Luciano Antonio Digiampietri

Genome features of Leptospira interrogans serovar Copenhageni

We report novel features of the genome sequence of Leptospira interrogans serovar Copenhageni, a highly invasive spirochete. Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in mammals. Genomic sequence analysis reveals the presence of a competent transport system with 13 families of genes encoding for major transporters including a three-member component efflux system compatible with the long-term survival of this organism. The leptospiral genome contains a broad array of genes encoding regulatory system, signal transduction and methyl-accepting chemotaxis proteins, reflecting the organisms ability to respond to diverse environmental stimuli. The identification of a complete set of genes encoding the enzymes for the cobalamin biosynthetic pathway and the novel coding genes related to lipopolysaccharide biosynthesis should bring new light to the study of Leptospira physiology. Genes related to toxins, lipoproteins and several surface-exposed proteins may facilitate a better understanding of the Leptospira pathogenesis and may serve as potential candidates for vaccine.

Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.

Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii

BackgroundCitrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C.ResultsWe have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein.ConclusionWe have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

Brazilian bibliometric coauthorship networks

The Brazilian Lattes Platform is an important academic/résumé data set that registers all academic activities of researchers associated with different major knowledge areas. The academic information collected in this data set is used to evaluate, analyze, and document the scientific production of research groups. Information about the interactions between Brazilian researchers in the form of coauthorships, however, has not been analyzed. In this article, we identified and characterized Brazilian academic coauthorship networks of researchers registered in the Lattes Platform using topological properties of graphs. For this purpose, we explored (a) strategies to develop a large Lattes curricula vitae data set, (b) an algorithm for identifying automatic coauthorships based on bibliographic information, and (c) topological metrics to investigate interactions among researchers. This study characterized coauthorship networks to gain an in‐depth understanding of the network structures and dynamics (social behavior) among researchers in all available major Brazilian knowledge areas. In this study, we evaluated information from a total of 1,131,912 researchers associated with the eight major Brazilian knowledge areas: agricultural sciences; biological sciences; exact and earth sciences; humanities; applied social sciences; health sciences; engineering; and linguistics, letters, and arts.

Automatic generation of workflow provenance

While workflow is playing an increasingly important role in e-Science, current systems lack support for the collection of provenance data. We argue that workflow provenance data should be automatically generated by the enactment engine and managed over time by an underlying storage service. We briefly describe our layered model for workflow execution provenance, which allows navigation from the conceptual model of an experiment to instance data collected during a specific experiment run, and back.

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.

Gene projects: a genome web tool for ongoing mining and annotation applied to CitEST

Genome projects, both genomic DNA and ESTs (cDNA), generate a large amount of information, demanding time and a well-structured bioinformatics laboratory to manage these data. These genome projects use information available in heterogeneous formats from different sources. The amount and heterogeneity of this information, as well as the absence of a world consensus pattern, make the integration of these data a difficult task. At the same time, sub-tasks, such as microarray analyses of these projects, are very complex. This creates a demand for the development of creative solutions for ongoing annotation, thematic projects, microarray experiments, etc. This paper presents Gene Projects, a system developed to integrate all kinds of solutions.

Comunicação científica no Brasil (1998-2012): indexação, crescimento, fluxo e dispersão

A producao cientifica brasileira vem demonstrando ascensao no cenario mundial, o que pode decorrer da internacionalizacao da ciencia nacional e/ou das revistas nacionais. Nesse contexto, este estudo reuniu a producao cientifica brasileira das bases Web of Science e Scientific Electronic Library Online entre 1998 e 2012, com o fim de analisar como a internacionalizacao tem influenciado a performance do pais. Com base em Zonas de Bradford da producao das diversas areas, buscou avaliar o aumento do numero de revistas em cada uma das zonas, assim como a proporcao de artigos publicados em revistas nacionais, ao longo de cinco trienios. Observou-se que o numero de revistas indexadas exclusivamente na Scientific Electronic Library Online cresceu no periodo, com excecao do trienio 4, quando aproximadamente 60% da producao nacional foi publicada em revistas estrangeiras ( Web of Science ). Notou-se que o aumento mais generalizado do numero de revistas das areas deu-se primeiramente na zona 3 (trienio 2004-2006), depois na zona 2 (trienio 2007-2009) e finalmente na zona 1 (trienio 2010-2012). Ja o percentual da producao em revistas nacionais diferenciou tres grupos de areas: ciencias sociais e humanas, onde as zonas 1 e 2 sao exclusivas de revistas nacionais, e a zona 3 vem dando lugar a publicacoes estrangeiras; Fisica, Ciencia do Espaco e Imunologia, cuja producao e exclusivamente internacional; e as demais areas, de ciencias exatas e da terra, saude e biologicas, que vem aumentando o percentual nas zonas 1 e 2, permanecendo a zona 3 direcionada a publicacoes internacionais. Palavras-chave : Avaliacao de pesquisa. Brasil. Producao cientifica. Revistas cientificas nacionais. Zonas de Bradford.

Implementation Issues for Automatic Composition of Web Services

Service Oriented Computing (SOC) is a computing paradigm for the agile development of software based on the orchestration of loosely-coupled services. Services perform functions from the solution of simple atomic requests to execution of complex business processes. Nowadays, new services are created from the manual composition of basic Web Services. It is an arduous and susceptible to errors task. To avoid this problem, it is necessary the existence of discovery and automatic composition mechanisms. This paper presents the specification of a architecture and implementation of a prototype for the automatic composition of Web Services using Artificial Intelligence planning techniques and the WSMO ontological model. Moreover, the paper contains a discussion about design and implementation choices and further improvements.

Analysis of an advisor-advisee relationship: an exploratory study of the area of exact and Earth sciences in Brazil.

Scientific collaboration has been studied by researchers for decades. Several approaches have been adopted to address the question of how collaboration has evolved in terms of publication output, numbers of coauthors, and multidisciplinary trends. One particular type of collaboration that has received very little attention concerns advisor and advisee relationships. In this paper, we examine this relationship for the researchers who are involved in the area of Exact and Earth Sciences in Brazil and its eight subareas. These pairs are registered in the Lattes Platform that manages the individual curricula vitae of Brazilian researchers. The individual features of these academic researchers and their coauthoring relationships were investigated. We have found evidence that there exists positive correlation between time of advisor–advisee relationship with the advisee’s productivity. Additionally, there has been a gradual decline in advisor–advisee coauthoring over a number of years as measured by the Kulczynski index, which could be interpreted as decline of the dependence.