Relevance of electron spin dissipative processes to dynamic nuclear polarization via thermal mixing

The available theoretical approaches aiming at describing Dynamic Nuclear spin Polarization (DNP) in solutions containing molecules of biomedical interest and paramagnetic centers are not able to model the behaviour observed upon varying the concentration of trityl radicals or the polarization enhancement caused by moderate addition of gadolinium complexes. In this manuscript, we first show experimentally that the nuclear steady state polarization reached in solutions of pyruvic acid with 15 mM trityl radicals is substantially independent from the average internuclear distance. This evidences a leading role of electron (over nuclear) spin relaxation processes in determining the ultimate performances of DNP. Accordingly, we have devised a variant of the Thermal Mixing model for inhomogenously broadened electron resonance lines which includes a relaxation term describing the exchange of magnetic anisotropy energy of the electron spin system with the lattice. Thanks to this additional term, the dependence of the nuclear polarization on the electron concentration can be properly accounted for. Moreover, the model predicts a strong increase of the final polarization on shortening the electron spin-lattice relaxation time, providing a possible explanation for the effect of gadolinium doping.Comment: 13 pages, 12 figure

Role of the glassy dynamics and thermal mixing in the dynamic nuclear polarization and relaxation mechanisms of pyruvic acid

The temperature dependence of $^1$H and $^{13}$C nuclear spin-lattice relaxation rate $1/T_1$ has been studied in the 1.6 K - 4.2 K temperature range in pure pyruvic acid and in pyruvic acid containing trityl radicals at a concentration of 15 mM. The temperature dependence of $1/T_1$ is found to follow a quadratic power law for both nuclei in the two samples. Remarkably the same temperature dependence is displayed also by the electron spin-lattice relaxation rate $1/T_{1e}$ in the sample containing radicals. These results are explained by considering the effect of the structural dynamics on the relaxation rates in pyruvic acid. Dynamic nuclear polarization experiments show that below 4 K the $^{13}$C build up rate scales with $1/T_{\text{1e}}$, in analogy to $^{13}$C $1/T_1$ and consistently with a thermal mixing scenario where all the electrons are collectively involved in the dynamic nuclear polarization process and the nuclear spin reservoir is in good thermal contact with the electron spin system.Comment: 14 pages, 13 figure

Antagonism between salicylate and the cAMP signal controls yeast cell survival and growth recovery from quiescence

Aspirin and its main metabolite salicylate are promising molecules in preventing cancer and metabolic diseases. S. cerevisiae cells have been used to study some of their effects: (i) salicylate induces the reversible inhibition of both glucose transport and the biosyntheses of glucose-derived sugar phosphates, (ii) Aspirin/salicylate causes apoptosis associated with superoxide radical accumulation or early cell necrosis in MnSOD-deficient cells growing in ethanol or in glucose, respectively. So, treatment with (acetyl)-salicylic acid can alter the yeast metabolism and is associated with cell death. We describe here the dramatic effects of salicylate on cellular control of the exit from a quiescence state. The growth recovery of long-term stationary phase cells was strongly inhibited in the presence of salicylate, to a degree proportional to the drug concentration. At high salicylate concentration, growth reactivation was completely repressed and associated with a dramatic loss of cell viability. Strikingly, both of these phenotypes were fully suppressed by increasing the cAMP signal without any variation of the exponential growth rate. Upon nutrient exhaustion, salicylate induced a premature lethal cell cycle arrest in the budded-G2/M phase that cannot be suppressed by PKA activation. We discuss how the dramatic antagonism between cAMP and salicylate could be conserved and impinge common targets in yeast and humans. Targeting quiescence of cancer cells with stem-like properties and their growth recovery from dormancy are major challenges in cancer therapy. If mechanisms underlying cAMP-salicylate antagonism will be defined in our model, this might have significant therapeutic implications

Role of guanine nucleotides in the regulation of the Ras/cAMP pathway in Saccharomyces cerevisiae

AbstractThe CDC25 gene product is a guanine nucleotide exchange factor for Ras proteins in yeast. Recently it has been suggested that the intracellular levels of guanine nucleotides may influence the exchange reaction. To test this hypothesis we measured the levels of nucleotides in yeast cells under different growth conditions and the relative amount of Ras2-GTP. The intracellular GTP/GDP ratio was found to be very sensitive to growth conditions: the ratio is high, close to that of ATP/ADP during exponential growth, but it decreases rapidly before the beginning of stationary phase, and it drops further under starvation conditions. The addition of glucose to glucose-starved cells causes a fast increase of the GTP/GDP ratio. The relative amount of Ras2-GTP changes in a parallel way suggesting that there is a correlation with the cytosolic GTP/GDP ratio. In addition ‘in vitro’ mixed-nucleotide exchange experiments done on purified Ras2 protein demonstrated that the GTP and GDP concentrations influence the extent of Ras2-GTP loading giving further support to their possible regulatory role

Activation State of the Ras2 Protein and Glucose-induced Signaling in Saccharomyces cerevisiae

The activity of adenylate cyclase in the yeast Saccharomyces cerevisiae is controlled by two G-protein systems, the Ras proteins and the Gα protein Gpa2. Glucose activation of cAMP synthesis is thought to be mediated by Gpa2 and its G-protein-coupled receptor Gpr1. Using a sensitive GTP-loading assay for Ras2 we demonstrate that glucose addition also triggers a fast increase in the GTP loading state of Ras2 concomitant with the glucose-induced increase in cAMP. This increase is severely delayed in a strain lacking Cdc25, the guanine nucleotide exchange factor for Ras proteins. Deletion of the Ras-GAPs IRA2 (alone or with IRA1) or the presence of RAS2Val19 allele causes constitutively high Ras GTP loading that no longer increases upon glucose addition. The glucose-induced increase in Ras2 GTP-loading is not dependent on Gpr1 or Gpa2. Deletion of these proteins causes higher GTP loading indicating that the two G-protein systems might directly or indirectly interact. Because deletion of GPR1 or GPA2 reduces the glucose-induced cAMP increase the observed enhancement of Ras2 GTP loading is not sufficient for full stimulation of cAMP synthesis. Glucose phosphorylation by glucokinase or the hexokinases is required for glucose-induced Ras2 GTP loading. These results indicate that glucose phosphorylation might sustain activation of cAWDP synthesis by enhancing Ras2 GTP loading likely through inhibition of the Ira proteins. Strains with reduced feedback inhibition on cAMP synthesis also display elevated basal and induced Ras2 GTP loading consistent with the Ras2 protein acting as a target of the feedback-inhibition mechanism

Electron and nuclear spin dynamics in the thermal mixing model of dynamic nuclear polarization

A novel mathematical treatment is proposed for computing the time evolution of dynamic nuclear polarization processes in the low temperature thermal mixing regime. Without assuming any a priori analytical form for the electron polarization, our approach provides a quantitative picture of the steady state that recovers the well known Borghini prediction based on thermodynamics arguments, as long as the electrons-nuclei transition rates are fast compared to the other relevant time scales. Substantially different final polarization levels are achieved instead when the latter assumption is relaxed in the presence of a nuclear leakage term, even though very weak, suggesting a possible explanation for the deviation between the measured steady state polarizations and the Borghini prediction. The proposed methodology also allows to calculate nuclear polarization and relaxation times, once specified the electrons/nuclei concentration ratio and the typical rates of the microscopic processes involving the two spin species. Numerical results are shown to account for the manifold dynamical behaviours of typical DNP samples.Comment: 11 pages, 11 figure

Amplifying the Effects of Contrast Agents on Magnetic Resonance Images Using a Deep Learning Method Trained on Synthetic Data

OBJECTIVES: Artificial intelligence (AI) methods can be applied to enhance contrast in diagnostic images beyond that attainable with the standard doses of contrast agents (CAs) normally used in the clinic, thus potentially increasing diagnostic power and sensitivity. Deep learning-based AI relies on training data sets, which should be sufficiently large and diverse to effectively adjust network parameters, avoid biases, and enable generalization of the outcome. However, large sets of diagnostic images acquired at doses of CA outside the standard-of-care are not commonly available. Here, we propose a method to generate synthetic data sets to train an "AI agent" designed to amplify the effects of CAs in magnetic resonance (MR) images. The method was fine-tuned and validated in a preclinical study in a murine model of brain glioma, and extended to a large, retrospective clinical human data set. MATERIALS AND METHODS: A physical model was applied to simulate different levels of MR contrast from a gadolinium-based CA. The simulated data were used to train a neural network that predicts image contrast at higher doses. A preclinical MR study at multiple CA doses in a rat model of glioma was performed to tune model parameters and to assess fidelity of the virtual contrast images against ground-truth MR and histological data. Two different scanners (3 T and 7 T, respectively) were used to assess the effects of field strength. The approach was then applied to a retrospective clinical study comprising 1990 examinations in patients affected by a variety of brain diseases, including glioma, multiple sclerosis, and metastatic cancer. Images were evaluated in terms of contrast-to-noise ratio and lesion-to-brain ratio, and qualitative scores. RESULTS: In the preclinical study, virtual double-dose images showed high degrees of similarity to experimental double-dose images for both peak signal-to-noise ratio and structural similarity index (29.49 dB and 0.914 dB at 7 T, respectively, and 31.32 dB and 0.942 dB at 3 T) and significant improvement over standard contrast dose (ie, 0.1 mmol Gd/kg) images at both field strengths. In the clinical study, contrast-to-noise ratio and lesion-to-brain ratio increased by an average 155% and 34% in virtual contrast images compared with standard-dose images. Blind scoring of AI-enhanced images by 2 neuroradiologists showed significantly better sensitivity to small brain lesions compared with standard-dose images (4.46/5 vs 3.51/5). CONCLUSIONS: Synthetic data generated by a physical model of contrast enhancement provided effective training for a deep learning model for contrast amplification. Contrast above that attainable at standard doses of gadolinium-based CA can be generated through this approach, with significant advantages in the detection of small low-enhancing brain lesions.</p

The interaction between the measles virus nucleoprotein and the Interferon Regulator Factor 3 relies on a specific cellular environment

<p>Abstract</p> <p>Background</p> <p>The genome of measles virus consists of a non-segmented single-stranded RNA molecule of negative polarity, which is encapsidated by the viral nucleoprotein (N) within a helical nucleocapsid. The N protein possesses an intrinsically disordered C-terminal domain (aa 401–525, N_TAIL) that is exposed at the surface of the viral nucleopcapsid. Thanks to its flexible nature, N_TAILinteracts with several viral and cellular partners. Among these latter, the Interferon Regulator Factor 3 (IRF-3) has been reported to interact with N, with the interaction having been mapped to the regulatory domain of IRF-3 and to N_TAIL. This interaction was described to lead to the phosphorylation-dependent activation of IRF-3, and to the ensuing activation of the pro-immune cytokine RANTES gene.</p> <p>Results</p> <p>After confirming the reciprocal ability of IRF-3 and N to be co-immunoprecipitated in 293T cells, we thoroughly investigated the N_TAIL-IRF-3 interaction using a recombinant, monomeric form of the regulatory domain of IRF-3. Using a large panel of spectroscopic approaches, including circular dichroism, fluorescence spectroscopy, nuclear magnetic resonance and electron paramagnetic resonance spectroscopy, we failed to detect any direct interaction between IRF-3 and either full-length N or N_TAILunder conditions where these latter interact with the C-terminal X domain of the viral phosphoprotein. Furthermore, such interaction was neither detected in <it>E. coli </it>nor in a yeast two hybrid assay.</p> <p>Conclusion</p> <p>Altogether, these data support the requirement for a specific cellular environment, such as that provided by 293T human cells, for the N_TAIL-IRF-3 interaction to occur. This dependence from a specific cellular context likely reflects the requirement for a human or mammalian cellular co-factor.</p