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  1. Book ; Online: Evolution, Composition and Regulation of Supernumerary B Chromosomes

    Houben, Andreas / Jones, Neil / Martins, Cesar / Trifonov, Vladimir

    2019  

    Abstract: Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi. Since their discovery more than a century ago, they have been a source of puzzlement, as they only occur in some ... ...

    Abstract Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi. Since their discovery more than a century ago, they have been a source of puzzlement, as they only occur in some members of a population and are absent from others. When they do occur, they are often harmful, and in the absence of "selfishness", based on mechanisms of mitotic and meiotic drive, there appears to be no obvious reason for their existence. Cytogeneticists have long wrestled with questions about the biological existence of these enigmatic elements, including their lack of any adaptive properties, apparent absence of functional genes, their origin, sequence organization, and co-evolution as nuclear parasites. Emerging new technologies are now enabling researchers to step up a gear, to look enthusiastically beyond the previous limits of the horizon, and to uncover the secrets of these "silent" chromosomes. This book provides a comprehensive guide to theoretical advancements in the field of B chromosome research in both animal and plant systems
    Keywords Science (General) ; Biology (General)
    Size 1 electronic resource (254 pages)
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Document type Book ; Online
    Note eng ; Open Access
    HBZ-ID HT020307443
    ISBN 9783038977865 ; 9783038977872 ; 3038977861 ; 303897787X
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Chromosome-Centric View of Genome Organization and Evolution.

    Sharakhova, Maria / Trifonov, Vladimir

    Genes

    2021  Volume 12, Issue 8

    Abstract: Genetic material in all cellular organisms is packed into chromosomes, which represent essential units of inheritance, recombination, and evolution [ ... ]. ...

    Abstract Genetic material in all cellular organisms is packed into chromosomes, which represent essential units of inheritance, recombination, and evolution [...].
    MeSH term(s) Animals ; Chromosomes ; Evolution, Molecular ; Genome
    Language English
    Publishing date 2021-08-12
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12081237
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: What is a B chromosome? Early definitions revisited.

    Ferree, Patrick M / Blagojević, Jelena / Houben, Andreas / Martins, Cesar / Trifonov, Vladimir A / Vujošević, Mladen

    G3 (Bethesda, Md.)

    2024  

    Abstract: Since the discovery of B chromosomes, multiple different definitions of these selfish genetic elements have been put forth. We reconsidered early definitions in light of recently published studies. While there are many characteristics that vary among ... ...

    Abstract Since the discovery of B chromosomes, multiple different definitions of these selfish genetic elements have been put forth. We reconsidered early definitions in light of recently published studies. While there are many characteristics that vary among different B chromosomes, such as their evolutionary origins, size, segregation behaviors, gene content, and function, there is one defining trait of all B chromosomes: they are nonessential for the organism. The points raised here may be useful for framing future B chromosome studies and help guide the categorization of new chromosomal elements that are uncovered in genomic studies.
    Language English
    Publishing date 2024-04-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkae068
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Chromosome-Centric View of Genome Organization and Evolution

    Sharakhova, Maria / Trifonov, Vladimir

    Genes. 2021 Aug. 12, v. 12, no. 8

    2021  

    Abstract: Genetic material in all cellular organisms is packed into chromosomes, which represent essential units of inheritance, recombination, and evolution [ ... ] ...

    Abstract Genetic material in all cellular organisms is packed into chromosomes, which represent essential units of inheritance, recombination, and evolution [...]
    Keywords chromosomes ; evolution ; genes ; materials ; organizations
    Language English
    Dates of publication 2021-0812
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12081237
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Conservation of Major Satellite DNAs in Snake Heterochromatin

    Lisachov, Artem / Rumyantsev, Alexander / Prokopov, Dmitry / Ferguson-Smith, M. A. / Trifonov, Vladimir

    Animals. 2023 Jan. 17, v. 13, no. 3

    2023  

    Abstract: Repetitive DNA sequences constitute a sizeable portion of animal genomes, and tandemly organized satellite DNAs are a major part of them. They are usually located in constitutive heterochromatin clusters in or near the centromeres or telomeres, and less ... ...

    Abstract Repetitive DNA sequences constitute a sizeable portion of animal genomes, and tandemly organized satellite DNAs are a major part of them. They are usually located in constitutive heterochromatin clusters in or near the centromeres or telomeres, and less frequently in the interstitial parts of chromosome arms. They are also frequently accumulated in sex chromosomes. The function of these clusters is to sustain the architecture of the chromosomes and the nucleus, and to regulate chromosome behavior during mitosis and meiosis. The study of satellite DNA diversity is important for understanding sex chromosome evolution, interspecific hybridization, and speciation. In this work, we identified four satellite DNA families in the genomes of two snakes from different families: Daboia russelii (Viperidae) and Pantherophis guttatus (Colubridae) and determine their chromosomal localization. We found that one family is localized in the centromeres of both species, whereas the others form clusters in certain chromosomes or subsets of chromosomes. BLAST with snake genome assemblies showed the conservation of such clusters, as well as a subtle presence of the satellites in the interspersed manner outside the clusters. Overall, our results show high conservation of satellite DNA in snakes and confirm the “library” model of satellite DNA evolution.
    Keywords DNA ; Daboia russelii ; Pantherophis guttatus ; centromeres ; chromosome mapping ; evolution ; genome ; heterochromatin ; interspecific hybridization ; meiosis ; mitosis ; models ; satellite DNA ; satellites ; sex chromosomes ; snakes ; telomeres
    Language English
    Dates of publication 2023-0117
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani13030334
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Preface.

    Trifonov, Vladimir A / Cioffi, Marcelo B / Liehr, Thomas

    Cytogenetic and genome research

    2021  Volume 161, Issue 1-2, Page(s) 5

    Language English
    Publishing date 2021-04-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2087824-2
    ISSN 1424-859X ; 1424-8581
    ISSN (online) 1424-859X
    ISSN 1424-8581
    DOI 10.1159/000513608
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 512: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article: Conservation of Major Satellite DNAs in Snake Heterochromatin.

    Lisachov, Artem / Rumyantsev, Alexander / Prokopov, Dmitry / Ferguson-Smith, Malcolm / Trifonov, Vladimir

    Animals : an open access journal from MDPI

    2023  Volume 13, Issue 3

    Abstract: Repetitive DNA sequences constitute a sizeable portion of animal genomes, and tandemly organized satellite DNAs are a major part of them. They are usually located in constitutive heterochromatin clusters in or near the centromeres or telomeres, and less ... ...

    Abstract Repetitive DNA sequences constitute a sizeable portion of animal genomes, and tandemly organized satellite DNAs are a major part of them. They are usually located in constitutive heterochromatin clusters in or near the centromeres or telomeres, and less frequently in the interstitial parts of chromosome arms. They are also frequently accumulated in sex chromosomes. The function of these clusters is to sustain the architecture of the chromosomes and the nucleus, and to regulate chromosome behavior during mitosis and meiosis. The study of satellite DNA diversity is important for understanding sex chromosome evolution, interspecific hybridization, and speciation. In this work, we identified four satellite DNA families in the genomes of two snakes from different families:
    Language English
    Publishing date 2023-01-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani13030334
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Addressing Long-Standing Questions with Advanced Approaches: The 4th B Chromosome Conference.

    Martins, Cesar / Trifonov, Vladimir / Houben, Andreas

    Cytogenetic and genome research

    2020  Volume 160, Issue 3, Page(s) 111–117

    Abstract: B chromosomes (Bs) are enigmatic accessory genomic elements extensively characterized in diverse eukaryotes. Since their discovery in the beginning of the 20th century, B chromosomes have been the subject of investigation in laboratories all around the ... ...

    Abstract B chromosomes (Bs) are enigmatic accessory genomic elements extensively characterized in diverse eukaryotes. Since their discovery in the beginning of the 20th century, B chromosomes have been the subject of investigation in laboratories all around the world. As a consequence, scientific meetings have dealt with B chromosomes, including the most specific and important conference in the field, "The B Chromosome Conference." The 4th B Chromosome Conference (4BCC) took place in Botucatu, Brazil, in 2019 and was an excellent opportunity to discuss the latest developments in the B chromosome research field. B chromosome science has advanced from classical and molecular cytogenetics to genomics and bioinformatics approaches. The recent advances in next-generation sequencing technologies and high-throughput molecular biology protocols have led Bs to be the subject of massive data analysis, thus enabling the investigation of structural and functional issues not considered before. Although extensive progress has been made, questions are still remaining to be answered. The advances in functional studies based on RNA, epigenetics, and gene ontologies open the perspective to a better understanding of the complex biology of B chromosomes.
    MeSH term(s) Brazil ; Chromosomes/genetics ; Cytogenetics ; Epigenomics ; Eukaryota/genetics ; Evolution, Molecular ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; RNA/genetics
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2020-03-07
    Publishing country Switzerland
    Document type Congress
    ZDB-ID 2087824-2
    ISSN 1424-859X ; 1424-8581
    ISSN (online) 1424-859X
    ISSN 1424-8581
    DOI 10.1159/000506695
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 512: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article: Evolution, Composition and Regulation of Supernumerary B Chromosomes.

    Houben, Andreas / Jones, Neil / Martins, Cesar / Trifonov, Vladimir

    Genes

    2019  Volume 10, Issue 2

    Abstract: Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi [ ... ]. ...

    Abstract Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi [...].
    MeSH term(s) Abnormal Karyotype ; Animals ; Evolution, Molecular
    Language English
    Publishing date 2019-02-20
    Publishing country Switzerland
    Document type Editorial ; Introductory Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes10020161
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Compound Activity Prediction with Dose-Dependent Transcriptomic Profiles and Deep Learning.

    Godinez, William J / Trifonov, Vladimir / Fang, Bin / Kuzu, Guray / Pei, Luying / Guiguemde, W Armand / Martin, Eric J / King, Frederick J / Jenkins, Jeremy L / Skewes-Cox, Peter

    Journal of chemical information and modeling

    2024  Volume 64, Issue 7, Page(s) 2695–2704

    Abstract: Predicting compound activity in assays is a long-standing challenge in drug discovery. Computational models based on compound-induced gene expression signatures from a single profiling assay have shown promise toward predicting compound activity in other, ...

    Abstract Predicting compound activity in assays is a long-standing challenge in drug discovery. Computational models based on compound-induced gene expression signatures from a single profiling assay have shown promise toward predicting compound activity in other, seemingly unrelated, assays. Applications of such models include predicting mechanisms-of-action (MoA) for phenotypic hits, identifying off-target activities, and identifying polypharmacologies. Here, we introduce transcriptomics-to-activity transformer (TAT) models that leverage gene expression profiles observed over compound treatment at multiple concentrations to predict the compound activity in other biochemical or cellular assays. We built TAT models based on gene expression data from a RASL-seq assay to predict the activity of 2692 compounds in 262 dose-response assays. We obtained useful models for 51% of the assays, as determined through a realistic held-out set. Prospectively, we experimentally validated the activity predictions of a TAT model in a malaria inhibition assay. With a 63% hit rate, TAT successfully identified several submicromolar malaria inhibitors. Our results thus demonstrate the potential of transcriptomic responses over compound concentration and the TAT modeling framework as a cost-efficient way to identify the bioactivities of promising compounds across many assays.
    MeSH term(s) Humans ; Transcriptome ; Deep Learning ; Drug Discovery/methods ; Gene Expression Profiling ; Malaria
    Language English
    Publishing date 2024-01-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01855
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
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