How efficiently do corn‐ and soybean‐based cropping systems use water? A systems modeling analysis

Agricultural systems are being challenged to decrease water use and increase production while climate becomes more variable and the world's population grows. Low water use efficiency is traditionally characterized by high water use relative to low grain production and usually occurs under dry conditions. However, when a cropping system fails to take advantage of available water during wet conditions, this is also an inefficiency and is often detrimental to the environment. Here, we provide a systems‐level definition of water use efficiency (sWUE) that addresses both production and environmental quality goals through incorporating all major system water losses (evapotranspiration, drainage, and runoff). We extensively calibrated and tested the Agricultural Production Systems sIMulator (APSIM) using 6 years of continuous crop and soil measurements in corn‐ and soybean‐based cropping systems in central Iowa, USA. We then used the model to determine water use, loss, and grain production in each system and calculated sWUE in years that experienced drought, flood, or historically average precipitation. Systems water use efficiency was found to be greatest during years with average precipitation. Simulation analysis using 28 years of historical precipitation data, plus the same dataset with ± 15% variation in daily precipitation, showed that in this region, 430 mm of seasonal (planting to harvesting) rainfall resulted in the optimum sWUE for corn, and 317 mm for soybean. Above these precipitation levels, the corn and soybean yields did not increase further, but the water loss from the system via runoff and drainage increased substantially, leading to a high likelihood of soil, nutrient, and pesticide movement from the field to waterways. As the Midwestern United States is predicted to experience more frequent drought and flood, inefficiency of cropping systems water use will also increase. This work provides a framework to concurrently evaluate production and environmental performance of cropping systems.     

Phosphorylation modulates the affinity of light-activated rhodopsin for G protein and arrestin

Reduced effector activity and binding of arrestin are widely accepted consequences of GPCR phosphorylation. However, the effect of receptor multiphosphorylation on G protein activation and arrestin binding parameters has not previously been quantitatively examined. We have found receptor phosphorylation to alter both G protein and arrestin binding constants for light-activated rhodopsin in proportion to phosphorylation stoichiometry. Rod disk membranes containing different average receptor phosphorylation stoichiometries were combined with G protein or arrestin, and titrated with a series of brief light flashes. Binding of G(t) or arrestin to activated rhodopsin augmented the 390 nm MII optical absorption signal by stabilizing MII as MII.G or MII.Arr. The concentration of active arrestin or G(t) and the binding constant of each to MII were determined using a nonlinear least-squares (Simplex) reaction model analysis of the titration data. The binding affinity of phosphorylated MII for G(t) decreased while that for arrestin increased with each added phosphate. G(t) binds more tightly to MII at phosphorylation levels less than or equal to two phosphates per rhodopsin; at higher phosphorylation levels, arrestin binding is favored. However, arrestin was found to bind much more slowly than G(t) at all phosphorylation levels, perhaps allowing time for phosphorylation to gradually reduce receptor-G protein interaction before arrestin capping of rhodopsin. Sensitivity of the binding constants to ionic strength suggests that a strong membrane electrostatic component is involved in both the reduction of G(t) binding and the increase of arrestin binding with increasing rhodopsin phosphorylation.     

Yeast ribosomal protein L24 affects the kinetics of protein synthesis and ribosomal protein L39 improves translational accuracy, while mutants lacking both remain viable

Four mutant strains from Saccharomyces cerevisiae were used to study ribosome structure and function. They included a strain carrying deletions of the two genes encoding ribosomal protein L24, a strain carrying a mutation spb2 in the gene for ribosomal protein L39, a strain carrying a deletion of the gene for L39, and a mutant lacking both L24 and L39. The mutant lacking only L24 showed just 25% of the normal polyphenylalanine-synthesizing activity followed by a decrease in P-site binding, suggesting the possibility that protein L24 is involved in the kinetics of translation. Each of the two L39 mutants displayed a 4-fold increase of their error frequencies over the wild type. This was accompanied by a substantial increase in A-site binding, typical of error-prone mutants. The absence of L39 also increased sensitivity to paromomycin, decreased the ribosomal subunit ratio, and caused a cold-sensitive phenotype. Mutant cells lacking both ribosomal proteins remained viable. Their ribosomes showed reduced initial rates caused by the absence of L24 but a normal extent of polyphenylalanine synthesis and a substantial in vivo reduction in the amount of 80S ribosomes compared to wild type. Moreover, this mutant displayed decreased translational accuracy, hypersensitivity to the antibiotic paromomycin, and a cold-sensitive phenotype, all caused mainly by the deletion of L39. Protein L39 is the first protein of the 60S ribosomal subunit implicated in translational accuracy.     

Can mineralization of soil organic nitrogen meet maize nitrogen demand?

Background and aims

It is generally assumed that very large herbivores, such as elephants, make foraging decisions at large spatial scales, but the extent to which seasonal foraging decisions are driven by soil quality, and its link to plant nutrient levels, is uncertain.

Methods

We studied the diet selection of African elephants Loxodonta africana in Ithala Game Reserve in northern KwaZulu-Natal, South Africa, using data on elephant feeding preferences and spatial distributions from a published paper. Elephants were present in the eastern half with granite soils in the wet season, and in the western half with sedimentary soils in the dry season. The quality of these two soil types and of seven key tree species for elephants was assessed in both seasons.

Results

Soil quality was higher on the sedimentary soils in terms of total nitrogen, soil respiration, water-holding capacity, organic carbon and pH. Leaf quality was higher on the sedimentary soils in the dry season, while in the wet season there was no significant difference in leaf quality of the seven key tree species growing on the two substrates.

Conclusion

Soil quality may explain elephants’ foraging decisions in the dry season, but not in the wet season. Elephants preferred trees with higher protein and lower concentrations of fibre on both granite and sedimentary soils.

     

Temperature and pH dependence of the metarhodopsin I-metarhodopsin II equilibrium and the binding of metarhodopsin II to G protein in rod disk membranes.

The equilibria between metarhodopsins I and II (MI and MII) and the binding of MII to retinal G protein (G) were investigated, using the dual wavelength absorbance response of rod disk membrane (RDM) suspensions to a series of small bleaches, together with a nonlinear least-squares fitting procedure that decouples the two reactions. This method has been subjected to a variety of theoretical and experimental tests that establish its validity. The two equilibrium constants, the amount of active G protein (that can bind to and stabilize MII) and the fraction bleached by the flash, have been determined without a priori assumptions about these values, at temperatures between 0 and 15 degrees C and pHs from 6.2 to 8.2. Binding of G to MII in normal RDM exhibits 1:1 stoichiometry (not cooperative), relatively weak, 2-4 x 10(4) M-1 affinity on the membrane, with a pH dependence maximal at pH 7.6, and a low thermal coefficient. The reported amount of active G remained constant even when its binding constant was reduced more than 10-fold at low pH. The method can readily be applied to the binding of MII to other proteins or polypeptides that stabilize its conformation as MII. It appears capable of determining many of the essential physical constants of G protein coupled receptor interaction with immediate signaling partners and the effect of perturbation of environmental parameters on these constants.     

Identification of physicochemical selective pressure on protein encoding nucleotide sequences

Background  

Statistical methods for identifying positively selected sites in protein coding regions are one of the most commonly used tools in evolutionary bioinformatics. However, they have been limited by not taking the physiochemical properties of amino acids into account.     

Permanent Preparations with the Thomas arginine Histochemical Test

A modification of Thomas' arginine histochemical method, yielding a stable coloration, is described. Elimination of some intermediary and clearing fluids which were found to have a dilatorious effect on the color, changes in the reaction times, and the use of mineral oil as mounting medium all contribute to color permanency. The method described is simpler than the original ones and offers considerable economy in time and material.     

Influence of Residue and Nitrogen Fertilizer Additions on Carbon Mineralization in Soils with Different Texture and Cropping Histories

To improve our ability to predict SOC mineralization response to residue and N additions in soils with different inherent and dynamic organic matter properties, a 330-day incubation was conducted using samples from two long-term experiments (clay loam Mollisols in Iowa [IAsoil] and silt loam Ultisols in Maryland [MDsoil]) comparing conventional grain systems (Conv) amended with inorganic fertilizers with 3 yr (Med) and longer (Long), more diverse cropping systems amended with manure. A double exponential model was used to estimate the size (C _a, C _s) and decay rates (k _a, k _s) of active and slow C pools which we compared with total particulate organic matter (POM) and occluded-POM (OPOM). The high-SOC IAsoil containing highly active smectite clays maintained smaller labile pools and higher decay rates than the low-SOC MDsoil containing semi-active kaolinitic clays. Net SOC loss was greater (2.6 g kg⁻¹; 8.6%) from the IAsoil than the MDsoil (0.9 g kg⁻¹, 6.3%); fractions and coefficients suggest losses were principally from IAsoil’s resistant pool. Cropping history did not alter SOC pool size or decay rates in IAsoil where rotation-based differences in OPOM-C were small. In MDsoil, use of diversified rotations and manure increased k _a by 32% and k _s by 46% compared to Conv; differences mirrored in POM- and OPOM-C contents. Residue addition prompted greater increases in C _a (340% vs 230%) and C _s (38% vs 21%) and decreases in k _a (58% vs 9%) in IAsoil than MDsoil. Reduced losses of SOC from residue-amended MDsoil were associated with increased OPOM-C. Nitrogen addition dampened CO₂-C release. Clay type and C saturation dominated the IAsoil’s response to external inputs and made labile and stable fractions more vulnerable to decay. Trends in OPOM suggest aggregate protection influences C turnover in the low active MDsoil. Clay charge and OPOM-C contents were better predictors of soil C dynamics than clay or POM-C contents.     

"Prion-proof" for [PIN+]: infection with in vitro-made amyloid aggregates of Rnq1p-(132-405) induces [PIN+

Prions are self-propagating, infectious protein conformations. The mammalian prion, PrP(Sc), responsible for neurodegenerative diseases like bovine spongiform encephalopathy (BSE; "mad cow" disease) and Creutzfeldt-Jakob's disease, appears to be a beta-sheet-rich amyloid conformation of PrP(c) that converts PrP(c) into PrP(Sc). However, an unequivocal demonstration of "protein-only" infection by PrP(Sc) is still lacking. So far, protein only infection has been proven for three prions, [PSI(+)], [URE3] and [Het-s], all of fungal origin. Considerable evidence supports the hypothesis that another protein, the yeast Rnq1p, can form a prion, [PIN(+)]. While Rnq1p does not lose any known function upon prionization, [PIN(+)] has interesting positive phenotypes: facilitating the appearance and destabilization of other prions as well as the aggregation of polyglutamine extensions of the Huntingtin protein. Here, we polymerize a Gln/Asn-rich recombinant fragment of Rnq1p into beta-sheet-rich amyloid-like aggregates. While the method used for [PSI(+)] and [URE3] infectivity assays did not yield protein-only infection for the Rnq1p aggregates, we did successfully obtain protein-only infection by modifying the protocol. This work proves that [PIN(+)] is a prion mediated by amyloid-like aggregates of Rnq1p, and supports the hypothesis that heterologous prions affect each other's appearance and propagation through interaction of their amyloid-like regions.