Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

Citation: Tanger, P., Klassen, S., Mojica, J. P., Lovell, J. T., Moyers, B. T., Baraoidan, M., . . . McKay, J. K. (2017). Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice. Scientific Reports, 7, 8. doi:10.1038/srep42839To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index. Genetic mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution

USP15 deubiquitinase safeguards hematopoiesis and genome integrity in hematopoietic stem cells and leukemia cells

Altering ubiquitination by disruption of individual deubiquitinating enzymes (DUBs) has proven to affect hematopoietic stem cell (HSC) maintenance. However, comprehensive knowledge of DUB function during hematopoiesis in vivo is lacking. To accomplish this goal, we systematically inactivated DUBs in mouse hematopoietic progenitors using in vivo small hairpin RNAs (shRNAs) screens. We found that multiple DUBs may be individually required for hematopoiesis and that the ubiquitin-specific protease 15 (USP15) is particularly important for the maintenance of murine hematopoietic stem and progenitor cells in vitro and in vivo. Consistently, Usp15 knockout mice exhibited a reduced HSC pool. The defect was intrinsic to HSCs, as demonstrated by competitive repopulation assays. Importantly, USP15 is highly expressed in normal human hematopoietic cells and leukemias, and USP15 depletion in murine early progenitors and myeloid leukemia cells impaired in vitro expansion and increased genotoxic stress. Our study underscores the importance of DUBs in preserving normal hematopoiesis and uncovers USP15 as a critical DUB in safeguarding genome integrity in HSC and in leukemia cells

A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring

Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables has rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as ‘‘Bison Pool’’ in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community.Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the composition of biomass and the environmental conditions

Subsurface hydrothermal processes and the bioenergetics of chemolithoautotrophy at the shallow-sea vents off Panarea Island (Italy)

The subsurface evolution of shallow-sea hydrothermal fluids is a function of many factors including fluid-mineral equilibria, phase separation, magmatic inputs, and mineral precipitation, all of which influence discharging fluid chemistry and consequently associated seafloor microbial communities. Shallow-sea vent systems, however, are understudied in this regard. In order to investigate subsurface processes in a shallow-sea hydrothermal vent, and determine how these physical and chemical parameters influence the metabolic potential of the microbial communities, three shallow-sea hydrothermal vents associated with Panarea Island (Italy) were characterized. Vent fluids, pore fluids and gases at the three sites were sampled and analyzed for major and minor elements, redox-sensitive compounds, free gas compositions, and strontium isotopes. The corresponding data were used to 1) describe the subsurface geochemical evolution of the fluids and 2) to evaluate the catabolic potential of 61 inorganic redox reactions for in situ microbial communities. Generally, the vent fluids can be hot (up to 135 °C), acidic (pH 1.9-5.7), and sulfidic (up to 2.5 mM H2S). Three distinct types of hydrothermal fluids were identified, each with higher temperatures and lower pH, Mg2 + and SO42 -, relative to seawater. Type 1 was consistently more saline than Type 2, and both were more saline than seawater. Type 3 fluids were similar to or slightly depleted in most major ions relative to seawater. End-member calculations of conservative elements indicate that Type 1 and Type 2 fluids are derived from two different sources, most likely 1) a deeper, higher salinity reservoir and 2) a shallower, lower salinity reservoir, respectively, in a layered hydrothermal system. The deeper reservoir records some of the highest end-member Cl concentrations to date, and developed as a result of recirculation of brine fluids with long term loss of steam and volatiles due to past phase separation. No strong evidence for ongoing phase separation is observed. Type 3 fluids are suggested to be mostly influenced by degassing of volatiles and subsequently dissolution of CO2, H2S, and other gases into the aqueous phase. Gibbs energies (ΔGr) of redox reactions that couple potential terminal electron acceptors (O2, NO3-, MnIV, FeIII, SO42 -, S0, CO2,) with potential electron donors (H2, NH4+, Fe2 +, Mn2 +, H2S, CH4) were evaluated at in situ temperatures and compositions for each site and by fluid type. When Gibbs energies of reaction are normalized per kilogram of hydrothermal fluid, sulfur oxidation reactions are the most exergonic, while the oxidation of Fe2 +, NH4+, CH4, and Mn2 + are moderately energy yielding. The energetics calculations indicate that the most robust microbial communities in the Panarea hot springs combine H2S from deep water-rock-gas interactions with O2 that is entrained via seawater mixing to fuel their activities, regardless of site location or fluid type

Network Competition with Income Effects

I generalize the workhorse model of network competition to include income effects in call demand. Empirical work has shown call demand to increase significantly with income. For any positive income effect, network operators prefer a termination rate above marginal cost if networks are sufficiently differentiated. This holds with or without call price discrimination. Under price discrimination, the networks charge a lower price for calls within the own network (on-net) than to other networks (off-net). Income effects thus deliver theoretical results consistent with stylized facts about call prices and in line with regulatory concern about excessive termination rates

Phase Behavior of Aqueous Na-K-Mg-Ca-CI-NO3 Mixtures: Isopiestic Measurements and Thermodynamic Modeling

A comprehensive model has been established for calculating thermodynamic properties of multicomponent aqueous systems containing the Na{sup +}, K{sup +}, Mg{sup 2+}, Ca{sup 2+}, Cl{sup -}, and NO{sub 3}{sup -} ions. The thermodynamic framework is based on a previously developed model for mixed-solvent electrolyte solutions. The framework has been designed to reproduce the properties of salt solutions at temperatures ranging from the freezing point to 300 C and concentrations ranging from infinite dilution to the fused salt limit. The model has been parameterized using a combination of an extensive literature database and new isopiestic measurements for thirteen salt mixtures at 140 C. The measurements have been performed using Oak Ridge National Laboratory's (ORNL) previously designed gravimetric isopiestic apparatus, which makes it possible to detect solid phase precipitation. Water activities are reported for mixtures with a fixed ratio of salts as a function of the total apparent salt mole fraction. The isopiestic measurements reported here simultaneously reflect two fundamental properties of the system, i.e., the activity of water as a function of solution concentration and the occurrence of solid-liquid transitions. The thermodynamic model accurately reproduces the new isopiestic data as well as literature data for binary, ternary and higher-order subsystems. Because of its high accuracy in calculating vapor-liquid and solid-liquid equilibria, the model is suitable for studying deliquescence behavior of multicomponent salt systems

Yardstick Competition and Quality

"This paper explores the consequences for quality of introducing yardstick competition in duopoly when a verifiable quality indicator is available. Yardstick competition can be implemented by a menu of transfers that are linear in the cost differential between the two firms and in quality. Cost- and quality incentives are stronger in larger firms when improvements are highly valued by consumers and firms can significantly influence quality. Expenditures on quality improvement can increase or decrease following the introduction of yardstick competition. The crucial factor is the likelihood ratio of productivity between the two firms, not productivity differences." Copyright (c) 2009, The Author(s) Journal Compilation (c) 2009 Wiley Periodicals, Inc..

Visual prey capture in larval zebrafish is controlled by identified reticulospinal neurons downstream of the tectum

Many vertebrates are efficient hunters and recognize their prey by innate neural mechanisms. During prey capture, the internal representation of the prey's location must be constantly updated and made available to premotor neurons that convey the information to spinal motor circuits. We studied the neural substrate of this specialized visuomotor system using high- speed video recordings of larval zebrafish and laser ablations of candidate brain structures. Seven-day-old zebrafish oriented toward, chased, and consumed paramecia with high accuracy. Lesions of the retinotectal neuropil primarily abolished orienting movements toward the prey. Wild-type fish tested in darkness, as well as blind mutants, were impaired similarly to tectum-ablated animals, suggesting that prey capture is mainly visually mediated. To trace the pathway further, we examined the role of two pairs of identified reticulospinal neurons, MeLc and MeLr, located in the nucleus of the medial longitudinal fasciculus of the tegmentum. These two neurons extend dendrites into the ipsilateral tectum and project axons into the spinal cord. Ablating MeLc and MeLr bilaterally impaired prey capture but spared several other behaviors. Ablating different sets of reticulospinal neurons did not impair prey capture, suggesting a selective function of MeLr and MeLc in this behavior. Ablating MeLc and MeLr neurons unilaterally in conjunction with the contralateral tectum also mostly abolished prey capture, but ablating them together with the ipsilateral tectum had a much smaller effect. These results suggest that MeLc and MeLr function in series with the tectum, as part of a circuit that coordinates prey capture movements