Exploring the diversity of promoter and 5’UTR sequences in ancestral, historic and modern wheat

A dataset of promoter and 5’UTR sequences of homoeo-alleles of 495 wheat genes that contribute to agriculturally important traits in 95 ancestral and commercial wheat cultivars is presented here. The high stringency myBaits technology used made individual capture of homoeo-allele promoters possible, which is reported here for the first time. Promoters of most genes are remarkably conserved across the 82 hexaploid cultivars used with <7 haplotypes per promoter and 21% being identical to the reference Chinese Spring. InDels and many high-confidence SNPs are located within predicted plant transcription factor binding sites, potentially changing gene expression. Most haplotypes found in the Watkins landraces and a few haplotypes found in T. monococcum, germplasms hitherto not thought to have been used in modern wheat breeding, are already found in many commercial hexaploid wheats. The full dataset which is useful for genomic and gene function studies and wheat breeding is available at https://rrescloud.rothamsted.ac.uk/index.php/s/3vc9QopcqYEbIUs/authenticate

Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions

BACKGROUND: Identifying pathogen virulence genes required to cause disease is crucial to understand the mechanisms underlying the pathogenic process. Plasmid insertion mutagenesis of fungal protoplasts is frequently used for this purpose in filamentous ascomycetes. Post transformation, the mutant population is screened for loss of virulence to a specific plant or animal host. Identifying the insertion event has previously met with varying degrees of success, from a cleanly disrupted gene with minimal deletion of nucleotides at the insertion point to multiple-copy insertion events and large deletions of chromosomal regions. Currently, extensive mutant collections exist in laboratories globally where it was hitherto impossible to identify all the affected genes. RESULTS: We used a whole-genome sequencing (WGS) approach using Illumina HiSeq 2000 technology to investigate DNA tag insertion points and chromosomal deletion events in mutagenised, reduced virulence F. graminearum isolates identified in disease tests on wheat (Triticum aestivum). We developed the FindInsertSeq workflow to localise the DNA tag insertions to the nucleotide level. The workflow was tested using four mutants showing evidence of single and multi-copy insertions in DNA blot analysis. FindInsertSeq was able to identify both single and multi-copy concatenation insertion sites. By comparing sequencing coverage, unexpected molecular recombination events such as large tagged and untagged chromosomal deletions, and DNA amplification were observed in three of the analysed mutants. A random data sampling approach revealed the minimum genome coverage required to survey the F. graminearum genome for alterations. CONCLUSIONS: This study demonstrates that whole-genome re-sequencing to 22x fold genome coverage is an efficient tool to characterise single and multi-copy insertion mutants in the filamentous ascomycete Fusarium graminearum. In some cases insertion events are accompanied with large untagged chromosomal deletions while in other cases a straight-forward insertion event could be confirmed. The FindInsertSeq analysis workflow presented in this study enables researchers to efficiently characterise insertion and deletion mutants. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1412-9) contains supplementary material, which is available to authorized users

A CRISPR-Cas9 sex-ratio distortion system for genetic control.

Genetic control aims to reduce the ability of insect pest populations to cause harm via the release of modified insects. One strategy is to bias the reproductive sex ratio towards males so that a population decreases in size or is eliminated altogether due to a lack of females. We have shown previously that sex ratio distortion can be generated synthetically in the main human malaria vector Anopheles gambiae, by selectively destroying the X-chromosome during spermatogenesis, through the activity of a naturally-occurring endonuclease that targets a repetitive rDNA sequence highly-conserved in a wide range of organisms. Here we describe a CRISPR-Cas9 sex distortion system that targets ribosomal sequences restricted to the member species of the Anopheles gambiae complex. Expression of Cas9 during spermatogenesis resulted in RNA-guided shredding of the X-chromosome during male meiosis and produced extreme male bias among progeny in the absence of any significant reduction in fertility. The flexibility of CRISPR-Cas9 combined with the availability of genomic data for a range of insects renders this strategy broadly applicable for the species-specific control of any pest or vector species with an XY sex-determination system by targeting sequences exclusive to the female sex chromosome

Apparatus for dimensional characterization of fused silica fibers for the suspensions of advanced gravitational wave detectors

Detection of gravitational waves from astrophysical sources remains one of the most challenging problems faced by experimental physicists. A significant limit to the sensitivity of future long-baseline interferometric gravitational wave detectors is thermal displacement noise of the test mass mirrors and their suspensions. Suspension thermal noise results from mechanical dissipation in the fused silica suspension fibers suspending the test mass mirrors and is therefore an important noise source at operating frequencies between ∼10 and 30 Hz. This dissipation occurs due to a combination of thermoelastic damping, surface and bulk losses. Its effects can be reduced by optimizing the thermoelastic and surface loss, and these parameters are a function of the cross sectional dimensions of the fiber along its length. This paper presents a new apparatus capable of high resolution measurements of the cross sectional dimensions of suspension fibers of both rectangular and circular cross section, suitable for use in advanced detector mirror suspensions

FRI0592-HPR Work rehabilitation in inflammatory arthritis: A pilot randomised controlled trial

Background Work problems are common in people with inflammatory arthritis (IA): with 28-40% of people with rheumatoid arthritis (RA) stopping work in 5y of diagnosis. There is little research into effectiveness of job retention vocational rehabilitation (JRVR)for employed people with IA. Brief JR-VR led to significantly fewer job losses at 3.5 years in the USA (Allaire et al, 2003) and a UK pilot trial demonstrated 6m improvements in work instability and work satisfaction (Macedo et al, 2009). Objectives: To conduct a pilot randomised controlled trial (RCT) evaluating a JR-VR intervention with employed people with IA,to facilitate planning a full RCT. Methods: Participants with IA were recruited from 6 Rheumatology departments and randomised to VR (delivered by Rheumatology OTs with VR training) or a control group. Both groups received written self-help information about managing work problems. The VR group could receive up to 6h JR-VR, including a work visit. Presenteeism outcomes included: RA-Work Instability Scale (RAWIS:0-23), Work Limitations Questionnaire Productivity Loss (WLQPL: %), Work Activities Limitations Scale (WALS:0-33). Absenteeism was measured using monthly work diaries. Health outcomes included: SF12v2 Physical component(SF12-PC), pain, fatigue and perceived health status VAS (0-100). Mean (SD) change scores and effect sizes were calculated. Results: 213 eligible employed patients with IA were identified, of whom 55 (26%) participated (34 with RA): 13M, 42F; aged 49y (SD 8.8); 7.9y (SD 8.9) disease duration; 33 worked full-time; job types were professional (27%), associated professional/skilled (15%), partly skilled/admin/caring/retain (53%), unskilled (5%). Both groups were comparable at baseline (see Table). At 9m: effect sizes were moderate to large for changes in work and health outcomes in the JR-VR group and none to small in the control group; %working days lost due to sickness: JR-VR =9.6% (SD 13.6); control = 20% (SD 27.1). JR-VR lasted on average 3.08 (SD 1.8)hours and cost £74.98 (SD £46.80) per patient. Conclusions: This pilot suggests brief JR-VR provided by Rheumatology OTs can improve presenteeism, absenteeism and health status, indicating a RCT is warranted. Recruitment was problematic, with many not consenting. Potential reasons include: fear about employers (in a recession) learning they have arthritis; concerns about time out of work attending VR; and not perceiving VR is needed as yet. JR-VR intends to prevent work problems. Support is needed to enable employed people with IA and work problems to attend JR-VR

Simple Impurity Embedded in a Spherical Jellium: Approximations of Density Functional Theory compared to Quantum Monte Carlo Benchmarks

We study the electronic structure of a spherical jellium in the presence of a central Gaussian impurity. We test how well the resulting inhomogeneity effects beyond spherical jellium are reproduced by several approximations of density functional theory (DFT). Four rungs of Perdew's ladder of DFT functionals, namely local density approximation (LDA), generalized gradient approximation (GGA), meta-GGA and orbital-dependent hybrid functionals are compared against our quantum Monte Carlo (QMC) benchmarks. We identify several distinct transitions in the ground state of the system as the electronic occupation changes between delocalized and localized states. We examine the parameter space of realistic densities ($1 \le r_s\le 5$) and moderate depths of the Gaussian impurity ($Z<7$). The selected 18 electron system (with closed-shell ground state) presents $1d \to 2s$ transitions while the 30 electron system (with open-shell ground state) exhibits $1f \to 2p$ transitions. For the former system, the accuracy for the transitions is clearly improving with increasing sophistication of functionals with meta-GGA and hybrid functionals having only small deviations from QMC. However, for the latter system, we find much larger differences for the underlying transitions between our pool of DFT functionals and QMC. We attribute this failure to treatment of the exact exchange within these functionals. Additionally, we amplify the inhomogeneity effects by creating the system with spherical shell which leads to even larger errors in DFT approximations.Comment: 8 pages, 4 figures, submitted to PRB as a regular article revisited version after revie

Silicon mirror suspensions for gravitational wave detectors

One of the most significant limits to the sensitivity of current, and future, long-baseline interferometric gravitational wave detectors is thermal displacement noise of the test masses and their suspensions. This paper reports results of analytical and experimental studies of the limits to thermal noise performance of cryogenic silicon test mass suspensions set by two constraints on suspension fibre dimensions: the minimum dimensions required to allow conductive cooling for extracting incident laser beam heat deposited in the mirrors; and the minimum dimensions of fibres (set by their tensile strength) which can support test masses of the size envisaged for use in future detectors. We report experimental studies of breaking strength of silicon ribbons, and resulting design implications for the feasibility of suspension designs for future gravitational wave detectors using silicon suspension fibres. We analyse the implication of this study for thermal noise performance of cryogenically cooled silicon suspensions

Few-body resonances of unequal-mass systems with infinite interspecies two-body s-wave scattering length

Two-component Fermi and Bose gases with infinitely large interspecies s-wave scattering length $a_s$ exhibit a variety of intriguing properties. Among these are the scale invariance of two-component Fermi gases with equal masses, and the favorable scaling of Efimov features for two-component Bose gases and Bose-Fermi mixtures with unequal masses. This paper builds on our earlier work [D. Blume and K. M. Daily, arXiv:1006.5002] and presents a detailed discussion of our studies of small unequal-mass two-component systems with infinite $a_s$ in the regime where three-body Efimov physics is absent. We report on non-universal few-body resonances. Just like with two-body systems on resonance, few-body systems have a zero-energy bound state in free space and a diverging generalized scattering length. Our calculations are performed within a non-perturbative microscopic framework and investigate the energetics and structural properties of small unequal-mass two-component systems as functions of the mass ratio $\kappa$, and the numbers $N_{1}$ and $N_2$ of heavy and light atoms. For purely attractive Gaussian two-body interactions, we find that the $(N_1,N_2)=(2,1)$ and $(3,1)$ systems exhibit three-body and four-body resonances at mass ratios $\kappa = 12.314(2)$ and 10.4(2), respectively. The three- and four-particle systems on resonance are found to be large. This suggests that the corresponding wave function has relatively small overlap with deeply-bound dimers, trimers or larger clusters and that the three- and four-body systems on resonance have a comparatively long lifetime. Thus, it seems feasible that the features discussed in this paper can be probed experimentally with present-day technology.Comment: 17 pages, 17 figure