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1.  Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses 
Pedrosa, Fábio O. | Monteiro, Rose Adele | Wassem, Roseli | Cruz, Leonardo M. | Ayub, Ricardo A. | Colauto, Nelson B. | Fernandez, Maria Aparecida | Fungaro, Maria Helena P. | Grisard, Edmundo C. | Hungria, Mariangela | Madeira, Humberto M. F. | Nodari, Rubens O. | Osaku, Clarice A. | Petzl-Erler, Maria Luiza | Terenzi, Hernán | Vieira, Luiz G. E. | Steffens, Maria Berenice R. | Weiss, Vinicius A. | Pereira, Luiz F. P. | Almeida, Marina I. M. | Alves, Lysangela R. | Marin, Anelis | Araujo, Luiza Maria | Balsanelli, Eduardo | Baura, Valter A. | Chubatsu, Leda S. | Faoro, Helisson | Favetti, Augusto | Friedermann, Geraldo | Glienke, Chirlei | Karp, Susan | Kava-Cordeiro, Vanessa | Raittz, Roberto T. | Ramos, Humberto J. O. | Ribeiro, Enilze Maria S. F. | Rigo, Liu Un | Rocha, Saul N. | Schwab, Stefan | Silva, Anilda G. | Souza, Eliel M. | Tadra-Sfeir, Michelle Z. | Torres, Rodrigo A. | Dabul, Audrei N. G. | Soares, Maria Albertina M. | Gasques, Luciano S. | Gimenes, Ciela C. T. | Valle, Juliana S. | Ciferri, Ricardo R. | Correa, Luiz C. | Murace, Norma K. | Pamphile, João A. | Patussi, Eliana Valéria | Prioli, Alberto J. | Prioli, Sonia Maria A. | Rocha, Carmem Lúcia M. S. C. | Arantes, Olívia Márcia N. | Furlaneto, Márcia Cristina | Godoy, Leandro P. | Oliveira, Carlos E. C. | Satori, Daniele | Vilas-Boas, Laurival A. | Watanabe, Maria Angélica E. | Dambros, Bibiana Paula | Guerra, Miguel P. | Mathioni, Sandra Marisa | Santos, Karine Louise | Steindel, Mario | Vernal, Javier | Barcellos, Fernando G. | Campo, Rubens J. | Chueire, Ligia Maria O. | Nicolás, Marisa Fabiana | Pereira-Ferrari, Lilian | da Conceição Silva, José L. | Gioppo, Nereida M. R. | Margarido, Vladimir P. | Menck-Soares, Maria Amélia | Pinto, Fabiana Gisele S. | Simão, Rita de Cássia G. | Takahashi, Elizabete K. | Yates, Marshall G. | Souza, Emanuel M.
PLoS Genetics  2011;7(5):e1002064.
The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.
Author Summary
In this work we describe the genome of H. seropedicae SmR1, a bacterium capable of fixing nitrogen and promoting the growth of important plant crops such as maize, rice, and sugar cane. Several investigations have shown that H. seropedicae supplies fixed nitrogen to the associated plant and increases grain productivity up to 50%. In the genome of H. seropedicae, we identified all the genes involved in the nitrogen fixation process and its regulation and, in addition, genes potentially involved in the establishment of efficient interaction with the host plant. Our analyses also revealed that this bacterium has a highly versatile metabolism capable of synthesizing and degrading a large number of organic and inorganic compounds. We believe that the knowledge of the genome of this bacterium will direct research to a better understanding of this important endophytic organism and allow the construction of new strains with enhanced agronomic efficiency.
doi:10.1371/journal.pgen.1002064
PMCID: PMC3093359  PMID: 21589895
2.  STINGRAY: system for integrated genomic resources and analysis 
BMC Research Notes  2014;7:132.
Background
The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms.
Findings
STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation.
Conclusion
STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.
doi:10.1186/1756-0500-7-132
PMCID: PMC4015962  PMID: 24606808
Genome; Annotation; Workflow; Next generation sequencing; Sanger; Data integration
3.  Trans-sialidase Stimulates Eat Me Response from Epithelial Cells 
Traffic (Copenhagen, Denmark)  2013;14(7):853-869.
Epithelial cell invasion by the protozoan parasite Trypanosoma cruzi is enhanced by the presence of an enzyme expressed on its cell surface during the trypomastigote life cycle stage. The enzyme, trans-sialidase (TS), is a member of one of the largest gene families expressed by the parasite and the role of its activity in mediating epithelial cell entry has not hitherto been understood. Here we show that the T. cruzi TS generates an eat me signal which is capable of enabling epithelial cell entry. We have utilized purified, recombinant, active (TcTS) and inactive (TcTS2V0) TS coated onto beads to challenge an epithelial cell line. We find that TS activity acts upon G protein coupled receptors present at the epithelial cell synapse with the coated bead, thereby enhancing cell entry. By so doing, we provide evidence that TS proteins bind glycans, mediate the formation of distinct synaptic domains and promote macropinocytotic uptake of microparticles into a perinuclear compartment in a manner which may emulate entosis.
doi:10.1111/tra.12078
PMCID: PMC3770925  PMID: 23601193
entosis; G-protein; host-parasite; lipid raft; trans-sialidase; Trypanosoma cruzi
4.  Predicting the Proteins of Angomonas deanei, Strigomonas culicis and Their Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family 
PLoS ONE  2013;8(4):e60209.
Endosymbiont-bearing trypanosomatids have been considered excellent models for the study of cell evolution because the host protozoan co-evolves with an intracellular bacterium in a mutualistic relationship. Such protozoa inhabit a single invertebrate host during their entire life cycle and exhibit special characteristics that group them in a particular phylogenetic cluster of the Trypanosomatidae family, thus classified as monoxenics. In an effort to better understand such symbiotic association, we used DNA pyrosequencing and a reference-guided assembly to generate reads that predicted 16,960 and 12,162 open reading frames (ORFs) in two symbiont-bearing trypanosomatids, Angomonas deanei (previously named as Crithidia deanei) and Strigomonas culicis (first known as Blastocrithidia culicis), respectively. Identification of each ORF was based primarily on TriTrypDB using tblastn, and each ORF was confirmed by employing getorf from EMBOSS and Newbler 2.6 when necessary. The monoxenic organisms revealed conserved housekeeping functions when compared to other trypanosomatids, especially compared with Leishmania major. However, major differences were found in ORFs corresponding to the cytoskeleton, the kinetoplast, and the paraflagellar structure. The monoxenic organisms also contain a large number of genes for cytosolic calpain-like and surface gp63 metalloproteases and a reduced number of compartmentalized cysteine proteases in comparison to other TriTryp organisms, reflecting adaptations to the presence of the symbiont. The assembled bacterial endosymbiont sequences exhibit a high A+T content with a total of 787 and 769 ORFs for the Angomonas deanei and Strigomonas culicis endosymbionts, respectively, and indicate that these organisms hold a common ancestor related to the Alcaligenaceae family. Importantly, both symbionts contain enzymes that complement essential host cell biosynthetic pathways, such as those for amino acid, lipid and purine/pyrimidine metabolism. These findings increase our understanding of the intricate symbiotic relationship between the bacterium and the trypanosomatid host and provide clues to better understand eukaryotic cell evolution.
doi:10.1371/journal.pone.0060209
PMCID: PMC3616161  PMID: 23560078
5.  Transcriptome analysis of Taenia solium cysticerci using Open Reading Frame ESTs (ORESTES) 
Parasites & Vectors  2009;2:35.
Background
Human infection by the pork tapeworm Taenia solium affects more than 50 million people worldwide, particularly in underdeveloped and developing countries. Cysticercosis which arises from larval encystation can be life threatening and difficult to treat. Here, we investigate for the first time the transcriptome of the clinically relevant cysticerci larval form.
Results
Using Expressed Sequence Tags (ESTs) produced by the ORESTES method, a total of 1,520 high quality ESTs were generated from 20 ORESTES cDNA mini-libraries and its analysis revealed fragments of genes with promising applications including 51 ESTs matching antigens previously described in other species, as well as 113 sequences representing proteins with potential extracellular localization, with obvious applications for immune-diagnosis or vaccine development.
Conclusion
The set of sequences described here will contribute to deciphering the expression profile of this important parasite and will be informative for the genome assembly and annotation, as well as for studies of intra- and inter-specific sequence variability. Genes of interest for developing new diagnostic and therapeutic tools are described and discussed.
doi:10.1186/1756-3305-2-35
PMCID: PMC2731055  PMID: 19646239
6.  Assessing the molecular divergence between Anopheles (Kerteszia) cruzii populations from Brazil using the timeless gene: further evidence of a species complex 
Malaria Journal  2009;8:60.
Background
Anopheles (Kerteszia) cruzii was the most important vector of human malaria in southern Brazil between 1930–1960. Nowadays it is still considered an important Plasmodium spp. vector in southern and south-eastern Brazil, incriminated for oligosymptomatic malaria. Previous studies based on the analysis of X chromosome banding patterns and inversion frequencies in An. cruzii populations from these areas have suggested the occurrence of three sibling species. In contrast, two genetically distinct groups among An. cruzii populations from south/south-east and north-east Brazil have been revealed by isoenzyme analysis. Therefore, An. cruzii remains unclear.
Methods
In this study, a partial sequence of the timeless gene (~400 bp), a locus involved in the control of circadian rhythms, was used as a molecular marker to assess the genetic differentiation between An. cruzii populations from six geographically distinct areas of Brazil.
Results
The timeless gene revealed that An. cruzii from Itaparica Island, Bahia State (north-east Brazil), constitutes a highly differentiated group compared with the other five populations from south and south-east Brazil. In addition, significant genetic differences were also observed among some of the latter populations.
Conclusion
Analysis of the genetic differentiation in the timeless gene among An. cruzii populations from different areas of Brazil indicated that this malaria vector is a complex of at least two cryptic species. The data also suggest that further work might support the occurrence of other siblings within this complex in Brazil.
doi:10.1186/1475-2875-8-60
PMCID: PMC2673228  PMID: 19358734
7.  Different serological cross-reactivity of Trypanosoma rangeli forms in Trypanosoma cruzi-infected patients sera 
Parasites & Vectors  2008;1:20.
Background
American Trypanosomiasis or Chagas disease is caused by Trypanosoma cruzi which currently infects approximately 16 million people in the Americas causing high morbidity and mortality. Diagnosis of American trypanosomiasis relies on serology, primarily using indirect immunofluorescence assay (IFA) with T. cruzi epimastigote forms. The closely related but nonpathogenic Trypanosoma rangeli has a sympatric distribution with T. cruzi and is carried by the same vectors. As a result false positives are frequently generated. This confounding factor leads to increased diagnostic test costs and where false positives are not caught, endangers human health due to the toxicity of the drugs used to treat Chagas disease.
Results
In the present study, serologic cross-reactivity between the two species was compared for the currently used epimastigote form and the more pathologically relevant trypomastigote form, using IFA and immunoblotting (IB) assays. Our results reveal an important decrease in cross reactivity when T. rangeli culture-derived trypomastigotes are used in IFA based diagnosis of Chagas disease. Western blot results using sera from both acute and chronic chagasic patients presenting with cardiac, indeterminate or digestive disease revealed similar, but not identical, antigenic profiles.
Conclusion
This is the first study addressing the serological cross-reactivity between distinct forms and strains of T. rangeli and T. cruzi using sera from distinct phases of the Chagasic infection. Several T. rangeli-specific proteins were detected, which may have potential as diagnostic tools.
doi:10.1186/1756-3305-1-20
PMCID: PMC2475519  PMID: 18611261
8.  ProtozoaDB: dynamic visualization and exploration of protozoan genomes 
Nucleic Acids Research  2007;36(Database issue):D547-D552.
ProtozoaDB (http://www.biowebdb.org/protozoadb) is being developed to initially host both genomics and post-genomics data from Plasmodium falciparum, Entamoeba histolytica, Trypanosoma brucei, T. cruzi and Leishmania major, but will hopefully host other protozoan species as more genomes are sequenced. It is based on the Genomics Unified Schema and offers a modern Web-based interface for user-friendly data visualization and exploration. This database is not intended to duplicate other similar efforts such as GeneDB, PlasmoDB, TcruziDB or even TDRtargets, but to be complementary by providing further analyses with emphasis on distant similarities (HMM-based) and phylogeny-based annotations including orthology analysis. ProtozoaDB will be progressively linked to the above-mentioned databases, focusing in performing a multi-source dynamic combination of information through advanced interoperable Web tools such as Web services. Also, to provide Web services will allow third-party software to retrieve and use data from ProtozoaDB in automated pipelines (workflows) or other interoperable Web technologies, promoting better information reuse and integration. We also expect ProtozoaDB to catalyze the development of local and regional bioinformatics capabilities (research and training), and therefore promote/enhance scientific advancement in developing countries.
doi:10.1093/nar/gkm820
PMCID: PMC2238986  PMID: 17981844
9.  The sialotranscriptome of the blood-sucking bug Triatoma brasiliensis (Hemiptera, Triatominae) 
Triatoma brasiliensis is the most important autochthon vector of Trypanosoma cruzi in Brazil, where it is widely distributed in the semiarid areas of the Northeast. In order to advance the knowledge of the salivary biomolecules of Triatominae, a salivary gland cDNA library of T. brasiliensis was mass sequenced and analyzed. Polypeptides were sequenced by HPLC/Edman degradation experiments. 1,712 cDNA sequences were obtained and grouped in 786 clusters. The housekeeping category had 24.4% and 17.8% of the clusters and sequences, respectively. The putatively secreted category contained 47.1% of the clusters and 68.2% of the sequences. Finally, 28.5% of the clusters, containing 14% of all sequences, were classified as unknown. The sialoma of T. brasiliensis showed a high amount and great variety of different lipocalins (93.8% of secreted proteins). Remarkably, a great number of serine proteases that were not observed in previous blood-sucking sialotranscriptomes were found. Nine Kazal peptides were identified, among them one with high homology to the tabanid vasodilator vasotab, suggesting that the Triatoma vasodilator could be a Kazal protein.
doi:10.1016/j.ibmb.2007.04.004
PMCID: PMC1896098  PMID: 17550826
Saliva; Transcriptome; Hematophagy; Salivary proteins; Triatoma brasiliensis
10.  Bat-transmitted Human Rabies Outbreaks, Brazilian Amazon 
Emerging Infectious Diseases  2006;12(8):1197-1202.
We describe 2 bat-transmitted outbreaks in remote, rural areas of Portel and Viseu Municipalities, Pará State, northern Brazil. Central nervous system specimens were taken after patients' deaths and underwent immunofluorescent assay and histopathologic examination for rabies antigens; also, specimens were injected intracerebrally into suckling mice in an attempt to isolate the virus. Strains obtained were antigenically and genetically characterized. Twenty-one persons died due to paralytic rabies in the 2 municipalities. Ten rabies virus strains were isolated from human specimens; 2 other cases were diagnosed by histopathologic examination. Isolates were antigenically characterized as Desmodus rotundus variant 3 (AgV3). DNA sequencing of 6 strains showed that they were genetically close to D. rotundus–related strains isolated in Brazil. The genetic results were similar to those obtained by using monoclonal antibodies and support the conclusion that the isolates studied belong to the same rabies cycle, the virus variants found in the vampire bat D. rotundus.
doi:10.3201/1208.050929
PMCID: PMC3291204  PMID: 16965697
human rabies virus, bat transmission, antigenic and genetic characterization; Brazilian Amazon
11.  Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae†  
Vasconcelos, Ana Tereza R. | Ferreira, Henrique B. | Bizarro, Cristiano V. | Bonatto, Sandro L. | Carvalho, Marcos O. | Pinto, Paulo M. | Almeida, Darcy F. | Almeida, Luiz G. P. | Almeida, Rosana | Alves-Filho, Leonardo | Assunção, Enedina N. | Azevedo, Vasco A. C. | Bogo, Maurício R. | Brigido, Marcelo M. | Brocchi, Marcelo | Burity, Helio A. | Camargo, Anamaria A. | Camargo, Sandro S. | Carepo, Marta S. | Carraro, Dirce M. | de Mattos Cascardo, Júlio C. | Castro, Luiza A. | Cavalcanti, Gisele | Chemale, Gustavo | Collevatti, Rosane G. | Cunha, Cristina W. | Dallagiovanna, Bruno | Dambrós, Bibiana P. | Dellagostin, Odir A. | Falcão, Clarissa | Fantinatti-Garboggini, Fabiana | Felipe, Maria S. S. | Fiorentin, Laurimar | Franco, Gloria R. | Freitas, Nara S. A. | Frías, Diego | Grangeiro, Thalles B. | Grisard, Edmundo C. | Guimarães, Claudia T. | Hungria, Mariangela | Jardim, Sílvia N. | Krieger, Marco A. | Laurino, Jomar P. | Lima, Lucymara F. A. | Lopes, Maryellen I. | Loreto, Élgion L. S. | Madeira, Humberto M. F. | Manfio, Gilson P. | Maranhão, Andrea Q. | Martinkovics, Christyanne T. | Medeiros, Sílvia R. B. | Moreira, Miguel A. M. | Neiva, Márcia | Ramalho-Neto, Cicero E. | Nicolás, Marisa F. | Oliveira, Sergio C. | Paixão, Roger F. C. | Pedrosa, Fábio O. | Pena, Sérgio D. J. | Pereira, Maristela | Pereira-Ferrari, Lilian | Piffer, Itamar | Pinto, Luciano S. | Potrich, Deise P. | Salim, Anna C. M. | Santos, Fabrício R. | Schmitt, Renata | Schneider, Maria P. C. | Schrank, Augusto | Schrank, Irene S. | Schuck, Adriana F. | Seuanez, Hector N. | Silva, Denise W. | Silva, Rosane | Silva, Sérgio C. | Soares, Célia M. A. | Souza, Kelly R. L. | Souza, Rangel C. | Staats, Charley C. | Steffens, Maria B. R. | Teixeira, Santuza M. R. | Urmenyi, Turan P. | Vainstein, Marilene H. | Zuccherato, Luciana W. | Simpson, Andrew J. G. | Zaha, Arnaldo
Journal of Bacteriology  2005;187(16):5568-5577.
This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.
doi:10.1128/JB.187.16.5568-5577.2005
PMCID: PMC1196056  PMID: 16077101
12.  Trypanocidal and Leishmanicidal Properties of Substitution-Containing Chalcones 
Ten chalcones were synthesized and tested as potential leishmanicidal and trypanocidal agents. All tested compounds caused concentration-dependent inhibition of the in vitro growth of Leishmania braziliensis and Trypanosoma cruzi with no significant toxic effect towards host macrophages. Our results show that the positions of the substituents seem to be critical for their antiprotozoal activities.
doi:10.1128/AAC.47.4.1449-1451.2003
PMCID: PMC152493  PMID: 12654691
13.  Salivaria or Stercoraria? The Trypanosoma rangeli dilemma 
The taxonomic status of Trypanosoma rangeli as well as the tools for its molecular characterization is briefly commented.
doi:10.1186/1475-9292-1-5
PMCID: PMC119326  PMID: 12234384

Results 1-13 (13)