Evolution of bacterial communities in the wheat crop rhizosphere

The gap between current average global wheat yields and that achievable through best agronomic management and crop genetics is large. This is notable in intensive wheat rotations which are widely used. Expectations are that this gap can be reduced by manipulating soil processes, especially those that involve microbial ecology. Cross‐year analysis of the soil microbiome in an intensive wheat cropping system revealed that rhizosphere bacteria changed much more than the bulk soil community. Dominant factors influencing populations included binding to roots, plant age, site and planting sequence. We demonstrated evolution of bacterial communities within the field rhizosphere. Early in the season, communities tightly bound to the root were simplest. These increased in diversity with plant age and senescence. Loosely bound communities also increased in diversity from vegetative to reproductive plant stages but were more stable than those tightly bound to roots. Planting sequence and, to a lesser extent, wheat genotype also significantly affected rhizosphere bacteria. Plasticity in the rhizosphere generated from crop root system management and genetics offers promise for manipulating the soil ecology of intense cereal systems. Analyses of soil microbiomes for the purpose of developing agronomic benefit should include roots as well as soil loosely adhered to the roots, and the bulk soil.     

Human macrophage migration inhibitory factor: a proven immunomodulatory cytokine?

Macrophage migration inhibitory factor (MIF) is a pro-inflammatory mediator with the ability to induce various immunomodulatory responses and override glucocorticoid-driven immunosuppression. Some of these functions have been linked to the unusual enzymatic properties of the protein, namely tautomerase and oxidoreductase activities. However, there are conflicting reports regarding the functional role of these enzymatic properties in normal physiological homeostasis and disease progression. Therefore, we have produced a highly pure, virtually endotoxin-free recombinant MIF preparation and fully characterized this using a variety of biochemical and biophysical approaches. The recombinant protein, with demonstrable enzymatic activity, was then used to systematically examine the biological activity of MIF. Surprisingly, treatment with MIF alone failed to induce cytokine expression, with the exception of IL-8. However, co-treatment of lipopolysaccharide (LPS) in conjunction with MIF produced synergistic secretion of tumor necrosis factor-alpha, interleukin (IL)-1, and IL-8 compared with LPS alone. The potentiating effect of MIF was seen at physiologically relevant concentrations. These data suggest that MIF has no conventional cytokine activity but, rather, acts to modulate and amplify the response to LPS.     

Network analysis identifies protein clusters of functional importance in juvenile idiopathic arthritis

Introduction

Our objective was to utilise network analysis to identify protein clusters of greatest potential functional relevance in the pathogenesis of oligoarticular and rheumatoid factor negative (RF-ve) polyarticular juvenile idiopathic arthritis (JIA).

Methods

JIA genetic association data were used to build an interactome network model in BioGRID 3.2.99. The top 10% of this protein:protein JIA Interactome was used to generate a minimal essential network (MEN). Reactome FI Cytoscape 2.83 Plugin and the Disease Association Protein-Protein Link Evaluator (Dapple) algorithm were used to assess the functionality of the biological pathways within the MEN and to statistically rank the proteins. JIA gene expression data were integrated with the MEN and clusters of functionally important proteins derived using MCODE.

Results

A JIA interactome of 2,479 proteins was built from 348 JIA associated genes. The MEN, representing the most functionally related components of the network, comprised of seven clusters, with distinct functional characteristics. Four gene expression datasets from peripheral blood mononuclear cells (PBMC), neutrophils and synovial fluid monocytes, were mapped onto the MEN and a list of genes enriched for functional significance identified. This analysis revealed the genes of greatest potential functional importance to be PTPN2 and STAT1 for oligoarticular JIA and KSR1 for RF-ve polyarticular JIA. Clusters of 23 and 14 related proteins were derived for oligoarticular and RF-ve polyarticular JIA respectively.

Conclusions

This first report of the application of network biology to JIA, integrating genetic association findings and gene expression data, has prioritised protein clusters for functional validation and identified new pathways for targeted pharmacological intervention.     

Soil Profile Arsenic Concentration Distributions in Missouri Soils Having Cambic and Argillic Soil Horizons

Understanding of the pedogenic pathways associated with arsenic (As) transformations in soil is important to understanding arsenic soil chemistry and discriminating between natural background and anthropogenic arsenic (As). Twenty-one soil series, some with multiple pedons, were assessed to determine if the As distributions in soil profiles exhibit discrete maxima that correspond to the presence of agrillic horizons. The majority of pedons exhibiting argillic horizon expression show a Fe-oxyhydroxide and As maxima corresponding precisely with the argillic horizon. Pearson correlation coefficients verify the close correspondence of Fe and As. Soil profiles having cambic horizons, and lacking argillic horizons, may also show As and Fe accumulations at soil depths. Some coarse-textured, well-drained to moderately well-drained Entisols and Inceptisols have Fe-oxyhydroxide accumulation in their cambic horizons, promoting As accumulation. Conversely, silty-textured and poorly drained to somewhat poorly drained Entisols and Inceptisols have C and Cg horizons that show somewhat uniform Fe and As concentrations throughout their soil profiles. Analysis of selected pedons having well-drained to moderately well-drained soil profiles demonstrates that clay fraction Fe and As concentrations are closely correlated and that the As and Fe concentrations are greater than those from the corresponding whole soil. The somewhat poorly drained Crowley pedon exhibited cohesive masses of Fe and Mn accumulation (sand separate) that had greater arsenic concentrations than those of the clay and silt separates. These pedogenic nodules with enhanced arsenic concentrations reveal alternative pathways involving arsenic transformation.     

Extracellular fibril production by freshwater algae and cyanobacteria

In order to study the ability of freshwater algae and cyanobacteria to form extracellular fibrils, a screening test using ruthenium red (RR) staining was carried out on 28 species. Five of these were examined for growth and production of fibrillar material in culture media of different phosphate (P;) contents. RR-staining and uronic acid determinations at various stages of algal growth were complemented by electron microscopy of the cells and of fibrillar material released into the medium. The lower P_i concentrations enhanced growth of Micrasterias radiata, Eremosphaera sp., and Microcystis aeruginosa, and had little or no effect on growth of a Xanthidium sp. and Scenedesmus quadricauda. Extracellular uronic acid production, which was higher in low P_i medium in M. radiata, M. aeruginosa, and Xanthidium sp., could reach levels of 50 mg/liter or more. Algae with high proportions of RR-positive cells (M. radiata, Eremosphaera sp., Xanthidium sp., and M. aeruginosa) produced high levels of slime-like material and distinct fibrils that were often seen attached to the cell surface and only slowly released into the medium. No such material was found in cultures (or supernatants) of Sc. quadricauda, which also produced relatively low amounts of polyuronic acids. Specific types of filaments, often forming fascicles with rectangular arrays of globular particles were observed by negative staining electron microscopy of some algal cultures. RR-positive material was also observed in the cytoplasm and on the cell walls and surfaces of M. radiata and M. aeruginosa.Offprint requests to: D. J. Kushner.     

Hydrilla control with split treatments of fluridone in Lake Harris, Florida

After several unsuccessful management efforts, a split treatment of fluridone was applied to the 6700 ha Lake Harris in March and June 1987, at a rate of 3.4 kg ha^–1 (680 and 340 kg fluridone, respectively) to two 3 m deep, hydrilla-infested bays. Fluridone concentrations in the water were sampled following the June treatment. Average fluridone concentrations were 2.1 µg l^–1 prior to this second application, and a maximum concentration of 30.2 µg l^–1 was detected in the treated area on the day following application. Fluridone residues dissipated out of the plot quickly due to dilution but concentrations declined lake-wide more slowly, following a logarithmic model, with an estimated fluridone half-life of 97 days. Control of hydrilla in Lake Harris resulted from the long exposure (over 25 weeks due to the split application) to fluridone concentrations of 2 µg l^–1, well below the maximum labelled rate of 150 µg l^–1.     

Biofeedback applications to migraine and tension headaches: A double-blinded outcome study

The efficacy of progressive relaxation, fingertip temperature training, and EMG training of the frontalis muscles was tested against chronic migraine and tension headaches in a double-blinded 3×2 design. All 56 subjects reported being conditioned in the course of the nine 1/2-hour training sessions. Detailed records of perceived severity and duration of the headaches were maintained by the subjects before the study and for at least 3 months after the training period. While even a conservativeF revealed a diminution of perceived severity, of hours/month of headache, and of an index conceived by Budzynski, Stoyva, Adler, and Mullaney (1973), across time, at beyond the .05 level of significance, no specific treatment emerged as clearly most effective for either type of headache. Over time, however, progressive relaxation was not as good as the other procedures in reducing the number of hours/month of headache.     

Chromosomal abnormalities in maternal and fetal tissues of magnesium- or zinc-deficient rats.

The effect of dietary deficiency during pregnancy of zinc or magnesium on maternal and fetal chromosomes was studied. Pregnant rats were given a zinc-deficient or a magnesium-deficient diet from the beginning of pregnancy and maternal bone marrow and fetal liver were removed on day 19 of gestation. Chromosome spreads were prepared and metaphases examined for abnormalities. Both magnesium- and zinc-deficient maternal bone-marrow and fetal liver cells showed significantly more chromosomal abnormalities than did those of controls. The chromosomal aberrations occurring in highest incidence in magnesium-deficient animals were terminal deletions and fragments. A higher than normal incidence of "stickiness" was also observed in cells from magnesium-deficient animals. In zinc-deficient animals, on the other hand, the chromosomal aberrations with the highest incidence were gaps and terminal deletions.     

Validation of an LC‐MS based approach for profiling histones in chronic lymphocytic leukemia

The in vitro evaluation of histones and their PTMs has drawn substantial interest in the development of epigenetic therapies. The differential expression of histone isoforms may serve as a potential marker in the classification of diseases affected by chromatin abnormalities. In this study, protein profiling by LC and MS was used to explore differences in histone composition in primary chronic lymphocytic leukemia (CLL) cells. Extensive method validations were performed to determine the experimental variances that would impact histone relative abundance. The resulting data demonstrated that the proposed methodology was suitable for the analysis of histone profiles. In 4 normal individuals and 40 CLL patients, a significant decrease in the relative abundance of histone H2A variants (H2AFL and H2AFA/M*) was observed in primary CLL cells as compared to normal B cells. Protein identities were determined using high mass accuracy MS and shotgun proteomics.     

Toxicity,persistence, and efficacy of spinosad,chlorfenapyr, and thiamethoxam on eggplant when applied against the eggplant flea beetle (Coleoptera: Chrysomelidae)

A laboratory bioassay was developed for determining the toxicity of spinosad, chlorfenapyr, and thiamethoxam against the eggplant flea beetle, Epitrix fuscula Crotch, on eggplant foliage. Four days after initial exposure, LC50 values were 1.99, 2.50, and 0.88 ppm for spinosad, chlorfenapyr, and thiamethoxam, respectively. By dividing the recommended field rate in ppm by the LC50 value, a field toxicity ratio was determined and ranged from 13.5 for spinosad to 73.9 for thiamethoxam. The high ratios suggest that field rates for all three insecticides could likely be reduced. This was supported by field studies in 2000 in which reduced rates of spinosad and thiamethoxam significantly reduced flea beetle numbers on eggplant. Mortality produced by thiamethoxam occurred more quickly than that for the other tested materials as shown with LT50 values of 1.8, 3.0, and 3.6 and days for thiamethoxam, chlorfenapyr, and spinosad, respectively. Persistence studies indicated that while all three of the tested compounds initially produced high levels of mortality, chlorfenapyr and thiamethoxam produced 50% or greater mortality after 6 d. Our data suggest that future management strategies for E. fuscula on eggplant can be successfully altered to meet the changing needs of the producer. Spinosad was recently registered, is effective against the E. fuscula, and offers a viable alternative to carbamate and pyrethroid insecticides. Thiamethoxam and chlorfenapyr offer high levels of toxicity to E. fuscula and upon registration will offer additional effective tools for management.