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Archives of 2014

  1. Ecological Models for Gene Therapy. I. Models for Intraorganismal Ecology

    Ecological Models for Gene Therapy. I. Models for Intraorganismal Ecology

    Biological Theory


    We discuss the perspective of intra-organismal ecology by investigating a family of ecological models. We consider first and second order models.

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    Abstract:

    In this article, we discuss the perspective of intraorganismal ecology by investigating a family of ecological models. We consider two types of models. First-order models describe the population dynamics as being directly affected by ecological factors (here understood as nutrients, space, etc). They might be thought of as analogous to Aristotelian physics. Second-order models describe the population dynamics as being indirectly affected, the ecological factors now affecting the derivative of the growth rate (that is, the population acceleration), possibly through an impact on nongenetically inherited factors. Second-order models might be thought of as analogous to Galilean physics. In a companion article, we apply these ideas to a situation of gene therapy.

    Keywords: Ecosystem engineering, Inertial dynamics, Intraorganismal ecology, Niche construction, Nongenetic inheritance

    Citation:

    Pocheville, A., and Maël Montévil. 2014. “Ecological Models for Gene Therapy. I. Models for Intraorganismal Ecology.” Biological Theory 9 (4): 401–13. https://doi.org/10.1007/s13752-014-0190-y

  2. Ecological Models for Gene Therapy. II. Niche Construction, Nongenetic Inheritance, and Ecosystem Perturbations

    Ecological Models for Gene Therapy. II. Niche Construction, Nongenetic Inheritance, and Ecosystem Perturbations

    Biological Theory


    We apply the perspective of intra-organismal ecology by investigating a family of ecological models suitable to describe a gene therapy.

    Manuscript Citation Publisher Full text

    Abstract:

    In this article, we apply the perspective of intraorganismal ecology by investigating a family of ecological models suitable to describe a gene therapy for a particular metabolic disorder, the adenosine deaminase deficiency. The gene therapy is modeled as the prospective ecological invasion of an organ (here, bone marrow) by genetically modified stem cells, which then operate niche construction in the cellular environment by releasing an enzyme they synthesize. We show that depending on the order chosen for the model (a choice that cannot be made on a priori assumptions), different kinds of dynamics are expected, possibly leading to different therapeutic strategies. This drives us to discuss several features of the extension of ecology to intraorganismal ecology.

    Keywords: Adenosine deaminase deficiency, Ecosystem engineering, Gene therapy, Intraorganismal ecology, Nongenetic inheritance, Severe combined immunodeficiency

    Citation:
  3. Introduction to New Perspectives in Biology

    Introduction to New Perspectives in Biology

    Essays for the Luca Cardelli Fest


    This note introduces work in Theoretical Biology in the book: Perspectives on Organisms: Biological Time, Symmetries and Singularities.

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    Abstract:

    This note introduces recent work in Theoretical Biology by borrowing from the Introduction (chapter 1) of the book by the authors: "Perspectives on Organisms: Biological Time, Symmetries and Singularities", Springer, 2014. The idea is to work towards a Theory of Organisms analogue and along the Theory of Evolution, where ontogenesis could be considered as part of phylogenesis. As a matter of fact, the latter is made out of "segments" of the first: phylogenesis is the "sum" of ontogenetic paths and they should be made intelligible by similar principles. To this aim, we look at ontogenesis from different perspectives. By this, we shed light on the unity of the organism from different points of view, yet constantly keeping that unity as a core invariant. The analysis of invariance, as the result of theoretical symmetries, and of symmetry changes, is a key theme of the approach in the book and in the discussion in this note.

    Citation:

    Longo, G., and Maël Montévil. 2014. “Introduction to New Perspectives in Biology.” In Essays for the Luca Cardelli Fest, edited by Martin Abadi, Philippa Gardner, Andrew D. Gordon, and Radu Mardare, 187–201. MSR-TR-2014-104. Microsoft Research. http://research.microsoft.com/apps/pubs/default.aspx?id=226237

  4. IAS-IHPST Workshop: Boundaries and levels of biological organization


    The workshop will discuss the notion of biological organization from a systemic- perspective. In particular it will focus on its intrinsic hierarchical dimension, and on the role organization plays in the understanding of the transition from pre-biotic to minimal living systems and of more complex …

  5. A Novel 3D Model to Study the Link Between Hormonal Exposure and Mammographic Density in Breast Cancer


    Lower type 1 collagen concentration (0.5 mg/ml) increases elongation of structures compared to 1 mg/ml. Fibroblasts enhances elongation of structures in 1 mg/ml, but not 0.5 mg/ml. In 1 mg/ml collagen, elongated epithelial structures had lumen formation when co­‐cultured with fibroblasts. Hormones …

  6. Development of Software for Automated Morphology Analysis (SAMA) to analyze morphogenic effects of mammotrophic hormones in vitro


    In vitro 3D simulations of biological systems are critical for understanding morphogenesis and patterns of normal and abnormal development in tissues. <br> Here we present SAMA, a novel method through which epithelial structures grown in 3D cultures can be imaged, reconstructed in 3D and analyzed with …

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