bluuebunny/crossref_metadata_2025 huggingface dataset:
Three‐dimensional structure of the summertime circulation in the Yellow Sea from a wave‐tide‐circulation coupled model
Authors: Xia Changshui , Qiao Fangli , Yang Yongzeng , Ma Jian , Yuan Yeli
Published: July 2006

The three‐dimensional structure of the summertime circulation of the Yellow Sea (hereafter YS) is studied by using a prognostic wave‐tide‐circulation coupled model based on the Princeton Ocean Model (POM) and a surface wave model. The simulated tidal harmonic constants and temperature structure agree with the observations well. The patterns of the simulated salinity generally agree also with the observations. The simulated results show that the horizontal circulation has a three‐layer structure: in the surface layer (0–4 m), the prevailing current direction is northeastward; in the upper layer (4–40 m) it is dominated by a basin scale anticlockwise (cyclonic) gyre; in the bottom layer (below 40 m) the water diverges from the center area and there exists a weak southward current along the YS trough. The stream function of the YS shows that the net circulation of the YS is an anticlockwise (cyclonic) one, and the net transport is about 0.1 Sv. Diagnostic analysis of the momentum balance and sensitivity show that the cyclonic circulation in the upper layers is mainly a quasi‐geostrophic flow along tidal‐induced temperature front, and it is also strengthened by the tide residual currents. The tidal residual current and the compensation for northward surface layer wind transport contribute to the formation of southward flow in the bottom layer. The vertical circulations vary along different sections. A circulation cell is found in the frontal area near the Korean coast, and an upwelling is found along the slope.
Inferring dust composition from wavelength‐dependent absorption in Aerosol Robotic Network (AERONET) data
Authors: Koven Charles D. , Fung Inez
Published: July 2006

Atmospheric mineral dust is an important component of the Earth system, affecting climate and biogeochemical cycling. We present an inverse method of inferring dust composition from wavelength dependence of light absorption and the complex refractive indices of aerosol components. Specifically, we separate absorption by black carbon from absorption by hematite and organic carbon. We apply this method to coarse‐mode‐dominated Aerosol Robotic Network (AERONET) observations in the “dust belt” region of the globe, and we identify differences between dust optical properties and composition in different locations. We solve for dust composition using two opposite, bracketing hypotheses of the state of mineralogical mixing: purely internal mixing and purely external mixing. We find that calculated absolute hematite concentrations are highly sensitive to mixing assumptions, while relative geographic and seasonal patterns are less sensitive to mixing assumptions. Internal mixing calculations appear to underestimate absolute hematite concentrations, while external mixing overestimates hematite concentrations. Inversions calculated assuming external mixing are better able to explain the wavelength dependence of dust absorption by only varying hematite concentration than inversions using internal mixing, which require substantial covariation between black carbon and hematite to match observations. Saharan and East Asian dust show higher hematite content than dust from Arabia. Saharan dust also shows seasonal variation in hematite content which may reflect seasonal shifts in dust source areas.
Secondary aerosol formation from the oxidation of biogenic hydrocarbons by chlorine atoms
Authors: Cai Xuyi , Griffin Robert J.
Published: July 2006

The chlorine atom (Cl) is a potential oxidant of volatile organic compounds (VOCs) in the atmosphere and is hypothesized to lead to secondary organic aerosol (SOA) formation in coastal and industrialized areas. The purpose of this paper is to test this hypothesis and to quantify the SOA formation potentials of the common monoterpenes α‐pinene, β‐pinene, and d‐limonene when oxidized by Cl in laboratory chamber experiments. Results indicate that the oxidation of these monoterpenes generates significant amounts of aerosol. The SOA yields of α‐pinene, β‐pinene, and d‐limonene in this study are comparable to those when they are oxidized by ozone, by nitrate radical, and in photooxidation scenarios. For aerosol mass up to 30.0 μg m−3, their yields reach approximately 0.20, 0.20, and 0.30, respectively. For d‐limonene, data indicate two yield curves that depend on the initial concentration ratio of Cl precursor to d‐limonene. It is argued theoretically that multiple SOA yield curves may be common for VOCs, depending on the initial concentration ratio of oxidant to VOC. SOA formation from the three typical monoterpenes when oxidized by Cl in the marine boundary layer, coastal areas, and inland industrialized areas could be a source of organic aerosol in the early morning.
Prediction uncertainty in a median‐based index flood method using L moments
Authors: Kjeldsen Thomas R. , Jones David A.
Published: July 2006

The standard for conducting flood frequency analysis in the UK, as set out in the Flood Estimation Handbook, is based on the index flood method, using the median of the annual maximum flood as the index flood. For a given target site, a region‐of‐influence approach is used, involving the creation of a collection of hydrologically similar catchments (pooling group). This paper examines the sampling uncertainty of quantile estimates on the basis of pooling groups and using the median as the index flood for both gauged and ungauged sites. Analytical approximations for the variance of the quantile estimates were derived, on the basis of asymptotic theory, and were used to calculate approximate confidence intervals for flood frequency curves obtained using both single‐site and pooled analysis at gauged and ungauged sites. A series of bootstrap experiments were conducted to quantify the intersite dependence and to develop generalized expressions to be included in the analysis. It is shown that the pooled analysis yields narrower confidence intervals than the single‐site analysis and that the presence of intersite correlations increases the sampling uncertainty. The method was extended to encompass estimation at ungauged sites in the UK on the basis of a regression model for the index flood, which significantly increases the prediction uncertainty compared with using an estimate of the index flood derived from observations at the target site.
Modeling of river dynamics of phosphorus under unsteady flow conditions
Authors: Kim Kyunghyun , Kalita Prasanta K. , Bowes Michael J. , Eheart J. Wayland
Published: July 2006

A model has been developed to investigate in‐river sediment and phosphorus dynamics. This advective‐dispersive model is coupled with hydrodynamics and sediment transport submodels to simulate suspended sediment, total dissolved phosphorus, total phosphorus, and particulate phosphorus concentrations under unsteady flow conditions. The model is applied to a 55‐km stretch of the River Swale in Yorkshire, UK, within the framework of the generalized likelihood uncertainty estimation (GLUE) methodology. First, simulations are conducted without in‐river interactions to separate the effects of the in‐river dynamics from the observed data at the downstream end. Results show that there was relatively minimal sediment and phosphorus mass exchange between the overlying water and the riverbed during low flow periods and active mass exchange during storm events. Also, there was net phosphorus diffusion from the riverbed throughout the entire period and particulate phosphorus gain during storm events, indicating higher phosphorus concentration in the riverbed sediment. The second group of simulations is conducted with in‐river interactions. The results show relatively strong simulation dependencies of particulate phosphorus and total phosphorus on both flow and suspended sediment. They indicate that the uncertainties of the flow and suspended sediment predictions considerably contribute to those in particulate phosphorus and total phosphorus predictions. However, the uncertainties of suspended sediment and total dissolved phosphorus predictions are already sufficient without including those propagated from the flow predictions. Finally, the results provide supporting evidence of a higher phosphorus concentration in the riverbed, which is obtained by assimilating all available data within the GLUE framework.
A Bayesian perspective on input uncertainty in model calibration: Application to hydrological model “abc”
Authors: Huard David , Mailhot Alain
Published: July 2006

The impact of input errors in the calibration of watershed models is a recurrent theme in the water science literature. It is now acknowledged that hydrological models are sensitive to errors in the measures of precipitation and that those errors bias the model parameters estimated via the standard least squares (SLS) approach. This paper presents a Bayesian uncertainty framework allowing one to account for input, output, and structural (model) uncertainties in the calibration of a model. Using this framework, we study the impact of input uncertainty on the parameters of the hydrological model “abc.” Mostly of academic interest, the “abc” model has a response linear to its input, allowing the closed form integration of nuisance variables under proper assumptions. Using those analytical solutions to compute the posterior density of the model parameters, some interesting observations can be made about their sensitivity to input errors. We provide an explanation for the bias identified in the SLS approach and show that in the input error context the prior on the input “true” value has a significant influence on the parameters' posterior density. Overall, the parameters obtained from the Bayesian method are more accurate, and the uncertainty over them is more realistic than with SLS. This method, however, is specific to linear models, while most hydrological models display strong nonlinearities. Further research is thus needed to demonstrate the applicability of the uncertainty framework to commonly used hydrological models.
Pathways of eddies in the South Atlantic Ocean revealed from satellite altimeter observations
Authors: Fu Lee‐Lueng
Published: July 2006

The majority of the kinetic energy of ocean currents is contained in the mesoscale eddies. The pathways of ocean eddies, which are the “weather” of ocean circulation, are mapped from space using a decade‐long record of sea surface height measured by two simultaneously flying satellite radar altimeters. The speed and direction of the propagation of eddies in the South Atlantic Ocean are presented in the paper. The patterns of the eddy propagation velocity reveal the effects of the interaction between mean flow and eddies with strong influence of bottom topography. The information describes a unique property of the ocean general circulation and serves as a basis for testing ocean models.
Intercomparison of kinetic temperature from 15 μm CO2 limb emissions and OH*(3,1) rotational temperature in nearly coincident air masses: SABER, GRIPS
Authors: Oberheide J. , Offermann D. , Russell J. M. , Mlynczak M. G.
Published: July 2006

Three years (2003–2005) of kinetic temperatures measured by the Sounding the Atmosphere using Broadband Emission Radiometry (SABER) instrument on board the TIMED satellite are compared to OH*(3,1) rotational temperatures measured by the Ground Based Infrared P‐Branch Spectrometer (GRIPS) located at 7.2°E, 51.3°N in Wuppertal, Germany. Comparisons are confined to nearly coincident air masses (miss distance: ∼600 km, miss time: 30 minutes). OH*(3,1) rotational temperatures are systematically higher by 7.5 K than OH equivalent SABER temperatures derived from 15 μm CO2 limb emissions which is just within the combined error bars. The bias is independent of year and season thus providing additional confidence into allocating the mean altitude of the OH* emission layer to a constant value of 87 km for long‐term trend analyses.
A Lagrangian analysis of the Indian‐Atlantic interocean exchange in a regional model
Authors: Doglioli A. M. , Veneziani M. , Blanke B. , Speich S. , Griffa A.
Published: July 2006

We present a new numerical Lagrangian technique based on the coupling of transport computation with spin analysis of trajectories. This method was applied to results from a high‐resolution numerical model of the oceanic region around South Africa. We estimated an Indian‐Atlantic leakage of about 14 Sv. In the western Cape Basin, approximately 30% of this transport is due to trapping eddies with a ratio between cyclones and anticyclones transport of 1.3. These findings are briefly discussed with respect to recent observations of the highly nonlinear regime found in this area of the Cape Basin.
Changes in the leading ENSO modes associated with the late 1970s climate shift: Role of surface zonal current
Authors: An Soon‐Il , Ye Zhengqing , Hsieh William W.
Published: July 2006

In this study, using the nonlinear principal analysis (NLPCA) technique, we demonstrated that the leading El Nino‐Southern Oscillation (ENSO) mode in a physical basis changed since the late 1970s. The ENSO mode during the pre‐1980s resembles the destabilized ‘ocean basin mode’, while during the post‐1980s does ‘the recharge‐mode’. In particular, for the pre‐1980s, the surface zonal current mainly acts as an intensifier of the ENSO, while that during post‐1980s it plays a role in the transition of the ENSO cycle. The NLPCA results are reconfirmed by the eigen analysis of the linearized intermediated ENSO model. Over a reasonable parameter range, the leading eigen modes associated with the pre‐1980s are completely separable from those associated with the post‐1980s. The eigen structures for each decadal‐period resemble the corresponding NLPCA patterns.
Modeling the heterogeneous reaction probability for chlorine nitrate hydrolysis on ice
Authors: Loerting Thomas , Voegele Andreas F. , Tautermann Christofer S. , Liedl Klaus R. , Molina Luisa T. , Molina Mario J.
Published: July 2006

We present a theoretical estimate of the reaction probability γ for the chlorine nitrate (ClONO2) hydrolysis on type II (water‐ice) polar stratospheric cloud material. This estimate is based on high‐level ab initio calculations in a supermolecule containing four molecules of water and one molecule of chlorine nitrate. To the best of our knowledge, this is the first estimate of γ that makes no a priori use of experimental data at all. Instead, the rate constants for association, surface reaction, and surface desorption as calculated by variational transition state theory enter the model. At 180 K we estimate γ ≈ 0.10−0.06+0.20, which is within the error bars of the agreeing recommendations of Jet Propulsion Laboratory and International Union of Pure and Applied Chemistry of 0.3−0.1+0.7. The temperature dependence between 75 and 150 K agrees with results obtained from laser‐induced thermal desorption. In particular, the temperature of 105 K above which γ becomes less than unity is reproduced well. A negative temperature dependence between 180 and 210 K is found, which has not yet been confirmed in the laboratory for ClONO2 hydrolysis but only for BrONO2 on ice. This qualitative agreement of a gas‐phase cluster calculation with experiments on hexagonal ice surfaces implies that a highly mobile and oxygen disordered ice surface rather than an ordered, immobile crystalline ice surface is experienced by chlorine nitrate molecules under polar stratospheric conditions.
Measurements of N2O5 near Fairbanks, Alaska
Authors: Ayers James D. , Simpson William R.
Published: July 2006

We report measurements of N2O5, CO, and O3 at a subarctic site near Fairbanks, Alaska (65°N), during two periods of approximately 2 weeks each, one in December 2002 and the other in February 2004. N2O5 mixing ratios range from below the instrument detection limit of 2 parts per trillion by volume (pptv) up to approximately 250 pptv. Ozone and carbon monoxide measurements help distinguish several different air mass types: “clean” (near background CO and ozone), “titrated” (ozone titrated to near zero and elevated CO), and “mixed” (intermediate ozone and some CO elevation). Observed N2O5 mixing ratios are near zero for air masses that are either clean or titrated. Times with measurable N2O5 are almost always associated with mixed air masses. Measurements of CO and the CO:NOx emissions ratio in Fairbanks are used to estimate NO2 mixing ratios and calculate steady state lifetimes for N2O5. The lifetime estimates vary from subminute to 4 hours, with a median for the February study of 10 min and a median for the December study of 4 min. These lifetimes are quite short compared to the lifetime of NO2 with respect to reaction with ozone and formation of NO3, suggesting that the rate limiting step of NOx oxidation in the nighttime atmosphere is the formation of NO3, not the losses of NO3 and N2O5. These data show sinks of N2O5 (presumably mostly heterogeneous hydrolysis) are an efficient mechanism of NOx removal near the surface in the dark, high‐latitude winter.
Revisiting China's CO emissions after the Transport and Chemical Evolution over the Pacific (TRACE‐P) mission: Synthesis of inventories, atmospheric modeling, and observations
Authors: Streets David G. , Zhang Qiang , Wang Litao , He Kebin , Hao Jiming , Wu Ye , Tang Youhua , Carmichael Gregory R.
Published: July 2006

A new inventory of CO emissions in China is presented for the year 2001. This inventory improves and updates the a priori CO emission inventory prepared in support of NASA's TRACE‐P mission in the spring of 2001. Analysis of CO observations using chemical transport models in inverse and forward modes suggested that China's emissions were underestimated by about 50%. We have reexamined the source characteristics and conclude that emissions from cement kilns, brick kilns, and the iron and steel industry were underestimated. Our new estimate for China's CO emissions in 2001 is 157 Tg, 36% higher than the TRACE‐P estimate for the year 2000 of 116 Tg. Bottom‐up and modeled emission estimates are now in good agreement, which represents a major success story for the TRACE‐P mission. The new inventory has been gridded at 30 min × 30 min resolution and tested with the CFORS/STEM‐2K1 model, considerably improving the correlation between model predictions and observations (bias reduced from 27% to 9%). Propagation‐of‐error estimates in the new inventory yield an uncertainty of ±68% (95% confidence intervals), lower than the TRACE‐P value of ±156%; however, the good agreement with results from inverse and forward models implies a greater level of confidence than this. The largest remaining uncertainties concern (1) characterization of open vegetation burning, which cannot be resolved without new field studies; (2) emission factors for small combustion devices, for which emissions testing is urgently needed; and (3) residential fuel consumption, which may require a reassessment of China's official statistics.
Heat equilibrium distribution in a turbulent flow
Authors: Haba Z.
Published: July 2006

We consider a shear flow of a scale invariant Gaussian random velocity field that does not depend on the coordinates in the direction of the flow. We investigate a heat advection coming from a Gaussian random homogeneous source. We discuss a relaxation at large time of a temperature distribution determined by the forced advection-diffusion equation. We represent the temperature correlation functions by means of the Feynman-Kac formula. Jensen inequalities are applied for lower and upper bounds on the correlation functions. We show that at finite time there is no velocity dependence of long range temperature correlations (low momentum asymptotics) in the direction of the flow but the equilibrium heat distribution has large distance correlations (low momentum behavior) with an index depending on the scaling index of the random flow and of the index of the random forcing. If the velocity has correlations growing with the distance (a turbulent flow), then the large distance correlations depend in a crucial way on the scaling index of the turbulent flow. In such a case the correlations increase in the direction of the flow and decrease in the direction perpendicular to the flow, making the stream of heat more coherent.
Explicit actions for electromagnetism with two gauge fields with only one electric and one magnetic physical field
Authors: Ferreira P. Castelo
Published: July 2006

We extend the work of Mello et al. based on Cabbibo and Ferrari concerning the description of electromagnetism with two gauge fields from a variational principle, i.e., an action. We provide a systematic independent derivation of the allowed actions that have only one magnetic and one electric physical field and are invariant under the discrete symmetries P and T. We conclude that neither the Lagrangian, nor the Hamiltonian, are invariant under the electromagnetic duality rotations. This agrees with the weak-strong coupling mixing characteristic of the duality due to the Dirac quantization condition providing a natural way to differentiate dual theories related by the duality rotations (the energy is not invariant). Also, the standard electromagnetic duality rotations considered in this work violate both P and T by inducing Hopf terms (theta terms) for each sector and a mixed Maxwell term. The canonical structure of the theory is briefly addressed and the magnetic gauge sector is interpreted as a ghost sector.
Detection mechanism for ferroelectric domain boundaries with lateral force microscopy
Authors: Jungk Tobias , Hoffmann Ákos , Soergel Elisabeth
Published: July 2006

The contrast mechanism for the visualization of ferroelectric domain boundaries with lateral force microscopy is generally assumed to be caused by mechanical deformation of the sample due to the converse piezoelectric effect. We show, however, that electrostatic interactions between the charged tip and the electric fields arising from the surface polarization charges dominate the contrast mechanism. This explanation is sustained by quantitative analysis of the measured forces as well as by comparative measurements on lithium niobate and potassium titanyl phosphate.
Quantitative microscopy of nonlinear dielectric constant using a scanning evanescent microwave microscopy
Authors: Hu Bo , Liu Wenhan , Gao Chen , Zhu Xiaohong , Zheng Dongning
Published: July 2006

Quantitative characterization of dielectric nonlinearity in ferroelectric materials has been successfully performed using a scanning evanescent microwave microscope, and a key calibration coefficient for quantitative microscopy of nonlinear dielectric constant is derived. This unique technique has advantages of high spatial resolution and simultaneously accessing of other related properties such as dielectric constant and magnetoelectric coefficient. Samples of LiNbO3 single crystal and PbTiO3 thin film are measured, which demonstrates that this technique can access the nonlinear dielectric constant of a microregion with a sensitivity of 1.0×10−21F∕V.
The Ets factor Spi-B is a direct critical target of the coactivator OBF-1
Authors: Bartholdy Boris , Du Roure Camille , Bordon Alain , Emslie Dianne , Corcoran Lynn M. , Matthias Patrick
Published: July 2006

OBF-1 (Bob.1, OCA-B) is a lymphoid-specific transcriptional coactivator that associates with the transcription factors Oct-1 or Oct-2 on the conserved octamer element present in the promoters of several ubiquitous and lymphoid-specific genes. OBF-1-deficient mice have B cell-intrinsic defects, lack germinal centers, and have severely impaired immune responses to T cell-dependent antigens. Crucial genes that are regulated by OBF-1 and that might explain the observed phenotype of OBF-1 deficiency have remained elusive to date. Here we have generated transgenic mice expressing OBF-1 specifically in T cells and examined these together with mice lacking OBF-1 to discover transcriptional targets of this coactivator. Using microarray analysis, we have identified the Ets transcription factor Spi-B as a direct target gene critically regulated by OBF-1 that can help explain the phenotype of OBF-1-deficient mice. Spi-B has been implicated in signaling pathways downstream of the B cell receptor and is essential for germinal center formation and maintenance. The present findings establish a hierarchy between these two factors and provide a molecular link between OBF-1 and B cell receptor signaling.
Regulation of neddylation and deneddylation of cullin1 in SCF
Skp2
ubiquitin ligase by F-box protein and substrate
Authors: Bornstein Gil , Ganoth Dvora , Hershko Avram
Published: July 2006

The activity of cullin-containing ubiquitin protein ligase complexes is stimulated by linkage to cullin of the ubiquitin-like protein Nedd8 (“neddylation”). Neddylation is inhibited by the tight binding of cullins to CAND1 (cullin-associated and neddylation-dissociated 1) protein, and Nedd8 is removed from cullins by specific isopeptidase activity of the COP9/signalosome (CSN) complex. The mechanisms that regulate neddylation and deneddylation of cullins were unknown. We examined this problem for the case of SCF
Skp2
, a cullin1 (Cul1)-containing ubiquitin ligase complex that contains the S phase-associated protein Skp2 as the substrate-binding F-box protein subunit. SCF
Skp2
targets for degradation the cyclin-dependent kinase (cdk) inhibitor p27 in the G
1
-to-S phase transition, a process that requires its phosphorylation and binding to cdk2-cyclin E. Because levels of Skp2, cyclin E, and the accessory protein Cks1 (cyclin kinase subunit 1) all rise at the end of G
1
phase, it seemed possible that the neddylation of Cul1 in SCF
Skp2
is regulated by the availability of the F-box protein and/or the substrate. We found that the supplementation of Skp2–Skp1 and substrate (along with further components necessary for substrate presentation to the ubiquitin ligase) to extracts of HeLa cells synergistically increased levels of neddylated Cul1. Skp2–Skp1 abrogates the inhibitory influence of CAND1 on the neddylation of Cul1 by promoting the dissociation of the cullin–CAND1 complex, whereas substrate, together with substrate-presenting components, prevents the action of CSN to deneddylate cullin. We propose a sequence of events in which the increased availability of Skp2 and substrate in the transition of cells to S phase promotes the neddylation and assembly of the SCF
Skp2
ubiquitin ligase complex.
Free-energy distribution of binary protein–protein binding suggests cross-species interactome differences
Authors: Shi Yi Y. , Miller Gerald A. , Qian Hong , Bomsztyk Karol
Published: July 2006

Major advances in large-scale yeast two-hybrid screening have provided a global view of binary protein–protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all species studied have a degree distribution of protein–protein binding that is approximately scale-free (varies as a power law) even though their evolutionary divergence times differ by billions of years. The universal power law shows only the surface of the rich information harbored by these high-throughput data. We develop a detailed mathematical model of the protein–protein interaction network based on association free energy, the biochemical quantity that determines protein–protein interaction strength. This model reproduces the degree distribution of all of the large-scale yeast two-hybrid data sets available and allows us to extract the distribution of free energy, the likelihood that a pair of proteins of a given species will bind. We find that across-species interactomes have significant differences that reflect the strengths of the protein–protein interaction. Our results identify a global evolutionary shift: more evolved organisms have weaker binary protein–protein binding. This result is consistent with the evolution of increased protein unfoldedness and challenges the dogma that only specific protein–protein interactions can be biologically functional.
Identification of a protein complex that assembles lipopolysaccharide in the outer membrane of
Escherichia coli
Authors: Wu Tao , McCandlish Andrew C. , Gronenberg Luisa S. , Chng Shu-Sin , Silhavy Thomas J. , Kahne Daniel
Published: July 2006

The outer membrane of most Gram-negative bacteria is made up of LPS, and in nearly all bacteria that contain LPS it is essential for the life of the organism. The lipid portion of this molecule, lipid A, also known as endotoxin, is a potent activator of the innate immune response. More than 50 genes are required to synthesize LPS and assemble it at the cell surface. Enormous progress has been made in elucidating the structure and biosynthesis of LPS, but until recently the cellular components required for its transport from its site of synthesis in the inner membrane to its final cellular location at the cell surface remained elusive. Here we describe the identification of a protein complex that functions to assemble LPS at the surface of the cell. This complex contains two proteins: Imp, already identified as an essential outer-membrane protein implicated in LPS assembly; and another protein, RlpB, heretofore identified only as a rare lipoprotein. We show that RlpB is also essential for cell viability and that the Imp/RlpB complex is responsible for LPS reaching the outer surface of the outer membrane.
The regulatory utilization of genetic redundancy through responsive backup circuits
Authors: Kafri Ran , Levy Melissa , Pilpel Yitzhak
Published: July 2006

Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes. One consequence of these redundancies is a tremendous increase to the robustness of organisms to mutations and other stresses. Yet, this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime. In contrast, numerous reports describe instances of functional overlaps that have been conserved throughout extended evolutionary periods. More interestingly, many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. By manual inspection of the literature, we have compiled a list of such “responsive backup circuits” in a diverse list of species. Reviewing these responsive backup circuits, we extract recurring principles characterizing their regulation. We then apply modeling approaches to explore further their dynamic properties. Our results demonstrate that responsive backup circuits may function as ideal devices for filtering nongenetic noise from transcriptional pathways and obtaining regulatory precision. We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation. In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.
Constraints on the Late Saalian to early Middle Weichselian ice sheet of Eurasia from field data and rebound modelling
Authors: LAMBECK KURT , PURCELL ANTHONY , FUNDER SVEND , KJæR KURT H. , LARSEN EILIV , MOLLER PER
Published: July 2006

Using glacial rebound models we have inverted observations of crustal rebound and shoreline locations to estimate the ice thickness for the major glaciations over northern Eurasia and to predict the palaeo‐topography from late MIS‐6 (the Late Saalian at c. 140 kyr BP) to MIS‐4e (early Middle Weichselian at c. 64 kyr BP). During the Late Saalian, the ice extended across northern Europe and Russia with a broad dome centred from the Kara Sea to Karelia that reached a maximum thickness of c. 4500 m and ice surface elevation of c. 3500 m above sea level. A secondary dome occurred over Finland with ice thickness and surface elevation of 4000 m and 3000 m, respectively. When ice retreat commenced, and before the onset of the warm phase of the early Eemian, extensive marine flooding occurred from the Atlantic to the Urals and, once the ice retreated from the Urals, to the Taymyr Peninsula. The Baltic‐White Sea connection is predicted to have closed at about 129 kyr BP, although large areas of arctic Russia remained submerged until the end of the Eemian. During the stadials (MIS‐5d, 5b, 4) the maximum ice was centred over the Kara‐Barents Seas with a thickness not exceeding c. 1200 m. Ice‐dammed lakes and the elevations of sills are predicted for the major glacial phases and used to test the ice models. Large lakes are predicted for west Siberia at the end of the Saalian and during MIS‐5d, 5b and 4, with the lake levels, margin locations and outlets depending inter alia on ice thickness and isostatic adjustment. During the Saalian and MIS‐5d, 5b these lakes overflowed through the Turgay pass into the Aral Sea, but during MIS‐4 the overflow is predicted to have occurred north of the Urals. West of the Urals the palaeo‐lake predictions are strongly controlled by whether the Kara Ice Sheet dammed the White Sea. If it did, then the lake levels are controlled by the topography of the Dvina basin with overflow directed into the Kama‐Volga river system. Comparisons of predicted with observed MIS‐5b lake levels of Komi Lake favour models in which the White Sea was in contact with the Barents Sea.
Eurasian ice‐sheet interaction in northwestern Russia throughout the late Quaternary
Authors: KJæR KURT H. , LARSEN EILIV , FUNDER SVEND , DEMIDOV IGOR N. , JENSEN MARIA , HAKANSSON LENA , MURRAY ANDREW
Published: July 2006

Sediment successions from the Kanin Peninsula and Chyoshskaya Bay in northwestern Russia contain information on the marginal behaviour of all major ice sheets centred in Scandinavia, the Barents Sea and the Kara Sea during the Eemian‐Weichselian. Extensive luminescence dating of regional lithostratigraphical units, supported by biostratigraphical evidence, identifies four major ice advances at 100–90, 70–65, 55–45 and 20–18 kyr ago interbedded with lacustrine, glaciolacustrine and marine sediments. The widespread occurrence of marine tidal sediments deposited c. 65–60 kyr ago allows a stratigraphical division of the Middle Weichselian Barents Sea and Kara Sea ice sheets into two shelf‐based glaciations separated by almost complete deglaciation. The first ice dispersal centre was in the Barents Sea and thereafter in the Kara Sea. It is possible to extract both flow patterns from ice marginal landforms inside the southward termination. Accordingly, it is proposed that the Markhida line and its western continuation are asynchronous and originate from two separate glaciations before and after the marine transgression. The marine sedimentation occurred during a eustatic sea‐level rise of up to 20 m/1000 yr, i.e. the Mezen Transgression. We speculate that the rapid eustatic sea‐level rise triggered a collapse of the Barents Sea Ice Sheet at the MIS (Marine Isotope Stage) 4 to 3 transition. This is motivated by lack of an early marine highstand, the timing of events, and the marginal position of Arkhangelsk relative to open marine conditions.
Cosmogenic 10Be exposure age dating across Early to Late Weichselian ice‐marginal zones in northwestern Russia
Authors: LINGE HENRIETTE , LARSEN EILIV , KJæR KURT H. , DEMIDOV IGOR N. , BROOK EDWARD J. , RAISBECK GRANT M. , YIOU FRANCOISE
Published: July 2006

Rock samples from the Kanin Peninsula and the Timan Ridge were analysed for in situ cosmogenic 10Be for exposure age dating purposes. Crystalline rocks were sampled at four sites on the Kanin Peninsula, either from bedrock outcrops or from glacial erratics, giving overall similar 10Be ages. Outcropping sandstone and crystalline erratics were available from three sites at the Timan Ridge. The highly weathered sandstone gives substantially younger 10Be ages than the adjacent erratics. The exposure ages from the Kanin Peninsula suggest that the last deglaciation of this area took place between 55 and 37 10Be kyr ago, in agreement with a preceding Kara Sea glaciation (55–45 kyr BP). The northwest coast of the peninsula was probably just outside the maximum limit of the last Scandinavian glaciation (20–17 kyr BP). Glacial erratic exposure ages from the Timan Ridge suggest that the 55–45 kyr BP Kara Sea glaciation reached the northern part of the ridge. The exposure dates do not show conclusive evidence regarding the existence of a Timan Ridge ice cap.
Optically Stimulated Luminescence (OSL) dating of glacial sediments from Arctic Russia ‐ depositional bleaching and methodological aspects
Authors: THOMAS PUTHUSSERRY J. , MURRAY ANDREW S. , KJæR KURT H. , FUNDER SVEND , LARSEN EILIV
Published: July 2006

Optical dating has been extensively used for stratigraphical correlation in the reconstruction of Eurasian ice‐sheet dynamics and palaeoenvironmental changes during the last glaciation. In recent terrestrial studies in Arctic Russia, Optically Stimulated Luminescence (OSL) is the main chronological tool, and has been used across the whole of the Eurasian north. We report new OSL ages obtained on glaciofluvial and glaciolacustrine sediments from the Arkhangelsk and Taymyr regions of Arctic Russia and discuss the characteristics of the quartz OSL signal in terms of its saturation limit, variability among samples from the same location, and initial signal resetting in different depositional environments. It is shown that effect of partial bleaching in our mainly Weichselian samples is trivial because: modern analogues are well zeroed; there is good agreement between OSL and 14C ages in young samples; and skewness in the dose distribution of relatively older samples is mainly due to varying shapes of the growth curves. The overall reliability of the OSL ages from Arctic Russia, when compared with the limited independent age controls available, appears to be good.
Are we there yet? Teachers, schools and electronic networks
Authors: Carmichael Patrick , Procter Richard
Published: July 2006

The ‘Learning How to Learn’ project of the ESRC Teaching and Learning Research Programme engaged teachers from primary and secondary schools in the UK in development and research of practice related to ‘assessment for learning’ between 2001 and 2005. As part of the project, we were concerned to discover what factors encouraged the development and sharing of practice within and between schools, including the use of electronic networking. A range of data about the use of electronic networks, tools and resources was collected through: a survey of over 250 teachers; an audit of participating schools' IT infrastructures and available resources; semi‐structured interviews; and a novel ‘network mapping’ task. We discovered that while use of IT is now a well‐established element of classroom practice, teachers made less use of electronic networks to develop their professional practice, even when their schools were part of networks designed to support them in so doing. Despite a range of barriers to the development of IT in teachers' practice, the overall impression presented by the data is one of optimism as to what new technologies can offer and a sense that while the journey may be onerous the benefits will make it all worth while.
Determinants of daily smoking in Estonia, Latvia, Lithuania, and Finland in 1994—2002
Authors: Helasoja Ville V. , Lahelma Eero , Prättälä Ritva S. , Patja Kristna M. , Klumbiene Jurate , Pudule Iveta , Kasmel Anu
Published: July 2006

Aims: To investigate time trends in the smoking prevalence and the sociodemographic and psychosocial background of smoking in the Baltic countries in comparison with Finland during 1994—2002. Methods: Differences in daily smoking according to age, education, urbanization, and psychological distress in the Baltic countries and Finland were studied using postal surveys in 1994, 1996, 1998, 2000, and 2002 among adults (20—64 years old) in Estonia (n=6,271), Latvia (n=6,106), Lithuania (n=9,824), and Finland (n=15,764). Results: In 1994, 1996, 1998, 2000, and 2002 the prevalence of smoking in Estonia, Latvia, Lithuania, and Finland was 47%, 54%, 46%, and 29% among men, and 21%, 19%, 11%, and 19% among women, respectively. Smoking increased among Lithuanian women from 6% in 1994 to 13% in 2002, but decreased among Estonian men and women. Smoking was generally more common among younger individuals, the less educated, and people with distress in all four countries. The odds ratios for smoking for those with low education compared with those with high education were 2.18 (1.69—2.81), 3.32 (2.55—4.31), 2.20 (1.79—2.70) and 2.80 (2.40—3.27) in men, and 1.90 (1.42—2.52). 3.09 (2.28—4.18), 0.86 (0.59—1.26), and 3.00 (2.53—3.55) in women, in Estonia, Latvia, Lithuania, and Finland, respectively. There were indications of increasing educational differences in Latvian men. Smoking was less common among rural women in all countries except Estonia. Conclusions: Estonia, Latvia, and Finland show characteristics of the ``mature'' phase of a smoking epidemic, and smoking may not increase in these countries. In Lithuanian women smoking may increase. Smoking may be increasingly unequally distributed in the future in all the studied countries.
A Shift of Phloem Unloading from Symplasmic to Apoplasmic Pathway Is Involved in Developmental Onset of Ripening in Grape Berry
Authors: Zhang Xiao-Yan , Wang Xiu-Ling , Wang Xiao-Fang , Xia Guo-Hai , Pan Qiu-Hong , Fan Ren-Chun , Wu Fu-Qing , Yu Xiang-Chun , Zhang Da-Peng
Published: July 2006

It remains unclear whether the phloem unloading pathway alters to adapt to developmental transition in fleshy fruits that accumulate high level of soluble sugars. Using a combination of electron microscopy, transport of the phloem-mobile symplasmic tracer carboxyfluorescein, movement of the companion cell-expressed and the green fluorescent protein-tagged viral movement protein, and assays of the sucrose cleavage enzymes, the pathway of phloem unloading was studied in the berries of a hybrid grape (Vitis vinifera × Vitis labrusca). Structural investigations showed that the sieve element-companion cell complex is apparently symplasmically connected through plasmodesmata with surrounding parenchyma cells throughout fruit development, though a small portion of plasmodesmata are apparently blocked in the ripening stage. Both carboxyfluorescein and the green fluorescent protein-tagged viral movement protein were released from the functional phloem strands during the early and middle stages of fruit development, whereas the two symplasmic tracers were confined to the phloem strands during the late stage. This reveals a shift of phloem unloading from symplasmic to apoplasmic pathway during fruit development. The turning point of the phloem unloading pathways was further shown to be at or just before onset of ripening, an important developmental checkpoint of grape berry. In addition, the levels of both the expression and activities of cell wall acid invertase increased around the onset of ripening and reached a high level in the late stage, providing further evidence for an operation of the apoplasmic unloading pathway after onset of ripening. These data demonstrate clearly the occurrence of an adaptive shift of phloem unloading pathway to developmental transition from growing phase to ripening in grape berry.
Genomic Organization, Differential Expression, and Interaction of SQUAMOSA Promoter-Binding-Like Transcription Factors and microRNA156 in Rice
Authors: Xie Kabin , Wu Congqing , Xiong Lizhong
Published: July 2006

Transcription factors play essential roles in the developmental processes of plants. Many such factors are regulated by microRNAs (miRNAs). SQUAMOSA (SQUA) promoter-binding-like (SPL) genes encode plant-specific transcription factors, some of which contain complementary sequences of miRNA156. In this study, 19 rice (Oryza sativa) SPL (OsSPL) genes and 12 rice miRNA156 (OsmiR156) precursors were identified in the rice genome. Sequence and experimental analysis suggested that 11 OsSPL genes were putative targets of OsmiR156. Plant SPL proteins were classified into six subgroups based on the phylogenetic analysis of SQUA promoter-binding protein domain. Diverse exon-intron structures and distinct organizations of putative motifs beyond the SQUA promoter-binding protein domains were identified in the OsSPL gene family. Transcript level analysis of OsSPL genes in various rice tissues and organs revealed different tempospatial expression patterns. More than half of the OsSPL genes including most OsmiR156-targeted genes are predominantly expressed in the young panicles, whereas OsmiR156 genes are predominantly expressed in the young shoots and leaves of rice. Overexpression of two OsmiR156 genes (OsmiR156b and OsmiR156h) in rice resulted in severe dwarfism, strongly reduced panicle size, and delayed flowering, suggesting that OsmiR156 and OsSPL target genes are involved in various developmental processes, especially the flower development of rice. Different patterns of transcript changes (decreased or unchanged) of different target genes in same tissue and of same target gene in different tissues detected in the OsmiR156-overexpressing plants suggested diverse interactions between OsmiR156 and OsSPL target genes in a tissue-specific manner.
Posttranscriptional Induction of Two Cu/Zn Superoxide Dismutase Genes in Arabidopsis Is Mediated by Downregulation of miR398 and Important for Oxidative Stress Tolerance
Authors: Sunkar Ramanjulu , Kapoor Avnish , Zhu Jian-Kang
Published: July 2006

MicroRNAs (miRNAs) are a class of regulatory RNAs of ∼21 nucleotides that posttranscriptionally regulate gene expression by directing mRNA cleavage or translational inhibition. Increasing evidence points to a potential role of miRNAs in diverse physiological processes. miR398 targets two closely related Cu/Zn superoxide dismutases (cytosolic CSD1 and chloroplastic CSD2) that can detoxify superoxide radicals. CSD1 and CSD2 transcripts are induced in response to oxidative stress, but the regulatory mechanism of the induction is unknown. Here, we show that miR398 expression is downregulated transcriptionally by oxidative stresses, and this downregulation is important for posttranscriptional CSD1 and CSD2 mRNA accumulation and oxidative stress tolerance. We also provide evidence for an important role of miR398 in specifying the spatial and temporal expression patterns of CSD1 and CSD2 mRNAs. Our results suggest that CSD1 and CSD2 expression is fine-tuned by miR398-directed mRNA cleavage. Additionally, we show that transgenic Arabidopsis thaliana plants overexpressing a miR398-resistant form of CSD2 accumulate more CSD2 mRNA than plants overexpressing a regular CSD2 and are consequently much more tolerant to high light, heavy metals, and other oxidative stresses. Thus, relieving miR398-guided suppression of CSD2 in transgenic plants is an effective new approach to improving plant productivity under oxidative stress conditions.
The role of regulatory T cells in alloantigen tolerance
Authors: Aluvihare Varuna R. , Betz Alexander G.
Published: July 2006

Summary:  The diversification mechanism used by the adaptive immune system to maximize the recognition of foreign antigens has the side effect of generating autoreactivity. This effect is counteracted by deletion of cells expressing receptors with high affinity to self (central tolerance) and suppression of autoreactive cells by regulatory T cells (Tregs; peripheral tolerance). This understanding led to the notion that Tregs represent a specialized subset of autoreactive T cells with inhibitory function. The process of generating a diverse repertoire of receptors recognizing antigen presented by major histocompatibility complex (MHC) intrinsically leads to the generation of cells recognizing foreign MHC (alloantigen). The precursor frequency of T cells responding to alloantigen is substantially higher than that responding to any exogenous antigen. The only physiological context in which this becomes a problem is placental viviparity. Although the maternal immune system has no intrinsic mechanism to distinguish between a pathogen and paternally derived fetal alloantigen, it has to neutralize the former and tolerate the latter. We review the function of Tregs from this perspective and propose that they may have evolved to promote tolerance to alloantigen in the context of pregnancy.