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  1. Article ; Online: Now that We Got There, What Next?

    Tanaka, Elly M

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

    2022  Volume 2562, Page(s) 471–479

    Abstract: As seen in the protocols in this book, the opportunities to pursue work at the cellular and molecular work in salamanders have considerably broadened over the last years. The availability of genomic information and genome editing, and the possibility to ... ...

    Abstract As seen in the protocols in this book, the opportunities to pursue work at the cellular and molecular work in salamanders have considerably broadened over the last years. The availability of genomic information and genome editing, and the possibility to image tissues live and other methods enhance the spectrum of biological questions accessible to all researchers. Here I provide a personal perspective on what I consider exciting future questions open for investigation.
    MeSH term(s) Animals ; Genome ; Urodela ; Genomics ; Gene Editing
    Language English
    Publishing date 2022-10-22
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2659-7_31
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  2. Article ; Online: Regenerating tissues.

    Tanaka, Elly M

    Science (New York, N.Y.)

    2018  Volume 360, Issue 6387, Page(s) 374–375

    MeSH term(s) Regeneration
    Language English
    Publishing date 2018--27
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.aat4588
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  3. Article ; Online: A new society for regenerative biologists.

    Poss, Kenneth D / Tanaka, Elly M

    Development (Cambridge, England)

    2021  Volume 148, Issue 3

    MeSH term(s) Animals ; Humans ; Regeneration/physiology ; Regenerative Medicine ; Societies ; Tissue Engineering
    Language English
    Publishing date 2021-02-12
    Publishing country England
    Document type Editorial
    ZDB-ID 90607-4
    ISSN 1477-9129 ; 0950-1991
    ISSN (online) 1477-9129
    ISSN 0950-1991
    DOI 10.1242/dev.199474
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  4. Article ; Online: Navigation and Use of Custom Tracks within the Axolotl Genome Browser.

    Nowoshilow, Sergej / Tanaka, Elly M

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

    2022  Volume 2562, Page(s) 273–289

    Abstract: The availability of the chromosome-scale axolotl genome sequences has made it possible to explore genome evolution, perform cross-species comparisons, and use additional sequencing data to analyze both genome-wide features and individual genes. Here, we ... ...

    Abstract The availability of the chromosome-scale axolotl genome sequences has made it possible to explore genome evolution, perform cross-species comparisons, and use additional sequencing data to analyze both genome-wide features and individual genes. Here, we will focus on the UCSC genome browser and demonstrate in a step-by-step manner how to use it to integrate different data to approach a broad question of the Fgf8 locus evolution and analyze the neighborhood of a gene that was reported missing in axolotl - Pax3.
    MeSH term(s) Animals ; Databases, Genetic ; Ambystoma mexicanum ; Software ; Genome ; Internet
    Language English
    Publishing date 2022-10-22
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2659-7_19
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  5. Article ; Online: Positional Memory in Vertebrate Regeneration: A Century's Insights from the Salamander Limb.

    Otsuki, Leo / Tanaka, Elly M

    Cold Spring Harbor perspectives in biology

    2022  Volume 14, Issue 6

    Abstract: Salamanders, such as axolotls and newts, can regenerate complex tissues including entire limbs. But what mechanisms ensure that an amputated limb regenerates a limb, and not a tail or unpatterned tissue? An important concept in regeneration is positional ...

    Abstract Salamanders, such as axolotls and newts, can regenerate complex tissues including entire limbs. But what mechanisms ensure that an amputated limb regenerates a limb, and not a tail or unpatterned tissue? An important concept in regeneration is positional memory-the notion that adult cells "remember" spatial identities assigned to them during embryogenesis (e.g., "head" or "hand") and use this information to restore the correct body parts after injury. Although positional memory is well documented at a phenomenological level, the underlying cellular and molecular bases are just beginning to be decoded. Herein, we review how major principles in positional memory were established in the salamander limb model, enabling the discovery of positional memory-encoding molecules, and advancing insights into their pattern-forming logic during regeneration. We explore findings in other amphibians, fish, reptiles, and mammals and speculate on conserved aspects of positional memory. We consider the possibility that manipulating positional memory in human cells could represent one route toward improved tissue repair or engineering of patterned tissues for therapeutic purposes.
    MeSH term(s) Animals ; Extremities ; Mammals ; Urodela ; Vertebrates
    Language English
    Publishing date 2022-06-14
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ISSN 1943-0264
    ISSN (online) 1943-0264
    DOI 10.1101/cshperspect.a040899
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  6. Article ; Online: Chromosome Conformation Capture for Large Genomes.

    Kawaguchi, Akane / Tanaka, Elly M

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

    2022  Volume 2562, Page(s) 291–318

    Abstract: The gigantic 32Gb Axolotl genome inspires fascinating questions such as: how such a big genome is organized and packed in nuclei and how regulation of gene transcription can happen over such large genomic distances. Currently, there are many technical ... ...

    Abstract The gigantic 32Gb Axolotl genome inspires fascinating questions such as: how such a big genome is organized and packed in nuclei and how regulation of gene transcription can happen over such large genomic distances. Currently, there are many technical challenges when we investigate chromatin architecture in axolotl. For example, probing promoter-enhancer interactions in such a large genome. Chromatin capture methods (e.g., Chromatin Conformation Capture) have been used in a variety of species. The large size of the axolotl nuclei and its genome requires the adaptation of such methods. Here, we describe a detailed protocol for high-throughput genome-wide conformation capture (Hi-C) using axolotl limb cells. This Hi-C library preparation protocol can also be used to prepare libraries from other nonmodel organisms such as Lungfish and Cephalopods. We believe that our protocol could be useful for a variety of animal systems including other salamanders.
    MeSH term(s) Animals ; High-Throughput Nucleotide Sequencing/methods ; Genome ; Chromosomes/genetics ; Chromatin/genetics ; Genomics/methods ; Nucleic Acid Conformation
    Chemical Substances Chromatin
    Language English
    Publishing date 2022-10-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2659-7_20
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  7. Article ; Online: Ethyl Cinnamate-Based Tissue Clearing Strategies.

    Masselink, Wouter / Tanaka, Elly M

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

    2022  Volume 2562, Page(s) 123–133

    Abstract: Tissue clearing turns otherwise turbid and opaque tissue transparent, enabling imaging deep within tissues. The nontransparent nature of most tissues is due to the refractive index mismatch between its three major constituent components (lipids, proteins, ...

    Abstract Tissue clearing turns otherwise turbid and opaque tissue transparent, enabling imaging deep within tissues. The nontransparent nature of most tissues is due to the refractive index mismatch between its three major constituent components (lipids, proteins, and water). All tissue clearing methods rectify this mismatch by homogenizing the refractive index within the tissue and carefully matching it to the surrounding media. Here we describe a detailed protocol to clear a wide range of salamander tissues. We also include several optional steps such as depigmentation, antibody staining, and tissue mounting. These steps are optional, and do not change anything in the steps needed for tissue clearing. Depending on the fluorescent signal and optics employed, images up to several millimeters inside of the tissue can be acquired.
    MeSH term(s) Staining and Labeling ; Cinnamates ; Lipids ; Water ; Imaging, Three-Dimensional/methods
    Chemical Substances ethyl cinnamate (C023P3M5JJ) ; Cinnamates ; Lipids ; Water (059QF0KO0R)
    Language English
    Publishing date 2022-10-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2659-7_7
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  8. Article ; Online: Transposon waves at the water-to-land transition.

    Falcon, Francisco / Tanaka, Elly M / Rodriguez-Terrones, Diego

    Current opinion in genetics & development

    2023  Volume 81, Page(s) 102059

    Abstract: The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome ... ...

    Abstract The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome duplication events occurred during the water-to-land transition, and it remains an open question how did genome dynamics contribute to this prominent evolutionary event. Indeed, the recent sequencing of sarcopterygian and amphibian genomes has revealed that the extant lineages immediately preceding and succeeding this transition harbor an exceptional number of transposable elements and it is tempting to speculate that these sequences might have catalyzed the adaptations that enabled vertebrates to venture into land. Here, we review the genome dynamics associated with the major transitions in vertebrate evolution and discuss how the highly repetitive genomic landscapes revealed by recent efforts to characterize the genomes of amphibians and sarcopterygians argue for turbulent genome dynamics occurring before the water-to-land transition and possibly enabling it.
    MeSH term(s) DNA Transposable Elements ; Biological Evolution ; Genomics ; Humans ; Animals ; Genome
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2023-06-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2023.102059
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  9. Article ; Online: The cellular and signaling dynamics of salamander limb regeneration.

    Bassat, Elad / Tanaka, Elly M

    Current opinion in cell biology

    2021  Volume 73, Page(s) 117–123

    Abstract: Limb amputation in salamanders yields a wound response that ultimately leads to replacement of the missing part. This unique-among-tetrapod trait involves the migration and recruitment of multiple cell types including epithelium, immune cells, axonal ... ...

    Abstract Limb amputation in salamanders yields a wound response that ultimately leads to replacement of the missing part. This unique-among-tetrapod trait involves the migration and recruitment of multiple cell types including epithelium, immune cells, axonal growth cones, and connective tissue cells to build the blastema which contains the proliferating stem and progenitor cells to rebuild the limb tissues. A number of the signaling and cell biological events have been defined. They point to the intimate coordination of physical events such as osmotic pressure, cell migration, and cell-cell communication with changes in cell identity such as dedifferentiation into embryonic-like epithelial and mesenchymal cells.
    MeSH term(s) Animals ; Extremities ; Signal Transduction ; Stem Cells ; Urodela
    Language English
    Publishing date 2021-09-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1026381-0
    ISSN 1879-0410 ; 0955-0674
    ISSN (online) 1879-0410
    ISSN 0955-0674
    DOI 10.1016/j.ceb.2021.07.010
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    Zs.A 2963: Show issues Location:
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  10. Article ; Online: Canonical Wnt signaling and the regulation of divergent mesenchymal Fgf8 expression in axolotl limb development and regeneration.

    Glotzer, Giacomo L / Tardivo, Pietro / Tanaka, Elly M

    eLife

    2022  Volume 11

    Abstract: The expression of fibroblast growth factors (Fgf) ligands in a specialized epithelial compartment, the Apical Ectodermal Ridge (AER), is a conserved feature of limb development across vertebrate species. In vertebrates, ...

    Abstract The expression of fibroblast growth factors (Fgf) ligands in a specialized epithelial compartment, the Apical Ectodermal Ridge (AER), is a conserved feature of limb development across vertebrate species. In vertebrates,
    MeSH term(s) Ambystoma mexicanum/genetics ; Animals ; Chickens/genetics ; Extremities/physiology ; Fibroblast Growth Factor 8/genetics ; Fibroblast Growth Factor 8/metabolism ; Fibroblast Growth Factors/metabolism ; Gene Expression Regulation, Developmental ; In Situ Hybridization, Fluorescence ; Ligands ; Vertebrates/genetics ; Wnt Signaling Pathway
    Chemical Substances Ligands ; Fibroblast Growth Factor 8 (148997-75-5) ; Fibroblast Growth Factors (62031-54-3)
    Language English
    Publishing date 2022-05-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.79762
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