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2. Isoprene hydrocarbons production upon heterologous transformation of Saccharomyces cerevisiae

Author

Hong, S‐Y, Zurbriggen, AS, and Melis, A

Subjects
Biological Sciences, Industrial Biotechnology, Genetics, Alkyl and Aryl Transferases, Butadienes, Codon, DNA, Ribosomal, Fermentation, Genetic Engineering, Hemiterpenes, Pentanes, Plasmids, Pueraria, Saccharomyces cerevisiae, Transformation, Genetic, Transgenes, biofuels, isoprene synthase, kudzu vine, methyl-butenol, renewable energy, yeast, Microbiology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

Aims  Isoprene (2-methyl-1,3-butadiene; C(5) H(8) ) is naturally produced by photosynthesis and emitted in the atmosphere by the leaves of many herbaceous, deciduous and woody plants. Fermentative yeast and fungi (Ascomycota) are not genetically endowed with the isoprene production process. The work investigated whether Ascomycota can be genetically modified and endowed with the property of constitutive isoprene production.Methods and results  Two different strategies for expression of the IspS gene in Saccharomyces cerevisiae were employed: (i) optimization of codon usage of the IspS gene for specific expression in S. cerevisiae and (ii) multiple independent integrations of the IspS gene in the rDNA loci of the yeast genome. Copy number analysis showed that IspS transgenes were on the average incorporated within about 25% of the endogenous rDNA. Codon use optimization of the Pueraria montana (kudzu vine) IspS gene (SckIspS) for S. cerevisiae showed fivefold greater expression of the IspS protein compared with that of nonoptimized IspS (kIspS). With the strategies mentioned earlier, heterologous expression of the kudzu isoprene synthase gene (kIspS) in S. cerevisiae was tested for stability and as a potential platform of fermentative isoprene production. The multi-copy IspS transgenes were stably integrated and expressed for over 100 generations of yeast cell growth and constitutively produced volatile isoprene hydrocarbons. Secondary chemical modification of isoprene to a number of hydroxylated isoprene derivatives in the sealed reactor was also observed.Conclusion  Transformation of S. cerevisiae with the Pueraria montana var. lobata (kudzu vine) isoprene synthase gene (IspS) conferred to the yeast cells constitutive isoprene hydrocarbons production in the absence of adverse or toxic effects.Significance and impact of the study  First-time demonstration of constitutive isoprene hydrocarbons production in a fermentative eukaryote operated through the mevalonic acid pathway. The work provides concept validation for the utilization of S. cerevisiae, as a platform for the production of volatile hydrocarbon biofuels and chemicals.

Published
2012

7. Update on World Health Organization HIV Drug Resistance Prevention and Assessment Strategy: 2004—2011

Author

Jordan, M. R., Bennett, D. E., Wainberg, M. A., Havlir, D., Hammer, S., Yang, C., Morris, L., Peeters, M., Wensing, A. M., Parkin, N., Nachega, J. B., Phillips, A., De Luca, A., Geng, E., Calmy, A., Raizes, E., Sandstrom, P., Archibald, C. P., Perriëns, J., McClure, C. M., Hong, S. Y., McMahon, J. H., Dedes, N., Sutherland, D., and Bertagnolio, S.

Published
2012
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23. The Impact of Microphysical Schemes on Intensity and Track of Hurricane

Author

Tao, W. K, Shi, J. J, Chen, S. S, Lang, S, Lin, P, Hong, S. Y, Peters-Lidard, C, and Hou, A

Subjects
Meteorology And Climatology
Abstract

During the past decade, both research and operational numerical weather prediction models [e.g. Weather Research and Forecasting Model (WRF)] have started using more complex microphysical schemes originally developed for high-resolution cloud resolving models (CRMs) with a 1-2 km or less horizontal resolutions. The WRF is a next-generation meso-scale forecast model and assimilation system that has incorporated a modern software framework, advanced dynamics, numeric and data assimilation techniques, a multiple moveable nesting capability, and improved physical packages. The WRF model can be used for a wide range of applications, from idealized research to operational forecasting, with an emphasis on horizontal grid sizes in the range of 1-10 km. The current WRF includes several different microphysics options. At Goddard, four different cloud microphysics schemes (warm rain only, two-class of ice, two three-class of ice with either graupel or hail) are implemented into the WRF. The performances of these schemes have been compared to those from other WRF microphysics scheme options for an Atlantic hurricane case. In addition, a brief review and comparison on the previous modeling studies on the impact of microphysics schemes and microphysical processes on intensity and track of hurricane will be presented. Generally, almost all modeling studies found that the microphysics schemes did not have major impacts on track forecast, but did have more effect on the intensity. All modeling studies found that the simulated hurricane has rapid deepening and/or intensification for the warm rain-only case. It is because all hydrometeors were very large raindrops, and they fell out quickly at and near the eye-wall region. This would hydrostatically produce the lowest pressure. In addition, these modeling studies suggested that the simulated hurricane becomes unrealistically strong by removing the evaporative cooling of cloud droplets and melting of ice particles. This is due to the much weaker downdraft simulated. However, there are many differences between different modeling studies and these differences were identified and discussed.

Published
2010

25. An Improved Bulk Microphysical Scheme for Studying Precipitation Processes: Comparisons with Other Schemes

Author

Tao, W. K, Shi, J. J, Lang, S, Chen, S, Hong, S-Y, and Peters-Lidard, C

Subjects
Meteorology And Climatology
Abstract

Cloud microphysical processes play an important role in non-hydrostatic high-resolution simulations. Over the past decade both research and operational numerical weather prediction models have started using more complex cloud microphysical schemes that were originally developed for high-resolution cloud-resolving models. An improved bulk microphysical parameterization (adopted from the Goddard microphysics schemes) has recently implemented into the Weather Research and Forecasting (WRF) model. This bulk microphysical scheme has three different options --- 2ICE (cloud ice & snow), 3ICE-graupel (cloud ice, snow & graupel) and 3ICE-hail (cloud ice, snow & hail). High-resolution model simulations are conducted to examine the impact of microphysical schemes on two different weather events (a midlatitude linear convective system and an Atlantic hurricane). In addition, this bulk microphysical parameterization is compared with WIRF's three other bulk microphysical schemes.

Published
2007

26. New, Improved Bulk-microphysical Schemes for Studying Precipitation Processes in WRF

Author

Tao, W.-K, Shi, J, Chen, S. S, Lang, S, Hong, S.-Y, Thompson, G, Peters-Lidard, C, Hou, A, Braun, S, and Simpson, J

Subjects
Meteorology And Climatology
Abstract

Advances in computing power allow atmospheric prediction models to be mn at progressively finer scales of resolution, using increasingly more sophisticated physical parameterizations and numerical methods. The representation of cloud microphysical processes is a key component of these models, over the past decade both research and operational numerical weather prediction models have started using more complex microphysical schemes that were originally developed for high-resolution cloud-resolving models (CRMs). A recent report to the United States Weather Research Program (USWRP) Science Steering Committee specifically calls for the replacement of implicit cumulus parameterization schemes with explicit bulk schemes in numerical weather prediction (NWP) as part of a community effort to improve quantitative precipitation forecasts (QPF). An improved Goddard bulk microphysical parameterization is implemented into a state-of the-art of next generation of Weather Research and Forecasting (WRF) model. High-resolution model simulations are conducted to examine the impact of microphysical schemes on two different weather events (a midlatitude linear convective system and an Atllan"ic hurricane). The results suggest that microphysics has a major impact on the organization and precipitation processes associated with a summer midlatitude convective line system. The 31CE scheme with a cloud ice-snow-hail configuration led to a better agreement with observation in terms of simulated narrow convective line and rainfall intensity. This is because the 3ICE-hail scheme includes dense ice precipitating (hail) particle with very fast fall speed (over 10 m/s). For an Atlantic hurricane case, varying the microphysical schemes had no significant impact on the track forecast but did affect the intensity (important for air-sea interaction)

Published
2007

40. Sulfur at nickel-alumina interfaces - Molecular orbital theory

Author

Hong, S. Y, Anderson, Alfred B, and Smialek, James L

Subjects
Inorganic And Physical Chemistry
Abstract

Previous studies on Al-Ni alloys containing sulfur as an impurity suggest that, when S is in the interface between a metal and an oxide scale, it weakens the chemical bonding between them. This paper investigates factors responsible for this effect, using a molecular orbital theory to predict sulfur structures and electronic properties on the Ni-Al2O3 interface. It is shown that, in absence of S, the basal plane of Al2O3 will bind strongly through the Al(3+) cation surface to Ni (111). When segregated S impurity is present on the Ni surface, there are too few interfacial AlS bonds to effect good adhesion, leading to an inhibition of the oxide scale adhesion in NiCrAl alloys.

Published
1990
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43. Carbon nanotubes synthesized by Ni-assisted atmospheric pressure thermal chemical vapor deposition.

Author

Choi, G. S., Cho, Y. S., Hong, S. Y., Park, J. B., Son, K. H., and Kim, D. J.

Subjects
NANOTUBES, MORPHOLOGY, SILICON, CHEMICAL vapor deposition
Abstract

A detailed systematic study on the growth morphology of carbon nanotubes (CNTs) on Si in atmospheric pressure thermal chemical vapor deposition was undertaken. The role of NH[sub 3] for vertical alignment of CNTs was investigated. The direct cause for the alignment was a dense distribution of the catalytic metal particles, but that the particles are maintained catalytically active under amorphous carbon deposits was established by NH[sub 3]. It allows a dense nucleation of the CNTs, and consequently, assists vertical alignment through entanglement and mechanical leaning among the tubes. The CNTs grew in a base growth mode. Since Ni is consumed both by silicide reaction and by capture into the growing tube, the growth stops when Ni is totally depleted. It occurs earlier for smaller particles, and thus a long time of growth results in a thin bottom with poor adhesion. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Published
2002
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44. Update on World Health Organization HIV Drug Resistance Prevention and Assessment Strategy: 2004-2011

Author

Jordan, M. R., Bennett, D. E., Wainberg, M. A., Havlir, D., Hammer, S., Yang, C., Morris, L., Peeters, M., Wensing, A. M., Parkin, N., Nachega, J. B., Phillips, A., De Luca, A., Geng, E., Calmy, A., Raizes, E., Sandstrom, P., Archibald, C. P., Perriëns, J., McClure, C. M., Hong, S. Y., McMahon, J. H., Dedes, N., Sutherland, D., Bertagnolio, S., Jordan, M. R., Bennett, D. E., Wainberg, M. A., Havlir, D., Hammer, S., Yang, C., Morris, L., Peeters, M., Wensing, A. M., Parkin, N., Nachega, J. B., Phillips, A., De Luca, A., Geng, E., Calmy, A., Raizes, E., Sandstrom, P., Archibald, C. P., Perriëns, J., McClure, C. M., Hong, S. Y., McMahon, J. H., Dedes, N., Sutherland, D., and Bertagnolio, S.

Abstract

The HIV drug resistance (HIVDR) prevention and assessment strategy, developed by the World Health Organization (WHO) in partnership with HIVResNet, includes monitoring of HIVDR early warning indicators, surveys to assess acquired and transmitted HIVDR, and development of an accredited HIVDR genotyping laboratory network to support survey implementation in resource-limited settings. As of June 2011, 52 countries had implemented at least 1 element of the strategy, and 27 laboratories had been accredited. As access to antiretrovirals expands under the WHO/Joint United Nations Programme on HIV/AIDS Treatment 2.0 initiative, it is essential to strengthen HIVDR surveillance efforts in the face of increasing concern about HIVDR emergence and transmission

Published
2017

45. Multivariate Variance Ratio Statistics

Author

Hong, S. Y., Linton, O., and Zhang, H. J.

Subjects
Martingale, Momentum, Predictability
Abstract

We propose several multivariate variance ratio statistics. We derive the asymptotic distribution of the statistics and scalar functions thereof under the null hypothesis that returns are unpredictable after a constant mean adjustment (i.e., under the Efficient Market Hypothesis). We do not impose the no leverage assumption of Lo and MacKinlay (1988) but our asymptotic standard errors are relatively simple and in particular do not require the selection of a bandwidth parameter. We extend the framework to allow for a smoothly varying risk premium in calendar time, and show that the limiting distribution is the same as in the constant mean adjustment case. We show the limiting behaviour of the statistic under a multivariate fads model and under a moderately explosive bubble process: these alternative hypotheses give opposite predictions with regards to the long run value of the statistics. We apply the methodology to three weekly size-sorted CRSP portfolio returns from 1962 to 2013 in three subperiods. We find evidence of a reduction of linear predictability in the most recent period, for small and medium cap stocks. We find similar results for the main UK stock indexes. The main findings are not substantially affected by allowing for a slowly varying risk premium.

Published
2016
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46. Isoprene hydrocarbons production upon heterologous transformation of Saccharomyces cerevisiae.

Author

Hong, S-Y, Hong, S-Y, Zurbriggen, AS, Melis, A, Hong, S-Y, Hong, S-Y, Zurbriggen, AS, and Melis, A

Abstract

Aims Isoprene (2-methyl-1,3-butadiene; C(5) H(8) ) is naturally produced by photosynthesis and emitted in the atmosphere by the leaves of many herbaceous, deciduous and woody plants. Fermentative yeast and fungi (Ascomycota) are not genetically endowed with the isoprene production process. The work investigated whether Ascomycota can be genetically modified and endowed with the property of constitutive isoprene production.Methods and results Two different strategies for expression of the IspS gene in Saccharomyces cerevisiae were employed: (i) optimization of codon usage of the IspS gene for specific expression in S. cerevisiae and (ii) multiple independent integrations of the IspS gene in the rDNA loci of the yeast genome. Copy number analysis showed that IspS transgenes were on the average incorporated within about 25% of the endogenous rDNA. Codon use optimization of the Pueraria montana (kudzu vine) IspS gene (SckIspS) for S. cerevisiae showed fivefold greater expression of the IspS protein compared with that of nonoptimized IspS (kIspS). With the strategies mentioned earlier, heterologous expression of the kudzu isoprene synthase gene (kIspS) in S. cerevisiae was tested for stability and as a potential platform of fermentative isoprene production. The multi-copy IspS transgenes were stably integrated and expressed for over 100 generations of yeast cell growth and constitutively produced volatile isoprene hydrocarbons. Secondary chemical modification of isoprene to a number of hydroxylated isoprene derivatives in the sealed reactor was also observed.Conclusion Transformation of S. cerevisiae with the Pueraria montana var. lobata (kudzu vine) isoprene synthase gene (IspS) conferred to the yeast cells constitutive isoprene hydrocarbons production in the absence of adverse or toxic effects.Significance and impact of the study First-time demonstration of constitutive isoprene hydrocarbons production in a fermentative eukaryote operated through the mevalonic acid

Published
2012

48. Fully Nonlinear Multidirectional Waves by a 3-D Viscous Numerical Wave Tank

Author

Kim, M. H., Niedzwecki, J. M., Roesset, J. M., Park, J. C., Hong, S. Y., and Tavassoli, A.

Subjects
Waves -- Analysis, Boundary value problems -- Analysis, Fluid dynamics -- Analysis, Science and technology
Abstract

A finite-difference scheme and a modified marker-and-cell (MAC) method are used for numerical wave tank (NWT) simulations to investigate the characteristics of nonlinear multidirectional waves. The Navier-Stokes (NS) equations are solved for two fluid layers and the boundary values updated at each time step by a finite-difference time-marching scheme in the frame of rectangular coordinate system. The fully nonlinear kinematic free-surface condition is satisfied by the density-function technique developed for two fluid layers. The directional incident waves are generated from the inflow boundary by prescribing a snakelike motion along the wavemaker direction. The outgoing waves are numerically dissipated inside an artificial damping zone located at the end of the tank. Using the NS-MAC NWT with both solid and transparent side-wall conditions, the effects of side-wall reflections are studied. Bull's-eye waves are also numerically generated by the phase control of neighboring wavemaker segments or the reverse process of cylindrical wavemakers. The simulation results are compared with the computations by an independently developed potential-based NWT and the experiments conducted in the Offshore Technology Research Center's 3-D wave basin. [DOI: 10.1115/1.1377598] Keywords: Numerical Wave Tank, Multidirectional Waves, Finite-Difference Method, Fully Nonlinear Free-Surface, Navier-Stokes Equation, Density Function, Two-Layer Flow, Side-Wall Reflection, Snakelike Wavemaker Motions, Bull's-Eye Waves

Published
2001

49. RF-bias effect on structural and magnetic properties in CoCrPt/[Cr.sub.25][Ti.sub.25]/CoTi trilayer type longitudinal recording media

Author

Hong, S. Y., Shin, K. H., and Lee, T. D.

Subjects
Magnetism -- Research, Magnetic recorders and recording -- Research, Business, Electronics, Electronics and electrical industries
Abstract

The effects of an rf substrate bias on the structural and magnetic properties of the CoCrPt/[Cr.sub.75][Ti.sub.25]/CoTi trilayer type longitudinal recording media deposited on glass substrate have been studied. It was found that the coercivity of 30 nm thick CoCrPt films deposited on [Cr.sub.75][Ti.sub.25]/CoTi underlayer was 4000 Oe by a substrate bias of 100 W rf, which is 800 Oe increase than the non-biased case. X-ray diffraction indicated that the rf-bias to substrate improved the Co (1010) and (1120) plane textures of the CoCrPt magnetic layer. From RBS analyses, Pt content of the CoCrPt magnetic layer increased with rf-bias power. In addition to the Pt increase, a better lattice matching between the CoCrPt magnetic layer and the [Cr.sub.75][Ti.sub.25]/CoTi underlayer was obtained through the expansion of the lattice parameter, 'a' and 'c' of Co in the CoCrPt with the substrate bias. These two factors are thought to be the origin of the coercivity increase. Index Terms--CoCrPt, [Cr.sub.75][Ti.sub.25]/CoTi underlayer, crystallographic texture, substrate bias

Published
1999

50. A Double Underlayer for Co-Based Longitudinal Recording Thin Film Media

Author

Lee, T. D., Hong, S. Y., Bae, Seung-Young, and Shin, K. H.

Subjects
Magnetic recorders and recording -- Research, Thin films -- Analysis, Business, Electronics, Electronics and electrical industries
Abstract

Magnetic and recording characteristics of CoCrPt thin film media deposited on [Cr.sub.75][Ti.sub.25]/CoTi double underlayers were investigated and compared to those on bare CoTi or Cr underlayer. Higher coercivity and improved SNR property were obtained compared to media that had CoTi or Cr underlayer. Transmission electron microscopy analysis showed that the crystal grain size and grain size distribution in the magnetic layer were reduced when the [Cr.sub.75][Ti.sub.25] double layer was used as underlayer. Furthermore, from the delta-M and magnetic force microscopy analyses, it was found that CoCrPt/[Cr.sub.75][Ti.sub.25]/CoTi triple layered thin films had higher magnetic decoupling of neighboring grains than that of CoCrPt deposited on CoTi or Cr underlayer. Index Terms--Coercivity, SNR, [Cr.sub.75][Ti.sub.25]/CoTi double underlayer, magnetic decoupling.

Published
1999

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