scholarly journals Early beginnings - the emergence of complex signaling systems and cell-to-cell communication

2010 ◽  
Vol 8 (1) ◽  
Author(s):  
Stephan M Feller
Keyword(s):  
Cell Communication ◽  
Signaling Systems ◽  
Complex Signaling

Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants

2019 ◽  
Vol 70 (1) ◽  
pp. 153-186 ◽  
Author(s):  
Vilde Olsson ◽  
Lisa Joos ◽  
Shanshuo Zhu ◽  
Kris Gevaert ◽  
Melinka A. Butenko ◽  
...  
Keyword(s):  
Cell Communication ◽  
Peptide Ligands ◽  
Biologically Active ◽  
Peptide Ligand ◽  
Long Distance ◽  
Signaling Systems ◽  
Experimental Approaches ◽  
Biologically Active Peptide ◽  
Subsequent Activation ◽  
Complex Signaling

During the past decade, a flurry of research focusing on the role of peptides as short- and long-distance signaling molecules in plant cell communication has been undertaken. Here, we focus on peptides derived from nonfunctional precursors, and we address several key questions regarding peptide signaling. We provide an overview of the regulatory steps involved in producing a biologically active peptide ligand that can bind its corresponding receptor(s) and discuss how this binding and subsequent activation lead to specific cellular outputs. We discuss different experimental approaches that can be used to match peptide ligands with their receptors. Lastly, we explore how peptides evolved from basic signaling units regulating essential processes in plants to more complex signaling systems as new adaptive traits developed and how nonplant organisms exploit this signaling machinery by producing peptide mimics.

scholarly journals Precancerous niche (PCN), a product of fibrosis with remodeling by incessant chronic inflammation

4open ◽  
2019 ◽  
Vol 2 ◽  
pp. 11 ◽  
Author(s):  
Björn L.D.M. Brücher ◽  
Ijaz S. Jamall
Keyword(s):  
Extracellular Matrix ◽  
Chronic Inflammation ◽  
Genetic Material ◽  
Cell Communication ◽  
Cell Types ◽  
Complex Signaling ◽  
Different Cell Types ◽  
Multiple Signaling ◽  
Extracellular Environment

Fibroblasts are actively involved in the creation of the stroma and the extracellular matrix which are important for cell adhesion, cell–cell communication, and tissue metabolism. The role of fibrosis in carcinogenesis can be examined by analogy to tissues of various cancers. The orchestration of letters in the interplay of manifold components with signaling and crosstalk is incompletely understood but available evidence suggests a hitherto underappreciated role for fibrosis in carcinogenesis. Complex signaling and crosstalk by pathogenic stimuli evoke persistent subclinical inflammation, which in turn, results in a cascade of different cell types, ubiquitous proteins and their corresponding enzymes, cytokine releases, and multiple signaling pathways promoting the onset of fibrosis. There is considerable evidence that the body's attempt to resolve such a modified extracellular environment leads to further disruption of homeostasis and the genesis of the precancerous niche as part of the six-step process that describes carcinogenesis. The precancerous niche is formed and can be understood to develop as a result of (1) pathogenic stimulus, (2) chronic inflammation, and (3) fibrosis with alterations of the extracellular matrix, stromal rigidity, and mechano-transduction. This is why carcinogenesis is not just a process of aberrant cell growth with damaged genetic material but the role of the PCN in its entirety reveals how carcinogenesis can occur without invoking the need for somatic mutations.

scholarly journals Function and Evolution of Nuclear Receptors in Environmental-Dependent Postembryonic Development

2021 ◽  
Vol 9 ◽  
Author(s):  
Jan Taubenheim ◽  
Constantin Kortmann ◽  
Sebastian Fraune
Keyword(s):  
Nuclear Receptors ◽  
Sexual Maturation ◽  
Steroid Receptors ◽  
Current Knowledge ◽  
Postembryonic Development ◽  
Model Organisms ◽  
Signaling Mechanism ◽  
Signaling Systems ◽  
Decision Points ◽  
Complex Signaling

Nuclear receptors (NRs) fulfill key roles in the coordination of postembryonal developmental transitions in animal species. They control the metamorphosis and sexual maturation in virtually all animals and by that the two main environmental-dependent developmental decision points. Sexual maturation and metamorphosis are controlled by steroid receptors and thyroid receptors, respectively in vertebrates, while both processes are orchestrated by the ecdysone receptor (EcR) in insects. The regulation of these processes depends on environmental factors like nutrition, temperature, or photoperiods and by that NRs form evolutionary conserved mediators of phenotypic plasticity. While the mechanism of action for metamorphosis and sexual maturation are well studied in model organisms, the evolution of these systems is not entirely understood and requires further investigation. We here review the current knowledge of NR involvement in metamorphosis and sexual maturation across the animal tree of life with special attention to environmental integration and evolution of the signaling mechanism. Furthermore, we compare commonalities and differences of the different signaling systems. Finally, we identify key gaps in our knowledge of NR evolution, which, if sufficiently investigated, would lead to an importantly improved understanding of the evolution of complex signaling systems, the evolution of life history decision points, and, ultimately, speciation events in the metazoan kingdom.

scholarly journals Parallel Tempering with Lasso for Model Reduction in Systems Biology

2019 ◽  
Author(s):  
Sanjana Gupta ◽  
Robin E.C. Lee ◽  
James R. Faeder
Keyword(s):  
Systems Biology ◽  
Model Reduction ◽  
Feedback Loops ◽  
Signaling Network ◽  
Parallel Tempering ◽  
Emergent Properties ◽  
Signaling Systems ◽  
Cellular Behaviors ◽  
Complex Signaling ◽  
The Bayesian Approach

AbstractSystems Biology models reveal relationships between signaling inputs and observable molecular or cellular behaviors. The complexity of these models, however, often obscures key elements that regulate emergent properties. We use a Bayesian model reduction approach that combines Parallel Tempering with Lasso regularization to identify minimal subsets of reactions in a signaling network that are sufficient to reproduce experimentally observed data. The Bayesian approach finds distinct reduced models that fit data equivalently. A variant of this approach based on Group Lasso is applied to the NF-κB signaling network to test the necessity of feedback loops for responses to pulsatile and continuous pathway stimulation. Taken together, our results demonstrate that Bayesian parameter estimation combined with regularization can isolate and reveal core motifs sufficient to explain data from complex signaling systems.

scholarly journals The context-dependent, combinatorial logic of BMP signaling

2020 ◽  
Author(s):  
Heidi Klumpe ◽  
Matthew A. Langley ◽  
James M. Linton ◽  
Christina J. Su ◽  
Yaron E. Antebi ◽  
...  
Keyword(s):  
Communication Systems ◽  
Cell Communication ◽  
Bmp Signaling ◽  
Receptor Expression ◽  
Signaling Systems ◽  
Morphogenetic Protein ◽  
Pathway Activation ◽  
Ligand Interactions ◽  
Context Dependent ◽  
Combinatorial Interactions

SummaryCell-cell communication systems typically comprise families of ligand and receptor variants that function together in combinations. Pathway activation depends in a complex way on which ligands are present and what receptors are expressed by the signal-receiving cell. To understand the combinatorial logic of such a system, we systematically measured pairwise Bone Morphogenetic Protein (BMP) ligand interactions in cells with varying receptor expression. Ligands could be classified into equivalence groups based on their profile of positive and negative synergies with other ligands. These groups varied with receptor expression, explaining how ligands can functionally replace each other in one context but not another. Context-dependent combinatorial interactions could be explained by a biochemical model based on competitive formation of alternative signaling complexes with distinct activities. Together, these results provide insights into the roles of BMP combinations in developmental and therapeutic contexts and establish a framework for analyzing other combinatorial, context-dependent signaling systems.

scholarly journals Animal personalities and their implications for complex signaling

2014 ◽  
Vol 60 (3) ◽  
pp. 381-386 ◽  
Author(s):  
Nicholas Dirienzo ◽  
Ann V Hedrick
Keyword(s):  
Sexual Selection ◽  
Behavioral Ecology ◽  
Ecological Processes ◽  
Signaling Systems ◽  
Signaling Complex ◽  
Selection For ◽  
Complex Signaling ◽  
Animal Personalities ◽  
Signaling Interactions

Abstract Animal personalities have been a major focus of behavioral ecology over the past decade. Consistent individual differences in behavior have been found across taxa, and have been shown to influence a range of ecological processes. The role of personalities in sexual selection has been considered, and examples exist that show selection for personality traits with both assortative and disassortative mating patterns between personality types. One overlooked aspect of the personality and sexual selection literature is the potential for personality-signaling interactions, specifically with complex signaling. Complex signaling is a diverse topic in itself, and in short, consists of multiple signals within one or more modalities that interact to elicit a receiver response. Research into complex signaling has been thorough, although at times studies discover complex signaling systems that fail to fit into one of the existing hypotheses in the literature. Here, we argue that personalities may interact with complex signaling, which should be considered by researchers of both personality and sexual selection and communication. We describe several ways in which personality-complex signaling interactions could affect both the signaler and receiver, and the way in which they may drive personality-specific signals as well as receiver preferences. Finally, we discuss how considering personality in complex signaling studies may inform theory as well as improve the ability of researchers to accurately describe its function.

scholarly journals Inference and analysis of cell-cell communication using CellChat

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Suoqin Jin ◽  
Christian F. Guerrero-Juarez ◽  
Lihua Zhang ◽  
Ivan Chang ◽  
Raul Ramos ◽  
...  
Keyword(s):  
Communication Networks ◽  
Cell Communication ◽  
Molecular Complexes ◽  
Web Based ◽  
Single Cell Rna Sequencing ◽  
Context Specific ◽  
Global Communications ◽  
Complex Signaling ◽  
Intercellular Communications ◽  
Cell Cell

AbstractUnderstanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.

Can regulatory peptides be regarded as words of a biological language

1991 ◽  
Vol 261 (2) ◽  
pp. G171-G184 ◽  
Author(s):  
E. A. Mayer ◽  
J. P. Baldi
Keyword(s):  
Growth Factor ◽  
Information Content ◽  
Cell Biology ◽  
Information Transfer ◽  
Cell Communication ◽  
Regulatory Peptides ◽  
Quantitative Information ◽  
Receptor Subtypes ◽  
Signaling Systems ◽  
Noise Interference

Despite the complexities of individual systems, neurocrine, endocrine, and growth factor-mediated signaling systems show striking similarities in the molecules they use for communication and in their signal-transduction mechanisms. In contrast to the traditional view in cell biology, which has focused on the regulatory aspects of neurocrine and endocrine messengers and growth factors, an analysis of various aspects of peptidergic cell-to-cell communication on the basis of information theory is suggested. According to theorems for efficient and error-free encoding, the differences in rate and distance of information transfer and in noise interference between neurocrine, endocrine, and growth factor-mediated messages require different encoding strategies. These differences are reflected in the use of plurichemical transmission (to increase information content) or in the number and sequence of amino acids within peptide molecules (to protect against noise interference). In contrast to the quantitative information content, the qualitative information of the messages is not transmitted but is retrieved when the message interacts with transduction networks at the receiver cell. The semantic information is contained within the rules specifying the conditional co-occurrences of signals. The suggested analysis provides a framework for the understanding of various aspects of cell-to-cell communication, such as structure-function relationship of regulatory peptides, multiple receptor subtypes, plurichemical transmission, and transduction networks. The data discussed are consistent with the role of regulatory peptides as signals in a universal structured code for biological communication.

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