Geometric slow-fast analysis of a hybrid pituitary cell model with stochastic ion channel dynamics

To obtain explicit understanding of the behavior of dynamical systems, geometrical methods and slow-fast analysis have proved to be highly useful. Such methods are standard for smooth dynamical systems, and increasingly used for continuous, non-smooth dynamical systems. However, they are much less used for random dynamical systems, in particular for hybrid models with discrete, random dynamics. Indeed, the analysis of such systems has typically been done by studying the corresponding deterministic system and considering how noise perturbs the deterministic geometrical structures. Here we propose a geometrical method that works directly with the hybrid system. We illustrate our approach through an application to a hybrid pituitary cell model in which the stochastic dynamics of very few active large-conductance potassium (BK) channels is coupled to a deterministic model of the other ion channels and calcium dynamics. To employ our geometric approach, we exploit the slow-fast structure of the model. The random fast subsystem is analyzed by considering discrete phase planes, corresponding to the discrete number of open BK channels, and stochastic events correspond to jumps between these planes. The evolution within each plane can be understood from nullclines and limit cycles, and the overall dynamics, e.g., whether the model produces a spike or a burst, is determined by the location at which the system jumps from one plane to another. Our approach is generally applicable to other scenarios to study discrete random dynamical systems defined by hybrid stochastic-deterministic models.Comment: 15 pages, 8 figure

Recent advances in mathematical modeling and statistical analysis of exocytosis in endocrine cells

open5noMost endocrine cells secrete hormones as a result of Ca(2+)-regulated exocytosis, i.e., fusion of the membranes of hormone-containing secretory granules with the cell membrane, which allows the hormone molecules to escape to the extracellular space. As in neurons, electrical activity and cell depolarization open voltage-sensitive Ca(2+) channels, and the resulting Ca(2+) influx elevate the intracellular Ca(2+) concentration, which in turn causes exocytosis. Whereas the main molecular components involved in exocytosis are increasingly well understood, quantitative understanding of the dynamical aspects of exocytosis is still lacking. Due to the nontrivial spatiotemporal Ca(2+) dynamics, which depends on the particular pattern of electrical activity as well as Ca(2+) channel kinetics, exocytosis is dependent on the spatial arrangement of Ca(2+) channels and secretory granules. For example, the creation of local Ca(2+) microdomains, where the Ca(2+) concentration reaches tens of µM, are believed to be important for triggering exocytosis. Spatiotemporal simulations of buffered Ca(2+) diffusion have provided important insight into the interplay between electrical activity, Ca(2+) channel kinetics, and the location of granules and Ca(2+) channels. By confronting simulations with statistical time-to-event (or survival) regression analysis of single granule exocytosis monitored with TIRF microscopy, a direct connection between location and rate of exocytosis can be obtained at the local, single-granule level. To get insight into whole-cell secretion, simplifications of the full spatiotemporal dynamics have shown to be highly helpful. Here, we provide an overview of recent approaches and results for quantitative analysis of Ca(2+) regulated exocytosis of hormone-containing granules.openPedersen, Morten Gram; Tagliavini, Alessia; Cortese, Giuliana; Riz, Michela; Montefusco, FrancescoPedersen, MORTEN GRAM; Tagliavini, Alessia; Cortese, Giuliana; Riz, Michela; Montefusco, Francesc

Implementing nonlinear feedback controllers using DNA strand displacement reactions

We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs

Analysis of a Cardiac-Necrosis-Biomarker Release in Patients with Acute Myocardial Infarction via Nonlinear Mixed-Effects Models

The release of the cardiac troponin T (cTnT) in patients with acute myocardial infarc tion (AMI) has been analyzed through a methodology based on nonlinear mixed-effects (NME) models. The aim of this work concerns the investigation of any possible relationship between clin ical covariates and the dynamics of the release of cTnT to derive more detailed and useful clinical information for the correct treatment of these patients. An ad-hoc mechanistic model describing the biomarker release process after AMI has been devised, assessed, and exploited to evaluate the im pact of the available clinical covariates on the cTnT release dynamic. The following approach was tested on a preliminary dataset composed of a small number of potential clinical covariates: em ploying an unsupervised approach, and despite the limited sample size, dyslipidemia, a known risk factor for cardiovascular disease, was found to be a statistically significant covariate. By increasing the number of covariates considered in the model, and patient cohort, we envisage that this approach may provide an effective means to automatically classify AMI patients and to investigate the role of interactions between clinical covariates and cTnT relea

Impact of Cytomegalovirus Replication and Cytomegalovirus Serostatus on the Outcome of Patients with B Cell Lymphoma after Allogeneic Stem Cell Transplantation

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Analysis of the phytochemical composition of pomegranate fruit juices, peels and kernels: A comparative study on four cultivars grown in Southern Italy

The increasing popularity of pomegranate (Punica granatum L.), driven by the awareness of its nutraceutical properties and excellent environmental adaptability, is promoting a global expansion of its production area. This investigation reports the variability in the weight, moisture, pH, total soluble solids, carbohydrates, organic acids, phenolic compounds, fatty acids, antioxidant activities, and element composition of different fruit parts (juices, peels, and kernels) from four (Ako, Emek, Kamel, and Wonderful One) of the most widely cultivated Israeli pomegranate varieties in Salento (South Italy). To the best of our knowledge, this is the first systematic characterization of different fruit parts from pomegranate cultivars grown simultaneously in the same orchard and subjected to identical agronomic and environmental conditions. Significant genotype-dependent variability was observed for many of the investigated parameters, though without any correlation among fruit parts. The levels of phenols, flavonoids, anthocyanins, and ascorbic and dehydroascorbic acids of all samples were higher than the literature-reported data, as was the antioxidant activity. This is likely due to positive interactions among genotypes, the environment, and good agricultural practices. This study also confirms that pomegranate kernels and peels are, respectively, rich sources of punicic acid and phenols together, with several other bioactive molecules. However, the variability in their levels emphasizes the need for further research to better exploit their agro-industrial potential and thereby increase juice-production chain sustainability. This study will help to assist breeders and growers to respond to consumer and industrial preferences and encourage the development of biorefinery strategies for the utilization of pomegranate by-products as nutraceuticals or value-added ingredients for custom-tailored supplemented foods

Bortezomib Plus Dexamethasone Followed by Escalating Donor Lymphocyte Infusions for Patients with Multiple Myeloma Relapsing or Progressing after Allogeneic Stem Cell Transplantation

Abstract Multiple myeloma relapsing after allogeneic stem cell transplantation (alloSCT) has a poor outcome. To assess the safety and efficacy of bortezomib and dexamethasone (VD) combination followed by donor lymphocyte infusions (DLIs) in myeloma patients relapsing or progressing after alloSCT, a prospective phase II study was designed. The treatment plan consisted of three VD courses followed by escalated doses of DLIs in case of response or at least stable disease. Nineteen patients were enrolled with a median age of 57 years (range, 33 to 67); 14 patients were allografted from human leukocyte antigen–identical siblings and 5 from alternative donors. Sixteen of 19 patients received the planned treatment, but 3 patients did not: 2 patients because of disease progression and 1 refused. After the VD phase the response rate was 62%, with 1 complete remission, 6 very good partial remissions, 5 partial remissions, 2 patients with stable disease, and 5 with progressive disease. After the DLI phase, the response rate was 68%, but a significant upgrade of response was observed: 3 stringent complete remissions, 2 complete remissions, 5 very good partial remissions, 1 partial remission, 4 with stable disease, and 1 with progressive disease. With a median follow-up of 40 months (range, 29 to 68), the 3-year progression-free survival and overall survival rates were 31% and 73%, respectively. Neither unexpected organ toxicities, in particular severe neuropathy, nor severe acute graft-versus-host disease flares were observed. VD-DLIs is a safe treatment for multiple myeloma patients relapsing or progressing after alloSCT and may be effective

Exogenous Liposomal ceramide-c6 ammeliorates lipidomic profile, energy homeostasis and anti-oxidant systems in NASH

In non-alcoholic steatohepatitis (NASH), many lines of investigation have reported a dysregulation in lipid homeostasis, leading to intrahepatic lipid accumulation. Recently, the role of dysfunctional sphingolipid metabolism has also been proposed. Human and animal models of NASH have been associated with elevated levels of long chain ceramides and pro-apoptotic sphingolipid metabolites, implicated in regulating fatty acid oxidation and inflammation. Importantly, inhibition of de novo ceramide biosynthesis or knock-down of ceramide synthases reverse some of the pathology of NASH. In contrast, cell permeable, short chain ceramides have shown anti-inflammatory actions in multiple models of inflammatory disease. Here, we investigated non-apoptotic doses of a liposome containing short chain C6-Ceramide (Lip-C6) administered to human hepatic stellate cells (hHSC), a key effector of hepatic fibrogenesis, and an animal model characterized by inflammation and elevated liver fat content. On the basis of the results from unbiased liver transcriptomic studies from non-alcoholic fatty liver disease patients, we chose to focus on adenosine monophosphate activated kinase (AMPK) and nuclear factor-erythroid 2-related factor (Nrf2) signaling pathways, which showed an abnormal profile. Lip-C6 administration inhibited hHSC proliferation while improving anti-oxidant protection and energy homeostasis, as indicated by upregulation of Nrf2, activation of AMPK and an increase in ATP. To confirm these in vitro data, we investigated the effect of a single tail-vein injection of Lip-C6 in the methionine-choline deficient (MCD) diet mouse model. Lip-C6, but not control liposomes, upregulated phospho-AMPK, without inducing liver toxicity, apoptosis, or exacerbating inflammatory signaling pathways. Alluding to mechanism, mass spectrometry lipidomics showed that Lip-C6-treatment reversed the imbalance in hepatic phosphatidylcholines and diacylglycerides species induced by the MCD-fed diet. These results reveal that short-term Lip-C6 administration reverses energy/metabolic depletion and increases protective anti-oxidant signaling pathways, possibly by restoring homeostatic lipid function in a model of liver inflammation with fat accumulation