Draft Genome Sequence of Amycolatopsis lurida NRRL 2430, Producer of the Glycopeptide Family Antibiotic Ristocetin.

We report here the first draft genome sequence for Amycolatopsis lurida NRRL 2430, the producer of the glycopeptide antibiotic ristocetin. The 9-Mbp genome is predicted to harbor 8,143 genes, including those belonging to the ristocetin biosynthesis cluster and 31 additional predicted secondary metabolite gene clusters.This work was supported by the grants from the Royal Society (516002.K5877/ROG) and the Medical Research Council (G0700141).This paper was originally published in Genome Announcements (Kwun MJ, Hong H-J, Genome Announcements 2014, 2(5):e01050-14. doi:10.1128/genomeA.01050-14)

The activity of glycopeptide antibiotics against resistant bacteria correlates with their ability to induce the resistance system.

Glycopeptide antibiotics containing a hydrophobic substituent display the best activity against vancomycin-resistant enterococci, and they have been assumed to be poor inducers of the resistance system. Using a panel of 26 glycopeptide derivatives and the model resistance system in Streptomyces coelicolor, we confirmed this hypothesis at the level of transcription. Identification of the structural glycopeptide features associated with inducing the expression of resistance genes has important implications in the search for more effective antibiotic structures.This work was supported by the Royal Society (516002.K5877/ROG) and the Medical Research Council (G0700141).This is the accepted manuscript version. The final version is available from ASM at http://aac.asm.org/content/early/2014/07/30/AAC.03668-14.abstract

Genome Sequence of Streptomyces toyocaensis NRRL 15009, Producer of the Glycopeptide Antibiotic A47934.

Here we report the draft genome sequence of Streptomyces toyocaensis strain NRRL 15009 which is the producer of the glycopeptide antibiotic A47934. The genome sequence is predicted to harbor a total of 26 secondary metabolite biosynthetic gene clusters including the A47934 cluster.This work was supported by grants from the Royal Society (516002.K5877/ ROG) and the Medical Research Council (G0700141).This is the final published version, also available from ASM at http://genomea.asm.org/content/2/4/e00749-14

In Vivo Characterization of the Activation and Interaction of the VanR-VanS Two-Component Regulatory System Controlling Glycopeptide Antibiotic Resistance in Two Related Streptomyces Species.

This is the author accepted manuscript. The final version is available from the American Society for Microbiology via http://dx.doi.org/10.1128/AAC.01367-15The VanR-VanS two-component system is responsible for inducing resistance to glycopeptide antibiotics in various bacteria. We have performed a comparative study of the VanR-VanS systems from two streptomyces strains, Streptomyces coelicolor and Streptomyces toyocaensis, to characterize how the two proteins cooperate to signal the presence of antibiotics and to define the functional nature of each protein in each strain background. The results indicate that the glycopeptide antibiotic inducer specificity is determined solely by the differences between the amino acid sequences of the VanR-VanS two-component systems present in each strain rather than by any inherent differences in general cell properties, including cell wall structure and biosynthesis. VanR of S. coelicolor (VanRsc) functioned with either sensor kinase partner, while VanR of S. toyocaensis (VanRst) functioned only with its cognate partner, S. toyocaensis VanS (VanSst). In contrast to VanRsc, which is known to be capable of phosphorylation by acetylphosphate, VanRst could not be activated in vivo independently of a VanS sensor kinase. A series of amino acid sequence modifications changing residues in the N-terminal receiver (REC) domain of VanRst to the corresponding residues present in VanRsc failed to create a protein capable of being activated by VanS of S. coelicolor (VanSsc), which suggests that interaction of the response regulator with its cognate sensor kinase may require a region more extended than the REC domain. A T69S amino acid substitution in the REC domain of VanRst produced a strain exhibiting weak constitutive resistance, indicating that this particular amino acid may play a key role for VanS-independent phosphorylation in the response regulator protein.This work was supported by funding from the Medical Research Council, UK (G0700141) and the Royal Society, UK (516002.K5877/ROG). the American Society for Microbiology

Proteomic Validation of Multifunctional Molecules in Mesenchymal Stem Cells Derived from Human Bone Marrow, Umbilical Cord Blood and Peripheral Blood

Mesenchymal stem cells (MSCs) are one of the most attractive therapeutic resources in clinical application owing to their multipotent capability, which means that cells can differentiate into various mesenchymal tissues such as bone, cartilage, fat, tendon, muscle and marrow stroma. Depending on the cellular source, MSCs exhibit different application potentials according to their different in vivo functions, despite similar phenotypic and cytological characteristics. To understand the different molecular conditions that govern the different application or differentiation potential of each MSC according to cellular source, we generated a proteome reference map of MSCs obtained from bone marrow (BM), umbilical cord blood (CB) and peripheral blood (PB). We identified approximately 30 differentially regulated (or expressed) proteins. Most up-regulated proteins show a cytoskeletal and antioxidant or detoxification role according to their functional involvement. Additionally, these proteins are involved in the increase of cell viability, engraftment and migration in pathological conditions in vivo. In summary, we examined differentially expressed key regulatory factors of MSCs obtained from several cellular sources, demonstrated their differentially expressed proteome profiles and discussed their functional role in specific pathological conditions. With respect to the field of cell therapy, it may be particularly crucial to determine the most suitable cell sources according to target disease

Effects of the energy spread of secondary electrons in a dc-biased single-surface multipactor

The effects of the energy spread of secondary electrons are theoretically investigated for a dc-biased single-surface multipactor. In our previous publication [S. G. Jeon et al., Phys. Plasmas 16, 073101 (2009)], we obtained the conditions for the phase lock of an electron bunch, assuming zero velocity spread of the secondary electrons. In this work, we extended our previous theory to derive a quadratic map, by which the stability and bifurcation of the electron bunch can be systematically investigated. For the study of the energy spread of the secondary electrons, a randomized term was added to this map. The modified map then showed significant smearing-out of the bifurcated branches. The theoretical results were verified by particle-in-cell simulations, which showed good agreement in wide parameter ranges for both cases of monoenergetic and energy-spread secondary electrons.open4

Electron bunching from a dc-biased, single-surface multipactor with realistically broad energy spectrum and emission angle of secondary electrons

We studied the influences of wide energy spectrum and emission angle of secondary electrons on electron bunching from a dc-biased single surface multipactor. In our previous study of the same system, an ideally narrow energy spread of secondary electrons without emission angle was used in the analysis of the electron trajectory [M. S. Hur, J.-I. Kim, G.-J. Kim, and S.-G. Jeon, Phys. Plasmas 18, 033103 (2011) and S.-G. Jeon, J.-I. Kim, S.-T. Han, S.-S. Jung, and J. U. Kim, Phys. Plasmas 16, 073101 (2009)]. In this paper, we investigated the cases with realistic energy spectrum, which is featured by a wide energy spread and significant emission angle. To theoretically approach the matter of emission angle, we employed a concept of effective longitudinal velocity distribution. The theoretical results are verified by particle-in-cell (PIC) simulations. We also studied the electron bunching from a copper by PIC simulations, where we observed stable electron bunches with bunch width of approximately 80 mu m.open3

Novel Diagnostic Model for the Deficient and Excess Pulse Qualities

The deficient and excess pulse qualities (DEPs) are the two representatives of the deficiency and excess syndromes, respectively. Despite its importance in the objectification of pulse diagnosis, a reliable classification model for the DEPs has not been reported to date. In this work, we propose a classification method for the DEPs based on a clinical study. First, through factor analysis and Fisher's discriminant analysis, we show that all the pulse amplitudes obtained at various applied pressures at Chon, Gwan, and Cheok contribute on equal orders of magnitude in the determination of the DEPs. Then, we discuss that the pulse pressure or the average pulse amplitude is appropriate for describing the collective behaviors of the pulse amplitudes and a simple and reliable classification can be constructed from either quantity. Finally, we propose an enhanced classification model that combines the two complementary variables sequentially

Effect of biochars pyrolyzed in N2 and CO2, and feedstock on microbial community in metal(loid)s contaminated soils

Little is known about the effects of applying amendments on soil for immobilizing metal(loid)s on the soil microbial community. Alterations in the microbial community were examined after incubation of treated contaminated soils. One soil was contaminated with Pb and As, a second soil with Cd and Zn. Red pepper stalk (RPS) and biochars produced from RPS in either N2 atmosphere (RPSN) or CO2 atmosphere (RPSC) were applied at a rate of 2.5% to the two soils and incubated for 30 days. Bacterial communities of control and treated soils were characterized by sequencing 16S rRNA genes using the Illumina MiSeq sequencing. In both soils, bacterial richness increased in the amended soils, though somewhat differently between the treatments. Evenness values decreased significantly, and the final overall diversities were reduced. The neutralization of pH, reduced available concentrations of Pb or Cd, and supplementation of available carbon and surface area could be possible factors affecting the community changes. Biochar amendments caused the soil bacterial communities to become more similar than those in the not amended soils. The bacterial community structures at the phylum and genus levels showed that amendment addition might restore the normal bacterial community of soils, and cause soil bacterial communities in contaminated soils to normalize and stabilize

Antibiotic resistance mechanisms inform discovery: identification and characterization of a novel amycolatopsis strain producing ristocetin.

Discovering new antibiotics is a major scientific challenge, made increasingly urgent by the continued development of resistance in bacterial pathogens. A fundamental understanding of the mechanisms of bacterial antibiotic resistance will be vital for the future discovery or design of new, more effective antibiotics. We have exploited our intimate knowledge of the molecular mechanism of glycopeptide antibiotic resistance in the harmless bacterium Streptomyces coelicolor to develop a new two-step cell wall bioactivity screen, which efficiently identified a new actinomycete strain containing a previously uncharacterized glycopeptide biosynthetic gene cluster. The screen first identifies natural product extracts capable of triggering a generalized cell wall stress response and then specifically selects for glycopeptide antibacterials by assaying for the induction of glycopeptide resistance genes. In this study, we established a diverse natural product extract library from actinomycete strains isolated from locations with widely varying climates and ecologies, and we screened them using the novel two-step bioassay system. The bioassay ultimately identified a single strain harboring the previously unidentified biosynthetic gene cluster for the glycopeptide ristocetin, providing a proof of principle for the effectiveness of the screen. This is the first report of the ristocetin biosynthetic gene cluster, which is predicted to include some interesting and previously uncharacterized enzymes. By focusing on screening libraries of microbial extracts, this strategy provides the certainty that identified producer strains are competent for growth and biosynthesis of the detected glycopeptide under laboratory conditions.This work was supported by funding from the Royal Society, UK (516002.K5877/ROG), the Medical Research council, UK (G0700141) and St. John’s College, University of CambridgeThis the the author accepted manuscript. The final version is available from ASM at http://aac.asm.org/content/early/2014/07/09/AAC.03349-14.abstract