15N NMR study of a mixture of uniformly labeled tRNAs

15N NMR spectra were taken of 15N-enriched tRNA extracted from bakers yeast; ammonium sulfate was used as a nitrogen source. The increase in the degree of denaturation of tRNA, which occurs with increase in temperature from 30 degrees C to 70 degrees C, resulted in no large changes in 15N chemical shifts at acidic and neutral pH but quite pronounced changes in proton-15N nuclear Overhauser effects

Phase separation of binary fluids with dynamic temperature

Phase separation of binary fluids quenched by contact with cold external walls is considered. Navier-Stokes, convection-diffusion, and energy equations are solved by lattice Boltzmann method coupled with finite-difference schemes. At high viscosity, different morphologies are observed by varying the thermal diffusivity. In the range of thermal diffusivities with domains growing parallel to the walls, temperature and phase separation fronts propagate towards the inner of the system with power-law behavior. At low viscosity hydrodynamics favors rounded shapes, and complex patterns with different lengthscales appear. Off-symmetrical systems behave similarly but with more ordered configurations.Comment: Accepted for publication in Phys. Rev. E, 11 figures, best quality figures available on reques

Cavitation inception of a van der Waals fluid at a sack-wall obstacle

Cavitation in a liquid moving past a constraint is numerically investigated by means of a free-energy lattice Boltzmann simulation based on the van der Waals equation of state. The fluid is streamed past an obstacle and, depending on the pressure drop between inlet and outlet, vapor formation underneath the corner of the sack-wall is observed. The circumstances of cavitation formation are investigated and it is found that the local bulk pressure and mean stress are insufficient to explain the phenomenon. Results obtained in this study strongly suggest that the viscous stress, interfacial contributions to the local pressure, and the Laplace pressure are relevant to the opening of a vapor cavity. This can be described by a generalization of Joseph's criterion that includes these contributions. A macroscopic investigation measuring mass flow rate behavior and discharge coefficient was also performed. As theoretically predicted, mass flow rate increases linearly with the square root of the pressure drop. However, when cavitation occurs, the mass flow growth rate is reduced and eventually it collapses into a choked flow state. In the cavitating regime, as theoretically predicted and experimentally verified, the discharge coefficient grows with the Nurick cavitation number

Monte Carlo study of the phase transition in the Critical behavior of the Ising model with shear

The critical behavior of the Ising model with non-conserved dynamics and an external shear profile is analyzed by studying its dynamical evolution in the short time regime. Starting from high temperature disordered configurations (FDC), the critical temperature $T_c$ is determined when the order parameter, defined as the absolute value of the transversal spin profile, exhibits a power-law behavior with an exponent that is a combination of some of the critical exponents of the transition. For each value of the shear field magnitude, labeled as $\dot{\gamma}$, $T_c$ has been estimated and two stages have been found: 1) a growing stage at low values of $\dot{\gamma}$, where $T_c\sim\dot{\gamma}^\psi$ and $\psi=0.52(3)$; 2) a saturation regime at large $\dot{\gamma}$. The same values of $T_c(\dot{\gamma})$ were found studying the dynamical evolution from the ground state configuration (GSC) with all spins pointing in the same direction. By combining the exponents of the corresponding power laws obtained from each initial configuration the set of critical exponents was calculated. These values, at large external field magnitude, define a new critical behavior different from that of the Ising model and of other driven lattice gases.Comment: 25 page

Response of Autonomic Nervous System to Body Positions: Fourier and Wavelet Analysis

Two mathematical methods, the Fourier and wavelet transforms, were used to study the short term cardiovascular control system. Time series, picked from electrocardiogram and arterial blood pressure lasting 6 minutes, were analyzed in supine position (SUP), during the first (HD1), and the second parts (HD2) of $90^{\circ}$ head down tilt and during recovery (REC). The wavelet transform was performed using the Haar function of period $T=2^j$ ($$,2,$...$,6) to obtain wavelet coefficients. Power spectra components were analyzed within three bands, VLF (0.003-0.04), LF (0.04-0.15) and HF (0.15-0.4) with the frequency unit cycle/interval. Wavelet transform demonstrated a higher discrimination among all analyzed periods than the Fourier transform. For the Fourier analysis, the LF of R-R intervals and VLF of systolic blood pressure show more evident difference for different body positions. For the wavelet analysis, the systolic blood pressures show much more evident difference than the R-R intervals. This study suggests a difference in the response of the vessels and the heart to different body positions. The partial dissociation between VLF and LF results is a physiologically relevant finding of this work.Comment: RevTex,8 figure

Folding transitions of the triangular lattice with defects

A recently introduced model describing the folding of the triangular lattice is generalized allowing for defects in the lattice and written as an Ising model with nearest-neighbor and plaquette interactions on the honeycomb lattice. Its phase diagram is determined in the hexagon approximation of the cluster variation method and the crossover from the pure Ising to the pure folding model is investigated, obtaining a quite rich structure with several multicritical points. Our results are in very good agreement with the available exact ones and extend a previous transfer matrix study.Comment: 16 pages, latex, 5 postscript figure

Ire1 alpha/xbp1 axis sustains primary effusion lymphoma cell survival by promoting cytokine release and stat3 activation

Primary Effusion Lymphoma (PEL) is a highly aggressive B cell lymphoma associated with Kaposi’s Sarcoma-associated Herpesvirus (KSHV). It is characterized by a high level of basal Endoplasmic Reticulum (ER) stress, Unfolded Protein Response (UPR) activation and constitutive phosphorylation of oncogenic pathways such as the Signal Transducer and activator of Transcription (STAT3). In this study, we found that the inositol requiring kinase (IRE) 1alpha/X-box binding protein (XBP1) axis of UPR plays a key role in the survival of PEL cells, while double stranded RNA-activated protein kinase-like ER kinase (PERK) and activating transcription factor (ATF) 6 slightly influence it, in correlation with the capacity of the IRE1alpha/XBP1 axis to induce the release of interleukin (IL)-6, IL-10 and Vascular-Endothelial Growth Factor (VEGF). Moreover, we found that IRE1alpha/XBP1 inhibition reduced STAT3 Tyr705 phosphorylation and induced a pro-survival autophagy in PEL cells. In conclusion, this study suggests that targeting the IRE1alpha/XBP1 axis represents a promising strategy against PEL cells and that the cytotoxic effect of this treatment may be potentiated by autophagy inhibition

Viral Infection and Autophagy Dysregulation. The Case of HHV-6, EBV and KSHV

Human Herpes Virus-6 (HHV-6), Epstein-Barr Virus (EBV) and Kaposi Sarcoma Herpes Virus (KSHV) are viruses that share with other member of the Herpesvirus family the capacity to interfere with the autophagic process. In this paper, mainly based on the findings of our laboratory, we describe how, through different mechanisms, these viruses converge in reducing autophagy to impair DC immune function and how, by infecting and dysregulating autophagy in different cell types, they promote the pathologies associated with their infection, from the neurodegenerative diseases such Alzheimer's disease to cancer

Concomitant Inhibition of IRE1α/XBP1 Axis of UPR and PARP. A Promising Therapeutic Approach against c-Myc and Gammaherpesvirus-Driven B-Cell Lymphomas

It is emerging that targeting the adaptive functions of Unfolded Protein Response (UPR) may represent a promising anti-cancer therapeutic approach. This is particularly relevant for B-cell lymphomas, characterized by a high level of constitutive stress due to high c-Myc expression. In this study, we found that IRE1α/XBP1 axis inhibition exerted a stronger cytotoxic effect compared to the inhibition of the other two UPR sensors, namely PERK and ATF6, in Burkitt lymphoma (BL) cells, in correlation with c-Myc downregulation. Interestingly, such an effect was more evident in Epstein-Barr virus (EBV)-negative BL cells or those cells expressing type I latency compared to type III latency BL cells. The other interesting finding of this study was that the inhibition of IRE1α/XBP1 downregulated BRCA-1 and RAD51 and potentiated the cytotoxicity of PARP inhibitor AZD2661 against BL cells and also against Primary Effusion Lymphoma (PEL), another aggressive B-cell lymphoma driven by c-Myc and associated with gammaherpesvirus infection. These results suggest that combining the inhibition of UPR sensors, particularly IRE1α/XBP1 axis, and molecules involved in DDR, such as PARP, could offer a new therapeutic opportunity for treating aggressive B-cell lymphomas such as BL and PEL