Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits

<p>Abstract</p> <p>Background</p> <p>Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (<it>Solanum tuberosum </it>L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to <it>Phytophthora infestans</it>) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits.</p> <p>Results</p> <p>Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by <it>ca</it>. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by <it>ca</it>. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes.</p> <p>Conclusions</p> <p>Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database.</p

3D radiation therapy boost improves the outcome of whole brain radiation therapy treated RPA II patients with one or two brain metastases

PURPOSE: to evaluate the role of whole brain radiotherapy (WBRT) and radiation boost (RB) for 208 patients recursive partitioning analysis (RPA) II with 1 or 2 brain metastases (BM) at a single institution. METHODS AND MATERIALS: the dose of WBRT was 30 Gy (10 fractions of 3 Gy). One hundred thirty-two patients (63.5%) benefited from RB of 9 Gy in 3 fractions of 3 Gy at the metastatic site. Patients had 1 or 2 BM in 122 (58.7%) and 86 cases (41.3%), respectively. RESULTS: patients with one or two metastases had similar survival (4.6 and 5.1 months, respectively) (p = 0.4). Median overall survival (OS) for patients treated with WBRT and RB, and with WBRT alone was 5.9 and 3.7 months, respectively (p = 0.03). The 6-, 12- and 24-month OS rates after WBRT and RB were 48.5%, 25% and 10.6%, respectively, while WBRT alone resulted in OS rates of 34%, 22.4% and 3.2%, respectively (p = 0.03). After WBRT and RB, the 6-, 12- and 24-month local control rates were 92%, 82% and 67%, respectively, while they were 81.2%, 75% and 37.5%, respectively, after WBRT alone (p = 0.03). The 6-, 12- and 24-month brain control rates after WBRT and RB were 88.7%, 75.8% and 62%, respectively, and after WBRT alone they were 78.5%, 59% and 37.7%, respectively (p = 0.03). CONCLUSION: additional boost delivered with 3D conformal radiotherapy improves local and brain control rates significantly as well as overall survival for RPA II patients with 1 or 2 unresectable BM

Assisted reproductive techniques do not impact late neurodevelopmental outcomes of preterm children

ObjectiveAssisted reproductive technology (ART) increases the rate of preterm births, though few studies have analyzed outcomes for these infants. No data are available on 4-year-old children born prematurely after ART. The objective was to investigate whether ART affect the neurodevelopmental outcomes at 4 years in preterm infants born before 34 weeks of gestational age (GA).Methods and resultsA total of 166 ART and 679 naturally conceived preterm infants born before 34 weeks GA between 2013 and 2015 enrolled in the Loire Infant Follow-up Team were included. Neurodevelopment was assessed at 4 years using the age and stage questionnaire (ASQ) and the need for therapy services. The association between the socio-economic and perinatal characteristics and non-optimal neurodevelopment at 4 years was estimated. After adjustment, the ART preterm group remained significantly associated with a lower risk of having at least two domains in difficulty at ASQ: adjusted odds ratio (aOR) 0.34, 95% confidence interval (CI) (0.13–0.88), p = 0.027. The factors independently associated with non-optimal neurodevelopment at 4 years were male gender, low socio-economic level, and 25–30 weeks of GA at birth. The need for therapy services was similar between groups (p = 0.079). The long-term neurodevelopmental outcomes of preterm children born after ART are very similar, or even better than that of the spontaneously conceived children

Visualising the visceral: using film to research the ineffable

While cheaper technology, wider training availability and the online digital learning environment have broadened the opportunities for geographers to use film and video, it has also led to calls to improve the discipline’s media literacy. This need is made even more urgent by the shift in qualitative research to practice-based methods targeted towards how we experience our lived environment. Other shifts in empirical and conceptual focus are also relevant, particularly interest in emotional beneath the surface geographies and calls for participation rather than observation encased in recent debates on the Anthropocene. The negative association of film with entertainment and marketeering has led to concerns about the suitability of film as a research output and has led some scholars to restrict themselves to a stringent use of real-time ‘video’ in a primarily data-collection context. This paper adopts a practice-based approach in order to identify some of the complex qualities that a research film holds and contribute to the debate about its future as a form of academic research and publication. Reflecting on a recent film-based research project on heritage tourism in Syria and Jordan I argue that the potential to manipulate, distort or entertain should not be ignored or refuted. Rather the wide range of relationships between people, objects and landscape within the frame such as depth of field, mise-en-scene and between the frames via editing (montage) give film a complex viscerality and multi-sensorial power that can help us explore how we communicate our feelings and connect the experiential qualities of filmic research methods to final outputs.This work was supported by the Economic and Social Research Council grant number RES-062-23-324

Archeohandi: protocol for a national disabilities database in archaeology in France

The archaeology of disability is a relatively recent and little-known approach in France. While the study of palaeopathology now goes hand in hand with funerary archaeology and osteoarchaeology, the French study of disabilities and disabling pathologies remains marginal and unevenly treated, depending on location, chronology and researcher’s interest. This paper focuses on highlighting the compatibility between this new research area, the obligations of osteoarchaeology, and the benefits of developing a national, diachronic, and interdisciplinary study. A database is designed within an interpretive, consensual framework, that can be adapted to overcome limitations and promote open-minded research on the care of the disabled in their own communities. A preliminary category selection of disabling pathologies has been made. These are trepanation, completely edentulous and/or compensating denture, neuronal impairment, severe scoliosis, Paget's disease, Diffuse Idiopathic Skeletal Hyperostosis (DISH), rickets, dwarfism, infectious diseases, unreduced fracture, amputation, severe degenerative disease and others. This list has been critically reviewed by experts in the field; it will evolve in a somewhat Darwinian fashion. Our database is hosted on the Huma-Num platform, with a management interface and quick access based on multiple tabs. The data includes information about archaeological operations, subjects, and pathologies; it is complemented by pictorial data stored on the Nakala platform. The development involved creating a prototype using HTML, CSS, JavaScript, SQL, and PHP, with features to display, add, modify, and delete operations and subjects. Enhancements have been made, including search optimization, charts, and the ability to export data in CSV format. The database, whose administrative interface can be accessed at archeohandi.huma-num.fr, contains so far 211 existing operations with a total of 1232 registered subjects spread throughout metropolitan France. These initial data reveal numerous research perspectives in osteoarchaeology that can be combined with other research topics, such as virtual reality

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Monitoring bee health in European agroecosystems using wing morphology and fat bodies

Current global change substantially threatens pollinators, which directly impacts the pollination services underpinning the stability, structure and functioning of ecosystems. Amongst these threats, many synergistic drivers, such as habitat destruction and fragmentation, increasing use of agrochemicals, decreasing resource diversity, as well as climate change, are known to affect wild and managed bees. Therefore, reliable indicators for pollinator sensitivity to such threats are needed. Biological traits, such as phenotype (e.g. shape, size and asymmetry) and storage reserves (e.g. fat body size), are important pollinator traits linked to reproductive success, immunity, resilience and foraging efficiency and, therefore, could serve as valuable markers of bee health and pollination service potential. This data paper contains an extensive dataset of wing morphology and fat body content for the European honeybee (Apis mellifera) and the buff-tailed bumblebee (Bombus terrestris) sampled at 128 sites across eight European countries in landscape gradients dominated by two major bee-pollinated crops (apple and oilseed rape), before and after focal crop bloom and potential pesticide exposure. The dataset also includes environmental metrics of each sampling site, namely landscape structure and pesticide use. The data offer the opportunity to test whether variation in the phenotype and fat bodies of bees is structured by environmental factors and drivers of global change. Overall, the dataset provides valuable information to identify which environmental threats predominantly contribute to the modification of these traits

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 - Meeting Abstracts - Antwerp, Belgium. 15–20 July 2017

This work was produced as part of the activities of FAPESP Research,\ud Disseminations and Innovation Center for Neuromathematics (grant\ud 2013/07699-0, S. Paulo Research Foundation). NLK is supported by a\ud FAPESP postdoctoral fellowship (grant 2016/03855-5). ACR is partially\ud supported by a CNPq fellowship (grant 306251/2014-0)