Solution structure of the Mesorhizobium loti K1 channel cyclic nucleotide‐binding domain in complex with cAMP

Cyclic nucleotide‐sensitive ion channels, known as HCN and CNG channels, are crucial in neuronal excitability and signal transduction of sensory cells. HCN and CNG channels are activated by binding of cyclic nucleotides to their intracellular cyclic nucleotide‐binding domain (CNBD). However, the mechanism by which the binding of cyclic nucleotides opens these channels is not well understood. Here, we report the solution structure of the isolated CNBD of a cyclic nucleotide‐sensitive K⁺ channel from Mesorhizobium loti. The protein consists of a wide anti‐parallel β‐roll topped by a helical bundle comprising five α‐helices and a short 3₁₀‐helix. In contrast to the dimeric arrangement (‘dimer‐of‐dimers’) in the crystal structure, the solution structure clearly shows a monomeric fold. The monomeric structure of the CNBD supports the hypothesis that the CNBDs transmit the binding signal to the channel pore independently of each other.     

LLWR Techniques for Quantifying Potential Soil Compaction Consequences of Crop Residue Removal

Harvesting crop residues for bioenergy or bio-product production may decrease soil organic matter (SOM) content, resulting in the degradation of soil physical properties and ultimately soil productivity. Using the least limiting water range (LLWR) to evaluate improvement or degradation of soil physical properties in response to SOM changes has generally been hampered by the extensive amount of data needed to parameterize limiting factor models for crop production. Our objective was to evaluate five pedotransfer functions to determine their effectiveness in predicting soil water holding capacity in response to different SOM levels. Similarly, two other pedotransfer functions were evaluated to determine the effects of SOM on cone index values. Predictions of field capacity and wilting point water content as well as the cone index–water content–bulk density relationship of soil strength using the pedotransfer functions were compared with field data from two tillage experiments near Akron, CO that had a range of SOM concentrations. Equations previously developed by da Silva and Kay gave the best estimates of LLWR for the pedotransfer functions we evaluated. These equations were then used to illustrate LLWR changes in response to different soil and crop management practices on a Duroc loam near Sidney, NE. The results showed that tillage and, possibly, soil erosion decreased the LLWR as tillage intensity increased. Therefore, we recommend that crop residue removal rates be limited to rates that maintain or increase SOM content to ensure soil physical conditions are not degraded.     

Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci

Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible “supergene” regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.     

Do pollen carryover and pollinator constancy mitigate effects of competition for pollination?

Pollinator constancy and pollen carryover are both thought to mitigate competitive effects that result when shared pollinators cause loss of pollen to heterospecific flowers. I present analytical and simulation models to investigate how pollinator constancy and pollen carryover interact with each other and with the relationship between pollen receipt and seed set to determine pollination success in competitive environments. With inconstant pollinators, increased pollen carryover reduces variance in pollen receipt without affecting average pollen receipt. Consequently, for flowers requiring at least a threshold quantity of pollen for success, rare flowers with inconstant pollinators benefit from reduced carryover, especially for high pollen receipt thresholds, whereas common flowers benefit from increased carryover, especially for low receipt thresholds. Pollinator constancy is predicted to increase pollen receipt, especially if pollen carryover rates are low. As a result, increased pollinator constancy reduces the range of pollen receipt thresholds for which carryover is beneficial. Similarly, for flowers whose pollination success is a convex function of pollen receipt, carryover is expected to increase fecundity if pollinators are inconstant, but with even a low degree of pollinator constancy, carryover reduces fecundity. These results predict that rare plants with many ovules per flower benefit from dispersing aggregations of pollen, especially if their pollinators exhibit constancy, whereas plants with inconstant pollinators and low thresholds of pollen receipt benefit from pollen grains dispersing individually to increase the number of flowers reached by the pollen.     

Using stable isotope analysis to assess the effects of hypolimnetic oxygenation on diet in a mixed cold- and warmwater fish community

Line-diffuser hypolimnetic oxygenation was initiated in North Twin Lake, Washington, in 2009 to mitigate reductions in Rainbow Trout (Oncorhynchus mykiss) and Brook Trout (Salvelinus fontinalis) habitat due to temperature-dissolved oxygen “habitat squeeze”. Previous studies demonstrated that trout populations rapidly expanded into increased hypolimnetic habitat within the first few years of oxygenation and previous short-term diet analyses indicated an effect on fish diet; however, the long-term effects on fish ecology have yet to be established. In this study, stable isotope analysis of fish liver tissue suggests relatively few differences in feeding ecology of principal coldwater fish species in North Twin Lake compared to unoxygenated South Twin Lake. When compared between lakes, Rainbow Trout and Brook Trout diets contained similar proportions of Daphnia, Chironomidae, and Chaoboridae. Littoral and epilimnetic-focused Golden Shiner (Notemigonus crysoleucas) diets were also similar between lakes. Observed similarities between Golden Shiner and trout diets suggest the effects of interspecific competition between salmonids and non-salmonids may be limiting trout growth and survival. Fisheries managers should therefore consider both habitat limitations and interspecific competition when managing for coldwater fish species in mesotrophic, dimictic lakes.     

Drosophila MUS312 interacts with the nucleotide excision repair endonuclease MEI-9 to generate meiotic crossovers

MEI-9 is the Drosophila homolog of the human structure-specific DNA endonuclease XPF. Like XPF, MEI-9 functions in nucleotide excision repair and interstrand crosslink repair. MEI-9 is also required to generate meiotic crossovers, in a function thought to be associated with resolution of Holliday junction intermediates. We report here the identification of MUS312, a protein that physically interacts with MEI-9. We show that mutations in mus312 elicit a meiotic phenotype identical to that of mei-9 mutants. A missense mutation in mei-9 that disrupts the MEI-9-MUS312 interaction abolishes the meiotic function of mei-9 but does not affect the DNA repair functions of mei-9. We propose that MUS312 facilitates resolution of meiotic Holliday junction intermediates by MEI-9.     

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

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Effects of aspirin on the development of Helicobacter pylori-induced gastric inflammation and heterotopic proliferative glands in Mongolian gerbils

Background: Helicobacter pylori infection is a major cause of gastritis and gastric carcinoma. Aspirin has anti‐inflammatory and antineoplastic activity. The aim of the present study was to determine the effects of aspirin on H. pylori‐induced gastritis and the development of heterotopic proliferative glands. Methods: H. pylori strain SS1 was inoculated into the stomachs of Mongolian gerbils. Two weeks after inoculation, the animals were fed with the powder diets containing 0 p.p.m. (n = 10), 150 p.p.m. (n = 10), or 500 p.p.m. (n = 10) aspirin. Mongolian gerbils were killed after 36 weeks of infection. Uninfected Mongolian gerbils (n = 10) were used as controls. Histologic changes, epithelial cell proliferation and apoptosis, and prostaglandin E₂ (PGE₂) levels of gastric tissue were determined. Results: H. pylori infection induced gastric inflammation. Administration of aspirin did not change H. pylori‐induced gastritis, but alleviated H. pylori‐induced hyperplasia and the development of heterotopic proliferative glands. Administration of aspirin accelerated H. pylori‐associated apoptosis but decreased H. pylori‐associated cell proliferation. In addition, the increased gastric PGE₂ levels due to H. pylori infection were suppressed by treatment with aspirin, especially at the dose of 500 p.p.m. Conclusions: Aspirin alleviates H. pylori‐induced hyperplasia and the development of heterotopic proliferative glands. Moreover, aspirin increases H. pylori‐induced apoptosis. We demonstrated the antineoplastic activities of aspirin in H. pylori‐related gastric carcinogenesis.