Application of bifurcation theory and siRNA-based control signal to restore the proper response of cancer cells to DNA damage

AbstractMany diseases with a genetic background such as some types of cancer are caused by damage in the p53 signaling pathway. The damage changes the system dynamics providing cancer cells with resistance to therapy such as radiation therapy. The change can be observed as the difference in bifurcation diagrams and equilibria type and location between normal and damaged cells, and summarized as the changes of the mathematical model parameters and following changes of the eigenvalues of Jacobian matrix. Therefore a change in other model parameters, such as mRNA degradation rates, may restore the proper eigenvalues and by that proper system dynamics. From the biological point of view, the change of mRNA degradation rate can be achieved by application of the small interfering RNA (siRNA). Here, we propose a general mathematical framework based on the bifurcation theory and siRNA-based control signal in order to study how to restore the proper response of cells with damaged p53 signaling pathway to therapy by using ionizing radiation (IR) therapy as an example. We show the difference between the cells with normal p53 signaling pathway and cells with abnormalities in the negative (as observed in SJSA-1 cell line) or positive (as observed in MCF-7 or PNT1a cell lines) feedback loop. Then we show how the dynamics of these cells can be restored to normal cell dynamics by using selected siRNA

Cutaneous Burn Injury Modulates Urinary Antimicrobial Peptide Responses and the Urinary Microbiome

OBJECTIVES: Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to identify potential mechanisms leading to urinary tract infections and associated morbidities in burn patients. DESIGN: Retrospective cohort study using human urine from control and burn subjects. SETTING: University research laboratory. PATIENTS: Burn patients. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Urine samples from catheterized burn patients were collected hourly for up to 40 hours. Control urine was collected from "healthy" volunteers. The urinary bacterial microbiome and antimicrobial peptide levels and activity were compared with patient outcomes. We observed a significant increase in urinary microbial diversity in burn patients versus controls, which positively correlated with a larger percent burn and with the development of urinary tract infection and sepsis postadmission, regardless of age or gender. Urinary psoriasin and β-defensin antimicrobial peptide levels were significantly reduced in burn patients at 1 and 40 hours postadmission. We observed a shift in antimicrobial peptide hydrophobicity and activity between control and burn patients when urinary fractions were tested against Escherichia coli and Enterococcus faecalis urinary tract infection isolates. Furthermore, the antimicrobial peptide activity in burn patients was more effective against E. coli than E. faecalis. Urinary tract infection-positive burn patients with altered urinary antimicrobial peptide activity developed either an E. faecalis or Pseudomonas aeruginosa urinary tract infection, suggesting a role for urinary antimicrobial peptides in susceptibility to select uropathogens. CONCLUSIONS: Our data reveal potential links for urinary tract infection development and several morbidities in burn patients through alterations in the urinary microbiome and antimicrobial peptides. Overall, this study supports the concept that early assessment of urinary antimicrobial peptide responses and the bacterial microbiome may be used to predict susceptibility to urinary tract infections and sepsis in burn patients

Tuning the Reactivity of Nanoenergetic Gas Generators Based on Bismuth and Iodine oxidizers

There is a growing interest on novel energetic materials called Nanoenergetic Gas- Generators (NGGs) which are potential alternatives to traditional energetic materials including pyrotechnics, propellants, primers and solid rocket fuels. NGGs are formulations that utilize metal powders as a fuel and oxides or hydroxides as oxidizers that can rapidly release large amount of heat and gaseous products to generate shock waves. The heat and pressure discharge, impact sensitivity, long term stability and other critical properties depend on the particle size and shape, as well as assembling procedure and intermixing degree between the components. The extremely high energy density and the ability to tune the dynamic properties of the energetic system makes NGGs ideal candidates to dilute or replace traditional energetic materials for emerging applications. In terms of energy density, performance and controllability of dynamic properties, the energetic materials based on bismuth and iodine compounds are exceptional among the NGGs. The thermodynamic calculations and experimental study confirm that NGGs based on iodine and bismuth compounds mixed with aluminum nanoparticles are the most powerful formulations to date and can be used potentially in microthrusters technology with high thrust-to-weight ratio with controlled combustion and exhaust velocity for space applications. The resulting nano thermites generated significant value of pressure discharge up to 14.8 kPa m3/g. They can also be integrated with carbon nanotubes to form laminar composite yarns with high power actuation of up to 4700 W/kg, or be used in other emerging applications such as biocidal agents to effectively destroy harmful bacteria in seconds, with 22 mg/m2 minimal content over infected area

Interfacial Chemistry in Al/CuO Reactive Nanomaterial and Its Role in Exothermic Reaction.

Interface layers between reactive and energetic materials in nanolaminates or nanoenergetic materials are believed to play a crucial role in the properties of nanoenergetic systems. Typically, in the case of Metastable Interstitial Composite nanolaminates, the interface layer between the metal and oxide controls the onset reaction temperature, reaction kinetics, and stability at low temperature. So far, the formation of these interfacial layers is not well understood for lack of in situ characterization, leading to a poor control of important properties. We have combined in situ infrared spectroscopy and ex situ X-ray photoelectron spectroscopy, differential scanning calorimetry, and high resolution transmission electron microscopy, in conjunction with firstprinciples calculations to identify the stable configurations that can occur at the interface and determine the kinetic barriers for their formation. We find that (i) an interface layer formed during physical deposition of aluminum is composed of a mixture of Cu, O, and Al through Al penetration into CuO and constitutes a poor diffusion barrier (i.e., with spurious exothermic reactions at lower temperature), and in contrast, (ii) atomic layer deposition (ALD) of alumina layers using trimethylaluminum (TMA)produces a conformal coating that effectively prevents Al diffusion even for ultrathin layer thicknesses (∼0.5 nm), resulting in better stability at low temperature and reduced reactivity. Importantly, the initial reaction of TMA with CuO leads to the extraction of oxygen from CuO to form an amorphous interfacial layer that is an important component for superior protection properties of the interface and is responsible for the high system stability. Thus, while Al e-beam evaporation and ALD growth of an alumina layer on CuO both lead to CuO reduction, the mechanism for oxygen removal is different, directly affecting the resistance to Al diffusion. This work reveals that it is the nature of the monolayer interface between CuO and alumina/Al rather than the thickness of the alumina layer that controls the kinetics of Al diffusion, underscoring the importance of the chemical bonding at the interface in these energetic materials

Toxic Diatom Aldehydes Affect Defence Gene Networks in Sea Urchins.

Marine organisms possess a series of cellular strategies to counteract the negative effects of toxic compounds, including the massive reorganization of gene expression networks. Here we report the modulated dose-dependent response of activated genes by diatom polyunsaturated aldehydes (PUAs) in the sea urchin Paracentrotus lividus. PUAs are secondary metabolites deriving from the oxidation of fatty acids, inducing deleterious effects on the reproduction and development of planktonic and benthic organisms that feed on these unicellular algae and with anti-cancer activity. Our previous results showed that PUAs target several genes, implicated in different functional processes in this sea urchin. Using interactomic Ingenuity Pathway Analysis we now show that the genes targeted by PUAs are correlated with four HUB genes, NF-κB, p53, δ-2-catenin and HIF1A, which have not been previously reported for P. lividus. We propose a working model describing hypothetical pathways potentially involved in toxic aldehyde stress response in sea urchins. This represents the first report on gene networks affected by PUAs, opening new perspectives in understanding the cellular mechanisms underlying the response of benthic organisms to diatom exposure

Modeling the Basal Dynamics of P53 System

The tumor suppressor p53 has become one of most investigated genes. Once activated by stress, p53 leads to cellular responses such as cell cycle arrest and apoptosis.Most previous models have ignored the basal dynamics of p53 under nonstressed conditions. To explore the basal dynamics of p53, we constructed a stochastic delay model by incorporating two negative feedback loops. We found that protein distribution of p53 under nonstressed condition is highly skewed with a fraction of cells showing high p53 levels comparable to those observed under stressed conditions. Under nonstressed conditions, asynchronous and spontaneous p53 pulses are triggered by basal DNA double strand breaks produced during normal cell cycle progression. The first peaking times show a predominant G1 distribution while the second ones are more widely distributed. The spontaneous pulses are triggered by an excitable mechanism. Once initiated, the amplitude and duration of pulses remain unchanged. Furthermore, the spontaneous pulses are filtered by ataxia telangiectasia mutated protein mediated posttranslational modifications and do not result in substantial p21 transcription. If challenged by externally severe DNA damage, cells generate synchronous p53 pulses and induce significantly high levels of p21. The high expression of p21 can also be partially induced by lowering the deacetylation rate.Our results demonstrated that the dynamics of p53 under nonstressed conditions is initiated by an excitable mechanism and cells become fully responsive only when cells are confronted with severe damage. These findings advance our understanding of the mechanism of p53 pulses and unlock many opportunities to p53-based therapy

Analysis and verification of the HMGB1 signaling pathway

Background\ud Recent studies have found that overexpression of the High-mobility group box-1 (HMGB1) protein, in conjunction with its receptors for advanced glycation end products (RAGEs) and toll-like receptors (TLRs), is associated with proliferation of various cancer types, including that of the breast and pancreatic.\ud \ud Results\ud We have developed a rule-based model of crosstalk between the HMGB1 signaling pathway and other key cancer signaling pathways. The model has been simulated using both ordinary differential equations (ODEs) and discrete stochastic simulation. We have applied an automated verification technique, Statistical Model Checking, to validate interesting temporal properties of our model.\ud \ud Conclusions\ud Our simulations show that, if HMGB1 is overexpressed, then the oncoproteins CyclinD/E, which regulate cell proliferation, are overexpressed, while tumor suppressor proteins that regulate cell apoptosis (programmed cell death), such as p53, are repressed. Discrete, stochastic simulations show that p53 and MDM2 oscillations continue even after 10 hours, as observed by experiments. This property is not exhibited by the deterministic ODE simulation, for the chosen parameters. Moreover, the models also predict that mutations of RAS, ARF and P21 in the context of HMGB1 signaling can influence the cancer cell's fate - apoptosis or survival - through the crosstalk of different pathways

Noise Amplification in Human Tumor Suppression following Gamma Irradiation

The influence of noise on oscillatory motion is a subject of permanent interest, both for fundamental and practical reasons. Cells respond properly to external stimuli by using noisy systems. We have clarified the effect of intrinsic noise on the dynamics in the human cancer cells following gamma irradiation. It is shown that the large amplification and increasing mutual information with delay are due to coherence resonance. Furthermore, frequency domain analysis is used to study the mechanisms