Dynamical behaviour of biological regulatory networks—I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state

1995 ◽  
Vol 57 (2) ◽  
pp. 247-276 ◽  
Author(s):  
René Thomas ◽  
Denis Thieffry ◽  
Marcelle Kaufman
Keyword(s):  
Regulatory Networks ◽  
Dynamical Behaviour ◽  
Feedback Loops ◽  
Biological Role ◽  
Characteristic State ◽  
Biological Regulatory Networks

The role of self-organisation in the emergence of phonological systems

1999 ◽  
Vol 3 (1) ◽  
pp. 21-48 ◽  
Author(s):  
Didier Demolin ◽  
Alain Soquet
Keyword(s):  
Environmental Variables ◽  
Regulatory Networks ◽  
Vocal Tract ◽  
Feedback Loops ◽  
Self Organization ◽  
Emergent Properties ◽  
External Influence ◽  
Self Organized ◽  
Sound Patterns

The origin of phonological systems is examined from the paradigm of self-organization. We claim that phonological systems could have emerged as the product of self-organizing processes. Self-organization may have facilitated the evolution of structures within the sounds that humans were able to produce. One of the main points of the paper concerns the identification of the processes which could account for the self-organized behavior of sound systems used in languages spoken by humans. In this paradigm, phonological systems or sound patterns of human languages are emergent properties of these systems rather than properties imposed by some external influence. Regulations are defined as the constraints that adjust the rate of production of the elements of a system to the state of the system and of relevant environmental variables. The main operators of these adjustments are feedback loops. Two types of processes can be distinguished in regulatory networks, homeostatic and epigenetic. Since the origin of sound patterns, of human languages, is in the vocal tract constraints, we make the hypothesis that sound change does not reflect any adaptive character but rather is the phonetic modality of differentiation understood as epigenetic regulation.

Gene Targeting and Gene Transfer Studies of the Biological Role of the Plasminogen/Plasmin System

1995 ◽  
Vol 74 (01) ◽  
pp. 429-436 ◽  
Author(s):  
Peter Carmeliet ◽  
Désiré Collen
Keyword(s):  
Gene Transfer ◽  
Gene Targeting ◽  
Biological Role

From Organizations of Processes to Organisms and Other Biological Individuals

2018 ◽  
Author(s):  
Argyris Arnellos
Keyword(s):  
Multicellular Organism ◽  
Collaborative Networks ◽  
Biological Role ◽  
Regulatory Processes ◽  
Different Types ◽  
Organizational Framework

The emphasis on the collaborative dimension of life overlooks the importance of biological individuals (conceived of as integrated, self-maintaining organizations) in the build-up of more complex collaborative networks in the course of evolution. This chapter proposes a process-based organizational ontology for biology, according to which the essential features of unicellular organismicality are captured by a self-maintaining organization of processes integrated by means of a special type of collaboration (realized through regulatory processes entailing an indispensable interdependence) between its constitutive and its interactive aspects. This ontology is then used to describe different types of collaborations among cells and to suggest the type that yields a multicellular organism. The proposed organizational framework enables us to critically assess hypercollaborative views of life, especially issues related to the distinction between biological individuals and organisms and between life and non-life, without however underestimating the central biological role of collaboration.

scholarly journals Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hong Wang ◽  
Aiping Duan ◽  
Jing Zhang ◽  
Qi Wang ◽  
Yuexian Xing ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Glucocorticoid Receptor ◽  
Protective Effect ◽  
Histone Modification ◽  
Regulatory Networks ◽  
Target Gene ◽  
Regulatory Elements ◽  
Chromatin Interactions ◽  
Super Enhancer

AbstractElucidating transcription mediated by the glucocorticoid receptor (GR) is crucial for understanding the role of glucocorticoids (GCs) in the treatment of diseases. Podocyte is a useful model for studying GR regulation because GCs are the primary medication for podocytopathy. In this study, we integrated data from transcriptome, transcription factor binding, histone modification, and genome topology. Our data reveals that the GR binds and activates selective regulatory elements in podocyte. The 3D interactome captured by HiChIP facilitates the identification of remote targets of GR. We found that GR in podocyte is enriched at transcriptional interaction hubs and super-enhancers. We further demonstrate that the target gene of the top GR-associated super-enhancer is indispensable to the effective functioning of GC in podocyte. Our findings provided insights into the mechanisms underlying the protective effect of GCs on podocyte, and demonstrate the importance of considering transcriptional interactions in order to fine-map regulatory networks of GR.

scholarly journals The Role of Autophagy and lncRNAs in the Maintenance of Cancer Stem Cells

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1239
Author(s):  
Leila Jahangiri ◽  
Tala Ishola ◽  
Perla Pucci ◽  
Ricky M. Trigg ◽  
Joao Pereira ◽  
...  
Keyword(s):  
Stem Cells ◽  
Cancer Stem Cells ◽  
Cancer Progression ◽  
Regulatory Networks ◽  
Epithelial To Mesenchymal Transition ◽  
Tumour Microenvironment ◽  
Repair Capacity ◽  
Mesenchymal Transition ◽  
Cellular Processes

Cancer stem cells (CSCs) possess properties such as self-renewal, resistance to apoptotic cues, quiescence, and DNA-damage repair capacity. Moreover, CSCs strongly influence the tumour microenvironment (TME) and may account for cancer progression, recurrence, and relapse. CSCs represent a distinct subpopulation in tumours and the detection, characterisation, and understanding of the regulatory landscape and cellular processes that govern their maintenance may pave the way to improving prognosis, selective targeted therapy, and therapy outcomes. In this review, we have discussed the characteristics of CSCs identified in various cancer types and the role of autophagy and long noncoding RNAs (lncRNAs) in maintaining the homeostasis of CSCs. Further, we have discussed methods to detect CSCs and strategies for treatment and relapse, taking into account the requirement to inhibit CSC growth and survival within the complex backdrop of cellular processes, microenvironmental interactions, and regulatory networks associated with cancer. Finally, we critique the computationally reinforced triangle of factors inclusive of CSC properties, the process of autophagy, and lncRNA and their associated networks with respect to hypoxia, epithelial-to-mesenchymal transition (EMT), and signalling pathways.

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