SimStack: An Intuitive Workflow Framework

Establishing a fundamental understanding of the nature of materials via computational simulation approaches requires knowledge from different areas, including physics, materials science, chemistry, mechanical engineering, mathematics, and computer science. Accurate modeling of the characteristics of a particular system usually involves multiple scales and therefore requires the combination of methods from various fields into custom-tailored simulation workflows. The typical approach to developing patch-work solutions on a case-to-case basis requires extensive expertise in scripting, command-line execution, and knowledge of all methods and tools involved for data preparation, data transfer between modules, module execution, and analysis. Therefore multiscale simulations involving state-of-the-art methods suffer from limited scalability, reproducibility, and flexibility. In this work, we present the workflow framework SimStack that enables rapid prototyping of simulation workflows involving modules from various sources. In this platform, multiscale- and multimodule workflows for execution on remote computational resources are crafted via drag and drop, minimizing the required expertise and effort for workflow setup. By hiding the complexity of high-performance computations on remote resources and maximizing reproducibility, SimStack enables users from academia and industry to combine cutting-edge models into custom-tailored, scalable simulation solutions

Biogeochemical limitations of carbon stabilization in forest subsoils

Background: Soils are important carbon (C) sinks or sources and thus of utmost importance for global carbon cycling. Particularly, subsoils are considered to have a high potential for additional C storage due to mineral surfaces still available for sorptive stabilization. Aims: Little information exists about the extent to which additional litter-derived C is transferred to and stabilized in subsoils. This study aimed at evaluating the role of litter-derived dissolved organic matter (DOM) inputs for the formation of stable mineral-associated C in subsoils. Methods: We carried out a multiple-method approach including field labeling with 13C-enriched litter, exposure of 13C-loaded reactive minerals to top- and subsoils, and laboratory sorption experiments. Results: For temperate forest soils, we found that the laboratory-based C sink capacity of subsoils is unlikely to be reached under field conditions. Surface C inputs via litter leachates are little conducive to the subsoil C pool. Only 0.5% of litter-derived C entered the subsoil as DOM within nearly 2 years and most of the recently sorbed C is prone to fast microbial mineralization rather than long-term mineral retention. Desorption to the soil solution and an adapted microbial community re-mobilize organic matter in subsoils faster than considered so far. Conclusions: We conclude that the factors controlling the current mineral retention and stabilization of C within temperate forest subsoils will likewise limit additional C uptake. Thus, in contrast to their widely debated potential to accrue more C, the role of forest subsoils as future C sink is likely overestimated and needs further reconsideration

An overview of data‐driven HADDOCK strategies in CAPRI rounds 38-45

Our information-driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part, to its ability to integrate data into the modeling process, and to the robustness of its scoring function. We participated in CAPRI both as server and manual predictors. In CAPRI rounds 38-45, we have used various strategies depending on the available information. These ranged from imposing restraints to a few residues identified from literature as being important for the interaction, to binding pockets identified from homologous complexes or template-based refinement/CA-CA restraint-guided docking from identified templates. When relevant, symmetry restraints were used to limit the conformational sampling. We also tested for a large decamer target a new implementation of the MARTINI coarse-grained force field in HADDOCK. Overall, we obtained acceptable or better predictions for 13 and 11 server and manual submissions, respectively, out of the 22 interfaces. Our server performance (acceptable or higher-quality models when considering the top 10) was better (59%) than the manual (50%) one, in which we typically experiment with various combinations of protocols and data sources. Again, our simple scoring function based on a linear combination of intermolecular van der Waals and electrostatic energies and an empirical desolvation term demonstrated a good performance in the scoring experiment with a 63% success rate across all 22 interfaces. An analysis of model quality indicates that, while we are consistently performing well in generating acceptable models, there is room for improvement for generating/identifying higher quality models

Seroepidemiological study on the spread of SARS-CoV-2 in Germany:

The SARS-CoV-2 coronavirus has spread rapidly across Germany. Infections are likely to be under-recorded in the notification data from local health authorities on laboratory-confirmed cases since SARS-CoV-2 infections can proceed with few symptoms and then often remain undetected. Seroepidemiological studies allow the estimation of the proportion in the population that has been infected with SARS-CoV-2 (seroprevalence) as well as the extent of undetected infections. The ‘CORONA-MONITORING bundesweit’ study (RKI-SOEP study) collects biospecimens and interview data in a nationwide population sample drawn from the German Socio-Economic Panel (SOEP). Participants are sent materials to self-collect a dry blood sample of capillary blood from their finger and a swab sample from their mouth and nose, as well as a questionnaire. The samples returned are tested for SARS-CoV-2 IgG antibodies and SARS-CoV-2 RNA to identify past or present infections. The methods applied enable the identification of SARS-CoV-2 infections, including those that previously went undetected. In addition, by linking the data collected with available SOEP data, the study has the potential to investigate social and health-related differences in infection status. Thus, the study contributes to an improved understanding of the extent of the epidemic in Germany, as well as identification of target groups for infection protection

Differentiated Human Midbrain-Derived Neural Progenitor Cells Express Excitatory Strychnine-Sensitive Glycine Receptors Containing α2β Subunits

BACKGROUND: Human fetal midbrain-derived neural progenitor cells (NPCs) may deliver a tissue source for drug screening and regenerative cell therapy to treat Parkinson's disease. While glutamate and GABA(A) receptors play an important role in neurogenesis, the involvement of glycine receptors during human neurogenesis and dopaminergic differentiation as well as their molecular and functional characteristics in NPCs are largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: Here we investigated NPCs in respect to their glycine receptor function and subunit expression using electrophysiology, calcium imaging, immunocytochemistry, and quantitative real-time PCR. Whole-cell recordings demonstrate the ability of NPCs to express functional strychnine-sensitive glycine receptors after differentiation for 3 weeks in vitro. Pharmacological and molecular analyses indicate a predominance of glycine receptor heteromers containing α2β subunits. Intracellular calcium measurements of differentiated NPCs suggest that glycine evokes depolarisations mediated by strychnine-sensitive glycine receptors and not by D-serine-sensitive excitatory glycine receptors. Culturing NPCs with additional glycine, the glycine-receptor antagonist strychnine, or the Na(+)-K(+)-Cl(-) co-transporter 1 (NKCC1)-inhibitor bumetanide did not significantly influence cell proliferation and differentiation in vitro. CONCLUSIONS/SIGNIFICANCE: These data indicate that NPCs derived from human fetal midbrain tissue acquire essential glycine receptor properties during neuronal maturation. However, glycine receptors seem to have a limited functional impact on neurogenesis and dopaminergic differentiation of NPCs in vitro

Seroepidemiologische Studie zur bundesweiten Verbreitung von SARS-CoV-2 in Deutschland: Studienprotokoll von CORONA-MONITORING bundesweit (RKI-SOEP-Studie)

Das Coronavirus SARS-CoV-2 hat sich in kurzer Zeit bundesweit ausgebreitet. In den Meldedaten der Gesundheitsämter zu laborbestätigten Infektionsfällen ist von einer Untererfassung des Infektionsgeschehens auszugehen, da Infektionen häufig unentdeckt bleiben, zum Beispiel weil sie symptomarm verlaufen. In seroepidemiologischen Studien kann der Bevölkerungsanteil mit durchgemachter SARS-CoV-2-Infektion (Seroprävalenz) wie auch der Umfang unentdeckter Infektionen abgeschätzt werden. In der Studie CORONA-MONITORING bundesweit (RKI-SOEP-Studie) werden Bioproben und Befragungsdaten in einer deutschlandweiten Bevölkerungsstichprobe des Sozio-oekonomischen Panels (SOEP) erhoben. Den Teilnehmenden werden Materialien zur selbstständigen Gewinnung einer Trockenblutprobe aus Kapillarblut des Fingers und einer Abstrichprobe aus Mund und Nase sowie ein Fragebogen postalisch zugesendet. Die zurückgesendeten Proben werden auf SARS-CoV-2-IgG-Antikörper und SARS-CoV-2-RNA zur Identifikation einer durchgemachten oder aktuellen Infektion untersucht. Die eingesetzten Methoden ermöglichen es, auch solche SARS-CoV-2-Infektionen zu erkennen, die bislang unentdeckt blieben. Durch die Verknüpfung mit bereits vorhandenen SOEP-Daten hat die Studie das Potenzial, auch soziale und gesundheitsbezogene Unterschiede im Infektionsstatus zu untersuchen. So kann die Studie zu einem verbesserten Verständnis des Ausmaßes der Epidemie in Deutschland wie auch zur Identifikation von Zielgruppen für den Infektionsschutz beitragen

A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis

A novel, high-affinity sucrose transporter identified in the plasma membrane of the plant pathogen Ustilago maydis is essential for fungal virulence and successful infection of maize

Assessment of contact predictions in CASP12: co-evolution and deep learning coming of age

Following up on the encouraging results of residue-residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of 34 groups for 38 domains classified as free modeling targets which are not accessible to homology-based modeling due to a lack of structural templates. CASP11 saw a rise of coevolution-based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12. In more than half of the targets, especially those with many homologous sequences accessible, precisions above 90% were achieved with the best predictors reaching a precision of 100% in some cases. We furthermore tested the impact of using these contacts as restraints in ab initio modeling of 14 single-domain free modeling targets using Rosetta. Adding contacts to the Rosetta calculations resulted in improvements of up to 26% in GDT_TS within the top five structures

Assessment of contact predictions in CASP12: co-evolution and deep learning coming of age

Following up on the encouraging results of residue-residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of 34 groups for 38 domains classified as free modeling targets which are not accessible to homology-based modeling due to a lack of structural templates. CASP11 saw a rise of coevolution-based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12. In more than half of the targets, especially those with many homologous sequences accessible, precisions above 90% were achieved with the best predictors reaching a precision of 100% in some cases. We furthermore tested the impact of using these contacts as restraints in ab initio modeling of 14 single-domain free modeling targets using Rosetta. Adding contacts to the Rosetta calculations resulted in improvements of up to 26% in GDT_TS within the top five structures

Influence of the hinge region and its adjacent domains on binding and signaling patterns of the thyrotropin and follitropin receptor.

Glycoprotein hormone receptors (GPHR) have a large extracellular domain (ECD) divided into the leucine rich repeat (LRR) domain for binding of the glycoprotein hormones and the hinge region (HinR), which connects the LRR domain with the transmembrane domain (TMD). Understanding of the activation mechanism of GPHRs is hindered by the unknown interaction of the ECD with the TMD and the structural changes upon ligand binding responsible for receptor activation. Recently, our group showed that the HinR of the thyrotropin receptor (TSHR) can be replaced by those of the follitropin (FSHR) and lutropin receptor (LHCGR) without effects on surface expression and hTSH signaling. However, differences in binding characteristics for bovine TSH at the various HinRs were obvious. To gain further insights into the interplay between LRR domain, HinR and TMD we generated chimeras between the TSHR and FSHR. Our results obtained by the determination of cell surface expression, ligand binding and G protein activation confirm the similar characteristics of GPHR HinRs but they also demonstrate an involvement of the HinR in ligand selectivity indicated by the observed promiscuity of some chimeras. While the TSHR HinR contributes to specific binding of TSH and its variants, no such contribution is observed for FSH and its analog TR4401 at the HinR of the FSHR. Furthermore, the charge distribution at the poorly characterized LRR domain/HinR transition affected ligand binding and signaling even though this area is not in direct contact with the ligand. In addition our results also demonstrate the importance of the TMD/HinR interface. Especially the combination of the TSHR HinR with the FSHR-TMD resulted in a loss of cell surface expression of the respective chimeras. In conclusion, the HinRs of GPHRs do not only share similar characteristics but also behave as ligand specific structural and functional entities