Genomes and Genes
Summary: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
Publications222 found, 100 shown here
- Post-transcriptional regulation of gene expression in trypanosomes and leishmaniasChristine Clayton
Zentrum für Molekualre Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
Mol Biochem Parasitol 156:93-101. 2007..Thus the regulation of gene expression is post-transcriptional. We here discuss recent results concerning the enzymes required for mRNA degradation, and components of the translation initiation machinery, and how both are regulated...
- Discovery of gene function by expression profiling of the malaria parasite life cycleKarine G Le Roch
Department of Cell Biology ICND202, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Science 301:1503-8. 2003..Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes...
- Analysis of a cation-transporting ATPase of Plasmodium falciparumM Dyer
Department of Zoology, University of Oxford, UK
Mol Biochem Parasitol 78:1-12. 1996....
- A universal framework for regulatory element discovery across all genomes and data typesOlivier Elemento
Lewis Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Mol Cell 28:337-50. 2007....
- Double-stranded RNA-mediated gene silencing of cysteine proteases (falcipain-1 and -2) of Plasmodium falciparumPawan Malhotra
International Centre for Genetic Engineering and Biotechnology, PPO Box 10504, Aruna Asaf Ali Marg, New Delhi 110 065, India
Mol Microbiol 45:1245-54. 2002..falciparum and also suggest possibilities for using RNAi as an effective tool to determine the functions of the genes identified from the P. falciparum genome sequencing project...
- TcUBP-1, a developmentally regulated U-rich RNA-binding protein involved in selective mRNA destabilization in trypanosomesA C Frasch
, , Universidad Nacional de General San Martin, 1650 San Martin, Provincia de Buenos Aires, Argentina
J Biol Chem 276:34801-9. 2001..Because TcUBP-1 is developmentally regulated, it might have a relevant role in regulating protein expression during trypanosome differentiation, allowing a correct expression pattern of U-rich-containing mRNAs...
- The genome of the kinetoplastid parasite, Leishmania majorAlasdair C Ivens
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
Science 309:436-42. 2005..Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression...
- Structural basis for double-stranded RNA processing by DicerIan J Macrae
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Science 311:195-8. 2006..The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end...
- U1 small nuclear RNP from Trypanosoma brucei: a minimal U1 snRNA with unusual protein componentsZsofia Palfi
Institut fur Biochemie, Justus Liebig Universität Giessen Heinrich Buff Ring 58, D 35392 Giessen, Germany
Nucleic Acids Res 33:2493-503. 2005..These data result in a model of the trypanosome U1 snRNP, which deviates substantially from our classical view of the U1 particle and may reflect the special requirements for splicing of a small set of cis-introns in trypanosomes...
- A surface transporter family conveys the trypanosome differentiation signalSamuel Dean
Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
Nature 459:213-7. 2009..As well as being molecular transducers of the differentiation signal in these parasites, PAD proteins provide the first example of a surface marker able to discriminate the transmission stage of trypanosomes in their mammalian host...
- Evolution of RNA editing in trypanosome mitochondriaL Simpson
Howard Hughes Medical Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
Proc Natl Acad Sci U S A 97:6986-93. 2000..The possible evolutionary relationship of the C to U and U-insertion editing systems is discussed...
- Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea:Entodiniomorphida) inferred from small subunit ribosomal RNA sequencesA D Wright
Department of Zoology, College of Biological Science, University of Guelph, Ontario, Canada
J Eukaryot Microbiol 44:61-7. 1997..The litostomes (Class Litostomatea), consisting of the haptorians and the rumen ciliates, are also a monophyletic group...
- Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa)David Bass
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Int J Syst Evol Microbiol 54:2393-404. 2004..Although Metromonas groups with weak to moderate support with Chlorarachnea, it is here placed in superclass Monadofilosa, to which it is morphologically more similar...
- Substitutional editing of transcripts from genes of cyanobacterial origin in the dinoflagellate Ceratium horridumStefan Zauner
Cell Biology, Philipps University Marburg, Karl von Frisch Strasse, D 35032 Marburg, Germany
FEBS Lett 577:535-8. 2004....
- A complex organization of the gene encoding cytochrome oxidase subunit 1 in the mitochondrial genome of the dinoflagellate, Crypthecodinium cohnii: homologous recombination generates two different cox1 open reading framesJ E Norman
Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Room 8F-2, Tupper Medical Building, 5859 University Avenue, Halifax, Nova Scotia B3H 4H7, Canada
J Mol Evol 53:351-63. 2001..Such recombining repeats are a characteristic feature of plant (angiosperm) mtDNA, but they have not previously been described in the mitochondrial genomes of protists...
- Naturally acquired Plasmodium knowlesi malaria in human, ThailandSomchai Jongwutiwes
Chulalongkorn University, Bangkok, Thailand
Emerg Infect Dis 10:2211-3. 2004..The occurrence of simian malaria in human has signified the roles of wild primate populations in disease transmission in some malaria-endemic areas...
- Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two speciesAnnie Rochette
Research Centre in Infectious Diseases, CHUL Research Centre and Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
BMC Genomics 9:255. 2008....
- A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analysesNeil Hall
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Science 307:82-6. 2005..We observed posttranscriptional gene silencing through translational repression of messenger RNA during sexual development, and a 47-base 3' untranslated region motif is implicated in this process...
- Regulation of sexual development of Plasmodium by translational repressionGunnar R Mair
Department of Parasitology, Leiden University Medical Centre, 2333 ZA Leiden, Netherlands
Science 313:667-9. 2006..Genetic disruption of pbdozi inhibits the formation of the ribonucleoprotein complexes, and instead, at least 370 transcripts are diverted to a degradation pathway...
- A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophaseKazufumi Mochizuki
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Genes Dev 19:77-89. 2005..Dcl1p also is required for proper mitotic and meiotic segregation of micronuclear chromosomes and for normal chromosome alignment in meiotic prophase, suggesting that DCL1 has multiple functions in regulating chromosome dynamics...
- tbCPSF30 depletion by RNA interference disrupts polycistronic RNA processing in Trypanosoma bruceiEdward F Hendriks
School of Biological Sciences, Division of Biochemistry, 2 205 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
J Biol Chem 278:26870-8. 2003..This study is the first to identify and characterize a core component of the T. brucei CPSF and show its involvement in polycistronic RNA processing...
- miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtiiAttila Molnar
Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK
Nature 447:1126-9. 2007..The common features of miRNAs and siRNAs in an alga and in higher plants indicate that complex RNA-silencing systems evolved before multicellularity and were a feature of primitive eukaryotic cells...
- Analysis of short RNAs in the malaria parasite and its red blood cell hostTina Rathjen
School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
FEBS Lett 580:5185-8. 2006..Interestingly, mir-451 was not detectable in a series of immortalised cell lines representing progenitor stages of all major blood lineages, suggesting that mir-451 may play a role in the differentiation of erythroid cells...
- Polyadenylated transcripts containing random gene fragments are expressed in dinoflagellate mitochondriaHélène Chaput
Departement de sciences biologiques, Universite de Montreal, Canada
Protist 153:111-22. 2002..Gene fragments or multiple copies of the cox3 and cob sequences may be abundant in the mitochondrial genome since Southern blots, using these sequences separately as probes, show multiple restriction fragments with several enzymes...
- RNA polymerase I transcribes procyclin genes and variant surface glycoprotein gene expression sites in Trypanosoma bruceiARTHUR GUNZL
Medizinisch Naturwissenschaftliches Forschungsinstitut der Universität Tübingen, 72074 Tubingen, Germany
Eukaryot Cell 2:542-51. 2003..Our studies unequivocally show that T. brucei harbors a multifunctional RNA pol I which, in addition to transcribing rDNA, transcribes procyclin genes and VSG gene expression sites...
- Genomic organization and gene expression in a chromosomal region of Leishmania majorSéverine Monnerat
Department of Biochemistry, University of Lausanne, Ch des Boveresses 155, 1066 Epalinges, Switzerland
Mol Biochem Parasitol 134:233-43. 2004..In conclusion, the transcriptional organization of the Leishmania genome is complex, raising the possibility that computer predictions may not be comprehensive...
- Targeted disruption of expression site-associated gene-1 in bloodstream-form Trypanosoma bruceiV B Carruthers
Laboratory of Molecular Parasitology, Rockefeller University, New York, NY 10021 6399, USA
Mol Biochem Parasitol 81:65-79. 1996..We have therefore been unable to determine whether esag1 is an essential gene, or what function it fulfils, or whether any competent Esag1 protein is expressed in the mutant trypanosomes...
- Developmentally regulated instability of the GPI-PLC mRNA is dependent on a short-lived protein factorHelena Webb
Department of Biochemistry 80 Tennis Court Road, Cambridge CB2 1GA, UK
Nucleic Acids Res 33:1503-12. 2005..Thus, the effect of protein synthesis inhibitors in stabilizing the GPI-PLC mRNA operates in trans through a short-lived factor dependent on protein synthesis...
- Variable var transition rates underlie antigenic variation in malariaPaul Horrocks
Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
Proc Natl Acad Sci U S A 101:11129-34. 2004..These findings have important implications for both the underlying molecular mechanisms of antigenic variation and the processes that promote chronicity of infection in vivo...
- The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomesClaudio H Slamovits
Department of Botany, University of British Columbia, Vancouver, BC, Canada
J Mol Biol 372:356-68. 2007..Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes...
- High diversity and rapid changeover of expressed var genes during the acute phase of Plasmodium falciparum infections in human volunteersJennifer Peters
Malaria Laboratory, Infectious Diseases Unit, Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Queensland 4029, Australia
Proc Natl Acad Sci U S A 99:10689-94. 2002....
- Characterization of a candidate Trypanosoma brucei U1 small nuclear RNA geneA Djikeng
Department of Internal Medicine, Yale University School of Medicine, PO Box 208022, 333 Cedar Street, New Haven, CT 06520-8022, USA
Mol Biochem Parasitol 113:109-15. 2001....
- Architecture of telomerase RNAA Bhattacharyya
Department of Microbiology and Immunology, University of California, San Francisco 94143
EMBO J 13:5721-31. 1994....
- Editing site recognition and nucleotide insertion are separable processes in Physarum mitochondriaElaine M Byrne
Center for RNA Molecular Biology, Case Western Reserve University, 2109 Adelbert Road, School of Medicine, Cleveland, OH 44106, USA
EMBO J 21:6154-61. 2002....
- Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondriaRyoma Kamikawa
Laboratory of Marine Microbiology, Division of Applied Biosciences, Department of Agriculture, Kyoto University, Kyoto 606 8502, Japan
Protist 158:239-45. 2007..However, current sequence data on dinoflagellate mitochondria are insufficient to reject the alternative scenario, in which the rRNA fragmentation evolved independently in apicomplexan and dinoflagellate mitochondria...
- Phylogenetic relationships amongst tetrahymenine ciliates inferred by a comparison of telomerase RNAsAmanda J Ye
Department of Pharmacology, Medical School, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA
Int J Syst Evol Microbiol 52:2297-302. 2002..The tetrahymenine phylogeny derived from distance analysis of TER sequences is largely consistent with those based on rRNA and histone sequences...
- Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysisKausik Chakrabarti
Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
RNA 13:1923-39. 2007..These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts...
- Toxoplasma gondii asexual development: identification of developmentally regulated genes and distinct patterns of gene expressionMichael D Cleary
Department of Microbiology and Immunology, Stanford University, Stanford, California 94305 5124, USA
Eukaryot Cell 1:329-40. 2002..This analysis permits the first in-depth look at changes in gene expression during development of this complex protozoan parasite...
- Genomic and proteomic expression analysis of Leishmania promastigote and amastigote life stages: the Leishmania genome is constitutively expressedKirk Leifso
Immunity and Infection Research Centre, Vancouver Coastal Health Research Institute, Canada
Mol Biochem Parasitol 152:35-46. 2007..The differential expression was validated by the identification of previously reported stage specific proteins and identified several amastigote and promastigote novel stage specific proteins...
- Virulence of malaria is associated with differential expression of Plasmodium falciparum var gene subgroups in a case-control studyMirjam Kaestli
Swiss Tropical Institute, Basel, Switzerland
J Infect Dis 193:1567-74. 2006..Furthermore, parasites forming rosettes showed a significant up-regulation of var group A transcripts...
- Developmental regulation of gene expression in trypanosomatid parasitic protozoaSimon Haile
Research Centre in Infectious Diseases, CHUL Research Centre of Laval University, CHUQ, 2705 Laurier Blvd, Quebec, QC, Canada G1V 4G2
Curr Opin Microbiol 10:569-77. 2007..Several of these developments have greatly benefited from the recently completed genomic sequences and functional genomic studies...
- Crystal structure of a group I ribozyme domain: principles of RNA packingJ H Cate
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Science 273:1678-85. 1996..Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome...
- The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparumRowena E Martin
School of Biochemistry and Molecular Biology, Faculty of Science, The Australian National University, Canberra, ACT 0200, Australia
Genome Biol 6:R26. 2005....
- A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modificationXue Hai Liang
Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
RNA 11:619-45. 2005..The large repertoire of modifications and guide RNAs in trypanosomes suggests that these modifications possibly play a central role in these parasites...
- A role for the exosome in the in vivo degradation of unstable mRNAsSimon Haile
Zentrum für Molekulare Biologie de Universität Heidelberg ZMBH, D 69120 Heidelberg, Germany
RNA 9:1491-501. 2003..We conclude that the exosome is required for the initiation of rapid degradation of unstable mRNAs in trypanosomes...
- Expressed sequence tag analysis of the dinoflagellate Lingulodinium polyedrum during dark phaseNaomi Tanikawa
Japan Science and Technology Agency PRESTO, Light and Control, Osaka, Japan
Photochem Photobiol 80:31-5. 2004..These cDNA clones and EST sequence data should provide a powerful resource for future genome-wide functional analyses for uncharacterized genes...
- Identification of the first trypanosome H/ACA RNA that guides pseudouridine formation on rRNAX H Liang
Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
J Biol Chem 276:40313-8. 2001..Mapping of the pseudouridine site indicated that the predicted U is indeed modified. However, in contrast to all H/ACA RNAs, h1 consists of a single hairpin structure and is the shortest H/ACA RNA described so far...
- Annealing of RNA editing substrates facilitated by guide RNA-binding protein gBP21U F Muller
Department of Microbiology and Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
EMBO J 20:1394-404. 2001..The data suggest a factor-like contribution of gBP21 to the RNA editing process by accelerating the rate of gRNA-pre-mRNA anchor formation...
- A filter paper method for the detection of Plasmodium falciparum gametocytes by reverse transcription polymerase chain reactionGodfree Mlambo
Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
Am J Trop Med Hyg 78:114-6. 2008..This assay will greatly facilitate bulk analysis of gametocyte RNA transcripts on filter paper, especially in areas where collection and preservation of liquid blood is not feasible...
- Temporal order of RNA-processing reactions in trypanosomes: rapid trans splicing precedes polyadenylation of newly synthesized tubulin transcriptsE Ullu
Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510 8056
Mol Cell Biol 13:720-5. 1993..Thus, trans splicing is cotranscriptional. In addition, we show that trans splicing precedes polyadenylation in the processing of trypanosome tubulin pre-mRNAs...
- Cloning and characterization of two guide RNA-binding proteins from mitochondria of Crithidia fasciculata: gBP27, a novel protein, and gBP29, the orthologue of Trypanosoma brucei gBP21D Blom
Department of Biochemistry, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
Nucleic Acids Res 29:2950-62. 2001..Together, these results suggest that the proteins are part of a large macromolecular complex(es). We infer that gBP29 and gBP27 are components of the C.fasciculata editing machinery that may interact with gRNAs...
- Identification of Leishmania selenoproteins and SECIS elementA Cassago
Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Caixa Postal 369, 13560 590 São Carlos, SP, Brazil
Mol Biochem Parasitol 149:128-34. 2006..To our knowledge this is the first report on the identification of selenocysteine insertion machinery in Kinetoplastida, more specifically in Leishmania, at the sequence level...
- Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lambliaMalin E L Weiland
Microbiology and Tumor Biology Center, Karolinska Institutet, Stockholm, Sweden
Int J Parasitol 35:617-26. 2005..These localisation experiments suggest alpha-giardins play a role in cell motility, attachment and membrane stability...
- Plasmodium berghei: analysis of the gamma-glutamylcysteine synthetase gene in drug-resistant linesJosé Pérez-Rosado
Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, San Juan 00936 5067, USA
Exp Parasitol 101:175-82. 2002..berghei with different drug resistance profiles. This work suggests a link between increased GSH levels and drug resistance in Plasmodium...
- A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparumKarine G Le Roch
Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA
BMC Genomics 9:513. 2008..Here we have employed transcriptome and proteome profiling analyses to characterize the global response of P. falciparum to T4 during the intraerythrocytic cycle of this parasite...
- Transcription in kinetoplastid protozoa: why be normal?David A Campbell
Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, 609 Charles E Young Drive East, Los Angeles, CA 90095 1489, USA
Microbes Infect 5:1231-40. 2003..Here, we present a broad overview of what is known about transcription in the kinetoplastids and what has yet to be determined...
- Characterisation of a new Leishmania META gene and genomic analysis of the META clusterCamila S Ramos
Department of Parasitology, Institute of Biomedical Sciences, Universidade de Sao Paulo, São Paulo 05508 900 SP, Brazil
FEMS Microbiol Lett 238:213-9. 2004....
- Trypanosome spliced leader RNA genes contain the first identified RNA polymerase II gene promoter in these organismsG Gilinger
Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
Nucleic Acids Res 29:1556-64. 2001..We show here that the in vitro transcription extract contains a binding activity that is specific for the initiator element and thus may participate in recruiting RNA polymerase II to the SL RNA gene promoter...
- Evolutionary relatedness of some primate models of PlasmodiumA P Waters
Laboratorium voor Parasitologie, Universiteit te Leiden, The Netherlands
Mol Biol Evol 10:914-23. 1993..What is considered to be the most ancient of the human malaria pathogens, P. malariae, was also included in the analysis and does not group at all with other simian or human parasites...
- Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 5'-cap structureAugusto Simoes-Barbosa
Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095 1489, USA
RNA 14:1617-31. 2008..Despite the lack of a cap structure, U1, U2, U4, and U5 genes are transcribed by RNA polymerase II, whereas the U6 gene is transcribed by RNA polymerase III...
- Analysis of the Leishmania donovani transcriptome reveals an ordered progression of transient and permanent changes in gene expression during differentiationA Saxena
Seattle Biomedical Research Institute, 307 Westlake Avenue N, Seattle, WA 98109 5219, USA
Mol Biochem Parasitol 152:53-65. 2007..This paper provides the first genome-scale quantitative analysis of gene expression during the transition from promastigotes to amastigotes and demonstrates the utility of the host-free differentiation system...
- Genomic organization and expression of the expanded SCG/L/R gene family of Leishmania major: internal clusters and telomeric localization of SCGs mediating species-specific LPG modificationsDeborah E Dobson
Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
Mol Biochem Parasitol 146:231-41. 2006..Potentially, telomeric localization of SCG genes may function primarily to facilitate gene conversion and the elaboration of functional evolutionary diversity in the degree of PG sc-galactosylation observed in other strains of L. major...
- The complex repeats of Dictyostelium discoideumG Glockner
IMB Jena, Department of Genome Analysis, D 07745 Jena, Germany
Genome Res 11:585-94. 2001..All elements show insertion preference into loci in which other elements of the same family reside. The analysis of the complex repeats is a valuable data resource for the ongoing assembly of whole D. discoideum chromosomes...
- Identification of species and sources of Cryptosporidium oocysts in storm waters with a small-subunit rRNA-based diagnostic and genotyping toolL Xiao
Division of Parasitic Diseases, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, USA
Appl Environ Microbiol 66:5492-8. 2000..Thus, this technique provides an alternative method for the detection and differentiation of Cryptosporidium parasites in environmental samples...
- A 100-kD complex of two RNA-binding proteins from mitochondria of Leishmania tarentolae catalyzes RNA annealing and interacts with several RNA editing componentsRuslan Aphasizhev
Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles 90095, USA
RNA 9:62-76. 2003..The Ltp26/Ltp28 RNP complex is a candidate for catalyzing the annealing of guide RNA and pre-edited mRNA in the initial step of RNA editing...
- Messenger RNA processing sites in Trypanosoma bruceiCorinna Benz
Zentrum fur Molekulare Biologie, Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
Mol Biochem Parasitol 143:125-34. 2005..The data from the genome analysis and the program are available from: ...
- A stem-loop of Tetrahymena telomerase RNA distant from the template potentiates RNA folding and telomerase activityJ M Sperger
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
Biochemistry 40:7005-16. 2001..Thus an RNA element far from the template makes a major contribution to Tetrahymena telomerase enzyme activity...
- In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteinsJohanna P Daily
Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115, USA
J Infect Dis 191:1196-203. 2005....
- PfMyb1, a Plasmodium falciparum transcription factor, is required for intra-erythrocytic growth and controls key genes for cell cycle regulationMathieu Gissot
INSERM U511, CHU Pitie Salpetriere, 91 Boulevard de l Hopital, 75013 Paris, France
J Mol Biol 346:29-42. 2005..This study provides the first evidence of a regulation network involving a Plasmodium transcription factor...
- Regulated expression of glycosomal phosphoglycerate kinase in Trypanosoma bruceiClaudia Colasante
Zentrum für Molekulare Biologie der Universität Heidelberg ZMBH, Im Neuenheimer Feld 282, D 69120 Heidelberg, Germany
Mol Biochem Parasitol 151:193-204. 2007..We also found that production of mRNAs using T7 polymerase can affect the apparent half-life, and that large amounts of CAT enzyme may be toxic in trypanosomes...
- MicroRNA switches in Trypanosoma bruceiBibekanand Mallick
Computational Biology Group, Indian Association for the Cultivation of Science, 2A and 2B, Raja S C Mullick Road, Jadavpur, Calcutta 700 032, India
Biochem Biophys Res Commun 372:459-63. 2008..2 corresponding to these clustered miRNAs play essential role in trypanosomiasis. These snippets can act as genetic switches modulating host-parasite interaction and provide useful clue toward treatment of trypanosomiasis...
- Comparative whole genome transcriptome analysis of three Plasmodium falciparum strainsManuel Llinas
Department of Molecular Biology, Lewis Sigler Institute for Integrative Genomics, Princeton University, 246 Carl Icahn Laboratory, Princeton, NJ 08544, USA
Nucleic Acids Res 34:1166-73. 2006..The majority of these genes are uncharacterized and have no homology to other species. These tractable transcriptional differences provide important phenotypes for these otherwise highly related strains of Plasmodium...
- A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst proteinBarbara J Davids
Department of Pathology, Division of Infectious Diseases, University of California, San Diego, California, United States of America
PLoS ONE 1:e44. 2006..HCNCp and the other HCMp provide a rich source for developing parasite-specific diagnostic reagents, vaccine candidates, and subjects for further research into Giardia biology...
- A novel protein kinase family in Plasmodium falciparum is differentially transcribed and secreted to various cellular compartments of the host cellMarta C Nunes
Unité de Biologie des Interactions Hôte Parasite, Institut Pasteur, CNRS, 75724 Paris, France
Mol Microbiol 63:391-403. 2007..Our data suggest a role of FIKK proteins in the remodelling of the erythrocyte surface and reveal the existence of an adaptable parasite system able to sense intra- and possibly extracellular changes...
- Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes, lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicanaTimothy R Holzer
Purdue University, Department of Biochemistry, West Lafayette, IN 47907 2063, USA
Mol Biochem Parasitol 146:198-218. 2006..Leishmania may represent an alternative paradigm for eukaryotic differentiation with minimal contributions from changes in mRNA abundance...
- Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasitesMiranda S M Oakley
Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases NIH, Rockville, MD 20892, USA
Infect Immun 75:2012-25. 2007..These studies enhance the possibility of designing vaccines and drugs on the basis of disruption in molecules and pathways of parasite survival and virulence activated in response to febrile temperatures...
- Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stageRichard Bishop
The International Livestock Research Institute ILRI, PO Box 30709, Nairobi, Kenya
Nucleic Acids Res 33:5503-11. 2005..The data suggests a low level of baseline transcription from the majority of protein-coding genes...
- Systematic study of sequence motifs for RNA trans splicing in Trypanosoma bruceiT Nicolai Siegel
Laboratory of Molecular Parasitology, Box 185, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Mol Cell Biol 25:9586-94. 2005..These findings should assist in the development of improved algorithms for computationally identifying a 3'SS and help to discriminate noncoding open reading frames from true genes in current efforts to annotate the T. brucei genome...
- Small sense and antisense RNAs derived from a telomeric retroposon family in Giardia intestinalisElisabetta Ullu
Department of Internal Medicine, Yale Medical School, BCMM 136D, 295 Congress Avenue, Box 9812, New Haven, CT 06536 8012, USA
Eukaryot Cell 4:1155-7. 2005..These small RNAs may contribute to silencing GilT expression via the RNA interference pathway...
- Plasmodium falciparum: genome wide perturbations in transcript profiles among mixed stage cultures after chloroquine treatmentAnusha M Gunasekera
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard University, Boston, MA 02115, USA
Exp Parasitol 117:87-92. 2007..Molecular Microbiology 50, 1229-1239]. These findings are important to report, given the striking contrast to similar studies in other model eukaryotic organisms...
- Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycleJennifer L Shock
Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street, San Francisco, California 94158 2330, USA
Genome Biol 8:R134. 2007..Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression...
- Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalisXiaowei Sylvia Chen
Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand
Nucleic Acids Res 35:4619-28. 2007..Subsequent computational analysis has revealed additional putative C/D-box snoRNAs. Our results will lead towards a future understanding of RNA metabolism in the deep-branching eukaryote Giardia, as more ncRNAs are characterized...
- Transcriptome analysis of antigenic variation in Plasmodium falciparum--var silencing is not dependent on antisense RNAStuart A Ralph
Institut Pasteur, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2581, F 75724 Paris Cedex 15, France
Genome Biol 6:R93. 2005..To investigate transcriptional features of this mechanism, we conducted a microarray analysis of parasites that were selected to express different var genes by adhesion to chondroitin sulfate A (CSA) or CD36...
- Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma bruceiSarah Kabani
Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, King s Buildings, University of Edinburgh, Edinburgh, UK
BMC Genomics 10:427. 2009..These developmental events are highly regulated, temporally reproducible and accompanied by expression changes mediated almost exclusively at the post-transcriptional level...
- Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma bruceiJurgen R Haanstra
Vrije Universiteit, BioCentrum Amsterdam, De Boelelaan 1085, Amsterdam, The Netherlands
J Biol Chem 283:2495-507. 2008..Yet regulation of mRNA levels does not occur by transcription, but by adjusting mRNA degradation. The contribution of splicing to regulation is negligible, as for all cases where splicing is faster than RNA precursor degradation...
- A selenocysteine tRNA and SECIS element in Plasmodium falciparumTobias Mourier
RNA 11:119-22. 2005..To our knowledge, this is the first report of an identification of protozoan selenocysteine insertion machinery at the sequence level...
- A study of var gene transcription in vitro using universal var gene primersH M Taylor
Institute of Molecular Medicine, Nuffield Department of Medicine, John Radcliffe Hospital, Headington, Oxford, UK
Mol Biochem Parasitol 105:13-23. 2000..In addition, we demonstrate that the choice of primers used for RT-PCR is crucial in data interpretation...
- Identification of stage-regulated and differentiation-enriched transcripts during transformation of the African trypanosome from its bloodstream to procyclic formK R Matthews
University of Manchester, UK
Mol Biochem Parasitol 95:81-95. 1998....
- TashHN, a Theileria annulata encoded protein transported to the host nucleus displays an association with attenuation of parasite differentiationDavid G Swan
Department of Veterinary Parasitology, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK
Cell Microbiol 5:947-56. 2003..In addition, analyses of multiple cell lines that have become severely attenuated in their potential to differentiate, indicated a substantial increase in TashHN expression, with host nuclear reactivity particularly enhanced...
- Regulated transcription of the histone H2B genes of Trypanosoma bruceiJ A García-Salcedo
Laboratory of Molecular Parasitology, Department of Molecular Biology, Free University of Brussels, Belgium
Eur J Biochem 264:717-23. 1999..Addition of hydroxyurea to procyclic forms in culture specifically decreased H2B mRNA levels by about twofold, an effect not linked to its 3' untranslated region. Inhibition of protein synthesis prevented this decrease...
- Role of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editingRobert P Igo
Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
Eukaryot Cell 1:112-8. 2002..ExoUase is stereospecific and cannot remove (Rp)alpha-thio-U. The specificity of the exoUase activity thus contributes to the precision of RNA editing...
- 3' UTR elements enhance expression of Pgs28, an ookinete protein of Plasmodium gallinaceumL M Golightly
Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
Mol Biochem Parasitol 105:61-70. 2000..The U-rich element and fifth eukaryotic polyadenylation consensus sequence within the pgs28 3' UTR are therefore necessary for Pgs28 protein expression...
- The two RNA ligases of the Trypanosoma brucei RNA editing complex: cloning the essential band IV gene and identifying the band V geneL N Rusché
Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Mol Cell Biol 21:979-89. 2001..The band IV and band V RNA ligases of the RNA editing complex therefore serve different functions. We also identified the gene for band V RNA ligase, a protein much more homologous to band IV than to other known ligases...
- An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma bruceiA Schnaufer
Seattle Biomedical Research Institute, Seattle, WA 98109, USA
Science 291:2159-62. 2001..The editing complex, which is present in all kinetoplastid parasites, may thus be a chemotherapeutic target...
- RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAsA Djikeng
Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520-8022, USA
RNA 7:1522-30. 2001..We speculate that RNAi in trypanosomes serves a housekeeping function and is likely to be involved in silencing retroposon transcripts...
- RNA editing in kinetoplastid protozoaK Stuart
Seattle Biomedical Research Institute, Washington 98109 1651, USA
Microbiol Mol Biol Rev 61:105-20. 1997..The origin of editing, its developmental regulation which helps control the switching between terminal respiratory systems during the life cycle of trypanosomes, and other areas for future study are discussed...
- Divergent regulation of dihydrofolate reductase between malaria parasite and human hostKai Zhang
Department of Biology, The Catholic University of America, Washington, DC 20064, USA
Science 296:545-7. 2002..Thus, antifolate treatment does not relieve translational inhibition and parasites cannot replenish dead enzyme...
- Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarrayZbynek Bozdech
Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143 0448, USA
Genome Biol 4:R9. 2003..The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development...
- Mechanisms underlying the evolution and maintenance of functionally heterogeneous 18S rRNA genes in ApicomplexansAlejandro P Rooney
Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U S Department of Agriculture, Peoria, Illinois, USA
Mol Biol Evol 21:1704-11. 2004..This represents the first case in which an rRNA gene family has been found to evolve under the birth-and-death model...
- Expression of a major surface protein of Trypanosoma brucei insect forms is controlled by the activity of mitochondrial enzymesErik Vassella
Institute of Cell Biology, University of Bern, CH 3012 Bern, Switzerland
Mol Biol Cell 15:3986-93. 2004..Our results reveal a new mechanism by which expression of a surface glycoprotein is controlled by the activity of mitochondrial enzymes...
- A selenoprotein in the plant kingdom. Mass spectrometry confirms that an opal codon (UGA) encodes selenocysteine in Chlamydomonas reinhardtii gluththione peroxidaseLian Hai Fu
Department of Fruit Tree Breeding and Molecular Genetics, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel
J Biol Chem 277:25983-91. 2002..Thus, our data present the first direct proof that a UGA opal codon is decoded in the plant kingdom to incorporate selenocysteine...
- Novel Anti-Malarials by Combinatorial PharmacogenomicsJoseph DeRisi; Fiscal Year: 2006..The compiled relationships from known anti-malarials, novel quinolines, and toxicology will then be used to guide and optimize additional synthesis efforts toward the ultimate goal of producing effective therapeutics. ..
- Allosteric DNAzyme sensors for practical detection of mycotoxinsSCOTT SILVERMAN; Fiscal Year: 2007..Improved sensors for detecting mycotoxins and thereby revealing the presence of fungi will allow proper remedial actions to be taken. [unreadable] [unreadable] [unreadable]..
- Drug resistance in Plasmodium falciparumJohanna Daily; Fiscal Year: 2007..abstract_text> ..
- 2006 Biology of Host-Parasite Interactions Gordon Research ConferenceElisabetta Ullu; Fiscal Year: 2006..Host-Cell Invasion (Discussion Leader: Barbara Burleigh: Harvard) Trichomonads and Amoebae (Discussion Leader: Patricia Johnson, UCLA) Parasite Membrane Biology (Discussion Leader: Scott Landfear: University of Oregon) ..
- Nucleic Acids Gordon Research ConferenceSCOTT STROBEL; Fiscal Year: 2006..Considerable time is allotted for discussion following formal lectures. Poster sessions and optional recreational activities will stimulate informal interactions. [unreadable] [unreadable] [unreadable] [unreadable]..
- 2006 Thiol-based Redox Regulation and Signaling Gordon Research ConferenceVADIM GLADYSHEV; Fiscal Year: 2006..A diverse mix of established and emerging leaders in the field, and of junior and senior investigators will be included in the program. [unreadable] [unreadable] [unreadable]..
- Development of a cell-based method for high-throughput drug screening in malaria Liwang Cui; Fiscal Year: 2008..To facilitate antimalarial drug discovery, we propose to develop a highly sensitive, cell-based, one-step luminescent drug screen assay for high throughput screening of large chemical libraries. [unreadable] [unreadable] [unreadable]..
- RNA METABOLISM IN TRYPANOSOMESElisabetta Ullu; Fiscal Year: 2009..3. Further characterize the RNAi pathway in terms of its components and how the interaction of TbAGO1 with translating ribosomes is brought about. ..
- RATIONAL DESIGN TOOLS FOR ANTISENSE NUCLEIC ACIDSYe Ding; Fiscal Year: 2007..In the post-genomic era, the availability of the software and the Web server will substantially facilitate applications of antisense nucleic acids in high throughput functional genomics. ..
- GENETIC ANALYSIS OF PURINE METABOLISM IN LEISHMANIA DONOBuddy Ullman; Fiscal Year: 2007..coli that overexpress hgprt genes, and[unreadable] intact parasites. ..
- Biology of Host-Parasite Interactions 2008 Gordon Research ConferenceElisabetta Ullu; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- Automated Macromolecular Crystallization SystemJEFFREY KIEFT; Fiscal Year: 2007..Cost savings. Cost of crystallization trials will decrease due to the use of smaller amounts of reagents, including solutions and protein/RNA samples. [unreadable] [unreadable] [unreadable]..
- Development of tools for structural genomics of viral RNAJEFFREY KIEFT; Fiscal Year: 2008..By solving the structures of these RNAs, we will inform and enable new strategies for developing therapeutics aimed at curing viral disease. [unreadable] [unreadable] [unreadable]..
- Complement mediated lysis resistance genes of LeishmaniaJEFFREY BEETHAM; Fiscal Year: 2008..abstract_text> ..
- USING THE CHEMISTRY OF IRON(II) TO STUDY DNA STRUCTURETHOMAS TULLIUS; Fiscal Year: 2002..The high resolution and structural sensitivity of the hydroxyl radical will be used to determine structural details of these DNA molecules in solution. ..
- Structure and function of SRP RNAChristian Zwieb; Fiscal Year: 2006..These studies will focus on the specific features of two critical interactions and define their dynamic relationship to SRP function. [unreadable] [unreadable]..
- Redox mechanism of cancer prevention by seleniumVADIM GLADYSHEV; Fiscal Year: 2002..These approaches should yield insight into the mechanism of the anticancer effect of selenium and may lead to the identification of human cancers most susceptible to selenium chemoprevention. ..
- FOOTPRINTING WITH IRON (II)-GENERATED HYDROXYL RADICALTHOMAS TULLIUS; Fiscal Year: 2003..abstract_text> ..
- EXPRESSION OF THE LEISHMANIA TARENTOLAE SL RNA GENEDavid Campbell; Fiscal Year: 2003..These unique features represent potential targets for selective therapeutic intervention. ..
- MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SABuddy Ullman; Fiscal Year: 2003..Concurrent experiments will determine how NTPase functions in AK HGXPRT-, and AT parasites, identify the protein(s) which regulate NTPase enzymatic activity, and evaluate the impact of abrogating NTPase expression on parasite viability. ..
- Structure of genomic DNA at single-nucleotide resolutionThomas D Tullius; Fiscal Year: 2010..Experimental data production and informatics pipelines, data verification and validation protocols, and plans for data deposition are detailed in the application. ..
- MOLECULAR ANALYSIS OF ANTIGENIC VARIATION IN MALARIAMary Galinski; Fiscal Year: 2004....
- EVOLUTION OF IMMUNE RECOGNITION AND EVASIONAustin L Hughes; Fiscal Year: 2010..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..
- Gene Duplication and Genome EvolutionAustin Hughes; Fiscal Year: 2004..5) Examining the role of transposable elements in duplication of genomic segments by testing for nonrandom association between these elements and putatively duplicated blocks in the yeast genome. ..
- Translational Control in Plasmodium Sexual DevelopmentLiwang Cui; Fiscal Year: 2005....
- Chromosome breakage and DNA detection in TetrahymenaMeng Chao Yao; Fiscal Year: 2006..abstract_text> ..
- Adherence of malaria-infected red cellsAlan Cowman; Fiscal Year: 2009..These studies will contribute to and increased understanding of the pathophysiology of falciparum malaria. ..
- PHYSICAL CHEMISTRY OF NUCLEIC ACIDSCarlos Bustamante; Fiscal Year: 2008..Finally, in the experiments described here, mechanical force will be used as a new controllable variable to characterize the process of mechanochemical transduction in this motor enzyme. ..
- DRUG RESISTANCE AND PTERIDINE METABOLISM IN LEISHMANIAStephen M Beverley; Fiscal Year: 2010..These studies have yielded new opportunities for chemotherapeutic attack and new directions for future study of pteridine metabolism and biology. [unreadable] ..
- Polyamine Metabolism in LeishmaniaBuddy Ullman; Fiscal Year: 2008..donovani. We propose, therefore, to ascertain whether the disparity in the abilities of ?lmarg L. mexicana and ?ldodc L. donovani to infect mice can be ascribed to species or gene differences. ..
- Plasmodium vivax:Proteomic Analysis of Asexual and Sporozoite StagesLiwang Cui; Fiscal Year: 2007..Its recent resurgence in prevalence and emergence of drug- resistant parasite strains have raised a great concern for the future control of malaria. [unreadable] [unreadable] [unreadable]..
- CONFERENCE PROPOSAL: CILIATE MOLECULAR BIOLOGYLAWRENCE KLOBUTCHER; Fiscal Year: 2003..abstract_text> ..
- Chlamydia trachomatis, Genital Flora, & STD PathogenesisGerald Byrne; Fiscal Year: 2004..This hypothesis will be tested by determining the effects of indole-producing normal flora on chlamydial genital tract disease in a well-characterized murine model. ..
- Study of permissive/non-permissive T. gondii infectionsJay Radke; Fiscal Year: 2004..abstract_text> ..
- Identification of Tetrahymena DNA Rearrangement GenesDOUGLAS LEE CHALKER; Fiscal Year: 2010..abstract_text> ..
- Nucleoside Transporters of Plasmodium falciparumBuddy Ullman; Fiscal Year: 2007..falciparum in order to test whether PfNT1 function is essential to the intact parasite. We will then characterize the resultant transport and growth phenotypes. ..
- R13 travel grant for Polyamine/parasite conference in Portland, ORBuddy Ullman; Fiscal Year: 2006..abstract_text> ..
- RNA Uridylytransferases of TrypanosomesRuslan Aphasizhev; Fiscal Year: 2009..Sequences of the newly identified UTP-specific transferases will be used to establish characteristic protein motifs for this family of enzymes. ..
- Role of iNOS and CAT-2 in defense against CP infectionJody Gookin; Fiscal Year: 2006..parvum infection. The PI is presently in the 3rd year of a 5-year K08 from NIDDK. These studies are anticipated to generate key preliminary data for the PI's first R01 application ..
- NO& Epithelial Repair in CryptosporidiosisJody Gookin; Fiscal Year: 2006..abstract_text> ..