Gamma-rays induced genome wide stable mutations in cowpea deciphered through whole genome sequencing

PURPOSE

Gamma rays are the most widely exploited physical mutagen in plant mutation breeding. They are known to be involved in the development of more than 60% of global cowpea (Vigna unguiculata (L.) Walp.) mutant varieties. Nevertheless, the nature and type of genome-wide mutations induced by gamma rays have not been studied in cowpea and therefore, the present investigation was undertaken.

MATERIALS AND METHODS

Genomic DNAs from three stable gamma rays-induced mutants (large seed size, small seed size and disease resistant mutant) of cowpea cultivar 'CPD103' in M6 generation along with its progenitor were used for Illumina-based whole-genome resequencing.

RESULTS

Gamma rays induced a relatively higher frequency (88.9%) of single base substitutions (SBSs) with an average transition to transversion ratio (Ti/Tv) of 3.51 in M6 generation. A > G transitions, including its complementary T > C transitions, predominated the transition mutations, while all four types of transversion mutations were detected with frequencies over 6.5%. Indels (small insertions and deletions) constituted about 11% of the total induced variations, wherein small insertions (6.3%) were relatively more prominent than small deletions (4.8%). Among the indels, single-base indels and, in particular, those involving A/T bases showed a preponderance, albeit indels of up to three bases were detected in low proportions. Distributed across all 11 chromosomes, only a fraction of SBSs (19.45%) and indels (20.2%) potentially altered the encoded amino acids/peptides. The inherent mutation rate induced by gamma rays in cowpea was observed to be in the order of 1.4 × 10-7 per base pair in M6 generation.

CONCLUSION

Gamma-rays with a greater tendency to induce SBSs and, to a lesser extent, indels could be efficiently and effectively exploited in cowpea mutation breeding.

Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience

The development of adaptation strategies for crops under ever-changing climate conditions is a critically important food security issue. Studies of barley responses to ionising radiation showed that this evolutionarily ancient stress factor can be successfully used to identify molecular pathways involved in adaptation to a range of abiotic stressors. In order to identify potential molecular contributors to abiotic stress resilience, we examined the transcriptomic profiles of barley seedlings after exposure to γ-rays, electrons, and protons. A total of 553 unique differentially expressed genes with increased expression and 124 with decreased expression were detected. Among all types of radiation, the highest number of differentially expressed genes was observed in electron-irradiated samples (428 upregulated and 56 downregulated genes). Significant upregulation after exposure to the three types of radiation was shown by a set of ROS-responsive genes, genes involved in DNA repair, cell wall metabolism, auxin biosynthesis and signalling, as well as photosynthesis-related genes. Most of these genes are known to be involved in plant ROS-mediated responses to other abiotic stressors, especially with genotoxic components, such as heavy metals and drought. Ultimately, the modulation of molecular pathways of plant responses to ionising radiation may be a prospective tool for stress tolerance programmes.

Mechanical, Morphological, Thermal and the Attenuation Properties of Heavy Mortars Doped with Nanoparticles for Gamma-Ray Shielding Applications

This study aimed to develop a mortar composite with improved gamma ray shielding properties using WO₃ and Bi₂O₃ nanoparticles, as well as granite residue as a partial replacement of sand. The physical properties and effects of sand substitution and nanoparticle addition on the mortar composite were analyzed. TEM analysis confirmed the size of Bi₂O₃ and WO₃ NPs to be 40 ± 5 nm and 35 ± 2 nm, respectively. SEM images showed that increasing the percentage of granite residues and nanoparticles improved the homogeneity of the mixture and decreased the percentage of voids. TGA analysis indicated that the thermal properties of the material improved with the increase in nanoparticles, without decreasing the material weight at higher temperatures. The linear attenuation coefficients were reported and we found that the LAC value at 0.06 MeV increases by a factor of 2.47 when adding Bi₂O₃, while it is enhanced by a factor of 1.12 at 0.662 MeV. From the LAC data, the incorporation of Bi₂O₃ nanoparticles can greatly affect the LAC at low energies, and still have a small but noticeable effect at higher energies. The addition of Bi₂O₃ nanoparticles into the mortars led to a decrease in the half value layer, resulting in excellent shielding properties against gamma rays. The mean free path of the mortars was found to increase with increasing photon energy, but the addition of Bi₂O₃ led to a decrease in MFP and better attenuation, making the CGN-20 mortar the most ideal in terms of shielding ability among the prepared mortars. Our findings on the improved gamma ray shielding properties of the developed mortar composite have promising implications for radiation shielding applications and granite waste recycling.

Shielding Properties of Epoxy Matrix Composites Reinforced with MgO Micro- and Nanoparticles

The aim of the current study is to investigate the impact of introducing micro- and nanoparticle MgO as a filler into epoxy resin on the radiation shielding abilities of the prepared samples. To this end, we performed a gamma-radiation spectroscopy experiment with the help of an HPGe detector and Am-241, Cs-137, and Co-60 sources. We evaluated the particle size effect (PSE) and detected the maximum PSE value with the addition of 50 wt% MgO particles, indicating that nanoparticle MgO was more successful in shielding against incoming radiation than microparticle MgO. We compared the half-value layer (HVL) for the samples with 10 wt%, 20 wt%, and 30 wt % micro-MgO and nano-MgO and found that the HVL values were lower for the nanoparticle samples than for the microparticles samples, confirming that smaller particle sizes enhanced the shielding ability of the samples against radiation. The MFP results showed that epoxy matrices containing micro-MgO, for all investigated energies, resulted in higher MFP values that those containing nano-MgO.

Wilczek] and its validation using linked molecular markers

PURPOSE

Mungbean yellow mosaic India virus (MYMIV) is a serious constraint in the mungbean which is a potential source of easily digestible high-quality proteins, fibers, minerals, and vitamins in Asian countries. Developing resistant cultivars is the most cost-effective, eco-friendly, and sustainable approach to protect mungbean from MYMIV damage. Mutation breeding provides a quick and cost-effective way of developing resistance as lack of genetic variability is the biggest bottleneck for other traditional breeding tools.

MATERIALS AND METHODS

Outstanding but MYMIV-sensitive varieties of mungbean, viz., MH 2-15 and MH 318 were mutagenized through various individual and combined doses of gamma-rays and Ethyl methanesulfonate (EMS) and evaluated in M₂ and M₃ generations for the appearance of resistance reactions. This was subsequently validated through marker-assisted genotyping using previously reported Yellow Mosaic Disease (YMD) linked markers.

RESULTS

The phenotyping in M₃ generation yielded 64 MYMIV resistant mutants whereas, marker-assisted genotyping identified the 22 mutants with true resistance. Markers YR4, CYR1, and CEDG180 were found associated with MYMIV resistance whereas, DMB-SSR158 did not show any amplification. Among identified resistant mutants, ten lines exhibited at par and two revealed a little higher seed yield over controls.

CONCLUSIONS

The mutagenesis created significant variability in MYMIV resistance as well as seed yield per plant. YR4, CYR1, and CEDG180 are found to be linked with the MYMIV loci in the mungbean and could be utilized for MYMIV resistance breeding. Mutant M-37 from MH 2-15 and M-104 from MH 318 exhibited more seed yield along with MYMIV resistance which upon further validation can be released as a variety. The induced mutagenesis integrated with powerful emerging molecular and next-generation sequencing (NGS) tools would be highly helpful in breeding mungbean for durable resistance against threatening MYMIV.

Genotype-by-Sequencing Analysis of Mutations and Recombination in Pepper Progeny of Gamma-Irradiated Gametophytes

The irradiation of dry seeds is the most widely-used irradiation method for improving seed-propagated crops; however, the irradiation of other tissues also has useful effects. The irradiation of plant reproductive organs, rather than seeds, for mutation breeding has advantages, such as producing non-chimeric progeny. However, the mutation frequency and spectrum produced using this method have not been analyzed on a genome-wide level. We performed a genotype-by-sequencing analysis to determine the frequencies of single-base substitutions and small (1–2 bp) insertions and deletions in hot pepper (Capsicum annuum L.) plants derived from crosses using gamma-irradiated female or male gametophytes. The progeny of irradiated gametophytes showed similar or higher DNA mutation frequencies, which were dependent on the irradiation dose and irradiated tissue, and less biased single base substitutions than progeny of irradiated seeds. These characteristics were expected to be beneficial for development of mutation population with a high frequency of small DNA mutations and performing reverse-genetics-based mutation screening. We also examined the possible use of this irradiation method in manipulating the meiotic recombination frequency; however, no statistically significant increase was detected. Our results provide useful information for further research and breeding using irradiated gametophytes.

Mutagenic Effect of Proton Beams Characterized by Phenotypic Analysis and Whole Genome Sequencing in Arabidopsis

Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M₂ lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects.

Radiation Response of Negative Gate Biased SiC MOSFETs

Silicon carbide (SiC) metal-oxide-semiconductor field effect transistors (MOSFETs) are expected as power electronic devices for high radiative conditions, including nuclear plants and space. Radiation response of commercial-grade prototype SiC MOSFETs with applying the gate bias is of interest, in terms of installation of the device in robots or sensors working under such radioactive circumstances. Due to gamma-rays irradiation, the threshold voltages (V_th) of samples with un- and negative-biased up to -4.5 V slightly shift toward the negative voltage side. In contrast, the positive bias of 2.25 V shifts V_th more negatively. Positive charge densities trapped in the gate oxide of un- and positive-biased samples increased with increasing dose. However, no significant increase was observed for negative-biased samples of -2.25 and -4.5 V. We calculated characteristic parameters for the accumulation of holes in the gate oxide, σ_pJ_p which is defined as the product of current density due to holes generated by irradiation and capture cross section for a hole in a trap, and it is lower for these negative biased samples compared with the unbiased case. Application of appropriate negative gate biases to SiC MOSFETs during irradiation suppresses accumulation of positive charges in the gate oxide and negative shift of V_th, due to irradiation.

Betatron radiation and emittance growth in plasma wakefield accelerators

Beam-driven plasma wakefield acceleration (PWFA) has demonstrated significant progress during the past two decades of research. The new Facility for Advanced Accelerator Experimental Tests (FACET) II, currently under construction, will provide 10 GeV electron beams with unprecedented parameters for the next generation of PWFA experiments. In the context of the FACET II facility, we present simulation results on expected betatron radiation and its potential application to diagnose emittance preservation and hosing instability in the upcoming PWFA experiments. This article is part of the Theo Murphy meeting issue 'Directions in particle beam-driven plasma wakefield acceleration'.

Lactoferrin-Immobilized Surfaces onto Functionalized PLA Assisted by the Gamma-Rays and Nitrogen Plasma to Create Materials with Multifunctional Properties

Both cold nitrogen radiofrequency plasma and gamma irradiation have been applied to activate and functionalize the polylactic acid (PLA) surface and the subsequent lactoferrin immobilization. Modified films were comparatively characterized with respect to the procedure of activation and also with unmodified sample by water contact angle measurements, mass loss, X-ray photoelectron spectroscopy (XPS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), atomic force microscopy (AFM), and chemiluminescence measurements. All modified samples exhibit enhanced surface properties mainly those concerning biocompatibility, antimicrobial, and antioxidant properties, and furthermore, they are biodegradable and environmentally friendly. Lactoferrin deposited layer by covalent coupling using carbodiimide chemistry showed a good stability. It was found that the lactoferrin-modified PLA materials present significantly increased oxidative stability. Gamma-irradiated samples and lactoferrin-functionalized samples show higher antioxidant, antimicrobial, and cell proliferation activity than plasma-activated and lactoferrin-functionalized ones. The multifunctional materials thus obtained could find application as biomaterials or as bioactive packaging films.

Protective role of miR-155 in breast cancer through RAD51 targeting impairs homologous recombination after irradiation. Proc Natl Acad Sci U S A. 2014;111:4536-4541. [PMID: 24616504 DOI: 10.1073/pnas.1402604111]

Cell survival after DNA damage relies on DNA repair, the abrogation of which causes genomic instability and development of cancer. However, defective DNA repair in cancer cells can be exploited for cancer therapy using DNA-damaging agents. DNA double-strand breaks are the major lethal lesions induced by ionizing radiation (IR) and can be efficiently repaired by DNA homologous recombination, a system that requires numerous factors including the recombinase RAD51 (RAD51). Therapies combined with adjuvant radiotherapy have been demonstrated to improve the survival of triple-negative breast cancer patients; however, such therapy is challenged by the emergence of resistance in tumor cells. It is, therefore, essential to develop novel therapeutic strategies to overcome radioresistance and improve radiosensitivity. In this study we show that overexpression of microRNA 155 (miR-155) in human breast cancer cells reduces the levels of RAD51 and affects the cellular response to IR. miR-155 directly targets the 3'-untranslated region of RAD51. Overexpression of miR-155 decreased the efficiency of homologous recombination repair and enhanced sensitivity to IR in vitro and in vivo. High miR-155 levels were associated with lower RAD51 expression and with better overall survival of patients in a large series of triple-negative breast cancers. Taken together, our findings indicate that miR-155 regulates DNA repair activity and sensitivity to IR by repressing RAD51 in breast cancer. Testing for expression levels of miR-155 may be useful in the identification of breast cancer patients who will benefit from an IR-based therapeutic approach.

Relative biological effects of neutron mixed-beam irradiation for boron neutron capture therapy on cell survival and DNA double-strand breaks in cultured mammalian cells

Understanding the biological effects of neutron mixed-beam irradiation used for boron neutron capture therapy (BNCT) is important in order to improve the efficacy of the therapy and to reduce side effects. In the present study, cell viability and DNA double-strand breaks (DNA-DSBs) were examined in Chinese hamster ovary cells (CHO-K1) and their radiosensitive mutant cells (xrs5, Ku80-deficient), following neutron mixed-beam irradiation for BNCT. Cell viability was significantly impaired in the neutron irradiation groups compared to the reference gamma-ray irradiation group. The relative biological effectiveness for 10% cell survival was 3.3 and 1.2 for CHO-K1 and xrs5 cells, respectively. There were a similar number of 53BP1 foci, indicators of DNA-DSBs, in the neutron mixed-beam and the gamma-ray groups. In addition, the size of the foci did not differ between groups. However, neutron mixed-beam irradiation resulted in foci with different spatial distributions. The foci were more proximal to each other in the neutron mixed-beam groups than the gamma-ray irradiation groups. These findings suggest that neutron beams may induce another type of DNA damage, such as clustered DNA-DSBs, as has been indicated for other high-LET irradiation.

Geological carbon sequestration: a new approach for near-surface assurance monitoring

There are two distinct objectives in monitoring geological carbon sequestration (GCS): Deep monitoring of the reservoir’s integrity and plume movement and near-surface monitoring (NSM) to ensure public health and the safety of the environment. However, the minimum detection limits of the current instrumentation for NSM is too high for detecting weak signals that are embedded in the background levels of the natural variations, and the data obtained represents point measurements in space and time. A new approach for NSM, based on gamma-ray spectroscopy induced by inelastic neutron scatterings (INS), offers novel and unique characteristics providing the following: (1) High sensitivity with a reducible error of measurement and detection limits, and, (2) temporal- and spatial-integration of carbon in soil that results from underground CO₂ seepage. Preliminary field results validated this approach showing carbon suppression of 14% in the first year and 7% in the second year. In addition the temporal behavior of the error propagation is presented and it is shown that for a signal at the level of the minimum detection level the error asymptotically approaches 47%.

Nuclear Orientation Thermometry

Low temperature nuclear orientation thermometry, in particular γ-ray anisotropy thermometry, is discussed both from a theoretical and practical point of view. Detailed information is given on the most often used γ-ray anisotropy thermometers, along with a comprehensive description of the γ-ray anisotropy technique. The ⁶⁰Co in (hcp) cobalt single crystal γ-ray anisotropy thermometer is discussed in considerable detail since it is used more frequently in comparison experiments with other primary thermometers. Recent experimental results using γ-ray anisotropy thermometers are also reviewed.