Recombinase technology: applications and possibilities

The use of recombinases for genomic engineering is no longer a new technology. In fact, this technology has entered its third decade since the initial discovery that recombinases function in heterologous systems (Sauer in Mol Cell Biol 7(6):2087–2096, 1987). The random insertion of a transgene into a plant genome by traditional methods generates unpredictable expression patterns. This feature of transgenesis makes screening for functional lines with predictable expression labor intensive and time consuming. Furthermore, an antibiotic resistance gene is often left in the final product and the potential escape of such resistance markers into the environment and their potential consumption raises consumer concern. The use of site-specific recombination technology in plant genome manipulation has been demonstrated to effectively resolve complex transgene insertions to single copy, remove unwanted DNA, and precisely insert DNA into known genomic target sites. Recombinases have also been demonstrated capable of site-specific recombination within non-nuclear targets, such as the plastid genome of tobacco. Here, we review multiple uses of site-specific recombination and their application toward plant genomic engineering. We also provide alternative strategies for the combined use of multiple site-specific recombinase systems for genome engineering to precisely insert transgenes into a pre-determined locus, and removal of unwanted selectable marker genes

Development of a Molecular Dynamics Simulation Model for Heat Transfer in Vapors

For many practical cases, such as gas-wall interactions, molecular dynamics simulations are aperfect tool. Here we use such molecular dynamics simulation to study the micro heat transfer ofgas in a nanochannel. However, to study larger microchannels molecular dynamics iscomputationally too expensive. Within the GASMEMS project, firstly an efficient parallel code willbe developed and a method for modeling complex wall geometries will be developed. Furthermore,a hybrid method with other particle based methods, like Monte Carlo method or with Continuummethods will be studied

Geometry effects on rarefied nanochannel flows

A three dimensional molecular dynamics method was used to study the effect of different geometries for rarefied gas flows in nanochannels. Argon molecules have been used. The velocity profiles in the channel were obtained and analyzed with three different channel geometries: a circular, a rectangular (square), and a slit channel. A channel width of 50 nm was used for the simulation. It was found that when using the same driving force, the maximum velocity of the flow increases when the geometry changes in the order from circular to rectangular to slit geometry, where the latter becomes 2–2.5 times as large compared with either the rectangular or circular channel. For Kn larger than 1.0, the rectangular channel showed a similar maximum and slip velocity as the circular channel while the velocity profile was qualitatively similar to the slit channel. The effect of different Knudsen numbers on the velocity profiles was also investigated. We found that for Kn larger than 2–3, the Knudsen number has a relatively small influence on the slip velocity for circular channels and rectangular channels. The effect of the accommodation coefficient on the average flow velocity for all three geometries was studied and expressed as an allometric equation mode

Molecular simulation of water vapor outgassing from silica nanopores

The outgassing problem is solved numerically by molecular dynamics. A slit-shaped nanopore consisting of cavity and channel is built with an implicit tabulated wall potential that describes the water–silicon/silica interaction. A\u3cbr/\u3eflexible three-point water model is used for the simulation. The effects of varying the system temperature, outlet pressure, geometry, and materials of the nanopore on the outgassing rate are investigated. The results show that the temperature plays an important role in the outgassing rate, while the effect\u3cbr/\u3eof the outlet pressure is negligible as long as it is in the high to medium vacuum range. The geometry of the channel also has an influence on the outgassing rate, but not as much as the surface material. Three different types of silica materials are tested: silicon, silica-cristobalite (hydrophilic material), and silica-quartz (super hydrophilic material). The fastest outgassing rate is found for a silicon nanopore. It is also found that a thin water film is formed on the surface of the silica-quartz nanopore. This material shows hardly any outgassing of water. The outgassing problem is solved numerically by molecular dynamics. A slit-shaped nanopore consisting of cavity and channel is built with an implicit tabulated wall potential that describes the water–silicon/silica interaction. A\u3cbr/\u3eflexible three-point water model is used for the simulation. The effects of varying the system temperature, outlet pressure, geometry, and materials of the nanopore on the outgassing rate are investigated. The results show that the temperature plays an important role in the outgassing rate, while the effect\u3cbr/\u3eof the outlet pressure is negligible as long as it is in the high to medium vacuum range. The geometry of the channel also has an influence on the outgassing rate, but not as much as the surface material. Three different types of silica materials are tested: silicon, silica-cristobalite (hydrophilic material), and silica-quartz (super hydrophilic material). The fastest outgassing\u3cbr/\u3erate is found for a silicon nanopore. It is also found that a thin water film is formed on the surface of the silica-quartz nanopore. This material shows hardly any outgassing of water

Development of KSTAR ECE imaging system for measurement of temperature fluctuations and edge density fluctuations

The ECE imaging (ECEI) diagnostic tested on the TEXTOR tokamak revealed the sawtooth reconnection physics in unprecedented detail, including the first observation of high-field-side crash and collective heat transport [ H. K. Park, N. C. Luhmann, Jr., A. J. H. Donné et al., Phys. Rev. Lett. 96, 195003 (2006) ]. An improved ECEI system capable of visualizing both high- and low-field sides simultaneously with considerably better spatial coverage has been developed for the KSTAR tokamak in order to capture the full picture of core MHD dynamics. Direct 2D imaging of other MHD phenomena such as tearing modes, edge localized modes, and even Alfvén eigenmodes is expected to be feasible. Use of ECE images of the optically thin edge region to recover 2D electron density changes during L/H mode transitions is also envisioned, providing powerful information about the underlying physics. The influence of density fluctuations on optically thin ECE is discussed. © 2010 American Institute of Physic

Development of KSTAR ECE imaging system for measurement of temperature fluctuations and edge density fluctuation

The ECE imaging (ECEI) diagnostic tested on the TEXTOR tokamak revealed the sawtooth reconnection physics in unprecedented detail, including the first observation of high-field-side crash and collective heat transport [H. K. Park, N. C. Luhmann, Jr., A. J. H. Donne et al., Phys. Rev. Lett. 96, 195003 (2006)]. An improved ECEI system capable of visualizing both high-and low-field sides simultaneously with considerably better spatial coverage has been developed for the KSTAR tokamak in order to capture the full picture of core MHD dynamics. Direct 2D imaging of other MHD phenomena such as tearing modes, edge localized modes, and even Alfven eigenmodes is expected to be feasible. Use of ECE images of the optically thin edge region to recover 2D electron density changes during L/H mode transitions is also envisioned, providing powerful information about the underlying physics. The influence of density fluctuations on optically thin ECE is discussed. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3483209]open116069sciescopu

Visualization of fusion plasma physics via millimeter wave imaging techniques

Advances in microwave technology and innovative ideas have enabled visualization of complex physics of the high temperature plasmas in magnetic fusion devices. ECE Imaging system becomes a powerful tool for MHD physics in various devices and the potential of the MIR system has been reassessed and a system design for KSTAR is in progress