CYP19A1 fine-mapping and Mendelian randomization: Estradiol is causal for endometrial cancer

Candidate gene studies have reported CYP19A1 variants to be associated with endometrial cancer and with estradiol (E2) concentrations. We analyzed 2937 single nucleotide polymorphisms (SNPs) in 6608 endometrial cancer cases and 37 925 controls and report the first genome wide-significant association between endometrial cancer and a CYP19A1 SNP (rs727479 in intron 2, P=4.8x10(-11)). SNP rs727479 was also among those most strongly associated with circulating E2 concentrations in 2767 post-menopausal controls (P=7.4x10(-8)). The observed endometrial cancer odds ratio per rs727479 A-allele (1.15, CI=1.11-1.21) is compatible with that predicted by the observed effect on E2 concentrations (1.09, CI=1.03-1.21), consistent with the hypothesis that endometrial cancer risk is driven by E2. From 28 candidate-causal SNPs, 12 co-located with three putative gene-regulatory elements and their risk alleles associated with higher CYP19A1 expression in bioinformatical analyses. For both phenotypes, the associations with rs727479 were stronger among women with a higher BMI (Pinteraction=0.034 and 0.066 respectively), suggesting a biologically plausible gene-environment interaction.

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

Nested association mapping (NAM) offers power to dissect complex, quantitative traits. This study made use of a recently developed sorghum backcross (BC)-NAM population to dissect the genetic architecture of flowering time in sorghum; to compare the QTL identified with other genomic regions identified in previous sorghum and maize flowering time studies and to highlight the implications of our findings for plant breeding. A subset of the sorghum BC-NAM population consisting of over 1,300 individuals from 24 families was evaluated for flowering time across multiple environments. Two QTL analysis methodologies were used to identify 40 QTLs with predominately small, additive effects on flowering time; 24 of these co-located with previously identified QTL for flowering time in sorghum and 16 were novel in sorghum. Significant synteny was also detected with the QTL for flowering time detected in a comparable NAM resource recently developed for maize (Zea mays) by Buckler et al. (Science 325:714-718, 2009). The use of the sorghum BC-NAM population allowed us to catalogue allelic variants at a maximal number of QTL and understand their contribution to the flowering time phenotype and distribution across diverse germplasm. The successful demonstration of the power of the sorghum BC-NAM population is exemplified not only by correspondence of QTL previously identified in sorghum, but also by correspondence of QTL in different taxa, specifically maize in this case. The unification across taxa of the candidate genes influencing complex traits, such as flowering time can further facilitate the detailed dissection of the genetic control and causal genes.

Origin of leaf rust adult plant resistance gene Rph20 in barley

Rph20 is the only reported, simply inherited gene conferring moderate to high levels of adult plant resistance (APR) to leaf rust (Puccinia hordei Otth) in barley (Hordeum vulgare L.). Key parental genotypes were examined to determine the origin of Rph20 in two-rowed barley. The Dutch cultivar 'Vada' (released in the 1950s) and parents, 'Hordeum laevigatum' and 'Gull' ('Gold'), along with the related cultivar 'Emir' (a derivative of 'Delta'), were assessed for APR to P. hordei in a disease screening nursery. The marker bPb-0837-PCR, co-located with Rph20 on the short arm of chromosome 5H (5HS), was used to screen genotypes for the resistance allele, Rph20.ai. Results from phenotypic assessment and DNA analysis confirmed that Rph20 originated from the landrace 'H. laevigatum' (i.e., Hordeum vulgare subsp. vulgare). Tracing back this gene through the pedigrees of two-rowed barley cultivars, indicated that Rph20 has contributed APR to P. hordei for more than 60 years. Although there have been no reports of an Rph20-virulent pathotype, the search for alternative sources of APR should continue to avoid widespread reliance upon a single resistance factor.

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria , Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. © 2014 Penton et al.

QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Tillering in sorghum can be associated with either the carbon supply–demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.

Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Key message “To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.” Abstract Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

Identifying the Function of Sorghum's Drought Tolerance Stay-Green QTL

The goal of this research is to understand the function of allelic variation of genes underpinning the stay-green drought adaptation trait in sorghum in order to enhance yield in water-limited environments. Stay-green, a delayed leaf senescence phenotype in sorghum, is primarily an emergent consequence of the improved balance between the supply and demand of water. Positional and functional fine-mapping of candidate genes associated with stay-green in sorghum is the focus of an international research partnership between Australian (UQ/DAFFQ) and US (Texas A&M University) scientists. Stay-green was initially mapped to four chromosomal regions (Stg1, Stg2, Stg3, and Stg4) by a number of research groups in the US and Australia. Physiological dissection of near-isolines containing single introgressions of Stg QTL (Stg1-4) indicate that these QTL reduce water demand before flowering by constricting the size of the canopy, thereby increasing water availability during grain filling and, ultimately, grain yield. Stg and root angle QTL are also co-located and, together with crop water use data, suggest the role of roots in the stay-green phenomenon. Candidate genes have been identified in Stg1-4, including genes from the PIN family of auxin efflux carriers in Stg1 and Stg2, with 10 of 11 PIN genes in sorghum co-locating with Stg QTL. Modified gene expression in some of these PIN candidates in the stay-green compared with the senescent types has been found in preliminary RNA expression profiling studies. Further proof-of-function studies are underway, including comparative genomics, SNP analysis to assess diversity at candidate genes, reverse genetics and transformation.

Conceptualising social media support for tacit knowledge sharing: physicians’ perspectives and experiences

Purpose – This paper aims to explore the potential contributions of social media in supporting tacit knowledge sharing, according to the physicians’ perspectives and experiences. Design/methodology/approach – Adopting a qualitative survey design, 24 physicians were interviewed. Purposive and snowball sampling were used to select the participants. Thematic analysis approach was used for data analysis. Findings – The study revealed five major themes and over 20 sub-themes as potential contributions of social media to tacit knowledge flow among physicians. The themes included socialising, practising, networking, storytelling and encountering. In addition, with the help of the literature and the supporting data, the study proposed a conceptual model that explains the potential contribution of social media to tacit knowledge sharing. Research limitations/implications – The study had both theoretical (the difficulty of distinguishing tacit and explicit knowledge in practice) and practical limitations (small sample size). The study findings have implications for the healthcare industry whose clinical teams are not always physically co-located but must exchange their critical experiential and tacit knowledge. Originality/value – The study has opened up a new discussion of this area by demonstrating and conceptualising how social media tools may facilitate tacit knowledge sharing.

Cost Sharing Mechanisms for Business Clusters with Strategic Firms

A business cluster is a co-located group of micro, small, medium scale enterprises. Such firms can benefit significantly from their co-location through shared infrastructure and shared services. Cost sharing becomes an important issue in such sharing arrangements especially when the firms exhibit strategic behavior. There are many cost sharing methods and mechanisms proposed in the literature based on game theoretic foundations. These mechanisms satisfy a variety of efficiency and fairness properties such as allocative efficiency, budget balance, individual rationality, consumer sovereignty, strategyproofness, and group strategyproofness. In this paper, we motivate the problem of cost sharing in a business cluster with strategic firms and illustrate different cost sharing mechanisms through the example of a cluster of firms sharing a logistics service. Next we look into the problem of a business cluster sharing ICT (information and communication technologies) infrastructure and explore the use of cost sharing mechanisms.

High-rate, Single-Symbol Decodable Distributed STBCs for Partially-Coherent Cooperative Networks

Space-time block codes (STBCs) that are single-symbol decodable (SSD) in a co-located multiple antenna setting need not be SSD in a distributed cooperative communication setting. A relay network with N relays and a single source-destination pair is called a partially-coherent relay channel (PCRC) if the destination has perfect channel state information (CSI) of an the channels and the relays have only the phase information of the source-to-relay channels. In our earlier work, we had derived a set of necessary and sufficient conditions for a distributed STBC (DSTBC) to be SSD for a PCRC. Using these conditions, in this paper we show that the possibility of channel phase compensation operation at the relay nodes using partial CSI at the relays increases the possible rate of SSD DSTBCs from 2/N when the relays do not have CSI to 1/2, which is independent of N. We also show that when a DSTBC is SSD for a PCRC, then arbitrary coordinate interleaving of the in-phase and quadrature-phase components of the variables does not disturb its SSD property. Using this property we are able to construct codes that are SSD and have higher rate than 2/N but giving full diversity only for signal constellations satisfying certain conditions.

Insights from stimulating creative behaviours in a project-based organization team

Novel and useful ideas and creative behaviours originate in varied work environments, yet the characteristics of work environments that stimulate and foster such creative behaviours are not well defined. The aim of this study was to identify the influences that contribute to creative behaviours in the work environment of a global project-based professional service organization. This article is based on an investigation of the work environment of one project team undertaking interdisciplinary work in the construction of a processing plant in a remote location. This multi-disciplinary team encouraged creative behaviours through regular team meetings, ensuring the presentation of diverse views and commitments to regular interaction and collaboration in co-located environments. In addition, a technology manager dedicated to identifying potential opportunities for patenting and commercialization further extended the creative behaviours of the team by focusing on the best solution for each situation. The study contributes new knowledge to research regarding work environments that facilitate creative behaviours.

Series-connected substrate-integrated lead-carbon hybrid ultracapacitors with voltage-management circuit

Cell voltage for a fully charged-substrate-integrated lead-carbon hybrid ultracapacitor is about 2.3 V. Therefore, for applications requiring higher DC voltage, several of these ultracapacitors need to be connected in series. However, voltage distribution across each series-connected ultracapacitor tends to be uneven due to tolerance in capacitance and parasitic parallel-resistance values. Accordingly, voltage-management circuit is required to protect constituent ultracapacitors from exceeding their rated voltage. In this study, the design and characterization of the substrate-integrated lead-carbon hybrid ultracapacitor with co-located terminals is discussed. Voltage-management circuit for the ultracapacitor is presented, and its effectiveness is validated experimentally.

ABSOLUTE/CONVECTIVE INSTABILITY TRANSITION IN A BACKWARD FACING STEP COMBUSTOR: FUNDAMENTAL MECHANISM AND INFLUENCE OF DENSITY GRADIENT

Hydrodynamic instabilities of the flow field in lean premixed gas turbine combustors can generate velocity perturbations that wrinkle and distort the flame sheet over length scales that are smaller than the flame length. The resultant heat release oscillations can then potentially result in combustion instability. Thus, it is essential to understand the hydrodynamic instability characteristics of the combustor flow field in order to understand its overall influence on combustion instability characteristics. To this end, this paper elucidates the role of fluctuating vorticity production from a linear hydrodynamic stability analysis as the key mechanism promoting absolute/convective instability transitions in shear layers occurring in the flow behind a backward facing step. These results are obtained within the framework of an inviscid, incompressible, local temporal and spatio-temporal stability analysis. Vorticity fluctuations in this limit result from interaction between two competing mechanisms - (1) production from interaction between velocity perturbations and the base flow vorticity gradient and (2) baroclinic torque in the presence of base flow density gradients. This interaction has a significant effect on hydrodynamic instability characteristics when the base flow density and velocity gradients are co-located. Regions in the space of parameters characterizing the base flow velocity profile, i.e. shear layer thickness and ratio of forward to reverse flow velocity, corresponding to convective and absolute instability are identified. The implications of the present results on prior observations of flow instability in other flows such as heated jets and bluff-body stabilized flames is discussed.

Investigations of aerosol black carbon from a semi-urban site in the Indo-Gangetic Plain region

Long-term (2009-2012) data from ground-based measurements of aerosol black carbon (BC) from a semi-urban site, Pantnagar (29.0 degrees N, 79.5 degrees E, 231 m amsl), in the Indo-Gangetic Plain (IGP) near the Himalayan foothills are analyzed to study the regional characterization. Large variations are seen in BC at both diurnal and seasonal scales, associated with the mesoscale and synoptic meteorological processes, and local/regional anthropogenic activities. BC diurnal variations show two peaks (morning and evening) arising from the combined effects of the atmospheric boundary layer (ABL) dynamics and local emissions. The diurnal amplitudes as well as the rates of diurnal evolution are the highest in winter season, followed by autumn, and the lowest in summer-monsoon. BC exhibits nearly an inverse relation with mixing layer depth in all seasons; being strongest in winter (R-2 = 0.89) and weakest (R-2 = 0.33) in monsoon (July-August). Unlike BC, co-located aerosol optical depths (AOD) and aerosol absorption are highest in spring over IGP, probably due to the presence of higher abundances of aerosols (including dust) above the ABL (in the free troposphere). AOD (500 nm) showed annual peak (>0.6) in May-June, dominated by coarse mode, while fine mode aerosols dominated in late autumn and early winter. Aerosols profiles from CALIPSO show highest values close to the surface in winter/autumn, similar to the feature seen in surface BC, whereas at altitudes > 2 km, the extinction is maximum in spring/summer. WRF-Chem model is used to simulate BC temporal variations and then compared with observed BC. The model captures most of the important features of the diurnal and seasonal variations but significantly underestimated the observed BC levels, suggesting improvements in diurnal and seasonal varying BC emissions apart from the boundary layer processes. (C) 2015 Elsevier Ltd. All rights reserved.