Does endophyte influence resource acquisition and allocation in defoliated tall fescue as a function of microsite conditions?

Tall fescue [Lolium arundinaceum (Schreb.) Darbysh.] often benefits in terms of productivity and persistence when infected with Neotyphodium coenophialum ([Morgan-Jones and Gams], Glenn, Bacon, and Hanlin) endophyte, but the influence of novel non-ergogenic endophytes is unclear. We conducted a field experiment using container-grown tall fescue plants to determine how plants allocated resources when clipped repeatedly in microsites differing in the amount of available light associated with open (full sun), and partially shaded (about 20 or 40% of full sun) conditions. Plants of the same tall fescue cultivar (Jesup) were host to either a native or novel non-ergogenic fungal endophyte (MaxQ™), or were devoid of endophyte. Seedlings of plants infected with the novel endophyte had slower germination, germinated later, and allocated more photosynthate to shoots than roots, when compared to J− or J+ plants. Herbage production of undisturbed canopies was not influenced by host–endophyte association within a microsite, with more herbage produced at the open than at the heavily shaded site. Clipping plants to a 5- or a 10-cm residue height tended to accentuate differences, with diminished productivity and greater variability occurring when plants were maintained at 5 cm. This trend was supported by allometric resource allocation patterns, and in terms of vegetative propagule mass relative to the number of propagules. Tall fescue, irrespective of host–endophyte association, grown as forage in silvopastoral situations should be managed to maintain no less than a 10-cm residual plant height. Trends in photosynthate allocation and plant size might influence persistence and should be investigated for more than two growing seasons.     

Spectral and kinetic studies on the formation of eosinophil peroxidase compound I and its reaction with halides and thiocyanate

Compound I of peroxidases takes part in both the peroxidation and the halogenation reaction. This study for the first time presents transient kinetic measurements of the formation of compound I of human eosinophil peroxidase (EPO) and its reaction with halides and thiocyanate, using the sequential-mixing stopped-flow technique. Addition of 1 equiv of hydrogen peroxide to native EPO leads to complete formation of compound I. At pH 7 and 15 degrees C, the apparent second-order rate constant is (4.3 +/- 0.4) x 10(7) M(-1) s(-1). The rate for compound I formation by hypochlorous acid is (5.6 +/- 0.7) x 10(7) M(-1) s(-1). EPO compound I is unstable and decays to a stable intermediate with a compound II-like spectrum. At pH 7, the two-electron reduction of compound I to the native enzyme by thiocyanate has a second-order rate constant of (1.0 +/- 0. 5) x 10(8) M(-1) s(-1). Iodide [(9.3 +/- 0.7) x 10(7) M(-1) s(-1)] is shown to be a better electron donor than bromide [(1.9 +/- 0.1) x 10(7) M(-1) s(-1)], whereas chloride oxidation by EPO compound I is extremely slow [(3.1 +/- 0.3) x 10(3) M(-1) s(-1)]. The pH dependence studies suggest that a protonated form of compound I is more competent in oxidizing the anions. The results are discussed in comparison with those of the homologous peroxidases myeloperoxidase and lactoperoxidase and with respect to the role of EPO in host defense and tissue injury.     

Effects of PM10 in human peripheral blood monocytes and J774 macrophages

Background

Asthma is characterized by type 2 T-helper cell (Th2) inflammation, goblet cell hyperplasia, airway hyperreactivity, and airway fibrosis. Monocyte chemoattractant protein-1 (MCP-1 or CCL2) and its receptor, CCR2, have been shown to play important roles in the development of Th2 inflammation. CCR2-deficient mice have been found to have altered inflammatory and physiologic responses in some models of experimental allergic asthma, but the role of CCR2 in contributing to inflammation and airway hyperreactivity appears to vary considerably between models. Furthermore, MCP-1-deficient mice have not previously been studied in models of experimental allergic asthma.

Methods

To test whether MCP-1 and CCR2 are each required for the development of experimental allergic asthma, we applied an Aspergillus antigen-induced model of Th2 cytokine-driven allergic asthma associated with airway fibrosis to mice deficient in either MCP-1 or CCR2. Previous studies with live Aspergillus conidia instilled into the lung revealed that MCP-1 and CCR2 play a role in anti-fungal responses; in contrast, we used a non-viable Aspergillus antigen preparation known to induce a robust eosinophilic inflammatory response.

Results

We found that wild-type C57BL/6 mice developed eosinophilic airway inflammation, goblet cell hyperplasia, airway hyperreactivity, elevations in serum IgE, and airway fibrosis in response to airway challenge with Aspergillus antigen. Surprisingly, mice deficient in either MCP-1 or CCR2 had responses to Aspergillus antigen similar to those seen in wild-type mice, including production of Th2 cytokines.

Conclusion

We conclude that robust Th2-mediated lung pathology can occur even in the complete absence of MCP-1 or CCR2.     

An edit script for taxonomic classifications

Background  

The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification.     

Oxidation of hydroquinone, 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone by human myeloperoxidase

Myeloperoxidase is very susceptible to reducing radicals because the reduction potential of the ferric/ferrous redox couple is much higher compared with other peroxidases. Semiquinone radicals are known to reduce heme proteins. Therefore, the kinetics and spectra of the reactions of p-hydroquinone, 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone with compounds I and II were investigated using both sequential-mixing stopped-flow techniques and conventional spectrophotometric measurements. At pH 7 and 15 degrees C the rate constants for compound I reacting with p-hydroquinone, 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone were determined to be 5.6+/-0.4 x 10(7) M(-1)s(-1), 1.3+/-0.1 x 10(6) M(-1)s(-1) and 3.1+/-0.3 x 10(6) M(-1)s(-1), respectively. The corresponding reaction rates for compound II reduction were calculated to be 4.5+/-0.3 x 10(6) M(-1)s(-1), 1.9+/-0.1 x 10(5) M(-1)s(-1) and 4.5+/-0.2 x 10(4) M(-1)s(-1), respectively. Semiquinone radicals, produced by compounds I and II in the classical peroxidation cycle, promote compound III (oxymyeloperoxidase) formation. We could monitor formation of ferrous myeloperoxidase as well as its direct transition to compound II by addition of molecular oxygen. Formation of ferrous myeloperoxidase is shown to depend strongly on the reduction potential of the corresponding redox couple benzoquinone/semiquinone. With 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone as substrate, myeloperoxidase is extremely quickly trapped as compound III. These MPO-typical features could have potential in designing specific drugs which inhibit the production of hypochlorous acid and consequently attenuate inflammatory tissue damage.     

Cytosolic isocitrate dehydrogenase in humans, mice, and voles and phylogenetic analysis of the enzyme family

In this study, we report cDNA sequences of the cytosolic NADP-dependent isocitrate dehydrogenase for humans, mice, and two species of voles (Microtus mexicanus and Microtus ochrogaster). Inferred amino acid sequences from these taxa display a high level of amino acid sequence conservation, comparable to that of myosin beta heavy chain, and share known structural features. A Caenorhabditis elegans enzyme that was previously identified as a protein similar to isocitrate dehydrogenase is most likely the NADP-dependent cytosolic isocitrate dehydrogenase enzyme equivalent, based on amino acid similarity to mammalian enzymes and phylogenetic analysis. We also suggest that NADP-dependent isocitrate dehydrogenases characterized from alfalfa, soybean, and eucalyptus are most likely cytosolic enzymes. The phylogenetic tree of various isocitrate dehydrogenases from eukaryotic sources revealed that independent gene duplications may have given rise to the cytosolic and mitochondrial forms of NADP-dependent isocitrate dehydrogenase in animals and fungi. There appears to be no statistical support for a hypothesis that the mitochondrial and cytosolic forms of the enzyme are orthologous in these groups. A possible scenario of the evolution of NADP-dependent isocitrate dehydrogenases is proposed.      

TBMap: a taxonomic perspective on the phylogenetic database TreeBASE

Background  

TreeBASE is currently the only available large-scale database of published organismal phylogenies. Its utility is hampered by a lack of taxonomic consistency, both within the database, and with names of organisms in external genomic, specimen, and taxonomic databases. The extent to which the phylogenetic knowledge in TreeBASE becomes integrated with these other sources is limited by this lack of consistency.     

Sampling beetle communities: Trap design interacts with weather and species traits to bias capture rates

Globally, many insect populations are declining, prompting calls for action. Yet these findings have also prompted discussion about sampling methods and interpretation of long‐term datasets. As insect monitoring and research efforts increase, it is critical to quantify the effectiveness of sampling methods. This is especially true if sampling biases of different methods covary with climate, which is also changing over time. We assess the effectiveness of two types of flight intercept traps commonly used for beetles, a diverse insect group responsible for numerous ecosystem services, under different climatic conditions in Norwegian boreal forest. One of these trap designs includes a device to prevent rainwater from entering the collection vial, diluting preservatives and flushing out beetles. This design is compared to a standard trap. We ask how beetle capture rates vary between these traps, and how these differences vary based on precipitation levels and beetle body size, an important species trait. Bayesian mixed models reveal that the standard and modified traps differ in their beetle capture rates, but that the magnitude and direction of these differences change with precipitation levels and beetle body size. At low rainfall levels, standard traps catch more beetles, but as precipitation increases the catch rates of modified traps overtake those of standard traps. This effect is most pronounced for large‐bodied beetles. Sampling methods are known to differ in their effectiveness. Here, we present evidence for a less well‐known but likely common phenomenon—an interaction between climate and sampling, such that relative effectiveness of trap types for beetle sampling differs depending on precipitation levels and species traits. This highlights a challenge for long‐term monitoring programs, where both climate and insect populations are changing. Sampling methods should be sought that eliminate climate interactions, any biases should be quantified, and all insect datasets should include detailed methodological metadata.     

Perennial Biomass Grasses and the Mason–Dixon Line: Comparative Productivity across Latitudes in the Southern Great Plains

Understanding latitudinal adaptation of switchgrass (Panicum virgatum L.) and Miscanthus (Miscanthus?×?giganteus J. M. Greef & Deuter ex Hodk. & Renvoize) to the southern Great Plains is key to maximizing productivity by matching each grass variety to its optimal production environment. The objectives of this study were: (1) to quantify latitudinal variation in production of representative upland switchgrass ecotypes (Blackwell, Cave-in-Rock, and Shawnee), lowland switchgrass ecotypes (Alamo, Kanlow), and Miscanthus in the southern half of the US Great Plains and (2) to investigate the environmental factors affecting yield variation. Leaf area and yield were measured on plots at 10 locations in Missouri, Arkansas, Oklahoma, and Texas. More cold winter days led to decreased subsequent Alamo switchgrass yields and increased subsequent upland switchgrass yields. More hot-growing season days led to decreased Kanlow and Miscanthus yields. Increased drought intensity also contributed to decreased Miscanthus yields. Alamo switchgrass had the greatest radiation use efficiency (RUE) with a mean of 4.3 g per megajoule intercepted PAR and water use efficiency (WUE) with a mean of 4.5 mg of dry weight per gram of water transpired. The representative RUE values for other varieties ranged from 67 to 80 % of Alamo’s RUE value and 67 to 87 % of Alamo’s WUE. These results will provide valuable inputs to process-based models to realistically simulate these important perennial grasses in this region and to assess the environmental impacts of production on water use and nutrient demands. In addition, it will also be useful for landowners and companies choosing the most productive perennial grasses for biofuel production.     

Loss of meiosis in Aspergillus

If strictly mitotic asexual fungi lack recombination, the conventional view predicts that they are recent derivatives from older meiotic lineages. We tested this by inferring phylogenetic relationships among closely related meiotic and strictly mitotic taxa with Aspergillus conidial (mitotic) states. Phylogenies were constructed by using DNA sequences from the mitochondrial small ribosomal subunit, the nuclear ribosomal internal transcribed spacers, and the nuclear 5.8S ribosomal gene. Over 920 bp of sequence was analyzed for each taxon. Phylogenetic analysis of both the mitochondrial and nuclear data sets showed at least four clades that possess both meiotic and strictly mitotic taxa. These results support the hypothesis that strictly mitotic lineages arise frequently from more ancient meiotic lineages with Aspergillus conidial states. Many of the strictly mitotic species examined retained characters that may be vestiges of a meiotic state, including the production of sclerotia, sclerotium-like structures, and hulle cells.