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Se Chang Park - One of the best experts on this subject based on the ideXlab platform.

  • complete genome sequence and characterization of a broad host range t4 like bacteriophage phias5 infecting aeromonas salmonicida subsp salmonicida
    2012
    Co-Authors: Yunjaie Choi, Casiano H Choresca, Sang Phil Shin, Se Chang Park
    Abstract:

    Abstract In this study, we report one lytic Myoviridae bacteriophage (phage) infecting Aeromonas salmonicida subsp. salmonicida . The phage (named as phiAS5) was isolated from environmental river waters in Korea, and showed broad infectivity to other bacterial species in the family Aeromonadaceae as well as antibiotic-resistant A. salmonicida subsp. salmonicida strains. The biological properties and complete genome of phiAS5 were simultaneously investigated. The complete genome of phiAS5 composed of linear double-stranded DNA of 225,268 bp with G + C content of 43.0%, and encoded 343 putative ORFs, 69 putative promoters, 33 transcriptional Terminator Regions and 24 tRNA-encoding genes. A high degree of similarity to other T4-like Aeromonas phage was found in most ORFs of phiAS5. Therefore, the genome of phiAS5 was further compared with T4 phage and the closest relative, Aeromonas phage Aeh1, and the result demonstrated that it could be classified as a new member of the T4-like group. The bacteriolytic activity of phiAS5 against A. salmonicida subsp. salmonicida was evaluated at different doses of multiplicity of infection using one each of virulent strain that possesses the ascV gene and multi-drug resistant strain, and the results proved to be efficient for the reduction of bacterial growth. Based on these results, phiAS5 may have the potential for reducing the impacts of virulent or antibiotic-resistant A. salmonicida subsp. salmonicida in aquaculture and may also advance our understanding of the biodiversity of T4-like Aeromonas phages.

  • complete genomic sequence of a t4 like bacteriophage phias4 infecting aeromonas salmonicida subsp salmonicida
    2012
    Co-Authors: Younho Choi, Casiano H Choresca, Sang Phil Shin, Se Chang Park
    Abstract:

    A newly identified virulent phage (named phiAS4) infecting Aeromonas salmonicida subsp. salmonicida was isolated from river water in Korea. Morphological analysis of phiAS4 by transmission electron microscopy revealed that it belonged to the family Myoviridae. The genome of phiAS4 comprised a linear double-stranded DNA of 163,875 bp with a G + C content of 41.3%, and genomic analysis revealed 271 putative ORFs, 67 putative promoters, 25 putative Terminator Regions, and 16 tRNA-encoding genes. Most of the ORFs of phiAS4 showed a high degree of similarity to those of Aeromonas phage 25, which belongs to the T4-like group. Moreover, the comparison of the genome of phiAS4 with those of its relatives demonstrated that phage phiAS4 is closely related to members of the T4-like group and can be classified as a new member of the T4-like phages infecting bacteria of the family Aeromonadaceae.

P Woitke - One of the best experts on this subject based on the ideXlab platform.

  • dynamic mineral clouds on hd 189733b i 3d rhd with kinetic non equilibrium cloud formation
    2016
    Co-Authors: Graham K H Lee, Ian Dobbsdixon, Christiane Helling, K Bognar, P Woitke
    Abstract:

    Context. Observations of exoplanet atmospheres have revealed the presence of cloud particles in their atmospheres. 3D modelling of cloud formation in atmospheres of extrasolar planets coupled to the atmospheric dynamics has long been a challenge. Aims. We investigate the thermo-hydrodynamic properties of cloud formation processes in the atmospheres of hot Jupiter exoplanets. Methods. We simulate the dynamic atmosphere of HD 189733b with a 3D model that couples 3D radiative-hydrodynamics with a kinetic, microphysical mineral cloud formation module designed for RHD/GCM exoplanet atmosphere simulations. Our simulation includes the feedback effects of cloud advection and settling, gas phase element advection and depletion/replenishment and the radiative effects of cloud opacity. We model the cloud particles as a mix of mineral materials which change in size and composition as they travel through atmospheric thermo-chemical environments. All local cloud properties such as number density, grain size and material composition are time-dependently calculated. Gas phase element depletion as a result of cloud formation is included in the model. In situ effective medium theory and Mie theory is applied to calculate the wavelength dependent opacity of the cloud component. Results. We present a 3D cloud structure of a chemically complex, gaseous atmosphere of the hot Jupiter HD 189733b. Mean cloud particle sizes are typically sub-micron (0.01−0.5 μ m) at pressures less than 1 bar with hotter equatorial Regions containing the smallest grains. Denser cloud structures occur near Terminator Regions and deeper (~1 bar) atmospheric layers. Silicate materials such as MgSiO 3 [s] are found to be abundant at mid-high latitudes, while TiO 2 [s] and SiO 2 [s] dominate the equatorial Regions. Elements involved in the cloud formation can be depleted by several orders of magnitude. Conclusions. The interplay between radiative-hydrodynamics and cloud kinetics leads to an inhomogeneous, wavelength dependent opacity cloud structure with properties differing in longitude, latitude and depth. This suggests that transit spectroscopy would sample a variety of cloud particles properties (sizes, composition, densities).

  • dynamic mineral clouds on hd 189733b i 3d rhd with kinetic non equilibrium cloud formation
    2016
    Co-Authors: Graham K H Lee, Ian Dobbsdixon, Christiane Helling, K Bognar, P Woitke
    Abstract:

    Observations of exoplanet atmospheres have revealed the presence of cloud particles in their atmospheres. 3D modelling of cloud formation in atmospheres of extrasolar planets coupled to the atmospheric dynamics has long been a challenge. We investigate the thermo-hydrodynamic properties of cloud formation processes in the atmospheres of hot Jupiter exoplanets. We simulate the dynamic atmosphere of HD 189733b with a 3D model that couples 3D radiative-hydrodynamics with a kinetic, microphysical mineral cloud formation module designed for RHD/GCM exoplanet atmosphere simulations. Our simulation includes the feedback effects of cloud advection and settling, gas phase element advection and depletion/replenishment and the radiative effects of cloud opacity. We model the cloud particles as a mix of mineral materials which change in size and composition as they travel through atmospheric thermo-chemical environments. All local cloud properties such as number density, grain size and material composition are time-dependently calculated. Gas phase element depletion as a result of cloud formation is included in the model. In-situ \textit{effective medium theory} and Mie theory is applied to calculate the wavelength dependent opacity of the cloud component. We present a 3D cloud structure of a chemically complex, gaseous atmosphere of the hot Jupiter HD 189733b. Mean cloud particle sizes are typically sub-micron (0.01-0.5 $\mu$m) at pressures less than 1 bar with hotter equatorial Regions containing the smallest grains. Denser cloud structures occur near Terminator Regions and deeper ($\sim$ 1 bar) atmospheric layers. Silicate materials such as MgSiO$_{3}$[s] are found to be abundant at mid-high latitudes, while TiO$_{2}$[s] and SiO$_{2}$[s] dominate the equatorial Regions.

  • Dynamic mineral clouds on HD 189733b
    2016
    Co-Authors: G. Lee, K Bognar, Ch. Helling, I. Dobbs-dixon, P Woitke
    Abstract:

    Context. Observations of exoplanet atmospheres have revealed the presence of cloud particles in their atmospheres. 3D modelling of cloud formation in atmospheres of extrasolar planets coupled to the atmospheric dynamics has long been a challenge. Aims. We investigate the thermo-hydrodynamic properties of cloud formation processes in the atmospheres of hot Jupiter exoplanets. Methods. We simulate the dynamic atmosphere of HD 189733b with a 3D model that couples 3D radiative-hydrodynamics with a kinetic, microphysical mineral cloud formation module designed for RHD/GCM exoplanet atmosphere simulations. Our simulation includes the feedback effects of cloud advection and settling, gas phase element advection and depletion/replenishment and the radiative effects of cloud opacity. We model the cloud particles as a mix of mineral materials which change in size and composition as they travel through atmospheric thermo-chemical environments. All local cloud properties such as number density, grain size and material composition are time-dependently calculated. Gas phase element depletion as a result of cloud formation is included in the model. In situ effective medium theory and Mie theory is applied to calculate the wavelength dependent opacity of the cloud component. Results. We present a 3D cloud structure of a chemically complex, gaseous atmosphere of the hot Jupiter HD 189733b. Mean cloud particle sizes are typically sub-micron (0.01−0.5 μm) at pressures less than 1 bar with hotter equatorial Regions containing the smallest grains. Denser cloud structures occur near Terminator Regions and deeper (~1 bar) atmospheric layers. Silicate materials such as MgSiO3[s] are found to be abundant at mid-high latitudes, while TiO2[s] and SiO2[s] dominate the equatorial Regions. Elements involved in the cloud formation can be depleted by several orders of magnitude. Conclusions. The interplay between radiative-hydrodynamics and cloud kinetics leads to an inhomogeneous, wavelength dependent opacity cloud structure with properties differing in longitude, latitude and depth. This suggests that transit spectroscopy would sample a variety of cloud particles properties (sizes, composition, densities)

Casiano H Choresca - One of the best experts on this subject based on the ideXlab platform.

  • complete genome sequence and characterization of a broad host range t4 like bacteriophage phias5 infecting aeromonas salmonicida subsp salmonicida
    2012
    Co-Authors: Yunjaie Choi, Casiano H Choresca, Sang Phil Shin, Se Chang Park
    Abstract:

    Abstract In this study, we report one lytic Myoviridae bacteriophage (phage) infecting Aeromonas salmonicida subsp. salmonicida . The phage (named as phiAS5) was isolated from environmental river waters in Korea, and showed broad infectivity to other bacterial species in the family Aeromonadaceae as well as antibiotic-resistant A. salmonicida subsp. salmonicida strains. The biological properties and complete genome of phiAS5 were simultaneously investigated. The complete genome of phiAS5 composed of linear double-stranded DNA of 225,268 bp with G + C content of 43.0%, and encoded 343 putative ORFs, 69 putative promoters, 33 transcriptional Terminator Regions and 24 tRNA-encoding genes. A high degree of similarity to other T4-like Aeromonas phage was found in most ORFs of phiAS5. Therefore, the genome of phiAS5 was further compared with T4 phage and the closest relative, Aeromonas phage Aeh1, and the result demonstrated that it could be classified as a new member of the T4-like group. The bacteriolytic activity of phiAS5 against A. salmonicida subsp. salmonicida was evaluated at different doses of multiplicity of infection using one each of virulent strain that possesses the ascV gene and multi-drug resistant strain, and the results proved to be efficient for the reduction of bacterial growth. Based on these results, phiAS5 may have the potential for reducing the impacts of virulent or antibiotic-resistant A. salmonicida subsp. salmonicida in aquaculture and may also advance our understanding of the biodiversity of T4-like Aeromonas phages.

  • complete genomic sequence of a t4 like bacteriophage phias4 infecting aeromonas salmonicida subsp salmonicida
    2012
    Co-Authors: Younho Choi, Casiano H Choresca, Sang Phil Shin, Se Chang Park
    Abstract:

    A newly identified virulent phage (named phiAS4) infecting Aeromonas salmonicida subsp. salmonicida was isolated from river water in Korea. Morphological analysis of phiAS4 by transmission electron microscopy revealed that it belonged to the family Myoviridae. The genome of phiAS4 comprised a linear double-stranded DNA of 163,875 bp with a G + C content of 41.3%, and genomic analysis revealed 271 putative ORFs, 67 putative promoters, 25 putative Terminator Regions, and 16 tRNA-encoding genes. Most of the ORFs of phiAS4 showed a high degree of similarity to those of Aeromonas phage 25, which belongs to the T4-like group. Moreover, the comparison of the genome of phiAS4 with those of its relatives demonstrated that phage phiAS4 is closely related to members of the T4-like group and can be classified as a new member of the T4-like phages infecting bacteria of the family Aeromonadaceae.

Sang Phil Shin - One of the best experts on this subject based on the ideXlab platform.

  • complete genome sequence and characterization of a broad host range t4 like bacteriophage phias5 infecting aeromonas salmonicida subsp salmonicida
    2012
    Co-Authors: Yunjaie Choi, Casiano H Choresca, Sang Phil Shin, Se Chang Park
    Abstract:

    Abstract In this study, we report one lytic Myoviridae bacteriophage (phage) infecting Aeromonas salmonicida subsp. salmonicida . The phage (named as phiAS5) was isolated from environmental river waters in Korea, and showed broad infectivity to other bacterial species in the family Aeromonadaceae as well as antibiotic-resistant A. salmonicida subsp. salmonicida strains. The biological properties and complete genome of phiAS5 were simultaneously investigated. The complete genome of phiAS5 composed of linear double-stranded DNA of 225,268 bp with G + C content of 43.0%, and encoded 343 putative ORFs, 69 putative promoters, 33 transcriptional Terminator Regions and 24 tRNA-encoding genes. A high degree of similarity to other T4-like Aeromonas phage was found in most ORFs of phiAS5. Therefore, the genome of phiAS5 was further compared with T4 phage and the closest relative, Aeromonas phage Aeh1, and the result demonstrated that it could be classified as a new member of the T4-like group. The bacteriolytic activity of phiAS5 against A. salmonicida subsp. salmonicida was evaluated at different doses of multiplicity of infection using one each of virulent strain that possesses the ascV gene and multi-drug resistant strain, and the results proved to be efficient for the reduction of bacterial growth. Based on these results, phiAS5 may have the potential for reducing the impacts of virulent or antibiotic-resistant A. salmonicida subsp. salmonicida in aquaculture and may also advance our understanding of the biodiversity of T4-like Aeromonas phages.

  • complete genomic sequence of a t4 like bacteriophage phias4 infecting aeromonas salmonicida subsp salmonicida
    2012
    Co-Authors: Younho Choi, Casiano H Choresca, Sang Phil Shin, Se Chang Park
    Abstract:

    A newly identified virulent phage (named phiAS4) infecting Aeromonas salmonicida subsp. salmonicida was isolated from river water in Korea. Morphological analysis of phiAS4 by transmission electron microscopy revealed that it belonged to the family Myoviridae. The genome of phiAS4 comprised a linear double-stranded DNA of 163,875 bp with a G + C content of 41.3%, and genomic analysis revealed 271 putative ORFs, 67 putative promoters, 25 putative Terminator Regions, and 16 tRNA-encoding genes. Most of the ORFs of phiAS4 showed a high degree of similarity to those of Aeromonas phage 25, which belongs to the T4-like group. Moreover, the comparison of the genome of phiAS4 with those of its relatives demonstrated that phage phiAS4 is closely related to members of the T4-like group and can be classified as a new member of the T4-like phages infecting bacteria of the family Aeromonadaceae.

Woitke P. - One of the best experts on this subject based on the ideXlab platform.

  • Sparkling nights and very hot days on WASP-18b : the formation of clouds and the emergence of an ionosphere
    2019
    Co-Authors: Ch. Helling, Gourbin P., Woitke P.
    Abstract:

    Context. WASP-18b is an ultra-hot Jupiter with a temperature difference of up to 2500 K between day and night. Such giant planets begin to emerge as a planetary laboratory for understanding cloud formation and gas chemistry in well-tested parameter regimes in order to better understand planetary mass loss and for linking observed element ratios to planet formation and evolution. Aims. We aim to understand where clouds form, their interaction with the gas-phase chemistry through depletion and enrichment, the ionisation of the atmospheric gas, and the possible emergence of an ionosphere on ultra-hot Jupiters. Methods. We used 1D profiles from a 3D atmosphere simulation for WASP-18b as input for kinetic cloud formation and gas-phase chemical equilibrium calculations. We solved our kinetic cloud formation model for these 1D profiles, which sample the atmosphere of WASP-18b at 16 different locations along the equator and in the mid-latitudes. We derived the gas-phase composition consistently. Results. The dayside of WASP-18b emerges as completely cloud-free as a result of the very high atmospheric temperatures. In contrast, the nightside is covered in geometrically extended and chemically heterogeneous clouds with dispersed particle size distributions. The atmospheric C/O ratio increases to >0.7 and the enrichment of the atmospheric gas with cloud particles is ρd/ρgas > 10−3. The clouds that form at the limbs appear located farther inside the atmosphere, and they are the least extended. Not all day- to nightside Terminator Regions form clouds. The gas phase is dominated by H2, CO, SiO, H2O, H2S, CH4, and SiS. In addition, the dayside has a substantial degree of ionisation that is due to ions such as Na+, K+, Ca+, and Fe+. Al+ and Ti+ are the most abundant of their element classes. We find that WASP-18b, as one example for ultra-hot Jupiters, develops an ionosphere on the dayside.PostprintPeer reviewe

  • Sparkling nights and very hot days on WASP-18b: the formation of clouds and the emergence of an ionosphere
    2019
    Co-Authors: Ch. Helling, Gourbin P., Woitke P.
    Abstract:

    WASP-18b is an utra-hot Jupiter with a temperature difference of upto 2500K between day and night. Such giant planets begin to emerge as planetary laboratory for understanding cloud formation and gas chemistry in well-tested parameter regimes in order to better understand planetary mass loss and for linking observed element ratios to planet formation and evolution. We aim to understand where clouds form, their interaction with the gas phase chemistry through depletion and enrichment, the ionisation of the atmospheric gas and the possible emergence of an ionosphere on ultra-hot Jupiters. We utilize 1D profiles from a 3D atmosphere simulations for WASP-18b as input for kinetic cloud formation and gas-phase chemical equilibrium calculations. We solve our kinetic cloud formation model for these 1D profiles that sample the atmosphere of WASP-18b at 16 different locations along the equator and in the mid-latitudes and derive consistently the gas-phase composition. The dayside of WASP-18b emerges as completely cloud-free due to the very high atmospheric temperatures. In contrast, the nightside is covered in geometrically extended and chemically heterogeneous clouds with disperse particle size distributions. The atmospheric C/O increases to $>0.7$ and the enrichment of the atmospheric gas with cloud particles is $\rho_{\rm d}/\rho_{\rm gas}>10^{-3}$. The clouds that form at the limbs appear located farther inside the atmosphere and they are the least extended. Not all day-night Terminator Regions form clouds. The gas-phase is dominated by H$_2$, CO, SiO, H$_2$O, H$_2$S, CH$_4$, SiS. In addition, the dayside has a substantial degree of ionisation due to ions like Na$^+$, K$^+$, Ca$^+$, Fe$^+$. Al$^+$ and Ti$^+$ are the most abundant of their element classes. We find that WASP-18b, as one example for ultra-hot Jupiters, develops an ionosphere on the dayside.Comment: 31 pages, accepted for publication in A&

  • Dynamic mineral clouds on HD 189733b I. 3D RHD with kinetic, non-equilibrium cloud formation
    2016
    Co-Authors: Lee G., Ch. Helling, Bognar K., Woitke P.
    Abstract:

    Observations of exoplanet atmospheres have revealed the presence of cloud particles in their atmospheres. 3D modelling of cloud formation in atmospheres of extrasolar planets coupled to the atmospheric dynamics has long been a challenge. We investigate the thermo-hydrodynamic properties of cloud formation processes in the atmospheres of hot Jupiter exoplanets. We simulate the dynamic atmosphere of HD 189733b with a 3D model that couples 3D radiative-hydrodynamics with a kinetic, microphysical mineral cloud formation module designed for RHD/GCM exoplanet atmosphere simulations. Our simulation includes the feedback effects of cloud advection and settling, gas phase element advection and depletion/replenishment and the radiative effects of cloud opacity. We model the cloud particles as a mix of mineral materials which change in size and composition as they travel through atmospheric thermo-chemical environments. All local cloud properties such as number density, grain size and material composition are time-dependently calculated. Gas phase element depletion as a result of cloud formation is included in the model. In-situ \textit{effective medium theory} and Mie theory is applied to calculate the wavelength dependent opacity of the cloud component. We present a 3D cloud structure of a chemically complex, gaseous atmosphere of the hot Jupiter HD 189733b. Mean cloud particle sizes are typically sub-micron (0.01-0.5 $\mu$m) at pressures less than 1 bar with hotter equatorial Regions containing the smallest grains. Denser cloud structures occur near Terminator Regions and deeper ($\sim$ 1 bar) atmospheric layers. Silicate materials such as MgSiO$_{3}$[s] are found to be abundant at mid-high latitudes, while TiO$_{2}$[s] and SiO$_{2}$[s] dominate the equatorial Regions.Comment: 24 pages, accepted to A&

  • Dynamic mineral clouds on HD 189733b : I. 3D RHD with kinetic, non-equilibrium cloud formation
    2016
    Co-Authors: Lee G., Ch. Helling, Bognar K., Woitke P.
    Abstract:

    Funding: European community under the FP7 ERC starting grant 257431 (G.L., Ch. H.).Context. Observations of exoplanet atmospheres have revealed the presence of cloud particles in their atmospheres. 3D modelling of cloud formation in atmospheres of extrasolar planets coupled to the atmospheric dynamics has long been a challenge. Aims. We investigate the thermo-hydrodynamic properties of cloud formation processes in the atmospheres of hot Jupiter exoplanets. Methods. We simulate the dynamic atmosphere of HD 189733b with a 3D model that couples 3D radiative-hydrodynamics with a kinetic, microphysical mineral cloud formation module designed for RHD/GCM exoplanet atmosphere simulations. Our simulation includes the feedback effects of cloud advection and settling, gas phase element advection and depletion/replenishment and the radiative effects of cloud opacity. We model the cloud particles as a mix of mineral materials which change in size and composition as they travel through atmospheric thermo-chemical environments. All local cloud properties such as number density, grain size and material composition are time-dependently calculated. Gas phase element depletion as a result of cloud formation is included in the model. In situ effective medium theory and Mie theory is applied to calculate the wavelength dependent opacity of the cloud component. Results. We present a 3D cloud structure of a chemically complex, gaseous atmosphere of the hot Jupiter HD 189733b. Mean cloud particle sizes are typically sub-micron (0.01−0.5 μm) at pressures less than 1 bar with hotter equatorial Regions containing the smallest grains. Denser cloud structures occur near Terminator Regions and deeper (~1 bar) atmospheric layers. Silicate materials such as MgSiO3[s] are found to be abundant at mid-high latitudes, while TiO2[s] and SiO2[s] dominate the equatorial Regions. Elements involved in the cloud formation can be depleted by several orders of magnitude. Conclusions. The interplay between radiative-hydrodynamics and cloud kinetics leads to an inhomogeneous, wavelength dependent opacity cloud structure with properties differing in longitude, latitude and depth. This suggests that transit spectroscopy would sample a variety of cloud particles properties (sizes, composition, densities).Publisher PDFPeer reviewe