Krafla magma testbed: Understanding and using the magma-hydrothermal connection

The Krafla Magma Testbed (KMT), Krafla Caldera, Iceland, is proposed to be the first magma observatory, an international multi-borehole facility where teams will conduct scientific experiments and engineering tests focused on the magma-hydrothermal interface in a superhot geothermal systems (SHGS). Objectives are to: 1) Core and monitor from the roots of the hydrothermal system to the top of the magma body; 2) Provide ground-truth testing of surface-based techniques for locating magma; 3) Perturb the deep system to understand signals interpreted as volcano “unrest”; 4) Advance drilling and completion technology so that superhot and supercritical fluids can be produced from the magma roof zone; and 5) Advance sensor technology so that magma bodies can be monitored directly, vastly improving the eruption warnings important to 10% of Earth's population. KMT will provide a vanguard view of magma and hydrothermal circulation as the single system that it is. It will integrate the separate communities of practice of geothermal energy, which relies heavily on direct drilling observations; and volcanology, which relies on surface observations and theoretical models. The driving force is that geothermal drilling hit magma in Iceland, Kenya, and Hawaii, revealing how close to the surface magma exists and how closely connected magma is to the hydrothermal system. KMT is a 3 rd path in efforts to expand geothermal use. One path is to go deeper in cooler places, the Enhanced Geothermal System (EGS) concept, relying on advances in drilling and reservoir stimulation for economic viability, e.g. Frontier Observatory for Research in Geothermal Energy (FORGE) of the U.S. Department of Energy. Another, within SHGS, is to drill to conditions where fluids should be supercritical, e.g. IDDP-2 of Iceland Deep Drilling Program (IDDP) at Reykjanes. The 3 rd , also SHGS and pursued by KMT, is to access the vicinity of a magma body. This takes advantage of magma's high energy density due to latent heat of crystallization and delivered by convection to sustain high power output. Not only have SHGS wells proximal to magma at Krafla Caldera, Iceland, exhibited high flow rates equivalent to >100 MWt, but the expected efficiency of conversion to electricity is ~30% vs. ~10% for conventional geothermal. When combined with the new efficiencies of High Voltage Direct Current (HVDC) tranmission, the economic balance could shift from low-grade geothermal sources near the consumer to high-grade sources farther from the consumer

Clinical and Pathologic Features of H-Type Bovine Spongiform Encephalopathy Associated with E211K Prion Protein Polymorphism

The majority of bovine spongiform encephalopathy (BSE) cases have been ascribed to the classical form of the disease. H-type and L-type BSE cases have atypical molecular profiles compared to classical BSE and are thought to arise spontaneously. However, one case of H-type BSE was associated with a heritable E211K mutation in the prion protein gene. The purpose of this study was to describe transmission of this unique isolate of H-type BSE when inoculated into a calf of the same genotype by the intracranial route. Electroretinograms were used to demonstrate preclinical deficits in retinal function, and optical coherence tomography was used to demonstrate an antemortem decrease in retinal thickness. The calf rapidly progressed to clinical disease (9.4 months) and was necropsied. Widespread distribution of abnormal prion protein was demonstrated within neural tissues by western blot and immunohistochemistry. While this isolate is categorized as BSE-H due to a higher molecular mass of the unglycosylated PrPSc isoform, a strong labeling of all 3 PrPSc bands with monoclonal antibodies 6H4 and P4, and a second unglycosylated band at approximately 14 kDa when developed with antibodies that bind in the C-terminal region, it is unique from other described cases of BSE-H because of an additional band 23 kDa demonstrated on western blots of the cerebellum. This work demonstrates that this isolate is transmissible, has a BSE-H phenotype when transmitted to cattle with the K211 polymorphism, and has molecular features that distinguish it from other cases of BSE-H described in the literature

Multiple QTLs linked to agro-morphological and physiological traits related to drought tolerance in potato.

Dissection of the genetic architecture of adaptation and abiotic stress-related traits is highly desirable for developing drought-tolerant potatoes and enhancing the resilience of existing cultivars, particularly as agricultural production in rain-fed areas may be reduced by up to 50 % by 2020. The “DMDD” potato progeny was developed at International Potato Center (CIP) by crossing the sequenced double monoploid line DM and a diploid cultivar of the Solanum tuberosum diploid Andigenum Goniocalyx group. Recently, a high-density integrated genetic map based on single nucleotide polymorphism (SNP), diversity array technology (DArT), simple sequence repeats (SSRs), and amplified fragment length polymorphism (AFLP) markers was also made available for this population. Two trials were conducted, in greenhouse and field, for drought tolerance with two treatments each, well-watered and terminal drought, in which watering was suspended 60 days after planting. The DMDD population was evaluated for agro-morphological and physiological traits before and after initiation of stress, at multiple time points. Two dense parental genetic maps were constructed using published genotypic data, and quantitative trait locus (QTL) analysis identified 45 genomic regions associated with nine traits in well-watered and terminal drought treatments and 26 potentially associated with drought stress. In this study, the strong influence of environmental factors besides water shortage on the expression of traits and QTLs reflects the multigenic control of traits related to drought tolerance. This is the first study to our knowledge in potato identifying QTLs for drought-related traits in field and greenhouse trials, giving new insights into genetic architecture of drought-related traits. Many of the QTLs identified have the potential to be used in potato breeding programs for enhanced drought tolerance

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD

Changes in Channel Trafficking and Protein Stability Caused by LQT2 Mutations in the PAS Domain of the HERG Channel

Inherited human long-QT2 syndrome (LQTS) results from mutations in the gene encoding the HERG channel. Several LQT2-associated mutations have been mapped to the amino terminal cytoplasmic Per-Arnt-Sim (PAS) domain of the HERG1a channel subunit. Here we have characterized the trafficking properties of some LQT2-associated PAS domain mutants and analyzed rescue of the trafficking mutants by low temperature (27°C) or by the pore blocker drug E4031. We show that the LQT2-associated mutations in the PAS domain of the HERG channel display molecular properties that are distinct from the properties of LQT2-associated mutations in the trans-membrane region. Unlike the latter, many of the tested PAS domain LQT2-associated mutations do not result in trafficking deficiency of the channel. Moreover, the majority of the PAS domain mutations that cause trafficking deficiencies are not rescued by a pore blocking drug. We have also explored the in vitro folding stability properties of isolated mutant PAS domain proteins using a thermal unfolding fluorescence assay and a chemical unfolding assay

The development of endomycorrhizal root systems VIII. Effects of soil phosphorus and fungal colonization on the concentration of soluble carbohydrates in roots

Concentrations of phosphorus in shoot and soluble carbohydrates (fructose, glucose, sucrose and fructans) in root were measured in non-mycorrhizal and vesicular-arbuscular (VA) mycorrhizal (Glomus mosseae) leek plants (Allium porrum) raised at six concentrations of soil phosphate. In conditions when an increased concentration of soil phosphate reduced VA mycorrhizal infection, the concentrations of soluble carbohydrates in the root were at a maximum. Therefore the hypothesis that greater concentrations of soluble carbohydrates in roots favour VA mycorrhizal infection is discounted. There was a specific effect of VA mycorrhizas, in that infected roots contained a larger concentration of sucrose than did uninfected roots, in plants with similar phosphorus concentrations in dry matter of shoots. We conclude, first, that increased phosphorus supply from either phosphate addition to soil or VA mycorrhizal infection increases concentration of soluble carbohydrates in leek roots and, secondly, that the VA mycorrhizal root behaves as a particularly strong physiological sink when there is an excess concentration of sucrose in the host

Barley sodium content is regulated by natural variants of the Na+ transporter HvHKT1;5

During plant growth, sodium (Na+) in the soil is transported via the xylem from the root to the shoot. While excess Na+ is toxic to most plants, non-toxic concentrations have been shown to improve crop yields under certain conditions, such as when soil K+ is low. We quantified grain Na+ across a barley genome-wide association study panel grown under non-saline conditions and identified variants of a Class 1 HIGH-AFFINITY-POTASSIUM-TRANSPORTER (HvHKT1;5)-encoding gene responsible for Na+ content variation under these conditions. A leucine to proline substitution at position 189 (L189P) in HvHKT1;5 disturbs its characteristic plasma membrane localisation and disrupts Na+ transport. Under low and moderate soil Na+, genotypes containing HvHKT1:5P189 accumulate high concentrations of Na+ but exhibit no evidence of toxicity. As the frequency of HvHKT1:5P189 increases significantly in cultivated European germplasm, we cautiously speculate that this non-functional variant may enhance yield potential in non-saline environments, possibly by offsetting limitations of low available K+

Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

Conventional marker-based genotyping platforms are widely available, but not without their limitations. In this context, we developed Sequence-Based Genotyping (SBG), a technology for simultaneous marker discovery and co-dominant scoring, using next-generation sequencing. SBG offers users several advantages including a generic sample preparation method, a highly robust genome complexity reduction strategy to facilitate de novo marker discovery across entire genomes, and a uniform bioinformatics workflow strategy to achieve genotyping goals tailored to individual species, regardless of the availability of a reference sequence. The most distinguishing features of this technology are the ability to genotype any population structure, regardless whether parental data is included, and the ability to co-dominantly score SNP markers segregating in populations. To demonstrate the capabilities of SBG, we performed marker discovery and genotyping in Arabidopsis thaliana and lettuce, two plant species of diverse genetic complexity and backgrounds. Initially we obtained 1,409 SNPs for arabidopsis, and 5,583 SNPs for lettuce. Further filtering of the SNP dataset produced over 1,000 high quality SNP markers for each species. We obtained a genotyping rate of 201.2 genotypes/SNP and 58.3 genotypes/SNP for arabidopsis (n = 222 samples) and lettuce (n = 87 samples), respectively. Linkage mapping using these SNPs resulted in stable map configurations. We have therefore shown that the SBG approach presented provides users with the utmost flexibility in garnering high quality markers that can be directly used for genotyping and downstream applications. Until advances and costs will allow for routine whole-genome sequencing of populations, we expect that sequence-based genotyping technologies such as SBG will be essential for genotyping of model and non-model genomes alike

Comparative Functional Genomics of Salt Stress in Related Model and Cultivated Plants Identifies and Overcomes Limitations to Translational Genomics

One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding, especially for complex traits like abiotic stress tolerance, remains uncertain. Using comparative genomics (ionomics, transcriptomics and metabolomics) we analyzed the responses to salinity of three model and three cultivated species of the legume genus Lotus. At physiological and ionomic levels, models responded to salinity in a similar way to crop species, and changes in the concentration of shoot Cl− correlated well with tolerance. Metabolic changes were partially conserved, but divergence was observed amongst the genotypes. Transcriptome analysis showed that about 60% of expressed genes were responsive to salt treatment in one or more species, but less than 1% was responsive in all. Therefore, genotype-specific transcriptional and metabolic changes overshadowed conserved responses to salinity and represent an impediment to simple translational genomics. However, ‘triangulation’ from multiple genotypes enabled the identification of conserved and tolerant-specific responses that may provide durable tolerance across species

The Skeletal Organic Matrix from Mediterranean Coral Balanophyllia europaea Influences Calcium Carbonate Precipitation

Scleractinian coral skeletons are made mainly of calcium carbonate in the form of aragonite. The mineral deposition occurs in a biological confined environment, but it is still a theme of discussion to what extent the calcification occurs under biological or environmental control. Hence, the shape, size and organization of skeletal crystals from the cellular level through the colony architecture, were attributed to factors as diverse as mineral supersaturation levels and organic mediation of crystal growth. The skeleton contains an intra-skeletal organic matrix (OM) of which only the water soluble component was chemically and physically characterized. In this work that OM from the skeleton of the Balanophyllia europaea, a solitary scleractinian coral endemic to the Mediterranean Sea, is studied in vitro with the aim of understanding its role in the mineralization of calcium carbonate. Mineralization of calcium carbonate was conducted by overgrowth experiments on coral skeleton and in calcium chloride solutions containing different ratios of water soluble and/or insoluble OM and of magnesium ions. The precipitates were characterized by diffractometric, spectroscopic and microscopic techniques. The results showed that both soluble and insoluble OM components influence calcium carbonate precipitation and that the effect is enhanced by their co-presence. The role of magnesium ions is also affected by the presence of the OM components. Thus, in vitro, OM influences calcium carbonate crystal morphology, aggregation and polymorphism as a function of its composition and of the content of magnesium ions in the precipitation media. This research, although does not resolve the controversy between environmental or biological control on the deposition of calcium carbonate in corals, sheds a light on the role of OM, which appears mediated by the presence of magnesium ions