Frequency correlation requirements on the biphoton wavefunction in an induced coherence experiment between separate sources

There is renewed interest in using the coherence between beams generated in separate down-converter sources for new applications in imaging, spectroscopy, microscopy and optical coherence tomography (OCT). These schemes make use of continuous wave (CW) pumping in the low parametric gain regime, which produces frequency correlations, and frequency entanglement, between signal-idler pairs generated in each single source. But can induced coherence still be observed if there is no frequency correlation, so the biphoton wavefunction is factorable? We will show that this is the case, and this might be an advantage for OCT applications. High axial resolution requires a large bandwidth. For CW pumping this requires the use of short nonlinear crystals. This is detrimental since short crystals generate small photon fluxes. We show that the use of ultrashort pump pulses allows improving axial resolution even for long crystal that produce higher photon fluxes

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.Authors wish to thank the Two Blades Foundation for financial support. Part of this work was supported through access to facilities managed by Bioplatforms Australia and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative

Genomics accelerated isolation of a new stem rust avirulence gene - wheat resistance gene pair

Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled by genetic resistance in the latter half of the 20th century, new strains of Pgt with increased virulence, such as Ug99, have evolved by somatic hybridisation and mutation. These newly emerged strains have caused significant losses in Africa and other regions and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases. A number of race-specific rust resistance genes have been characterised in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class. These receptors recognize pathogen effector proteins often known as avirulence (Avr) proteins. However, only two Avr genes have been identified in Pgt to date, AvrSr35 and AvrSr50 and none in other cereal rusts, which hinders efforts to understand the evolution of virulence in rust populations. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale) which is a wheat-rye hybrid and is a host for Pgt. Sr27 is effective against Ug99 and other recently emerged Pgt strains. Here we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus

Nucleation of the electroactive γ phase and enhancement of the optical transparency in low filler content poly(vinylidene)/clay nanocomposites

Poly(vinylidene fluoride), PVDF, based nanocomposites with different clays structures have been processed by solvent casting and melt crystallisation. Depending on the melting temperature of the polymer, the nanocomposite recrystalises in the electroactive or non electroactive β-phase of the polymer. This fact is related to the thermal behaviour of the clay. For montmorillonite clay, the full crystallisation of the electroactiveγ-phase occurs for clay contents lower than 0.5 wt%, allowing the nanocomposites to maintain the mechanical properties of the polymer matrix. The electroactivity of the material has been proven by measuring the piezoelectric d33 response of the material. The obtained value of d33 is -7 pC/N, lower than in β-PVDF obtained by mechanical stretching, but still among the largest coefficients obtained for polymers. Further, the optical transmittance in the visible range is strongly enhanced with respect to the transmittance of the pure polymer. Finally, it is demonstrated that the nucleation of the β-phase can be also obtained in other clays, such as in kaolinite and laponite.Fundação para a Ciência e a Tecnologia (FCT) - NANO/NMed-SD/0156/2007, PTDC/CTM/69316/2006, PTDC/CTM-NAN/112574/2009, SFRH/BD/62507/2009.FEDER funds through the "Programa Operacional Factores de Competitividade – COMPETECOST Action MP1003, the ‘European Scientific Network for Artificial Muscles’ (ESNAM)

Linkage map construction involving a reciprocal translocation

This paper is concerned with a novel statistical–genetic approach for the construction of linkage maps in populations obtained from reciprocal translocation heterozygotes of barley (Hordeum vulgare L.). Using standard linkage analysis, translocations usually lead to ‘pseudo-linkage’: the mixing up of markers from the chromosomes involved in the translocation into a single linkage group. Close to the translocation breakpoints recombination is severely suppressed and, as a consequence, ordering markers in those regions is not feasible. The novel strategy presented in this paper is based on (1) disentangling the “pseudo-linkage” using principal coordinate analysis, (2) separating individuals into translocated types and normal types and (3) separating markers into those close to and those more distant from the translocation breakpoints. The methods make use of a consensus map of the species involved. The final product consists of integrated linkage maps of the distal parts of the chromosomes involved in the translocation

Introgression of Aegilops speltoides segments in Triticum aestivum and the effect of the gametocidal genes

• Background and Aims Bread wheat (Triticum aestivum) has been through a severe genetic bottleneck as a result of its evolution and domestication. It is therefore essential that new sources of genetic variation are generated and utilized. This study aimed to generate genome-wide introgressed segments from Aegilops speltoides. Introgressions generated from this research will be made available for phenotypic analysis. • Methods Aegilops speltoides was crossed as the male parent to T. aestivum ‘Paragon’. The interspecific hybrids were then backcrossed to Paragon. Introgressions were detected and characterized using the Affymetrix Axiom Array and genomic in situ hybridization (GISH). • Key Results Recombination in the gametes of the F₁ hybrids was at a level where it was possible to generate a genetic linkage map of Ae. speltoides. This was used to identify 294 wheat/Ae. speltoides introgressions. Introgressions from all seven linkage groups of Ae. speltoides were found, including both large and small segments. Comparative analysis showed that overall macro-synteny is conserved between Ae. speltoides and T. aestivum, but that Ae. speltoides does not contain the 4A/5A/7B translocations present in wheat. Aegilops speltoides has been reported to carry gametocidal genes, i.e. genes that ensure their transmission through the gametes to the next generation. Transmission rates of the seven Ae. speltoides linkage groups introgressed into wheat varied. A 100 % transmission rate of linkage group 2 demonstrates the presence of the gametocidal genes on this chromosome. • Conclusions A high level of recombination occurs between the chromosomes of wheat and Ae. speltoides, leading to the generation of large numbers of introgressions with the potential for exploitation in breeding programmes. Due to the gametocidal genes, all germplasm developed will always contain a segment from Ae. speltoides linkage group 2S, in addition to an introgression from any other linkage group

Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis

Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goat grass species Aegilops sharonesis (Sharon goatgrass) as a substantial reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F6 recombinant inbred line and an F2 population, two genes were identified that mapped to the short arm of chromosome 1Ssh, designated as Sr-1644-1Sh, and the long arm of chromosome 5Ssh, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (one of the Ug99 lineage races), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors

Using virulence mutants to identify Avr genes in the wheat stem rust fungus, Puccinia graminis f. sp. tritici

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. Resistance of host lines is often governed by recognition of fungal effector proteins (avirulence/virulence proteins) by plant resistance proteins (R proteins). We have taken a mutational genomics approach to identify Avr genes in Pgt. We isolated spontaneous mutants with virulence for Sr50, Sr5, Sr27, Sr21 or Sr45 by selection on resistant host lines. Sequence analysis of the Sr50 virulent mutant revealed that virulence resulted from the exchange of a whole chromosome between the two haploid nuclei of this dikaryotic organism, resulting in loss of the avirulence allele. This confirms the important role of somatic exchange events in virulence evolution in Pgt. The AvrSr50 gene was identified from the 25 candidate effector genes from this chromosome by transient co-expression with the cloned Sr50 gene in N. benthamiana. AvrSr50 recognition was confirmed in wheat by viral expression. Recognition of the AvrSr50 protein by the host Sr50 immune receptor is based on direct interaction and we have identified critical amino acid polymorphisms contributing to the escape from recognition in virulent isolates. Identification of AvrSr50 has enabled development of tools for testing effector function in wheat including viral overexpression and wheat protoplast transient expression assays. Spontaneous mutants for several other Avr loci have also been sequenced and a new Pacbio-based genome assembly for the Australian parental Pgt isolate has facilitated the delineation of these loci. Three mutants with virulence for Sr27 contain overlapping deletions and a single candidate gene for AvrSr27 has been identified. Likewise, AvrSr5 mutants contain large deletions spanning several candidate effector genes