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  • 1
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    Stage-specific transcription of distinct repertoires of a multigene family during Plasmodium life cycle (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-12
    Description: Members of a multigene family in the rodent malaria parasite Plasmodium yoelii yoelii code for 235-kilodalton proteins (Py235) that are located in the merozoite apical complex, are implicated in virulence, and may determine red blood cell specificity. We show that distinct subsets of py235 genes are expressed in sporozoites and hepatic and erythrocytic stages. Antibodies to Py235 inhibited sporozoite invasion of hepatocytes. The switch in expression profile occurred immediately after transition from one stage to another. The results suggest that this differential expression is driven by strong biological requirements and provide evidence that hepatic and erythrocytic merozoites differ.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Preiser, P R -- Khan, S -- Costa, F T M -- Jarra, W -- Belnoue, E -- Ogun, S -- Holder, A A -- Voza, T -- Landau, I -- Snounou, G -- Renia, L -- MC_U117532067/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2002 Jan 11;295(5553):342-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Parasitology, National Institute for Medical Research, The Ridgeway, London, NW7 1AA, UK. ppreise@nimr.mrc.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11786645" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anopheles/parasitology ; Cells, Cultured ; Erythrocytes/parasitology ; Fluorescent Antibody Technique ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Genes, Protozoan ; Hepatocytes/parasitology ; Life Cycle Stages ; Malaria/parasitology ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; *Multigene Family ; Plasmodium yoelii/*genetics/*growth & development/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Salivary Glands/parasitology ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Accuracy of timescales retrieved from diffusion modeling in olivine: A 3D perspective (2015)
    Mineralogical Society of America
    Details
    Publication Date: 2015-10-02
    Description: Diffusion modeling in olivine is a useful tool to resolve the timescales of various magmatic processes. Practical olivine geospeedometry applications employ 1D chemical transects across sections that are randomly sampled from a given 3D crystal population, but the accuracy and precision with which timescales can be retrieved from this procedure are not well constrained. Here, we use numerical 3D diffusion models of Fe-Mg to evaluate and quantify the uncertainties associated with their 1D counterparts. The 3D diffusion models were built using both simple and realistic olivine morphologies, and incorporate diffusion anisotropy as well as different zoning styles. The 3D model crystals were sectioned along ideal or random planes, which were used to perform 1D models and timescale comparisons. Results show that the timescales retrieved from 1D profiles are highly inaccurate and can vary by factors of 0.1–25 if diffusion anisotropy is not taken into account. Even when anisotropy is corrected for, timescales can still vary between 0.2–10 times the true 3D diffusion time due to crystal shape and sectioning effects. Simple grain selection procedures are described to reduce the misfit between calculated and actual diffusion times, and achieve an accuracy and precision of ~5% and ~15–25% relative, respectively. Provided that the grains are carefully selected, about 20 concentration profiles and associated 1D models suffice to achieve this accuracy.
    Print ISSN: 0003-004X
    Electronic ISSN: 1945-3027
    Topics: Geosciences
    Published by Mineralogical Society of America
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  • 3
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    RNAcommender: genome-wide recommendation of RNA-protein interactions (2016)
    Oxford University Press
    Details
    Publication Date: 2016-11-30
    Description: Motivation: Information about RNA–protein interactions is a vital pre-requisite to tackle the dissection of RNA regulatory processes. Despite the recent advances of the experimental techniques, the currently available RNA interactome involves a small portion of the known RNA binding proteins. The importance of determining RNA–protein interactions, coupled with the scarcity of the available information, calls for in silico prediction of such interactions. Results: We present RNAcommender, a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information taking into account the protein domain composition and the RNA predicted secondary structure. Our results show that RNAcommender is able to successfully suggest RNA interactors for RNA binding proteins using little or no interaction evidence. RNAcommender was tested on a large dataset of human RBP-RNA interactions, showing a good ranking performance (average AUC ROC of 0.75) and significant enrichment of correct recommendations for 75% of the tested RBPs. RNAcommender can be a valid tool to assist researchers in identifying potential interacting candidates for the majority of RBPs with uncharacterized binding preferences. Availability and Implementation: The software is freely available at http://rnacommender.disi.unitn.it . Contact: gianluca.corrado@unitn.it or andrea.passerini@unitn.it Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Stage-Specific Transcription of Distinct Repertoires of a Multigene Family During Plasmodium Life Cycle (2002)
    American Association for the Advancement of Science
    Details
    Publication Date: 2002-01-11
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science
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