# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Structural and mechanistic insights into bacterial phospholipase A involved in membrane phospholipid degradation and virulence

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Cells steadily adapt their membrane glycerophospholipid (GPL) composition to changing environmental and developmental conditions. While the regulation of membrane homeostasis via GPL synthesis in bacteria has been studied in detail, the mechanisms underlying the controlled degradation of endogenous GPLs remain unknown. Thus far, the function of intracellular phospholipases A (PLAs) in GPL remodeling (Lands cycle) in bacteria is not clearly established. Here, we identified the first cytoplasmic membrane-bound phospholipase A1 (PlaF) from Pseudomonas aeruginosa, which might be involved in the Lands cycle. PlaF is an important virulence factor, as the P. aeruginosa ΔplaF mutant showed strongly attenuated virulence in Galleria mellonella and macrophages. We present a 2.0-Å-resolution crystal structure of PlaF, the first structure that reveals homodimerization of a single-pass transmembrane (TM) full-length protein. PlaF dimerization, mediated solely through the intermolecular interactions of TM and juxtamembrane regions, inhibits its activity. The dimerization site and the catalytic sites are linked by an intricate ligand-mediated interaction network, which might explain the product (fatty acid) feedback inhibition observed with the purified PlaF protein. We used molecular dynamics simulations and configurational free energy computations to suggest a model of PlaF activation through a coupled monomerization and tilting of the monomer in the membrane, which constrains the active site cavity into contact with the GPL substrates. Thus, these data indicate the importance of the PlaF mediated GPL remodeling pathway for virulence and could pave the way for the development of novel therapeutics targeting PlaF.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Structural and mechanistic insights into bacterial phospholipase A involved in membrane phospholipid degradation and virulence

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Three-dimensional brain organoids from human pluripotent stem cells are a powerful tool for studying human neural networks. This article presents a refined protocol for generating robust brain organoid slices derived from regionalized cortical organoids and grown at the air-liquid interphase. The procedures for slicing organoids and maintaining them in long-term culture are described. We then detail approaches for quality control including evaluation of cell death and cellular identity. Finally, we describe procedures for expression of a genetically-encoded nanosensor for ATP.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title.alternative[].value
Protocol for the generation of cultured cortical brain organoid slices (cBOS)

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled asgard archaea

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Supplement to a paper in GBE (title: Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled asgard archaea)

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.sponsorship[].value
This study was supported by the National Science Foundation of China (Nos. 91851210,
41530105), the Shenzhen Key Laboratory of Marine Archaea Geo-Omics, the Shenzhen
Science and Technology Innovation Commission (JCYJ20180305123458107), Southern
University of Science and Technology (No. ZDSYS20180208184349083), and the Southern
Marine Science and Engineering Guangdong Laboratory (Guangzhou) (No. K19313901).
This research was also funded by the Moore–Simons Project on the Origin of the Eukaryotic
Cell GBMF9743 to W.F.M. W.F.M. also would like to thank the ERC (666053), the VW
Foundation (93046 and 96742), and the DFG (Ma 1426/21-1) for funding.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.subject[].value
Metagenomics, binning, eukaryogenesis, phylogenetics, asgard archaea, candidate phylum radiation (CPR)

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled asgard archaea

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Loss of Bmal1 impairs the glutamatergic light input to the SCN in mice

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Introduction: Glutamate represents the dominant neurotransmitter that conveys the light information to the brain, including the suprachiasmatic nucleus (SCN), the central pacemaker for the circadian system. The neuronal and astrocytic glutamate transporters are crucial for maintaining efficient glutamatergic signaling. In the SCN, glutamatergic nerve terminals from the retina terminate on vasoactive intestinal polypeptide (VIP) neurons, which are essential for circadian functions. Up-to-date, little is known about the role of the core circadian clock gene, Bmal1, in glutamatergic neurotransmission of light signal to various brain regions. Methods: The aim of this study was to further elucidate the role of Bmal1 in glutamatergic neurotransmission from the retina to the SCN. We therefore examined the spontaneous rhythmic locomotor activity, neuronal and glial glutamate transporters, as well as the ultrastructure of the synapse between the retinal ganglion cells (RGCs) and the SCN in adult male Bmal1-/- mice. Results: We found that the deletion of Bmal1 affects the light-mediated behavior in mice, decreases the retinal thickness and affects the vesicular glutamate transporters (vGLUT1,2) in the retina. Within the SCN, the immunoreaction of vGLUT1,2, glial glutamate transporters (GLAST) and VIP was decreased while the glutamate concentration was elevated. At the ultrastructure level, the presynaptic terminals were enlarged and the distance between the synaptic vesicles and the synaptic cleft was increased, indicative of a decrease in the readily releasable pool at the excitatory synapses in Bmal1-/-. Conclusion: Our data suggests that Bmal1 deletion affects the glutamate transmission at the tripartite synapse between the ipRGCs and the VIP neurons in the SCN and affects the behavioral responses to light.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.subject[].value
Bmal1, circadian system, SCN, vGLUT, GLAST, VIP, synapses

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Loss of Bmal1 impairs the glutamatergic light input to the SCN in mice

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Three-dimensional brain organoids from human pluripotent stem cells are a powerful tool for studying human neural networks. This article presents a refined protocol for generating robust brain organoid slices derived from regionalized cortical organoids and grown at the air-liquid interphase. The procedures for slicing organoids and maintaining them in long-term culture are described. We then detail approaches for quality control including evaluation of cell death and cellular identity. Finally, we describe procedures for expression of a genetically-encoded nanosensor for ATP.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title.alternative[].value
Protocol for the generation of cultured cortical brain organoid slices (cBOS)

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Table S1: Measured density of the solution of anisole in ethyl acetate versus the weight fraction between 0 and 0.013 of the solute between 258K and 348K. The densities are given as kg/m^-3.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Measured density of the solution of anisole in ethyl acetate versus the weight fraction between 0 and 0.013 of the solute between 258 K and 348 K.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.identifier.citation[].value
Lindic, M. M.; Zajonz, M.; Hebestreit, M.-L.; Schneider, M.; Meerts, W. L.; Schmitt, M. Additional data for evaluation of the excited state dipole moments of anisole. Data in Brief 2018, 21, 313 – 315.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.subject[].value
Temperature and weight fraction dependent density measurements

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Table S1: Measured density of the solution of anisole in ethyl acetate versus the weight fraction between 0 and 0.013 of the solute between 258K and 348K. The densities are given as kg/m^-3.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
MD simulation data for: "Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
PlaF is a membrane-bound phospholipase A1 from P. aeruginosa that is involved in remodeling membrane glycerophospholipids (GPLs) and modulation of virulence-associated signaling and metabolic pathways. Previously, we identified the role of medium-chain free fatty acids (FFA) in inhibiting PlaF activity and promoting homodimerization, yet the underlying molecular mechanism remained elusive. Here, we used unbiased and biased molecular dynamics simulations and free energy computations to assess how PlaF interacts with FFAs localized in the water milieu surrounding the bilayer or within the bilayer, and how these interactions regulate PlaF activity. Medium-chain FFAs localized in the upper bilayer leaflet can stabilize inactive dimeric PlaF, likely through interactions with charged surface residues as experimentally validated. Potential of mean force (PMF) computations indicate that membrane-bound FFAs may facilitate the activation of monomeric PlaF by lowering the activation barrier of changing into a tilted, active configuration. We estimated that the coupled equilibria of PlaF monomerization-dimerization and tilting at the physiological concentration of PlaF lead to the majority of PlaF forming inactive dimers when in a cell membrane loaded with decanoic acid (C10). This is in agreement with a suggested in vivo product feedback loop and GC-MS profiling results indicating that PlaF catalyzes the release of C10 from P. aeruginosa membranes. Additionally, we found that C10 in the water milieu can access the catalytic site of active monomeric PlaF, contributing to the competitive component of C10-mediated PlaF inhibition. Our study provides mechanistic insights into how medium-chain FFA may regulate the activity of PlaF, a potential bacterial drug target.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
MD simulation data for: "Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-regulated Activity of the Phospholipase PlaF from Pseudomonas aeruginosa"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Simulation data for "Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates has remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by fatty acid-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Simulation data for "Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Petersilie et al. 2024 - Supplementary Figure

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Brain organoids derived from human pluripotent stem cells are a promising tool for studying human
neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain
organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We show that cBOS host mature neurons and astrocytes organized in complex architecture. Whole-cell patch clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Brief metabolic inhibition to mimic transient energy restriction in the ischemic brain induced reversible intracellular calcium loading of cBOS. Moreover, metabolic inhibition induced a reversible decline in neuronal ATP as revealed by ATeam1.03YEMK. Overall, cBOS provide a powerful platform to assess morphological and functional aspects of human neural cells in intact minimal networks and to address the pathways that drive cellular damage during brain ischemia.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Petersilie et al. 2024 - Supplementary Figure

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title.alternative[].value
Cortical brain organoid slices (cBOS) for the study of human neural cells in minimal networks

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Molecular dynamics simulations data and analysis scripts used for Grx5 in the publication "Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
The files in this directory contain the molecular dynamics simulations data and analysis scripts for Grx5 used in the publication
"Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Molecular dynamics simulations data and analysis scripts used for Grx5 in the publication "Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Beteiligte Forschungsprojekte und deren FDM Anforderungen

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
An den drei Standorten gab es verschiedene Bedarfe der bestehenden (oder geplanten) Forschungsprojekte. In dieser Tabelle sind die wichtigsten Eckdaten der Projekte vermerkt.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Beteiligte Forschungsprojekte und deren FDM Anforderungen

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Brain organoids derived from human pluripotent stem cells are a promising tool for studying human
neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain
organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We show that cBOS host mature neurons and astrocytes organized in complex architecture. Whole-cell patch clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Brief metabolic inhibition to mimic transient energy restriction in the ischemic brain induced reversible intracellular calcium loading of cBOS. Moreover, metabolic inhibition induced a reversible decline in neuronal ATP as revealed by ATeam1.03YEMK. Overall, cBOS provide a powerful platform to assess morphological and functional aspects of human neural cells in intact minimal networks and to address the pathways that drive cellular damage during brain ischemia.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title.alternative[].value
Cortical brain organoid slices (cBOS) for the study of human neural cells in minimal networks

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Structural models of SFV Bet protein as SI for "Foamy Viruses, Bet, and APOBEC3 Restriction"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Domain boundaries within the sequence of the SFV-chimpanzee Bet protein sequence were predicted with TopDomain. 
The two domains were modeled using the ROBETTA webserver. 
For each domain, ROBETTA generated five models. The best model was chosen based on the lowest Cα atom RMSD 
between the generated models and the corresponding ab initio modeled domain of PFV Bet. 
This consensus approach was also validated by TopScore in that domains with the lowest RMSD also have the 
lowest TopScore compared to the other four models. 
For the N-terminal domain, the overall TopScore is 0.47 and for the C-terminal one 0.45, indicating a moderate quality of the models. 
In the N-terminal domain, the helical part of the structure has low local TopScores, indicating good quality, 
but the N-terminal loops high local TopScores, indicating low quality. 
In the C-terminal domain, the β-strands have low local TopScores, indicating good quality, 
but helices and loops from residues 358–403 have high local TopScores, indicating low quality.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Structural models of SFV Bet protein as SI for "Foamy Viruses, Bet, and APOBEC3 Restriction"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Table S2: Absorption spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K. These data are available as Table S2.doc and Table S2.csv. The raw data (in nm) are available as Table 2.dat

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Absorption spectra (in wavenumber) of anisole in ethyl acetate between 258K
and 348K in steps of 5K.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Table S2: Absorption spectra (in wavenumber) of anisole in ethyl acetate between 258K and 348K in steps of 5K. These data are available as Table S2.doc and Table S2.csv. The raw data (in nm) are available as Table 2.dat

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Brain organoids derived from human pluripotent stem cells are a promising tool for studying human
neurodevelopment and related disorders. Here, we generated long-term cultures of cortical brain
organoid slices (cBOS) grown at the air-liquid interphase from regionalized cortical organoids. We show that cBOS host mature neurons and astrocytes organized in complex architecture. Whole-cell patch clamp demonstrated subthreshold synaptic inputs and action potential firing of neurons. Spontaneous intracellular calcium signals turned into synchronous large-scale oscillations upon combined disinhibition of NMDA receptors and blocking of GABAA receptors. Brief metabolic inhibition to mimic transient energy restriction in the ischemic brain induced reversible intracellular calcium loading of cBOS. Moreover, metabolic inhibition induced a reversible decline in neuronal ATP as revealed by ATeam1.03YEMK. Overall, cBOS provide a powerful platform to assess morphological and functional aspects of human neural cells in intact minimal networks and to address the pathways that drive cellular damage during brain ischemia.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title.alternative[].value
Cortical brain organoid slices (cBOS) for the study of human neural cells in minimal networks

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Subacute thyroiditis – Is it really linked to viral infection? - Supplemental material

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.contributor.author[].value
Hans Martin Orth,  Alexander Killer,  Smaranda Gliga,  Michael Böhm, Torsten Feldt,  Björn-Erik O. Jensen, Tom Luedde, Rolf Kaiser, Martin Pirkl

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
This document includes additional figures for the study "Subacute thyroiditis – Is it really linked to viral infection?"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.subject.ddc[].value
600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::616 Krankheiten

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Subacute thyroiditis – Is it really linked to viral infection? - Supplemental material

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Supporting Information for "Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
The dataset contains: I. 3D structural models of esterases generated by a AlphaFold2-based workflow of ColabFold, II. predicted catalytic triads of esterases and their substrate accessibilities analyzed by CAVER 3.0.3 PyMOL Plugin, III. input and output files for molecular dynamics (MD) simulations performed by Amber21, and, IV. Tp-values of esterases predicted by Constraint Network Analysis (CNA). We added template scripts and a readme file for further explanations.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Supporting Information for "Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes"

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.name
Table S4: Linearized laser induced fluroescence Stark spectrum of anisole at an electric field strength of 819:09Vcm􀀀1. The first column gives the relative frequeny in 1MHz increment, the second column the relative intensities.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Linearized laser induced fluroescence Stark spectrum of anisole at an electric
field strength of 819:09V/cm. The first column gives the relative frequeny in 1MHz
increment, the second column the relative intensities.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.subject[].value
Laser induced fluorescence Stark spectrum

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title[].value
Table S4: Linearized laser induced fluroescence Stark spectrum of anisole at an electric field strength of 819:09Vcm􀀀1. The first column gives the relative frequeny in 1MHz increment, the second column the relative intensities.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Presentation slides for the training seminar about Open Science in Research Data Management of the FoDaKo-project: https://fodako.de

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.description.abstract[].value
Three-dimensional brain organoids from human pluripotent stem cells are a powerful tool for studying human neural networks. This article presents a refined protocol for generating robust brain organoid slices derived from regionalized cortical organoids and grown at the air-liquid interphase. The procedures for slicing organoids and maintaining them in long-term culture are described. We then detail approaches for quality control including evaluation of cell death and cellular identity. Finally, we describe procedures for expression of a genetically-encoded nanosensor for ATP.

# _embedded.searchResult._embedded.objects[]._embedded.indexableObject.metadata.dc.title.alternative[].value
Protocol for the generation of cultured cortical brain organoid slices (cBOS)