Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme.

Massively parallel, quantitative measurements of biomolecular activity across sequence space can greatly expand our understanding of RNA sequence-function relationships. We report the development of an RNA-array assay to perform such measurements and its application to a model RNA: the core glmS ribozyme riboswitch, which performs a ligand-dependent self-cleavage reaction. We measure the cleavage rates for all possible single and double mutants of this ribozyme across a series of ligand concentrations, determining kcat and KM values for active variants. These systematic measurements suggest that evolutionary conservation in the consensus sequence is driven by maintenance of the cleavage rate. Analysis of double-mutant rates and associated mutational interactions produces a structural and functional mapping of the ribozyme sequence, revealing the catalytic consequences of specific tertiary interactions, and allowing us to infer structural rearrangements that permit certain sequence variants to maintain activity

Spectral densities for hot QCD plasmas in a leading log approximation

We compute the spectral densities of $T^{\mu\nu}$ and $J^{\mu}$ in high temperature QCD plasmas at small frequency and momentum,\, $\omega,k \sim g^4 T$. The leading log Boltzmann equation is reformulated as a Fokker Planck equation with non-trivial boundary conditions, and the resulting partial differential equation is solved numerically in momentum space. The spectral densities of the current, shear, sound, and bulk channels exhibit a smooth transition from free streaming quasi-particles to ideal hydrodynamics. This transition is analyzed with conformal and non-conformal second order hydrodynamics, and a second order diffusion equation. We determine all of the second order transport coefficients which characterize the linear response in the hydrodynamic regime.Comment: 39 pages, 6 figures. v3 contains an analysis of the bulk channel with non-conformal hydrodynamics. Otherwise no significant change

Static cylindrically symmetric spacetimes

We prove existence of static solutions to the cylindrically symmetric Einstein-Vlasov system, and we show that the matter cylinder has finite extension. The same results are also proved for a quite general class of equations of state for perfect fluids coupled to the Einstein equations, extending the class of equations of state considered in \cite{BL}. We also obtain this result for the Vlasov-Poisson system.Comment: Added acknowledgemen

Ohm's Law in the Fast Lane: General Relativistic Charge Dynamics

Fully relativistic and causal equations for the flow of charge in curved spacetime are derived. It is believed that this is the first set of equations to be published that correctly describes the flow of charge, and evolution of the electromagnetic field, in highly dynamical relativistic environments on time scales much shorter than the collapse time ($GM/c^3$). The equations will be important for correctly investigating problems such as the dynamical collapse of magnetized stellar cores to black holes and the production of jets and gravitational waves. This system of equations, given the name of `charge dynamics', is analogous to those of hydrodynamics (which describe the flow of {\em mass} in spacetime rather than the flow of charge). The most important one in the system is the relativistic generalized Ohm's law, which is used to compute time-dependent four-current. Unlike previous equations for the current, this one ensures that charge drift velocities remain less than the speed of light, takes into account the finite current rise time, is expressed in a covariant form, and is suitable for general relativistic computations in an arbitrary metric. It includes the standard known effects (Lorentz force, Hall effect, pressure effect, and resistivity) and reduces to known forms of Ohm's law in the appropriate limits. In addition, the plasma particles are allowed to have highly relativistic drift velocities, resulting in an implicit equation for the `current beaming factor' $\gamma_q$.Comment: 23 pages, 0 figures; accepted for publication in the Astrophysical Journa

Design and development of photoswitchable DFG-Out RET kinase inhibitors

REarranged during Transfection (RET) is a transmembrane receptor tyrosine kinase that is required for development of multiple human tissues, but which is also an important contributor to human cancers. RET activation through rearrangement or point mutations occurs in thyroid and lung cancers. Furthermore, activation of wild type RET is an increasingly recognized mechanism promoting tumor growth and dissemination of a much broader group of cancers. RET is therefore an attractive therapeutic target for small-molecule kinase inhibitors. Non-invasive control of RET signaling with light offers the promise of unveiling its complex spatiotemporal dynamics in vivo. In this work, photoswitchable DFG-out RET kinase inhibitors based on heterocycle-derived azobenzenes were developed, enabling photonic control of RET activity. Based on the binding mode of DFG-out kinase inhibitors and using RET kinase as the test model, we developed a photoswitchable inhibitor with a quinoline “head” constituting the azoheteroarene. This azo compound was further modified by three different strategies to increase the difference in biological activity between the E-isomer and the light enriched Z-isomer. Stilbene-based derivatives were used as model compounds to guide in the selection of substituents that could eventually be introduced to the corresponding azo compounds. The most promising quinoline-based compound showed more than a 15-fold difference in bioactivity between the two isomers in a biochemical assay. However, the same compound showed a decreased Z/E (IC50) ratio in the cellular assay, tentatively assigned to stability issues. The corresponding stilbene compound gave a Z/E (IC50) ratio well above 100, consistent with that measured in the biochemical assay. Ultimately, a 7-azaindole based photoswitchable DFG-out kinase inhibitor was shown to display more than a 10-fold difference in bioactivity between the two isomers, in both a biochemical and a cell-based assay, as well as excellent stability even under reducing conditions

Compact medical fluorosensor for minimally invasive tissue characterization

A compact fiber-optic point-measuring fluorosensor fully adapted to clinical studies is described. The system can use two excitation wavelengths, 337 and 405 nm, obtained from a nitrogen laser directly, or after dye laser conversion, respectively. The image intensifier used in the spectrometer can be gated with a variable time delay, allowing also time-resolved spectra to be extracted, with a time resolution of about 4 ns. Moreover, diffusely scattered white light can be spectrally recorded. The system is fully computer controlled enabling short recording times in clinical application, which are illustrated

Lumbar and ventricular CSF concentrations of extracellular matrix proteins before and after shunt surgery in idiopathic normal pressure hydrocephalus

Background: Idiopathic normal pressure hydrocephalus (iNPH) is a reversible CNS disease characterized by disturbed cerebrospinal fluid (CSF) dynamics. Changes in the extracellular matrix (ECM) composition might be involved in the pathophysiology of iNPH. The aim of this study was to explore possible differences between lumbar and ventricular CSF concentrations of the ECM markers brevican and neurocan, matrix metalloproteinases (MMPs) and tissue inhibitor of metalloproteinase-1 (TIMP-1) and their relation to clinical symptoms in iNPH patients before and after shunt surgery. Methods: Paired lumbar and ventricular CSF was collected from 31 iNPH patients, before and four months after shunt surgery. CSF was analysed for concentrations of tryptic peptides originating from brevican and neurocan using a mass spectrometry-based panel, and for MMP-1, -2, -9, -10 and TIMP-1 using fluorescent or electrochemiluminescent immunoassays. Results: Brevican and neurocan peptide levels were not influenced by CSF origin, but MMP-1, -2, -10 and TIMP-1 were increased (p ≤ 0.0005), and MMP-9 decreased (p ≤ 0.0003) in lumbar CSF compared with ventricular CSF. There was a general trend of ECM proteins to increase following shunt surgery. Ventricular TIMP-1 was inversely correlated with overall symptoms (rho = − 0.62, p < 0.0001). CSF concentrations of the majority of brevican and neurocan peptides were increased in iNPH patients with a history of cardiovascular disease (p ≤ 0.001, AUC = 0.84–0.94) compared with those without. Conclusion: Levels of the CNS-specific proteins brevican and neurocan did not differ between the lumbar and ventricular CSF, whereas the increase of several CNS-unspecific MMPs and TIMP-1 in lumbar CSF suggests contribution from peripheral tissues. The increase of ECM proteins in CSF following shunt surgery could indicate disturbed ECM dynamics in iNPH that are restored by restitution of CSF dynamics

Gravastar energy conditions revisited

We consider the gravastar model where the vacuum phase transition between the de Sitter interior and the Schwarzschild or Schwarzschild-de Sitter exterior geometries takes place at a single spherical delta-shell. We derive sharp analytic bounds on the surface compactness (2m/r) that follow from the requirement that the dominant energy condition (DEC) holds at the shell. In the case of Schwarzschild exterior, the highest surface compactness is achieved with the stiff shell in the limit of vanishing (dark) energy density in the interior. In the case of Schwarzschild-de Sitter exterior, in addition to the gravastar configurations with the shell under surface pressure, gravastar configurations with vanishing shell pressure (dust shells), as well as configurations with the shell under surface tension, are allowed by the DEC. Respective bounds on the surface compactness are derived for all cases. We also consider the speed of sound on the shell as derived from the requirement that the shell is stable against the radial perturbations. The causality requirement (sound speed not exceeding that of light) further restricts the space of allowed gravastar configurations.Comment: LaTeX/IOP-style, 16 pages, 2 figures, changes wrt v1: motivation for eq. (6) clarified, several referecnes added (to appear in Class. Quantum Grav.