Custom Types

The Multiple Layers of the Tumor Environment, new paper by Laplane et al.

If and how a tumor develops, depends in large part on its surroundings. While scientists agree on the importance of the tumor environment (TE), there is no consensus on how to define and spatially delineate it.
A new paper by Lucie Laplane, Dorothée Duluc, Nicolas Larmonier, Thomas Pradeu and Andreas Bikfalvi lays out six clearly defined layers that surround the tumor: (i) the tumor cell-only environment, (ii) the niche, and the (iii) confined, (iv) proximal, (v) peripheral, and (vi) organismal tumor environment. The authors show the different tumor-promoting or -suppressing mechanisms at work in the different layers and how they impact therapeutic approaches.
 

Click here for more information: The Multiple Layers of the Tumor Environment
Click here for the PDF

Dissecting the meanings of physiology, new paper by Lemoine & Pradeu in Physiology

Lemoine M. & Pradeu T. (2018)
Dissecting the meanings of ‘Physiology’ to assess the vitality of the discipline
Physiology 33(4), 236-245. (Open Access PDF) (PDF of final draft).

Abstract:
The vitality of physiology is currently under debate. Some say that physiology is a dying discipline in the era of molecular medicine and systems biology, whereas others claim that physiology remains a key biological and medical discipline, due in part to its integrative nature. In this conceptual review, we argue that any assessment of the vitality of physiology depends heavily on the definition of this discipline adopted. We examine two main conceptions of physiology, one focusing on its object (what physiology is about), and the other on the methods used (how physiologists study the biological reality). We contend that physiology no longer encompasses all biological disciplines and may no longer be the only synoptic biological science. However, far from indicating a sterility of this discipline, this situation should drive physiology to re-invent its relationship with these other biological domains.

Immunological memory, New paper by Pradeu & Du Pasquier in Immunological Reviews

Immunological memory: What’s in a name?

Thomas Pradeu & Louis Du Pasquier

Immunological Reviews (May 2018), Volume 283, Issue 1 (Special Issue: Immunologic Memory),

Pages 7-20.

 

Summary

Immunological memory is one of the core topics of contemporary immunology. Yet there are many discussions about what this concept precisely means, which components of the immune system display it, and in which phyla it exists. Recent years have seen the multiplication of claims that immunological memory can be found in “innate” immune cells and in many phyla beyond vertebrates (including invertebrates, plants, but also bacteria and archaea), as well as the multiplication of concepts to account for these phenomena, such as “innate immune memory” or “trained immunity”. The aim of this critical review is to analyze these recent claims and concepts, and to distinguish ideas that have often been misleadingly associated, such as memory, adaptive immunity, and specificity. We argue that immunological memory is a gradual and multidimensional phenomenon, irreducible to any simple dichotomy, and we show why adopting this new view matters from an experimental and therapeutic point of view.

Robustness in the tissue reconstruction system, New paper by Truchetet & Pradeu

New paper by M-E. Truchetet & T. Pradeu, Re-thinking our understanding of immunity: Robustness in the tissue reconstruction system. Seminars in Immunology (2018). (PDF of final draft).

Abstract

Robustness, understood as the maintenance of specific functionalities of a given system against internal and external perturbations, is pervasive in today’s biology. Yet precise applications of this notion to the immune system have been scarce. Here we show that the concept of robustness sheds light on tissue repair, and particularly on the crucial role the immune system plays in this process. We describe the specific mechanisms, including plasticity and redundancy, by which robustness is achieved in the tissue reconstruction system (TRS). In turn, tissue repair offers a very important test case for assessing the usefulness of the concept of robustness, and identifying different varieties of robustness.

Keywords
Tissue repair
Tissue regeneration
Robustness
Redundancy
Plasticity
Surveillance

Towards a General Theory of Immunity? New paper by Eberl & Pradeu

New paper in Trends in Immunology (2018), by Gérard Eberl (Institut Pasteur, Paris) & Thomas Pradeu (ImmunoConcept, Bordeaux)

Abstract
Theories are indispensable to organize immunological data into coherent, explanatory, and predictive frameworks. We propose to combine different models to develop a unifying theory of immunity which situates immunology in the wider context of physiology. We believe that the immune system will be increasingly understood as a central component of a network of partner physiological systems that interconnect to maintain homeostasis.
 
 

Protective Microbiota & Co-Immunity, New OA paper by Chiu, Bazin, et al.

New paper by Lynn Chiu, Thomas Bazin (co-first authors), Marie-Elise Truchetet, Thierry Schaeverbeke, Laurence Delhaes &  Thomas Pradeu
Frontiers in Immunology (Dec 2017). Full text in Open Access.

Abstract:
Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota.
 

What is metaphysics of science? New paper in Synthese by Guay & Pradeu

Right out of the box: how to situate metaphysics of science in relation to other metaphysical approaches
Alexandre Guay & Thomas Pradeu
Free full text: http://rdcu.be/wulr

Abstract
Several advocates of the lively field of “metaphysics of science” have recently argued that a naturalistic metaphysics should be based solely on current science, and that it should replace more traditional, intuition-based, forms of metaphysics. The aim of the present paper is to assess that claim by examining the relations between metaphysics of science and general metaphysics. We show that the current metaphysical battlefield is richer and more complex than a simple dichotomy between “metaphysics of science” and “traditional metaphysics”, and that it should instead be understood as a three dimensional “box”, with one axis distinguishing “descriptive metaphysics” from “revisionary metaphysics”, a second axis distinguishing a priori from a posteriori metaphysics, and a third axis distinguishing “commonsense metaphysics”, “traditional metaphysics” and “metaphysics of science”. We use this three-dimensional figure to shed light on the project of current metaphysics of science, and to demonstrate that, in many instances, the target of that project is not defined with enough precision and clarity.

New open access paper on dysbiosis, by Hooks & O’Malley

Hooks K. & O’Malley M. (2017) Dysbiosis and Its Discontents. mBio 8:e01492-17. (Open Access).
 
Abstract
Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states. Although some questions have been raised about how this term is applied, its use continues undiminished in the literature. We investigate the ways in which microbiome researchers discuss dysbiosis and then assess the impact of different concepts of dysbiosis on microbiome research. After an overview of the term’s historical roots, we conduct quantitative and qualitative analyses of a large selection of contemporary dysbiosis statements. We categorize both short definitions and longer conceptual statements about dysbiosis. Further analysis allows us to identify the problematic implications of how dysbiosis is used, particularly with regard to causal hypotheses and normal-abnormal distinctions. We suggest that researchers should reflect carefully on the ways in which they discuss dysbiosis, in order for the field to continue to develop greater predictive scope and explanatory depth.