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This article presents the findings from systematically reviewing 26 empirical research studies published from 2005 to 2014 on the use of GIS for learning and teaching. By employing methods of narrative synthesis and qualitative content analysis, the study gives evidence about the state of knowledge of competence-based GIS education. The results explain what factors and variables effect GIS learning in terms of technology use, major subject contents, learning contexts, and didactic and pedagogical aspects. They also show what facets of knowledge, process skills, and affect the research literature has investigated. The analysis of the type and quality of the methods used indicates that current GIS education research is a heterogeneous field that needs a systematic research framework for future efforts, according to empirical education research.
1. Plant-fungal interactions are important for plant community assembly, but quantifying these relationships remains challenging. High throughput sequencing of fungal communities allows us to identify plant-fungal associations at a high level of resolution, but often fails to provide information on taxonomic and functional assignment of fungi. 2. We transplanted seeds of Pinus cembra across an elevational gradient (1850–2250 m a.s.l.) and identified environmental factors and known fungal associates important for seedling establishment and survival. We then applied null model tests to identify taxonomically unassigned fungi associated with pine recruitment. 3. Early seedling establishment was determined by abiotic environmental factors, while seedling survival was predominantly affected by biotic environmental factors (i.e., the abundance of a fungal pathogen known from literature and the distance to adult trees). Null model tests identified known mycorrhizal partners and a large number of unknown operational taxonomic units (OTUs) associated with seedling survival, including saprotrophic and pathogenic species. These results highlight that unknown fungal OTUs, which are usually discarded from analyses, could play a crucial role for plant survival. 4. Synthesis. We conclude that high throughput metabarcoding paired with null model tests, is a valuable approach for identifying hidden plant-fungal associations within large and complex DNA metabarcoding datasets. Such an approach can be an important tool in illuminating the black box of plant-microbe interactions, and thus understanding ecosystem dynamics.
This paper explores the many interesting implications for oscillator design, with optimized phase-noise performance, deriving from a newly proposed model based on the concept of oscillator conjugacy. For the case of 2-D (planar) oscillators, the model prominently predicts that only circuits producing a perfectly symmetric steady-state can have zero amplitude-to-phase (AM-PM) noise conversion, a so-called zero-state. Simulations on standard industry oscillator circuits verify all model predictions and, however, also show that these circuit classes cannot attain zero-states except in special limit-cases which are not practically relevant. Guided by the newly acquired design rules, we describe the synthesis of a novel 2-D reduced-order LC oscillator circuit which achieves several zero-states while operating at realistic output power levels. The potential future application of this developed theoretical framework for implementation of numerical algorithms aimed at optimizing oscillator phase-noise performance is briefly discussed.
We report here the in-cell NMR-spectroscopic observation of the binding of the cognate ligand 2′-deoxyguanosine to the aptamer domain of the bacterial 2′-deoxyguanosine-sensing riboswitch in eukaryotic cells, namely Xenopus laevis oocytes and in human HeLa cells. The riboswitch is sufficiently stable in both cell types to allow for detection of binding of the ligand to the riboswitch. Most importantly, we show that the binding mode established by in vitro characterization of this prokaryotic riboswitch is maintained in eukaryotic cellular environment. Our data also bring important methodological insights: Thus far, in-cell NMR studies on RNA in mammalian cells have been limited to investigations of short (<15 nt) RNA fragments that were extensively modified by protecting groups to limit their degradation in the intracellular space. Here, we show that the in-cell NMR setup can be adjusted for characterization of much larger (≈70 nt) functional and chemically non-modified RNA.
We developed three bathochromic, green-light activatable, photolabile protecting groups based on a nitrodibenzofuran (NDBF) core with D-π-A push–pull structures. Variation of donor substituents (D) at the favored ring position enabled us to observe their impact on the photolysis quantum yields. Comparing our new azetidinyl-NDBF (Az-NDBF) photolabile protecting group with our earlier published DMA-NDBF, we obtained insight into its excitation-specific photochemistry. While the “two-photon-only” cage DMA-NDBF was inert against one-photon excitation (1PE) in the visible spectral range, we were able to efficiently release glutamic acid from azetidinyl-NDBF with irradiation at 420 and 530 nm. Thus, a minimal change (a cyclization adding only one carbon atom) resulted in a drastically changed photochemical behavior, which enables photolysis in the green part of the spectrum.
Some realists in political theory deny that the notion of feasibility has any place in realist theory, while others claim that feasibility constraints are essential elements of realist normative theorising. But none have so far clarified what exactly they are referring to when thinking of feasibility and political realism together. In this article, we develop a conception of the realist feasibility frontier based on an appraisal of how political realism should be distinguished from non-ideal theories. In this realist framework, political standards are feasible if they meet three requirements: they are (i) politically intelligible, (ii) contextually recognisable as authoritative, and (iii) contestable. We conclude by suggesting that our conception of realist feasibility might be compatible with utopian demands, thereby possibly finding favour with realists who otherwise refuse to resort to the notion of feasibility.
Nano-granular metals are materials that fall into the general class of granular electronic systems in which the interplay of electronic correlations, disorder and finite size effects can be studied. The charge transport in nano-granular metals is dominated by thermally-assisted, sequential and correlated tunneling over a temperature-dependent number of metallic grains. Here we study the frequency-dependent conductivity (AC conductivity) of nano-granular Platinum with Pt nano-grains embedded into amorphous carbon (C). We focus on the transport regime on the insulating side of the insulator metal transition reflected by a set of samples covering a range of tunnel-coupling strengths. In this transport regime polarization contributions to the AC conductivity are small and correlation effects in the transport of free charges are expected to be particularly pronounced. We find a universal behavior in the frequency dependence that can be traced back to the temperature-dependent zero-frequency conductivity (DC conductivity) of Pt/C within a simple lumped-circuit analysis. Our results are in contradistinction to previous work on nano-granular Pd/ZrO2ZrO2 in the very weak coupling regime where polarization contributions to the AC conductivity dominated. We describe possible future applications of nano-granular metals in proximity impedance spectroscopy of dielectric materials.
A general circulation model is used to study the interaction between parameterized gravity waves (GWs) and large-scale Kelvin waves in the tropical stratosphere. The simulation shows that Kelvin waves with substantial amplitudes (∼10 m s−1) can significantly affect the distribution of GW drag by modulating the local shear. Furthermore, this effect is localized to regions above strong convective organizations that generate large-amplitude GWs, so that at a given altitude it occurs selectively in a certain phase of Kelvin waves. Accordingly, this effect also contributes to the zonal-mean GW drag, which is large in the middle stratosphere during the phase transition of the quasi-biennial oscillation (QBO). Furthermore, we detect an enhancement of Kelvin-wave momentum flux due to GW drag modulated by Kelvin waves. The result implies an importance of GW dynamics coupled to Kelvin waves in the QBO progression.
Plain Language Summary: The variability of the tropical atmosphere at altitudes of about 18–40 km is dominated by a large-amplitude long-term oscillation of wind, the quasi-biennial oscillation, which has a broad impact on the climate and seasonal forecasting. This oscillation is known to be driven by various types of atmospheric waves with multiple spatial scales. Using a numerical model, this study reports a process of interaction between those waves on different scales, which has not been illuminated before. The result implies a potential importance of this process in the progression of the quasi-biennial oscillation. Proper model representations of these multiscale waves and tropical convection are required to simulate this process.
The acetogenic model bacterium Acetobacterium woodii is well-known to produce acetate by homoacetogenesis from sugars, but under certain conditions minor amounts of ethanol are produced in addition. Here, we have aimed to identify physiological conditions that increase electron and carbon flow towards ethanol production. Ethanol was only produced from fructose but not from H2 + CO2, formate, pyruvate, lactate or alanine. In the absence of Na+, the Wood–Ljungdahl pathway (WLP) of acetate formation is not functional. Therefore, the ethanol yield increased to 0.42 mol/mol (ethanol/fructose) with an ethanol/acetate ratio of 0.28 mol/mol. The presence of bicarbonate/CO2 stimulated electron and carbon flow through the WLP and led to less ethanol produced. Of the 11 potential alcohol dehydrogenase genes, the most upregulated during ethanologenesis was adh4. A deletion of adh4 led to an increase in ethanol production by 100% to a yield of 0.79 mol/mol (ethanol/fructose); this correlated with an increase in transcript abundance of adh6. In sum, our studies revealed low Na+ and bicarbonate/CO2 as factors that trigger ethanol formation and that a deletion of adh4 drastically increased ethanol formation in A. woodii.
Acinetobacter baumannii is outstanding for its ability to cope with low water activities which significantly contributes to its persistence in hospital environments. The vast majority of bacteria are able to prevent loss of cellular water by amassing osmoactive compatible solutes or their precursors into the cytoplasm. One such precursor of an osmoprotectant is choline that is taken up from the environment and oxidized to the compatible solute glycine betaine. Here, we report the identification of the osmotic stress operon betIBA in A. baumannii. This operon encodes the choline oxidation pathway important for the production of the solute glycine betaine. The salt-sensitive phenotype of a betA deletion strain could not be rescued by addition of choline, which is consistent with the role of BetA in choline oxidation. We found that BetA is a choline dehydrogenase but also mediates in vitro the oxidation of glycine betaine aldehyde to glycine betaine. BetA was found to be associated with the membrane and to contain a flavin, indicative for BetA donating electrons into the respiratory chain. The choline dehydrogenase activity was not salt dependent but was stimulated by the compatible solute glutamate.
Long-term effects on cirrhosis and portal hypertension of direct antiviral agent (DAA)-based eradication of hepatitis C virus (HCV) are still under debate. We analysed dynamics of liver and spleen elastography to assess potential regression of cirrhosis and portal hypertension 3 years post-treatment. Fifty-four patients with HCV-associated cirrhosis and DAA-induced SVR were included. Liver and spleen stiffness were measured at baseline (BL), end of treatment (EOT), 24 weeks after EOT (FU24) and 1, 2 and 3 (FU144) years post-treatment by transient liver elastography (L-TE) and point shear wave elastography (pSWE) using acoustic radiation force impulse (ARFI) of the liver (L-ARFI) and spleen (S-ARFI). Biochemical, virological and clinical data were also obtained. Liver stiffness assessed by L-TE decreased between BL [median (range), 32.5(9.1–75) kPa] and EOT [21.3(6.7–73.5) kPa; p < .0001] and EOT and FU144 [16(4.1–75) kPa; p = .006]. L-ARFI values improved between EOT [2.5(1.2–4.1) m/s] and FU144 [1.7(0.9–4.1) m/s; p = .001], while spleen stiffness remained unchanged. Overall, L-TE improved in 38 of 54 (70.4%) patients at EOT and 29 of 38 (76.3%) declined further until FU144, whereas L-ARFI values decreased in 30/54 (55.6%) patients at EOT and continued to decrease in 28/30 (93.3%) patients at FU144. Low bilirubin and high albumin levels at BL were associated with improved L-ARFI values (p = .048) at EOT or regression of cirrhosis (<12.5 kPa) by L-TE at FU144 (p = .005), respectively. Liver stiffness, but not spleen stiffness, continued to decline in a considerable proportion of patients with advanced liver disease after HCV eradication.
Beneficial acute effects of resistance exercise on cognitive functions may be modified by exercise intensity or by habitual physical activity. Twenty-six participants (9 female and 17 male; 25.5 ± 3.4 years) completed four resistance exercise interventions in a randomized order on separate days (≥48 h washout). The intensities were set at 60%, 75%, and 90% of the one repetition maximum (1RM). Three interventions had matched workloads (equal resistance*nrepetitions). One intervention applied 75% of the 1RM and a 50% reduced workload (resistance*nrepetitions = 50%). Cognitive attention (Trail Making Test A—TMTA), task switching (Trail Making Test B—TMTB), and working memory (Digit Reading Spans Backward) were assessed before and immediately after exercise. Habitual activity was assessed as MET hours per week using the International Physical Activity Questionnaire. TMTB time to completion was significantly shorter after exercise with an intensity of 60% 1RM and 75% 1RM and 100% workload. Friedman test indicated a significant effect of exercise intensity in favor of 60% 1RM. TMTA performance was significantly shorter after exercise with an intensity of 60% 1RM, 90% 1RM, and 75% 1RM (50% workload). Habitual activity with vigorous intensity correlated positively with the baseline TMTB and Digit Span Forward performance but not with pre- to post-intervention changes. Task switching, based on working memory, mental flexibility, and inhibition, was beneficially influenced by acute exercise with moderate intensity whereas attention performance was increased after exercise with moderate and vigorous intensity. The effect of regular activity had no impact on acute exercise effects.
An exploration of the relationship between recruitment communication and foraging in stingless bees
(2021)
Social information is widely used in the animal kingdom and can be highly adaptive. In social insects, foragers can use social information to find food, avoid danger, or choose a new nest site. Copying others allows individuals to obtain information without having to sample the environment. When foragers communicate information they will often only advertise high-quality food sources, thereby filtering out less adaptive information. Stingless bees, a large pantropical group of highly eusocial bees, face intense inter- and intra-specific competition for limited resources, yet display disparate foraging strategies. Within the same environment there are species that communicate the location of food resources to nest-mates and species that do not. Our current understanding of why some species communicate foraging sites while others do not is limited. Studying freely foraging colonies of several co-existing stingless bee species in Brazil, we investigated if recruitment to specific food locations is linked to 1) the sugar content of forage, 2) the duration of foraging trips, and 3) the variation in activity of a colony from 1 day to another and the variation in activity in a species over a day. We found that, contrary to our expectations, species with recruitment communication did not return with higher quality forage than species that do not recruit nestmates. Furthermore, foragers from recruiting species did not have shorter foraging trip durations than those from weakly recruiting species. Given the intense inter- and intraspecific competition for resources in these environments, it may be that recruiting species favor food resources that can be monopolized by the colony rather than food sources that offer high-quality rewards.
Droughts are anticipated to intensify in many parts of the world due to climate change. However, the issue of drought definition, namely the diversity of drought indices, makes it difficult to compare drought assessments. This issue is widely known, but its relative importance has never been quantitatively evaluated in comparison to other sources of uncertainty. Here, encompassing three drought categories (meteorological, agricultural, and hydrological droughts) with four temporal scales of interest, we evaluated changes in the drought frequency using multi-model and multi-scenario simulations to identify areas where the definition issue could result in pronounced uncertainties and to what extent. We investigated the disagreement in the signs of changes between drought definitions and decomposed the variance into four main factors: drought definitions, greenhouse gas concentration scenarios, global climate models, and global water models, as well as their interactions. The results show that models were the primary sources of variance over 82% of the global land area. On the other hand, the drought definition was the dominant source of variance in the remaining 17%, especially in parts of northern high-latitudes. Our results highlight specific regions where differences in drought definitions result in a large spread among projections, including areas showing opposite signs of significant changes. At a global scale, 7% of the variance resulted independently from the definition issue, and that value increased to 44% when 1st and 2nd order interactions were considered. The quantitative results suggest that by clarifying hydrological processes or sectors of interest, one could avoid these uncertainties in drought assessments to obtain a clearer picture of future drought change.
Purpose: 10-year retrospective study to assess burden of illness in individuals with tuberous sclerosis complex (TSC) identified from German healthcare data. Methods: Patients with TSC were identified by International Classification of Diseases code Q85.1. Patients with epilepsy were identified by epilepsy diagnosis or antiseizure medication (ASM) prescription after TSC diagnosis. Results: Using data from 2016 (final study year), 100 patients with TSC were identified (mean [range] age: 38 [1–86] years; male: 40%); prevalence: 7.9 per 100,000 (TSC), 2.2 per 100,000 (TSC with epilepsy). During the 10-year study period (2007–2016), 256 patients with TSC were identified and followed up for 1,784 patient- years (epilepsy: 36%, 616 patient-years). TSC manifestations/comorbidities (apart from epilepsy) were identi- fied more frequently in patients with epilepsy than without. Mean annual healthcare costs for patients with TSC were €6,139 per patient-year (PPY), mostly attributable to medication (35%) and inpatient care (29%). Patients with epilepsy incurred costs more than double those without. Mean (standard deviation [SD]) annual hospi- talisation rate (AHR) and length of stay (LOS) PPY: 0.5 (1.0) and 5.9 (18.6) days for TSC. AHR and LOS were greater in patients with epilepsy than without. Mean (SD) number of ASMs prescribed (TSC with epilepsy): 3.0 (2.3) over the entire observable time per patient. Mortality rates (vs. control): 5.08% (vs. 1.69%, p<0.001) for TSC, 7.53% (vs. 0.98%, p<0.001) for TSC with epilepsy, 3.68% (vs. 2.03%, p = 0.003) for TSC without epilepsy. Conclusion: Healthcare costs, resource utilisation, and mortality were greater in patients with TSC and epilepsy than those without epilepsy.
An exploratory latent class analysis of student expectations towards learning analytics services
(2021)
For service implementations to be widely adopted, it is necessary for the expectations of the key stakeholders to be considered. Failure to do so may lead to services reflecting ideological gaps, which will inadvertently create dissatisfaction among its users. Learning analytics research has begun to recognise the importance of understanding the student perspective towards the services that could be potentially offered; however, student engagement remains low. Furthermore, there has been no attempt to explore whether students can be segmented into different groups based on their expectations towards learning analytics services. In doing so, it allows for a greater understanding of what is and is not expected from learning analytics services within a sample of students. The current exploratory work addresses this limitation by using the three-step approach to latent class analysis to understand whether student expectations of learning analytics services can clearly be segmented, using self-report data obtained from a sample of students at an Open University in the Netherlands. The findings show that student expectations regarding ethical and privacy elements of a learning analytics service are consistent across all groups; however, those expectations of service features are quite variable. These results are discussed in relation to previous work on student stakeholder perspectives, policy development, and the European General Data Protection Regulation (GDPR).
Glioblastoma is the most common malignant primary brain tumor. To date, clinically relevant biomarkers are restricted to isocitrate dehydrogenase (IDH) gene 1 or 2 mutations and O6-methylguanine DNA methyltransferase (MGMT) promoter methylation. Long non-coding RNAs (lncRNAs) have been shown to contribute to glioblastoma pathogenesis and could potentially serve as novel biomarkers. The clinical significance of HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) was determined by analyzing HOTAIRM1 in multiple glioblastoma gene expression data sets for associations with prognosis, as well as, IDH mutation and MGMT promoter methylation status. Finally, the role of HOTAIRM1 in glioblastoma biology and radiotherapy resistance was characterized in vitro and in vivo. We identified HOTAIRM1 as a candidate lncRNA whose up-regulation is significantly associated with shorter survival of glioblastoma patients, independent from IDH mutation and MGMT promoter methylation. Glioblastoma cell line models uniformly showed reduced cell viability, decreased invasive growth and diminished colony formation capacity upon HOTAIRM1 down-regulation. Integrated proteogenomic analyses revealed impaired mitochondrial function and determination of reactive oxygen species (ROS) levels confirmed increased ROS levels upon HOTAIRM1 knock-down. HOTAIRM1 knock-down decreased expression of transglutaminase 2 (TGM2), a candidate protein implicated in mitochondrial function, and knock-down of TGM2 mimicked the phenotype of HOTAIRM1 down-regulation in glioblastoma cells. Moreover, HOTAIRM1 modulates radiosensitivity of glioblastoma cells both in vitro and in vivo. Our data support a role for HOTAIRM1 as a driver of biological aggressiveness, radioresistance and poor outcome in glioblastoma. Targeting HOTAIRM1 may be a promising new therapeutic approach.
In this thesis we investigate the thermodynamic and dynamic properties of the D-dimensional quantum Heisenberg ferromagnet within the spin functional renormalization group (FRG); a
formalism describing the evolution of the system’s observables as the magnetic exchange inter-action is artificially deformed. Following an introduction providing a self contained summary of the conceptual and mathematical background, we present the spin FRG as developed by Krieg and Kopietz in references [1] and [2] in chapter two. Thereto, the generating functional of the imaginary time-spin correlation functions and its exact flow equation describing the deformation process of the exchange interaction are introduced. In addition, it is highlighted that - in contrast to conventional field-theoretic FRG approaches - the related Legendre trans-formed functional cannot be defined if the exchange interaction is initially switched off. Next, we show that this limitation can be circumvented within an alternativ hybrid approach, which treats transverse and longitudinal spin fluctuations differently. The relevant functionals are introduced and the relations of the corresponding functional Taylor coefficients with the spin correlation functions are discussed. Lastly, the associated flow equations are derived and the possibility of explicit or spontaneous symmetry breaking is taken into account.
In chapter three, we benchmark the hybrid formalism against a calculation of the thermo-dynamic properties of the one and two-dimensional Heisenberg model at low temperatures T and finite magnetic field H. For this purpose, we devise an anisotropic deformation scheme of the exchange interaction which allows for a controlled truncation of the infinite hierarchy of FRG flow equations. Thereby, contact with mean-field and spin-wave theory is made and the violation of the Mermin-Wagner theorem is discussed. To fulfill the latter, the truncation scheme is then complemented by a Ward identity relating the transverse self-energy and the magnetization. The resulting magnetization M (H, T ) and isothermal susceptibility χ(H, T ) are in quantitative agreement with the literature and the established behavior of the transverse correlation length and the zero-field susceptibility close to the critical point is qualitatively reproduced in the limit H → 0.
Finally, we investigate the longitudinal dynamics at low temperatures. To this end, the hierarchy of flow equations is solved within the same anisotropic deformation scheme complemented by an expansion in the inverse interaction range, and the resulting longitudinal dynamic structure factor is calculated within a low-momentum expansion. In D = 3, the large phase space accessible for the decay into transverse magnons yields only a broad hump centered at zero frequency whose width scales linearly in momentum. In contrast, at low temperatures and in a certain range of magnetic fields, a well-defined quasiparticle peak with linear dispersion emerges in D ≤ 2, which we identify as zero-magnon sound. Sound velocity and damping are discussed as a function of temperature and magnetic field, and the relevant momentum-frequency window is estimated and compared to the hydrodynamic
second-magnon regime.
By the latter half of the twentieth century, a documented, substantial quantitative increase had occurred in the total number of Christian political organizations operating in Washington, D.C. with the sole purpose of influencing Congress and the administration through direct lobbying. This study seeks to understand what were the contributing historical factors that influenced the rise of Christian Lobby Organizations (CLOs), resulting in their normalization in American society?
Background: Breast cancer (BC) is the most frequent female cancer and preferentially metastasizes to bone. The transcription factor TGFB-induced factor homeobox 1 (TGIF) is involved in bone metabolism. However, it is not yet known whether TGIF is associated with BC bone metastasis or patient outcome and thus of potential interest. Methods: TGIF expression was analyzed by immunohistochemistry in 1197 formalin-fixed, paraffin-embedded tissue samples from BC patients treated in the GAIN (German Adjuvant Intergroup Node-Positive) study with two adjuvant dose-dense schedules of chemotherapy with or without bisphosphonate ibandronate. TGIF expression was categorized into negative/low and moderate/strong staining. Endpoints were disease-free survival (DFS), overall survival (OS) and time to primary bone metastasis as first site of relapse (TTPBM). Results: We found associations of higher TGIF protein expression with smaller tumor size (p= 0.015), well differentiated phenotype (p< 0.001) and estrogen receptor (ER)-positive BC (p< 0.001). Patients with higher TGIF expression levels showed a significantly longer disease-free (DFS: HR 0.75 [95%CI 0.59–0.95], log-rank p=0.019) and overall survival (OS: HR 0.69 [95%CI 0.50–0.94], log-rank p= 0.019), but no association with TTPBM (HR 0.77 [95%CI 0.51–1.16]; p= 0.213). Univariate analysis in molecular subgroups emphasized that elevated TGIF expression was prognostic for both DFS and OS in ER-positive BC patients (DFS: HR 0.68 [95%CI 0.51–0.91]; log-rank p= 0.009, interaction p= 0.130; OS: HR 0.60 [95%CI 0.41–0.88], log-rank p= 0.008, interaction p= 0.107) and in the HER2-negative subgroup (DFS:HR 0.67 [95%CI 0.50–0.88], log-rank p= 0.004, interaction p= 0.034; OS: HR 0.57 [95%CI 0.40–0.81], log-rank p= 0.002, interaction p= 0.015). Conclusions: Our results suggest that moderate to high TGIF expression is a common feature of breast cancer cells and that this is not associated with bone metastases as first site of relapse. However, a reduced expression is linked to tumor progression, especially in HER2-negative breast cancer.
Obligate endoparasitic oomycetes are known to ubiquitously occur in marine and freshwater diatoms, but their diversity is still largely unexplored. Many of these parasitoids are members of the early-diverging oomycete lineages (Miracula, Diatomophthora), others are within the Leptomitales of the Saprolegniomycetes (Ectrogella, Lagenisma) and some have been described in the Peronosporomycetes (Aphanomycopsis, Lagenidium). Even though some species have been recently described and two new genera were introduced (Miracula and Diatomophthora), the phylogeny and taxonomy of most of these organisms remain unresolved. This is contrasted by the high number of sequences from unclassified species, as recently revealed from environmental sequencing, suggesting the presence of several undiscovered species. In this study, a new species of Miracula is reported from a marine centric diatom (Minidiscus sp.) isolated from Skagaströnd harbor in Northwest Iceland. The morphology and life cycle traits of this novel oomycete parasite are described herein, and its taxonomic placement within the genus Miracula is confirmed by molecular phylogeny. As it cannot be assigned to any previously described species, it is introduced as Miracula islandica in this study. The genus Miracula thus contains three described holocarpic species (M. helgolandica, M. islandica, M. moenusica) to which likely additional species will need to be added in the future, considering the presence of several lineages known only from environmental sequencing that clustered within the Miracula clade.
High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed opensource and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain ‘layerification’ and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.
Aims: Cardio-oncology is a growing interdisciplinary field which aims to improve cardiological care for cancer patients in order to reduce morbidity and mortality. The impact of cardiac biomarkers, echocardiographic parameters, and cardiological assessment regarding risk stratification is still unclear. We aimed to identify potential parameters that allow an early risk stratification of cancer patients. Methods and results: In this cohort study, we evaluated 930 patients that were admitted to the cardio-oncology outpatient clinic of the University Hospital Heidelberg from January 2016 to January 2019. We performed echocardiography, including Global Longitudinal Strain (GLS) analysis and measured cardiac biomarkers including N-terminal pro brain-type natriuretic peptide (NT-proBNP) and high-sensitivity cardiac troponin T levels (hs-cTnT). Most patients were suffering from breast cancer (n = 450, 48.4%), upper gastrointestinal carcinoma (n = 99, 10.6%) or multiple myeloma (n = 51, 5.5%). At the initial visit, we observed 86.7% of patients having a preserved left ventricular ejection fraction (LVEF >50%). At the second follow up, still 78.9% of patients showed a preserved LVEF. Echocardiographic parameters or elevation of NT-proBNP did not significantly correlate with all-cause mortality (ACM) (logistic regression LVEF <50%: P = 0.46, NT-proBNP: P = 0.16) and failed to identify high-risk patients. In contrast, hs-cTnT above the median (≥7 ng/L) was an independent marker to determine ACM (multivariant logistic regression, OR: 2.21, P = 0.0038) among all included patients. In particular, hs-cTnT levels before start of a chemotherapy were predictive for ACM. Conclusions: Based on our non-selected cohort of cardio-oncological patients, hs-cTnT was able to identify patients with high mortality by using a low cutoff of 7 ng/L. We conclude that measurement of hs-cTnT is an important tool to stratify the risk for mortality of cancer patients before starting chemotherapy.
We retrospectively investigated histopathological growth patterns in individuals with advanced nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) treated within the randomized HD18 study. In all, 35/60 patients (58%) presented with atypical growth patterns. Patients with atypical growth patterns more often had stage IV disease (P = 0·0354) and splenic involvement (P = 0·0048) than patients with typical growth patterns; a positive positron emission tomography after two cycles of chemotherapy (PET-2) tended to be more common (P = 0·1078). Five-year progression-free survival [hazard ratio (HR) = 0·86; 95% confidence interval (CI) = 0·49–1·47] and overall survival (HR = 0·85; 95% CI = 0·49–1·51) did not differ between the groups after study treatment with PET-2-guided escalated BEACOPP (bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, prednisone). Thus, advanced NLPHL is often associated with atypical growth patterns but their prognostic impact is compensated by PET-2-guided escalated BEACOPP.
Since the early 1970s several studies have reported distal splenic artery embolization, better known as partial spleen embolization (PSE), as an efficacious treatment of portal hypertensive variceal bleeding and hypersplenism in cirrhosis.(1, 2) However, the effect of PSE on portal pressure is secondary to the induction of splenic infarction. Depending on both the infarct volume and possible infection, PSE can induce serious complications including death.(2, 3) On the other hand, proximal splenic artery embolization (PSAE), which mimics surgical splenic artery ligation, prevents large infarction of the spleen, favoring collateral perfusion of its intact distal vasculature.(3) For this, PSAE has been extensively preferred over PSE for reducing portal hyperflow and treating refractory ascites (RA) after whole or partial liver transplantation (LT).(3, 4) We report here a case of PSAE used to treat RA in a patient with cirrhosis not eligible for transjugular intrahepatic portosystemic shunt (TIPS) and LT.
A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.
Inhibition of fatty acid synthesis (FAS) stimulates tumor cell death and reduces angiogenesis. When SH-SY5Y cells or primary neurons are exposed to hypoxia only, inhibition of FAS yields significantly enhanced cell injury. The pathophysiology of stroke, however, is not only restricted to hypoxia but also includes reoxygenation injury. Hence, an oxygen-glucose-deprivation (OGD) model with subsequent reoxygenation in both SH-SY5Y cells and primary neurons as well as a murine stroke model were used herein in order to study the role of FAS inhibition and its underlying mechanisms. SH-SY5Y cells and cortical neurons exposed to 10 h of OGD and 24 h of reoxygenation displayed prominent cell death when treated with the Acetyl-CoA carboxylase inhibitor TOFA or the fatty acid synthase inhibitor cerulenin. Such FAS inhibition reduced the reduction potential of these cells, as indicated by increased NADH2+/NAD+ ratios under both in vitro and in vivo stroke conditions. As observed in the OGD model, FAS inhibition also resulted in increased cell death in the stroke model. Stroke mice treated with cerulenin did not only display increased brain injury but also showed reduced neurological recovery during the observation period of 4 weeks. Interestingly, cerulenin treatment enhanced endothelial cell leakage, reduced transcellular electrical resistance (TER) of the endothelium and contributed to poststroke blood-brain barrier (BBB) breakdown. The latter was a consequence of the activated NF-κB pathway, stimulating MMP-9 and ABCB1 transporter activity on the luminal side of the endothelium. In conclusion, FAS inhibition aggravated poststroke brain injury as consequence of BBB breakdown and NF-κB-dependent inflammation.
In the last decade, the Climate Limited-area Modeling Community (CLM-Community) has contributed to the Coordinated Regional Climate Downscaling Experiment (CORDEX) with an extensive set of regional climate simulations. Using several versions of the COSMO-CLM-Community model, ERA-Interim reanalysis and eight global climate models from phase 5 of the Coupled Model Intercomparison Project (CMIP5) were dynamically downscaled with horizontal grid spacings of 0.44∘ (∼ 50 km), 0.22∘ (∼ 25 km), and 0.11∘ (∼ 12 km) over the CORDEX domains Europe, South Asia, East Asia, Australasia, and Africa. This major effort resulted in 80 regional climate simulations publicly available through the Earth System Grid Federation (ESGF) web portals for use in impact studies and climate scenario assessments. Here we review the production of these simulations and assess their results in terms of mean near-surface temperature and precipitation to aid the future design of the COSMO-CLM model simulations. It is found that a domain-specific parameter tuning is beneficial, while increasing horizontal model resolution (from 50 to 25 or 12 km grid spacing) alone does not always improve the performance of the simulation. Moreover, the COSMO-CLM performance depends on the driving data. This is generally more important than the dependence on horizontal resolution, model version, and configuration. Our results emphasize the importance of performing regional climate projections in a coordinated way, where guidance from both the global (GCM) and regional (RCM) climate modeling communities is needed to increase the reliability of the GCM–RCM modeling chain.
In this study, we determine spectral characteristics and amplitude decays of wind turbine induced seismic signals in the far field of a wind farm (WF) close to Uettingen, Germany. Average power spectral densities (PSDs) are calculated from 10 min time segments extracted from (up to) 6 months of continuous recordings at 19 seismic stations, positioned along an 8 km profile starting from the WF. We identify seven distinct PSD peaks in the frequency range between 1 and 8 Hz that can be observed to at least 4 km distance; lower-frequency peaks are detectable up to the end of the profile. At distances between 300 m and 4 km the PSD amplitude decay can be described by a power law with exponent b. The measured b values exhibit a linear frequency dependence and range from b=0.39 at 1.14 Hz to b=3.93 at 7.6 Hz. In a second step, the seismic radiation and amplitude decays are modeled using an analytical approach that approximates the surface wave field. Since we observe temporally varying phase differences between seismograms recorded directly at the base of the individual wind turbines (WTs), source signal phase information is included in the modeling approach. We show that phase differences between source signals have significant effects on the seismic radiation pattern and amplitude decays. Therefore, we develop a phase shift elimination method to handle the challenge of choosing representative source characteristics as an input for the modeling. To optimize the fitting of modeled and observed amplitude decay curves, we perform a grid search to constrain the two model parameters, i.e., the seismic shear wave velocity and quality factor. The comparison of modeled and observed amplitude decays for the seven prominent frequencies shows very good agreement and allows the constraint of shear velocities and quality factors for a two-layer model of the subsurface. The approach is generalized to predict amplitude decays and radiation patterns for WFs of arbitrary geometry.
Hyrrokkin sarcophaga is a parasitic foraminifera that is commonly found in cold-water coral reefs where it infests the file clam Acesta excavata and the scleractinian coral Desmophyllum pertusum (formerly known as Lophelia pertusa). Here, we present measurements of the trace element and isotopic composition of these parasitic foraminifera, analyzed by inductively coupled optical emission spectrometry (ICP-OES), electron probe microanalysis (EPMA) and mass spectrometry (gas-source MS and inductively-coupled-plasma MS). Our results reveal that the geochemical signature of H. sarcophaga depends on the host organism it infests. Sr / Ca ratios are 1.1 mmol mol−1 higher in H. sarcophaga that infest D. pertusum, which could be an indication that dissolved host carbonate material is utilized in shell calcification, given that the aragonite of D. pertusum has a naturally higher Sr concentration compared to the calcite of A. excavata. Similarly, we measure 3.1 ‰ lower δ13C and 0.25 ‰ lower δ18O values in H. sarcophaga that lived on D. pertusum, which might be caused by the direct uptake of the host's carbonate material with a more negative isotopic composition or different pH regimes in these foraminifera (pH can exert a control on the extent of CO2 hydration/hydroxylation) due to the uptake of body fluids of the host. We also observe higher Mn / Ca ratios in foraminifera that lived on A. excavata but did not penetrate the host shell compared to specimen that penetrated the shell, which could be interpreted as a change in food source, changes in the calcification rate, Rayleigh fractionation or changing oxygen conditions. While our measurements provide an interesting insight into the calcification process of this unusual foraminifera, these data also indicate that the geochemistry of this parasitic foraminifera is unlikely to be a reliable indicator of paleoenvironmental conditions using Sr / Ca, Mn / Ca, δ18O or δ13C unless the host organism is known and its geochemical composition can be accounted for.
Evidence of hydrothermal activity is reported for the Mesozoic pre- and syn-rift successions of the western Adriatic palaeomargin of the Alpine Tethys, preserved in the Western Southalpine Domain (NW Italy). The products of hydrothermal processes are represented by vein and breccia cements, as well as dolomitization and silicification of the host rocks. In the eastern part of the study area, interpreted as part of the necking zone of the continental margin, Middle Triassic dolostones and Lower Jurassic sediments are crossed by veins and hydrofracturing breccias cemented by saddle dolomite. The precipitation of dolomite cements occurred within the stratigraphic succession close to the sediment–water interface. Despite the shallow burial depth, fluid inclusion microthermometry and clumped isotopes show that hydrothermal fluids were relatively hot (80–150°C). In the western part of the study area, interpreted as part of the hyperextended distal zone, a polyphase history of host-rock fracturing is recorded, with at least two generations of veins cemented by calcite, dolomite and quartz. Vein opening and cementation occurred at shallow burial depth around the time of deposition of the syn-rift clastic succession. Fluid inclusion microthermometry on both quartz and dolomite cements indicates a fluid temperature of 90–130°C, again pointing to hydrothermal fluids. Both in Fenera-Sostegno and Montalto Dora areas, O, C and Sr isotope values, coupled with fluid inclusion and clumped isotope data, indicate that hydrothermal fluids derived from seawater interacted with crustal rocks during hydrothermal circulation. Stratigraphic and petrographic evidence, and U–Pb dating of dolomitized clasts within syn-rift sediments, document that hydrothermal fluids circulated through sediments from the latest Triassic to the Toarcian, corresponding to the entire syn-rift evolution of the western portion of the Adriatic palaeomargin. The documented hydrothermal processes are temporally correlated with regional-scale thermal events that took place in the same time interval at deeper crustal levels.
Background: No simple staging system has emerged for basal cell carcinomas (BCCs), since they do not follow the TNM process, and practitioners failed to agree on simple clinical or pathological criteria as a basis for a classification. Operational classification of BCCs is required for decision-making, trials and guidelines. Unsupervised clustering of real cases of difficult-to-treat BCCs (DTT-BCCs; part 1) has demonstrated that experts could blindly agree on a five groups classification of DTT-BCCs based on five patterns of clinical situations. Objective: Using this five patterns to generate an operational and comprehensive classification of BCCs. Method: Testing practitioner's agreement, when using the five patterns classification to ensure that it is robust enough to be used in the practice. Generating the first version of a staging system of BCCs based on pattern recognition. Results: Sixty-two physicians, including 48 practitioners and the 14 experts who participated in the generation of the five different patterns of DTT-BCCs, agreed on 90% of cases when classifying 199 DTT-BCCs cases using the five patterns classification (part 1) attesting that this classification is understandable and usable in practice. In order to cover the whole field of BCCs, these five groups of DTT-BCCs were added a group representing the huge number of easy-to-treat BCCs, for which sub-classification has little interest, and a group of very rare metastatic cases, resulting in a four-stage and seven-substage staging system of BCCs. Conclusion: A practical classification adapted to the specificities of BCCs is proposed. It is the first tumour classification based on pattern recognition of clinical situations, which proves to be consistent and usable. This EADO staging system version 1 will be improved step by step and tested as a decision tool and a prognostic instrument.
National greenhouse gas inventories (GHGIs) are submitted annually to the United Nations Framework Convention on Climate Change (UNFCCC). They are estimated in compliance with Intergovernmental Panel on Climate Change (IPCC) methodological guidance using activity data, emission factors and facility-level measurements. For some sources, the outputs from these calculations are very uncertain. Inverse modelling techniques that use high-quality, long-term measurements of atmospheric gases have been developed to provide independent verification of national GHGIs. This is considered good practice by the IPCC as it helps national inventory compilers to verify reported emissions and to reduce emission uncertainty. Emission estimates from the InTEM (Inversion Technique for Emission Modelling) model are presented for the UK for the hydrofluorocarbons (HFCs) reported to the UNFCCC (HFC-125, HFC-134a, HFC-143a, HFC-152a, HFC-23, HFC-32, HFC-227ea, HFC-245fa, HFC-43-10mee and HFC-365mfc). These HFCs have high global warming potentials (GWPs), and the global background mole fractions of all but two are increasing, thus highlighting their relevance to the climate and a need for increasing the accuracy of emission estimation for regulatory purposes. This study presents evidence that the long-term annual increase in growth of HFC-134a has stopped and is now decreasing. For HFC-32 there is an early indication, its rapid global growth period has ended, and there is evidence that the annual increase in global growth for HFC-125 has slowed from 2018. The inverse modelling results indicate that the UK implementation of European Union regulation of HFC emissions has been successful in initiating a decline in UK emissions from 2018. Comparison of the total InTEM UK HFC emissions in 2020 with the average from 2009–2012 shows a drop of 35 %, indicating progress toward the target of a 79 % decrease in sales by 2030. The total InTEM HFC emission estimates (2008–2018) are on average 73 (62–83) % of, or 4.3 (2.7–5.9) Tg CO2-eq yr−1 lower than, the total HFC emission estimates from the UK GHGI. There are also significant discrepancies between the two estimates for the individual HFCs.
The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.
When a nanoparticle is irradiated by an intense laser pulse, it turns into a nanoplasma, a transition that is accompanied by many interesting nonequilibrium dynamics. So far, most experiments on nanoplasmas use ion measurements, reflecting the outside dynamics in the nanoparticle. Recently, the direct observation of the ultrafast structural dynamics on the inside of the nanoparticle also became possible with the advent of x-ray free electron lasers (XFELs). Here, we report on combined measurements of structural dynamics and speeds of ions ejected from nanoplasmas produced by intense near-infrared laser irradiations, with the control of the initial plasma conditions accomplished by widely varying the laser intensity (9×1014 W/cm2 to 3×1016 W/cm2). The structural change of nanoplasmas is examined by time-resolved x-ray diffraction using an XFEL, while the kinetic energies of ejected ions are measured by an ion time-of-fight method under the same experimental conditions. We find that the timescale of crystalline disordering in nanoplasmas strongly depends on the laser intensity and scales with the inverse of the average speed of ions ejected from the nanoplasma. The observations support a recently suggested scenario for nanoplasma dynamics in the wide intensity range, in which crystalline disorder in nanoplasmas is caused by a rarefaction wave propagating at a speed comparable with the average ion speed from the surface toward the inner crystalline core. We demonstrate that the scenario is also applicable to nanoplasma dynamics in the hard x-ray regime. Our results connect the outside nanoplasma dynamics to the loss of structure inside the sample on the femtosecond timescale.
Destruction of the cosmic γ-ray emitter 26Al in massive stars: study of the key 26Al(n,p) reaction
(2021)
The 26Al(n,p)26Mg reaction is the key reaction impacting on the abundances of the cosmic γ-ray emitter 26Al produced in massive stars and impacts on the potential pollution of the early solar system with 26Al by asymptotic giant branch stars. We performed a measurement of the 26Al(n,p)26Mg cross section at the high-flux beam line EAR-2 at the n_TOF facility (CERN). We report resonance strengths for eleven resonances, nine being measured for the first time, while there is only one previous measurement for the other two. Our resonance strengths are significantly lower than the only previous values available. Our cross-section data range to 150 keV neutron energy, which is sufficient for a reliable determination of astrophysical reactivities up to 0.5 GK stellar temperature.
Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.
The term structure of interest rates is crucial for the transmission of monetary policy to financial markets and the macroeconomy. Disentangling the impact of monetary policy on the components of interest rates, expected short rates, and term premia is essential to understanding this channel. To accomplish this, we provide a quantitative structural model with endogenous, time-varying term premia that are consistent with empirical findings. News about future policy, in contrast to unexpected policy shocks, has quantitatively significant effects on term premia along the entire term structure. This provides a plausible explanation for partly contradictory estimates in the empirical literature.
CrB4O6N crystallizes in the non-centrosymmetric space group P63mc (no. 186) with the lattice parameters a=5.1036(1), c=8.3519(3) Å, and a volume of 188.40(1) Å3. It was synthesized in a high-pressure/high-temperature experiment at 7 GPa and 1673 K and represents the first high-pressure oxonitridoborate. It is built up of starlike-shaped entities of four BO3N tetrahedra, connected via one common nitrogen atom that resembles the fourfold-coordinated nitrogen atoms in the homeotypic nitridosilicates MYbSi4N7 (M=Sr, Ba). Building up a network with channels that contain the Cr3+ ions, CrB4O6N contains for the first time a tetrahedral building unit in contrast to trigonal planar B(O/N)3 entities in all other known oxonitridoborates. The structural relations as well as the results of spectroscopic measurements and calculations on the chromium oxonitridoborate are discussed.
The relationship between exhaustion and work engagement has received considerable attention during the past decades. Although the theoretical proposition exists that work engagement may increase exhaustion over time, previous research has been mixed. Drawing on the transactional stress model and applying latent growth modeling, we aim to provide a more comprehensive picture of the work engagement–exhaustion relationship over time. In two longitudinal studies, with four measurement points each, we found consistent evidence that a higher initial work engagement related to increased exhaustion over time. Consistent with our hypotheses, a higher initial work engagement also related to less initial exhaustion, and increases in work engagement related to decreases in exhaustion over time. However, contrary to our expectations, a higher initial exhaustion related to elevated work engagement over time. In conclusion, our findings suggest that engaged employees are less exhausted but face a higher risk of exhaustion over time. At the same time, exhausted employees are less engaged, but they have the potential to become more so over time. The theoretical and practical implications of these findings will be discussed in this paper.
Acinetobacter baumannii is an opportunistic pathogen, which has become a rising threat in healthcare facilities worldwide due to increasing antibiotic resistances and optimal adaptation to clinical environments and the human host. We reported in a former publication on the identification of three phopholipases of the phospholipase D (PLD) superfamily in A. baumannii ATCC 19606T acting in concerted manner as virulence factors in Galleria mellonella infection and lung epithelial cell invasion. This study focussed on the function of the three PLDs. A Δpld1-3 mutant was defect in biosynthesis of the phospholipids cardiolipin (CL) and monolysocardiolipin (MLCL), whereas the deletion of pld2 and pld3 abolished the production of MLCL. Complementation of the Δpld1-3 mutant with pld1 restored CL biosynthesis demonstrating that the PLD1 is implicated in CL biosynthesis. Complementation of the Δpld1-3 mutant with either pld2 or pld3 restored MLCL and CL production leading to the conclusion that PLD2 and PLD3 are implicated in CL and MLCL production. Mutant studies revealed that two catalytic motifs are essential for the PLD3-mediated biosynthesis of CL and MLCL. The Δpld1-3 mutant exhibited a decreased colistin and polymyxin B resistance indicating a role of CL in cationic antimicrobial peptides (CAMPs) resistance.
The genome of the halophilic archaeon Haloferax volcanii encodes more than 40 one-domain zinc finger µ-proteins. Only one of these, HVO_2753, contains four C(P)XCG motifs, suggesting the presence of two zinc binding pockets (ZBPs). Homologs of HVO_2753 are widespread in many euryarchaeota. An in frame deletion mutant of HVO_2753 grew indistinguishably from the wild-type in several media, but had a severe defect in swarming and in biofilm formation. For further analyses, the protein was produced homologously as well as heterologously in Escherichia coli. HVO_2753 was stable and folded in low salt, in contrast to many other haloarchaeal proteins. Only haloarchaeal HVO_2753 homologs carry a very hydrophilic N terminus, and NMR analysis showed that this region is very flexible and not part of the core structure. Surprisingly, both NMR analysis and a fluorimetric assay revealed that HVO_2753 binds only one zinc ion, despite the presence of two ZBPs. Notably, the analysis of cysteine to alanine mutant proteins by NMR as well by in vivo complementation revealed that all four C(P)XCG motifs are essential for folding and function. The NMR solution structure of the major conformation of HVO_2753 was solved. Unexpectedly, it was revealed that ZBP1 was comprised of C(P)XCG motifs 1 and 3, and ZBP2 was comprised of C(P)XCG motifs 2 and 4. There are several indications that ZBP2 is occupied by zinc, in contrast to ZBP1. To our knowledge, this study represents the first in-depth analysis of a zinc finger µ-protein in all three domains of life.
We report here the nuclear magnetic resonance 19F screening of 14 RNA targets with different secondary and tertiary structure to systematically assess the druggability of RNAs. Our RNA targets include representative bacterial riboswitches that naturally bind with nanomolar affinity and high specificity to cellular metabolites of low molecular weight. Based on counter-screens against five DNAs and five proteins, we can show that RNA can be specifically targeted. To demonstrate the quality of the initial fragment library that has been designed for easy follow-up chemistry, we further show how to increase binding affinity from an initial fragment hit by chemistry that links the identified fragment to the intercalator acridine. Thus, we achieve low-micromolar binding affinity without losing binding specificity between two different terminator structures.
Phytochrome photoreceptors operate via photoisomerization of a bound bilin chromophore. Their typical architecture consists of GAF, PAS and PHY domains. Knotless phytochromes lack the PAS domain, while retaining photoconversion abilities, with some being able to photoconvert with just the GAF domain. Therefore, we investigated the ultrafast photoisomerization of the Pr state of a knotless phytochrome to reveal the effect of the PHY domain and its “tongue” region on the transduction of the light signal. We show that the PHY domain does not affect the initial conformational dynamics of the chromophore. However, it significantly accelerates the consecutively induced reorganizational dynamics of the protein, necessary for the progression of the photoisomerization. Consequently, the PHY domain keeps the bilin and its binding pocket in a more reactive conformation, which decreases the extent of protein reorganization required for the chromophore isomerization. Thereby, less energy is lost along nonproductive reaction pathways, resulting in increased efficiency.
The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus lævis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
BAG3 is a negative regulator of ciliogenesis in glioblastoma and triple-negative breast cancer cells
(2021)
By regulating several hallmarks of cancer, BAG3 exerts oncogenic functions in a wide variety of malignant diseases including glioblastoma (GBM) and triple-negative breast cancer (TNBC). Here we performed global proteomic/phosphoproteomic analyses of CRISPR/Cas9-mediated isogenic BAG3 knockouts of the two GBM lines U343 and U251 in comparison to parental controls. Depletion of BAG3 evoked major effects on proteins involved in ciliogenesis/ciliary function and the activity of the related kinases aurora-kinase A and CDK1. Cilia formation was significantly enhanced in BAG3 KO cells, a finding that could be confirmed in BAG3-deficient versus -proficient BT-549 TNBC cells, thus identifying a completely novel function of BAG3 as a negative regulator of ciliogenesis. Furthermore, we demonstrate that enhanced ciliogenesis and reduced expression of SNAI1 and ZEB1, two key transcription factors regulating epithelial to mesenchymal transition (EMT) are correlated to decreased cell migration, both in the GBM and TNBC BAG3 knockout cells. Our data obtained in two different tumor entities identify suppression of EMT and ciliogenesis as putative synergizing mechanisms of BAG3-driven tumor aggressiveness in therapy-resistant cancers.
Purpose: Auditory functional MRI (fMRI) often uses silent inter-volume delays for stimulus presentation. However, maintaining the steady-state of the magnetization usually requires constant delays. Here, a novel acquisition scheme dubbed “pre-Saturated EPI using Multiple delays in Steady-state” (SEPIMS) is proposed, using spin saturation at a fixed delay before each volume to maintain steady-state conditions, independent of previous spin history. This concept allows for variable inter-volume delays and thus for flexible stimulus design in auditory fMRI. The purpose was to compare the signal stability of SEPIMS and conventional sparse EPI (CS-EPI). Methods: The saturation module comprises two non-selective adiabatic saturation pulses. The efficiency of the saturation and its effect on the SEPIMS signal stability is tested in vitro and in vivo. Results: Data show that SEPIMS yields the same signal stability as CS-EPI, even for extreme variations between inter-volume delay durations. However, dual saturation pulses are required to achieve sufficiently high saturation efficiency in compartments with long T1 values. Importantly, spoiler gradient pulses after the EPI readout have to be optimized to avoid eddy-current-induced image distortions. Conclusion: The proposed SEPIMS sequence maintains high signal stability in the presence of variable inter-volume durations, thus allowing for flexible stimulus design.
The C40A/C82A double mutant of barstar has been shown to undergo cold denaturation above the water freezing point. By rapidly applying radio-frequency power to lossy aqueous samples, refolding of barstar from its cold-denatured state can be followed by real-time NMR spectroscopy. Since temperature-induced unfolding and refolding is reversible for this double mutant, multiple cycling can be utilized to obtain 2D real-time NMR data. Barstar contains two proline residues that adopt a mix of cis and trans conformations in the low-temperature-unfolded state, which can potentially induce multiple folding pathways. The high time resolution real-time 2D-NMR measurements reported here show evidence for multiple folding pathways related to proline isomerization, and stable intermediates are populated. By application of advanced heating cycles and state-correlated spectroscopy, an alternative folding pathway circumventing the rate-limiting cis-trans isomerization could be observed. The kinetic data revealed intermediates on both, the slow and the fast folding pathway.