Using systems biology approaches to identify signalling pathways activated during chronic wound initiation

2021 ◽  
Author(s):  
Proma Basu ◽  
Jane Hannah Kim ◽  
Shayan Saeed ◽  
Manuela Martins‐Green
Keyword(s):  
Systems Biology ◽  
Chronic Wound ◽  
Signalling Pathways

scholarly journals Exploring the intrinsic behaviour of multisite phosphorylation systems as part of signalling pathways

2018 ◽  
Vol 15 (143) ◽  
pp. 20180109 ◽  
Author(s):  
Thapanar Suwanmajo ◽  
J. Krishnan
Keyword(s):  
Information Processing ◽  
Systems Biology ◽  
Synthetic Biology ◽  
Cell Signalling ◽  
Enzyme Activation ◽  
Signalling Pathways ◽  
Chemical Information ◽  
Intrinsic Kinetics ◽  
Multisite Phosphorylation

Multisite phosphorylation is a basic way of chemically encoding substrate function and a recurring feature of cell signalling pathways. A number of studies have explored information processing characteristics of multisite phosphorylation, through studies of the intrinsic kinetics. Many of these studies focus on the module in isolation. In this paper, we build a bridge to connect the behaviour of multisite modification in isolation to that as part of pathways. We study the effect of activation of the enzymes (which are basic ways in which the module may be regulated), as well the effects of the modified substrates being involved in further modifications or exiting reaction compartments. We find that these effects can induce multiple kinds of transitions, including to behaviour not seen intrinsically in the multisite modification module. We then build on these insights to investigate how these multisite modification systems can be tuned by enzyme activation to realize a range of information processing outcomes for the design of synthetic phosphorylation circuits. Connecting the complexity of multisite modification kinetics, with the pathways in which they are embedded, serves as a basis for teasing out many aspects of their interaction, providing insights of relevance in systems biology, synthetic biology/chemistry and chemical information processing.

scholarly journals Cellular Signalling and Photobiomodulation in Chronic Wound Repair

2021 ◽  
Vol 22 (20) ◽  
pp. 11223
Author(s):  
Thobekile S. Leyane ◽  
Sandy W. Jere ◽  
Nicolette N. Houreld
Keyword(s):  
Wound Healing ◽  
Growth Factors ◽  
Wound Repair ◽  
Cellular Proliferation ◽  
Chronic Wounds ◽  
Chronic Wound ◽  
Cell Signalling ◽  
Signalling Pathways ◽  
Atp Production ◽  
Therapeutic Benefits

Photobiomodulation (PBM) imparts therapeutically significant benefits in the healing of chronic wounds. Chronic wounds develop when the stages of wound healing fail to progress in a timely and orderly frame, and without an established functional and structural outcome. Therapeutic benefits associated with PBM include augmenting tissue regeneration and repair, mitigating inflammation, relieving pain, and reducing oxidative stress. PBM stimulates the mitochondria, resulting in an increase in adenosine triphosphate (ATP) production and the downstream release of growth factors. The binding of growth factors to cell surface receptors induces signalling pathways that transmit signals to the nucleus for the transcription of genes for increased cellular proliferation, viability, and migration in numerous cell types, including stem cells and fibroblasts. Over the past few years, significant advances have been made in understanding how PBM regulates numerous signalling pathways implicated in chronic wound repair. This review highlights the significant role of PBM in the activation of several cell signalling pathways involved in wound healing.

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Experimental Design ◽  
Integrated Systems ◽  
Microbiome Research ◽  
Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

Caspases and apoptosis

2002 ◽  
Vol 38 ◽  
pp. 9-19 ◽  
Author(s):  
Guy S Salvesen
Keyword(s):  
Cysteine Proteases ◽  
Signalling Pathways ◽  
Term Survival ◽  
Mature Adult ◽  
Intracellular Signalling Pathways ◽  
Adult Cell ◽  
Caspase Family ◽  
Cell Fragments ◽  
Pro Inflammatory Cytokines

The ability of metazoan cells to undergo programmed cell death is vital to both the precise development and long-term survival of the mature adult. Cell deaths that result from engagement of this programme end in apoptosis, the ordered dismantling of the cell that results in its 'silent' demise, in which packaged cell fragments are removed by phagocytosis. This co-ordinated demise is mediated by members of a family of cysteine proteases known as caspases, whose activation follows characteristic apoptotic stimuli, and whose substrates include many proteins, the limited cleavage of which causes the characteristic morphology of apoptosis. In vertebrates, a subset of caspases has evolved to participate in the activation of pro-inflammatory cytokines, and thus members of the caspase family participate in one of two very distinct intracellular signalling pathways.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

Systems Biology

2009 ◽  
Author(s):  
Bernhard O. Palsson ◽  
Marc Abrams
Keyword(s):  
Systems Biology
Sign in / Sign up

Export Citation Format

Share Document