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  1. Book ; Online ; E-Book: Mechanisms of morphogenesis

    Davies, Jamie A.

    2023  

    Author's details Jamie A. Davies
    MeSH term(s) Morphogenesis ; Growth and Development
    Keywords Morphogenesis ; Developmental biology
    Subject code 571.833
    Language English
    Size 1 online resource (534 pages)
    Edition Third edition.
    Publisher Stacy Masucci
    Publishing place Kidlington, England
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 0-323-98528-9 ; 9780323999656 ; 978-0-323-98528-4 ; 0323999654
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: SynPharm and the guide to pharmacology database: A toolset for conferring drug control on engineered proteins.

    Davies, Jamie A

    Protein science : a publication of the Protein Society

    2020  Volume 30, Issue 1, Page(s) 160–167

    Abstract: Optimizing synthetic biological systems, for example novel metabolic pathways, becomes more complicated with more protein components. One method of taming the complexity and allowing more rapid optimization is engineering external control into components. ...

    Abstract Optimizing synthetic biological systems, for example novel metabolic pathways, becomes more complicated with more protein components. One method of taming the complexity and allowing more rapid optimization is engineering external control into components. Pharmacology is essentially the science of controlling proteins using (mainly) small molecules, and a great deal of information, spread between different databases, is known about structural interactions between these ligands and their target proteins. In principle, protein engineers can use an inverse pharmacological approach to include drug response in their design, by identifying ligand-binding domains from natural proteins that are amenable to being included in a designed protein. In this context, "amenable" means that the ligand-binding domain is in a relatively self-contained subsequence of the parent protein, structurally independent of the rest of the molecule so that its function should be retained in another context. The SynPharm database is a tool, built on to the Guide to Pharmacology database and connected to various structural databases, to help protein engineers identify ligand-binding domains suitable for transfer. This article describes the tool, and illustrates its use in seeking candidate domains for transfer. It also briefly describes already-published proof-of-concept studies in which the CRISPR effectors Cas9 and Cpf1 were placed separately under the control of tamoxifen and mefipristone, by including ligand-binding domains of the Estrogen Receptor and Progesterone Receptor in modified versions of Cas9 and Cpf1. The advantages of drug control or the rival protein-control technology of optogenetics, for different purposes and in different situations, are also briefly discussed.
    MeSH term(s) Databases, Pharmaceutical ; Databases, Protein ; Ligands ; Protein Domains ; Protein Engineering ; Proteins/chemistry ; Proteins/genetics
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2020-11-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.3971
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Introducing blood flow in kidney explants by engraftment onto the chick chorioallantoic membrane is not sufficient to induce arterial smooth muscle cell development.

    Tarnick, Julia / Davies, Jamie A

    Biology open

    2022  Volume 11, Issue 7

    Abstract: Kidney explant cultures are an important tool to gain insights into developmental processes, insights that can be used to develop strategies for engineering kidneys from stem cells. However, explants are not connected to a perfused vascular system. This ... ...

    Abstract Kidney explant cultures are an important tool to gain insights into developmental processes, insights that can be used to develop strategies for engineering kidneys from stem cells. However, explants are not connected to a perfused vascular system. This limits their survival and limits physiological studies, for example of blood filtration, the main function of the kidney. Previous studies have shown that grafting kidneys onto avian chorioallantoic membrane (CAM) can establish perfusion and enable glomerular vascularization, but the realism and maturity of the resultant vasculature has not been examined. Here, we show that vasculature of kidney explants grafted onto CAM is very different from natural kidney vasculature, showing excessive growth of endothelial cells, absence of a hierarchical arterio-venous network and no vascular smooth muscle cell recruitment. The model therefore has serious limits.
    MeSH term(s) Animals ; Cell Differentiation ; Chorioallantoic Membrane ; Endothelial Cells ; Kidney/blood supply ; Myocytes, Smooth Muscle
    Language English
    Publishing date 2022-07-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2632264-X
    ISSN 2046-6390 ; 2046-6390
    ISSN (online) 2046-6390
    ISSN 2046-6390
    DOI 10.1242/bio.059459
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Introducing blood flow in kidney explants by engraftment onto the chick chorioallantoic membrane is not sufficient to induce arterial smooth muscle cell development

    Julia Tarnick / Jamie A. Davies

    Biology Open, Vol 11, Iss

    2022  Volume 7

    Abstract: Kidney explant cultures are an important tool to gain insights into developmental processes, insights that can be used to develop strategies for engineering kidneys from stem cells. However, explants are not connected to a perfused vascular system. This ... ...

    Abstract Kidney explant cultures are an important tool to gain insights into developmental processes, insights that can be used to develop strategies for engineering kidneys from stem cells. However, explants are not connected to a perfused vascular system. This limits their survival and limits physiological studies, for example of blood filtration, the main function of the kidney. Previous studies have shown that grafting kidneys onto avian chorioallantoic membrane (CAM) can establish perfusion and enable glomerular vascularization, but the realism and maturity of the resultant vasculature has not been examined. Here, we show that vasculature of kidney explants grafted onto CAM is very different from natural kidney vasculature, showing excessive growth of endothelial cells, absence of a hierarchical arterio-venous network and no vascular smooth muscle cell recruitment. The model therefore has serious limits.
    Keywords kidney development ; arterial differentiation ; cam grafting ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher The Company of Biologists
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Stratified tissue biofabrication by rotational internal flow layer engineering.

    Holland, Ian / Shu, Wenmiao / Davies, Jamie A

    Biofabrication

    2023  Volume 15, Issue 4

    Abstract: The bioassembly of layered tissue that closely mimics human histology presents challenges for tissue engineering. Existing bioprinting technologies lack the resolution and cell densities necessary to form the microscale cell-width layers commonly ... ...

    Abstract The bioassembly of layered tissue that closely mimics human histology presents challenges for tissue engineering. Existing bioprinting technologies lack the resolution and cell densities necessary to form the microscale cell-width layers commonly observed in stratified tissue, particularly when using low-viscosity hydrogels, such as collagen. Here we present rotational internal flow layer engineering (RIFLE), a novel, low-cost biofabrication technology for assembling tuneable, multi-layered tissue-like structures. Using high-speed rotating tubular moulds, small volumes of cell-laden liquids added to the inner surface were transitioned into thin layers and gelled, progressively building macroscale tubes composed of discrete microscale strata with thicknesses a function of rotational speed. Cell encapsulation enabled the patterning of high-density layers (10
    MeSH term(s) Humans ; Tissue Engineering ; Hydrogels/chemistry ; Technology ; Tissue Scaffolds/chemistry ; Bioprinting ; Printing, Three-Dimensional
    Chemical Substances Hydrogels
    Language English
    Publishing date 2023-07-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2500944-8
    ISSN 1758-5090 ; 1758-5082
    ISSN (online) 1758-5090
    ISSN 1758-5082
    DOI 10.1088/1758-5090/ace2ed
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Real-World Synthetic Biology: Is It Founded on an Engineering Approach, and Should It Be?

    Davies, Jamie A

    Life (Basel, Switzerland)

    2019  Volume 9, Issue 1

    Abstract: Authors often assert that a key feature of 21st-century synthetic biology is its use of an 'engineering approach'; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using ... ...

    Abstract Authors often assert that a key feature of 21st-century synthetic biology is its use of an 'engineering approach'; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey of synthetic biology projects that have reached, or are near to, commercial application outside laboratories shows that they showed very few of these attributes. Instead, they featured much trial and error, and the use of specialized, custom components and assays. What is more, consideration of the special features of living systems suggest that a conventional engineering approach will often not be helpful. The article concludes that the engineering approach may be useful in some projects, but it should not be used to define or constrain synthetic biological endeavour, and that in fact the conventional engineering has more to gain by expanding and embracing more biological ways of working.
    Language English
    Publishing date 2019-01-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life9010006
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  7. Article ; Online: The inter-dependence of basic and applied biomedical sciences: Lessons from kidney development and tissue-engineering.

    Davies, Jamie A

    Porto biomedical journal

    2017  Volume 2, Issue 5, Page(s) 136–139

    Language English
    Publishing date 2017-09-01
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2444-8672
    ISSN (online) 2444-8672
    DOI 10.1016/j.pbj.2017.05.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Organizing Organoids: Stem Cells Branch Out.

    Davies, Jamie A

    Cell stem cell

    2017  Volume 21, Issue 6, Page(s) 705–706

    Abstract: In this issue of Cell Stem Cell, Taguchi and Nishinakamura (2017) describe a carefully optimized method for making a branch-competent ureteric bud, a tissue fundamental to kidney development, from mouse embryonic stem cells and human induced pluripotent ... ...

    Abstract In this issue of Cell Stem Cell, Taguchi and Nishinakamura (2017) describe a carefully optimized method for making a branch-competent ureteric bud, a tissue fundamental to kidney development, from mouse embryonic stem cells and human induced pluripotent stem cells. The work illuminates embryology and has important implications for making more realistic kidney organoids.
    MeSH term(s) Animals ; Cell Culture Techniques ; Cell Differentiation ; Humans ; Induced Pluripotent Stem Cells ; Mice ; Organogenesis ; Organoids ; Pluripotent Stem Cells
    Language English
    Publishing date 2017-12-08
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2375354-7
    ISSN 1875-9777 ; 1934-5909
    ISSN (online) 1875-9777
    ISSN 1934-5909
    DOI 10.1016/j.stem.2017.11.011
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  9. Article ; Online: Real-World Synthetic Biology

    Jamie A. Davies

    Life, Vol 9, Iss 1, p

    Is It Founded on an Engineering Approach, and Should It Be?

    2019  Volume 6

    Abstract: Authors often assert that a key feature of 21st-century synthetic biology is its use of an ‘engineering approach’; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using ... ...

    Abstract Authors often assert that a key feature of 21st-century synthetic biology is its use of an ‘engineering approach’; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey of synthetic biology projects that have reached, or are near to, commercial application outside laboratories shows that they showed very few of these attributes. Instead, they featured much trial and error, and the use of specialized, custom components and assays. What is more, consideration of the special features of living systems suggest that a conventional engineering approach will often not be helpful. The article concludes that the engineering approach may be useful in some projects, but it should not be used to define or constrain synthetic biological endeavour, and that in fact the conventional engineering has more to gain by expanding and embracing more biological ways of working.
    Keywords standardization ; modularity ; abstraction ; modelling ; design ; assay ; Science ; Q
    Subject code 501
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Adaptive self-organization in the embryo: its importance to adult anatomy and to tissue engineering.

    Davies, Jamie A

    Journal of anatomy

    2017  Volume 232, Issue 4, Page(s) 524–533

    Abstract: The anatomy of healthy humans shows much minor variation, and twin-studies reveal at least some of this variation cannot be explained genetically. A plausible explanation is that fine-scale anatomy is not specified directly in a genetic programme, but ... ...

    Abstract The anatomy of healthy humans shows much minor variation, and twin-studies reveal at least some of this variation cannot be explained genetically. A plausible explanation is that fine-scale anatomy is not specified directly in a genetic programme, but emerges from self-organizing behaviours of cells that, for example, place a new capillary where it happens to be needed to prevent local hypoxia. Self-organizing behaviour can be identified by manipulating growing tissues (e.g. putting them under a spatial constraint) and observing an adaptive change that conserves the character of the normal tissue while altering its precise anatomy. Self-organization can be practically useful in tissue engineering but it is limited; generally, it is good for producing realistic small-scale anatomy but large-scale features will be missing. This is because self-organizing organoids miss critical symmetry-breaking influences present in the embryo: simulating these artificially, for example, with local signal sources, makes anatomy realistic even at large scales. A growing understanding of the mechanisms of self-organization is now allowing synthetic biologists to take their first tentative steps towards constructing artificial multicellular systems that spontaneously organize themselves into patterns, which may soon be extended into three-dimensional shapes.
    MeSH term(s) Anatomic Variation ; Animals ; Dogs ; Embryo, Mammalian/physiology ; Embryonic Development/physiology ; Feedback, Physiological/physiology ; Humans ; Mice ; Organogenesis/physiology ; Organoids/physiology ; Synthetic Biology/methods ; Tissue Engineering/methods
    Language English
    Publishing date 2017-10-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2955-5
    ISSN 1469-7580 ; 0021-8782
    ISSN (online) 1469-7580
    ISSN 0021-8782
    DOI 10.1111/joa.12691
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