Trait-based frameworks are promising tools to understand the functional consequences of community shifts in response to environmental change. The applicability of these tools to soil microbes is limited by a lack of functional trait data and a focus on categorical traits. To address this gap for an important group of soil microorganisms, we identify trade-offs underlying a fungal economics spectrum based on a large trait collection in 28 saprobic fungal isolates, derived from a common grassland soil and grown in culture plates. In this dataset, ecologically relevant trait variation is best captured by a three-dimensional fungal economics space. The primary explanatory axis represents a dense-fast continuum, resembling dominant life-history trade-offs in other taxa. A second significant axis reflects mycelial flexibility, and a third one carbon acquisition traits. All three axes correlate with traits involved in soil carbon cycling. Since stress tolerance and fundamental niche gradients are primarily related to the dense-fast continuum, traits of the 2nd (carbon-use efficiency) and especially the 3rd (decomposition) orthogonal axes are independent of tested environmental stressors. These findings suggest a fungal economics space which can now be tested at broader scales.
View lessThe increasing pressure on freshwater systems due to intensive anthropogenic use is a big challenge in central-northern Namibia and its catchment areas, the Kunene and the Kavango Rivers, and the Cuvelai-Etosha Basin, that provide water for more than 1 million people. So far, there is no comprehensive knowledge about the ecological status and only few knowledge about the water quality. Therefore, it is crucial to learn about the state of the ecosystem and the ecological effects of pollutants to ensure the safe use of these resources. The surface waters of the three systems were sampled, and three bioassays were applied on three trophic levels: algae, daphnia, and zebrafish embryos. Additionally, in vitro assays were performed to analyze mutagenicity (Ames fluctuation), dioxin-like potential (micro-EROD), and estrogenicity (YES) by mechanism-specific effects. The results show that acute toxicity to fish embryos and daphnia has mainly been detected at all sites in the three catchment areas. The systems differ significantly from each other, with the sites in the Iishana system showing the highest acute toxicity. At the cellular level, only weak effects were identified, although these were stronger in the Iishana system than in the two perennial systems. Algae growth was not inhibited, and no cytotoxic effects could be detected in any of the samples. Mutagenic effects and an estrogenic potential were detected at three sites in the Iishana system. These findings are critical in water resource management as the effects can adversely impact the health of aquatic ecosystems and the organisms within them.
View lessTropical theileriosis is an important protozoan tick-borne disease in cattle. Vaccination using attenuated schizont-infected cell lines is one of the methods used for controlling the disease. This study describes the production of attenuated schizont-infected cell lines from Egypt and an evaluation of its use as a vaccine to protect calves against clinical disease upon field challenge. Two groups of exotic and crossbred male calves were divided into vaccinated and control groups. The vaccinated groups were inoculated with 4 ml (1 × 106 cells/ml) of the attenuated cell line. Three weeks after vaccination, calves of both groups were transported to the New Valley Governorate (Egyptian oasis) where they were kept under field conditions and exposed to the natural Theileria annulata challenge. All animals in the control group showed severe clinical signs and died despite treatment with buparvaquone, which was administered after two days of persistent fever due to a severe drop in packed cell volume (PCV). Animals in the vaccinated group became seropositive without developing severe clinical signs other than transient fever. Post-mortem examinations revealed enlarged and fragile lymph nodes, spleen, and liver with necrosis and hemorrhages. These findings indicate that the Egyptian attenuated cell line was successful in protecting both exotic and crossbred animals against tropical theileriosis under field conditions.
View lessBackground
Broiler chickens are frequently colonized with Extended-Spectrum Beta-Lactamase- (ESBL-) and plasmid mediated AmpC Beta-Lactamase- (pAmpC-) producing Enterobacterales, and we are confronted with the potential spread of these resistant bacteria in the food chain, in the environment, and to humans. Research focused on identifying of transmission routes and investigating potential intervention measures against ESBL- and pAmpC- producing bacteria in the broiler production chain. However, few data are available on the effects of cleaning and disinfection (C&D) procedures in broiler stables on ESBL- and pAmpC- producing bacteria. Results
We systematically investigated five broiler stables before and after C&D and identified potential ESBL- and pAmpC- colonization sites after C&D in the broiler stables, including the anteroom and the nearby surrounding environment of the broiler stables. Phenotypically resistant E. coli isolates grown on MacConkey agar with cefotaxime were further analyzed for their beta-lactam resistance genes and phylogenetic groups, as well as the relation of isolates from the investigated stables before and after C&D by whole genome sequencing. Survival of ESBL- and pAmpC- producing E. coli is highly likely at sites where C&D was not performed or where insufficient cleaning was performed prior to disinfection. For the first time, we showed highly related ESBL-/pAmpC- producing E. coli isolates detected before and after C&D in four of five broiler stables examined with cgMLST. Survival of resistant isolates in investigated broiler stables as well as transmission of resistant isolates from broiler stables to the anteroom and surrounding environment and between broiler farms was shown. In addition, enterococci (frequently utilized to detect fecal contamination and for C&D control) can be used as an indicator bacterium for the detection of ESBL-/pAmpC- E. coli after C&D. Conclusion
We conclude that C&D can reduce ESBL-/pAmpC- producing E. coli in conventional broiler stables, but complete ESBL- and pAmpC- elimination does not seem to be possible in practice as several factors influence the C&D outcome (e.g. broiler stable condition, ESBL-/pAmpC- status prior to C&D, C&D procedures used, and biosecurity measures on the farm). A multifactorial approach, combining various hygiene- and management measures, is needed to reduce ESBL-/pAmpC- E. coli in broiler farms.
View lessTranscription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Here, our cryo-EM structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ may be detrimental.
View lessRfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an α-helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a β-barrel, which binds the ribosome. Here, we report structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH, which reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life.
View lessFear of falling might result in overprotection by one's social environment. In turn, feeling dependent could increase fear of falling. However, the association between fear of falling and perceived overprotection and its temporal order is unknown. This longitudinal study explores this potential mutual longitudinal association. This study presents secondary analyses from a larger trial. We tested the association between fear of falling and perceived overprotection in a cross-lagged path model controlled for falls, health-related quality of life, age, gender, and trial condition. N = 310 participants (M = 70 years, range: 64–92) completed self-reports at Time 1, 7 (Time 2), and 11 weeks (Time 3) after baseline assessment. We found a positive association from fear of falling to perceived overprotection (β = .12, 95% CI[0.02, 0.21], p = .02; β = .10; [0.01, 0.18], p = .03). The reversed cross-lagged paths were not significant. Findings suggest higher fear of falling translates into perceived overprotection, which may in turn increase loss of independence in old age.
View lessWe show that covalent labelling of sialic acids on live cell surfaces or mucin increases the fluorescence of the fluorescence molecular rotors (FMRs) CCVJ, Cy3 and thioazole orange, enabling wash-free imaging of cell surfaces. Dual labelling with an FMR and an environmentally insensitive dye allows detection of changes that occur, for example, when cross-linking is altered.
Detection of pathogenic viruses for point-of-care applications has attracted great attention since the COVID-19 pandemic. Current virus diagnostic tools are laborious and expensive, while requiring medically trained staff. Although user-friendly and cost-effective biosensors are utilized for virus detection, many of them rely on recognition elements that suffer major drawbacks. Herein, computationally designed epitope-imprinted polymers (eIPs) are conjugated with a portable piezoelectric sensing platform to establish a sensitive and robust biosensor for the human pathogenic adenovirus (HAdV). The template epitope is selected from the knob part of the HAdV capsid, ensuring surface accessibility. Computational simulations are performed to evaluate the conformational stability of the selected epitope. Further, molecular dynamics simulations are executed to investigate the interactions between the epitope and the different functional monomers for the smart design of eIPs. The HAdV epitope is imprinted via the solid-phase synthesis method to produce eIPs using in silico-selected ingredients. The synthetic receptors show a remarkable detection sensitivity (LOD: 102 pfu mL–1) and affinity (dissociation constant (Kd): 6.48 × 10–12 M) for HAdV. Moreover, the computational eIPs lead to around twofold improved binding behavior than the eIPs synthesized with a well-established conventional recipe. The proposed computational strategy holds enormous potential for the intelligent design of ultrasensitive imprinted polymer binders.
View lessWhen 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 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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