Impact of Low-Energy Ion Beam Implantation on the Expression of Ty1-copia-like Retrotransposons in Wheat(Triticum aestivum)

Retrotransposon-like elements are major constituents of most eukaryotic genomes. For example, they account for roughly 90% of the wheat （Triticum aestivum） genome, Previous study on a wheat strain treated by low-energy N^＋ ions indicated the variations in AFLP （Amplified Fragment Length Polymorphism ） markers, One such variation was caused by the re-activation of Tyl-copia-like retrotransposons, implying that the mutagenic effects of lowenergy ions might work through elevated activation of retrotransposons, In this paper an expression profile of Tyl-copia-like retrotransposons in wheat treated by low-energy N^＋ ions is reported, The reverse transcriptase （RT） domains of these retrotransposons were amplified by reverse-transcriptional polymerase chain reaction （RT-PCR） and sequentially cloned, 42 and 65 clones were obtained from the treated （CL） and control materials （CK）, respectively, Sequence analysis of each clone was performed by software. Phylogeny and classification were calculated responding to the sequences of the RT domains. All the results show that there is much difference in the RT domain between the control sample and the treated sample, Especially, the RT domains from the treated group encode significantly more functional ORF （open reading frames） than those from the control sample, This observation suggests that the treated sample has higher activation of retrotransposons, possibly as a consequence of low-energy ion beam irradiation, It also suggests that retrotransposons in the two groups impact the host gene expression in two different ways and carry out different functions in wheat cells.

Damage of low-energy ion irradiation on copper nanowire:molecular dynamics simulation

Physical and chemical phenomena of low-energy ion irradiation on solid surfaces have been studied systematically for many years, due to the wide applications in surface modification, ion implantation and thin-film growth. Recently the bombardment of nano-scale materials with low-energy ions gained much attention. Comared to bulk materials, nano-scale materials show different physical and chemical properties. In this article, we employed molecular dynamics simulations to study the damage caused by low-energy ion irradiation on copper nanowires. By simulating the ion bombardment of 5 different incident energies, namely, 1 keV, 2 keV, 3 keV, 4 keV and 5 keV, we found that the sputtering yield of the incident ion is linearly proportional to the energies of incident ions. Low-energy impacts mainly induce surface damage to the nanowires, and only a few bulk defects were observed. Surface vacancies and adatoms accumulated to form defect clusters on the surface, and their distribution are related to the type of crystal plane, e.g. surface vacancies prefer to stay on （100） plane, while adatoms prefer （110） plane. These results reveal that the size effect will influence the interaction between low-energy ion and nanowire.

Improvement of L(+)-Lactic Acid Production of Rhizopus Oryzae by Low-Energy Ions and Analysis of Its Mechanism

The wild type strain Rhizopus oryzae PW352 was mutated by means of nitrogen ion implantation （15 keV, 7.8×10^14 ～ 2.08 ×10^15 ions/cm^2） to find an industrial strain with a higher L（＋）-lactic acid yield, and two mutants RE3303 and RF9052 were isolated. In order to discuss the mechanism primarily, Lactate Dehydrogenase of Rhizopus oryzae was studied. While the two mutants produced L（＋）-lactic acid by 75% more than the wild strain did, their specific activity of Lactate Dehydrogenase was found to be higher than that in the wild strain. The optimum temperature of Lactate Dehydrogenase in Rhizopus oryzae RF9052 was higher. Compared to the wild strain, the Michaelis constant （Km） value of Lactate Dehydrogenase in the mutants was Changed. All these changes show that L（＋）-lactic acid production has a correlation with the specific activity of Lactate Dehydrogenase. The low-energy ions, implanted into the strain, may improve the specific activity of Lactate Dehydrogenase by influencing its gene structure and protein structure.

Modeling of Inner Surface Modification of a Cylindrical Tube by Plasma-Based Low-Energy Ion Implantation

The inner surface modification process by plasma-based low-energy ion implantation（PBLEII）with an electron cyclotron resonance（ECR）microwave plasma source located at the central axis of a cylindrical tube is modeled to optimize the low-energy ion implantation parameters for industrial applications.In this paper,a magnetized plasma diffusion fluid model has been established to describe the plasma nonuniformity caused by plasma diffusion under an axial magnetic field during the pulse-off time of low pulsed negative bias.Using this plasma density distribution as the initial condition,a sheath collisional fluid model is built up to describe the sheath evolution and ion implantation during the pulse-on time.The plasma nonuniformity at the end of the pulse-off time is more apparent along the radial direction compared with that in the axial direction due to the geometry of the linear plasma source in the center and the difference between perpendicular and parallel plasma diffusion coefficients with respect to the magnetic field.The normalized nitrogen plasma densities on the inner and outer surfaces of the tube are observed to be about 0.39 and 0.24,respectively,of which the value is 1 at the central plasma source.After a 5μs pulse-on time,in the area less than 2 cm from the end of the tube,the nitrogen ion implantation energy decreases from 1.5 keV to 1.3 keV and the ion implantation angle increases from several degrees to more than 40°;both variations reduce the nitrogen ion implantation depth.However,the nitrogen ion implantation dose peaks of about 2×10^（10）-7×10^（10）ions/cm^2 in this area are 2-4 times higher than that of 1.18×10^（10）ions/cm^2 and 1.63×10^（10）ions/cm^2 on the inner and outer surfaces of the tube.The sufficient ion implantation dose ensures an acceptable modification effect near the end of the tube under the low energy and large angle conditions for nitrogen ion implantation,because the modification effect is mainly determined by the ion implantation dose,just as the mass transfer process in PBLEII is dominated by low-energy ion implantation and thermal diffusion.Therefore,a comparatively uniform surface modification by the low-energy nitrogen ion implantation is achieved along the cylindrical tube on both the inner and outer surfaces.

Studies on Mutation Breeding of High-Yielding Xylanase Strains by Low-Energy Ion Beam Implantation

As a new mutagenetic method, low-energy ion implantation has been used widely in many research areas in recent years. In order to obtain some industrial strains with high xylanase yield, the wild type strain Aspergillus niger A3 was mutated by means of nitrogen ions implantation （10 keV, 2.6× 10^14 ～ 1.56 × 10^15 ions/cm^2） and a mutant N212 was isolated subsequently. However, it was found that the initial screening means of the high-yielding xylanase strains such as transparent halos was unfit for first screening. Compared with that of the wild type strain, xylanase production of the mutant N212 was increased from 320 IU/ml to 610 IU/ml, and the optimum fermentation temperature was increased from 28 ℃ to 30 ℃.

Optimization of L(+)-Lactic Acid Production from Xylose with Rhizopus Oryzae Mutant RLC41-6 Breeding by Low-Energy Ion Implantation

In order to obtain an industrial strain with a higher L（＋）-lactic acid yield, the strain Rhizopus oryzae PW352 was mutated by means of nitrogen ion beam implantation and the mutant strain Rhizopus oryzae RLC41-6 was obtained. An experimental finding was made in surprise that Rhizopus oryzae mutant RLC41-6 is not only an L（＋）-lactic acid producer from corn starch but also an efficient producer of L（＋）-lactic acid from xylose. Under optimal conditions, the production of L（＋）-lactic acid from 100 g/L xylose reached 77.39 g/L after 144 h fed-batch fermentation, A high mutation rate and a wide mutation spectrum of low-energy ion implantation were observed in the experiment.

Breeding of Coenzyme Q_(10) Produced Strain by Low-Energy Ion Implantation and Optimization of Coenzyme Q_(10) Fermentation

In order to increase the production efficiency of coenzyme Q10, the original strain Agrobacterium tumefaciens ATCC 4452 was mutated by means of Nitrogen ions implantation. A mutant strain, ATX 12, with high contents of coenzyme Q10 was selected. Subsequently, the conditions such as carbohydrate concentration, nitrogen source concentration, inoculum＇s size, seed age, aeration and temperature which might affect the production of CoQ10 were investigated in detail. Under optimal conditions, the maximum concentration of the intracellular CoQ10 reached 200.3 mg/L after 80 h fed-batch fermentation, about 245% increasing in CoQ10 production after ion implantation, compared to the original strain.

Surface Etching and DNA Damage Induced by Low-Energy Ion Irradiation in Yeast

Bio-effects of survival and etching damage on cell surface and DNA strand breaks were investigated in the yeast saccharomyces cerevisiae after exposure by nitrogen ion with an energy below 40 keV. The result showed that 16% of trehalose provided definite protection for cells against vacuum stress compared with glycerol. In contrast to vacuum control, significant morpho- logical damage and DNA strand breaks were observed, in yeast cells bombarded with low-energy nitrogen, by scanning electron microscopy （SEM） and terminal deoxynucleotidyl transferase- mediated dUTP nick end labeling （TUNEL） immunofluorescence assays. Moreover, PI （propidium iodide） fluorescent staining indicated that cell integrity could be destroyed by ion irradiation. Cell damage eventually affected cell viability and free radicals were involved in cell damage as shown by DMSO （dimethyl sulfoxide） rescue experiment. Our primary experiments demonstrated that yeast cells can be used as an optional experimental model to study the biological effects of low energy ions and be applied to further investigate the mechanism（s） underlying the bio-effects of eukaryotic cells.

A Preliminary Study of the Application of a Model Animal-Caenorhabidity elegans'Exposure to a Low-Energy Ion Irradiation System

Because of the lack of suitable animal models adapted to high vacuum stress in the low-energy ion implantation system, the bio-effects ion irradiation with an energy less than 50 keV on multi-cellular animal individuals have never been investigated so far. The nematode Caenorhabditis elegans has proved to be an excellent animal model used for the study of a broad spectrum of biological issues. The purpose of this work was to investigate the viability of this animal under ion irradiation. We studied the protection effects of glycerol and trehalose on the enhancement of nematodes＇ ability to bear the vacuum stress. The results showed that the survival of the nematodes was enhanced remarkably under long and slow desiccation, even without glycerol and trehalose. 159 glycerol showed a better anti-vacuum stress effect on the nematodes than trehalose did under short-time desiccation. Low-temperature pre-treatment or post-treatment of the samples had no obvious effect on the survival scored after argon ion irradiation. Moreover, little effect was induced by 15% glycerol- and vacuum-exposure on germ cell apoptosis, compared to the untreated control sample. It issuggested that such treatment would provide relatively low background for genotoxic evaluations with ion irradiation.

Simulations of guiding of low-energy ions through a single nanocapillary in insulating materials

Simulations of guiding of low-energy ions through a single nanocapillary in insulating polymers are reported. The nanocapillary has a diameter of 100 nm and a length of 10 μm. Different from previous work, in our simulations a hyperbolic function is used to describe the decay of the charges deposited on the capillary surface. The present simulations reproduce the self-organized charge-up process occurring in the capillary. It is shown that lower-energy ions undergo more oscillations to get guiding equilibrium than those of higher-energy ions, resulting in a longer charging time, which is in good agreement with previous experimental results. Moreover, the experimentally observed mass independence of ion guiding is proved in our simulations. In particular, it is found that the maximum of the repulsive field within the capillary is independent of the ion energy as well as the tilt angle. To counterbalance the increasing of the transversal energy caused by increasing the tilt angle or incident energy, the effective length of the repulsive field is expanded in a self-organizing manner.

Morphological and Anatomical Assessment of KDML 105 (Oryza sativa L.spp.indica) and Its Mutants Induced by Low-Energy Ion Beam

Thai jasmine rice KDML 105 is consumed around the world. BKOS, PKOS and TKOS are new cultivars produced from low-energy ion beam induction in KDML 105. The purpose of this study is to compare the morphology and anatomy between KDML 105 and the three new cultivars. Seeds of the four cultivars were germinated and grown in pots until flowering phase. The plants＇ organs were observed and the lengths of culms, ligules, leaves and panicles were measured. Leaf surface area was calculated and numbers of roots, spikelets and tillers were counted. BKOS and PKOS had significantly shorter culms than KDML 105 and TKOS. The largest leaf area was found in KDML 105 followed by TKOS, BKOS and PKOS, respectively. Numbers of roots and tillers in BKOS and TKOS were significantly fewer than those in KDML 105 and PKOS. The number of spikelets per plant in BKOS was the lowest among all cultivars. For anatomical comparison, cross sections of culms and roots were observed. All plants had a similar arrangement of tissues, but the number and size of cells were different. Furthermore, longitudinal sections of culms showed that the lengths of epidermal and parenchyma cells were directly related with the length of the culm. To compare the leaves, both stomata and epidermal cells were counted and the lengths of the guard cells were measured. The lengths of guard cells of BKOS and PKOS were shorter, but the stomatal density and the stomatal index were significantly greater than those of KDML 105. For TKOS, though the length of guard cells was shorter than that in KDML 105, the difference was not significant. However, the stomatal density and stomatal index were significantly higher than those in KDML 105.

Research on the Distant Hybrids of Wheat Obtained via Low-Energy Ion-Beam Implantation

The whole DNA of soybean was implanted into four varieties of wheat of Zhongyu 5, Huaiyin 9628, Wenyou 1, Jimai 5 respectively via ion-beam mediation. There were 5 plants obtained whose protein content was higher than 18.5 %, the highest one was 21.44 %. There were 3 plants obtained whose protein content was lower than 11.5%, the lowest one was 10.96%. We can see that the whole DNA of soybean transformed into wheat via ion beam implantation can induce the increase in wheat protein content dramatically. The result also shows that the transformation efficiency of different gene types of wheat receptor varies greatly that the implanting time has a certain effect on the efficiency of transformation.

Optimization of L(+)-Lactic Acid Fermentation Without Neutralisation of Rhizopus Oryzae Mutant RK02 by Low-Energy Ion Implantation

In order to get an industrial strain which can yield a high concentration of lactic acid for ISPR （in situ product removal）, the original strain Rhizopus oryzae RE3303 was mutated by low-energy ion beam implantation. A mutant RK02 was screened, and the factors such as the substrate concentration, nitrogen source concentration, inoculum size, seed age, aeration and temperature that affect the production of lactic acid were studied in detail. Under optimal con- ditions, the maximum concentration of L（＋）-lactic acid reached 34.85 g/L after 30 h shake-flask cultivation without adding any neutralisation （5% Glucose added）, which was a 146% increase in lactic acid production after ion implantation compared with the original strain. It was also shown that RK02 can be used in ISPR to reduce the number of times of separation.

Mutagenic Effects of BM302:GO112 Induced by Low-Energy Ion Beam Implantation

Mutant strains of GO112 and BM302 with a high 2-keto-L-gulonic acid （2KLG） transformation rate induced by ion beam implantation were separately and combinatorially compared with the original strains GO29 and BM80 to study the mutagenic effects of ion beam implantation. Both the sole GOl12 and mixed BM302：GOl12 demonstrated improved SNDH activity and 2KLG yield compared to the original strains. The mutant combinations of BM302：GOl12 showed a longer stationary phase and higher biomass than BM80：GO29. The mutant BM302 exhibited a stronger capacity to maintain a stable pH environment at mixed fermentation with Gluconobacter oxydans （G. oxydans） for 2KLG transformation and facilitated the growth of G. oxydans compared with the original strain BM80. The promotive capacity to L-sorbosone dehydrogenase （L-SNDH） from the supernate of BM302 was 1.6-fold higher than that of BM80. Genes encoded SNDH in GO29 and GOl12 were amplified and sequenced, and mutations including three transitions （CG →TA, CG →TA, GC → AT） and one transversion （AT→ TA） were confirmed from GO29 to GOl12. The corresponding amino acid was changed as Leu →Phe, Arg → Gln and Asn → Lys.

Apoptosis and necrosis of HeLa cells in response to low-energy ion radiation

The aim of this study was to investigate the damage of low-energy ions to HeLa cells and to particularly examine the relationship between apoptotic and necrotic effects and the low-energy ion radiation. In this study, HeLa cells were irradiated by low-energy ions (30keV N+) at different doses. The level of apoptosis and necrosis was evalu- ated using flow cytometry. Since vacuum is required for experimental low-energy ion generation and irradiation, the cells must be placed in vacuum. Mineral oil was used to prevent dehydration of cells. The results show that the apoptotic rate reached 7.09% when the ion implantation dose was 1 × 1015 ions/cm2; and when the cells were exposed to and implanted at 2 × 1015 ions/cm2 dose, the apoptotic rate was higher than that at 1 × 1015 ions/cm2, and the necrotic rate was 15.63%. In addition, the survival fraction gradually decreased with the increase in implantation dose. Some rela- tionships have been found between the radiation-induced apoptosis and the incubated time after irradiation.

Low-energy ion channeling in nanocubes

Focused ion beam(FIB)processing with low-energy ions has become a standard technique for the manipulation of nanostructures.Many underlying ion beam effects that deviate from conventional high-energy ion irradiation of bulk systems are considered today;however,ion channeling with its consequence of significant deeper penetration depth has been only theoretically investigated in this regime.We present here an experimental approach to determine the channeling of low-energy ions in crystalline nanoparticles by measuring the sputter yield derived from scanning electron microscopy(SEM)images taken after irradiation under various incident ion angles.Channeling maps of 30 and 20 keV Ga+ions in Ag nanocubes have been identified and fit well with the theory.Indeed,channeling has a significant impact on the transport of energetic ions in crystals due to the large critical angle at low ion energies,thus being relevant for any FIB-application.Consequently,the obtained sputter yield clearly differs from amorphous materials;therefore,it is recommended not to rely only on,e.g.,ion distribution depths predicted by standard Monte-Carlo(MC)algorithms for amorphous materials.

A refined Monte Carlo code for low-energy electron emission from gold material irradiated with sub-keV electrons

Considering the significance of low-energy electrons(LEEs;0–20 eV) in radiobiology, the sensitization potential of gold nanoparticles(AuNPs) as high-flux LEE emitters when irradiated with sub-keV electrons has been suggested. In this study, a track-structure Monte Carlo simulation code using the dielectric theory was developed to simulate the transport of electrons below 50 keV in gold. In this code, modifications, particularly for elastic scattering, are implemented for a more precise description of the LEE emission in secondary electron emission. This code was validated using the secondary electron yield and backscattering coefficient. To ensure dosimetry accuracy, we further verified the code for energy deposition calculations using the Monte Carlo toolkit, Geant4. The development of this code provides a basis for future studies regarding the role of AuNPs in targeted radionuclide radiotherapy.

Influence of extraction voltage on electron and ion behavior characteristics

The characteristics of the extracted ion current have a significant impact on the design and testing of ion source performance.In this paper,a 2D in space and 3D in velocity space particle in cell(2D3V PIC)method is utilized to simulate plasma motion and ion extraction characteristics under various initial plasma velocity distributions and extraction voltages in a Cartesian coordinate system.The plasma density is of the order of 10^(15)m^(-3)-10^(16)m^(-3)and the extraction voltage is of the order of 100 V-1000 V.The study investigates the impact of various extraction voltages on the velocity and density distributions of electrons and positive ions,and analyzes the influence of different initial plasma velocity distributions on the extraction current.The simulation results reveal that the main reason for the variation of extraction current is the spacecharge force formed by the relative aggregation of positive and negative net charges.This lays the foundation for a deeper understanding of extraction beam characteristics.

Bio-cementation for tidal erosion resistance improvement of foreshore slopes based on microbially induced magnesium and calcium precipitation

In most coastal and estuarine areas,tides easily cause surface erosion and even slope failure,resulting in severe land losses,deterioration of coastal infrastructure,and increased floods.The bio-cementation technique has been previously demonstrated to effectively improve the erosion resistance of slopes.Seawater contains magnesium ions(Mg^(2+))with a higher concentration than calcium ions(Ca^(2+));therefore,Mg^(2+)and Ca^(2+)were used together for bio-cementation in this study at various Mg^(2+)/Ca^(2+)ratios as the microbially induced magnesium and calcium precipitation(MIMCP)treatment.Slope angles,surface strengths,precipitation contents,major phases,and microscopic characteristics of precipitation were used to evaluate the treatment effects.Results showed that the MIMCP treatment markedly enhanced the erosion resistance of slopes.Decreased Mg^(2+)/Ca^(2+)ratios resulted in a smaller change in angles and fewer soil losses,especially the Mg^(2+)concentration below 0.2 M.The decreased Mg^(2+)/Ca^(2+)ratio achieved increased precipitation contents,which contributed to better erosion resistance and higher surface strengths.Additionally,the production of aragonite would benefit from elevated Mg^(2+)concentrations and a higher Ca^(2+)concentration led to more nesquehonite in magnesium precipitation crystals.The slopes with an initial angle of 53°had worse erosion resistance than the slopes with an initial angle of 35°,but the Mg^(2+)/Ca^(2+)ratios of 0.2:0.8,0.1:0.9,and 0:1.0 were effective for both slope stabilization and erosion mitigation to a great extent.The results are of great significance for the application of MIMCP to improve erosion resistance of foreshore slopes and the MIMCP technique has promising application potential in marine engineering.

Experimental results of a magnetic field modification to the radio frequency driver of a negative ion source

A magnetic field produced by a current flowing through the plasma grid(PG) is one of the solutions to reduce the collisional loss of negative ions in a negative ion source, which reduces the electron temperature in front of the PG. However, the magnetic field diffused into the driver has some influence on the plasma outflowing. In order to investigate the effect of changing this magnetic field on the outflowing of plasma from the driver, a circular ring(absorber) of high permeability iron has been introduced at the driver exit, which can reduce the magnetic field around it and improve plasma outflowing. With the application of the absorber, the electron density is increased by about 35%, and the extraction current measured from the extraction grid is increased from 1.02 A to 1.29 A. The results of the extraction experiment with cesium injection show that both the extraction grid(EG) current and H-current are increased when the absorber is introduced.