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TriTrypDB: a functional genomic resource for the Trypanosomatidae
2009
Nucleic Acids Research
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TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation ...
and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. ...
community via TriTrypDB in advance to publication. ...
doi:10.1093/nar/gkp851
pmid:19843604
pmcid:PMC2808979
fatcat:qyypxtdzkrcelht7rbvhkok5tq
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis
2017
Database: The Journal of Biological Databases and Curation
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These data were organized in a public repository named LeishDB (www.leishdb.com), which represents an improvement on the publicly available data related to genomic annotation for L. braziliensis. ...
Moreover, we identified for the first time the repertoire of 11 243 ncRNAs belonging to different classes distributed along the genome. ...
Rubens Monte-Neto for the helpful discussions during the development of LeishDB and the preparation of this manuscript. ...
doi:10.1093/database/bax047
pmid:29220437
pmcid:PMC5502370
fatcat:5nvrydnrkngezneltah6r7rj3m
EuPathDB: a portal to eukaryotic pathogen databases
2009
Nucleic Acids Research
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While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage ...
orthology for searches across genera. ...
ACKNOWLEDGEMENTS The authors wish to acknowledge the contribution of numerous members of the eukaryotic pathogen research community, in the form of advice, suggestions and/or data-often made available ...
doi:10.1093/nar/gkp941
pmid:19914931
pmcid:PMC2808945
fatcat:wvtdhudoo5fgjiclufxahkzhuy
Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli
2014
PLoS Neglected Tropical Diseases
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We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian ...
Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) ...
Our release of the T. rangeli genome casts further light on the evolutionary origins and relationships of trypanosomes, and provides a resource for better understanding the function of genes and factors ...
doi:10.1371/journal.pntd.0003176
pmid:25233456
pmcid:PMC4169256
fatcat:ebprlwbi5jbe3k7twqrpil6r2u
Evolutionary analyses of myosin genes in trypanosomatids show a history of expansion, secondary losses and neofunctionalization
2018
Scientific Reports
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Myosins are motor proteins that comprise a large and diversified family important for a broad range of functions. ...
evolution of new genes and functions. ...
Acknowledgements We are very grateful to Maykol Adrian Noll for the support with Perl programming code and to Instituto Carlos Chagas (ICC/Fiocruz) and its graduation programme "Programa de Pós-Graduação ...
doi:10.1038/s41598-017-18865-y
pmid:29358582
pmcid:PMC5778035
fatcat:lo7tyse5ifg3haddw7vetbuhwe
Ku80 is involved in telomere maintenance but dispensable for genomic stability in Leishmania mexicana
2021
PLoS Neglected Tropical Diseases
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Telomeres are indispensable for genome stability maintenance. They are maintained by the telomere-associated protein complex, which include Ku proteins and a telomerase among others. ...
Here, we investigated a role of Ku80 in Leishmania mexicana. Leishmania is a genus of parasitic protists of the family Trypanosomatidae causing a vector-born disease called leishmaniasis. ...
Acknowledgments We thank members of our laboratories for stimulating discussions and Dr. C. Janzen (University of Wu ¨rzburg) for sharing the plasmid pSP73 bearing the telomeric probe. ...
doi:10.1371/journal.pntd.0010041
pmid:34965251
pmcid:PMC8716037
fatcat:x4k6na3vk5gzdp4nwuc2mln6am
Investigation on Nuclear Transport of Trypanosoma brucei: An in silico Approach
[chapter]
2012
Bioinformatics
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The non-redundant data set was subjected to BLASTp [11] analyses against an integrated genomic and functional genomic database for eukaryotic pathogens of the family Trypanosomatidae, TriTrypDB. ...
The identified protein sequences then were then retrieved from the TriTrypDB. A portion of protein that can evolve, function, and exist independently is called protein domain. ...
doi:10.5772/48108
fatcat:nlmmw5eqa5gehb57zuuiwzkcl4
Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites
2019
PLoS Neglected Tropical Diseases
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and the signals required for differentiation to an adherent form. ...
For each species, this includes a stage in which parasites adhere to insect tissue via a hemidesmosome-like structure. ...
Roos for input on the project. We thank Omar S. Harb for help in obtaining the KEGG gene sets from TriTrypDB. ...
doi:10.1371/journal.pntd.0007570
pmid:31356610
pmcid:PMC6687205
fatcat:gpck7gbdcbc75ayquhevaqiwci
Specific and Nonhomologous Isofunctional Enzymes of the Genetic Information Processing Pathways as Potential Therapeutical Targets for Tritryps
2011
Enzyme Research
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From public data of the Tritryps' genomes, we reconstructed the Genetic Information Processing Pathways (GIPPs). ...
We then used AnEnPi to look for the presence of these enzymes betweenHomo sapiensand Tritryps, as well as specific enzymes of the parasites. ...
Acknowledgments The authors thank CAPES, CNPq, FAPERJ, PDTIS/Fiocruz, and PAPES/Fiocruz for financial support. They are grateful to Dr. Wim Degrave for the valuable discussions and support. ...
doi:10.4061/2011/543912
pmid:21808726
pmcid:PMC3145330
fatcat:6odkp2syybb7tfyo4r264zt5ji
Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease
2021
PLoS Pathogens
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The extreme genome flexibility evident in T. cruzi also appears to create unique challenges with respect to preserving core genome functions and gene expression that sets this species apart from related ...
However, the highly repetitive nature of the genome–largely a result of these same extensive families of genes–have prevented a full understanding of the extent of gene diversity and its maintenance in ...
Benedikt Brink from Ludwig-Maximilians-Universität for advice and for testing our data in his genome phasing pipeline. ...
doi:10.1371/journal.ppat.1009254
pmid:33508020
fatcat:ec2htafezvhovgqka6bwligi5a
A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major
2017
Bioinformatics and Biology Insights
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This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary ...
Among the 40 strictly specific enzymes, we identified sterol 24-C-methyltransferase, pyruvate phosphate dikinase, trypanothione synthetase, and RNA-editing ligase as 4 essential enzymes for L major that ...
Acknowledgements The authors thank members of the Plataforma de Bioinformática Fiocruz RPT04-A/RJ for technological support and David William Provance Jr for reading and editing the manuscript. ...
doi:10.1177/1177932217712471
pmid:28638238
pmcid:PMC5470852
fatcat:ngf2vo44orb4tgtf3cl7i6ln6e
Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
2021
Scientific Reports
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The increasing number of available genomic data allowed the development of phylogenomic analytical tools. ...
Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. ...
This work utilized the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov).
Author contributions ...
doi:10.1038/s41598-021-81926-w
pmid:33589693
pmcid:PMC7884790
fatcat:d46rbinlz5acxlpxye5mgeizru
Molecular Characterization of Tc964, A Novel Antigenic Protein from Trypanosoma cruzi
2020
International Journal of Molecular Sciences
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Tc964 is annotated in the T. cruzi genome as a hypothetical protein. ...
The Tc964 protein was initially identified by its presence in the interactome associated with the LYT1 mRNAs, which code for a virulence factor of Trypanosoma cruzi. ...
A question for the future will be to establish whether a functional role is shared between the proteins SPR54 and Tc964. ...
doi:10.3390/ijms21072432
pmid:32244527
pmcid:PMC7177413
fatcat:7leecorlrzfmvhuotbt5w6zpny
Discovery and Genetic Validation of Chemotherapeutic Targets for Chagas' Disease
2019
Frontiers in Cellular and Infection Microbiology
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At the TDR Targets database, a chemogenomics resource for neglected diseases, information about published structures for these genes was only found for three of these genes, and annotation of validated ...
This review provides a streamlined approach for identifying drug targets using freely available chemogenetic databases and outlines the relevant characteristics of an ideal chemotherapeutic target. ...
TRITRYPDB AS A TOOL FOR TARGET SELECTION TriTrypDB (http://tritrypdb.org) is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both ...
doi:10.3389/fcimb.2018.00439
pmid:30666299
pmcid:PMC6330712
fatcat:xysopid7pnc3vauujb57dvm4z4
Replication origin location might contribute to genetic variability in Trypanosoma cruzi
2020
BMC Genomics
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DNA replication in trypanosomatids operates in a uniquely challenging environment, since most of their genomes are constitutively transcribed. ...
The putative origins identified in T. cruzi show a notable enrichment of GC content, a preferential position at subtelomeric regions, coinciding with genes transcribed towards the telomeres, and a pronounced ...
Acknowledgments Authors are grateful to José Franco da Silveira for grateful discussions and to Marcelo S Reis and Flavio Lichtenstein for helping with statistical analyses. ...
doi:10.1186/s12864-020-06803-8
pmid:32571205
fatcat:jnp3evc4njailj4aelcgw6mj7e
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