scholarly journals Applying the Tuple Space-Based Approach to the Simulation of the Caspases, an Essential Signalling Pathway

2013 ◽  
Vol 10 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Maura Cárdenas-García ◽  
Pedro Pablo González-Pérez
Keyword(s):  
Apoptotic Cell ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Interaction Patterns ◽  
Simulation Approach ◽  
Tuple Space ◽  
Intracellular Signalling Pathway ◽  
First Approximation ◽  
Tuple Spaces ◽  
Mitochondrial Permeabilization

Summary Apoptotic cell death plays a crucial role in development and homeostasis. This process is driven by mitochondrial permeabilization and activation of caspases. In this paper we adopt a tuple spaces-based modelling and simulation approach, and show how it can be applied to the simulation of this intracellular signalling pathway. Specifically, we are working to explore and to understand the complex interaction patterns of the caspases apoptotic and the mitochondrial role. As a first approximation, using the tuple spacesbased in silico approach, we model and simulate both the extrinsic and intrinsic apoptotic signalling pathways and the interactions between them. During apoptosis, mitochondrial proteins, released from mitochondria to cytosol are decisively involved in the process. If the decision is to die, from this point there is normally no return, cancer cells offer resistance to the mitochondrial induction.

scholarly journals Network Pharmacology-Based Study of the Underlying Mechanisms of Huangqi Sijunzi Decoction for Alzheimer’s Disease

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Wei Zhang ◽  
Mingti Lv ◽  
Yating Shi ◽  
Yonghui Mu ◽  
Zhaoyang Yao ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Neuroprotective Effect ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Network Pharmacology ◽  
Neuroprotective Effects ◽  
Target Network ◽  
Compound Target

Background. Huangqi Sijunzi decoction (HQSJZD) is a commonly used conventional Chinese herbal medicine prescription for invigorating Qi, tonifying Yang, and removing dampness. Modern pharmacology and clinical applications of HQSJZD have shown that it has a certain curative effect on Alzheimer’s disease (AD). Methods. The active components and targets of HQSJZD were searched in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The genes corresponding to the targets were retrieved using UniProt and GeneCard database. The herb-compound-target network and protein-protein interaction (PPI) network were constructed by Cytoscape. The core targets of HQSJZD were analysed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The main active compounds of HQSJZD were docked with acetylcholinesterase (AChE). In vitro experiments were conducted to detect the inhibitory and neuroprotective effects of AChE. Results. Compound-target network mainly contained 132 compounds and 255 corresponding targets. The main compounds contained quercetin, kaempferol, formononetin, isorhamnetin, hederagenin, and calycosin. Key targets contained AChE, PTGS2, PPARG, IL-1B, GSK3B, etc. There were 1708 GO items in GO enrichment analysis and 310 signalling pathways in KEGG, mainly including the cAMP signalling pathway, the vascular endothelial growth factor (VEGF) signalling pathway, serotonergic synapses, the calcium signalling pathway, type II diabetes mellitus, arginine and proline metabolism, and the longevity regulating pathway. Molecular docking showed that hederagenin and formononetin were the top 2 compounds of HQSJZD, which had a high affinity with AChE. And formononetin has a good neuroprotective effect, which can improve the oxidative damage of nerve cells. Conclusion. HQSJZD was found to have the potential to treat AD by targeting multiple AD-related targets. Formononetin and hederagenin in HQSJZD may regulate multiple signalling pathways through AChE, which might play a therapeutic role in AD.

110 Temporal Changes in Endometrial Gene Expression Between Ipsi- and Contralateral Uterine Horns in Cattle

2018 ◽  
Vol 30 (1) ◽  
pp. 194
Author(s):  
J. M. Sánchez ◽  
C. Passaro ◽  
N. Forde ◽  
S. Behura ◽  
J. A. Browne ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Luteal Phase ◽  
Expression Patterns ◽  
Uterine Horn ◽  
Oestrous Cycle ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Robust Analysis ◽  
The Impact

The transfer of an embryo into the uterine horn contralateral to the ovary bearing the corpus luteum has been associated with a decreased pregnancy rate in cattle compared with transfer into the ipsilateral horn. These findings suggest that the environment in the contralateral horn is less conducive to supporting conceptus development than that of the ipsilateral horn. Therefore, this study compared the endometrial transcriptome of the ipsi- and contralateral uterine horns during the luteal phase. Endometrial samples from the ipsi- (IPSI) and contralateral (CONTRA) horns were collected from synchronized nonpregnant beef heifers on Days 5, 7, 13 or 16 post-oestrus (n = 5 heifers per time point). Total RNA was isolated and sequenced. Differences in the transcriptome were determined by edgeR-robust analysis. Principal component analysis found that IPSI and CONTRA have distinct patterns of gene expression on each day, with Day 5 exhibiting the most variation and Day 16 being least variable. Further, the 2 uterine horns had distinct expression patterns on Day 5, with IPSI exhibiting significantly higher variation in gene expression compared twitho CONTRA. EdgeR-robust analysis found 217 (201 up- and 16 down-regulated), 54 (44 up- and 10 down-regulated), 14 (13 up- and 1 down-regulated), and 18 (14 up- and 4 down-regulated) differentially expressed genes (DEG; >2-fold change, false discovery rate P < 0.05) between IPSI and CONTRA endometria on Days 5, 7, 13, and 16 of the oestrous cycle, respectively. The top 5 canonical pathways associated with DEG between IPSI and CONTRA during the luteal phase of the oestrous cycle were involved in signalling pathways regulating pluripotency of stem cells (73/138), progesterone-mediated oocyte maturation (55/89), endometrial cancer (31/51), ErbB signalling pathway (50/87), and mTOR signalling pathway (36/61). The impact of DEG on signalling pathways was assessed using a pathway perturbation algorithm called Signalling Pathway Impact Analysis (SPIA). This topology-based pathway analysis was conducted using the Bioconductor ToPAseq package (https://bioconductor.org/packages/release/bioc/html/ToPASeq.html) and revealed that signalling pathways regulating pluripotency of stem cells showed the highest perturbation score when IPSI was compared with CONTRA irrespective of day. Discovering and cataloguing which pathways are perturbed in each uterine horn throughout the oestrous cycle may contribute to our understanding of the mechanisms underlying early embryonic loss. Ths study was supported by Science Foundation Ireland (13/IA/1983) and the Irish Department of Agriculture, Food and The Marine (13S528).

Significance of PI3K signalling pathway in clear cell renal cell carcinoma in relation to VHL and HIF status

2020 ◽  
pp. jclinpath-2020-206693
Author(s):  
Raviprakash Tumkur Sitaram ◽  
Maréne Landström ◽  
Göran Roos ◽  
Börje Ljungberg
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Tumour Progression ◽  
Recent Decade ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Cell Renal Cell Carcinoma ◽  
Von Hippel Lindau

Renal cell carcinoma (RCC) includes diverse tumour types characterised by various genetic abnormalities. The genetic changes, like mutations, deletions and epigenetic alterations, play a crucial role in the modification of signalling networks, tumour pathogenesis and prognosis. The most prevalent RCC type, clear cell RCC (ccRCC), is asymptomatic in the early stages and has a poorer prognosis compared with the papillary and the chromophobe types RCCs. Generally, ccRCC is refractory to chemotherapy and radiation therapy. Loss of von Hippel-Lindau (VHL) gene and upregulation of hypoxia-inducible factors (HIF), the signature of most sporadic ccRCC, promote multiple growth factors. Hence, VHL/HIF and a variety of pathways, including phosphatase and TEnsin homolog on chromosome 10/phosphatidylinositol-3-kinase (PI3K)/AKT, are closely connected and contribute to the ontogeny of ccRCC. In the recent decade, multiple targeting agents have been developed based on blocking major signalling pathways directly or indirectly involved in ccRCC tumour progression, metastasis, angiogenesis and survival. However, most of these drugs have limitations; either metastatic ccRCC develops resistance to these agents, or despite blocking receptors, tumour cells use alternate signalling pathways. This review compiles the state of knowledge about the PI3K/AKT signalling pathway confined to ccRCC and its cross-talks with VHL/HIF pathway.

scholarly journals Agonists for endothelial P2 purinoceptors trigger a signalling pathway producing Ca2+ responses in lymphocytes adherent to endothelial cells

1995 ◽  
Vol 311 (2) ◽  
pp. 589-594 ◽  
Author(s):  
J S Wiley ◽  
J R Chen ◽  
G P Jamieson ◽  
P J Thurlow
Keyword(s):  
Endothelial Cells ◽  
Lymphocytic Leukaemia ◽  
Umbilical Vein ◽  
Cell Types ◽  
The Body ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Transient Rise ◽  
Umbilical Vein Endothelial Cells ◽  
Stimulation Of

Recirculation of lymphocytes through the body involves their frequent adhesion to endothelial cells but little is known of the signalling pathways between these two cell types. Lymphocytes from patients with chronic lymphocytic leukaemia were loaded with the Ca(2+)-sensitive indicator, fura 2, and allowed to adhere to either glass or monolayers of human umbilical-vein endothelial cells. Addition of ATP or UTP (1-10 microM) to the superfusate produced a transient rise in cytosolic Ca2+ concentration in the lymphocytes adherent to endothelium (24 of 35 cells). In contrast, ATP or UTP (1-10 microM) had no effect on the cytosolic Ca2+ of lymphocytes attached to glass. As the only lymphocyte receptor for ATP (P2Z class) requires higher ATP concentrations (> 50 microM) for Ca2+ influx and is unresponsive to UTP, the involvement of a lymphocyte P2Z purinoceptor is unlikely. Various agonists including ATP, UTP, 2-methylthioATP, ADP and histamine all stimulated increases in endothelial cytosolic Ca2+ but only ATP and UTP (both agonists for endothelial P2U purinoceptors) triggered Ca2+ transients in adherent lymphocytes. Removal of extracellular Ca2+ did not abolish the ATP-induced rise in cytosolic Ca2+ concentration in lymphocytes adherent to endothelial cells. These findings show that stimulation of endothelial P2U purinoceptors triggers an endothelial-lymphocyte signalling pathway which releases internal Ca2+ in adherent lymphocytes.

Regulation of MEK/ERK pathway output by subcellular localization of B-Raf

2012 ◽  
Vol 40 (1) ◽  
pp. 67-72 ◽  
Author(s):  
Catherine Andreadi ◽  
Catherine Noble ◽  
Bipin Patel ◽  
Hong Jin ◽  
Maria M. Aguilar Hernandez ◽  
...  
Keyword(s):  
Growth Factor ◽  
Subcellular Localization ◽  
Signalling Pathway ◽  
Erk Activation ◽  
Extracellular Signal Regulated Kinase ◽  
Intracellular Signalling Pathway ◽  
Pathway Activation ◽  
Extracellular Signal ◽  
A Cell ◽  
Phase Entry

The strength and duration of intracellular signalling pathway activation is a key determinant of the biological outcome of cells in response to extracellular cues. This has been particularly elucidated for the Ras/Raf/MEK [mitogen-activated growth factor/ERK (extracellular-signal-regulated kinase) kinase]/ERK signalling pathway with a number of studies in fibroblasts showing that sustained ERK signalling is a requirement for S-phase entry, whereas transient ERK signalling does not have this capability. A major unanswered question, however, is how a cell can sustain ERK activation, particularly when ERK-specific phosphatases are transcriptionally up-regulated by the pathway itself. A major point of ERK regulation is at the level of Raf, and, to sustain ERK activation in the presence of ERK phosphatases, sustained Raf activation is a requirement. Three Raf proteins exist in mammals, and the activity of all three is induced following growth factor stimulation of cells, but only B-Raf activity is maintained at later time points. This observation points to B-Raf as a regulator of sustained ERK activation. In the present review, we consider evidence for a link between B-Raf and sustained ERK activation, focusing on a potential role for the subcellular localization of B-Raf in this key physiological event.

scholarly journals Targeting mediators of Wnt signalling pathways by GnRH in gonadotropes

2010 ◽  
Vol 44 (4) ◽  
pp. 195-201 ◽  
Author(s):  
Samantha Gardner ◽  
Emmanouil Stavrou ◽  
Patricia E Rischitor ◽  
Elena Faccenda ◽  
Adam J Pawson
Keyword(s):  
Signal Transduction ◽  
Gnrh Receptor ◽  
Wnt Signalling ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Signal Transduction Pathways ◽  
Cellular Processes ◽  
Key Players ◽  
Canonical Wnt ◽  
Recent Demonstration

The binding of GnRH to its receptor on pituitary gonadotropes leads to the targeting of a diverse array of signalling mediators. These mediators drive multiple signal transduction pathways, which in turn regulate a variety of cellular processes, including the biosynthesis and secretion of the gonadotropins LH and FSH. Advances in our understanding of the mechanisms and signalling pathways that are recruited to regulate gonadotrope function are continually being made. This review will focus on the recent demonstration that key mediators of the canonical Wnt signalling pathway are targeted by GnRH in gonadotropes, and that these may play essential roles in regulating the expression of many of the key players in gonadotrope biology, including the GnRH receptor and the gonadotropins.

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