A screen for hoxb1-regulated genes identifies ppp1r14al as a regulator of the rhombomere 4 Fgf-signaling center

AbstractSegmentation of the vertebrate hindbrain into multiple rhombomeres is essential for proper formation of the cerebellum, cranial nerves and cranial neural crest. Paralog group 1 (PG1) hox genes are expressed early in the caudal hindbrain and are required for rhombomere formation. Accordingly, loss of PG1 hox function disrupts development of caudal rhombomeres in model organisms and causes brainstem defects, associated with cognitive impairment, in humans. In spite of this important role for PG1 hox genes, transcriptional targets of PG1 proteins are not well characterized. Here we use ectopic expression together with embryonic dissection to identify novel targets of the zebrafish PG1 gene hoxb1b. Of 100 genes up-regulated by hoxb1b, 54 were examined and 25 were found to represent novel hoxb1b regulated hindbrain genes. The ppp1r14al gene was analyzed in greater detail and our results indicate that Hoxb1b is likely to directly regulate ppp1r14al expression in rhombomere 4. Furthermore, ppp1r14al is essential for establishment of the earliest hindbrain signaling-center in rhombomere 4 by regulating expression of fgf3

Probing Noncommutative Space-Time in the Laboratory Frame

The phenomenological investigation of noncommutative space-time in the laboratory frame are presented. We formulate the apparent time variation of noncommutativity parameter $\theta_{\mu\nu}$ in the laboratory frame due to the earth's rotation. Furthermore, in the noncommutative QED, we discuss how to probe the electric-like component $\overrightarrow{\theta_{E}}=(\theta_{01},\theta_{02},\theta_{03})$ by the process $e^-e^+\to\gamma\gamma$ at future $e^-e^+$ linear collider. We may determine the magnitude and the direction of $\overrightarrow{\theta_{E}}$ by detailed study of the apparent time variation of total cross section. In case of us observing no signal, the upper limit on the magnitude of $\overrightarrow{\theta_E^{}}$ can be determined independently of its direction.Comment: 12 pages, 7 figures, typos are corrected, one graph have been added in figure

Cosmological evolution of interacting dark energy in Lorentz violation

The cosmological evolution of an interacting scalar field model in which the scalar field interacts with dark matter, radiation, and baryon via Lorentz violation is investigated. We propose a model of interaction through the effective coupling $\bar{\beta}$. Using dynamical system analysis, we study the linear dynamics of an interacting model and show that the dynamics of critical points are completely controlled by two parameters. Some results can be mentioned as follows. Firstly, the sequence of radiation, the dark matter, and the scalar field dark energy exist and baryons are sub dominant. Secondly, the model also allows the possibility of having a universe in the phantom phase with constant potential. Thirdly, the effective gravitational constant varies with respect to time through $\bar{\beta}$. In particular, we consider a simple case where $\bar{\beta}$ has a quadratic form and has a good agreement with the modified $\Lambda$CDM and quintessence models. Finally, we also calculate the first post--Newtonian parameters for our model.Comment: 14 pages, published versio

Discerning Noncommutative Extra Dimensions

Experimental limits on the violation of four-dimensional Lorentz invariance imply that noncommutativity among ordinary spacetime dimensions must be small. Noncommutativity among extra, compactified spatial dimensions, however, is far less constrained and may have discernable collider signatures. Here we study the experimental consequences of noncommutative QED in six dimensions, with noncommutativity restricted to a TeV-scale bulk. Assuming the orbifold T^2/Z_2, we construct the effective four-dimensional theory and study interactions unique to the noncommutative case. New vertices involving the Kaluza-Klein (KK) excitations of the photon yield order 100% corrections to the pair production and to the decays of some of the lighter modes. We show that these effects are difficult to resolve at the LHC, but are likely within the reach of a future Very Large Hadron Collider (VLHC).Comment: 20 pages LaTeX, 8 eps figures (minor revisions, version to appear in Phys. Rev. D

VFISV: Very Fast Inversion of the Stokes Vector for the Helioseismic and Magnetic Imager

In this paper we describe in detail the implementation and main properties of a new inversion code for the polarized radiative transfer equation (VFISV: Very Fast inversion of the Stokes vector). VFISV will routinely analyze pipeline data from the Helioseismic and Magnetic Imager (HMI) on-board of the Solar Dynamics Observatory (SDO). It will provide full-disk maps (4096$\times$4096 pixels) of the magnetic field vector on the Solar Photosphere every 10 minutes. For this reason VFISV is optimized to achieve an inversion speed that will allow it to invert 16 million pixels every 10 minutes with a modest number (approx. 50) of CPUs. Here we focus on describing a number of important details, simplifications and tweaks that have allowed us to significantly speed up the inversion process. We also give details on tests performed with data from the spectropolarimeter on-board of the Hinode spacecraft.Comment: 23 pages, 9 figures (2 color). Submitted for publication to Solar Physic

A-dependence of nuclear transparency in quasielastic A(e,e'p) at high Q^2

The A-dependence of the quasielastic A(e,e'p) reaction has been studied at SLAC with H-2, C, Fe, and Au nuclei at momentum transfers Q^2 = 1, 3, 5, and 6.8 (GeV/c)^2. We extract the nuclear transparency T(A,Q^2), a measure of the average probability that the struck proton escapes from the nucleus A without interaction. Several calculations predict a significant increase in T with momentum transfer, a phenomenon known as Color Transparency. No significant rise within errors is seen for any of the nuclei studied.Comment: 5 pages incl. 2 figures, Caltech preprint OAP-73

Insights into the complex regulation of rpoS in Borrelia burgdorferi

Co-ordinated regulation of gene expression is required for the transmission and survival of Borrelia burgdorferi in different hosts. The sigma factor RpoS (σS), as regulated by RpoN (σ54), has been shown to regulate key virulence factors (e.g. OspC) required for these processes. As important, multiple signals (e.g. temperature, pH, cell density, oxygen) have been shown to increase the expression of σS-dependent genes; however, little is known about the signal transduction mechanisms that modulate the expression of rpoS. In this report we show that: (i) rpoS has a σ54-dependent promoter that requires Rrp2 to activate transcription; (ii) Rrp2Δ123, a constitutively active form of Rrp2, activated σ54-dependent transcription of rpoS/P-lacZ reporter constructs in Escherichia coli; (iii) quantitative reverse transcription polymerase chain reaction (QRT-PCR) experiments with reporter cat constructs in B. burgdorferi indicated that Rrp2 activated transcription of rpoS in an enhancer-independent fashion; and finally, (iv) rpoN is required for cell density- and temperature-dependent expression of rpoS in B. burgdorferi, but histidine kinase Hk2, encoded by the gene immediately upstream of rrp2, is not essential. Based on these findings, a model for regulation of rpoS has been proposed which provides mechanisms for multiple signalling pathways to modulate the expression of the σS regulon in B. burgdorferi

Modeling the Subsurface Structure of Sunspots

While sunspots are easily observed at the solar surface, determining their subsurface structure is not trivial. There are two main hypotheses for the subsurface structure of sunspots: the monolithic model and the cluster model. Local helioseismology is the only means by which we can investigate subphotospheric structure. However, as current linear inversion techniques do not yet allow helioseismology to probe the internal structure with sufficient confidence to distinguish between the monolith and cluster models, the development of physically realistic sunspot models are a priority for helioseismologists. This is because they are not only important indicators of the variety of physical effects that may influence helioseismic inferences in active regions, but they also enable detailed assessments of the validity of helioseismic interpretations through numerical forward modeling. In this paper, we provide a critical review of the existing sunspot models and an overview of numerical methods employed to model wave propagation through model sunspots. We then carry out an helioseismic analysis of the sunspot in Active Region 9787 and address the serious inconsistencies uncovered by \citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find that this sunspot is most probably associated with a shallow, positive wave-speed perturbation (unlike the traditional two-layer model) and that travel-time measurements are consistent with a horizontal outflow in the surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic

Nuclear transparency from quasielastic A(e,e'p) reactions uo to Q^2=8.1 (GeV/c)^2

The quasielastic (e,e$^\prime$p) reaction was studied on targets of deuterium, carbon, and iron up to a value of momentum transfer $Q^2$ of 8.1 (GeV/c)$^2$. A nuclear transparency was determined by comparing the data to calculations in the Plane-Wave Impulse Approximation. The dependence of the nuclear transparency on $Q^2$ and the mass number $A$ was investigated in a search for the onset of the Color Transparency phenomenon. We find no evidence for the onset of Color Transparency within our range of $Q^2$. A fit to the world's nuclear transparency data reflects the energy dependence of the free proton-nucleon cross section.Comment: 11 pages, 6 figure

Lorentz breaking Effective Field Theory and observational tests

Analogue models of gravity have provided an experimentally realizable test field for our ideas on quantum field theory in curved spacetimes but they have also inspired the investigation of possible departures from exact Lorentz invariance at microscopic scales. In this role they have joined, and sometime anticipated, several quantum gravity models characterized by Lorentz breaking phenomenology. A crucial difference between these speculations and other ones associated to quantum gravity scenarios, is the possibility to carry out observational and experimental tests which have nowadays led to a broad range of constraints on departures from Lorentz invariance. We shall review here the effective field theory approach to Lorentz breaking in the matter sector, present the constraints provided by the available observations and finally discuss the implications of the persisting uncertainty on the composition of the ultra high energy cosmic rays for the constraints on the higher order, analogue gravity inspired, Lorentz violations.Comment: 47 pages, 4 figures. Lecture Notes for the IX SIGRAV School on "Analogue Gravity", Como (Italy), May 2011. V.3. Typo corrected, references adde