An evaluation of genotyping by sequencing (GBS) to map the <em>Breviaristatum-e (ari-e)</em> locus in cultivated barley

ABSTRACT: We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed cultivar ‘Morex’ (Ari-e/vrs1) to map plant height. We identified three Quantitative Trait Loci (QTL), the first in a region encompassing the spike architecture gene Vrs1 on chromosome 2H, the second in an uncharacterised centromeric region on chromosome 3H, and the third in a region of chromosome 5H coinciding with the previously described dwarfing gene Breviaristatum-e (Ari-e). BACKGROUND: Barley cultivars in North-western Europe largely contain either of two dwarfing genes; Denso on chromosome 3H, a presumed ortholog of the rice green revolution gene OsSd1, or Breviaristatum-e (ari-e) on chromosome 5H. A recessive mutant allele of the latter gene, ari-e.GP, was introduced into cultivation via the cv. ‘Golden Promise’ that was a favourite of the Scottish malt whisky industry for many years and is still used in agriculture today. RESULTS: Using GBS mapping data and phenotypic measurements we show that ari-e.GP maps to a small genetic interval on chromosome 5H and that alternative alleles at a region encompassing Vrs1 on 2H along with a region on chromosome 3H also influence plant height. The location of Ari-e is supported by analysis of near-isogenic lines containing different ari-e alleles. We explored use of the GBS to populate the region with sequence contigs from the recently released physically and genetically integrated barley genome sequence assembly as a step towards Ari-e gene identification. CONCLUSIONS: GBS was an effective and relatively low-cost approach to rapidly construct a genetic map of the GPMx population that was suitable for genetic analysis of row type and height traits, allowing us to precisely position ari-e.GP on chromosome 5H. Mapping resolution was lower than we anticipated. We found the GBS data more complex to analyse than other data types but it did directly provide linked SNP markers for subsequent higher resolution genetic analysis

Abelian Hidden Sectors at a GeV

We discuss mechanisms for naturally generating GeV-scale hidden sectors in the context of weak-scale supersymmetry. Such low mass scales can arise when hidden sectors are more weakly coupled to supersymmetry breaking than the visible sector, as happens when supersymmetry breaking is communicated to the visible sector by gauge interactions under which the hidden sector is uncharged, or if the hidden sector is sequestered from gravity-mediated supersymmetry breaking. We study these mechanisms in detail in the context of gauge and gaugino mediation, and present specific models of Abelian GeV-scale hidden sectors. In particular, we discuss kinetic mixing of a U(1)_x gauge force with hypercharge, singlets or bi-fundamentals which couple to both sectors, and additional loop effects. Finally, we investigate the possible relevance of such sectors for dark matter phenomenology, as well as for low- and high-energy collider searches.Comment: 43 pages, no figures; v2: to match JHEP versio

Community Occupational Therapy in Dementia intervention for people with mild to moderate dementia and their family carers in the UK: the VALID research programme including RCT

BACKGROUND: People with dementia find it increasingly difficult to carry out daily activities (activities of daily living), and may require increasing support from family carers. Researchers in the Netherlands developed the Community Occupational Therapy in Dementia intervention, which was delivered in 10 1-hour sessions over 5 weeks to people with dementia and their family carers at home. Community Occupational Therapy in Dementia was found to be clinically effective and cost-effective. OBJECTIVES: Translate and adapt Community Occupational Therapy in Dementia to develop the Community Occupational Therapy in Dementia - the UK version intervention and training programme and to optimise its suitability for use within the UK. To estimate the clinical effectiveness and cost-effectiveness of Community Occupational Therapy in Dementia - the UK version for people with mild to moderate dementia and their family carers compared with treatment as usual. DESIGN: The development phase used mixed methods to develop Community Occupational Therapy in Dementia - the UK version: translation, expert review, and adaptation of the manual and training materials; training occupational therapists; focus groups and interviews, including occupational therapists, managers, people with dementia and family carers; consensus conference; and an online survey of occupational therapists to scope UK practice. A multicentre, two-arm, parallel-group, single-blind individually randomised pragmatic trial was preceded by an internal pilot. Pairs were randomly allocated between Community Occupational Therapy in Dementia - the UK version and treatment as usual. A cost–utility analysis, fidelity study and qualitative study were also completed. SETTING: Community services for people with dementia across England. PARTICIPANTS: People with mild to moderate dementia recruited in pairs with a family carer/supporter. INTERVENTIONS: Community Occupational Therapy in Dementia - the UK version is an activity-based, goal-setting approach for people with dementia and family carers, and is delivered at home by an occupational therapist for 10 hours over 10 weeks. Treatment as usual comprised the usual local service provision, which may or may not include standard occupational therapy. MAIN OUTCOMES MEASURES: Data were collected through interviews conducted in person with dyads at baseline and at 12 and 26 weeks post randomisation, and then over the telephone with a reduced sample of just carers at 52 and 78 weeks post randomisation. The primary outcome was the Bristol Activities of Daily Living Scale at 26 weeks. The secondary outcomes were as follows: person with dementia – cognition, activities of daily living, quality of life and mood; carer – sense of competence, quality of life and mood; all participants – social contacts, leisure activities and serious adverse events. RESULTS: The Community Occupational Therapy in Dementia manual and training materials were translated and reviewed. In total, 44 occupational therapists were trained and delivered Community Occupational Therapy in Dementia to 130 pairs. A total of 197 occupational therapists completed the survey, of whom 138 also provided qualitative data. In total, 31 people attended the consensus conference. Community Occupational Therapy in Dementia - the UK version has more flexibility than Community Occupational Therapy in Dementia in terms of content and delivery; for example, occupational therapists can use the wider range of assessment tools that are already in regular use within UK practice and the time span for delivery is 10 weeks to better meet the needs of pairs and be more feasible for services to deliver. In total, 31 occupational therapists provided Community Occupational Therapy in Dementia - the UK version within the randomised controlled trial. A total of 468 pairs were randomised (249 pairs to Community Occupational Therapy in Dementia - the UK version, 219 pairs to treatment as usual). People with dementia ranged in age from 55 to 97 years (mean 78.6 years), and family carers ranged in age from 29 to 94 years (mean 69.1 years). The majority of those with dementia (74.8%) were married; 19.2% lived alone. Most family carers (72.6%) were spouses but 22.2% were adult children. At 26 weeks, 406 (87%) pairs remained in the trial, and the Bristol Activities of Daily Living Scale total score did not differ at the 5% level when comparing groups (adjusted mean difference estimate 0.35, 95% confidence interval –0.81 to 1.51; p = 0.55). The adjusted (for baseline Bristol Activities of Daily Living Scale total score and randomised group) intracluster correlation coefficient estimate at week 26 was 0.043. There were no significant differences in secondary outcomes. At 52 and 78 weeks, there were no differences between the two groups in Bristol Activities of Daily Living Scale total score and secondary outcomes. The probability that Community Occupational Therapy in Dementia - the UK version is cost-effective at a threshold of willingness to pay per quality-adjusted life-year of £20,000 is 0.02%. In the qualitative interviews, participants reported positive benefits and outcomes. Of the 249 pairs allocated to Community Occupational Therapy in Dementia - the UK version, 227 reached the goal-setting phase, and 838 of the 920 goals set (90.8%) were fully or partially achieved. LIMITATIONS: The development phase took longer than estimated because of translation time and organisational delays in delivering the intervention. Recruitment to the randomised controlled trial took longer than expected. Fidelity overall was moderate, with variation across sites and therapists. It is possible that Community Occupational Therapy in Dementia - the UK version did not work well in the UK service model in which usual care differs from that in the Netherlands. CONCLUSIONS: This programme used a rigorous process to develop Community Occupational Therapy in Dementia - the UK version but found no statistical evidence of clinical effectiveness or cost-effectiveness compared with usual care. Qualitative findings provided positive examples of how Community Occupational Therapy in Dementia - the UK version had enabled people to live well with dementia. FUTURE WORK: Developing tools to measure more meaningful outcomes, such as goals achieved or the quantity and quality of activity participation, with less reliance on proxy data, to collect the views and experiences of people with dementia themselves. TRIAL REGISTRATION: This trial was registered as ISRCTN10748953 (WP3 and WP4). FUNDING: This project was funded by the National Institute for Health and Care Research (NIHR) Programme Grants for Applied Research programme and will be published in full in Programme Grants for Applied Research; Vol. 11, No. 5. See the NIHR Journals Library website for further project information

Candidates for Inelastic Dark Matter

Although we have yet to determine whether the DAMA data represents a true discovery of new physics, among such interpretations inelastic dark matter (IDM) can match the energy spectrum of DAMA very well while not contradicting the results of other direct detection searches. In this paper we investigate the general properties that a viable IDM candidate must have and search for simple models that realize these properties in natural ways. We begin by determining the regions of IDM parameter space that are allowed by direct detection searches including DAMA, paying special attention to larger IDM masses. We observe that an inelastic dark matter candidate with electroweak interactions can naturally satisfy observational constraints while simultaneously yielding the correct thermal relic abundance. We comment on several other proposed dark matter explanations for the DAMA signal and demonstrate that one of the proposed alternatives -- elastic scattering of dark matter off electrons -- is strongly disfavored when the modulated and unmodulated DAMA spectral data are taken into account. We then outline the general essential features of IDM models in which inelastic scattering off nuclei is mediated by the exchange of a massive gauge boson, and construct natural models in the context of a warped extra dimension and supersymmetry.Comment: 44 pages, 6 figures, added reference

The USDA Barley Core Collection:Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections

Post-depositional fracturing and subsidence of pumice flow deposits: Lascar Volcano, Chile

Unconsolidated pyroclastic flow deposits of the 1993 eruption of Lascar Volcano, Chile, have, with time, become increasingly dissected by a network of deeply penetrating fractures. The fracture network comprises orthogonal sets of decimeter-wide linear voids that form a pseudo-polygonal grid visible on the deposit surface. In this work, we combine shallow surface geophysical imaging tools with remote sensing observations and direct field measurements of the deposit to investigate these fractures and their underlying causal mechanisms. Based on ground penetrating radar images, the fractures are observed to have propagated to depths of up to 10 m. In addition, orbiting radar interferometry shows that deposit subsidence of up to 1 cm/year occurred between 1993 and 1996 with continued subsidence occurring at a slower rate thereafter. In situ measurements show that 1 m below the surface, the 1993 deposits remain 5°C to 15°C hotter, 18 years after emplacement, than adjacent deposits. Based on the observed subsidence as well as estimated cooling rates, the fractures are inferred to be the combined result of deaeration, thermal contraction, and sedimentary compaction in the months to years following deposition. Significant environmental factors, including regional earthquakes in 1995 and 2007, accelerated settling at punctuated moments in time. The spatially variable fracture pattern relates to surface slope and lithofacies variations as well as substrate lithology. Similar fractures have been reported in other ignimbrites but are generally exposed only in cross section and are often attributed to formation by external forces. Here we suggest that such interpretations should be invoked with caution, and deformation including post-emplacement subsidence and fracturing of loosely packed ash-rich deposits in the months to years postemplacement is a process inherent in the settling of pyroclastic material

Growth of a human mammary tumor cell line is blocked by galangin, a naturally occurring bioflavonoid, and is accompanied by down-regulation of cyclins D3, E, and A

INTRODUCTION: This study was designed to determine if and how a non-toxic, naturally occurring bioflavonoid, galangin, affects proliferation of human mammary tumor cells. Our previous studies demonstrated that, in other cell types, galangin is a potent inhibitor of the aryl hydrocarbon receptor (AhR), an environmental carcinogen-responsive transcription factor implicated in mammary tumor initiation and growth control. Because some current breast cancer therapeutics are ineffective in estrogen receptor (ER) negative tumors and since the AhR may be involved in breast cancer proliferation, the effects of galangin on the proliferation of an ER(-), AhR(high )line, Hs578T, were studied. METHODS: AhR expression and function in the presence or absence of galangin, a second AhR inhibitor, α-naphthoflavone (α-NF), an AhR agonist, indole-3-carbinol, and a transfected AhR repressor-encoding plasmid (FhAhRR) were studied in Hs578T cells by western blotting for nuclear (for instance, constitutively activated) AhR and by transfection of an AhR-driven reporter construct, pGudLuc. The effects of these agents on cell proliferation were studied by (3)H-thymidine incorporation and by flow cytometry. The effects on cyclins implicated in mammary tumorigenesis were evaluated by western blotting. RESULTS: Hs578T cells were shown to express high levels of constitutively active AhR. Constitutive and environmental chemical-induced AhR activity was profoundly suppressed by galangin as was cell proliferation. However, the failure of α-NF or FhAhRR transfection to block proliferation indicated that galangin-mediated AhR inhibition was either insufficient or unrelated to its ability to significantly block cell proliferation at therapeutically relevant doses (IC(50 )= 11 μM). Galangin inhibited transition of cells from the G(0)/G(1 )to the S phases of cell growth, likely through the nearly total elimination of cyclin D3. Expression of cyclins A and E was also suppressed. CONCLUSION: Galangin is a strong inhibitor of Hs578T cell proliferation that likely mediates this effect through a relatively unique mechanism, suppression of cyclin D3, and not through the AhR. The results suggest that this non-toxic bioflavonoid may be useful as a chemotherapeutic, particularly in combination with agents that target other components of the tumor cell cycle and in situations where estrogen receptor-specific therapeutics are ineffective

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq) is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP) detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%). However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis

Stochastic Modeling of B Lymphocyte Terminal Differentiation and Its Suppression by Dioxin

<p>Abstract</p> <p>Background</p> <p>Upon antigen encounter, naïve B lymphocytes differentiate into antibody-secreting plasma cells. This humoral immune response is suppressed by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other dioxin-like compounds, which belong to the family of aryl hydrocarbon receptor (AhR) agonists.</p> <p>Results</p> <p>To achieve a better understanding of the immunotoxicity of AhR agonists and their associated health risks, we have used computer simulations to study the behavior of the gene regulatory network underlying B cell terminal differentiation. The core of this network consists of two coupled double-negative feedback loops involving transcriptional repressors Bcl-6, Blimp-1, and Pax5. Bifurcation analysis indicates that the feedback network can constitute a bistable system with two mutually exclusive transcriptional profiles corresponding to naïve B cells and plasma cells. Although individual B cells switch to the plasma cell state in an all-or-none fashion when stimulated by the polyclonal activator lipopolysaccharide (LPS), stochastic fluctuations in gene expression make the switching event probabilistic, leading to heterogeneous differentiation response among individual B cells. Moreover, stochastic gene expression renders the dose-response behavior of a population of B cells substantially graded, a result that is consistent with experimental observations. The steepness of the dose response curve for the number of plasma cells formed vs. LPS dose, as evaluated by the apparent Hill coefficient, is found to be inversely correlated to the noise level in Blimp-1 gene expression. Simulations illustrate how, through AhR-mediated repression of the AP-1 protein, TCDD reduces the probability of LPS-stimulated B cell differentiation. Interestingly, stochastic simulations predict that TCDD may destabilize the plasma cell state, possibly leading to a reversal to the B cell phenotype.</p> <p>Conclusion</p> <p>Our results suggest that stochasticity in gene expression, which renders a graded response at the cell population level, may have been exploited by the immune system to launch humoral immune response of a magnitude appropriately tuned to the antigen dose. In addition to suppressing the initiation of the humoral immune response, dioxin-like compounds may also disrupt the maintenance of the acquired immunity.</p

A chromosome conformation capture ordered sequence of the barley genome

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