Bacterial associations with salmonid eggs

Rainbow trout eggs Salmo gairdneri, Richardson, were incubated under a range of different environmental conditions. Recovery of bacteria from egg surfaces revealed that increased water temperature, slow water flow rates and high egg density all significantly increased egg surface bacterial populations. Live eggs were mainly colonized by Cytophaga sp., pseudomonas fluorescens and Aeromonas hydrophila. In contrast, dead eggs supported considerable numbers of fluorescent Pseudomonas sp. Analysis of potential nutrient sources for bacteria colonizing live egg surfaces revealed that small amounts of amino acids, phosphate and potassium may be lost by incubating eggs. Subsequently these nutrients were shown to be capable of supporting limited bacterial growth and reproduction. Dead eggs `leaked' increased amounts of the above nutrients which in turn supported higher bacterial numbers. In addition, biochemical analysis of eggs revealed amino acids and fatty acids that might be utilized by bacteria colonizing dead egg surfaces. Assessment of adhesion properties of bacteria frequently recovered from egg surfaces revealed high cell surface hydrophobicity as an important factor in successful egg colonization. Analysis of egg mortalities from groups of rainbow trout and brown trout (S.trutta L.) eggs maintained under two different incubation systems revealed that potentially a close correlation existed between egg surface bacterial numbers and mortalities in the egg during incubation. Innoculation of newly-fertilized eggs with bacteria demonstrated that groups of eggs supporting high numbers of P.fluorescens suffered significantly higher mortalities during the early part of their incubation. Exposure of incubating eggs to oxolinic acid, chlortetracycline and chloramphenicol demonstrated that numbers of bacteria on egg surfaces could be significantly reduced. However, as no corresponding increase in egg hatching success was revealed, the treatment of incubating eggs with antibiotics or antimicrobial compounds can not be recommended. In commercial hatcheries bacteria are only likely to be responsible for egg deaths during incubation when environmental conditions are unfavourable. High water temperatures, slow water flow rates and high egg density all lead to increased bacterial number of egg surfaces, reduced water circulation and low levels of dissolved oxygen. Under such circumstances sufficient amounts of dissolved oxygen may not be available to support developing embryos

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

MOTIVATION: Untargeted mass spectrometry is a powerful method for detecting metabolites in biological samples. However, fast and accurate identification of the metabolites' structures from MS/MS spectra is still a great challenge.RESULTS: We present a new analysis method, called SF-Matching, that is based on the hypothesis that molecules with similar structural features will exhibit similar fragmentation patterns. We combine information on fragmentation patterns of molecules with shared substructures and then use random forest models to predict whether a given structure can yield a certain fragmentation pattern. These models can then be used to score candidate molecules for a given mass spectrum. For rapid identification, we pre-compute such scores for common biological molecular structure databases. Using benchmarking datasets, we find that our method has similar performance to CSI:FingerID and that very high accuracies can be achieved by combining our method with CSI:FingerID. Rarefaction analysis of the training dataset shows that the performance of our method will increase as more experimental data become available. AVAILABILITY: SF-Matching is available from http://www.bork.embl.de/Docu/sf_matching. CONTACT: [email protected] (M.K.), [email protected] (P.B.

The Rotating Quantum Thermal Distribution

We show that the rigidly rotating quantum thermal distribution on flat space-time suffers from a global pathology which can be cured by introducing a cylindrical mirror if and only if it has a radius smaller than that of the speed-of-light cylinder. When this condition is met, we demonstrate numerically that the renormalized expectation value of the energy-momentum stress tensor corresponds to a rigidly rotating thermal bath up to a finite correction except on the mirror where there are the usual Casimir divergences.Comment: 8 pages, 2 PostScript figure

An horizon scan of biogeography

The opportunity to reflect broadly on the accomplishments, prospects, and reach of a field may present itself relatively infrequently. Each biennial meeting of the International Biogeography Society showcases ideas solicited and developed largely during the preceding year, by individuals or teams from across the breadth of the discipline. Here, we highlight challenges, developments, and opportunities in biogeography from that biennial synthesis. We note the realized and potential impact of rapid data accumulation in several fields, a renaissance for inter-disciplinary research, the importance of recognizing the evolution-ecology continuum across spatial and temporal scales and at different taxonomic, phylogenetic and functional levels, and re-exploration of classical assumptions and hypotheses using new tools. However, advances are taxonomically and geographically biased, and key theoretical frameworks await tools to handle, or strategies to simplify, the biological complexity seen in empirical systems. Current threats to biodiversity require unprecedented integration of knowledge and development of predictive capacity that may enable biogeography to unite its descriptive and hypothetico-deductive branches and establish a greater role within and outside academia

Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum

Protein-metabolite interactions play an important role in the cell's metabolism and many methods have been developed to screen them in vitro. However, few methods can be applied at a large scale and not alter biological state. Here we describe a proteometabolomic approach, using chromatography to generate cell fractions which are then analyzed with mass spectrometry for both protein and metabolite identification. Integrating the proteomic and metabolomic analyses makes it possible to identify protein-bound metabolites. Applying the concept to the thermophilic fungus Chaetomium thermophilum, we predict 461 likely protein-metabolite interactions, most of them novel. As a proof of principle, we experimentally validate a predicted interaction between the ribosome and isopentenyl adenine

TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome

G-protein-coupled receptors (GPCRs) remain major drug targets, despite our incomplete understanding of how they signal through 16 non-visual G-protein signal transducers (collectively named the transducerome) to exert their actions. To address this gap, we have developed an open-source suite of 14 optimized bioluminescence resonance energy transfer (BRET) Gαβγ biosensors (named TRUPATH) to interrogate the transducerome with single pathway resolution in cells. Generated through exhaustive protein engineering and empirical testing, the TRUPATH suite of Gαβγ biosensors includes the first Gα15 and GαGustducin probes. In head-to-head studies, TRUPATH biosensors outperformed first-generation sensors at multiple GPCRs and in different cell lines. Benchmarking studies with TRUPATH biosensors recapitulated previously documented signaling bias and revealed new coupling preferences for prototypic and understudied GPCRs with potential in vivo relevance. To enable a greater understanding of GPCR molecular pharmacology by the scientific community, we have made TRUPATH biosensors easily accessible as a kit through Addgene

Clostridium difficile sortase recognizes a (S/P)PXTG sequence motif and can accommodate diaminopimelic acid as a substrate for transpeptidation

AbstractCovalent attachment of surface proteins to the cell wall of Gram-positive bacteria requires a sortase-mediated transpeptidation reaction. In almost all Gram-positive bacteria, the housekeeping sortase, sortase A, recognizes the canonical recognition sequence LPXTG (X=any amino acid). The human pathogen Clostridium difficile carries a single putative sortase gene (cd2718) but neither transpeptidation activity nor specificity of CD2718 has been investigated. We produced recombinant CD2718 and examined its transpeptidation activity in vitro using synthetic peptides and MALDI-ToF(-ToF) MS analysis. We demonstrate that CD2718 has sortase activity with specificity for a (S/P)PXTG motif and can accommodate diaminopimelic acid as a substrate for transpeptidation

Constraining the mass of dark photons and axion-like particles through black-hole superradiance

Ultralight bosons and axion-like particles appear naturally in different scenarios and could solve some long-standing puzzles. Their detection is challenging, and all direct methods hinge on unknown couplings to the Standard Model of particle physics. However, the universal coupling to gravity provides model-independent signatures for these fields. We explore here the superradiant instability of spinning black holes triggered in the presence of such fields. The instability taps angular momentum from and limits the maximum spin of astrophysical black holes. We compute, for the first time, the spectrum of the most unstable modes of a massive vector (Proca) field for generic black-hole spin and Proca mass. The observed stability of the inner disk of stellar-mass black holes can be used to derive \emph{direct} constraints on the mass of dark photons in the mass range $10^{-13}\,{\rm eV}\lesssim m_V \lesssim 3\times 10^{-12}\,{\rm eV}$. By including also higher azimuthal modes, similar constraints apply to axion-like particles in the mass range $6\times10^{-13}\,{\rm eV}\lesssim m_{\rm ALP} \lesssim 10^{-11}\, {\rm eV}$. Likewise, mass and spin distributions of supermassive BHs --~as measured through continuum fitting, K$\alpha$ iron line, or with the future space-based gravitational-wave detector LISA~-- imply indirect bounds in the mass range approximately $10^{-19}\,{\rm eV}\lesssim m_V, m_{\rm ALP} \lesssim 10^{-13}\, {\rm eV}$, for both axion-like particles and dark photons. Overall, superradiance allows to explore a region of approximately $8$ orders of magnitude in the mass of ultralight bosons

Present Status and Future of DCC Analysis

Disoriented Chiral Condensates (DCC) have been predicted to form in high energy heavy ion collisions where the approximate chiral symmetry of QCD has been restored. This leads to large imbalances in the production of charged to neutral pions. Sophisticated analysis methods are being developed to disentangle DCC events out of the large background of events with conventionally produced particles. We present a short review of current analysis methods and future prospects.Comment: 12 pages, 5 figures. Invited talk presented at the 13th International Conference on Ultrarelativistic Nucleus-Nucleus Collisions (Quark Matter 97), Tsukuba, Japan, 1-5 Dec 199

Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors

The peptidergic system is the most abundant network of ligand-receptor-mediated signaling in humans. However, the physiological roles remain elusive for numerous peptides and more than 100 G protein-coupled receptors (GPCRs). Here we report the pairing of cognate peptides and receptors. Integrating comparative genomics across 313 species and bioinformatics on all protein sequences and structures of human class A GPCRs, we identify universal characteristics that uncover additional potential peptidergic signaling systems. Using three orthogonal biochemical assays, we pair 17 proposed endogenous ligands with five orphan GPCRs that are associated with diseases, including genetic, neoplastic, nervous and reproductive system disorders. We also identify additional peptides for nine receptors with recognized ligands and pathophysiological roles. This integrated computational and multifaceted experimental approach expands the peptide-GPCR network and opens the way for studies to elucidate the roles of these signaling systems in human physiology and disease. Video Abstract: Features learned from comparative sequence and structural analyses enabled prediction of peptide ligands for orphan GPCRs that, when coupled with functional validation, expose physiologically relevant signaling systems. © 2019 The Author(s