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  • 1
    Electronic Resource
    Electronic Resource
    Molecular characterization of hpuAB, the haemoglobin–haptoglobin-utilization operon of Neisseria meningitidis (1997)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 23 (1997), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: We previously identified HpuB, an 85 kDa Fe-repressible protein required for utilization of Fe from, and binding to, haemoglobin and the haemoglobin–haptoglobin complex. The gene for hpuB was cloned from Neisseria meningitidis strain DNM2 and the predicted amino acid sequence indicates that HpuB is an outer membrane receptor belonging to the TonB family of high-affinity transport proteins. A second open reading frame, predicted to encode a 34.8 kDa lipoprotein, was discovered 5′ to hpuB, and was designated hpuA. HpuA was identified in a total-membrane-protein preparation by construction of a mutant lacking HpuA. Acylation of HpuA was confirmed by [3H]-palmitic acid labelling of meningococci. Consensus promoter sequences were not apparent 5′ to hpuB. The hpuA insertion mutation exerted a polar effect, abolishing expression of hpuB, suggesting that hpuA and hpuB are co-transcribed. The 3.5 kb polycistronic hpuAB mRNA was identified and shown to be transcriptionally repressed by iron. The transcriptional start site was identified 33 nucleotides 5′ to the hpuA translational start site, appropriately positioned around consensus promoter and ferric uptake regulator (Fur)-box sequences. The structure of this operon suggests that HpuA–HpuB is a two-component receptor analogous to the bipartite transferrin receptor TbpB–TbpA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1997.2501619.x
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  • 2
    Electronic Resource
    Electronic Resource
    Parameter estimation in surface exchange models using nonlinear inversion: how many parameters can we estimate and which measurements are most useful? (2001)
    Oxford, UK : Blackwell Science Ltd
    Global change biology 7 (2001), S. 0 
    Details
    ISSN: 1365-2486
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Notes: Models of mass and energy exchanges between the biosphere and the atmosphere generally contain a nonlinear dependence between fluxes and model parameters, and thus estimation of these parameters from measurements in a heterogeneous landscape depends on the scale of the observations. The scale-dependence of a typical surface-exchange model (the CSIRO Biospheric Model, CBM) is examined using the diurnal variation of hourly fluxes of CO2, latent heat, sensible heat and soil heat. The fluxes were measured using micrometeorological techniques over six sites in a grazing/pasture system in SE Australia during a period of three weeks in 1995. Nonlinear parameter inversion was used to determine model parameters.Analysis of the covariance of the estimates of the parameters and the unexplained residuals of the model showed that a maximum of three or four parameters could be determined independently from the observations for all six sites. Estimates of a key model parameter, jmax, the mean of maximum potential electron transport rate of all leaves within the canopy, was best determined by the measurements of net CO2 flux at all sites examined. Measurements of ground heat flux provide little information about any of the model parameters in CBM.Because of nonlinearities in the surface exchange model, calculated fluxes will be in error if parameters for the component vegetation types are simply averaged in proportion to their areal fraction. The magnitude of these errors was examined for CBM using a hypothetical land surface consisting of two surface types, each with different parameter values. Predictions of net CO2, latent heat and ground heat fluxes using a linear combination of model parameters for the two surface types were quite similar with those found using optimal estimates of the parameters for the landscape, but were significantly poorer for sensible heat fluxes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2486.2001.00434.x
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  • 3
    Electronic Resource
    Electronic Resource
    A conserved region in the σ54-dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation (1997)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 26 (1997), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Rhizobium melioti DctD activates transcription from the dctA promoter by catalysing the isomerization of closed complexes between σ54-RNA polymerase holoenzyme and the promoter to open complexes. DctD must make productive contact with σ54-holoenzyme and hydrolyse ATP to catalyse this isomerization. To define further the activation process, we sought to isolate mutants of DctD that had reduced affinities for σ54-holoenzyme. Mutagenesis was confined to the well-conserved C3 region of the protein, which is required for coupling ATP hydrolysis to open complex formation in σ54-dependent activators. Mutant forms of DctD that failed to activate transcription and had substitutions in the C-terminal half of the C3 region were efficiently cross-linked to σ54 and the β-subunit of RNA polymerase, suggesting that they bound normally to σ54-holoenzyme. In contrast, some mutant forms of DctD with amino acid substitutions in the N-terminal half of the C3 region had reduced affinities for σ54 and the β-subunit in the cross-linking assay. These data suggest that the N-terminal half of the C3 region of DctD contains a site that may contact σ54-holoenzyme during open complex formation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1997.5851955.x
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  • 4
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    Transient dynamics of terrestrial carbon storage: mathematical foundation and its applications (2017)
    Copernicus
    Details
    Publication Date: 2017-01-12
    Description: Terrestrial ecosystems have absorbed roughly 30 % of anthropogenic CO2 emissions over the past decades, but it is unclear whether this carbon (C) sink will endure into the future. Despite extensive modeling and experimental and observational studies, what fundamentally determines transient dynamics of terrestrial C storage under global change is still not very clear. Here we develop a new framework for understanding transient dynamics of terrestrial C storage through mathematical analysis and numerical experiments. Our analysis indicates that the ultimate force driving ecosystem C storage change is the C storage capacity, which is jointly determined by ecosystem C input (e.g., net primary production, NPP) and residence time. Since both C input and residence time vary with time, the C storage capacity is time-dependent and acts as a moving attractor that actual C storage chases. The rate of change in C storage is proportional to the C storage potential, which is the difference between the current storage and the storage capacity. The C storage capacity represents instantaneous responses of the land C cycle to external forcing, whereas the C storage potential represents the internal capability of the land C cycle to influence the C change trajectory in the next time step. The influence happens through redistribution of net C pool changes in a network of pools with different residence times. Moreover, this and our other studies have demonstrated that one matrix equation can replicate simulations of most land C cycle models (i.e., physical emulators). As a result, simulation outputs of those models can be placed into a three-dimensional (3-D) parameter space to measure their differences. The latter can be decomposed into traceable components to track the origins of model uncertainty. In addition, the physical emulators make data assimilation computationally feasible so that both C flux- and pool-related datasets can be used to better constrain model predictions of land C sequestration. Overall, this new mathematical framework offers new approaches to understanding, evaluating, diagnosing, and improving land C cycle models.
    Print ISSN: 1726-4170
    Electronic ISSN: 1726-4189
    Topics: Biology , Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 5
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    Transient Dynamics of Terrestrial Carbon Storage: Mathematical foundation and Numeric Examples (2016)
    Copernicus
    Details
    Publication Date: 2016-09-16
    Description: Terrestrial ecosystems absorb roughly 30 % of anthropogenic CO2 emissions since preindustrial era, but it is unclear whether this carbon (C) sink will endure into the future. Despite extensive modeling, experimental, and observational studies, what fundamentally determines transient dynamics of terrestrial C storage under climate change is still not very clear. Here we develop a new framework for understanding transient dynamics of terrestrial C storage through mathematical analysis and numerical experiments. Our analysis indicates that the ultimate force driving ecosystem C storage change is the C storage capacity, which is jointly determined by ecosystem C input (e.g., net primary production, NPP) and residence time. Since both C input and residence time vary with time, the C storage capacity is time-dependent and acts as a moving attractor that actual C storage chases. The rate of change in C storage is proportional to the C storage potential, the difference between the current storage and the storage capacity. The C storage capacity represents instantaneous responses of the land C cycle to external forcing, whereas the C storage potential represents the internal capability of the land C cycle to influence the C change trajectory in the next time step. The influence happens through redistribution of net C pool changes in a network of pools with different residence times. Moreover, this and our other studies have demonstrated that one matrix equation can exactly replicate simulations of most land C cycle models (i.e., physical emulators). As a result, simulation outputs of those models can be placed into a three-dimensional (3D) parameter space to measure their differences. The latter can be decomposed into traceable components to track the origins of model uncertainty. Moreover, the emulators make data assimilation computationally feasible so that both C flux- and pool-related datasets can be used to better constrain model predictions of land C sequestration. We also propose that the C storage potential be the targeted variable for research, market trading, and government negotiation for C credits.
    Print ISSN: 1810-6277
    Electronic ISSN: 1810-6285
    Topics: Biology , Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 6
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    Contribution of hydroxymethanesulfonate (HMS) to severe winter haze in the North China Plain (2020)
    Copernicus
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    Publication Date: 2020-05-18
    Description: Severe winter haze accompanied by high concentrations of fine particulate matter (PM2.5) occurs frequently in the North China Plain and threatens public health. Organic matter (OM) and sulfate are recognized as major components of PM2.5, while atmospheric models often fail to predict their high concentrations during severe winter haze due to incomplete understanding of secondary aerosol formation mechanisms. By using a novel combination of single-particle mass spectrometry and an optimized ion chromatography method, here we show that hydroxymethanesulfonate (HMS), formed by the reaction between formaldehyde (HCHO) and dissolved SO2 in aerosol water, is ubiquitous in Beijing during winter. The HMS concentration and the molar ratio of HMS to sulfate increased with the deterioration of winter haze. High concentrations of precursors (SO2 and HCHO) coupled with low oxidant levels, low temperature, high relative humidity, and moderately acidic pH facilitate the heterogeneous formation of HMS, which could account for up to 15 % of OM in winter haze and lead to up to 36 % overestimates of sulfate when using traditional ion chromatography. Despite the clean air actions having substantially reduced SO2 emissions, the HMS concentration and molar ratio of HMS to sulfate during severe winter haze increased from 2015 to 2016 with the growth in HCHO concentration. Our findings illustrate the significant contribution of heterogeneous HMS chemistry to severe winter haze in Beijing, which helps to improve the prediction of OM and sulfate and suggests that the reduction in HCHO can help to mitigate haze pollution.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 7
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    Possible heterogeneous chemistry of hydroxymethanesulfonate (HMS) in northern China winter haze (2019)
    Copernicus
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    Publication Date: 2019-02-01
    Description: The chemical mechanisms responsible for rapid sulfate production, an important driver of winter haze formation in northern China, remain unclear. Here, we propose a potentially important heterogeneous hydroxymethanesulfonate (HMS) chemical mechanism. Through analyzing field measurements with aerosol mass spectrometry, we show evidence for a possible significant existence in haze aerosols of organosulfur primarily as HMS, misidentified as sulfate in previous observations. We estimate that HMS can account for up to about one-third of the sulfate concentrations unexplained by current air quality models. Heterogeneous production of HMS by SO2 and formaldehyde is favored under northern China winter haze conditions due to high aerosol water content, moderately acidic pH values, high gaseous precursor levels, and low temperature. These analyses identify an unappreciated importance of formaldehyde in secondary aerosol formation and call for more research on sources and on the chemistry of formaldehyde in northern China winter.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 8
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    Lower tropospheric distributions of O3 and aerosol over Raoyang, a rural site in the North China Plain (2017)
    Copernicus
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    Publication Date: 2017-03-21
    Description: The North China Plain (NCP) has become one of the most polluted regions in China, with the rapidly increasing economic growth in the past decades. High concentrations of ambient O3 and aerosol have been observed at urban as well as rural sites in the NCP. Most of the in situ observations of air pollutants have been conducted near the ground so that current knowledge about the vertical distributions of tropospheric O3 and aerosol over the NCP region is still limited. In this study, vertical profiles of O3 and size-resolved aerosol concentrations below 2.5 km were measured in summer 2014 over a rural site in the NCP, using an unmanned aerial vehicle (UAV) equipped with miniature analyzers. In addition, vertical profiles of aerosol scattering property in the lower troposphere and vertical profiles of O3 below 1 km were also observed at the site using a lidar and tethered balloon, respectively. The depths of the mixed layer and residual layer were determined according to the vertical gradients of lidar particle extinction and aerosol number concentration. Average O3 and size-resolved aerosol number concentration in both the mixed and residual layer were obtained from the data observed in seven UAV flights. The results show that during most of the flights the O3 levels above the top of mixed layer were higher than those below. Such a positive gradient in the vertical distribution of O3 makes the residual layer an important source of O3 in the mixed layer, particularly during the morning when the top of mixed layer is rapidly elevated. In contrast to O3, aerosol number concentration was normally higher in the mixed layer than in the residual layer, particularly in the early morning. Aerosol particles were overwhelmingly distributed in the size range  
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 9
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    First simultaneous measurements of peroxyacetyl nitrate (PAN) and ozone at Nam Co in the central Tibetan Plateau: impacts from the PBL evolution and transport processes (2018)
    Copernicus
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    Publication Date: 2018-04-17
    Description: Both peroxyacetyl nitrate (PAN) and ozone (O3) are key photochemical products in the atmosphere. Most of the previous in situ observations of both gases have been made in polluted regions and at low-altitude sites. Here we present the first simultaneous measurements of PAN and O3 at Nam Co (NMC; 30°46′ N, 90°57′ E, 4745 m a.s.l.), a remote site in the central Tibetan Plateau (TP). The observations were made during summer periods in 2011 and 2012. The PAN levels averaged 0.36 ppb (range: 0.11–0.76 ppb) and 0.44 ppb (range: 0.21–0.99 ppb) during 17–24 August 2011 and 15 May to 13 July 2012, respectively. The O3 level varied from 27.9 to 96.4 ppb, with an average of 60.0 ppb. Profound diurnal cycles of PAN and O3 were observed with minimum values around 05:00 LT, steep rises in the early morning, and broader platforms of high values during 09:00–20:00 LT. The evolution of the planetary boundary layer (PBL) played a key role in shaping the diurnal patterns of both gases, particularly the rapid increases of PAN and O3 in the early morning. Air entrainment from the free troposphere into the PBL seemed to cause the early-morning increase and be a key factor for sustaining the daytime high concentrations of both gases. The days with higher daytime PBL (about 3 km) showed stronger diurnal variations in both gases and were mainly distributed in the drier pre-monsoon period, while those with shallower daytime PBL (about 2 km) showed minor diurnal variations and were mainly distributed in the humid monsoon period. Episodes of higher PAN levels were occasionally observed at NMC. These PAN episodes were caused either by rapid downward transport of air masses from the middle/upper troposphere or by long-range transport of PAN plumes from north India, north Pakistan, and Nepal. The maximum PAN level in the downward transport cases ranged from 0.5 to 0.7 ppb. In the long-range transport case, the PAN level varied in the range of 0.3–1.0 ppb, with an average of 0.6 ppb. This long-range transport process influenced most of the western and central TP region for about a week in early June 2012. Our results suggest that polluted air masses from South Asia can significantly enhance the PAN level over the TP. As PAN acts as a reservoir of NOx, the impacts of pollution transport from South Asia on tropospheric photochemistry over the TP region deserve further studies.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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  • 10
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    Role of ambient ammonia in particulate ammonium formation at a rural site in the North China Plain (2018)
    Copernicus
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    Publication Date: 2018-01-08
    Description: The real-time measurements of NH3 and trace gases were conducted, in conjunction with semi-continuous measurements of water-soluble ions in PM2.5 at a rural site in the North China Plain (NCP) from May to September 2013 in order to better understand chemical characteristics of ammonia and the impact of secondary ammonium aerosols on formation in the NCP. Extremely high NH3 and NH4+ concentrations were observed after a precipitation event within 7–10 days following urea application. Elevated NH3 levels coincided with elevated NH4+, indicating that NH3 likely influenced particulate ammonium mass. For the sampling period, the average conversion ∕ oxidation ratios for NH4+ (NHR), SO42- (SOR), and NO3- (NOR) were estimated to be 0.30, 0.64, and 0.24, respectively. The increased NH3 concentrations, mainly from agricultural activities and regional transport, coincided with the prevailing meteorological conditions. The high NH3 level with NHR of about 0.30 indicates that the emission of NH3 in the NCP is much higher than needed for aerosol acid neutralisation, and NH3 plays an important role in the formation of secondary aerosols as a key neutraliser. The hourly data obtained were used to investigate gas–aerosol partitioning characteristics using the thermodynamic equilibrium model ISORROPIA-II. Modelled SO42-, NO3-, and NH3 values agree well with the measurements, while the modelled NH4+ values largely underestimate the measurements. Our observation and modelling results indicate that strong acids in aerosol are completely neutralised. Additional NH4+ exists in aerosol, probably a result of the presence of a substantial amount of oxalic and other diacids.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
    Topics: Geosciences
    Published by Copernicus on behalf of European Geosciences Union.
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