The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data.

The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. This extremely small coccus (200-300 nm) has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of an Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase, thereby killing its host. This first completed genome (705 kb) for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity. Comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host. Transcriptomic and metabolomic profiles provided the first indications, to our knowledge, that there is signaling interaction between TM7x and XH001. Furthermore, the induction of TNF-α production in macrophages by XH001 was repressed in the presence of TM7x, suggesting its potential immune suppression ability. Overall, our data provide intriguing insights into the uncultivability, pathogenicity, and unique lifestyle of this previously uncharacterized oral TM7 phylotype.TM7 | human-associated | epibiont | oral microbiome | interspecies interaction

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In all probability, natural selection began as ancient marine microorganisms were required to compete for limited resources. These pressures resulted in the evolution of diverse genetically encoded small molecules with a variety of ecological and metabolic roles. Remarkably, many of these same biologically active molecules have potential utility in modern medicine and biomedical research. The most promising of these natural products often derive from organisms richly populated by associated microorganisms (e.g., marine sponges and ascidians), and often there is great uncertainty about which organism in these assemblages is making these intriguing metabolites. To use the molecular machinery responsible for the biosynthesis of potential drug-lead natural products, new tools must be applied to delineate their genetic and enzymatic origins. The aim of this perspective is to highlight both traditional and emerging techniques for the localization of metabolic pathways within complex marine environments. Examples are given from the literature as well as recent proof-of-concept experiments from the authors' laboratories.

Neurotransmitter release is well known to occur at specialized synaptic regions that include presynaptic active zones and postsynaptic densities. At cholinergic synapses in the chick ciliary ganglion, however, membrane formations and physiological measurements suggest that release distant from postsynaptic densities can activate the predominantly extrasynaptic α7 nicotinic receptor subtype. We explored such ectopic neurotransmission with a novel model synapse that combines Monte Carlo simulations with high-resolution serial electron microscopic tomography. Simulated synaptic activity is consistent with experimental recordings of miniature excitatory postsynaptic currents only when ectopic transmission is included in the model, broadening the possibilities for mechanisms of neuronal communication.Throughout the nervous system, release of synaptic vesicles from presynaptic nerve terminals is thought to be associated with pre-and post-synaptic specializations, including active zones (AZs) and postsynaptic densities (PSDs). Release of neurotransmitter vesicles at extrasynaptic sites (ectopic release) has been suggested by the presence of morphologically docked vesicles distant from PSDs in electron micrographs from tissues, including the ribbon synapses of bipolar neurons (1) and saccular hair cells (2). Recently, direct measurements of quantal release have been made from climbing fibers in the cerebellar cortex onto the closely apposed Bergmann glia (3). Despite these findings, there † To whom correspondence should be addressed: terry@salk.edu. * These authors contributed equally to this work. HHMI Author Manuscript HHMI Author Manuscript HHMI Author Manuscripthas been no demonstration of the participation of ectopic release of neurotransmitter in the course of interneuronal synaptic transmission.At the structurally complex and umbrella-like calyceal synapse of the ciliary ganglion (CG), the case for ectopic release has been growing. Two major classes of kinetically distinct nicotinic acetylcholine receptors (nAChRs) are spatially segregated in the CG (4-6). The α7-nAChRs are expressed on matted spines but are largely excluded from PSDs regardless of where they occur (7-9). The α3*-nAChRs (6) are primarily localized to PSDs (whether on spines or somatic membrane) but are present at lower density on non-PSD membrane (4,9,10). The α7-nAChRs exhibit profound desensitization, an order of magnitude faster decay time, and an open probability lower by a factor of 30 than that of α3*-nAChRs (11-13).The segregation of the two nAChR subtypes, especially the exclusion of α7-nAChRs from PSDs, has made it difficult to interpret physiological measurements that show that the α7-nAChRs account for the majority of current in evoked EPSCs (11,12), are necessary to sustain higher frequency throughput (11,14), and produce distinct Ca signals localized to spines (15). Images of presynaptic vesicles within docking distance (ready to release), as well as Ω profiles (the image capture of fusing vesicles), are seen throughout the ...