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  1. Article ; Online: Finding motivation in the lighter side of science.

    Ivancevic, Atma

    Nature

    2020  Volume 581, Issue 7806, Page(s) 108

    MeSH term(s) Humans ; Internet ; Mental Health ; Motivation ; Newspapers as Topic ; Research Personnel/education ; Research Personnel/psychology ; Science/education ; Social Distance ; Social Media ; Uncertainty ; Webcasts as Topic ; Wit and Humor as Topic
    Language English
    Publishing date 2020-04-20
    Publishing country England
    Document type News
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-020-01151-9
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  2. Article ; Online: Transposable elements teach T cells new tricks.

    Ivancevic, Atma / Chuong, Edward Boyi

    Proceedings of the National Academy of Sciences of the United States of America

    2020  Volume 117, Issue 17, Page(s) 9145–9147

    MeSH term(s) DNA Transposable Elements ; Regulatory Sequences, Nucleic Acid ; T-Lymphocytes
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2020-04-20
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2004493117
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  3. Article ; Online: Detecting Horizontal Transfer of Transposons.

    Galbraith, James D / Ivancevic, Atma M / Qu, Zhipeng / Adelson, David L

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2607, Page(s) 45–62

    Abstract: Transposable elements (TEs) are prevalent genomic components which can replicate as a function of mobilization in eukaryotes. Not only do they alter genome structure, they also play regulatory functions or organize chromatin structure. In addition to ... ...

    Abstract Transposable elements (TEs) are prevalent genomic components which can replicate as a function of mobilization in eukaryotes. Not only do they alter genome structure, they also play regulatory functions or organize chromatin structure. In addition to vertical parent-to-offspring inheritance, TEs can also horizontally "jump" between species, known as horizontal transposon transfer (HTT). This can rapidly alter the course of genome evolution. In this chapter, we provide a practical framework to detect HTT events. Our HTT detection framework is based on the use of sequence alignment to determine the divergence/conservation profiles of TE families to determine the history of expansion events. In summary, it includes (a) workflow of HTT detection from Ab initio identified TEs; (b) workflow for detecting HTT for specific, curated TEs; and (c) workflow for validating detected HTT candidates. Our framework covers two common scenarios of HTT detection in the modern omics era, and we believe it will serve as a valuable toolbox for the TE and genomics research community.
    MeSH term(s) Humans ; DNA Transposable Elements/genetics ; Eukaryota ; Genomics ; Inheritance Patterns ; Sequence Alignment
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2022-11-30
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2883-6_3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Regulation of human interferon signaling by transposon exonization.

    Pasquesi, Giulia Irene Maria / Allen, Holly / Ivancevic, Atma / Barbachano-Guerrero, Arturo / Joyner, Olivia / Guo, Kejun / Simpson, David M / Gapin, Keala / Horton, Isabella / Nguyen, Lily / Yang, Qing / Warren, Cody J / Florea, Liliana D / Bitler, Benjamin G / Santiago, Mario L / Sawyer, Sara L / Chuong, Edward B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a ... ...

    Abstract Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.
    Language English
    Publishing date 2023-09-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.11.557241
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Horizontal transfer of BovB and L1 retrotransposons in eukaryotes.

    Ivancevic, Atma M / Kortschak, R Daniel / Bertozzi, Terry / Adelson, David L

    Genome biology

    2018  Volume 19, Issue 1, Page(s) 85

    Abstract: Background: Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a ... ...

    Abstract Background: Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events.
    Results: Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms.
    Conclusions: We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.
    MeSH term(s) Animals ; DNA Transposable Elements/genetics ; Eukaryota/genetics ; Gene Transfer, Horizontal/genetics ; Genomics/methods ; Insect Vectors/genetics ; Long Interspersed Nucleotide Elements/genetics ; Mammals/genetics ; Phylogeny ; Retroelements/genetics
    Chemical Substances DNA Transposable Elements ; Retroelements
    Language English
    Publishing date 2018-07-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-018-1456-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Aicardi Syndrome Is a Genetically Heterogeneous Disorder.

    Ha, Thuong T / Burgess, Rosemary / Newman, Morgan / Moey, Ching / Mandelstam, Simone A / Gardner, Alison E / Ivancevic, Atma M / Pham, Duyen / Kumar, Raman / Smith, Nicholas / Patel, Chirag / Malone, Stephen / Ryan, Monique M / Calvert, Sophie / van Eyk, Clare L / Lardelli, Michael / Berkovic, Samuel F / Leventer, Richard J / Richards, Linda J /
    Scheffer, Ingrid E / Gecz, Jozef / Corbett, Mark A

    Genes

    2023  Volume 14, Issue 8

    Abstract: Aicardi Syndrome (AIC) is a rare neurodevelopmental disorder recognized by the classical triad of agenesis of the corpus callosum, chorioretinal lacunae and infantile epileptic spasms syndrome. The diagnostic criteria of AIC were revised in 2005 to ... ...

    Abstract Aicardi Syndrome (AIC) is a rare neurodevelopmental disorder recognized by the classical triad of agenesis of the corpus callosum, chorioretinal lacunae and infantile epileptic spasms syndrome. The diagnostic criteria of AIC were revised in 2005 to include additional phenotypes that are frequently observed in this patient group. AIC has been traditionally considered as X-linked and male lethal because it almost exclusively affects females. Despite numerous genetic and genomic investigations on AIC, a unifying X-linked cause has not been identified. Here, we performed exome and genome sequencing of 10 females with AIC or suspected AIC based on current criteria. We identified a unique de novo variant, each in different genes:
    MeSH term(s) Male ; Female ; Animals ; Mice ; Aicardi Syndrome/genetics ; Zebrafish/genetics ; Chromosome Mapping ; Genes, X-Linked/genetics ; Biological Assay
    Language English
    Publishing date 2023-07-31
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14081565
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  7. Article: Horizontal transfer of BovB and L1 retrotransposons in eukaryotes

    Ivancevic, Atma M / Kortschak, R. Daniel / Bertozzi, Terry / Adelson, David L

    Genome biology. 2018 Dec., v. 19, no. 1

    2018  

    Abstract: BACKGROUND: Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a ... ...

    Abstract BACKGROUND: Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events. RESULTS: Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today’s mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms. CONCLUSIONS: We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.
    Keywords Chiroptera ; Cimicidae ; DNA ; bioinformatics ; eukaryotic cells ; frogs ; fungi ; genome ; genomics ; mammals ; retrotransposons ; ticks ; transposons ; viruses
    Language English
    Dates of publication 2018-12
    Size p. 85.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/s13059-018-1456-7
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life.

    Ivancevic, Atma M / Kortschak, R Daniel / Bertozzi, Terry / Adelson, David L

    Genome biology and evolution

    2016  Volume 8, Issue 11, Page(s) 3301–3322

    Abstract: LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to 'jump' around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active ...

    Abstract LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to 'jump' around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterized domain organization. For the past 30 years, model organisms have been used to define L1s as 6-8 kb sequences containing a 5'-UTR, two open reading frames working harmoniously in cis, and a 3'-UTR with a polyA tail. In this study, we demonstrate the remarkable and overlooked diversity of L1s via a comprehensive phylogenetic analysis of elements from over 500 species from widely divergent branches of the tree of life. The rapid and recent growth of L1 elements in mammalian species is juxtaposed against the diverse lineages found in other metazoans and plants. In fact, some of these previously unexplored mammalian species (e.g. snub-nosed monkey, minke whale) exhibit L1 retrotranspositional 'hyperactivity' far surpassing that of human or mouse. In contrast, non-mammalian L1s have become so varied that the current classification system seems to inadequately capture their structural characteristics. Our findings illustrate how both long-term inherited evolutionary patterns and random bursts of activity in individual species can significantly alter genomes, highlighting the importance of L1 dynamics in eukaryotes.
    MeSH term(s) Animals ; Eukaryota/classification ; Eukaryota/genetics ; Evolution, Molecular ; Long Interspersed Nucleotide Elements ; Phylogeny ; Plants/genetics
    Language English
    Publishing date 2016-12-14
    Publishing country England
    Document type Journal Article
    ISSN 1759-6653
    ISSN (online) 1759-6653
    DOI 10.1093/gbe/evw243
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  9. Article ; Online: Aicardi Syndrome Is a Genetically Heterogeneous Disorder

    Ha, Thuong T. / Burgess, Rosemary / Newman, Morgan / Moey, Ching / Mandelstam, Simone A. / Gardner, Alison E. / Ivancevic, Atma M. / Pham, Duyen / Kumar, Raman / Smith, Nicholas / Patel, Chirag / Malone, Stephen / Ryan, Monique M. / Calvert, Sophie / van Eyk, Clare L. / Lardelli, Michael / Berkovic, S. F. / Leventer, Richard J. / Richards, Linda J. /
    Scheffer, Ingrid E. / Gecz, Jozef / Corbett, Mark A.

    Genes (Basel). 2023 July 31, v. 14, no. 8

    2023  

    Abstract: Aicardi Syndrome (AIC) is a rare neurodevelopmental disorder recognized by the classical triad of agenesis of the corpus callosum, chorioretinal lacunae and infantile epileptic spasms syndrome. The diagnostic criteria of AIC were revised in 2005 to ... ...

    Abstract Aicardi Syndrome (AIC) is a rare neurodevelopmental disorder recognized by the classical triad of agenesis of the corpus callosum, chorioretinal lacunae and infantile epileptic spasms syndrome. The diagnostic criteria of AIC were revised in 2005 to include additional phenotypes that are frequently observed in this patient group. AIC has been traditionally considered as X-linked and male lethal because it almost exclusively affects females. Despite numerous genetic and genomic investigations on AIC, a unifying X-linked cause has not been identified. Here, we performed exome and genome sequencing of 10 females with AIC or suspected AIC based on current criteria. We identified a unique de novo variant, each in different genes: KMT2B, SLF1, SMARCB1, SZT2 and WNT8B, in five of these females. Notably, genomic analyses of coding and non-coding single nucleotide variants, short tandem repeats and structural variation highlighted a distinct lack of X-linked candidate genes. We assessed the likely pathogenicity of our candidate autosomal variants using the TOPflash assay for WNT8B and morpholino knockdown in zebrafish (Danio rerio) embryos for other candidates. We show expression of Wnt8b and Slf1 are restricted to clinically relevant cortical tissues during mouse development. Our findings suggest that AIC is genetically heterogeneous with implicated genes converging on molecular pathways central to cortical development.
    Keywords Danio rerio ; genome ; genomics ; males ; mice ; pathogenicity ; patients
    Language English
    Dates of publication 2023-0731
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14081565
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: A systematic review and meta-analysis of 271 PCDH19-variant individuals identifies psychiatric comorbidities, and association of seizure onset and disease severity.

    Kolc, Kristy L / Sadleir, Lynette G / Scheffer, Ingrid E / Ivancevic, Atma / Roberts, Rachel / Pham, Duyen H / Gecz, Jozef

    Molecular psychiatry

    2018  Volume 24, Issue 2, Page(s) 241–251

    Abstract: Epilepsy and Mental Retardation Limited to Females (EFMR) is an infantile onset disorder characterized by clusters of seizures. EFMR is due to mutations in the X-chromosome gene PCDH19, and is underpinned by cellular mosaicism due to X-chromosome ... ...

    Abstract Epilepsy and Mental Retardation Limited to Females (EFMR) is an infantile onset disorder characterized by clusters of seizures. EFMR is due to mutations in the X-chromosome gene PCDH19, and is underpinned by cellular mosaicism due to X-chromosome inactivation in females or somatic mutation in males. This review characterizes the neuropsychiatric profile of this disorder and examines the association of clinical and molecular factors with neuropsychiatric outcomes. Data were extracted from 38 peer-reviewed original articles including 271 individual cases. We found that seizure onset ≤12 months was significantly associated (p = 4.127 × 10
    MeSH term(s) Cadherins/genetics ; Cadherins/metabolism ; Comorbidity ; Epilepsy/genetics ; Female ; Genetic Association Studies ; Humans ; Infant ; Infant, Newborn ; Intellectual Disability/genetics ; Male ; Mutation ; Protocadherins ; Seizures/genetics ; Spasms, Infantile/genetics
    Chemical Substances Cadherins ; PCDH19 protein, human ; Protocadherins
    Language English
    Publishing date 2018-06-11
    Publishing country England
    Document type Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Systematic Review
    ZDB-ID 1330655-8
    ISSN 1476-5578 ; 1359-4184
    ISSN (online) 1476-5578
    ISSN 1359-4184
    DOI 10.1038/s41380-018-0066-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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