LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 373

Search options

  1. Article ; Online: The chromosome hoarding syndrome of (some) ferns and lycophytes.

    Li, Fay-Wei

    Nature reviews. Genetics

    2023  Volume 24, Issue 11, Page(s) 737

    Language English
    Publishing date 2023-07-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/s41576-023-00639-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 5474: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 40: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: Decolonizing botanical genomics.

    Li, Fay-Wei

    Nature plants

    2021  Volume 7, Issue 12, Page(s) 1542–1543

    Language English
    Publishing date 2021-10-21
    Publishing country England
    Document type Journal Article ; Comment
    ISSN 2055-0278
    ISSN (online) 2055-0278
    DOI 10.1038/s41477-021-01041-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: PURC Provides Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem.

    Schafran, Peter / Li, Fay-Wei / Rothfels, Carl J

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

    2023  Volume 2545, Page(s) 189–206

    Abstract: Inferring the true biological sequences from amplicon mixtures remains a difficult bioinformatics problem. The traditional approach is to cluster sequencing reads by similarity thresholds and treat the consensus sequence of each cluster as an " ... ...

    Abstract Inferring the true biological sequences from amplicon mixtures remains a difficult bioinformatics problem. The traditional approach is to cluster sequencing reads by similarity thresholds and treat the consensus sequence of each cluster as an "operational taxonomic unit" (OTU). Recently, this approach has been improved by model-based methods that correct PCR and sequencing errors in order to infer "amplicon sequence variants" (ASVs). To date, ASV approaches have been used primarily in metagenomics, but they are also useful for determining homeologs in polyploid organisms. To facilitate the usage of ASV methods among polyploidy researchers, we incorporated ASV inference alongside OTU clustering in PURC v2.0, a major update to PURC (Pipeline for Untangling Reticulate Complexes). In addition, PURC v2.0 features faster demultiplexing than the original version and has been updated to be compatible with Python 3. In this chapter we present results indicating that using the ASV approach is more likely to infer the correct biological sequences in comparison to the earlier OTU-based PURC and describe how to prepare sequencing data, run PURC v2.0 under several different modes, and interpret the output.
    MeSH term(s) Humans ; Phylogeny ; Cluster Analysis ; Computational Biology ; Consensus Sequence ; Polyploidy
    Language English
    Publishing date 2023-01-31
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2561-3_10
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Twelve new metagenome-assembled genomes from non-axenic culture of

    Rizzieri, Yanã C / Lipari, August / Gunn, Laura / Li, Fay-Wei

    Microbiology resource announcements

    2023  Volume 13, Issue 1, Page(s) e0072823

    Abstract: We report 12 metagenome-assembled genomes from a non-axenic culture of the red ... ...

    Abstract We report 12 metagenome-assembled genomes from a non-axenic culture of the red alga
    Language English
    Publishing date 2023-12-01
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00728-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Accelerating gametophytic growth in the model hornwort Anthoceros agrestis

    Andika Gunadi / Fay‐Wei Li / Joyce Van Eck

    Applications in Plant Sciences, Vol 10, Iss 2, Pp n/a-n/a (2022)

    2022  

    Abstract: Abstract Premise Hornworts belong to a unique lineage of bryophytes with critical traits for elucidating the evolution of land plants; however, the development of functional genetic tools for hornworts has been hampered by their relatively slow ... ...

    Abstract Abstract Premise Hornworts belong to a unique lineage of bryophytes with critical traits for elucidating the evolution of land plants; however, the development of functional genetic tools for hornworts has been hampered by their relatively slow gametophytic growth. Methods To identify the external factors that influence the development of hornwort gametophytes and potentially augment their growth, we evaluated the contributions of several culture medium components on the axenic gametophytic growth of Anthoceros agrestis, a model hornwort. A streamlined growth assay utilizing semiautomated image analysis was developed to rapidly quantify and compare tissue development spanning four weeks of culture on solidified medium. Results The addition of sucrose, ammonium nitrate, activated charcoal, pH buffering, and growth regulators (2,4‐dichlorophenoxyacetic acid, 6‐benzylaminopurine, and thidiazuron) affected gametophyte tissue survival, growth patterns, and the rate of thalli growth. Subsequently, an optimized medium composition and growth regimen for accelerating A. agrestis gametophytic growth were formulated, which at four weeks of culture increased the tissue wet weight by 2.1‐ to 8.5‐fold compared with other previously utilized hornwort growth media. Discussion Our protocol for generating vigorous starting material and accelerated tissue regeneration is pertinent for advancing gene function characterization and genome editing in hornworts.
    Keywords Anthocerotophyta ; growth medium ; image analysis ; plant growth regulator ; plant tissue culture ; Biology (General) ; QH301-705.5 ; Botany ; QK1-989
    Subject code 580
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a 'diploids-first' approach to conservation.

    Wickell, David / Landis, Jacob / Zimmer, Elizabeth / Li, Fay-Wei

    Annals of botany

    2023  Volume 133, Issue 2, Page(s) 261–272

    Abstract: Background and aims: Allopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However, many studies have questioned the importance of extant polyploid lineages, suggesting that the vast ... ...

    Abstract Background and aims: Allopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However, many studies have questioned the importance of extant polyploid lineages, suggesting that the vast majority may constitute evolutionary 'dead ends'. This has important implications for conservation efforts where polyploids and diploid progenitors often compete for wildlife management resources. Isoetes appalachiana is an allotetraploid that is broadly distributed throughout the eastern USA alongside its diploid progenitors, I. valida and I. engelmannii. As such, this species complex provides an excellent opportunity to investigate the processes that underpin the formation and survival of allopolyploid lineages.
    Methods: Here we utilized RADseq and whole-chloroplast sequencing to unravel the demographic and evolutionary history of hybridization in this widespread species complex. We developed a modified protocol for phasing RADseq loci from an allopolyploid in order to examine each progenitor's genetic contribution independently in a phylogenetic context. Additionally, we conducted population-level analyses to examine genetic diversity and evidence of gene flow within species.
    Key results: Isoetes appalachiana is the product of multiple phylogenetic origins, suggesting that formation and establishment of allopolyploids are common in this group. Hybridization appears to be unidirectional, with I. engelmannii consistently being the maternal progenitor. Additionally, we find that polyploid lineages are genetically isolated, rarely if ever experiencing gene flow between geographically distinct populations.
    Conclusions: Allopolyploid lineages of I. appalachiana appear to form frequently and experience a high degree of genetic isolation following formation. Thus, our results appear to corroborate the hypothesis that the vast majority of recently formed polyploids may represent evolutionary dead ends. However, this does not necessarily lessen the evolutionary importance or ecological impact of polyploidy per se. Accordingly, we propose a conservation strategy that prioritizes diploid taxa, thus preserving downstream processes that recurrently generate allopolyploid diversity.
    MeSH term(s) Phylogeny ; Diploidy ; Metagenomics ; Biological Evolution ; Tracheophyta ; Polyploidy
    Language English
    Publishing date 2023-11-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1461328-1
    ISSN 1095-8290 ; 0305-7364
    ISSN (online) 1095-8290
    ISSN 0305-7364
    DOI 10.1093/aob/mcad180
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article: Accelerating gametophytic growth in the model hornwort

    Gunadi, Andika / Li, Fay-Wei / Van Eck, Joyce

    Applications in plant sciences

    2022  Volume 10, Issue 2, Page(s) e11460

    Abstract: Premise: Hornworts belong to a unique lineage of bryophytes with critical traits for elucidating the evolution of land plants; however, the development of functional genetic tools for hornworts has been hampered by their relatively slow gametophytic ... ...

    Abstract Premise: Hornworts belong to a unique lineage of bryophytes with critical traits for elucidating the evolution of land plants; however, the development of functional genetic tools for hornworts has been hampered by their relatively slow gametophytic growth.
    Methods: To identify the external factors that influence the development of hornwort gametophytes and potentially augment their growth, we evaluated the contributions of several culture medium components on the axenic gametophytic growth of
    Results: The addition of sucrose, ammonium nitrate, activated charcoal, pH buffering, and growth regulators (2,4-dichlorophenoxyacetic acid, 6-benzylaminopurine, and thidiazuron) affected gametophyte tissue survival, growth patterns, and the rate of thalli growth. Subsequently, an optimized medium composition and growth regimen for accelerating
    Discussion: Our protocol for generating vigorous starting material and accelerated tissue regeneration is pertinent for advancing gene function characterization and genome editing in hornworts.
    Language English
    Publishing date 2022-03-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2699923-7
    ISSN 2168-0450
    ISSN 2168-0450
    DOI 10.1002/aps3.11460
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article: Characterizing Culturable Bacterial Endophytes of Five Lycopodiaceae Species

    Petlewski, Alaina R. / Patterson, Ariel / Li, Fay-Wei

    American fern journal. 2022 Apr. 26, v. 112, no. 2

    2022  

    Abstract: Microbial endophytes are integral factors in plant evolution, ecology, and physiology. However, the endophyte communities across all major plant lineages have yet to be characterized, and data are particularly scarce for lycophytes. Here we used a ... ...

    Abstract Microbial endophytes are integral factors in plant evolution, ecology, and physiology. However, the endophyte communities across all major plant lineages have yet to be characterized, and data are particularly scarce for lycophytes. Here we used a culture-based approach to survey the diversity of endophytic bacteria in five sympatric Lycopodiaceae species in central New York. The most notable endophyte isolated from this study is a bacterial species Allobranchiibius huperziae, which was only recently described from the roots of Huperzia serrata in China. The fact that the same endophyte was also found in our North American samples suggest a possible specific association with Lycopodiaceae species. The data and cultures from this study provide an important foundation for future metagenomic and functional studies to characterize better the diversity and significance of plant endophytes.
    Keywords Huperzia serrata ; endophytes ; evolution ; ferns and fern allies ; physiology ; sympatry ; China ; New York
    Language English
    Dates of publication 2022-0426
    Size p. 79-92.
    Publishing place American Fern Society
    Document type Article
    ZDB-ID 2175903-0
    ISSN 1938-422X ; 0002-8444
    ISSN (online) 1938-422X
    ISSN 0002-8444
    DOI 10.1640/0002-8444-112.2.79
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article: Accelerating gametophytic growth in the model hornwort Anthoceros agrestis

    Gunadi, Andika / Li, Fay‐Wei / Van Eck, Joyce

    Applications in plant sciences. 2022 Mar., v. 10, no. 2

    2022  

    Abstract: PREMISE: Hornworts belong to a unique lineage of bryophytes with critical traits for elucidating the evolution of land plants; however, the development of functional genetic tools for hornworts has been hampered by their relatively slow gametophytic ... ...

    Abstract PREMISE: Hornworts belong to a unique lineage of bryophytes with critical traits for elucidating the evolution of land plants; however, the development of functional genetic tools for hornworts has been hampered by their relatively slow gametophytic growth. METHODS: To identify the external factors that influence the development of hornwort gametophytes and potentially augment their growth, we evaluated the contributions of several culture medium components on the axenic gametophytic growth of Anthoceros agrestis, a model hornwort. A streamlined growth assay utilizing semiautomated image analysis was developed to rapidly quantify and compare tissue development spanning four weeks of culture on solidified medium. RESULTS: The addition of sucrose, ammonium nitrate, activated charcoal, pH buffering, and growth regulators (2,4‐dichlorophenoxyacetic acid, 6‐benzylaminopurine, and thidiazuron) affected gametophyte tissue survival, growth patterns, and the rate of thalli growth. Subsequently, an optimized medium composition and growth regimen for accelerating A. agrestis gametophytic growth were formulated, which at four weeks of culture increased the tissue wet weight by 2.1‐ to 8.5‐fold compared with other previously utilized hornwort growth media. DISCUSSION: Our protocol for generating vigorous starting material and accelerated tissue regeneration is pertinent for advancing gene function characterization and genome editing in hornworts.
    Keywords 2,4-D ; ammonium nitrate ; benzyladenine ; charcoal ; gametophytes ; genes ; image analysis ; pH ; sucrose ; thallus ; thidiazuron ; tissue repair
    Language English
    Dates of publication 2022-03
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2699923-7
    ISSN 2168-0450
    ISSN 2168-0450
    DOI 10.1002/aps3.11460
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article: Nostoc

    Chatterjee, Poulami / Schafran, Peter / Li, Fay-Wei / Meeks, John C

    Molecular plant-microbe interactions : MPMI

    2022  Volume 35, Issue 10, Page(s) 917–932

    Abstract: Endosymbiotic associations between hornworts and nitrogen-fixing cyanobacteria form when the plant is limited for combined nitrogen (N). We generated RNA-seq data to examine temporal gene expression patterns during the culturing of N- ... ...

    Abstract Endosymbiotic associations between hornworts and nitrogen-fixing cyanobacteria form when the plant is limited for combined nitrogen (N). We generated RNA-seq data to examine temporal gene expression patterns during the culturing of N-starved
    MeSH term(s) Ammonium Compounds ; Anthocerotophyta/genetics ; Chlorophyll ; Gene Expression ; Nitrogen ; Nostoc/genetics ; Symbiosis/genetics
    Chemical Substances Ammonium Compounds ; Chlorophyll (1406-65-1) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2022-09-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 743331-1
    ISSN 1943-7706 ; 0894-0282
    ISSN (online) 1943-7706
    ISSN 0894-0282
    DOI 10.1094/MPMI-05-22-0101-R
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3530: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top