Functional studies of the ‘GAFTGA’ motif of Escherichia coli Phage Shock Protein F

In the archetypal bacterial transcription, the multi-subunit core RNA polymerase (RNAP) is specifically bound to the promoter through the sigma factor (σ), forming a closed complex where DNA remains double-stranded. The promoter DNA is initially spontaneously melted by the σ factor within the core enzyme and subsequently loaded into the active channel of the holoenzyme. However, a major alternative transcription paradigm that depends on the sigma factor σ54 also exists in bacteria and controls pathogenicity, biofilm formation, bioluminescence, nitrogen fixation and stress responses. σ54 forms inhibitory interactions with DNA in the closed complex, which can only be alleviated by ATP hydrolysis-driven remodelling catalysed by bacterial enhancer binding proteins (bEBPs). In this regard, σ54- dependent transcription can be viewed analogous to the eukaryotic RNA Pol II system. This study was initiated to advance the understanding of: (i) how the ATP hydrolysis energy is relayed from the ATPase catalytic site to the closed complex for remodelling, (ii) the hexameric interface organisation of bEBPs for ATP hydrolysis, and (iii) the role of core RNAP in σ54-dependent transcription. A newly devised cross-linking technique combined with the DNA footprinting methods provided new insights of the organisation of each transcription component. The data gathered from this study updated the current working model for ATPdependent transcription. In addition, the cross-linking method proved to be an excellent tool to study protein-protein and nucleo-protein interactions

Reexamination of inflation in noncommutative space-time after Planck results

An inflationary model in the framework of noncommutative space-time may generate a nontrivial running of the scalar spectral index, but usually induces a large tensor-to-scalar ratio simultaneously. With the latest observational data from the Planck mission, we reexamine the inflationary scenarios in a noncommutative space-time. We find that either the running of the spectral index is tiny compared with the recent observational result, or the tensor-to-scalar ratio is too large to allow a sufficient number of $e$-folds. As examples, we show that the chaotic and power-law inflation models with the noncommutative effects are not favored by the current Planck data.Comment: 8 pages, 4 figures; version published in Physical Review

Cosmology-Independent Distance Moduli of 42 Gamma-Ray Bursts between Redshift of 1.44 and 6.60

This report is an update and extension of our paper accepted for publication in ApJ (arXiv:0802.4262). Since objects at the same redshift should have the same luminosity distance and the distance moduli of type Ia supernovae (SNe Ia) obtained directly from observations are completely cosmology independent, we obtain the distance modulus of a gamma-ray burst (GRB) at a given redshift by interpolating or iterating from the Hubble diagram of SNe Ia. Then we calibrate five GRB relations without assuming a particular cosmological model, from different regression methods, and construct the GRB Hubble diagram to constrain cosmological parameters. Based upon these relations we list the cosmology-independent distance moduli of 42 GRBs between redshift of 1.44 and 6.60, with the 1-$\sigma$ uncertainties of 1-3%.Comment: 6 pages, 2 figures, 3 tables. To appear in the proceedings of "2008 Nanjing GRB conference", Nanjing, 23-27 June 200

Rotational Behaviors and Magnetic Field Evolution of Radio Pulsars

The observed long-term spin-down evolution of isolated radio pulsars cannot be explained by the standard magnetic dipole radiation with a constant braking torque. However how and why the torque varies still remains controversial, which is an outstanding problem in our understanding of neutron stars. We have constructed a phenomenological model of the evolution of surface magnetic fields of pulsars, which contains a long-term decay modulated by short-term oscillations; a pulsar's spin is thus modified by its magnetic field evolution. The predictions of this model agree with the precisely measured spin evolutions of several individual pulsars; the derived parameters suggest that the Hall drift and Hall waves in the NS crusts are probably responsible for the long-term change and short-term quasi-periodical oscillations, respectively. Many statistical properties of the timing noise of pulsars can be well re-produced with this model, including correlations and the distributions of the observed braking indices of the pulsars, which span over a range of more than 100 millions. We have also presented a phenomenological model for the recovery processes of classical and slow glitches, which can successfully model the observed slow and classical glitch events without biases.Comment: 6 pages, 9 figures, submitted to conference proceedings of SMFNS2013 (Strong electromagnetic field and neutron stars 2013