MediaDive: the expert-curated cultivation media database.

We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms.

Therapeutic Peptides Are Preferentially Solubilized in Specific Microenvironments within PEG-PLGA Polymer Nanoparticles.

Polymeric nanoparticles are a highly promising drug delivery formulation. However, a lack of understanding of the molecular mechanisms that underlie their drug solubilization and controlled release capabilities has hindered the efficient clinical translation of such technologies. Polyethylene glycol-poly(lactic-co-glycolic) acid (PEG-PLGA) nanoparticles have been widely studied as cancer drug delivery vehicles. In this letter, we use unbiased coarse-grained molecular dynamics simulations to model the self-assembly of a PEG-PLGA nanoparticle and its solubulization of the anticancer peptide, EEK, with good agreement with previously reported experimental structural data. We applied unsupervised machine learning techniques to quantify the conformations that polymers adopt at various locations within the nanoparticle. We find that the local microenvironments formed by the various polymer conformations promote preferential EEK solubilization within specific regions of the NP. This demonstrates that these microenvironments are key in controlling drug storage locations within nanoparticles, supporting the rational design of nanoparticles for therapeutic applications.

Proline-Tyrosine Ring Interactions in Black Widow Dragline Silk Revealed by Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulations.

Selective one-dimensional 13C-13C spin-diffusion solid-state nuclear magnetic resonance (SSNMR) provides evidence for CH/π ring packing interactions between Pro and Tyr residues in 13C-enriched Latrodectus hesperus dragline silk. The secondary structure of Pro-containing motifs in dragline spider silks consistently points to an elastin-like type II ß-turn conformation based on 13C chemical shift analysis. 13C-13C spin diffusion measurements as a function of mixing times allow for the measurement of spatial proximity between the Pro and Tyr rings to be ∼0.5-1 nm, supporting strong Pro-Tyr ring interactions that likely occur through a CH/π mechanism. These results are supported by molecular dynamics (MD) simulations and analysis and reveals new insights into the secondary structure and Pro-Tyr ring stacking interactions for one of nature's toughest biomaterials.

BacDive in 2022: the knowledge base for standardized bacterial and archaeal data.

The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms.

Resilience of Xanthoria parietina under Mars-like conditions: photosynthesis and oxidative stress response.

MAIN CONCLUSION: Xanthoria parietina survivability in Mars-like conditions was supported by water-lysis efficiency recovery and antioxidant content balancing with ROS production after 30 days of exposure. Xanthoria parietina (L.) Th. Fr. is a widespread lichen showing tolerance against air pollutants and UV-radiation. It has been tested under space-like and Mars-like conditions resulting in high recovery performances. Hereby, we aim to assess the mechanisms at the basis of the thalli resilience against multiple space stress factors. Living thalli of X. parietina were exposed to simulated Martian atmospheric conditions (Dark Mars) and UV radiation (Full Mars). Then, we monitored as vitality indicator the photosynthetic efficiency, assessed by in vivo chlorophyll emission fluorescence measurements (FM; FV/F0). The physiological defense was evaluated by analyzing the thalli antioxidant capacity. The drop of FM and FV/F0 immediately after the exposure indicated a reduction of photosynthesis. After 24 h from exposure, photosynthetic efficiency began to recover suggesting the occurrence of protective mechanisms. Antioxidant concentrations were higher during the exposure, only decreasing after 30 days. The recovery of photosynthetic efficiency in both treatments suggested a strong resilience by the photosynthetic apparatus against combined space stress factors, likely due to the boosted antioxidants at the beginning and their depletion at the end of the exposure. The overall results indicated that the production of antioxidants, along with the occurrence of photoprotection mechanisms, guarantee X. parietina survivability in Mars-like environment.

Modular Software for Generating and Modeling Diverse Polymer Databases.

Machine learning methods offer the opportunity to design new functional materials on an unprecedented scale; however, building the large, diverse databases of molecules on which to train such methods remains a daunting task. Automated computational chemistry modeling workflows are therefore becoming essential tools in this data-driven hunt for new materials with novel properties, since they offer a means by which to create and curate molecular databases without requiring significant levels of user input. This ensures that well-founded concerns regarding data provenance, reproducibility, and replicability are mitigated. We have developed a versatile and flexible software package, PySoftK (Python Soft Matter at King's College London) that provides flexible, automated computational workflows to create, model, and curate libraries of polymers with minimal user intervention. PySoftK is available as an efficient, fully tested, and easily installable Python package. Key features of the software include the wide range of different polymer topologies that can be automatically generated and its fully parallelized library generation tools. It is anticipated that PySoftK will support the generation, modeling, and curation of large polymer libraries to support functional materials discovery in the nanotechnology and biotechnology arenas.

Temporin B Forms Hetero-Oligomers with Temporin L, Modifies Its Membrane Activity, and Increases the Cooperativity of Its Antibacterial Pharmacodynamic Profile.

The pharmacodynamic profile of antimicrobial peptides (AMPs) and their in vivo synergy are two factors that are thought to restrict resistance evolution and ensure their conservation. The frog Rana temporaria secretes a family of closely related AMPs, temporins A-L, as an effective chemical dermal defense. The antibacterial potency of temporin L has been shown to increase synergistically in combination with both temporins B and A, but this is modest. Here we show that the less potent temporin B enhances the cooperativity of the in vitro antibacterial activity of the more potent temporin L against EMRSA-15 and that this may be associated with an altered interaction with the bacterial plasma membrane, a feature critical for the antibacterial activity of most AMPs. Addition of buforin II, a histone H2A fragment, can further increase the cooperativity. Molecular dynamics simulations indicate temporins B and L readily form hetero-oligomers in models of Gram-positive bacterial plasma membranes. Patch-clamp studies show transmembrane ion conductance is triggered with lower amounts of both peptides and more quickly when used in combination, but conductance is of a lower amplitude and pores are smaller. Temporin B may therefore act by forming temporin L/B hetero-oligomers that are more effective than temporin L homo-oligomers at bacterial killing and/or by reducing the probability of the latter forming until a threshold concentration is reached. Exploration of the mechanism of synergy between AMPs isolated from the same organism may therefore yield antibiotic combinations with advantageous pharmacodynamic properties.

ILC1 drive intestinal epithelial and matrix remodelling.

Organoids can shed light on the dynamic interplay between complex tissues and rare cell types within a controlled microenvironment. Here, we develop gut organoid cocultures with type-1 innate lymphoid cells (ILC1) to dissect the impact of their accumulation in inflamed intestines. We demonstrate that murine and human ILC1 secrete transforming growth factor ß1, driving expansion of CD44v6+ epithelial crypts. ILC1 additionally express MMP9 and drive gene signatures indicative of extracellular matrix remodelling. We therefore encapsulated human epithelial-mesenchymal intestinal organoids in MMP-sensitive, synthetic hydrogels designed to form efficient networks at low polymer concentrations. Harnessing this defined system, we demonstrate that ILC1 drive matrix softening and stiffening, which we suggest occurs through balanced matrix degradation and deposition. Our platform enabled us to elucidate previously undescribed interactions between ILC1 and their microenvironment, which suggest that they may exacerbate fibrosis and tumour growth when enriched in inflamed patient tissues.

Asymmetric glycerophospholipids impart distinctive biophysical properties to lipid bilayers.

Phospholipids are a diverse group of biomolecules consisting of a hydrophilic headgroup and two hydrophobic acyl tails. The nature of the head and length and saturation of the acyl tails are important for defining the biophysical properties of lipid bilayers. It has recently been shown that the membranes of certain yeast species contain high levels of unusual asymmetric phospholipids consisting of one long and one medium-chain acyl moiety, a configuration not common in mammalian cells or other well-studied model yeast species. This raises the possibility that structurally asymmetric glycerophospholipids impart distinctive biophysical properties to the yeast membranes. Previously, it has been shown that lipids with asymmetric length tails form a mixed interdigitated gel phase and exhibit unusual endotherm behavior upon heating and cooling. Here, however, we address physiologically relevant temperature conditions and, using atomistic molecular dynamics simulations and environmentally sensitive fluorescent membrane probes, characterize key biophysical parameters (such as lipid packing, diffusion coefficient, membrane thickness, and area per lipid) in membranes composed of both length-asymmetric glycerophospholipids and ergosterol. Interestingly, we show that saturated but asymmetric glycerophospholipids maintain membrane lipid order across a wide range of temperatures. We also show that these asymmetric lipids can substiture of unsaturated symmetric lipids in the phase behaviour of ternary lipid bilayers. This may allow cells to maintain membrane fluidity, even in environments that lack oxygen, which is required for the synthesis of unsaturated lipids and sterols.

The Impact of Lipid Digestion on the Dynamic and Structural Properties of Micelles.

Self-assembled, lipid-based micelles, such as those formed by the short-chain phosphocholine, dihexanoylphosphatidylcholine (2C6PC), are degraded by the pancreatic enzyme, phospholipase A2 (PLA2). Degradation yields 1-hexanoyl-lysophosphocholine (C6LYSO) and hexanoic acid (C6FA) products. However, little is known about the behavior of these products during and after the degradation of 2C6PC. In this work, a combination of static and time-resolved small angle neutron scattering, as well as all-atom molecular dynamics simulations, is used to characterize the structure of 2C6PC micelles. In doing so a detailed understanding of the substrate and product aggregation behavior before, during and after degradation is gained. Consequently, the formation of mixed micelles containing 2C6PC, C6LYSO and C6FA is shown at every stage of the degradation process, as well as the formation of mixed C6LYSO/C6FA micelles after degradation is complete. The use of atomistic molecular dynamics has allowed us to characterize the structure of 2C6PC, 2C6PC/C6LYSO/C6FA, and C6LYSO/C6FA micelles throughout the degradation process, showing the localization of the different molecular species within the aggregates. In addition, the hydration of the 2C6PC, C6LYSO, and C6FA species both during micellization and as monomers in aqueous solution is documented to reveal the processes driving their micellization.

Effects of lipid heterogeneity on model human brain lipid membranes.

Cell membranes naturally contain a heterogeneous lipid distribution. However, homogeneous bilayers are commonly preferred and utilised in computer simulations due to their relative simplicity, and the availability of lipid force field parameters. Recently, experimental lipidomics data for the human brain cell membranes under healthy and Alzheimer's disease (AD) conditions were investigated, since disruption to the lipid composition has been implicated in neurodegenerative disorders, including AD [R. B. Chan et al., J. Biol. Chem., 2012, 287, 2678-2688]. In order to observe the effects of lipid complexity on the various bilayer properties, molecular dynamics simulations were used to study four membranes with increasing heterogeneity: a pure POPC membrane, a POPC and cholesterol membrane in a 1 : 1 ratio (POPC-CHOL), and to our knowledge, the first realistic models of a healthy brain membrane and an Alzheimer's diseased brain membrane. Numerous structural, interfacial, and dynamical properties, including the area per lipid, interdigitation, dipole potential, and lateral diffusion of the two simple models, POPC and POPC-CHOL, were analysed and compared to those of the complex brain models consisting of 27 lipid components. As the membranes gain heterogeneity, a number of alterations were found in the structural and dynamical properties, and more significant differences were observed in the lateral diffusion. Additionally, we observed snorkeling behaviour of the lipid tails that may play a role in the permeation of small molecules across biological membranes. In this work, atomistic description of realistic brain membrane models is provided, which can add insight towards the permeability and transport pathways of small molecules across these membrane barriers.

BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.

The bacterial metadatabase BacDive (http://bacdive.dsmz.de) has become a comprehensive resource for structured data on the taxonomy, morphology, physiology, cultivation, isolation and molecular data of prokaryotes. With its current release (7/2018) the database offers information for 63 669 bacterial and archaeal strains including 12 715 type strains. During recent developments of BacDive, the enrichment of information on existing strains was prioritized. This has resulted in a 146% increase of database content over the past three years. Especially rich datasets were integrated from 4782 manual annotated species descriptions in the International Journal of Systematic and Evolutionary Microbiology which yielded standardized phenotypic data for 5468 type strains. Another important improvement of content was achieved through the mobilization of 8977 Analytical Profile Index (API®) test results that constitute physiological data for the identification of 5237 strains. BacDive offers a unique API® data collection with respect to size and diversity. In addition, data on fatty acid profiles and antibiotic susceptibility tests were integrated. A revised graphical user interface and new search tools such as the API® test finder, the TAXplorer, or the Microbial Isolation Source Search significantly improve the user experience.

Transcriptional Responses of Pseudomonas aeruginosa to Inhibition of Lipoprotein Transport by a Small Molecule Inhibitor.

Lipoprotein transport from the inner to the outer membrane, carried out by the Lol machinery, is essential for the biogenesis of the Gram-negative cell envelope and, consequently, for bacterial viability. Recently, small molecule inhibitors of the Lol system in Escherichia coli have been identified and shown to inhibit the growth of this organism by interfering with the function of the LolCDE complex. Analysis of the transcriptome of E. coli treated with one such molecule (compound 2) revealed that a number of envelope stress response pathways were induced in response to LolCDE inhibition. However, Pseudomonas aeruginosa is refractory to inhibition by the same small molecule, but we could demonstrate that E. colilolCDE could be substituted for the P. aeruginosa orthologues, where it functions in the correct transport of Pseudomonas lipoproteins, and the cells are inhibited by the more potent compound 2A. In the present study, we took advantage of the functionality of E. coli LolCDE in P. aeruginosa and determined the P. aeruginosa transcriptional response to LolCDE inhibition by compound 2A. We identified key genes that responded to LolCDE inhibition and also demonstrated that the same genes appeared to be affected by genetic depletion of the native P. aeruginosa LolCDE proteins. Several of the major changes were in an upregulated cluster of genes that encode determinants of alginate biosynthesis and transport, and the levels of alginate were found to be increased either by treatment with the small molecule inhibitor or upon depletion of native LolCDE. Finally, we tested several antibiotics with differing mechanisms of action to identify potential specific reporter genes for the further development of compounds that would inhibit the native P. aeruginosa Lol system.IMPORTANCE A key set of lipoprotein transport components, LolCDE, were inhibited by both a small molecule as well as genetic downregulation of their expression. The data show a unique signature in the Pseudomonas aeruginosa transcriptome in response to perturbation of outer membrane biogenesis. In addition, we demonstrate a transcriptional response in key genes with marked specificity compared to several antibiotic classes with different mechanisms of action. As a result of this work, we identified genes that could be of potential use as biomarkers in a cell-based screen for novel antibiotic inhibitors of lipoprotein transport in P. aeruginosa.

Time-Resolved Fluorescence Anisotropy of a Molecular Rotor Resolves Microscopic Viscosity Parameters in Complex Environments.

Understanding viscosity in complex environments remains a largely unanswered question despite its importance in determining reaction rates in vivo. Here, time-resolved fluorescence anisotropy imaging (TR-FAIM) is combined with fluorescent molecular rotors (FMRs) to simultaneously determine two non-equivalent viscosity-related parameters in complex heterogeneous environments. The parameters, FMR rotational correlation time and lifetime, are extracted from fluorescence anisotropy decays, which in heterogeneous environments show dip-and-rise behavior due to multiple dye populations. Decays of this kind are found both in artificially constructed adiposomes and in live cell lipid droplet organelles. Molecular dynamics simulations are used to assign each population to nano-environments within the lipid systems. The less viscous population corresponds to the state showing an average 25° tilt to the lipid membrane normal, and the more viscous population to the state showing an average 55° tilt. This combined experimental and simulation approach enables a comprehensive description of the FMR probe behavior within viscous nano-environments in complex, biological systems.

Two Coexisting Membrane Structures Are Defined by Lateral and Transbilayer Interactions between Sphingomyelin and Cholesterol.

The structure of fully hydrated bilayers composed of equimolar proportions of palmitoylsphingomyelin (PSM) and cholesterol has been examined by synchrotron X-ray powder diffraction and atomistic molecular dynamics (MD) simulations. Two coexisting bilayer structures, which are distinguished by the transbilayer phosphate-phosphate distance of coupled PSM molecules, are observed by diffraction at 37 °C. The MD simulations reveal that PSM molecules in the thicker membrane are characterized by more ordered, more extended, and less interdigitated hydrocarbon tails compared to those in the thinner membrane. Intermolecular hydrogen bonds further distinguish the two bilayer structures, and we observe the disruption of a sphingomyelin intermolecular hydrogen bond network induced by the proximity of cholesterol. Through an unsupervised clustering of interatomic distances, we show for the first time that the asymmetry of phospholipids is important in driving their interactions with cholesterol. We identify four distinct modes of interaction, two of which lead to the dehydration of cholesterol. These two modes of interaction provide the first description of precise physical mechanisms underlying the umbrella model, which itself explains how phospholipids may shield cholesterol from water. The most dehydrating mode of interaction is particular to the N-acylated fatty acid moiety of PSM and thus may explain the long-held observation that cholesterol preferentially mixes with sphingomyelins over glycerophospholipids.

Structure and Dynamics of Nanoconfined Water Between Surfactant Monolayers.

The properties of nanoconfined water arise in direct response to the properties of the interfaces that confine it. A great deal of research has focused on understanding how and why the physical properties of confined water differ greatly from the bulk. In this work, we have used all-atom molecular dynamics (MD) simulations to provide a detailed description of the structural and dynamical properties of nanoconfined water between two monolayers consisting of an archetypal ionic surfactant, cetrimonium bromide (CTAB, [CH3(CH2)15N(CH3)3]+Br-). Small differences in the area per surfactant of the monolayers impart a clear effect on the intrinsic density, mobility, and ordering of the interfacial water layer confined by the monolayers. We find that as the area per surfactant within a monolayer decreases, the mobility of the interfacial water molecules decreases in response. As the monolayer packing density decreases, we find that each individual CTAB molecule has a greater effect on the ordering of water molecules in its first hydration shell. In a denser monolayer, we observe that the effect of individual CTAB molecules on the ordering of water molecules is hindered by increased competition between headgroups. Therefore, when two monolayers with different areas per surfactant are used to confine a nanoscale water layer, we observe the emergence of noncentrosymmetry.

On the microscopic origin of the cryoprotective effect in lysine solutions.

The amino acid lysine has been shown to prevent water crystallization at low temperatures in saturated aqueous solutions [S. Cerveny and J. Swenson, Phys. Chem. Chem. Phys., 2014, 16, 22382-22390]. Here, we investigate two ratios of water and lysine (5.4 water molecules per lysine (saturated) and 11 water molecules per lysine) by means of the complementary use of computer simulations and neutron diffraction. By performing a detailed structural analysis we have been able to explain the anti-freeze properties of lysine by the strong hydrogen bond interactions of interstitial water molecules with lysine that prevent them from forming crystalline seeds. Additional water molecules beyond the 1 : 5.4 proportion are no longer tightly bonded to lysine and therefore are free to form crystals.

Designer tRNAs for efficient incorporation of non-canonical amino acids by the pyrrolysine system in mammalian cells.

The pyrrolysyl-tRNA synthetase/tRNAPyl pair is the most versatile and widespread system for the incorporation of non-canonical amino acids (ncAAs) into proteins in mammalian cells. However, low yields of ncAA incorporation severely limit its applicability to relevant biological targets. Here, we generate two tRNAPyl variants that significantly boost the performance of the pyrrolysine system. Compared to the original tRNAPyl, the engineered tRNAs feature a canonical hinge between D- and T-loop, show higher intracellular concentrations and bear partially distinct post-transcriptional modifications. Using the new tRNAs, we demonstrate efficient ncAA incorporation into a G-protein coupled receptor (GPCR) and simultaneous ncAA incorporation at two GPCR sites. Moreover, by incorporating last-generation ncAAs for bioorthogonal chemistry, we achieve GPCR labeling with small organic fluorophores on the live cell and visualize stimulus-induced GPCR internalization. Such a robust system for incorporation of single or multiple ncAAs will facilitate the application of a wide pool of chemical tools for structural and functional studies of challenging biological targets in live mammalian cells.

On the Structure of Solid Lipid Nanoparticles.

Solid lipid nanoparticles (SLNs) have a crystalline lipid core which is stabilized by interfacial surfactants. SLNs are considered favorable candidates for drug delivery vehicles since their ability to store and release organic molecules can be tailored through the identity of the lipids and surfactants used. When stored, polymorphic transitions in the core of drug-loaded SLNs lead to the premature release of drug molecules. Significant experimental studies have been conducted with the aim of investigating the physicochemical properties of SLNs, however, no molecular scale investigations have been reported on the behaviors that drive SLN formation and their polymorphic transitions. A combination of small angle neutron scattering and all-atom molecular dynamics simulations is therefore used to yield a detailed atomistic description of the internal structure of an SLN comprising triglyceride, tripalmitin, and the nonionic surfactant, Brij O10 (C18:1 E10 ). The molecular scale mechanisms by which the surfactants stabilize the crystalline structure of the SLN lipid core are uncovered. By comparing these results to simulated liquid and solid aggregates of tripalmitin lipids, how the morphology of the lipids vary between these systems is demonstrated providing further insight into the mechanisms that control drug encapsulation and release from SLNs.

On the interaction of hyaluronic acid with synovial fluid lipid membranes.

All-atom molecular dynamics simulations have been used to investigate the adsorption of low molecular weight hyaluronic acid to lipid membranes. We have determined the interactions that govern the adsorption of three different molecular weight hyaluronic acid molecules (0.4, 3.8 & 15.2 kDa) to lipid bilayers that are representative of the surface-active phospholipid bilayers found in synovial joints. We have found that both direct hydrogen bonds and water-mediated interactions with the lipid headgroups play a key role in the binding of hyaluronic acid to the lipid bilayer. The water-mediated interactions become increasingly important in stabilising the adsorbed hyaluronic acid molecules as the molecular weight of hyaluronic acid increases. We also observe a redistribution of ions around bound hyaluronic acid molecules and the associated lipid headgroups, and that the degree of redistribution increases with the molecular weight of hyaluronic acid. By comparing this behaviour to that observed in simulations of the charge-neutral polysaccharide dextran (MW ∼ 15 kDa), we show that this charge redistribution leads to an increased alignment of the lipid headgroups with the membrane normal, and therefore to more direct and water-mediated interactions between hyaluronic acid and the lipid membrane. These findings provide a detailed understanding of the general structure of hyaluronic acid-lipid complexes that have recently been presented experimentally, as well as a potential mechanism for their enhanced tribological properties.