Small molecule in situ resin capture provides a compound first approach to natural product discovery.

Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.

MAR4 Streptomyces: A Unique Resource for Natural Product Discovery.

Marine-derived Streptomyces have long been recognized as a source of novel, pharmaceutically relevant natural products. Among these bacteria, the MAR4 clade within the genus Streptomyces has been identified as metabolically rich, yielding over 93 different compounds to date. MAR4 strains are particularly noteworthy for the production of halogenated hybrid isoprenoid natural products, a relatively rare class of bacterial metabolites that possess a wide range of biological activities. MAR4 genomes are enriched in vanadium haloperoxidase and prenyltransferase genes, thus accounting for the production of these compounds. Functional characterization of the enzymes encoded in MAR4 genomes has advanced our understanding of halogenated, hybrid isoprenoid biosynthesis. Despite the exceptional biosynthetic capabilities of MAR4 bacteria, the large body of research they have stimulated has yet to be compiled. Here we review 35 years of natural product research on MAR4 strains and update the molecular diversity of this unique group of bacteria.

Seamless Multilayer─A Novel Total Energy Partition Scheme for Embedded and Hybrid Calculations.

In this paper, we provide general formulation of a multilayer approach, covering both additive and subtractive quantum mechanics/molecular mechanics (QM/MM) as special cases. After that, we suggest a novel definition of QM/MM total energy based on the consideration of a system divided into three layers. In a simplified form, it is E=EQM(1+2)-EQM(2)+EMM(2+3), where layers 1, 2, and 3 represent inner QM, outer QM, and classical MM regions, respectively. The novel formulation is also not limited by only QM/MM combination of methods─in fact, any computational methods can be combined in a hybrid calculation. In this paper, we call the new approach seamless multilayer. Test calculations performed for silica and boric oxide show that the new approach requires no QM/MM interface parameterization as well as no or very simple correction terms for boundary atoms. This can greatly facilitate QM/MM studies of covalent inorganic solids. However, test calculations of α-Al2O3 show that for ionic compounds, the new method requires some additional development.

Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery.

Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.

Biogeographic patterns of biosynthetic potential and specialized metabolites in marine sediments.

While the field of microbial biogeography has largely focused on the contributions of abiotic factors to community patterns, the potential influence of biotic interactions in structuring microbial communities, such as those mediated by the production of specialized metabolites, remains largely unknown. Here, we examined the relationship between microbial community structure and specialized metabolism at local spatial scales in marine sediment samples collected from the Long-Term Ecological Research (LTER) site in Moorea, French Polynesia. By employing a multi-omic approach to characterize the taxonomic, functional, and specialized metabolite composition within sediment communities, we find that biogeographic patterns were driven by local scale processes (e.g., biotic interactions) and largely independent of dispersal limitation. Specifically, we observed high variation in biosynthetic potential (based on Bray-Curtis dissimilarity) between samples, even within 1 m2 plots, that reflected uncharacterized chemical space associated with site-specific metabolomes. Ultimately, connecting biosynthetic potential to community metabolomes facilitated the in situ detection of natural products and revealed new insights into the complex metabolic dynamics associated with sediment microbial communities. Our study demonstrates the potential to integrate biosynthetic genes and metabolite production into assessments of microbial community dynamics.

New Insights into the Crystal Chemistry of Elpidite, Na2Zr[Si6O15]·3H2O and (Na1+YCax□1-X-Y)Σ=2Zr[Si6O15]·(3-X)H2O, and Ab Initio Modeling of IR Spectra.

Elpidite belongs to a special group of microporous zirconosilicates, which are of great interest due to their capability to uptake various molecules and ions, e.g., some radioactive species, in their structural voids. The results of a combined electron probe microanalysis and single-crystal X-ray diffraction study of the crystals of elpidite from Burpala (Russia) and Khan-Bogdo (Mongolia) deposits are reported. Some differences in the chemical compositions are observed and substitution at several structural positions within the structure of the compounds are noted. Based on the obtained results, a detailed crystal-chemical characterization of the elpidites under study was carried out. Three different structure models of elpidite were simulated: Na2ZrSi6O15·3H2O (related to the structure of Russian elpidite), partly Ca-replaced Na1.5Ca0.25ZrSi6O15·2.75H2O (close to elpidite from Mongolia), and a hypothetical CaZrSi6O15·2H2O. The vibration spectra of the models were obtained and compared with the experimental one, taken from the literature. The strong influence of water molecule vibrations on the shape of IR spectra of studied structural models of elpidite is discussed in the paper.

Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria.

A diverse set of bacteria live on the above-ground parts of plants, composing the phyllosphere, and play important roles for plant health. Phyllosphere microbial communities assemble in a predictable manner and diverge from communities colonizing other plant organs or the soil. However, how these communities differ functionally remains obscure. We assembled a collection of 258 bacterial isolates representative of the most abundant taxa of the phyllosphere of Arabidopsis and a shared soil inoculum. We screened the collection for the production of metabolites that inhibit the growth of Gram-positive and Gram-negative bacteria either in isolation or in co-culture. We found that isolates capable of constitutive antibiotic production in monoculture were significantly enriched in the soil fraction. In contrast, the proportion of binary cultures resulting in the production of growth inhibitory compounds differed only marginally between the phyllosphere and soil fractions. This shows that the phyllosphere may be a rich resource for potentially novel molecules with antibiotic activity, but that production or activity is dependent upon induction by external signals or cues. Finally, we describe the isolation of antimicrobial acyloin metabolites from a binary culture of Arabidopsis phyllosphere isolates, which inhibit the growth of clinically relevant Acinetobacter baumannii.

Metabolome of the Phyllidiella pustulosa Species Complex (Nudibranchia, Heterobranchia, Gastropoda) Reveals Rare Dichloroimidic Sesquiterpene Derivatives from a Phylogenetically Distinct and Undescribed Clade.

Phyllidiid nudibranchs are brightly colored gastropod mollusks, frequently encountered in coral reefs of the tropical Indo-Pacific. The lack of a protective shell is suggested to be compensated by toxic secondary metabolites that are sequestered from specific prey sponges. Our ongoing reconstruction of phyllidiid phylogeny using molecular data of more than 700 specimens, based on published data and newly collected specimens in various seasons and localities around North Sulawesi (Indonesia), demonstrates that Phyllidiella pustulosa is a species complex with at least seven well-supported clades. A metabolomic analysis of 52 specimens from all seven clades of P. pustulosa was performed. Secondary metabolite profiles were found to correlate with the phylogenetic study and not the prevailing food sponges as expected. GNPS molecular networking revealed a unique chemotype in clade 6. Detailed chemical analysis of a specimen from this chemically and genetically distinct P. pustulosa clade led to the identification of seven new sesquiterpenoids with a rare dichloroimidic moiety (1 and 4) and derivatives thereof (2, 3, 5-7). Our findings suggest that P. pustulosa clades should be raised to the species level.

Astroglia-Derived BDNF and MSK-1 Mediate Experience- and Diet-Dependent Synaptic Plasticity.

Experience- and diet-dependent regulation of synaptic plasticity can underlie beneficial effects of active lifestyle on the aging brain. Our previous results demonstrate a key role for brain-derived neurotrophic factor (BDNF) and MSK1 kinase in experience-related homeostatic synaptic scaling. Astroglia has been recently shown to release BDNF via a calcium-dependent mechanism. To elucidate a role for astroglia-derived BDNF in homeostatic synaptic plasticity in the aging brain, we explored the experience- and diet-related alterations of synaptic transmission and plasticity in transgenic mice with impairment of the BDNF/MSK1 pathway (MSK1 kinase dead knock-in mice, MSK1 KD) and impairment of glial exocytosis (dnSNARE mice). We found that prolonged tonic activation of astrocytes caused BDNF-dependent increase in the efficacy of excitatory synapses accompanied by enlargement of synaptic boutons. We also observed that exposure to environmental enrichment (EE) and caloric restriction (CR) enhanced the Ca2+ signalling in cortical astrocytes and strongly up-regulated the excitatory and down-regulated inhibitory synaptic currents in old wild-type mice, thus counterbalancing the impact of ageing on astroglial and synaptic signalling. The EE- and CR-induced up-scaling of excitatory synaptic transmission in neocortex was accompanied by the enhancement of long-term synaptic potentiation. Importantly, effects of EE and CR on synaptic transmission and plasticity was significantly reduced in the MSK1 KD and dnSNARE mice. Combined, our results suggest that astroglial release of BDNF is important for the homeostatic regulation of cortical synapses and beneficial effects of EE and CR on synaptic transmission and plasticity in aging brain.

Optical properties of SrF2 and SrF2:Ce3+ crystals codoped with In3.

The paper presents the results of a comprehensive study of effects that In3+ ion impurities have on the optical properties of SrF2 and SrF2:Ce3+ crystals. The investigations were carried out both by optical spectroscopy methods and ab initio quantum chemical calculations. To estimate the effect of indium impurities on the optical band gap of the crystals, the DFT calculations were performed for SrF2 crystals doped with different concentrations of In3+ ions. The study of SrF2 crystals co-doped with Ce and In ions reveals the highly effective role of indium ions in reducing the electron trapping efficiency in the processes of excitation transfer to an activator. This improvement is associated with some change in the band gap of the crystals caused by indium doping, which is confirmed by both theoretical and experimental results.

Ontologic Model of Diagnostics and Treatment of Gastrointestinal Bleedings of Unknown Origin.

The article presents the semantic model of diagnostics and treatment of patients with gastrointestinal bleedings when the reasons of bleeding cannot be establihed by means of a laboratory tests, endoscopy and colonoscopy.

Age- and Experience-Related Plasticity of ATP-Mediated Signaling in the Neocortex.

There is growing recognition of the important role of interaction between neurons and glial cells for brain longevity. The extracellular ATP have been shown to bring significant contribution into bi-directional glia-neuron communications, in particular into astrocyte-driven modulation of synaptic plasticity. To elucidate a putative impact of brain aging on neuron-glia networks, we explored the aging-related plasticity of the purinoreceptors-mediated signaling in cortical neurons and astrocytes. We investigated the age- and experience-related alterations in purinergic components of neuronal synaptic currents and astroglial calcium signaling in the layer2/3 of neocortex of mice exposed to the mild caloric restriction (CR) and environmental enrichment (EE) which included ad libitum physical exercise. We observed the considerable age-related decline in the neuronal P2X receptor-mediated miniature spontaneous currents which originated from the release of ATP from both synapses and astrocytes. We also found out that purinergic astrocytic Ca2+-signaling underwent the substantial age-related decline but EE and CR rescued astroglial signaling, in particular mediated by P2X1, P2X1/5, and P2Y1 receptors. Our data showed that age-related attenuation in the astroglial calcium signaling caused a substantial decrease in the exocytosis of ATP leading to impairment of astroglia-derived purinergic modulation of excitatory synaptic currents and GABAergic tonic inhibitory currents. On a contrary, exposure to EE and CR, which enhanced purinergic astrocytic calcium signaling, up-regulated the excitatory and down-regulated the inhibitory currents in neurons of old mice, thus counterbalancing the impact of aging on synaptic signaling. Combined, our results strongly support the physiological importance of ATP-mediated signaling for glia-neuron interactions and brain function. Our data also show that P2 purinoreceptor-mediated communication between astrocytes and neurons in the neocortex undergoes remodeling during brain aging and decrease in the ATP release may contribute to the age-related impairment of synaptic transmission.

Diversity of Astroglial Effects on Aging- and Experience-Related Cortical Metaplasticity.

Activity-dependent regulation of synaptic plasticity, or metaplasticity, plays a key role in the adaptation of neuronal networks to physiological and biochemical changes in aging brain. There is a growing evidence that experience-related alterations in the mechanisms of synaptic plasticity can underlie beneficial effects of physical exercise and caloric restriction (CR) on brain health and cognition. Astrocytes, which form neuro-vascular interface and can modulate synaptic plasticity by release of gliotransmitters, attract an increasing attention as important element of brain metaplasticity. We investigated the age- and experience-related alterations in astroglial calcium signaling and stimulus-dependence of long-term synaptic plasticity in the neocortex of mice exposed to the mild CR and environmental enrichment (EE) which included ad libitum physical exercise. We found out that astrocytic Ca2+-signaling underwent considerable age-related decline but EE and CR enhanced astroglial signaling, in particular mediated by noradrenaline (NA) and endocannabinoid receptors. The release of ATP and D-Serine from astrocytes followed the same trends of age-related declined and EE-induced increase. Our data also showed that astrocyte-derived ATP and D-Serine can have diverse effects on the threshold and magnitude of long-term changes in the strength of neocortical synapses; these effects were age-dependent. The CR- and EE-induced enhancement of astroglial Ca2+-signaling had more stronger effect on synaptic plasticity in the old (14-18 months) than in the young (2-5 months) wild-type (WT) mice. The effects of CR and EE on synaptic plasticity were significantly altered in both young and aged dnSNARE mice. Combined, our data suggest astrocyte-neuron interactions are important for dynamic regulation of cortical synaptic plasticity. This interaction can significantly decline with aging and thus contributes to the age-related cognitive impairment. On another hand, experience-related increase in the astroglial Ca2+-signaling can ameliorate the age-related decline.

Secondary metabolome and its defensive role in the aeolidoidean Phyllodesmium longicirrum, (Gastropoda, Heterobranchia, Nudibranchia).

Phyllodesmium longicirrum is the largest aeolidoidean species known to date, and extremely rich in terpenoid chemistry. Herein we report the isolation of a total of 19 secondary metabolites from a single specimen of this species, i.e., steroids 1-4, cembranoid diterpenes 5-13, complex biscembranoids 14 and 15, and the chatancin-type diterpenes 16-19. These compounds resemble those from soft corals of the genus Sarcophyton, of which to date, however, only S. trocheliophorum is described as a food source for P. longicirrum. Fish feeding deterrent activity was determined using the tropical puffer fish Canthigaster solandri, and showed activity for (2S)-isosarcophytoxide (10), cembranoid bisepoxide 12 and 4-oxochatancin (16). Determining the metabolome of P. longicirrum and its bioactivity, makes it evident that this seemingly vulnerable soft bodied animal is well protected from fish by its chemical arsenal.

Modelling the structure of Zr-rich Pb(Zr1-xTix)O3, x = 0.4 by a multiphase approach.

Solid solution perovskite Pb(Zr1-xTix)O3 (PZT) is an industrially important material. Despite the long history of experimental and theoretical studies, the structure of this material is still under intensive discussion. In this work, we have applied structure searching coupled with density functional theory methods to provide a multiphase description of this material at x = 0.4. We demonstrate that the permutational freedom of B-site cations leads to the stabilisation of a variety of local phases reflecting a relatively flat energy landscape of PZT. Using a set of predicted local phases we reproduce the experimental pair distribution function (PDF) profile with high accuracy. We introduce a complex multiphase picture of the structure of PZT and show that additional monoclinic and rhombohedral phases account for a better description of the experimental PDF profile. We propose that such a multiphase picture reflects the entropy reached in the sample during the preparation process.

Defensive Diterpene from the Aeolidoidean Phyllodesmium longicirrum.

Phyllodesmium is a tropical marine slug genus with about 30 described species. None of them have a protective shell, and all of them feed on octocorals that are generally known to provide defensive compounds and thus help to defend the naked slugs against sympatric predators, such as fish, crabs, cephalopods, and echinoderms. Phyllodesmium longicirrum is the species that grows the biggest and that is least protected by camouflage on its respective food, usually a soft coral of the genus Sarcophyton. Investigation of the lipophilic extract of a single specimen of P. longicirrum from the Great Barrier Reef (Australia) led to the isolation of four new polycyclic diterpenes. Compound 1 showed significant deterrent activity in a fish feeding assay.

Defense in the aeolidoidean genus Phyllodesmium (Gastropoda).

The genus Phyllodesmium (Aeolidoidea, Gastropoda) comprises shell-less marine snails, whose defense strategies are not well investigated yet. Here we report results of the first chemical investigation of P. briareum, as well as a re-investigation of P. longicirrum and P. magnum. Briarane diterpenes were isolated from P. briareum, and their origin could be traced to its prey organism Briareum sp. (Octocorallia). Considerable enrichment of the soft coral secondary metabolites in the slug was shown. Re-investigation of P. magnum led to isolation of cembrane diterpenes, 2-phenylethylamide, and furano sesquiterpenes. Sequestration of chemicals seems to have influenced speciation and evolution of Phyllodesmium species. Structural similarity or dissimilarity of particular slug metabolites suggests a closer, or more distant relationship of the respective Phyllodesmium taxa.