Reduced mutation rate and increased transformability of transposon-free Acinetobacter baylyi ADP1-ISx

ABSTRACT The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a designed function. We deleted all six copies of IS 1236 from the genome of the naturally transformable bacterium Acinetobacter baylyi ADP1. The natural competence of ADP1 made it possible to rapidly repair deleterious point mutations that arose during strain construction. In the resulting ADP1-ISx strain, the rates of mutations inactivating a reporter gene were reduced by 7- to 21-fold. This reduction was higher than expected from the incidence of new IS 1236 insertions found during a 300-day mutation accumulation experiment with wild-type ADP1 that was used to estimate spontaneous mutation rates in the strain. The extra improvement appears to be due in part to eliminating large deletions caused by IS 1236 activity, as the point mutation rate was unchanged in ADP1-ISx. Deletion of an error-prone polymerase ( dinP ) and a DNA damage response regulator ( umuD Ab [the umuD gene of A. baylyi ]) from the ADP1-ISx genome did not further reduce mutation rates. Surprisingly, ADP1-ISx exhibited increased transformability. This improvement may be due to less autolysis and aggregation of the engineered cells than of the wild type. Thus, deleting IS elements from the ADP1 genome led to a greater than expected increase in evolutionary reliability and unexpectedly enhanced other key strain properties, as has been observed for other clean-genome bacterial strains. ADP1-ISx is an improved chassis for metabolic engineering and other applications. IMPORTANCE Acinetobacter baylyi ADP1 has been proposed as a next-generation bacterial host for synthetic biology and genome engineering due to its ability to efficiently take up DNA from its environment during normal growth. We deleted transposable elements that are capable of copying themselves, inserting into other genes, and thereby inactivating them from the ADP1 genome. The resulting “clean-genome” ADP1-ISx strain exhibited larger reductions in the rates of inactivating mutations than expected from spontaneous mutation rates measured via whole-genome sequencing of lineages evolved under relaxed selection. Surprisingly, we also found that IS element activity reduces transformability and is a major cause of cell aggregation and death in wild-type ADP1 grown under normal laboratory conditions. More generally, our results demonstrate that domesticating a bacterial genome by removing mobile DNA elements that have accumulated during evolution in the wild can have unanticipated benefits. </jats:p

Longitudinal Ion Acceleration from High-Intensity Laser Interactions with Underdense Plasma

Longitudinal ion acceleration from high-intensity (I ~ 10^20 Wcm^-2) laser interactions with helium gas jet targets (n_e ~ 0.04 n_c) have been observed. The ion beam has a maximum energy for He^2+ of approximately 40 MeV and was directional along the laser propagation path, with the highest energy ions being collimated to a cone of less than 10 degrees. 2D particle-in-cell simulations have been used to investigate the acceleration mechanism. The time varying magnetic field associated with the fast electron current provides a contribution to the accelerating electric field as well as providing a collimating field for the ions. A strong correlation between the plasma density and the ion acceleration was found. A short plasma scale-length at the vacuum interface was observed to be beneficial for the maximum ion energies, but the collimation appears to be improved with longer scale-lengths due to enhanced magnetic fields in the ramp acceleration region.Comment: 18 pages, 6 figure

Focusing of laser-generated ion beams by a plasma cylinder: similarity theory and the thick lens formula

It is shown that plasma-based optics can be used to guide and focus highly divergent laser-generated ion beams. A hollow cylinder is considered, which initially contains a hot electron population. Plasma streaming toward the cylinder axis maintains a focusing electrostatic field due to the positive radial pressure gradient. The cylinder works as thick lens, whose parameters are obtained from similarity theory for freely expanding plasma in cylindrical geometry. Because the lens parameters are energy dependent, the lens focuses a selected energy range of ions and works as a monochromator. Because the focusing is due to the quasineutral part of the expanding plasma, the lens parameters depend on the hot electron temperature $T_e$ only, and not their density

Absolute calibration of GafChromic film for very high flux laser driven ion beams.

We report on the calibration of GafChromic HD-v2 radiochromic film in the extremely high dose regime up to 100 kGy together with very high dose rates up to 7 × 1011 Gy/s. The absolute calibration was done with nanosecond ion bunches at the Neutralized Drift Compression Experiment II particle accelerator at Lawrence Berkeley National Laboratory (LBNL) and covers a broad dose dynamic range over three orders of magnitude. We then applied the resulting calibration curve to calibrate a laser driven ion experiment performed on the BELLA petawatt laser facility at LBNL. Here, we reconstructed the spatial and energy resolved distributions of the laser-accelerated proton beams. The resulting proton distribution is in fair agreement with the spectrum that was measured with a Thomson spectrometer in combination with a microchannel plate detector

Three dimensional asset documentation using terrestrial laser scanner technology

Asset documentation is a detailed record or inventory of the properties located within a room or a building. It is important to record the assets in case of property loss happen inside the premise especially when that premise caught fire, earthquake, robbery and others. The instrument used in this study is Faro Laser Scanner Photon 120/20. The object of the study is the computer room of Photogrammetry Lab, Faculty of Geoinformation and Real Estate. The final output of this study is the 3D model of the assets available inside the building. Before 3D model can be formed, the scanned data which is in the form of point cloud generated from the laser scanner have to be registered and georeferenced in order to combine the scans. The combine scans is the representation of the whole area of work surveyed from every scan points. These processes use Faro Scene, software that comes together with the laser scanner. By introducing this method, large scale asset documentation such as for factories and schools would be very beneficial rather than conventional method. The next process is to model the point cloud using AutoCAD 2011. Every item available on the room such as desks, chairs, cubicles, computers, whiteboard, projectors and cupboard are modeled and each of these items was inserted with attributes so that we can know the information of each item

Seasonal and annual heat budgets offshore the Hanko Peninsula, Gulf of Finland

Peer reviewe

Continuous mHealth Patch Monitoring for the Algorithm-Based Detection of Atrial Fibrillation: Feasibility and Diagnostic Accuracy Study

Peer reviewe