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  1. Article ; Online: The mitochondrial genome of the black-tailed dusky antechinus (

    Geng, Yuepan / Yang, Chen / Guo, Han / Thomas, Patrick B / Jeffery, Penny L / Chopin, Lisa K / Baker, Andrew M / Tian, Ran / Seim, Inge

    Mitochondrial DNA. Part B, Resources

    2020  Volume 5, Issue 4, Page(s) 3835–3837

    Abstract: In this study, we report the mitochondrial genome of the black-tailed antechinus ( ...

    Abstract In this study, we report the mitochondrial genome of the black-tailed antechinus (
    Language English
    Publishing date 2020-12-24
    Publishing country England
    Document type Journal Article
    ISSN 2380-2359
    ISSN (online) 2380-2359
    DOI 10.1080/23802359.2020.1840940
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Modelling the tumor immune microenvironment for precision immunotherapy.

    Mackenzie, Nathan J / Nicholls, Clarissa / Templeton, Abby R / Perera, Mahasha Pj / Jeffery, Penny L / Zimmermann, Kate / Kulasinghe, Arutha / Kenna, Tony J / Vela, Ian / Williams, Elizabeth D / Thomas, Patrick B

    Clinical & translational immunology

    2022  Volume 11, Issue 6, Page(s) e1400

    Abstract: The complexity of the cellular and acellular players within the tumor microenvironment (TME) allows for significant variation in TME constitution and role in anticancer treatment response. Spatial alterations in populations of tumor cells and adjacent ... ...

    Abstract The complexity of the cellular and acellular players within the tumor microenvironment (TME) allows for significant variation in TME constitution and role in anticancer treatment response. Spatial alterations in populations of tumor cells and adjacent non-malignant cells, including endothelial cells, fibroblasts and tissue-infiltrating immune cells, often have a major role in determining disease progression and treatment response in cancer. Many current standard systemic antineoplastic treatments target the cancer cells and could be further refined to directly target commonly dysregulated cell populations of the TME. Recent developments in immuno-oncology and bioengineering have created an attractive potential to model these complexities at the level of the individual patient. These developments, along with the increasing momentum in precision medicine research and application, have catalysed exciting new discoveries in understanding drug-TME interactions, target identification, and improved efficacy of therapies. While rapid progress has been made, there are still many challenges to overcome in the development of accurate
    Language English
    Publishing date 2022-06-26
    Publishing country Australia
    Document type Journal Article ; Review
    ZDB-ID 2694482-0
    ISSN 2050-0068
    ISSN 2050-0068
    DOI 10.1002/cti2.1400
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The mitochondrial genome of the black-tailed dasyure (

    Tian, Ran / Geng, Yuepan / Thomas, Patrick B / Jeffery, Penny L / Mutton, Thomas Y / Chopin, Lisa K / Baker, Andrew M / Seim, Inge

    Mitochondrial DNA. Part B, Resources

    2019  Volume 4, Issue 2, Page(s) 3598–3600

    Abstract: In this study, we report the mitochondrial genome of the black-tailed dasyure ( ...

    Abstract In this study, we report the mitochondrial genome of the black-tailed dasyure (
    Language English
    Publishing date 2019-10-16
    Publishing country England
    Document type Journal Article
    ISSN 2380-2359
    ISSN (online) 2380-2359
    DOI 10.1080/23802359.2019.1677526
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Patient-Derived Explants as a Precision Medicine Patient-Proximal Testing Platform Informing Cancer Management.

    Templeton, Abby R / Jeffery, Penny L / Thomas, Patrick B / Perera, Mahasha P J / Ng, Gary / Calabrese, Alivia R / Nicholls, Clarissa / Mackenzie, Nathan J / Wood, Jack / Bray, Laura J / Vela, Ian / Thompson, Erik W / Williams, Elizabeth D

    Frontiers in oncology

    2021  Volume 11, Page(s) 767697

    Abstract: Precision medicine approaches that inform clinical management of individuals with cancer are progressively advancing. Patient-derived explants (PDEs) provide a patient- ... ...

    Abstract Precision medicine approaches that inform clinical management of individuals with cancer are progressively advancing. Patient-derived explants (PDEs) provide a patient-proximal
    Language English
    Publishing date 2021-12-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2021.767697
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Modelling the tumor immune microenvironment for precision immunotherapy

    Nathan J Mackenzie / Clarissa Nicholls / Abby R Templeton / Mahasha PJ Perera / Penny L Jeffery / Kate Zimmermann / Arutha Kulasinghe / Tony J Kenna / Ian Vela / Elizabeth D Williams / Patrick B Thomas

    Clinical & Translational Immunology, Vol 11, Iss 6, Pp n/a-n/a (2022)

    2022  

    Abstract: Abstract The complexity of the cellular and acellular players within the tumor microenvironment (TME) allows for significant variation in TME constitution and role in anticancer treatment response. Spatial alterations in populations of tumor cells and ... ...

    Abstract Abstract The complexity of the cellular and acellular players within the tumor microenvironment (TME) allows for significant variation in TME constitution and role in anticancer treatment response. Spatial alterations in populations of tumor cells and adjacent non‐malignant cells, including endothelial cells, fibroblasts and tissue‐infiltrating immune cells, often have a major role in determining disease progression and treatment response in cancer. Many current standard systemic antineoplastic treatments target the cancer cells and could be further refined to directly target commonly dysregulated cell populations of the TME. Recent developments in immuno‐oncology and bioengineering have created an attractive potential to model these complexities at the level of the individual patient. These developments, along with the increasing momentum in precision medicine research and application, have catalysed exciting new discoveries in understanding drug–TME interactions, target identification, and improved efficacy of therapies. While rapid progress has been made, there are still many challenges to overcome in the development of accurate in vitro, in vivo and ex vivo models incorporating the cellular interactions that take place in the TME. In this review, we describe how advances in immuno‐oncology and patient‐derived models, such as patient‐derived organoids and explant cultures, have enhanced the landscape of personalised immunotherapy prediction and treatment of solid organ malignancies. We describe and compare different immunological targets and perspectives on two‐dimensional and three‐dimensional modelling approaches that may be used to better rationalise immunotherapy use, ultimately providing a knowledge base for the integration of the autologous TME into these predictive models.
    Keywords co‐culture ; immuno‐oncology ; immunotherapy ; patient‐derived explants ; patient‐derived organoids ; precision medicine ; Immunologic diseases. Allergy ; RC581-607
    Subject code 610
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Turtle ghrelin.

    Seim, Inge / Jeffery, Penny L / Herington, Adrian C / Chopin, Lisa K

    Nature genetics

    2014  Volume 46, Issue 6, Page(s) 525–526

    MeSH term(s) Animals ; Turtles/genetics
    Language English
    Publishing date 2014-05-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng.2964
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: 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 46: Show issues

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  7. Article ; Online: Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines.

    Seim, Inge / Jeffery, Penny L / Thomas, Patrick B / Nelson, Colleen C / Chopin, Lisa K

    G3 (Bethesda, Md.)

    2017  Volume 7, Issue 6, Page(s) 1731–1741

    Abstract: The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing ( ... ...

    Abstract The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing (WGS) and
    MeSH term(s) Cell Line, Tumor ; Computational Biology/methods ; DNA Copy Number Variations ; Databases, Nucleic Acid ; Genome, Human ; Genome-Wide Association Study ; Genomics/methods ; Humans ; INDEL Mutation ; Male ; Neoplasm Metastasis ; Polymorphism, Single Nucleotide ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/mortality ; Prostatic Neoplasms/pathology ; Whole Genome Sequencing
    Language English
    Publishing date 2017-06-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.117.039909
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Comparative analysis reveals loss of the appetite-regulating peptide hormone ghrelin in falcons.

    Seim, Inge / Jeffery, Penny L / Herington, Adrian C / Chopin, Lisa K

    General and comparative endocrinology

    2015  Volume 216, Page(s) 98–102

    Abstract: Ghrelin and leptin are key peripherally secreted appetite-regulating hormones in vertebrates. Here we consider the ghrelin gene (GHRL) of birds (class Aves), where it has been reported that ghrelin inhibits rather than augments feeding. Thirty-one bird ... ...

    Abstract Ghrelin and leptin are key peripherally secreted appetite-regulating hormones in vertebrates. Here we consider the ghrelin gene (GHRL) of birds (class Aves), where it has been reported that ghrelin inhibits rather than augments feeding. Thirty-one bird species were compared, revealing that most species harbour a functional copy of GHRL and the coding region for its derived peptides ghrelin and obestatin. We provide evidence for loss of GHRL in saker and peregrine falcons, and this is likely to result from the insertion of an ERVK retrotransposon in intron 0. We hypothesise that the loss of anorexigenic ghrelin is a predatory adaptation that results in increased food-seeking behaviour and feeding in falcons.
    MeSH term(s) Amino Acid Sequence ; Animals ; Appetite Regulation/physiology ; Falconiformes/physiology ; Ghrelin/metabolism ; Molecular Sequence Data ; Peptide Hormones/metabolism ; Phylogeny ; Sequence Homology, Amino Acid
    Chemical Substances Ghrelin ; Peptide Hormones
    Language English
    Publishing date 2015-05-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1851-x
    ISSN 1095-6840 ; 0016-6480
    ISSN (online) 1095-6840
    ISSN 0016-6480
    DOI 10.1016/j.ygcen.2014.11.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 164: 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 ; Online: Culture of Bladder Cancer Organoids as Precision Medicine Tools.

    Thomas, Patrick B / Perera, Mahasha P J / Alinezhad, Saeid / Joshi, Andre / Saadat, Paria / Nicholls, Clarissa / Devonport, Caitlin P / Calabrese, Alivia R / Templeton, Abby R / Wood, Jack R / Mackenzie, Nathan J / Jeffery, Penny L / Vela, Ian / Williams, Elizabeth D

    Journal of visualized experiments : JoVE

    2021  , Issue 178

    Abstract: Current in vitro therapeutic testing platforms lack relevance to tumor pathophysiology, typically employing cancer cell lines established as two-dimensional (2D) cultures on tissue culture plastic. There is a critical need for more representative models ... ...

    Abstract Current in vitro therapeutic testing platforms lack relevance to tumor pathophysiology, typically employing cancer cell lines established as two-dimensional (2D) cultures on tissue culture plastic. There is a critical need for more representative models of tumor complexity that can accurately predict therapeutic response and sensitivity. The development of three-dimensional (3D) ex vivo culture of patient-derived organoids (PDOs), derived from fresh tumor tissues, aims to address these shortcomings. Organoid cultures can be used as tumor surrogates in parallel to routine clinical management to inform therapeutic decisions by identifying potential effective interventions and indicating therapies that may be futile. Here, this procedure aims to describe strategies and a detailed step-by-step protocol to establish bladder cancer PDOs from fresh, viable clinical tissue. Our well-established, optimized protocols are practical to set up 3D cultures for experiments using limited and diverse starting material directly from patients or patient-derived xenograft (PDX) tumor material. This procedure can also be employed by most laboratories equipped with standard tissue culture equipment. The organoids generated using this protocol can be used as ex vivo surrogates to understand both the molecular mechanisms underpinning urological cancer pathology and to evaluate treatments to inform clinical management.
    MeSH term(s) Humans ; Organoids/pathology ; Precision Medicine ; Urinary Bladder Neoplasms/pathology ; Urologic Neoplasms/pathology
    Language English
    Publishing date 2021-12-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/63192
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Culture of bladder cancer organoids as precision medicine tools

    Thomas, Patrick B. / Perera, Mahasha P. J. / Alinezhad, Saeid / Joshi, Andre / Saadat, Paria / Nicholls, Clarissa / Devonport, Caitlin P. / Calabrese, Alivia R. / Templeton, Abby R. / Wood, Jack R. / Mackenzie, Nathan J. / Jeffery, Penny L. / Vela, Ian / Williams, Elizabeth D.

    Journal of visualized experiments. 2021 Dec. 28, , no. 178

    2021  

    Abstract: Current in vitro therapeutic testing platforms lack relevance to tumor pathophysiology, typically employing cancer cell lines established as two-dimensional (2D) cultures on tissue culture plastic. There is a critical need for more representative models ... ...

    Abstract Current in vitro therapeutic testing platforms lack relevance to tumor pathophysiology, typically employing cancer cell lines established as two-dimensional (2D) cultures on tissue culture plastic. There is a critical need for more representative models of tumor complexity that can accurately predict therapeutic response and sensitivity. The development of three-dimensional (3D) ex vivo culture of patient-derived organoids (PDOs), derived from fresh tumor tissues, aims to address these shortcomings. Organoid cultures can be used as tumor surrogates in parallel to routine clinical management to inform therapeutic decisions by identifying potential effective interventions and indicating therapies that may be futile. Here, this procedure aims to describe strategies and a detailed step-by-step protocol to establish bladder cancer PDOs from fresh, viable clinical tissue. Our well-established, optimized protocols are practical to set up 3D cultures for experiments using limited and diverse starting material directly from patients or patient-derived xenograft (PDX) tumor material. This procedure can also be employed by most laboratories equipped with standard tissue culture equipment. The organoids generated using this protocol can be used as ex vivo surrogates to understand both the molecular mechanisms underpinning urological cancer pathology and to evaluate treatments to inform clinical management.
    Keywords equipment ; neoplasm cells ; organoids ; pathophysiology ; plastics ; precision medicine ; protocols ; tissue culture ; urinary bladder neoplasms ; xenotransplantation
    Language English
    Dates of publication 2021-1228
    Size p. e63192.
    Publishing place Journal of Visualized Experiments
    Document type Article
    ZDB-ID 2259946-0
    ISSN 1940-087X
    ISSN 1940-087X
    DOI 10.3791/63192
    Database NAL-Catalogue (AGRICOLA)

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