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TriTrypDB: a functional genomic resource for the Trypanosomatidae

Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P. Brunk, Mark Carrington, Daniel P. Depledge, Steve Fischer, Bindu Gajria, Xin Gao, Malcolm J. Gardner, Alan Gingle (+32 others)
2009 Nucleic Acids Research  
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

Felipe Torres, Raúl Arias-Carrasco, José C. Caris-Maldonado, Aldina Barral, Vinicius Maracaja-Coutinho, Artur T. L. De Queiroz
2017 Database: The Journal of Biological Databases and Curation  
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

Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice (+14 others)
2009 Nucleic Acids Research  
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

Patrícia Hermes Stoco, Glauber Wagner, Carlos Talavera-Lopez, Alexandra Gerber, Arnaldo Zaha, Claudia Elizabeth Thompson, Daniella Castanheira Bartholomeu, Débora Denardin Lückemeyer, Diana Bahia, Elgion Loreto, Elisa Beatriz Prestes, Fábio Mitsuo Lima (+26 others)
2014 PLoS Neglected Tropical Diseases  
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

Denise Andréa Silva de Souza, Daniela Parada Pavoni, Marco Aurélio Krieger, Adriana Ludwig
2018 Scientific Reports  
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

Ester Poláková, Amanda T. S. Albanaz, Alexandra Zakharova, Tatiana S. Novozhilova, Evgeny S. Gerasimov, Vyacheslav Yurchenko, Hans-Peter Fuehrer
2021 PLoS Neglected Tropical Diseases  
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]

Mohd Fakharul Zaman Raja Yahya, Umi Marshida Abdul Hamid, Farida Zuraina Mohd Yusof
2012 Bioinformatics  
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

John N. Filosa, Corbett T. Berry, Gordon Ruthel, Stephen M. Beverley, Wesley C. Warren, Chad Tomlinson, Peter J. Myler, Elizabeth A. Dudkin, Megan L. Povelones, Michael Povelones, Alvaro Acosta-Serrano
2019 PLoS Neglected Tropical Diseases  
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

Monete Rajão Gomes, Ana Carolina Ramos Guimarães, Antonio Basílio de Miranda
2011 Enzyme Research  
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

Wei Wang, Duo Peng, Rodrigo P. Baptista, Yiran Li, Jessica C. Kissinger, Rick L. Tarleton, Nicolai Siegel
2021 PLoS Pathogens  
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

Larissa Catharina, Carlyle Ribeiro Lima, Alexander Franca, Ana Carolina Ramos Guimarães, Marcelo Alves-Ferreira, Pierre Tuffery, Philippe Derreumaux, Nicolas Carels
2017 Bioinformatics and Biology Insights  
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

Sandra Regina Maruyama, Luana Aparecida Rogerio, Patricia Domingues Freitas, Marta Maria Geraldes Teixeira, José Marcos Chaves Ribeiro
2021 Scientific Reports  
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

Elizabeth Ruiz-Márvez, César Augusto Ramírez, Eliana Rocío Rodríguez, Magda Mellisa Flórez, Gabriela Delgado, Fanny Guzmán, Paulino Gómez-Puertas, José María Requena, Concepción J. Puerta
2020 International Journal of Molecular Sciences  
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

Juan Felipe Osorio-Méndez, Ana María Cevallos
2019 Frontiers in Cellular and Infection Microbiology  
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

Christiane Bezerra de Araujo, Julia Pinheiro Chagas da Cunha, Davi Toshio Inada, Jeziel Damasceno, Alex Ranieri Jerônimo Lima, Priscila Hiraiwa, Catarina Marques, Evonnildo Gonçalves, Milton Yutaka Nishiyama-Junior, Richard McCulloch, Maria Carolina Elias
2020 BMC Genomics  
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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