A theoretical modeling for frequency modulation of Ca2+ signal on activation of MAPK cascade

Integrated transcriptome and miRNA sequencing approaches provide insights into salt tolerance in allotriploid Populus cathayana

Some salt-stress responsive DEGs, mainly involved in ion transmembrane transport, hormone regulation, antioxidant system, osmotic regulation, and some miRNA jointly regulated the salt response process in allotriploid Populus cathayana. The molecular mechanism of plant polyploid stress resistance has been a hot topic in biological research. In this study, Populus diploids and first division restitution (FDR) and second division restitution (SDR) triploids were selected as research materials. All materials were treated with 70 mM NaCl solutions for 30 days in the same pot environment. We observed the growth state of triploids and diploids and determined the ratio of potassium and sodium ions, peroxidase (POD) activity, proline content, and ABA and jasmonic acid (JA) hormone content in leaves in the same culture environment with the same concentration of NaCl solution treatment. In addition, RNA-seq technology was used to study the differential expression of mRNA and miRNA. The results showed that triploid Populus grew well and the K⁺ content and the K⁺/Na⁺ ratio in the salt treatment were significantly lower than those in the control. The contents of ABA, JA, POD, and proline were increased compared with contents in diploid under salt stress. The salt-stress responsive DEGs were mainly involved in ion transport, cell homeostasis, the MAPK signaling pathway, peroxisome, citric acid cycle, and other salt response and growth pathways. The transcription factors mainly included NAC, MYB, MYB_related and AP2/ERF. Moreover, the differentially expressed miRNAs involved 32 families, including 743 miRNAs related to predicted target genes, among which 22 miRNAs were significantly correlated with salt-stress response genes and related to the regulation of hormones, ion transport, reactive oxygen species (ROS) and other biological processes. Our results provided insights into the physiological and molecular aspects for further research into the response mechanisms of allotriploid Populus cathayana to salt stress. This study provided valuable information for the salt tolerance mechanism of allopolyploids.

In vitro differentiation of W8B2+ human cardiac stem cells: gene expression of ionic channels and spontaneous calcium activity

Background

Human cardiac stem cells expressing the W8B2 marker (W8B2⁺ CSCs) were recently identified and proposed as a new model of multipotent CSCs capable of differentiating into smooth muscle cells, endothelial cells and immature myocytes. Nevertheless, no characterization of ion channel or calcium activity during the differentiation of these stem cells has been reported.

Methods

The objectives of this study were thus to analyze (using the TaqMan Low-Density Array technique) the gene profile of W8B2⁺ CSCs pertaining to the regulation of ion channels, transporters and other players involved in the calcium homeostasis of these cells. We also analyzed spontaneous calcium activity (via the GCaMP calcium probe) during the in vitro differentiation of W8B2⁺ CSCs into cardiac myocytes.

Results

Our results show an entirely different electrophysiological genomic profile between W8B2⁺ CSCs before and after differentiation. Some specific nodal genes, such as Tbx3, HCN, ICaT, L, KV, and NCX, are overexpressed after this differentiation. In addition, we reveal spontaneous calcium activity or a calcium clock whose kinetics change during the differentiation process. A pharmacological study carried out on differentiated W8B2⁺ CSCs showed that the NCX exchanger and IP3 stores play a fundamental role in the generation of these calcium oscillations.

Conclusions

Taken together, the present results provide important information on ion channel expression and intrinsic calcium dynamics during the differentiation process of stem cells expressing the W8B2 marker.

Propagation of Oscillating Chemical Signals through Reaction Networks

Akin to electronic systems that can tune to and process signals of select frequencies, systems/networks of chemical reactions also "propagate" time-varying concentration inputs in a frequency-dependent manner. Whereas signals of low frequencies are transmitted, higher frequency inputs are dampened and converted into steady-concentration outputs. Such behavior is observed in both idealized reaction chains as well as realistic signaling cascades, in the latter case explaining the experimentally observed responses of such cascades to input calcium oscillations. These and other results are supported by numerical simulations within the freely available Kinetix web application we developed to study chemical systems of arbitrary architectures, reaction kinetics, and boundary conditions.

Ca2+ Requirements for Long-Term Depression Are Frequency Sensitive in Purkinje Cells

Cerebellar long-term depression (LTD) is a form of synaptic plasticity dependent on postsynaptic Ca²⁺ changes. One fundamental question is how LTD is selectively induced by specific numbers of Ca²⁺ pulses and which are the frequency and duration of this train of pulses required for LTD induction. The molecular mechanism which leads the integration of postsynaptic Ca²⁺ pulses in the LTD signaling network has not been elucidated either. Recent publications have shown that Ca²⁺/calmodulin-dependent protein kinase II (CaMKII) is required for LTD induction. Additionally, protein kinase C (PKC), CaMKII, and MAPK play an important role to transduce the frequency of Ca²⁺ pulses into their enzymatic activity levels; however, it is still unknown which enzymes are involved in decoding Ca²⁺ pulses in LTD. We have extended a stochastic model of LTD by adding the molecular network regulating CaMKII activity and its activation. We solved this model with stochastic engine for pathway simulation to include the effect of biochemical noise in LTD. We systematically investigated the dependence of LTD induction on stimulus frequencies, and we found that LTD is selectively induced by a specific number of Ca²⁺ spikes at different frequencies. We observed that CaMKII is essential to induce LTD, and LTD is only weakly induced when its Thr286 phosphorylation site has been deleted. We found that CaMKII decodes the frequency of Ca²⁺ spikes into different amounts of kinase activity during LTD induction. In addition, PKC and ERK enzyme activity is highly sensitive to the frequency and the number of Ca²⁺ pulses and this sensitivity has an important effect on LTD activation. This research predicts the postsynaptic Ca²⁺ requirements to induce LTD using a typical synaptic activation sequence and explains how LTD is selectively induced by specific number of Ca²⁺ pulses at different frequencies.

Calcium as a signal integrator in developing epithelial tissues

Decoding how tissue properties emerge across multiple spatial and temporal scales from the integration of local signals is a grand challenge in quantitative biology. For example, the collective behavior of epithelial cells is critical for shaping developing embryos. Understanding how epithelial cells interpret a diverse range of local signals to coordinate tissue-level processes requires a systems-level understanding of development. Integration of multiple signaling pathways that specify cell signaling information requires second messengers such as calcium ions. Increasingly, specific roles have been uncovered for calcium signaling throughout development. Calcium signaling regulates many processes including division, migration, death, and differentiation. However, the pleiotropic and ubiquitous nature of calcium signaling implies that many additional functions remain to be discovered. Here we review a selection of recent studies to highlight important insights into how multiple signals are transduced by calcium transients in developing epithelial tissues. Quantitative imaging and computational modeling have provided important insights into how calcium signaling integration occurs. Reverse-engineering the conserved features of signal integration mediated by calcium signaling will enable novel approaches in regenerative medicine and synthetic control of morphogenesis.

Acid-sensing ion channel 1a mediates acid-induced inhibition of matrix metabolism of rat articular chondrocytes via the MAPK signaling pathway

The acid-sensing ion channel 1a (ASIC1a), which is activated by extracellular acid, contributes to the pathogenesis of rheumatoid arthritis. However, it remains unclear whether ASIC1a mediates acid-induced matrix metabolism in rat articular chondrocytes via activation of the MAPK signaling pathway. In the current study, we found that extracellular acidification (pH 6.0) inhibited proliferation and induced apoptosis of articular chondrocytes in a dose-dependent manner, while the expression of phosphorylated ERK1/2 and P38 MAPK increased, but, this effect was blocked by the Ca²⁺ chelator BAPTA-AM and the ASIC1a-specific blocker PcTx-1. In addition, extracellular acidification increased the expression of c-fos, GAG, HYP, and TIM1/2. These effects were inhibited by the Ca²⁺ chelator BAPTA-AM, ERK1/2 inhibitor PD98059, and ASIC1a-specific blocker PcTx-1, but not the P38 MAPK inhibitor SB203580. Finally, extracellular acidification increased the expression of c-jun and MMP-2/9, and these effects were blocked by the Ca²⁺ chelator BAPTA-AM, P38 MAPK inhibitor SB203580, and ASIC1a-specific blocker PcTx-1, but not the ERK1/2 inhibitor PD98059. In conclusion, ASIC1a inhibits the expression of MMP-2/9, GAG, HYP, and TIMP-1/2 by the Ca²⁺-dependent P38 MAPK/c-jun and ERK/c-fos signaling pathways.

Dihydroberberine exhibits synergistic effects with sunitinib on NSCLC NCI-H460 cells by repressing MAP kinase pathways and inflammatory mediators

Highly effective and attenuated dose schedules are good regimens for drug research and development. Combination chemotherapy is a good strategy in cancer therapy. We evaluated the antitumour effects of dihydroberberine combined with sunitinib (DCS) on the human non-small cell lung cancer cell lines (NSCLC), A549, NCI-H460, and NCI-H1299 in vitro and in vivo. DCS showed synergic effects on NCI-H460 cell proliferation, colony formation and transplantable tumour growth, which suggested dihydroberberine increases the sensitivity of lung carcinoma to sunitinib. Further studies indicated that DCS down-regulated phosphorylation of JNK, p38, and NF-κB in NCI-H460 cells and tumours and suppressed the IκB and COX-2 expression. In addition, DCS reduced the secretion of the pro-inflammatory cytokine, interleukin-1 (IL-1), in tumours. Inhibition of p38 activation by DCS was a likely contributing factor in IL-1 and COX-2 down-regulation. Consistent with these results, a genomewide microarray analysis found that DCS induced the expression of cell cycle signal molecules that are known to be affected by JNK and p38. The change of cell cycle, in turn, led to down-regulation of JNK and p38, and further reduced IL-1 secretion. Collectively, these findings highlight potential molecular mechanisms of DCS chemotherapeutic activity and suggest that DCS is an efficacious strategy in NSCLC therapy.

Minimal oscillating subnetwork in the Huang-Ferrell model of the MAPK cascade

Prompted by the recent growing evidence of oscillatory behavior involving MAPK cascades we present a systematic approach of analyzing models and elucidating the nature of biochemical oscillations based on reaction network theory. In particular, we formulate a minimal biochemically consistent mass action subnetwork of the Huang-Ferrell model of the MAPK signalling that provides an oscillatory response when a parameter controlling the activation of the top-tier kinase is varied. Such dynamics are either intertwined with or separated from the earlier found bistable/hysteretic behavior in this model. Using the theory of stability of stoichiometric networks, we reduce the original MAPK model, convert kinetic to convex parameters and examine those properties of the minimal subnetwork that underlie the oscillatory dynamics. We also use the methods of classification of chemical oscillatory networks to explain the rhythmic behavior in physicochemical terms, i.e., we identify of the role of individual biochemical species in positive and negative feedback loops and describe their coordinated action leading to oscillations. Our approach provides an insight into dynamics without the necessity of knowing rate coefficients and thus is useful prior the statistical evaluation of parameters.

Isofraxidin exhibited anti-inflammatory effects in vivo and inhibited TNF-α production in LPS-induced mouse peritoneal macrophages in vitro via the MAPK pathway

Isofraxidin (IF) is a Coumarin compound that can be isolated from medicinal plants, such as Sarcandra glabra (Thunb.). Nakai is widely used in Asian countries for the treatment of anti-bacterial, anti-inflammatory and anti-tumour action. The present investigation was designed to evaluate the effect of IF on inflammation and nociception. In addition, we investigated a potential novel mechanism to explain the anti-inflammatory properties of IF. In vivo, xylene-induced mouse ear edema, carrageenan-induced rat paw edema, LPS-induced mouse endotoxic shock, acetic acid-induced mice writhing and formalin-induced mouse pain models were used to evaluate the anti-inflammatory activity of IF. In vitro, we examined the effects of IF inhibition on TNF-α production and the regulation of ERK1/2 and p38 phosphorylation activity in LPS-induced mouse peritoneal macrophages. Our results demonstrated that IF can significantly decrease xylene-induced ear edema, carrageenan-induced paw edema, acetic acid-induced writhing and formalin-induced pain. Moreover, IF greatly inhibited the production of TNF-α in the serum of LPS-stimulated mice and peritoneal macrophages, and it decreased phospho-p38 and ERK1/2 protein expression in LPS-stimulated mouse peritoneal macrophages. Overall, our data suggest that IF possesses significant analgesic and anti-inflammatory activities that may be mediated through the regulation of pro-inflammatory cytokines, TNF-α and the phosphorylation of p38 and ERK1/2.