Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification

[1]  C. Frey,et al.  Tritrichomonas foetus: prevalence study in naturally mating bulls in Switzerland. , 2014, Veterinary parasitology.

[2]  Indra Neil Sarkar,et al.  Drug repurposing: mining protozoan proteomes for targets of known bioactive compounds , 2014, J. Am. Medical Informatics Assoc..

[3]  J. Gookin,et al.  Twice-daily dosing of RDZ no longer recommended for treatment of intestinal Tritrichomonas foetus infection , 2014, Journal of feline medicine and surgery.

[4]  Hans-Jörg Balzer,et al.  Enteropathogen co-infection in UK cats with diarrhoea , 2014, BMC Veterinary Research.

[5]  Neil D. Rawlings,et al.  MEROPS: the database of proteolytic enzymes, their substrates and inhibitors , 2013, Nucleic Acids Res..

[6]  Relationship between 5′ UTR length and gene expression pattern in chicken , 2013, Genetica.

[7]  Po-Jung Huang,et al.  Functional profiling of the Tritrichomonas foetus transcriptome and proteome. , 2013, Molecular and biochemical parasitology.

[8]  C. Yao.  Diagnosis of Tritrichomonas foetus-infected bulls, an ultimate approach to eradicate bovine trichomoniasis in US cattle? , 2013, Journal of medical microbiology.

[9]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[10]  J. Šlapeta,et al.  Comparative analysis of Tritrichomonas foetus (Riedmüller, 1928) cat genotype, T. foetus (Riedmüller, 1928) cattle genotype and Tritrichomonas suis (Davaine, 1875) at 10 DNA loci. , 2012, International journal for parasitology.

[11]  Joaquín Dopazo,et al.  Qualimap: evaluating next-generation sequencing alignment data , 2012, Bioinform..

[12]  I. Nookaew,et al.  A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae , 2012, Nucleic acids research.

[13]  K. Osoro,et al.  High prevalence of Tritrichomonas foetus infection in Asturiana de la Montaña beef cattle kept in extensive conditions in Northern Spain. , 2012, Veterinary journal.

[14]  J. Šlapeta,et al.  Sequence differences in the diagnostic region of the cysteine protease 8 gene of Tritrichomonas foetus parasites of cats and cattle. , 2012, Veterinary parasitology.

[15]  Joachim Müller,et al.  Tritrichomonas foetus isolates from cats and cattle show minor genetic differences in unrelated loci ITS-2 and EF-1α. , 2012, Veterinary parasitology.

[16]  David S. Roos,et al.  Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy , 2012, PLoS pathogens.

[17]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[18]  L. Varuzza,et al.  A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages. , 2012, International journal for parasitology.

[19]  S. Salzberg,et al.  Repetitive DNA and next-generation sequencing: computational challenges and solutions , 2011, Nature Reviews Genetics.

[20]  D. Sept,et al.  Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites , 2011, PLoS pathogens.

[21]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[22]  R. S. Ferreira,et al.  In silico screening strategies for novel inhibitors of parasitic diseases , 2011, Expert opinion on drug discovery.

[23]  James R. Brown,et al.  Computational biology approaches for selecting host-pathogen drug targets. , 2011, Drug discovery today.

[24]  Jaideep P. Sundaram,et al.  Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome , 2010, BMC Genomics.

[25]  J. Šlapeta,et al.  Tritrichomonas foetus from domestic cats and cattle are genetically distinct. , 2010, Experimental parasitology.

[26]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[27]  J. Gookin,et al.  Documentation of in vivo and in vitro aerobic resistance of feline Tritrichomonas foetus isolates to ronidazole. , 2010, Journal of veterinary internal medicine.

[28]  I. Čepička,et al.  Critical taxonomic revision of Parabasalids with description of one new genus and three new species. , 2010, Protist.

[29]  Federico Abascal,et al.  TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations , 2010, Nucleic Acids Res..

[30]  Jun Yu,et al.  KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies , 2010, Genom. Proteom. Bioinform..

[31]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

[32]  Neil D. Rawlings,et al.  MEROPS: the peptidase database , 2009, Nucleic Acids Res..

[33]  Patricia C Babbitt,et al.  The global cysteine peptidase landscape in parasites. , 2009, Trends in parasitology.

[34]  T. Lavstsen,et al.  An Upstream Open Reading Frame Controls Translation of var2csa, a Gene Implicated in Placental Malaria , 2009, PLoS pathogens.

[35]  Eileen Kraemer,et al.  GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis , 2008, Nucleic Acids Res..

[36]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[37]  J. J. Lucas,et al.  Characterization of a cysteine protease from Tritrichomonas foetus that induces host-cell apoptosis. , 2008, Archives of biochemistry and biophysics.

[38]  M. Stephens,et al.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.

[39]  R. Bondurant,et al.  Experimental infection of cats (Felis catus) with Tritrichomonas foetus isolated from cattle. , 2008, Veterinary parasitology.

[40]  Risk factors associated with Tritrichomonas foetus infection in beef herds in the Province of Buenos Aires, Argentina. , 2008, Veterinary parasitology.

[41]  M. Gonzalo Claros,et al.  A Web Tool to Discover Full-Length Sequences - Full-Lengther , 2008, Innovations in Hybrid Intelligent Systems.

[42]  H. Stockdale,et al.  EXPERIMENTAL INFECTION OF CATTLE WITH A FELINE ISOLATE OF TRITRICHOMONAS FOETUS , 2007, The Journal of parasitology.

[43]  L. Sibley,et al.  Rhoptries: an arsenal of secreted virulence factors. , 2007, Current opinion in microbiology.

[44]  Richard D. Hayes,et al.  Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis , 2007, Science.

[45]  Christopher H. Bryant,et al.  A First Step towards Learning which uORFs Regulate Gene Expression , 2006, J. Integr. Bioinform..

[46]  Peer Bork,et al.  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..

[47]  H. Hsu,et al.  Multifarious Transcriptional Regulation of Adhesion Protein Gene ap65-1 by a Novel Myb1 Protein in the Protozoan Parasite Trichomonas vaginalis , 2006, Eukaryotic Cell.

[48]  L. Paillard,et al.  AU-rich elements and associated factors: are there unifying principles? , 2006, Nucleic acids research.

[49]  T. Fenchel.  Cosmopolitan microbes and their cryptic species , 2005 .

[50]  J. Gookin,et al.  Histologic Features Associated with Tritrichomonas foetus-induced Colitis in Domestic Cats , 2005, Veterinary pathology.

[51]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[52]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[53]  J. J. Lucas,et al.  In vitro cytopathic effects of a cysteine protease of Tritrichomonas foetus on cultured bovine uterine epithelial cells. , 2005, American journal of veterinary research.

[54]  J. J. Lucas,et al.  Identification of Trichomonas vaginalis Cysteine Proteases That Induce Apoptosis in Human Vaginal Epithelial Cells* , 2005, Journal of Biological Chemistry.

[55]  Catherine Vaquero,et al.  PfMyb1, a Plasmodium falciparum transcription factor, is required for intra-erythrocytic growth and controls key genes for cell cycle regulation. , 2005, Journal of molecular biology.

[56]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[57]  G. Garber,et al.  Treatment of Infections Caused by Metronidazole-Resistant Trichomonas vaginalis , 2004, Clinical Microbiology Reviews.

[58]  D. O. Rae,et al.  Epidemiology of Tritrichomonas foetus in beef bull populations in Florida. , 2004, Theriogenology.

[59]  Graziano Pesole,et al.  PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences , 2003, Nucleic Acids Res..

[60]  D. Klumpp,et al.  Iron and contact with host cells induce expression of adhesins on surface of Trichomonas vaginalis , 2003, Molecular microbiology.

[61]  Vasudevan Seshadri,et al.  Translational control by the 3'-UTR: the ends specify the means. , 2003, Trends in biochemical sciences.

[62]  J. Rushton,et al.  Distinct changes in gene expression induced by A-Myb, B-Myb and c-Myb proteins , 2003, Oncogene.

[63]  F. Gillin,et al.  A novel Myb‐related protein involved in transcriptional activation of encystation genes in Giardia lamblia , 2002, Molecular microbiology.

[64]  M. Van Ranst,et al.  Cattle Pathogen Tritrichomonas foetus (Riedmüller, 1928) and Pig Commensal Tritrichomonas suis (Gruby & Delafond, 1843) Belong to the Same Species , 2002, The Journal of eukaryotic microbiology.

[65]  J. Tai,et al.  Characterization of an Iron-responsive Promoter in the Protozoan Pathogen Trichomonas vaginalis * , 2002, The Journal of Biological Chemistry.

[66]  Graziano Pesole,et al.  UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002 , 2002, Nucleic Acids Res..

[67]  P. Sarnow,et al.  Internal ribosome entry sites in eukaryotic mRNA molecules. , 2001, Genes & development.

[68]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[69]  Ziheng Yang,et al.  Statistical methods for detecting molecular adaptation , 2000, Trends in Ecology & Evolution.

[70]  D. Morris,et al.  Upstream Open Reading Frames as Regulators of mRNA Translation , 2000, Molecular and Cellular Biology.

[71]  D. Hartl,et al.  Deletion of a conserved regulatory element in the Drosophila Adh gene leads to increased alcohol dehydrogenase activity but also delays development. , 2000, Genetics.

[72]  B. T. ter Kuile,et al.  The Length of the Combined 3′ Untranslated Region and Poly(A) Tail Does Not Control Rates of Glyceraldehyde-3-Phosphate Dehydrogenase mRNA Translation in Three Species of Parasitic Protists , 2000, Journal of bacteriology.

[73]  L. Corbeil,et al.  TRITRICHOMONAS FOETUS EXTRACELLULAR CYSTEINE PROTEINASE CLEAVAGE OF BOVINE IgG2 ALLOTYPES , 2000, Journal of Parasitology.

[74]  Graziano Pesole,et al.  UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs , 2000, Nucleic Acids Res..

[75]  Graziano Pesole,et al.  The Untranslated Regions of Eukaryotic MRNAs: Structure, Function, Evolution and Bioinformatic Tools for Their Analysis , 2000, Briefings Bioinform..

[76]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[77]  J. Gookin,et al.  Diarrhea associated with trichomonosis in cats. , 1999, Journal of the American Veterinary Medical Association.

[78]  G. Pesole,et al.  Internet resources for the functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs. , 1999, Trends in genetics : TIG.

[79]  J. J. Lucas,et al.  Adhesion of Tritrichomonas foetus to Bovine Vaginal Epithelial Cells , 1999, Infection and Immunity.

[80]  W Stephan,et al.  A highly conserved sequence in the 3'-untranslated region of the drosophila Adh gene plays a functional role in Adh expression. , 1999, Genetics.

[81]  G. Scheper,et al.  Regulation of translation initiation factors by signal transduction. , 1998, European journal of biochemistry.

[82]  R. Corbeil,et al.  Female Reproductive Tract Immunity in Bovine Trichomoniasis , 1998, American journal of reproductive immunology.

[83]  D. Andrews,et al.  A single nucleotide is a sufficient 5′ untranslated region for translation in an eukaryotic in vitro system , 1997, FEBS letters.

[84]  G. Brugerolle,et al.  Molecular cloning of actin genes in Trichomonas vaginalis and phylogeny inferred from actin sequences. , 1997, FEMS microbiology letters.

[85]  A. Solé-Cava,et al.  Fine structure and isozymic characterization of trichomonadid protozoa , 1997, Parasitology Research.

[86]  Natalie L. Catlett,et al.  Actin and myosin function in directed vacuole movement during cell division in Saccharomyces cerevisiae , 1996, The Journal of cell biology.

[87]  L. Corbeil,et al.  Characterization of extracellular proteinases of Tritrichomonas foetus. , 1996, The Journal of parasitology.

[88]  Robert L. Tanguay,et al.  Translational efficiency is regulated by the length of the 3' untranslated region , 1996, Molecular and cellular biology.

[89]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its new supplement TREMBL , 1996, Nucleic Acids Res..

[90]  C. Lauriano,et al.  Cloning and molecular characterization of two genes encoding adhesion proteins involved in Trichomonas vaginalis cytoadherence , 1995, Molecular microbiology.

[91]  J. McCarthy,et al.  Cytoplasmic mRNA-protein interactions in eukaryotic gene expression. , 1995, Trends in biochemical sciences.

[92]  D. E. Burgess,et al.  Cytotoxic and hemolytic effects of Tritrichomonas foetus on mammalian cells , 1990, Infection and immunity.

[93]  M. Shago,et al.  Translation of the Saccharomyces cerevisiae tcm1 gene in the absence of a 5'-untranslated leader. , 1990, Nucleic acids research.

[94]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[95]  Eugene W. Myers,et al.  Basic local alignment search tool. Journal of Molecular Biology , 1990 .

[96]  J. Rhyan,et al.  Fetal and Placental Lesions in Bovine Abortion Due to Tritrichomonas foetus , 1988, Veterinary pathology.

[97]  I. Parsonson,et al.  Early pathogenesis and pathology of Tritrichomonas foetus infection in virgin heifers. , 1976, Journal of comparative pathology.