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      Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites

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          Abstract

          Kinetoplastids are a group of parasites that includes several medically-important species. These human-infective species are transmitted by insect vectors in which the parasites undergo specific developmental transformations. For each species, this includes a stage in which parasites adhere to insect tissue via a hemidesmosome-like structure. Although this structure has been described morphologically, it has never been molecularly characterized. We are using Crithidia fasciculata, an insect parasite that produces large numbers of adherent parasites inside its mosquito host, as a model kinetoplastid to investigate both the mechanism of adherence and the signals required for differentiation to an adherent form. An advantage of C. fasciculata is that adherent parasites can be generated both in vitro, allowing a direct comparison to cultured swimming forms, as well as in vivo within the mosquito. Using RNAseq, we identify genes associated with adherence in C. fasciculata. As almost all of these genes have orthologs in other kinetoplastid species, our findings may reveal shared mechanisms of adherence, allowing investigation of a crucial step in parasite development and disease transmission. In addition, dual-RNAseq allowed us to explore the interaction between the parasites and the mosquito. Although the infection is well-tolerated, anti-microbial peptides and other components of the mosquito innate immune system are upregulated. Our findings indicate that C. fasciculata is a powerful model system for probing kinetoplastid-insect interactions.

          Author summary

          Kinetoplastids are single-celled parasites that cause devastating human diseases worldwide. Although this group includes many species that infect a variety of hosts, they have a great deal of shared biology. One relatively unexplored aspect of the kinetoplastid life cycle is their ability to adhere to insect tissue. For pathogenic species, adherence is critical for transmission by insect vectors. We have used an insect parasite called Crithidia fasciculata as a model kinetoplastid to reveal shared mechanisms of insect adherence. We have compared gene expression profiles of motile, non-adherent C. fasciculata to those of C. fasciculata adhered to non-living substrates and those attached to the hindgut of mosquitoes. Through this analysis, we have identified a large number of candidate proteins that may mediate adhesion in these and related parasites. In addition, our findings suggest that the mosquito immune system is responding to the presence of parasites in the gut. These results establish a new, robust system to explore the interaction between kinetoplastids and their insect hosts.

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          A whole-genome assembly of Drosophila.

          We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.
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            Post-transcriptional regulation of gene expression in trypanosomes and leishmanias.

            Gene expression in Kinetoplastids is very unusual in that the open reading frames are arranged in long polycistronic arrays, monocistronic mRNAs being created by post-transcriptional processing. 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.
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              Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

              Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. Availability: The software is available at http://icorn.sourceforge.net Contact: tdo@sanger.ac.uk; cnewbold@hammer.imm.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Formal analysisRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – review & editing
                Role: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Negl Trop Dis
                PLoS Negl Trop Dis
                plos
                plosntds
                PLoS Neglected Tropical Diseases
                Public Library of Science (San Francisco, CA USA )
                1935-2727
                1935-2735
                29 July 2019
                July 2019
                : 13
                : 7
                : e0007570
                Affiliations
                [1 ] Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
                [2 ] Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
                [3 ] University of Missouri, Bond Life Sciences Center, Columbia, Missouri, United States of America
                [4 ] McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
                [5 ] Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
                [6 ] Department of Global Health, University of Washington, Seattle, Washington, United States of America
                [7 ] Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America
                [8 ] Department of Biology, Penn State Brandywine, Media, Pennsylvania, United States of America
                Liverpool School of Tropical Medicine, UNITED KINGDOM
                Author notes

                The authors have declared that no competing interests exist.

                [¤]

                Current address: School of Biomedical Engineering, Science, and Health Systems, Drexel University, Pennsylvania, United States of America

                Author information
                http://orcid.org/0000-0001-9348-2034
                http://orcid.org/0000-0003-2612-6413
                http://orcid.org/0000-0002-3766-2097
                Article
                PNTD-D-19-00291
                10.1371/journal.pntd.0007570
                6687205
                31356610
                97d1df3f-4657-4471-80e4-8cc0f9ee61ae
                © 2019 Filosa et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 21 February 2019
                : 22 June 2019
                Page count
                Figures: 9, Tables: 1, Pages: 29
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000076, Directorate for Biological Sciences;
                Award ID: MCB-1651517
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: AI29646
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: AI103858
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: 5U54HG00307907
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: S10 OD021633-01
                This work was supported by the National Science Foundation under grant number MCB-1651517 to MLP. https://www.nsf.gov. The PennVet Imaging Core (GR) is supported by a National Institutes of Health Shared Instrument Grant S10 OD021633-01 to Bruce Freedman. This study was financially supported in part by NIH grant AI29646 to SMB, NIH-NHGRI grant 5U54HG00307907 to Richard K. Wilson, Director of the Genome Institute at Washington University, and NIH-NIAID grant AI103858 to PJM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Physiology
                Biological Locomotion
                Swimming
                Medicine and Health Sciences
                Physiology
                Biological Locomotion
                Swimming
                Medicine and Health Sciences
                Parasitic Diseases
                Biology and Life Sciences
                Microbiology
                Protozoology
                Kinetoplastids
                Medicine and Health Sciences
                Infectious Diseases
                Disease Vectors
                Insect Vectors
                Mosquitoes
                Biology and Life Sciences
                Species Interactions
                Disease Vectors
                Insect Vectors
                Mosquitoes
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Insects
                Mosquitoes
                Biology and Life Sciences
                Genetics
                Gene Expression
                Medicine and Health Sciences
                Infectious Diseases
                Disease Vectors
                Insect Vectors
                Biology and Life Sciences
                Species Interactions
                Disease Vectors
                Insect Vectors
                Biology and Life Sciences
                Cell Biology
                Cell Processes
                Cell Cycle and Cell Division
                Biology and Life Sciences
                Genetics
                Gene Expression
                Gene Regulation
                Custom metadata
                vor-update-to-uncorrected-proof
                2019-08-08
                Data is contained within the manuscript and supporting files. The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE132641 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132641). As such, they are will also be available to the community through both SRA as well as TriTrypDB http://tritrypdb.org/tritrypdb/ and VectorBase https://www.vectorbase.org.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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