When exposed to low temperatures, plants undergo a drastic reprogramming of their transcriptome in order to adapt to their new environmental conditions, which primes them for potential freezing temperatures. While the involvement of transcription factors in this process, termed cold acclimation, has been deeply investigated, the potential contribution of chromatin regulation remains largely unclear. A large proportion of cold-inducible genes carries the repressive mark histone 3 lysine 27 trimethylation (H3K27me3), which has been hypothesized as maintaining them in a silenced state in the absence of stress, but which would need to be removed or counteracted upon stress perception. However, the fate of H3K27me3 during cold exposure has not been studied genome-wide. In this study, we offer an epigenome profiling of H3K27me3 and its antagonistic active mark H3K4me3 during short-term cold exposure. Both chromatin marks undergo rapid redistribution upon cold exposure, however, the gene sets undergoing H3K4me3 or H3K27me3 differential methylation are distinct, refuting the simplistic idea that gene activation relies on a switch from an H3K27me3 repressed chromatin to an active form enriched in H3K4me3. Coupling the ChIP-seq experiments with transcriptome profiling reveals that differential histone methylation only weakly correlates with changes in expression. Interestingly, only a subset of cold-regulated genes lose H3K27me3 during their induction, indicating that H3K27me3 is not an obstacle to transcriptional activation. In the H3K27me3 methyltransferase curly leaf (clf) mutant, many cold regulated genes display reduced H3K27me3 levels but their transcriptional activity is not altered prior or during a cold exposure, suggesting that H3K27me3 may serve a more intricate role in the cold response than simply repressing the cold-inducible genes in naïve conditions.
View lessSalt structures and their surroundings can play an important role in the energy transition related to a number of storage and energy applications. Thus, it is important to assess the current and future stability of salt bodies in their specific geological settings. We investigate the influence of ice sheet loading and unloading on subsurface salt structures using physical models based on the geological setting of northern Germany, which was repeatedly glaciated by the Scandinavian Ice Sheet during the Pleistocene. Apparent spatial correlations between subsurface salt structures in northern Germany and Weichselian ice marginal positions have been observed before, and the topic is a matter of ongoing debate. Recently described geomorphological features – termed surface cracks – have been interpreted as a direct result of ice-sheet-induced salt movement resulting in surface expansion. The spatial clustering and orientation of these surface cracks has not been well understood so far, owing to only a limited number of available studies dealing with the related salt tectonic processes. Thus, we use four increasingly complex physical models to test the basic loading and unloading principle, to analyze flow patterns within the salt source layer and within salt structures, and to examine the influence of the shape and orientation of the salt structures with respect to a lobate ice margin in a three-dimensional laboratory environment. Three salt structures of the northern German basin were selected as examples that were replicated in the laboratory. Salt structures were initially grown by differential loading and buried before loading. The ice load was simulated by a weight that was temporarily placed on a portion of the surface of the models. The replicated salt structures were either completely covered by the load, partly covered by the load, or situated outside the load extent. In all scenarios, a dynamic response of the system to the load could be observed; while the load was applied, the structures outside the load margin started to rise, with a decreasing tendency with distance from the load margin, and, at the same time, the structures under the load subsided. After the load was removed, a flow reversal set in, and previously loaded structures started to rise, whereas the structures outside the former load margin began to subside. The vertical displacements during the unloading stage were not as strong as during the load stage, and thus the system did not return to its pre-glaciation status. Modeled salt domes that were located at distance from the load margin showed a comparably weak reaction. A more extreme response was shown by modeled salt pillows whose margins varied from sub-parallel to sub-perpendicular to the load margin and were partly covered by the load. Under these conditions, the structures showed a strong reaction in terms of strain and vertical displacement. The observed strain patterns at the surface were influenced by the shape of the load margin and the shape of the salt structure at depth, resulting in complex deformation patterns. These physical modeling results provide more evidence for a possible interplay between ice sheets and subsurface salt structures, highlighting the significance of three-dimensional effects in dynamic geological settings. Our results lead to a better understanding of spatial patterns of the surface cracks that were mapped at the surface above salt structures and offer further room for interpretation of the influence of salt movements on the present-day landscape.
View lessThe Multi-Spectral Imager (MSI) on board the Earth Cloud, Aerosol and Radiation Explorer (EarthCARE) will provide horizontal information about aerosols and clouds. These measurements are needed to extend vertical cloud and aerosol property information, which is obtained from EarthCARE's active sensors, in order to obtain a full three-dimensional view of cloud and aerosol conditions. Mesoscale weather systems, in particular, will be characterized. The discovery of a non-compliance of the MSI visible–near-infrared–shortwave infrared (VNS) camera’s visible (VIS) and shortwave infrared (SWIR1) channels regarding a spectral central wavelength (CWVL) shift across-track of up to 14 nm (VIS) and 20 nm (SWIR1) led to the need for an analysis regarding its impact on MSI Level-2A aerosol and cloud products. A significant influence of the spectral misalignment effect (SMILE) on MSI retrievals is identified due to the spectral variation in gas absorption, surface reflectance, and aerosol and cloud properties within the spectral ranges of these MSI bands. For example, the VIS channel is positioned in close proximity to the red edge of green vegetation and is impacted by residual absorption of water vapor and ozone. Small central wavelength variations introduce uncertainties due to the rapid change in surface reflectance for conditions with low optical thickness. The present central wavelength shift in the VIS towards shorter wavelengths than at nadir introduces a relative error in transmission of up to 3.3 % due to the increasing influence of water vapor and ozone absorption. We found relative errors in the top-of-atmosphere (TOA) signal due to the SMILE of up to 30 % for low optical thickness over a land surface in that band. Since the magnitude of the impact strongly depends on the underlying surface and atmospheric conditions, we conclude that accounting for the SMILE in Level-2 retrievals or correcting the Level-1 signal will improve MSI aerosol and cloud product quality.
View lessAnnual maxima of daily precipitation sums can be typically described well with a stationary generalized extreme value (GEV) distribution. In many regions of the world, such a description does also work well for monthly maxima for a given month of the year. However, the description of seasonal and interannual variations requires the use of non-stationary models. Therefore, in this paper we propose a non-stationary modeling strategy applied to long time series from rain gauges in Germany. Seasonal variations in the GEV parameters are modeled with a series of harmonic functions and interannual variations with higher-order orthogonal polynomials. By including interactions between the terms, we allow for the seasonal cycle to change with time. Frequently, the shape parameter ξ of the GEV is estimated as a constant value also in otherwise instationary models. Here, we allow for seasonal–interannual variations and find that this is beneficial. A suitable model for each time series is selected with a stepwise forward regression method using the Bayesian information criterion (BIC). A cross-validated verification with the quantile skill score (QSS) and its decomposition reveals a performance gain of seasonally–interannually varying return levels with respect to a model allowing for seasonal variations only. Some evidence can be found that the impact of climate change on extreme precipitation in Germany can be detected, whereas changes are regionally very different. In general, an increase in return levels is more prevalent than a decrease. The median of the extreme precipitation distribution (2-year return level) generally increases during spring and autumn and is shifted to later times in the year; heavy precipitation (100-year return level) rises mainly in summer and occurs earlier in the year.
View lessThe radiative effects of biomass burning aerosols (BBAs) on low-level atmospheric circulation over southern Africa are investigated on 5 September 2017 during the Aerosols, Radiation and Clouds in southern Africa (AEROCLO-sA) field campaign. This is conducted using a variety of in situ and remote sensing observations, as well as two 5 d ensemble simulations made with the Meso-NH mesoscale model, one including the direct and semi-direct radiative effects of aerosols and one in which these effects are not included. We show that the radiative impact of BBA building up over a period of 5 d in the Meso-NH simulations can lead to significantly different circulations at low and middle levels, thereby affecting dust emissions over southern Namibia and northwestern South Africa as well as the transport of BBA in a so-called “river of smoke”. While most of the regional-scale dynamics, thermodynamics and composition features are convincingly represented in the simulation with BBA radiative effects, neglecting the radiative impact of BBA leads to unrealistic representations of (i) the low-level jet (LLJ) over the plateau, which is the main low-level dynamic feature fostering dust emission, and (ii) the mid-level dynamics pertaining to the transport of BBA from the fire-prone regions in the tropics to the mid-latitudes. For instance, when the BBA radiative impacts are not included, the LLJ is too weak and not well established over night, and the developing convective planetary boundary layer (PBL) is too deep compared to observations. The deeper convective PBL over Etosha and surrounding areas is related to the enhanced anomalous upward motion caused by the eastern displacement of the river of smoke. This eastern displacement is, in turn, related to the weaker southerly African easterly jet. Both ensemble simulations provide clear evidence that the enhanced near-surface extinction coefficient values detected from observations over Etosha are related to the downward mixing of BBA in the developing convective boundary layer rather than dust being emitted as a result of the LLJ breakdown after sunrise. This study suggests that the radiative effect of BBAs needs to be taken into account to properly forecast dust emissions in Namibia.
View lessWe present a seismic catalog (Bindi et al., 2024, https://doi.org/10.5880/GFZ.2.6.2023.010) including energy magnitude Me estimated from P waves recorded at teleseismic distances in the range 20° ≤ Δ ≤ 98° and for depths shorter than 80 km. The catalog is built starting from the event catalog disseminated by GEOFON (GEOFOrschungsNetz), considering 6349 earthquakes with moment magnitude Mw≥5 occurring between 2011 and 2023. Magnitudes are computed using 1 031 396 freely available waveforms archived in EIDA (European Integrated Data Archive) and IRIS (Incorporated Research Institutions for Seismology) repositories, retrieved through the standard International Federation of Digital Seismograph Networks (FDSN) web services (https://www.fdsn.org/webservices/, last access: March 2024). A reduced, high-quality catalog for events with Mw≥5.8 and from which stations and events with only few recordings were removed forms the basis of a detailed analysis of the residuals of individual station measurements, which are decomposed into station- and event-specific terms and a term accounting for remaining variability. The derived Me values are compared to Mw computed by GEOFON and with the Me values calculated by IRIS. Software and tools developed for downloading and processing waveforms for bulk analysis and an add-on for SeisComP for real-time assessment of Me in a monitoring context are also provided alongside the catalog. The SeisComP add-on has been part of the GEOFON routine processing since December 2021 to compute and disseminate Me for major events via the existing services.
View lessThe width of fluvial valley floors is a key parameter to quantifying the morphology of mountain regions. Valley floor width is relevant to diverse fields including sedimentology, fluvial geomorphology, and archaeology. The width of valleys has been argued to depend on climatic and tectonic conditions, on the hydraulics and hydrology of the river channel that forms the valley, and on sediment supply from valley walls. Here, we derive a physically based model that can be used to predict valley width and test it against three different datasets. The model applies to valleys that are carved by a river migrating laterally across the valley floor. We conceptualize river migration as a Poisson process, in which the river changes its direction stochastically at a mean rate determined by hydraulic boundary conditions. This approach yields a characteristic timescale for the river to cross the valley floor from one wall to the other. The valley width can then be determined by integrating the speed of migration over this timescale. For a laterally unconfined river that is not uplifting, the model predicts that the channel-belt width scales with river flow depth. Channel-belt width corresponds to the maximum width of a fluvial valley. We expand the model to include the effects of uplift and lateral sediment supply from valley walls. Both of these effects lead to a decrease in valley width in comparison to the maximum width. We identify a dimensionless number, termed the mobility–uplift number, which is the ratio between the lateral mobility of the river channel and uplift rate. The model predicts two limits: at high values of the mobility–uplift number, the valley evolves to the channel-belt width, whereas it corresponds to the channel width at low values. Between these limits, valley width is linked to the mobility–uplift number by a logarithmic function. As a consequence of the model, valley width increases with increasing drainage area, with a scaling exponent that typically has a value between 0.4 and 0.5, but can also be lower or higher. We compare the model to three independent datasets of valleys in experimental and natural uplifting landscapes and show that it closely predicts the first-order relationship between valley width and the mobility–uplift number.
View lessMineral dust aerosols are composed of a complex assemblage of various minerals depending on the region in which they originated. Given the different mineral composition of desert dust aerosols, different physicochemical properties and therefore varying climate effects are expected.
Despite the known regional variations in mineral composition, chemical transport models typically assume that mineral dust aerosols have uniform composition. This study adds, for the first time, mineralogical information to the mineral dust emission scheme used in the chemical transport model COSMO–MUSCAT. We provide a detailed description of the implementation of the mineralogical database, GMINER (Nickovic et al., 2012), together with a specific set of physical parameterizations in the model's mineral dust emission module, which led to a general improvement of the model performance when comparing the simulated mineral dust aerosols with measurements over the Sahara region for January–February 2022.
The simulated mineral dust aerosol vertical distribution is tested by a comparison with aerosol lidar measurements from the lidar system PollyXT, located at Cape Verde. For a lofted mineral dust aerosol layer on 2 February at 05:00 UTC the lidar retrievals yield a dust mass concentration peak of 156 µg m−3, while the model calculates the mineral dust peak at 136 µg m−3. The results highlight the possibility of using the model with resolved mineral dust composition for interpretation of the lidar measurements since a higher absorption in the UV–Vis wavelengths is correlated with particles having a higher hematite content. Additionally, the comparison with in situ mineralogical measurements of dust aerosol particles shows that more of them are needed for model evaluation.
View lessThis paper presents the first investigation of the solubility of iron in mineral dust aerosols collected at the Henties Bay Aerosol Observatory (HBAO), in Namibia, from April to December 2017. During the study period, 10 intense dust events occurred. Elemental iron reached peak concentrations as high as 1.5 µg m−3, significantly higher than background levels. These events are attributed to wind erosion of natural soils from the surrounding gravel plains of the Namib desert. The composition of the sampled dust is found to be overall similar to that of aerosols from northern Africa but is characterized by persistent and high concentrations of fluorine which are attributed to local fugitive dust.
The fractional solubility of Fe (%SFe) for both the identified dust episodes and background conditions ranged between 1.3 % and 20 % and averaged at 7.9 % (±4.1 %) and 6.8 (±3.3 %), respectively. Even under background conditions, the %SFe was correlated with that of Al and Si. The solubility was lower between June and August and increased from September onwards during the austral spring. The relation to measured concentrations of particulate MSA (methane sulfonic acid), solar irradiance, and wind speed suggests a possible two-way interaction whereby marine biogenic emissions from the coastal Benguela upwelling to the atmosphere would increase the solubility of iron-bearing dust according to the photo-reduction processes. This first investigation points to the western coast of southern Africa as a complex environment with multiple processes and active exchanges between the atmosphere and the Atlantic Ocean, requiring further research.
View lessThe objective of the Earth Cloud, Aerosol, and Radiation Explorer (EarthCARE) mission is to infer attributes of cloud, aerosol, precipitation, and radiation from observations made by four complementary instruments. This requires the development of single-instrument and multiple-instrument (i.e. synergistic) retrieval algorithms that employ measurements made by one, or more, of EarthCARE's cloud-profiling radar (CPR), atmospheric lidar (ATLID), and multi-spectral imager (MSI); its broadband radiometer (BBR) places the retrieved quantities in the context of the surface–atmosphere radiation budget. To facilitate the development and evaluation of ESA's EarthCARE production model prior to launch, sophisticated instrument simulators were developed to produce realistic synthetic EarthCARE measurements for simulated conditions provided by cloud-resolving models. While acknowledging that the physical and radiative representations of cloud, aerosol, and precipitation in the test scenes are based on numerical models, the opportunity to perform detailed evaluations wherein the “truth” is known provides insights into the performance of EarthCARE's instruments and retrieval algorithms. This level of omniscience will not be available for the evaluation of in-flight EarthCARE retrieval products, even during validation activities coordinated with ground-based and airborne measurements. In this study, we compare EarthCARE retrieval products both statistically across all simulated scenes and from a specific time series from a single scene.
For ice clouds, it is shown that retrieved profiles of ice water content and effective particle size made by the ATLID-CPR-MSI cloud, aerosols, and precipitation (ACM-CAP) synergistic algorithm are consistently more accurate than those from its single-instrument counterparts. While liquid clouds are often difficult to detect from satellite-borne sensors, especially for multi-layered clouds, ACM-CAP benefits from combined constraints from lidar backscatter, solar radiances, and radar-path-integrated attenuation but still exhibits non-trivial random error. For precipitation retrievals, the CPR cloud and precipitation product (C-CLD) and ACM-CAP have a similar performance when well-constrained by CPR measurements. The greatest differences are in coverage, with ACM-CAP reporting retrievals in the melting layer, and in heavy precipitation, where CPR signals are dominated by multiple scattering and attenuation. Aerosol retrievals from ATLID compensate for a high degree of measurement noise in a number of ways, with the ATLID extinction, backscatter, and depolarisation (A-EBD) product and ACM-CAP demonstrating similar performance. The multi-spectral imager (MSI) cloud optical properties (M-COP) product performs very well for unambiguous cloud layers. Similarly, the MSI aerosol optical thickness (M-AOT) product performs well when radiances are unaffected by cloud, but both products provide little information about vertical profiles of properties. Finally, a summary of the performance of all retrieval products and their random errors is provided.
View lessThe Earth Cloud, Aerosol and Radiation Explorer (EarthCARE) is a combination of multiple active and passive instruments on a single platform. The Atmospheric Lidar (ATLID) provides vertical information of clouds and aerosol particles along the satellite track. In addition, the Multi-Spectral Imager (MSI) collects multi-spectral information from the visible to the infrared wavelengths over a swath width of 150 km across the track. The ATLID–MSI Column Products processor (AM-COL) described in this paper combines the high vertical resolution of the lidar along track and the horizontal resolution of the imager across track to better characterize a three-dimensional scene. ATLID Level 2a (L2a) data from the ATLID Layer Products processor (A-LAY), MSI L2a data from the MSI Cloud Products processor (M-CLD) and the MSI Aerosol Optical Thickness processor (M-AOT), and MSI Level 1c (L1c) data are used as input to produce the synergistic columnar products: the ATLID–MSI Cloud Top Height (AM-CTH) and the ATLID–MSI Aerosol Column Descriptor (AM-ACD). The coupling of ATLID (measuring at 355 nm) and MSI (at ≥670 nm) provides multi-spectral observations of the aerosol properties. In particular, the Ångström exponent from the spectral aerosol optical thickness (AOT 355/670 nm) adds valuable information for aerosol typing. The AOT across track, the Ångström exponent and the dominant aerosol type are stored in the AM-ACD product. The accurate detection of the cloud top height (CTH) with lidar is limited to the ATLID track. The difference in the CTH detected by ATLID and retrieved by MSI is calculated along track. The similarity of MSI pixels across track with those along track is used to transfer the calculated CTH difference to the entire MSI swath. In this way, the accuracy of the CTH is increased to achieve the EarthCARE mission's goal of deriving the radiative flux at the top of the atmosphere with an accuracy of 10 W m−2 for a 100 km2 snapshot view of the atmosphere. The synergistic CTH difference is stored in the AM-CTH product. The quality status is provided with the products. It depends, e.g., on day/night conditions and the presence of multiple cloud layers. The algorithm was successfully tested using the common EarthCARE test scenes. Two definitions of the CTH from the model truth cloud extinction fields are compared: an extinction-based threshold of 20 Mm−1 provides the geometric CTH, and a cloud optical thickness threshold of 0.25 describes the radiative CTH. The first CTH definition was detected with ATLID and the second one with MSI. The geometric CTH is always higher than or equal to the radiative CTH.
View lessMonolayers of transition metal dichalcogenides (TMDCs) are direct-gap semiconductors with strong light–matter interactions featuring tightly bound excitons, while plasmonic crystals (PCs), consisting of metal nanoparticles that act as meta-atoms, exhibit collective plasmon modes and allow one to tailor electric fields on the nanoscale. Recent experiments show that TMDC-PC hybrids can reach the strong-coupling limit between excitons and plasmons, forming new quasiparticles, so-called plexcitons. To describe this coupling theoretically, we develop a self-consistent Maxwell-Bloch theory for TMDC-PC hybrid structures, which allows us to compute the scattered light in the near- and far-fields explicitly and provide guidance for experimental studies. One of the key findings of the developed theory is the necessity to differentiate between bright and originally momentum-dark excitons. Our calculations reveal a spectral splitting signature of strong coupling of more than 100 meV in gold-MoSe2 structures with 30 nm nanoparticles, manifesting in a hybridization of the plasmon mode with momentum-dark excitons into two effective plexcitonic bands. The semianalytical theory allows us to directly infer the characteristic asymmetric line shape of the hybrid spectra in the strong coupling regime from the energy distribution of the momentum-dark excitons. In addition to the hybridized states, we find a remaining excitonic mode with significantly smaller coupling to the plasmonic near-field, emitting directly into the far-field. Thus, hybrid spectra in the strong coupling regime can contain three emission peaks.
View lessIn this study, we examine the surface-derived electronic and chemical structures of nanostructured GaRh alloys as a model system for supported catalytically active liquid metal solutions (SCALMS), a novel catalyst candidate for dehydrogenation reactions that are important for the petrochemical and hydrogen energy industry. It is reported that under ambient conditions, SCALMS tends to form a gallium oxide shell, which can be removed by an activation treatment at elevated temperatures and hydrogen flow to enhance the catalytic reactivity. We prepared a 7 at. % Rh containing the GaRh sample and interrogated the evolution of the surface chemical and electronic structure by photoelectron spectroscopy (complemented by scanning electron microscopy) upon performing surface oxidation and (activation treatment mimicking) annealing treatments in ultrahigh vacuum conditions. The initially pronounced Rh 4d and Fermi level-derived states in the valence band spectra disappear upon oxidation (due to formation of a GaOx shell) but reemerge upon annealing, especially for temperatures of 600 °C and above, i.e., when the GaOx shell is efficiently being removed and the Ga matrix is expected to be liquid. At the same temperature, new spectroscopic features at both the high and low binding energy sides of the Rh 3d5/2 spectra are observed, which we attribute to new GaRh species with depleted and enriched Rh contents, respectively. A liquefied and GaOx-free surface is also expected for GaRh SCALMS at reaction conditions, and thus the revealed high-temperature properties of the GaRh alloy provide insights about respective catalysts at work.
View lessChromium (Cr) leached from iron (Fe) (oxyhydr)oxide-rich tropical laterites can substantially impact downstream groundwater, ecosystems, and human health. However, its partitioning into mineral hosts, its binding, oxidation state, and potential release are poorly defined. This is in part due to the current lack of well-designed and validated Cr-specific sequential extraction procedures (SEPs) for laterites. To fill this gap, we have (i) first optimized a Cr SEP for Fe (oxyhydr)oxide-rich laterites using synthetic and natural Cr-bearing minerals and laterite references, (ii) used a complementary suite of techniques and critically evaluated existing non-laterite and non-Cr-optimized SEPs, compared to our optimized SEP, and (iii) confirmed the efficiency of our new SEP through analyses of laterites from the Philippines. Our results show that other SEPs inadequately leach Cr host phases and underestimate the Cr fractions. Our SEP recovered up to seven times higher Cr contents because it (a) more efficiently dissolves metal-substituted Fe phases, (b) quantitatively extracts adsorbed Cr, and (c) prevents overestimation of organic Cr in laterites. With this new SEP, we can estimate the mineral-specific Cr fractionation in Fe-rich tropical soils more quantitatively and thus improve our knowledge of the potential environmental impacts of Cr from lateritic areas.
View lessNaturally available, stable, and heavy water molecules such as HDO and HO have a lower saturation vapour pressure than the most abundant light water molecule HO; therefore, these heavy water molecules preferentially condense and rain out during cloud formation. Stable water isotope observations thus have the potential to provide information on cloud processes in the trade-wind region, in particular when combined with high-resolution model simulations. In order to evaluate this potential, nested COSMOiso (isotope-enabled Consortium for Small Scale Modelling; Steppeler et al., 2003; Pfahl et al., 2012) simulations with explicit convection and horizontal grid spacings of 10, 5, and 1 km were carried out in this study over the tropical Atlantic for the time period of the EUREC4A (Elucidating the role of clouds-circulation coupling in climate; Stevens et al., 2021) field experiment. The comparison to airborne in situ and remote sensing observations shows that the three simulations are able to distinguish between different mesoscale cloud organisation patterns as well as between periods with comparatively high and low rain rates. Cloud fraction and liquid water content show a better agreement with aircraft observations with higher spatial resolution, because they show strong spatial variations on the scale of a few kilometres. A low-level cold-dry bias, including too depleted vapour in the subcloud and cloud layer and too enriched vapour in the free troposphere, is found in all three simulations. Furthermore, the simulated secondary isotope variable d-excess in vapour is overestimated compared to observations. Special attention is given to the cloud base level, which is the formation altitude of shallow cumulus clouds. The temporal variability of the simulated isotope variables at cloud base agrees reasonably well with observations, with correlations of the flight-to-flight data as high as 0.7 for δ2H and d-excess. A close examination of isotopic characteristics under precipitating clouds, non-precipitating clouds, clear-sky and dry-warm patches at the altitude of cloud base shows that these different environments are represented faithfully in the model with similar frequencies of occurrence, isotope signals, and specific-humidity anomalies as found in the observations. Furthermore, it is shown that the δ2H of cloud base vapour at the hourly timescale is mainly controlled by mesoscale transport and not by local microphysical processes, while the d-excess is mainly controlled by large-scale drivers. Overall, this evaluation of COSMOiso, including the isotopic characterisation of different cloud base environments, suggests that the simulations can be used for investigating the role of atmospheric circulations on different scales for controlling the formation of shallow cumulus clouds in the trade-wind region, as will be done in part 2 of this study.
View lessSystematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan–glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.
View lessThis study presents the simulated response of regional climate and the oxygen isotopic composition of precipitation (δ18Op) to different along-strike topographic evolution scenarios. These simulations are conducted to determine if the previously hypothesized diachronous surface uplift in the Western and Eastern Alps would produce δ18Op signals in the geologic record that are sufficiently large and distinct to be detected using stable isotope paleoaltimetry. We present a series of topographic sensitivity experiments conducted with the water-isotope-tracking atmospheric general circulation model (GCM) ECHAM5-wiso. The topographic scenarios are created from the variation of two free parameters, (1) the elevation of the Western–Central Alps and (2) the elevation of the Eastern Alps. The results indicate Δδ18Op values (i.e., the difference between δ18Op values at the low- and high-elevation sites) of up to −8 ‰ along the strike of the Alps for the diachronous uplift scenarios, primarily due to changes in orographic precipitation and adiabatic lapse rate driven localized changes in near-surface variables. These simulated magnitudes of Δδ18Op values suggest that the expected isotopic signal would be significant enough to be preserved and measured in geologic archives. Moreover, the simulated slight δ18Op differences of 1 ‰–2 ‰ across the low-elevation sites support the use of the δ–δ paleoaltimetry approach and highlight the importance of sampling far-field low-elevation sites to differentiate between the different surface uplift scenarios. The elevation-dependent rate of change in δ18Op (“isotopic lapse rate”) varies depending on the topographic configuration and the extent of the surface uplift. Most of the changes are significant (e.g., −1.04 ‰ km−1 change with slope error of ±0.09 ‰ km−1), while others were within the range of the statistical uncertainties (e.g., −0.15 ‰ km−1 change with slope error of ±0.13 ‰ km−1). The results also highlight the plausible changes in atmospheric circulation patterns and associated changes in moisture transport pathways in response to changes in the topography of the Alps. These large-scale atmospheric dynamics changes can complicate the underlying assumption of stable isotope paleoaltimetry and therefore require integration with paleoclimate modeling to ensure accurate reconstruction of the paleoelevation of the Alps.
View lessAt the interface of Chinese diaspora studies, migration studies, and urban studies, this introduction argues for a shift towards city-based migration studies. The city is understood here not as a self-contained social cosmos, but as a globally and socially embedded urban level that opens up a more flexible perspective on the unfolding of migration processes at the micro, meso, and macro levels. It begins with a brief overview of recent trends in Chinese diaspora studies, global migration and urbanisation trends, and debates in critical geography on multi-scale urban theories. Then, it raises the question of the empirical feasibility of such an approach and argues for conceptualising migrants’ agency as a starting point for migration research, rather than pursuing a policy-driven, normative approach. Finally, it presents the five empirical contributions to this Special Issue. They are based on fieldwork in Paris, Berlin, Manchester (UK), Mexico City, Lagos, Gaborone, and Windhoek.
View lessIntroduction/objective: Suppression of the SOS response in combination with drugs damaging DNA has been proposed as a potential target to tackle antimicrobial resistance. The SOS response is the pathway used to repair bacterial DNA damage induced by antimicrobials such as quinolones. The extent of lexA-regulated protein expression and other associated systems under pressure of agents that damage bacterial DNA in clinical isolates remains unclear. The aim of this study was to assess the impact of this strategy consisting on suppression of the SOS response in combination with quinolones on the proteome profile of Escherichia coli clinical strains.
Materials and methods: Five clinical isolates of E. coli carrying different chromosomally- and/or plasmid-mediated quinolone resistance mechanisms with different phenotypes were selected, with E. coli ATCC 25922 as control strain. In addition, from each clinical isolate and control, a second strain was created, in which the SOS response was suppressed by deletion of the recA gene. Bacterial inocula from all 12 strains were then exposed to 1xMIC ciprofloxacin treatment (relative to the wild-type phenotype for each isogenic pair) for 1 h. Cell pellets were collected, and proteins were digested into peptides using trypsin. Protein identification and label-free quantification were done by liquid chromatography-mass spectrometry (LC–MS) in order to identify proteins that were differentially expressed upon deletion of recA in each strain. Data analysis and statistical analysis were performed using the MaxQuant and Perseus software.
Results: The proteins with the lowest expression levels were: RecA (as control), AphA, CysP, DinG, DinI, GarL, PriS, PsuG, PsuK, RpsQ, UgpB and YebG; those with the highest expression levels were: Hpf, IbpB, TufB and RpmH. Most of these expression alterations were strain-dependent and involved DNA repair processes and nucleotide, protein and carbohydrate metabolism, and transport. In isolates with suppressed SOS response, the number of underexpressed proteins was higher than overexpressed proteins.
Conclusion: High genomic and proteomic variability was observed among clinical isolates and was not associated with a specific resistant phenotype. This study provides an interesting approach to identify new potential targets to combat antimicrobial resistance.
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