Using Microbial Community Interactions within Plant Microbiomes to Advance an Evergreen Agricultural Revolution

Innovative plant breeding and technology transfer fostered the Green Revolution (GR), which transformed agriculture worldwide by increasing grain yields in developing countries. The GR temporarily alleviated world hunger, but also reduced biodiversity, nutrient cycling, and carbon (C) sequestration that agricultural lands can provide. Meanwhile, economic disparity and food insecurity within and among countries continues. Subsequent agricultural advances, focused on objectives such as increasing crop yields or reducing the risk of a specific pest, have failed to meet food demands at the local scale or to restore lost ecosystem services. An increasing human population, climate change, growing per capita food and energy demands, and reduced ecosystem potential to provide agriculturally relevant services have created an unrelenting need for improved crop production practices. Meeting this need in a sustainable fashion will require interdisciplinary approaches that integrate plant and microbial ecology with efforts to advance crop production while mitigating effects of a changing climate. Metagenomic advances are revealing microbial dynamics that can simultaneously improve crop production and soil restoration while enhancing crop resistance to environmental change. Restoring microbial diversity to contemporary agroecosystems could establish ecosystem services while reducing production costs for agricultural producers. Our framework for examining plant-microbial interactions at multiple scales, modeling outcomes to broadly explore potential impacts, and interacting with extension and training networks to transfer microbial based agricultural technologies across socioeconomic scales, offers an integrated strategy for advancing agroecosystem sustainability while minimizing potential for the kind of negative ecological and socioeconomic feedbacks that have resulted from many widely adopted agricultural technologies

Structural Probe of a Glass Forming Liquid: Generalized Compressibility

We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming liquid consisting of a two component mixture of soft spheres in three dimensions. As the temperature is lowered (or as the density is increased), the generalized compressibility drops sharply at the glass transition, with the drop becoming more and more abrupt as the measurement time increases. At our longest measurement times, the drop occurs approximately at the mode coupling temperature $T_C$. The drop in the linear generalized compressibility occurs at the same temperature as the peak in the specific heat. By examining the inherent structure energy as a function of temperature, we find that our results are consistent with the kinetic view of the glass transition in which the system falls out of equilibrium. We find no size dependence and no evidence for a second order phase transition though this does not exclude the possibility of a phase transition below the observed glass transition temperature. We discuss the relation between the linear generalized compressibility and the ordinary isothermal compressibility as well as the static structure factor.Comment: 18 pages, Latex, 26 encapsulated postscript figures, revised paper is shorter, to appear in Phys. Rev.

Evidence for structural and electronic instabilities at intermediate temperatures in κ\kappa-(BEDT-TTF)2_{2}X for X=Cu[N(CN)2_{2}]Cl, Cu[N(CN)2_{2}]Br and Cu(NCS)2_{2}: Implications for the phase diagram of these quasi-2D organic superconductors

We present high-resolution measurements of the coefficient of thermal expansion $\alpha (T)=\partial \ln l(T)/\partial T$ of the quasi-twodimensional (quasi-2D) salts $\kappa$-(BEDT-TTF)$_2$X with X = Cu(NCS)$_2$, Cu[N(CN)$_2$]Br and Cu[N(CN)$_2$]Cl. At intermediate temperatures (B), distinct anomalies reminiscent of second-order phase transitions have been found at $T^\ast = 38$ K and 45 K for the superconducting X = Cu(NCS)$_2$ and Cu[N(CN)$_2$]Br salts, respectively. Most interestingly, we find that the signs of the uniaxial pressure coefficients of $T^\ast$ are strictly anticorrelated with those of $T_c$. We propose that $T^\ast$ marks the transition to a spin-density-wave (SDW) state forming on minor, quasi-1D parts of the Fermi surface. Our results are compatible with two competing order parameters that form on disjunct portions of the Fermi surface. At elevated temperatures (C), all compounds show $\alpha (T)$ anomalies that can be identified with a kinetic, glass-like transition where, below a characteristic temperature $T_g$, disorder in the orientational degrees of freedom of the terminal ethylene groups becomes frozen in. We argue that the degree of disorder increases on going from the X = Cu(NCS)$_2$ to Cu[N(CN)$_2$]Br and the Cu[N(CN)$_2$]Cl salt. Our results provide a natural explanation for the unusual time- and cooling-rate dependencies of the ground-state properties in the hydrogenated and deuterated Cu[N(CN)$_2$]Br salts reported in the literature.Comment: 22 pages, 7 figure

A survey of psychosocial adaptation in long-term survivors of pediatric liver transplants

We assessed 41 children and adolescents who had received liver transplants at least 4 years ago, for social, behavioral, and emotional adaptation; physical function; and family stress. We compared their level of adaptive functioning to published data from chronically ill and medically well children. On many measures, transplant recipients had equivalent levels of function to the comparison groups. However, 6- to 11-year-old patients showed mild social and scholastic deficits. Patients' parents report less negative impact of the illness on the family than do parents of other chronically ill children. A listing of medication side effects and the degree to which they are problematic was obtained.published_or_final_versio

Calibration and Physics with ARA Station 1: A Unique Askaryan Radio Array Detector

The Askaryan Radio Array Station 1 (A1), the first among five autonomous stations deployed for the ARA experiment at the South Pole, is a unique ultra-high energy neutrino (UHEN) detector based on the Askaryan effect that uses Antarctic ice as the detector medium. Its 16 radio antennas (distributed across 4 strings, each with 2 Vertically Polarized (VPol), 2 Horizontally Polarized (HPol) receivers), and 2 strings of transmitting antennas (calibration pulsers, CPs), each with 1 VPol and 1 HPol channel, are deployed at depths less than 100 m within the shallow firn zone of the 2.8 km thick South Pole (SP) ice. We apply different methods to calibrate its Ice Ray Sampler second generation (IRS2) chip for timing offset and ADC-to-Voltage conversion factors using a known continuous wave input signal to the digitizer, and achieve a precision of sub-nanoseconds. We achieve better calibration for odd, compared to even samples, and also find that the HPols under-perform relative to the VPol channels. Our timing calibrated data is subsequently used to calibrate the ADC-to-Voltage conversion as well as precise antenna locations, as a precursor to vertex reconstruction. The calibrated data will then be analyzed for UHEN signals in the final step of data compression. The ability of A1 to scan the firn region of SP ice sheet will contribute greatly towards a 5-station analysis and will inform the design of the planned IceCube Gen-2 radio array.Comment: 10 page

Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening

<p>Abstract</p> <p>Background</p> <p>Cluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no transcriptomic data have been reported describing the mechanisms that underlie the agronomic and biochemical effects of thinning.</p> <p>Results</p> <p>We profiled the transcriptome of <it>Vitis vinifera </it>cv. Sangiovese berries before and after thinning at veraison using a genome-wide microarray representing all grapevine genes listed in the latest V1 gene prediction. Thinning increased the source/sink ratio from 0.6 to 1.2 m²leaf area per kg of berries and boosted the sugar and anthocyanin content at harvest. Extensive transcriptome remodeling was observed in thinned vines 2 weeks after thinning and at ripening. This included the enhanced modulation of genes that are normally regulated during berry development and the induction of a large set of genes that are not usually expressed.</p> <p>Conclusion</p> <p>Cluster thinning has a profound effect on several important cellular processes and metabolic pathways including carbohydrate metabolism and the synthesis and transport of secondary products. The integrated agronomic, biochemical and transcriptomic data revealed that the positive impact of cluster thinning on final berry composition reflects a much more complex outcome than simply enhancing the normal ripening process.</p

Exercise therapy for prevention of falls in people with Parkinson's disease: A protocol for a randomised controlled trial and economic evaluation

<p>Abstract</p> <p>Background</p> <p>People with Parkinson's disease are twice as likely to be recurrent fallers compared to other older people. As these falls have devastating consequences, there is an urgent need to identify and test innovative interventions with the potential to reduce falls in people with Parkinson's disease. The main objective of this randomised controlled trial is to determine whether fall rates can be reduced in people with Parkinson's disease using exercise targeting three potentially remediable risk factors for falls (reduced balance, reduced leg muscle strength and freezing of gait). In addition we will establish the cost effectiveness of the exercise program from the health provider's perspective.</p> <p>Methods/Design</p> <p>230 community-dwelling participants with idiopathic Parkinson's disease will be recruited. Eligible participants will also have a history of falls or be identified as being at risk of falls on assessment. Participants will be randomly allocated to a usual-care control group or an intervention group which will undertake weight-bearing balance and strengthening exercises and use cueing strategies to address freezing of gait. The intervention group will choose between the home-based or support group-based mode of the program. Participants in both groups will receive standardized falls prevention advice. The primary outcome measure will be fall rates. Participants will record falls and medical interventions in a diary for the duration of the 6-month intervention period. Secondary measures include the Parkinson's Disease Falls Risk Score, maximal leg muscle strength, standing balance, the Short Physical Performance Battery, freezing of gait, health and well being, habitual physical activity and positive and negative affect schedule.</p> <p>Discussion</p> <p>No adequately powered studies have investigated exercise interventions aimed at reducing falls in people with Parkinson's disease. This trial will determine the effectiveness of the exercise intervention in reducing falls and its cost effectiveness. This pragmatic program, if found to be effective, has the potential to be implemented within existing community services.</p> <p>Trial registration</p> <p>The protocol for this study is registered with the Australian New Zealand Clinical Trials Registry (ACTRN12608000303347).</p

Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip

UMR AGAP - équipe DAAV - Diversité, adaptation et amélioration de la vigne[b]Background[/b] [br/]The increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci). [br/][b]Results[/b] [br/]Ten stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered. [br/][b]Conclusions[/b] [br/]This study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variatio

The Microphenotron: a robotic miniaturized plant phenotyping platform with diverse applications in chemical biology

Background Chemical genetics provides a powerful alternative to conventional genetics for understanding gene function. However, its application to plants has been limited by the lack of a technology that allows detailed phenotyping of whole-seedling development in the context of a high-throughput chemical screen. We have therefore sought to develop an automated micro-phenotyping platform that would allow both root and shoot development to be monitored under conditions where the phenotypic effects of large numbers of small molecules can be assessed. Results The ‘Microphenotron’ platform uses 96-well microtitre plates to deliver chemical treatments to seedlings of Arabidopsis thaliana L. and is based around four components: (a) the ‘Phytostrip’, a novel seedling growth device that enables chemical treatments to be combined with the automated capture of images of developing roots and shoots; (b) an illuminated robotic platform that uses a commercially available robotic manipulator to capture images of developing shoots and roots; (c) software to control the sequence of robotic movements and integrate these with the image capture process; (d) purpose-made image analysis software for automated extraction of quantitative phenotypic data. Imaging of each plate (representing 80 separate assays) takes 4 min and can easily be performed daily for time-course studies. As currently configured, the Microphenotron has a capacity of 54 microtitre plates in a growth room footprint of 2.1 m², giving a potential throughput of up to 4320 chemical treatments in a typical 10 days experiment. The Microphenotron has been validated by using it to screen a collection of 800 natural compounds for qualitative effects on root development and to perform a quantitative analysis of the effects of a range of concentrations of nitrate and ammonium on seedling development. Conclusions The Microphenotron is an automated screening platform that for the first time is able to combine large numbers of individual chemical treatments with a detailed analysis of whole-seedling development, and particularly root system development. The Microphenotron should provide a powerful new tool for chemical genetics and for wider chemical biology applications, including the development of natural and synthetic chemical products for improved agricultural sustainability

From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation

The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the -to- atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance