E. coli tRNA Leucine Identity and Recognition Sets

E. coli contains five different tRNAs which recognize the six leucine codons. These tRNAs are all recognized by the single leucyl-tRNA synthetase (LeuRS). We have used in vitro and in vivo methods to determine the set of identity elements which distinguish the set of leucine tRNAs from all other tRNAs allowing the faithful translation of the leucine codons. An identity swap experiment has been used to determine which of the nucleotides conserved in all leucine tRNAs are identity elements. In this experiment the identity of an amber suppressor tRNASer was changed completely to leucine. This experiment was effective because the anticodons in tRNASer and tRNALeu are not recognized by their respective synthetases and consequently in both cases tRNAs containing the CUA anticodon required in amber suppressors are fully active. In its minimal form the Ser-Leu swap required six changes, five of which altered the tertiary structure of the tRNA: the G15-C48 tertiary "Levitt base-pair" in tRNASer was changed to Al5-U48 found in all leucine tRNAs; it was necessary to insert one nucleotide and to delete one nucleotide so as to position the conserved D-loop Gl8, Gl9 nucleotides as they are in all leucine tRNAs; a base was inserted at position 47n between the base-paired extra stem and the T-stem to achieve a configuration found in all leucine tRNAs; in addition it was necessary to change the G73 "discriminator" base in tRNASer to A73, found in all leucine tRNAs. This minimally altered tRNASer inserted exclusively leucine as an amber suppressor and it was an excellent in vitro substrate for LeuRS. Both tRNASer and tRNALeu are type II tRNAs containing large base-paired extra stem loops. In the case of tRNASer the extra stem loop is a crucial identity element but for tRNALeu earlier in vitro and in vivo experiments had indicated that it is not an identity element. To investigate the role of tRNA tertiary structure in leucine identity we carried out a parallel swap experiment in which the glutamine identity of the amber suppressor tRNASerΔ (in which the type II extra stem loop had been replaced by a consensus type I loop) was converted to leucine. This "type I" swap experiment was also successful both in vivo and in vitro. Interesting differences in the role of conserved leucine base-pairs in the acceptor stems of leucine tRNAs were observed in the two experiments. In the type II swap the conserved acceptor stem bases were not important. In the type I swap their absence had a large effect both in vivo and in vitro. This result indicates that the presence of the extra stem loop in leucine tRNAs has an effect on the tertiary structure of the tRNA. When this structure is altered conserved nucleotides, unimportant in its presence, take on an important role. Possible reasons for this effect are discussed.</p

Non-parametric reconstruction of the primordial power spectrum at horizon scales from WMAP data

We extend to large scales a method proposed in previous work that reconstructs non-parametrically the primordial power spectrum from cosmic microwave background data at high resolution. The improvement is necessary to account for the non-gaussianity of the Wilkinson Microwave Anisotropy Probe (WMAP) likelihood due primarily to cosmic variance. We assume the concordance LambdaCDM cosmology, utilise a smoothing prior and perform Monte Carlo simulations around an initial power spectrum that is scale-free and with spectral index n_s=0.97, very close to the concordance spectrum. The horizon scale for the model we are considering corresponds to the wavenumber k_h=4.52X10^{-4} Mpc^{-1}. We find some evidence for the presence of features and we quantify the probabilities of exceeding the observed deviations in WMAP data with respect to the fiducial models. We detect the following marginal departures from a scale-free (spectral index n_s=0.97) initial spectrum: a cut-off at 0.0001<k<0.001 Mpc^{-1} at 79.5% (92%), a dip at 0.001<k<0.003 Mpc^{-1} at 87.2% (98%) and a bump at 0.003<k<0.004 Mpc^{-1} at 90.3% (55.5%) confidence level. These frequentist confidence levels are calculated by integrating over the distribution of the Monte Carlo reconstructions built around the fiducial models. The frequentist analysis finds the low k cutoff of the estimated power spectrum to be about 2.5 sigma away from the n_s=0.97 model, while in the Bayesian analysis the model is about 1.5 sigma away from the estimated spectrum. (The sigma's are different for the two different methods.)Comment: 9 pages, 8 figures. Revised version accepted for publication in MNRA

The nature of dark energy

According to a variety of cosmological observations at small and large redshifts, the universe is composed by a large fraction of a weakly clustered component with negative pressure, called dark energy. The nature of the dark energy, i.e. its interaction and self-interaction properties, is still largely unknown. In this contribution we review the properties of dark energy as inferred from observations, with particular emphasis on the cosmic microwave background. We argue that the current dataset imposes strong constraints on the coupling of dark energy to dark matter, while it is still insufficient to constrain the equation of state or potential. Future data will dramatically improve the prospects

A new search for features in the primordial power spectrum

We develop a new approach toward a high resolution non-parametric reconstruction of the primordial power spectrum using WMAP cosmic microwave background temperature anisotropies that we confront with SDSS large-scale structure data in the range k~0.01-0.1 h/Mpc. We utilise the standard LambdaCDM cosmological model but we allow the baryon fraction to vary. In particular, for the concordance baryon fraction, we compare indications of a possible feature at k~0.05 h/Mpc in WMAP data with suggestions of similar features in large scale structure surveys.Comment: revised version, conclusions unchanged, 7 figures, accepted for publication in MNRA

Cosmology with massive neutrinos coupled to dark energy

Cosmological consequences of a coupling between massive neutrinos and dark energy are investigated. In such models, the neutrino mass is a function of a scalar field, which plays the role of dark energy. The evolution of the background and cosmological perturbations are discussed. We find that mass-varying neutrinos can leave a significant imprint on the anisotropies in the cosmic microwave background and even lead to a reduction of power on large angular scales

Dark Energy and Dark Matter

It is a puzzle why the densities of dark matter and dark energy are nearly equal today when they scale so differently during the expansion of the universe. This conundrum may be solved if there is a coupling between the two dark sectors. In this paper we assume that dark matter is made of cold relics with masses depending exponentially on the scalar field associated to dark energy. Since the dynamics of the system is dominated by an attractor solution, the dark matter particle mass is forced to change with time as to ensure that the ratio between the energy densities of dark matter and dark energy become a constant at late times and one readily realizes that the present-day dark matter abundance is not very sensitive to its value when dark matter particles decouple from the thermal bath. We show that the dependence of the present abundance of cold dark matter on the parameters of the model differs drastically from the familiar results where no connection between dark energy and dark matter is present. In particular, we analyze the case in which the cold dark matter particle is the lightest supersymmetric particle.Comment: 4 pages latex, 2 figure

Primordial Power Spectrum Reconstruction

In order to reconstruct the initial conditions of the universe it is important to devise a method that can efficiently constrain the shape of the power spectrum of primordial matter density fluctuations in a model-independent way from data. In an earlier paper we proposed a method based on the wavelet expansion of the primordial power spectrum. The advantage of this method is that the orthogonality and multiresolution properties of wavelet basis functions enable information regarding the shape of $P_{\rm in}(k)$ to be encoded in a small number of non-zero coefficients. Any deviation from scale-invariance can then be easily picked out. Here we apply this method to simulated data to demonstrate that it can accurately reconstruct an input $P_{\rm in}(k)$, and present a prescription for how this method should be used on future data.Comment: 4 pages, 2 figures. JCAP accepted versio

Mass-Varying Neutrinos from a Variable Cosmological Constant

We consider, in a completely model-independent way, the transfer of energy between the components of the dark energy sector consisting of the cosmological constant (CC) and that of relic neutrinos. We show that such a cosmological setup may promote neutrinos to mass-varying particles, thus resembling a recently proposed scenario of Fardon, Nelson, and Weiner (FNW), but now without introducing any acceleronlike scalar fields. Although a formal similarity of the FNW scenario with the variable CC one can be easily established, one nevertheless finds different laws for neutrino mass variation in each scenario. We show that as long as the neutrino number density dilutes canonically, only a very slow variation of the neutrino mass is possible. For neutrino masses to vary significantly (as in the FNW scenario), a considerable deviation from the canonical dilution of the neutrino number density is also needed. We note that the present `coincidence' between the dark energy density and the neutrino energy density can be obtained in our scenario even for static neutrino masses.Comment: 8 pages, minor corrections, two references added, to apear in JCA

Le Chatelier-Braun principle in cosmological physics

Assuming that dark energy may be treated as a fluid with a well defined temperature, close to equilibrium, we argue that if nowadays there is a transfer of energy between dark energy and dark matter, it must be such that the latter gains energy from the former and not the other way around.Comment: 6 pages, revtex file, no figures; version accepted for publication in General Relativity and Gravitatio