Excitation of Giant Monopole Resonance in 208^{208}Pb and 116^{116}Sn Using Inelastic Deuteron Scattering

The excitation of the isoscalar giant monopole resonance (ISGMR) in $^{116}$Sn and $^{208}$Pb has been investigated using small-angle (including $0^\circ$) inelastic scattering of 100 MeV/u deuteron and multipole-decomposition analysis (MDA). The extracted strength distributions agree well with those from inelastic scattering of 100 MeV/u $\alpha$ particles. These measurements establish deuteron inelastic scattering at E$_d \sim$ 100 MeV/u as a suitable probe for extraction of the ISGMR strength with MDA, making feasible the investigation of this resonance in radioactive isotopes in inverse kinematics.Comment: 5 pages, 4 figures. To be published in Phys. Lett.

Effect of promoter architecture on the cell-to-cell variability in gene expression

According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effort that addresses the question of how changes in promoter architecture affect noise in gene expression in a systematic rather than case-by-case fashion. In this article, we make such a systematic investigation, based on a simple microscopic model of gene regulation that incorporates stochastic effects. In particular, we show how operator strength and operator multiplicity affect this variability. We examine different modes of transcription factor binding to complex promoters (cooperative, independent, simultaneous) and how each of these affects the level of variability in transcription product from cell-to-cell. We propose that direct comparison between in vivo single-cell experiments and theoretical predictions for the moments of the probability distribution of mRNA number per cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte

Observations of the dispersion characteristics and meridional sea level structure of equatorial waves in the Pacific Ocean

Author Posting. © American Meteorological Society, 2008. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 38 (2008): 1669-1689, doi:10.1175/2007JPO3890.1.Spectral techniques applied to altimetry data are used to examine the dispersion relation and meridional sea level structure of wavelike variability with periods of about 20 to 200 days in the equatorial Pacific Ocean. Zonal wavenumber–frequency power spectra of sea surface height, when averaged over about 7°S–7°N, exhibit spectral peaks near the theoretical dispersion curves of first baroclinic-mode equatorial Kelvin and Rossby waves. There are distinct, statistically significant ridges of power near the first and second meridional-mode Rossby wave dispersion curves. Sea level variability near the theoretical Kelvin wave and first meridional-mode Rossby wave dispersion curves is dominantly (but not perfectly) symmetric about the equator, while variability near the theoretical second meridional-mode Rossby wave dispersion curve is dominantly antisymmetric. These results are qualitatively consistent with expectations from classical or shear-modified theories of equatorial waves. The meridional structures of these modes resemble the meridional modes of equatorial wave theory, but there are some robust features of the meridional profiles that were not anticipated. The meridional sea level structure in the intraseasonal Kelvin wave band closely resembles the theoretically expected Gaussian profile, but sea level variability coherent with that at the equator is detected as far away as 11.75°S, possibly as a result of the forced nature of these Kelvin waves. Both first and second meridional-mode Rossby waves have larger amplitude in the Northern Hemisphere. The meridional sea level structure of tropical instability waves closely resembles that predicted by Lyman et al. using a model linearized about a realistic equatorial zonal current system.This work was supported in part by the NOAA Climate Prediction Program for the Americas (Grant NA17RJ1223)

Intraseasonal variability near 10°N in the eastern tropical Pacific Ocean

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 111 (2006): C05015, doi:10.1029/2005JC002989.New in situ observations from 10°N, 125°W during 1997–1998 show strong intraseasonal variability in meridional velocity and sea surface temperature. The 50- to 100-day oscillations in sea surface height (SSH) have long been recognized as a prominent aspect of oceanic variability in the region of 9–13°N in the eastern Pacific Ocean. We use in situ and satellite data to more fully characterize this variability. The oscillations have zonal wavelengths of 550–1650 km and propagate westward in a manner consistent with the dispersion relation for first baroclinic mode, free Rossby waves in the presence of a mean westward flow. Analysis of 9 years of altimetry data shows that the amplitude of the 50- to 100-day SSH variability at 10°N is largest on 90–115°W, with peak amplitudes occurring around April. Some eddies traveling westward at 10–13°N emanate from near the gulfs of Tehuantepec and Papagayo, but eddies sometimes also appear to intensify well away from the coast while in the North Equatorial Current (NEC). The hypothesis that the intraseasonal variability and its annual cycle are associated with baroclinic instability of the NEC is supported by a spatiotemporal correlation between the amplitude of 50- to 100-day variability and the occurrence of westward zonal flows meeting an approximate necessary condition for baroclinic instability. The notion that baroclinic instability may be involved is further corroborated by the tendency of the NEC to weaken while the eddies intensify, even as the wind works to strengthen the current.The authors gratefully acknowledge support for the fieldwork under the NOAA Office of Global Programs Pan American Climate Studies program (grants NA66GPO130 and NA96GPO428) and for analysis and publication (grants NA87RJ0445 and NA17RJ1223)

A model of multiple zonal jets in the oceans : dynamical and kinematical analysis

Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 2711-2734, doi:10.1175/2009JPO4093.1.Multiple alternating zonal jets observed in the ocean are studied with an idealized quasigeostrophic zonal-channel model, with the supercritical, zonal background flow imposed. Both eastward and westward background flows with vertical shear are considered. The underlying nonlinear dynamics is illuminated with analysis of the vertical-mode interactions and time-mean eddy fluxes. Interactions between the vertical modes are systematically studied. The barotropic component of the jets is maintained by both barotropic–barotropic and baroclinic–baroclinic time-mean interactions; thus, the barotropic component of the jets cannot be accurately simulated with a randomly forced barotropic model. The roles of the vertical-mode interactions in driving the baroclinic component of the jets are also characterized. Not only the first but also the second baroclinic mode is found to be important for maintaining the baroclinic component of the jets, whereas the barotropic component of the jets is maintained mostly by the barotropic and first baroclinic modes. The properties of the eddy forcing were systematically studied. It is shown that the baroclinic component of the jets is maintained by Reynolds stress forcing and resisted by form stress forcing only in the eastward background flow. In the westward background flow, the jets are maintained by form stress forcing and resisted by Reynolds stress forcing. The meridional scaling and kinematical properties of the jets are studied as well as the roles of meridional boundaries. The Rhines scaling for meridional spacing of the jets is not generally confirmed, and it is also shown that there are multiple stable equilibria with different numbers of the time-mean jets. It is also found that the jets are associated with alternating weak barriers to the meridional material transport, but the locations of these barriers are not unique and depend on the direction of the background flow and depth. Finally, if the channel is closed with meridional walls, then the jets become more latent but the eddy forcing properties do not change qualitatively.Funding for PB was provided by NSF Grants OCE 0344094 and OCE 0725796 and by the research grant from the Newton Trust of the University of Cambridge. Funding for IK was provided by NSF Grants OCE 0346178 and 0749722. Funding for JP was provided by NSF Grant OCE 0451086

A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix

Direct targeting of critical DNA-binding elements of a repressor by its cognate antirepressor is an effective means to sequester the repressor and remove a transcription initiation block. Structural descriptions for this, though often proposed for bacterial and phage repressor–antirepressor systems, are unavailable. Here, we describe the structural and functional basis of how the Myxococcus xanthus CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible promoter. CarA and CarH repress the carB operon in the dark. CarS, produced in the light, physically interacts with the MerR-type winged-helix DNA-binding domain of these repressors leading to activation of carB. The NMR structure of CarS1, a functional CarS variant, reveals a five-stranded, antiparallel β-sheet fold resembling SH3 domains, protein–protein interaction modules prevalent in eukaryotes but rare in prokaryotes. NMR studies and analysis of site-directed mutants in vivo and in vitro unveil a solvent-exposed hydrophobic pocket lined by acidic residues in CarS, where the CarA DNA recognition helix docks with high affinity in an atypical ligand-recognition mode for SH3 domains. Our findings uncover an unprecedented use of the SH3 domain-like fold for protein–protein recognition whereby an antirepressor mimics operator DNA in sequestering the repressor DNA recognition helix to activate transcription

Accuracy assessment of recent ocean tide models

Over 20 global ocean tide models have been developed since 1994, primarily as a consequence of analysis of the precise altimetric measurements from TOPEX/POSEIDON and as a result of parallel developments numerical tidal modeling and data assimilation. This paper provides an accuracy assessment of 10 such tide models and discusses their benefits in many fields including geodesy, oceanography, and geophysics. A variety of tests indicate that all these tide models agree within 2-3 cm in the deep ocean, and they represent significant improvement over the classical Schwidersk1i 1980 model by approximately 5 cm rms. As a result, two tide models were selected for the reprocessing of TOPEX/POSEIDON Geophysical Data Records in late 1995. Current ocean tide models allow an improved observation of deep ocean surface dynamic topography using satellite altimetry. Other significant contributions include their applications in an improved orbit computation for TOPEX/POSEIDON and other geodetic satellites, to yield accurate predictions of Earth rotation excitations and improved estimates of ocean loading corrections for geodetic observatories, and to allow better separation of astronomical tides from phenomena with meteorological and geophysical origins. The largest differences between these tide models occur in shallow waters, indicating that the current models are still problematic in these areas. Future improvement of global tide models is anticipated with additional high-quality altimeter data and with advances in numerical techniques to assimilate data into high-resolution hydrodynamic models.Copyrighted by American Geophysical Union