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      Toxoplasma infection in male mice alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease

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          Abstract

          During chronic infection, the single celled parasite, Toxoplasma gondii, can migrate to the brain where it has been associated with altered dopamine function and the capacity to modulate host behavior, increasing risk of neurocognitive disorders. Here we explore alterations in dopamine-related behavior in a new mouse model based on stimulant (cocaine)-induced hyperactivity. In combination with cocaine, infection resulted in heightened sensorimotor deficits and impairment in prepulse inhibition response, which are commonly disrupted in neuropsychiatric conditions. To identify molecular pathways in the brain affected by chronic T. gondii infection, we investigated patterns of gene expression. As expected, infection was associated with an enrichment of genes associated with general immune response pathways, that otherwise limits statistical power to identify more informative pathways. To overcome this limitation and focus on pathways of neurological relevance, we developed a novel context enrichment approach that relies on a customized ontology. Applying this approach, we identified genes that exhibited unexpected patterns of expression arising from the combination of cocaine exposure and infection. These include sets of genes which exhibited dampened response to cocaine in infected mice, suggesting a possible mechanism for some observed behaviors and a neuroprotective effect that may be advantageous to parasite persistence. This model offers a powerful new approach to dissect the molecular pathways by which T. gondii infection contributes to neurocognitive disorders.

          Author summary

          Infecting 1 in 3 worldwide, the single-celled parasite T. gondii causes a chronic infection whereby it can migrate to the brain and promote low-grade neuroinflammation. Given this intimate association, infection with T. gondii has the capacity to induce changes in brain morphology and behavior as well as modulate the production of neurotransmitters, such as dopamine. Consequently, T. gondii has been linked with several neurocognitive disorders including schizophrenia, dementia, and Parkinson’s disease, in addition to a loss of fear response. To examine how infection impacts pathways utilizing neurotransmitters, we used a mouse model, based on stimulant-induced (cocaine) hyperactivity. Infection with T. gondii did not alter fear behavior but did impact motor activity and neuropsychiatric-related behaviors. Gene expression analysis revealed an initial enrichment of uninformative immune-response pathways. By applying a novel context enrichment approach, we identified significant associations with neurologically relevant genes involved in multiple pathways. These include sets of genes which exhibited dampened response to cocaine exposure in the context of T. gondii infection, suggestive of a neuroprotective effect that may be advantageous to parasite persistence. We suggest this novel mouse model offers a new perspective to dissect the molecular pathways by which T. gondii infection contributes to neuropsychiatric disorders.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              STAR: ultrafast universal RNA-seq aligner.

              Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – review & editing
                Role: Data curationRole: Investigation
                Role: Investigation
                Role: Investigation
                Role: InvestigationRole: Methodology
                Role: Formal analysisRole: Visualization
                Role: Data curationRole: Formal analysisRole: Investigation
                Role: Methodology
                Role: MethodologyRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Negl Trop Dis
                PLoS Negl Trop Dis
                plos
                PLoS Neglected Tropical Diseases
                Public Library of Science (San Francisco, CA USA )
                1935-2727
                1935-2735
                20 July 2022
                July 2022
                : 16
                : 7
                : e0010600
                Affiliations
                [1 ] Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
                [2 ] Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Canada
                [3 ] Dept. of Biochemistry, University of Toronto, Toronto, Canada
                [4 ] Dept. of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, Canada
                [5 ] Dept. of Physiology, University of Toronto, Toronto, Canada
                [6 ] Institute of Medical Sciences, University of Toronto, Toronto, Canada
                [7 ] Dept. of Psychology, University of Toronto, Toronto, Canada
                [8 ] Dept. of Molecular Genetics, University of Toronto, Toronto, Canada
                Washington University in St Louis School of Medicine, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                [¤]

                Current address: Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada

                ‡ Lead contact.

                Author information
                https://orcid.org/0000-0001-9815-1189
                Article
                PNTD-D-22-00218
                10.1371/journal.pntd.0010600
                9342775
                35857765
                24660909-20e6-49b8-8bb8-abeb7977c4d8
                © 2022 Cromar 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
                : 16 February 2022
                : 21 June 2022
                Page count
                Figures: 6, Tables: 0, Pages: 29
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100006126, Hospital for Sick Children;
                Award ID: “Chase an Idea” grant
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000024, Canadian Institutes of Health Research;
                Award ID: PJT-152921
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
                Award ID: RGPIN-2015-03923
                Award Recipient :
                This work was supported by a “Chase an Idea” grant provided by the Centre for Brain and Mental Health, Hospital for Sick Children to JE, JP and PWF. Additional funding was provided by the Canadian Institute for Health Research (PJT - 152921 to JP) and a Natural Sciences and Engineering Research Council of Canada award to PWF (RGPIN-2015-03923). 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
                Organisms
                Eukaryota
                Protozoans
                Parasitic Protozoans
                Toxoplasma
                Toxoplasma Gondii
                Physical Sciences
                Chemistry
                Chemical Compounds
                Alkaloids
                Cocaine
                Medicine and Health Sciences
                Pharmacology
                Behavioral Pharmacology
                Recreational Drug Use
                Cocaine
                Biology and Life Sciences
                Psychology
                Behavior
                Animal Behavior
                Social Sciences
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                Animal Behavior
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                Zoology
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                Biology and Life Sciences
                Zoology
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                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
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                Research and Analysis Methods
                Model Organisms
                Mouse Models
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Animal Models
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                Biology and Life Sciences
                Genetics
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                Biology and Life Sciences
                Anatomy
                Brain
                Hippocampus
                Medicine and Health Sciences
                Anatomy
                Brain
                Hippocampus
                Biology and Life Sciences
                Neuroscience
                Cognitive Science
                Cognitive Psychology
                Perception
                Sensory Perception
                Biology and Life Sciences
                Psychology
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                Perception
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                Social Sciences
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                Perception
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                Biology and Life Sciences
                Neuroscience
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                Custom metadata
                vor-update-to-uncorrected-proof
                2022-08-01
                The sequencing data associated with this study have been deposited with links to BioProject accession number PRJNA750929 in the NCBI BioProject database ( https://www.ncbi.nlm.nih.gov/bioproject/).

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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