Effects of neutron irradiation on the brittle to ductile transition in single crystal tungsten

Only limited data exist on the effect of neutron irradiation on the brittle to ductile transition (BDT) in tungsten. This work investigates the increase in brittle to ductile transition temperature (BDTT) following neutron irradiation to 1.67 displacements per atom, using four-point bend tests over a range of temperatures (623–1173 K) and strain rates (3.5 × 10−7 - 2.5 × 10−5 s−1). The BDTT was found to increase by 500 K after irradiation. The activation energy for the BDT was determined using Arrhenius analysis of the four-point bend tests. Nanoindentation strain-rate jump tests were used to characterise the activation volume for dislocation motion. These were quantified as 1.05 eV and 18 b3 respectively, very close to values found for unirradiated tungsten. This suggests that kink-pair formation is the controlling mechanism for the BDT before and after irradiation. This work also carries out a unique verification of inventory-code-modelling (via FISPACT-II) of transmutation of tungsten to rhenium and osmium under neutron irradiation using two independent techniques (X-ray and gamma-ray spectroscopy). These results show that modelling can correctly predict this transmutation, provided that an accurate neutron spectrum is used. This is a critical result given the widespread use of inventory codes such as FISPACT-II, and the associated nuclear data libraries, for modelling transmutation of tungsten

Effects of neutron irradiation on the brittle to ductile transition in single crystal tungsten

Only limited data exist on the effect of neutron irradiation on the brittle to ductile transition (BDT) in tungsten. This work investigates the increase in brittle to ductile transition temperature (BDTT) following neutron irradiation to 1.67 displacements per atom, using four-point bend tests over a range of temperatures (623-1173 K) and strain rates (3.5 x 10$^{-7}$- 2.5 x 10$^{-5}$ s$^{-1}$). The BDTT was found to increase by 500 K after irradiation. The activation energy for the BDT was determined using Arrhenius analysis of the four-point bend tests. Nanoindentation strain-rate jump tests were used to characterise the activation volume for dislocation motion. These were quantified as 1.05 eV and 4.6 b³ respectively, very close to values found for unirradiated tungsten. This suggests that kink-pair formation is the controlling mechanism for the BDT before and after irradiation. This work also carries out a unique verification of inventory-code-modelling (via FISPACT-II) of transmutation of tungsten to rhenium and osmium under neutron irradiation using two independent techniques (X-ray and gamma-ray spectroscopy). These results show that modelling can correctly predict this transmutation, provided that an accurate neutron spectrum is used. This is a critical result given the widespread use of inventory codes such as FISPACT-II, and the associated nuclear data libraries, for modelling transmutation of tungsten

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

Background: Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. Results: The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. Conclusions: The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene

Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Citation: Chapman, J. A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., . . . Rokhsar, D. S. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16(1). doi:10.1186/s13059-015-0582-8Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. © 2015 Chapman et al. licensee BioMed Central.Additional Authors: Muehlbauer, G. J.;Stein, N.;Rokhsar, D. S