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  1. Book: Plant genomic and cytogenetic databases

    García, Sonia / Nualart, Neus

    (Methods in molecular biology ; 2703 ; Springer protocols)

    2023  

    Author's details edited by Sònia Garcia, Neus Nualart
    Series title Methods in molecular biology ; 2703
    Springer protocols
    Collection
    Keywords Plant genomes/Databases ; Cytogenetics/Databases
    Subject code 572.8620285574
    Language English
    Size xiii, 249 Seiten, Illustrationen
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT030348771
    ISBN 9781071633885 ; 9781071633892 ; 1071633880 ; 1071633899
    Database Catalogue ZB MED Medicine, Health

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  2. Book: Plant cytogenetics and cytogenomics

    Heitkam, Tony / García, Sonia

    methods and protocols

    (Methods in molecular biology ; 2672 ; Springer protocols)

    2023  

    Author's details edited by Tony Heitkam, Sònia Garcia
    Series title Methods in molecular biology ; 2672
    Springer protocols
    Collection
    Keywords Plant cytogenetics ; Genomics
    Subject code 572.82
    Language English
    Size xviii, 562 Seiten, Illustrationen, 26 cm
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT030059922
    ISBN 978-1-0716-3225-3 ; 9781071632260 ; 1-0716-3225-6 ; 1071632264
    Database Catalogue ZB MED Medicine, Health

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  3. Article: Pandemics and Traditional Plant-Based Remedies. A Historical-Botanical Review in the Era of COVID19.

    Garcia, Sònia

    Frontiers in plant science

    2020  Volume 11, Page(s) 571042

    Abstract: Pandemics are as old as humanity and since ancient times we have turned to plants to find solutions to health-related problems. Traditional medicines based mostly on plants are still the only therapeutic possibility in many developing countries, but even ...

    Abstract Pandemics are as old as humanity and since ancient times we have turned to plants to find solutions to health-related problems. Traditional medicines based mostly on plants are still the only therapeutic possibility in many developing countries, but even in the richest ones, herbal formulation currently receives increased attention. Plants are natural laboratories whose complex secondary metabolism produces a wealth of chemical compounds, leading to drug discovery - 25% of widespread use drugs are indeed of plant origin. Their therapeutic potential is even bigger: although many plant-based compounds show inhibitory effects against a myriad of pathogens, few reach the stage of clinical trials. Their mechanism of action is often unknown, yet traditional plant-based remedies have the advantage of a long-term experience in their use, usually of hundreds to thousands of years, and thus a precious experience on their safety and effects. Here I am providing a non-systematic historical-botanical review of some of the most devastating pandemics that humanity has faced, with a focus on plant therapeutic uses. I will revisit the Middle Ages black death, in which a plant-based lotion (the four thieves vinegar) showed some effectiveness; the smallpox, a viral disease that lead to the discovery of vaccination but for which the native Americans had a plant ally, an interesting carnivorous plant species; tuberculosis and the use of garlic; the Spanish flu and the widespread recommendation of eating onions, among other plant-based treatments; and malaria, whose first effective treatment, quinine, came from the bark of a Peruvian tree, properties already known by the Quechua people. Synthetic analogues of quinine such as chloroquine or hydroxychloroquine are now being revisited for the treatment of COVID19 symptoms, as they are artemisinin and derivatives, other plant-based compounds effective against malaria. Finally, I will give some hints on another facet of plants to aid us in the prevention of infectious diseases: the production of biotechnological plant-based vaccines. Altogether, my aim is to stress the significant role of plants in global health (past, present and future) and the need of enhancing and protecting the botanical knowledge, from systematics to conservation, from ecology to ethnobotany.
    Keywords covid19
    Language English
    Publishing date 2020-08-28
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2020.571042
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes.

    Maiwald, Sophie / Mann, Ludwig / Garcia, Sònia / Heitkam, Tony

    Molecular biology and evolution

    2024  Volume 41, Issue 2

    Abstract: The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to the 5S preservation we observe the occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandras. Cassandras harbor highly conserved 5S ... ...

    Abstract The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to the 5S preservation we observe the occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandras. Cassandras harbor highly conserved 5S rDNA-related sequences within their long terminal repeats, advantageously providing them with the 5S internal promoter. However, the dynamics of Cassandra retrotransposon evolution in the context of 5S rRNA gene sequence information and structural arrangement are still unclear, especially: (1) do we observe repeated or gradual domestication of the highly conserved 5S promoter by Cassandras and (2) do changes in 5S organization such as in the linked 35S-5S rDNA arrangements impact Cassandra evolution? Here, we show evidence for gradual co-evolution of Cassandra sequences with their corresponding 5S rDNAs. To follow the impact of 5S rDNA variability on Cassandra TEs, we investigate the Asteraceae family where highly variable 5S rDNAs, including 5S promoter shifts and both linked and separated 35S-5S rDNA arrangements have been reported. Cassandras within the Asteraceae mirror 5S rDNA promoter mutations of their host genome, likely as an adaptation to the host's specific 5S transcription factors and hence compensating for evolutionary changes in the 5S rDNA sequence. Changes in the 5S rDNA sequence and in Cassandras seem uncorrelated with linked/separated rDNA arrangements. We place all these observations into the context of angiosperm 5S rDNA-Cassandra evolution, discuss Cassandra's origin hypotheses (single or multiple) and Cassandra's possible impact on rDNA and plant genome organization, giving new insights into the interplay of ribosomal genes and transposable elements.
    MeSH term(s) RNA, Ribosomal, 5S/genetics ; Retroelements/genetics ; Genes, rRNA ; Base Sequence ; DNA, Ribosomal/genetics ; Genome, Plant ; Mutation ; Evolution, Molecular
    Chemical Substances RNA, Ribosomal, 5S ; Retroelements ; DNA, Ribosomal
    Language English
    Publishing date 2024-01-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msae010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Pandemics and Traditional Plant-Based Remedies. A Historical-Botanical Review in the Era of COVID19

    Garcia, Sònia

    Frontiers in Plant Science

    2020  Volume 11

    Keywords Plant Science ; covid19
    Publisher Frontiers Media SA
    Publishing country ch
    Document type Article ; Online
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2020.571042
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Sacubitril/valsartan: Where mechanism meets evidence-based medicine.

    Rivas García, Sonia / Álvarez-García, Jesús

    European journal of heart failure

    2023  Volume 26, Issue 1, Page(s) 127–129

    MeSH term(s) Humans ; Heart Failure/drug therapy ; Evidence-Based Medicine ; Valsartan ; Aminobutyrates/therapeutic use ; Biphenyl Compounds ; Drug Combinations ; Tetrazoles/therapeutic use ; Angiotensin Receptor Antagonists/therapeutic use ; Stroke Volume
    Chemical Substances sacubitril (17ERJ0MKGI) ; Valsartan (80M03YXJ7I) ; Aminobutyrates ; Biphenyl Compounds ; Drug Combinations ; Tetrazoles ; Angiotensin Receptor Antagonists
    Language English
    Publishing date 2023-12-12
    Publishing country England
    Document type Editorial
    ZDB-ID 1483672-5
    ISSN 1879-0844 ; 1388-9842
    ISSN (online) 1879-0844
    ISSN 1388-9842
    DOI 10.1002/ejhf.3100
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Ultraviolet light spectroscopic characterization of ibuprofen acid aggregation in deionized water.

    Marbán, Gregorio / Fernández-Pérez, Amparo / Álvarez-García, Sonia

    Heliyon

    2023  Volume 9, Issue 11, Page(s) e21260

    Abstract: This work provides a description of the aggregation equilibria of ibuprofen acid in deionized water at temperatures between 20 and 40 °C in the 0.1-20.1 ppm concentration range. For this goal, we have made use of UV-Visible spectroscopy. A calculation ... ...

    Abstract This work provides a description of the aggregation equilibria of ibuprofen acid in deionized water at temperatures between 20 and 40 °C in the 0.1-20.1 ppm concentration range. For this goal, we have made use of UV-Visible spectroscopy. A calculation algorithm was developed to obtain the aggregate orders and thermodynamic parameters from the experimental absorbance values. Monomeric ibuprofen acid was found to be absent in water solutions. In addition to the dimer, two aggregates formed by 32 and 128 monomeric units were found to co-exist in solution at the highest concentration tested. A critical micelle concentration of 7.8 ppm was estimated for this system. The appearance of the first aggregate occurs when the pH drops below the
    Language English
    Publishing date 2023-10-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e21260
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Can we have it all? Repurposing target capture for repeat genomics. A commentary on: 'Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA'.

    Heitkam, Tony / Garcia, Sònia

    Annals of botany

    2021  Volume 128, Issue 7, Page(s) iii–v

    MeSH term(s) DNA ; Genomics ; Sequence Analysis, DNA
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2021-07-05
    Publishing country England
    Document type Editorial ; Comment
    ZDB-ID 1461328-1
    ISSN 1095-8290 ; 0305-7364
    ISSN (online) 1095-8290
    ISSN 0305-7364
    DOI 10.1093/aob/mcab080
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol.

    Garcia, Sònia / Pascual-Díaz, Joan Pere / Krumpolcová, Alice / Kovarík, Ales

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

    2023  Volume 2672, Page(s) 501–512

    Abstract: The ribosomal RNA genes (rDNA) are universal genome components with a housekeeping function, given the crucial role of ribosomal RNA in the synthesis of ribosomes and thus for life-on-Earth. Therefore, their genomic organization is of considerable ... ...

    Abstract The ribosomal RNA genes (rDNA) are universal genome components with a housekeeping function, given the crucial role of ribosomal RNA in the synthesis of ribosomes and thus for life-on-Earth. Therefore, their genomic organization is of considerable interest for biologists, in general. Ribosomal RNA genes have also been largely used to establish phylogenetic relationships, and to identify allopolyploid or homoploid hybridization.Here, we demonstrate how high-throughput sequencing data, through graph clustering implemented in RepeatExplorer2 pipeline ( https://repeatexplorer-elixir.cerit-sc.cz/galaxy/ ), can be helpful to decipher the genomic organization of 5S rRNA genes. We show that the linear shapes of cluster graphs are reminiscent to the linked organization of 5S and 35S rDNA (L-type arrangement) while the circular graphs correspond to their separate arrangement (S-type). We further present a simplified protocol based on the paper by (Garcia et al., Front Plant Sci 11:41, 2020) about the use of graph clustering of 5S rDNA homoeologs (S-type) to identify hybridization events in the species history. We found that the graph complexity (i.e., graph circularity in this case) is related to ploidy and genome complexity, with diploids typically showing circular-shaped graphs while allopolyploids and other interspecific hybrids display more complex graphs, with usually two or more interconnected loops representing intergenic spacers. When a three-genomic comparative clustering analysis from a given hybrid (homoploid/allopolyploid) and its putative progenitor species (diploids) is performed, it is possible to identify the corresponding homoeologous 5S rRNA gene families, and to elucidate the contribution of each putative parental genome to the 5S rDNA pool of the hybrid. Thus, the analysis of 5S rDNA cluster graphs by RepeatExplorer, together with information coming from other sources (e.g., morphology, cytogenetics) is a complementary approach for the determination of allopolyploid or homoploid hybridization and even ancient introgression events.
    MeSH term(s) DNA, Ribosomal/genetics ; Phylogeny ; RNA, Ribosomal, 5S/genetics ; Genes, rRNA ; Genomics
    Chemical Substances DNA, Ribosomal ; RNA, Ribosomal, 5S
    Language English
    Publishing date 2023-06-19
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3226-0_30
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Sex-chrom v. 2.0: a database of green plant species with sex chromosomes.

    Garcia, Sònia / Janousek, Bohuslav / Pascual-Díaz, Joan Pere / Renner, Susanne S

    Chromosoma

    2023  Volume 132, Issue 1, Page(s) 55–58

    MeSH term(s) Sex Chromosomes/genetics ; Viridiplantae
    Language English
    Publishing date 2023-02-02
    Publishing country Austria
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 203083-4
    ISSN 1432-0886 ; 0009-5915
    ISSN (online) 1432-0886
    ISSN 0009-5915
    DOI 10.1007/s00412-023-00786-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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