Escobedo-Galván Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Jalisco, Mexico P. Siroski Laboratorio de Ecología Molecular Aplicada-ICiVet UNL/ CONICET, Santa Fe, Argentina e-mail: psiroski@fcv.unl.edu.ar W. E. Magnusson Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil e-mail: bill@inpa.gov.br

Microsatellite DNA markers have been used to assess genetic diversity and to study ecological beh... more Microsatellite DNA markers have been used to assess genetic diversity and to study ecological behavioral character-istics in animals. Although these markers are powerful tools, their development is labor intensive and costly. Thus, before new markers are developed it is important to prospect the use of markers from related species. In the present study we investigated the possibility of using microsatellite markers developed for Alligator mississipiensis and Cai-man latirostris in South American crocodilians. Our results demonstrate the use of microsatellite markers for Paleosuchus palpebrosus, Caiman crocodilus and Caiman yacare.

This final chapter summarizes the main concepts expressed in this book, condensing the main findi... more This final chapter summarizes the main concepts expressed in this book, condensing the main findings developed over many years through genetic research in crocodile populations of the New World. Since the development of new technologies, researchers from the New World have been applying them successfully in the species that concern us. In this way, a large amount of information has been collected over time, as displayed throughout the reading of this book, obtaining a body of knowledge that contributes to the conservation of its populations. Basic data have been obtained, such as population parameters of genetic diversity up to applied data, for example, determining the species or population of origin to which a commercial product belongs. A large part of the successful results was obtained thanks to the collaboration between working groups of crocodile specialists, which allows extending the sampling, and the genetic information or markers to be used or increase the depth of the analysis. The fundamental ideas developed in each of the previous chapters are organized here with the aim of elaborating on the final conclusions of this book.

Microsatellite markers have been applied to conservation genetic studies of crocodilians since th... more Microsatellite markers have been applied to conservation genetic studies of crocodilians since the second half of 90's. The identification of highly transferable markers would be very important to crocodilian genetic studies. Here is described the identification of twenty-five new microsatellite markers from Alligator mississippiensis (Daudin, 1802) EST sequences and discussed their expected efficiency for the amplification of DNA of other crocodilian species.

RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avali... more RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avaliados, como parte do Programa Nacional do Livro para o Ensino Médio (PNLEM). Neste artigo, relatamos resultados dessa avaliação. Os critérios e o processo de avaliação são apresentados de modo detalhado, bem como os principais problemas das obras não-recomendadas para compra pelo MEC e os principais aspectos positivos das obras recomendadas. Das 18 obras submetidas à avaliação, nove satisfizeram os critérios mínimos de qualidade para aprovação. Sete obras didáticas excluídas apresentaram problemas em todas as classes de critérios de avaliação. Todas as nove obras excluídas exibiram problemas relativos à correção e adequação conceituais, e à precisão da informação básica fornecida. As qualidades mais frequentes nas obras recomendadas diziam respeito à adequação metodológica e à construção do conhecimento. Não encontramos evidências claras de que a frequência de escolha pelos professores do ensino médio refletiu a qualidade dos itens avaliados, conforme estabelecida pela equipe que analisou as obras.

Journal of Experimental Zoology

RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avali... more RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avaliados, como parte do Programa Nacional do Livro para o Ensino Médio (PNLEM). Neste artigo, relatamos resultados dessa avaliação. Os critérios e o processo de avaliação são apresentados de modo detalhado, bem como os principais problemas das obras não-recomendadas para compra pelo MEC e os principais aspectos positivos das obras recomendadas. Das 18 obras submetidas à avaliação, nove satisfizeram os critérios mínimos de qualidade para aprovação. Sete obras didáticas excluídas apresentaram problemas em todas as classes de critérios de avaliação. Todas as nove obras excluídas exibiram problemas relativos à correção e adequação conceituais, e à precisão da informação básica fornecida. As qualidades mais frequentes nas obras recomendadas diziam respeito à adequação metodológica e à construção do conhecimento. Não encontramos evidências claras de que a frequência de escolha pelos professores do ensino médio refletiu a qualidade dos itens avaliados, conforme estabelecida pela equipe que analisou as obras.

Journal of experimental …, Jan 1, 2002

In theory, geographic scale is related to genetic variation at the population level, whereas micr... more In theory, geographic scale is related to genetic variation at the population level, whereas microgeographic scale may reveal intra-population structure such as social groups and families. In the present work, both levels of genetic variation in the broad-snouted caiman (Caiman latirostris) were evaluated in small wetlands associated with the Piracicaba River and some of its tributaries in the state of São Paulo, Brazil. Genetic variation was determined using microsatellite DNA markers originally developed for the American alligator (Alligator mississipiensis) and previously tested in pedigreed captive broad-snouted caimans. Using these markers, we were able to detect variability among individuals from different sites, even those within a small geographic distance. Genetic results suggest that the groups sampled at each site are composed predominantly of related individuals. A possible combination of high mortality and low natality rates results in a low number of successfully dispersed individuals per generation. Future studies using a recently constructed Caiman latirostris microsatellite library might help us to understand metapopulation processes that may be occurring within this species.

Journal of Experimental …, Jan 1, 2002

New genetic markers were characterized for the broad-snouted caiman (Caiman latirostris) by const... more New genetic markers were characterized for the broad-snouted caiman (Caiman latirostris) by constructing libraries enriched for microsatellite DNA. Construction and characterization of these libraries are described in the present study. One microsatellite marker was developed from a (ACC-TGG) n enriched microsatellite DNA library, and 12 microsatellite markers were developed from a (AC-TG) n enriched microsatellite DNA library. These markers were tested in wild-caught animals, and these tests resulted in ten new polymorphic microsatellites for C. latirostris.

Microsatellite DNA markers have been used to assess genetic diversity and to study ecological beh... more Microsatellite DNA markers have been used to assess genetic diversity and to study ecological behavioral characteristics in animals. Although these markers are powerful tools, their development is labor intensive and costly. Thus, before new markers are developed it is important to prospect the use of markers from related species. In the present study we investigated the possibility of using microsatellite markers developed for Alligator mississipiensis and Caiman latirostris in South American crocodilians. Our results demonstrate the use of microsatellite markers for Paleosuchus palpebrosus, Caiman crocodilus and Caiman yacare.

PCR-Polymerase Chain Reaction (Reação em cadeia da polimerase). RAPD-Randon Amplified Polymorphic... more PCR-Polymerase Chain Reaction (Reação em cadeia da polimerase). RAPD-Randon Amplified Polymorphic DNA (Polimorfismo de DNA amplificado ao acaso). AFLP-Amplified Fragment Lenght Polymorphism (Polimorfismo de comprimento de fragmento amplificado). RWR-Rockfeller Wild Refuge.

Journal of Experimental Zoology, 2002

Journal of Experimental Zoology, 2002

2014 IEEE International Conference on Cluster Computing (CLUSTER), 2014

ABSTRACT Many e-science applications can benefit from the elasticity of resources provided by vol... more ABSTRACT Many e-science applications can benefit from the elasticity of resources provided by volunteer and distributed platforms. While the former is based on resources assigned voluntarily by its owners, the second is based on resources specially configured for this purpose. In this paper, we present the integration of BOINC and Hadoop, two of the most popular middlewares available today, at the infrastructure level of mc2 , a platform designed to support scientific applications. We discuss some case studies related to DNA sequencing running in CloudBurst, model selection running in the MEGA Computational Core and similarity searches running in BLAST. Our results show scientific users can run their experiments in our platform with a high level of abstraction and, in some cases, with very good performance.

ABSTRACT Dissertação (Mestrado)--Centro de Energia Nuclear na Agricultura.

Genetics and Molecular Biology, 2009

Global Ecology and Conservation

Conservation Genetics of New World Crocodilians

The chapter gives an introductory overview on the biology of the 11 species of crocodilians inhab... more The chapter gives an introductory overview on the biology of the 11 species of crocodilians inhabiting the Americas. Geographical distribution is broadly discussed in the light of biogeographical and evolutionary origins. As a broad generalization, crocodilians are morphologically, genetically, and ecologically conservative and show a high dispersal ability, which together complicate the delimitation of species boundaries. Furthermore, distinct clades of crocodilians are a result of environmental selection for different adaptive characteristics. Gene flow occurs between clades, but distinct morphological varieties are sometimes a result of environmental filters. Thus, many taxa of crocodilians can be considered ecological species. Reproductive characteristics, such as nest-site choice and female reproductive output, influence reproductive success and thus population trends, so we discuss reproductive and habitat characteristics in the light of conservation genetics. Finally, the status of crocodilians is discussed both in terms of past hunting pressure and current conservation and management initiatives. In general, crocodilians can look after themselves if they have sufficient habitat, but some species are critically endangered by hunting, even though much of their original habitat remains intact. Conservation actions must be applied locally, taking into account threats and dispersal between source and sink populations. Given the difficulty of studying the F. Villamarín (*) Grupo de Biogeografía y Ecología Espacial (BioGeoE2). Universidad Regional Amazónica Ikiam, Km 7 vía Muyuna., Tena, Ecuador A. H. Escobedo-Galván Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Jalisco, Mexico P. Siroski Laboratorio de Ecología Molecular Aplicada-ICiVet UNL/ CONICET, Santa Fe, Argentina e-mail: psiroski@fcv.unl.edu.ar W. E. Magnusson Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil e-mail: bill@inpa.gov.br

Microsatellite DNA markers have been used to assess genetic diversity and to study ecological beh... more Microsatellite DNA markers have been used to assess genetic diversity and to study ecological behavioral character-istics in animals. Although these markers are powerful tools, their development is labor intensive and costly. Thus, before new markers are developed it is important to prospect the use of markers from related species. In the present study we investigated the possibility of using microsatellite markers developed for Alligator mississipiensis and Cai-man latirostris in South American crocodilians. Our results demonstrate the use of microsatellite markers for Paleosuchus palpebrosus, Caiman crocodilus and Caiman yacare.

This final chapter summarizes the main concepts expressed in this book, condensing the main findi... more This final chapter summarizes the main concepts expressed in this book, condensing the main findings developed over many years through genetic research in crocodile populations of the New World. Since the development of new technologies, researchers from the New World have been applying them successfully in the species that concern us. In this way, a large amount of information has been collected over time, as displayed throughout the reading of this book, obtaining a body of knowledge that contributes to the conservation of its populations. Basic data have been obtained, such as population parameters of genetic diversity up to applied data, for example, determining the species or population of origin to which a commercial product belongs. A large part of the successful results was obtained thanks to the collaboration between working groups of crocodile specialists, which allows extending the sampling, and the genetic information or markers to be used or increase the depth of the analysis. The fundamental ideas developed in each of the previous chapters are organized here with the aim of elaborating on the final conclusions of this book.

Microsatellite markers have been applied to conservation genetic studies of crocodilians since th... more Microsatellite markers have been applied to conservation genetic studies of crocodilians since the second half of 90's. The identification of highly transferable markers would be very important to crocodilian genetic studies. Here is described the identification of twenty-five new microsatellite markers from Alligator mississippiensis (Daudin, 1802) EST sequences and discussed their expected efficiency for the amplification of DNA of other crocodilian species.

RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avali... more RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avaliados, como parte do Programa Nacional do Livro para o Ensino Médio (PNLEM). Neste artigo, relatamos resultados dessa avaliação. Os critérios e o processo de avaliação são apresentados de modo detalhado, bem como os principais problemas das obras não-recomendadas para compra pelo MEC e os principais aspectos positivos das obras recomendadas. Das 18 obras submetidas à avaliação, nove satisfizeram os critérios mínimos de qualidade para aprovação. Sete obras didáticas excluídas apresentaram problemas em todas as classes de critérios de avaliação. Todas as nove obras excluídas exibiram problemas relativos à correção e adequação conceituais, e à precisão da informação básica fornecida. As qualidades mais frequentes nas obras recomendadas diziam respeito à adequação metodológica e à construção do conhecimento. Não encontramos evidências claras de que a frequência de escolha pelos professores do ensino médio refletiu a qualidade dos itens avaliados, conforme estabelecida pela equipe que analisou as obras.

Journal of Experimental Zoology

RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avali... more RESUMO: Em 2005, os livros didáticos de Biologia do ensino médio publicados no Brasil foram avaliados, como parte do Programa Nacional do Livro para o Ensino Médio (PNLEM). Neste artigo, relatamos resultados dessa avaliação. Os critérios e o processo de avaliação são apresentados de modo detalhado, bem como os principais problemas das obras não-recomendadas para compra pelo MEC e os principais aspectos positivos das obras recomendadas. Das 18 obras submetidas à avaliação, nove satisfizeram os critérios mínimos de qualidade para aprovação. Sete obras didáticas excluídas apresentaram problemas em todas as classes de critérios de avaliação. Todas as nove obras excluídas exibiram problemas relativos à correção e adequação conceituais, e à precisão da informação básica fornecida. As qualidades mais frequentes nas obras recomendadas diziam respeito à adequação metodológica e à construção do conhecimento. Não encontramos evidências claras de que a frequência de escolha pelos professores do ensino médio refletiu a qualidade dos itens avaliados, conforme estabelecida pela equipe que analisou as obras.

Journal of experimental …, Jan 1, 2002

In theory, geographic scale is related to genetic variation at the population level, whereas micr... more In theory, geographic scale is related to genetic variation at the population level, whereas microgeographic scale may reveal intra-population structure such as social groups and families. In the present work, both levels of genetic variation in the broad-snouted caiman (Caiman latirostris) were evaluated in small wetlands associated with the Piracicaba River and some of its tributaries in the state of São Paulo, Brazil. Genetic variation was determined using microsatellite DNA markers originally developed for the American alligator (Alligator mississipiensis) and previously tested in pedigreed captive broad-snouted caimans. Using these markers, we were able to detect variability among individuals from different sites, even those within a small geographic distance. Genetic results suggest that the groups sampled at each site are composed predominantly of related individuals. A possible combination of high mortality and low natality rates results in a low number of successfully dispersed individuals per generation. Future studies using a recently constructed Caiman latirostris microsatellite library might help us to understand metapopulation processes that may be occurring within this species.

Journal of Experimental …, Jan 1, 2002

New genetic markers were characterized for the broad-snouted caiman (Caiman latirostris) by const... more New genetic markers were characterized for the broad-snouted caiman (Caiman latirostris) by constructing libraries enriched for microsatellite DNA. Construction and characterization of these libraries are described in the present study. One microsatellite marker was developed from a (ACC-TGG) n enriched microsatellite DNA library, and 12 microsatellite markers were developed from a (AC-TG) n enriched microsatellite DNA library. These markers were tested in wild-caught animals, and these tests resulted in ten new polymorphic microsatellites for C. latirostris.