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  1. Article ; Online: Genetics, Transcriptomics and Meta-Taxonomics in Visceral Leishmaniasis.

    Blackwell, Jenefer M / Fakiola, Michaela / Singh, Om Prakash

    Frontiers in cellular and infection microbiology

    2020  Volume 10, Page(s) 590888

    Abstract: Visceral leishmaniasis (VL) caused by parasites of ... ...

    Abstract Visceral leishmaniasis (VL) caused by parasites of the
    MeSH term(s) Genome-Wide Association Study ; Humans ; India ; Leishmania donovani/genetics ; Leishmaniasis, Visceral ; RNA, Ribosomal, 16S ; Transcriptome
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2020-11-25
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2020.590888
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  2. Article ; Online: Human genetics of leishmania infections.

    Blackwell, Jenefer M / Fakiola, Michaela / Castellucci, Léa C

    Human genetics

    2020  Volume 139, Issue 6-7, Page(s) 813–819

    Abstract: Identifying genetic risk factors for parasitic infections such as the leishmaniases could provide important leads for improved therapies and vaccines. Until recently most genetic studies of human leishmaniasis were underpowered and/or not replicated. ... ...

    Abstract Identifying genetic risk factors for parasitic infections such as the leishmaniases could provide important leads for improved therapies and vaccines. Until recently most genetic studies of human leishmaniasis were underpowered and/or not replicated. Here, we focus on recent genome-wide association studies of visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). For VL, analysis across 2287 cases and 2692 controls from three cohorts identified a single major peak of genome-wide significance (P
    MeSH term(s) Gene Expression Regulation ; Genetic Predisposition to Disease ; HLA Antigens/genetics ; HLA Antigens/immunology ; Human Genetics ; Humans ; Leishmania/genetics ; Leishmania/immunology ; Leishmaniasis/genetics ; Leishmaniasis/immunology ; Leishmaniasis/parasitology ; Polymorphism, Single Nucleotide
    Chemical Substances HLA Antigens
    Language English
    Publishing date 2020-02-13
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 223009-4
    ISSN 1432-1203 ; 0340-6717
    ISSN (online) 1432-1203
    ISSN 0340-6717
    DOI 10.1007/s00439-020-02130-w
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    Zs.A 256: Show issues Location:
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  3. Article ; Online: Personalised analytics for rare disease diagnostics

    Denise Anderson / Gareth Baynam / Jenefer M. Blackwell / Timo Lassmann

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 8

    Abstract: Genome sequencing is being widely adopted for diagnosis of genetic diseases, but identifying the causal variants remains challenging. Here, the authors introduce a tool that incorporates tissue-specific gene expression data into predicting variant ... ...

    Abstract Genome sequencing is being widely adopted for diagnosis of genetic diseases, but identifying the causal variants remains challenging. Here, the authors introduce a tool that incorporates tissue-specific gene expression data into predicting variant pathogenicity, improving accuracy.
    Keywords Science ; Q
    Language English
    Publishing date 2019-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
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  4. Article ; Online: Personalised analytics for rare disease diagnostics.

    Anderson, Denise / Baynam, Gareth / Blackwell, Jenefer M / Lassmann, Timo

    Nature communications

    2019  Volume 10, Issue 1, Page(s) 5274

    Abstract: Whole genome and exome sequencing is a standard tool for the diagnosis of patients suffering from rare and other genetic disorders. The interpretation of the tens of thousands of variants returned from such tests remains a major challenge. Here we focus ... ...

    Abstract Whole genome and exome sequencing is a standard tool for the diagnosis of patients suffering from rare and other genetic disorders. The interpretation of the tens of thousands of variants returned from such tests remains a major challenge. Here we focus on the problem of prioritising variants with respect to the observed disease phenotype. We hypothesise that linking patterns of gene expression across multiple tissues to the phenotypes will aid in discovering disease causing variants. To test this, we construct classifiers that learn associations between tissue-specific gene expression and disease phenotypes. We find that using Genotype-Tissue Expression project (GTEx) expression data in conjunction with disease agnostic variant prioritisation methods (CADD or MetaSVM) results in consistent improvements in classification accuracy. Our method represents a previously overlooked avenue of utilising existing expression data for clinical diagnostics, and also opens the door to use of other functional genomic data sets in the same manner.
    MeSH term(s) Gene Expression Profiling ; Gene Expression Regulation ; Genetic Variation ; Genome, Human/genetics ; Genome-Wide Association Study/methods ; Genotype ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Phenotype ; Precision Medicine/methods ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Exome Sequencing/methods
    Language English
    Publishing date 2019-11-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-019-13345-5
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  5. Article ; Online: Toxoplasma gondii

    Syn, Genevieve / Anderson, Denise / Blackwell, Jenefer M / Jamieson, Sarra E

    Frontiers in cellular and infection microbiology

    2017  Volume 7, Page(s) 512

    Abstract: Upon invasion of host cells, the ubiquitous ... ...

    Abstract Upon invasion of host cells, the ubiquitous pathogen
    MeSH term(s) Cells, Cultured ; Fibroblasts/parasitology ; Gene Expression Profiling ; Humans ; Mitochondria/metabolism ; Mitochondria/pathology ; Toxoplasma/growth & development ; Toxoplasmosis/pathology
    Language English
    Publishing date 2017-12-12
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2017.00512
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  6. Article ; Online: An in silico pipeline to filter the Toxoplasma gondii proteome for proteins that could traffic to the host cell nucleus and influence host cell epigenetic regulation.

    Syn, Genevieve / Blackwell, Jenefer M / Jamieson, Sarra E / Francis, Richard W

    Memorias do Instituto Oswaldo Cruz

    2018  Volume 113, Issue 6, Page(s) e170471

    Abstract: Toxoplasma gondii uses epigenetic mechanisms to regulate both endogenous and host cell gene expression. To identify genes with putative epigenetic functions, we developed an in silico pipeline to interrogate the T. gondii proteome of 8313 proteins. Step ... ...

    Abstract Toxoplasma gondii uses epigenetic mechanisms to regulate both endogenous and host cell gene expression. To identify genes with putative epigenetic functions, we developed an in silico pipeline to interrogate the T. gondii proteome of 8313 proteins. Step 1 employs PredictNLS and NucPred to identify genes predicted to target eukaryotic nuclei. Step 2 uses GOLink to identify proteins of epigenetic function based on Gene Ontology terms. This resulted in 611 putative nuclear localised proteins with predicted epigenetic functions. Step 3 filtered for secretory proteins using SignalP, SecretomeP, and experimental data. This identified 57 of the 611 putative epigenetic proteins as likely to be secreted. The pipeline is freely available online, uses open access tools and software with user-friendly Perl scripts to automate and manage the results, and is readily adaptable to undertake any such in silico search for genes contributing to particular functions.
    MeSH term(s) Cell Nucleus/parasitology ; Computer Simulation ; Epigenesis, Genetic/genetics ; Host-Parasite Interactions/physiology ; Proteome/genetics ; Toxoplasma/genetics ; Toxoplasma/physiology
    Chemical Substances Proteome
    Language English
    Publishing date 2018
    Publishing country Brazil
    Document type Journal Article
    ZDB-ID 953293-6
    ISSN 1678-8060 ; 0074-0276
    ISSN (online) 1678-8060
    ISSN 0074-0276
    DOI 10.1590/0074-02760170471
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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.33: Show issues Location:
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  7. Article ; Online: Epigenetic dysregulation of host gene expression in Toxoplasma infection with specific reference to dopamine and amyloid pathways.

    Syn, Genevieve / Anderson, Denise / Blackwell, Jenefer M / Jamieson, Sarra E

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2018  Volume 65, Page(s) 159–162

    Abstract: Recent interest has focussed on the influence of infectious disease organisms on the host epigenome. Toxoplasma gondii infection acquired congenitally or in early life is associated with severe ocular and brain developmental anomalies, while persistent ... ...

    Abstract Recent interest has focussed on the influence of infectious disease organisms on the host epigenome. Toxoplasma gondii infection acquired congenitally or in early life is associated with severe ocular and brain developmental anomalies, while persistent asymptomatic infection is a proposed risk factor for neurodegenerative and psychiatric disorders, including Parkinson's and Alzheimer's Diseases, and schizophrenia. Genome-wide analysis of the host methylome and transcriptome following T. gondii infection in a retinal cell line identified genes (132, 186 and 128 genes at 2, 6 and 24 h post-infection) concordant for methylation and expression, i.e. hypermethylated and decreased expression or hypomethylated and increased expression. Pathway analyses showed perturbation of two neurologically-associated pathways: dopamine-DARPP32 feedback in cAMP signalling (p-value = 8.3 × 10
    MeSH term(s) Amyloid/genetics ; Amyloid/metabolism ; Cell Line ; Dopamine/genetics ; Dopamine/metabolism ; Epigenesis, Genetic ; Eye/cytology ; Eye Infections, Parasitic/genetics ; Eye Infections, Parasitic/metabolism ; Gene Expression Regulation ; Host-Parasite Interactions/genetics ; Humans ; Toxoplasma/pathogenicity ; Toxoplasmosis/genetics ; Toxoplasmosis/metabolism
    Chemical Substances Amyloid ; Dopamine (VTD58H1Z2X)
    Language English
    Publishing date 2018-07-26
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2018.07.034
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    Zs.A 5645: Show issues Location:
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  8. Article ; Online: Common and Rare Genetic Variants That Could Contribute to Severe Otitis Media in an Australian Aboriginal Population.

    Jamieson, Sarra E / Fakiola, Michaela / Tang, Dave / Scaman, Elizabeth / Syn, Genevieve / Francis, Richard W / Coates, Harvey L / Anderson, Denise / Lassmann, Timo / Cordell, Heather J / Blackwell, Jenefer M

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

    2021  Volume 73, Issue 10, Page(s) 1860–1870

    Abstract: Background: Our goal was to identify genetic risk factors for severe otitis media (OM) in Aboriginal Australians.: Methods: Illumina® Omni2.5 BeadChip and imputed data were compared between 21 children with severe OM (multiple episodes chronic ... ...

    Abstract Background: Our goal was to identify genetic risk factors for severe otitis media (OM) in Aboriginal Australians.
    Methods: Illumina® Omni2.5 BeadChip and imputed data were compared between 21 children with severe OM (multiple episodes chronic suppurative OM and/or perforations or tympanic sclerosis) and 370 individuals without this phenotype, followed by FUnctional Mapping and Annotation (FUMA). Exome data filtered for common (EXaC_all ≥ 0.1) putative deleterious variants influencing protein coding (CADD-scaled scores ≥15] were used to compare 15 severe OM cases with 9 mild cases (single episode of acute OM recorded over ≥3 consecutive years). Rare (ExAC_all ≤ 0.01) such variants were filtered for those present only in severe OM. Enrichr was used to determine enrichment of genes contributing to pathways/processes relevant to OM.
    Results: FUMA analysis identified 2 plausible genetic risk loci for severe OM: NR3C1 (Pimputed_1000G = 3.62 × 10-6) encoding the glucocorticoid receptor, and NREP (Pimputed_1000G = 3.67 × 10-6) encoding neuronal regeneration-related protein. Exome analysis showed: (i) association of severe OM with variants influencing protein coding (CADD-scaled ≥ 15) in a gene-set (GRXCR1, CDH23, LRP2, FAT4, ARSA, EYA4) enriched for Mammalian Phenotype Level 4 abnormal hair cell stereociliary bundle morphology and related phenotypes; (ii) rare variants influencing protein coding only seen in severe OM provided gene-sets enriched for "abnormal ear" (LMNA, CDH23, LRP2, MYO7A, FGFR1), integrin interactions, transforming growth factor signaling, and cell projection phenotypes including hair cell stereociliary bundles and cilium assembly.
    Conclusions: This study highlights interacting genes and pathways related to cilium structure and function that may contribute to extreme susceptibility to OM in Aboriginal Australian children.
    MeSH term(s) Australia/epidemiology ; Continental Population Groups ; Humans ; Otitis Media/genetics ; Phenotype ; Trans-Activators
    Chemical Substances EYA4 protein, human ; Trans-Activators
    Language English
    Publishing date 2021-03-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1099781-7
    ISSN 1537-6591 ; 1058-4838
    ISSN (online) 1537-6591
    ISSN 1058-4838
    DOI 10.1093/cid/ciab216
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    Zs.A 1505: Show issues Location:
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    Zs.MO 480: Show issues

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  9. Article ; Online: Transketolase and vitamin B1 influence on ROS-dependent neutrophil extracellular traps (NETs) formation.

    Riyapa, Donporn / Rinchai, Darawan / Muangsombut, Veerachat / Wuttinontananchai, Chayanin / Toufiq, Mohammed / Chaussabel, Damien / Ato, Manabu / Blackwell, Jenefer M / Korbsrisate, Sunee

    PloS one

    2019  Volume 14, Issue 8, Page(s) e0221016

    Abstract: Neutrophil extracellular traps (NETs) are a recently identified, web-like, extracellular structure composed of decondensed nuclear DNA and associated antimicrobial granules. NETs are extruded into the extracellular environment via the reactive oxygen ... ...

    Abstract Neutrophil extracellular traps (NETs) are a recently identified, web-like, extracellular structure composed of decondensed nuclear DNA and associated antimicrobial granules. NETs are extruded into the extracellular environment via the reactive oxygen species (ROS)-dependent cell death pathway participating in inflammation and autoimmune diseases. Transketolase (TKT) is a thiamine pyrophosphate (vitamin B1)-dependent enzyme that links the pentose phosphate pathway with the glycolytic pathway by feeding excess sugar phosphates into the main carbohydrate metabolic pathways to generate biosynthetic reducing capacity in the form of NADPH as a substrate for ROS generation. In this work, TKT was selected as a lead candidate from 24 NET-associated proteins obtained by literature screening and knowledge gap assessment. Consequently, we determined whether TKT influenced NET formation in vitro. We firstly established that the release of ROS-dependent NETs was significantly decreased after purified human PMNs were pretreated with oxythiamine, a TKT inhibitor, and in a concentration dependent manner. As a cofactor for TKT reaction, we evaluated the release of NET formation either in vitamin B1 treatment or in combined use of oxythiamine and vitamin B1, and found that those treatments also exerted a significant suppressive effect on the amount of NET-DNA and ROS production. The regulation of TKT by oxythiamine and/or vitamin B1 may therefore be associated with response to the modulation of NET formation by preventing generation of excessive NETs in inflammatory diseases.
    MeSH term(s) Extracellular Traps/metabolism ; Humans ; Inflammation/metabolism ; Inflammation/pathology ; Neutrophils/metabolism ; Neutrophils/pathology ; Reactive Oxygen Species/metabolism ; Thiamine/metabolism ; Transketolase/metabolism
    Chemical Substances Reactive Oxygen Species ; Transketolase (EC 2.2.1.1) ; Thiamine (X66NSO3N35)
    Language English
    Publishing date 2019-08-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0221016
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  10. Article ; Online: Reference exome data for a Northern Brazilian population

    Alexia L. Weeks / Richard W. Francis / Joao I. C. F. Neri / Nathaly M. C. Costa / Nivea M. R. Arrais / Timo Lassmann / Jenefer M. Blackwell / Selma M. B. Jeronimo

    Scientific Data, Vol 7, Iss 1, Pp 1-

    2020  Volume 5

    Abstract: Measurement(s) exome • Exon Mutation Technology Type(s) DNA sequencing assay • comparison analysis operation Sample Characteristic - Organism Homo sapiens Sample Characteristic - Location Rio Grande do Norte State Machine-accessible metadata file ... ...

    Abstract Measurement(s) exome • Exon Mutation Technology Type(s) DNA sequencing assay • comparison analysis operation Sample Characteristic - Organism Homo sapiens Sample Characteristic - Location Rio Grande do Norte State Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.12839735
    Keywords Science ; Q
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
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