Influence of two management practices in the Canadian Prairies on radiative forcing.

Surface albedo and soil carbon sequestration are influenced by agricultural management practices which impact the Earth's radiation budget and climate change. In this study we investigate the impact of reduced summer fallowing and reduced tillage in the Canadian Prairies on climate change by estimating the change in radiative forcing due to albedo and soil carbon sequestration. Seasonal variations of albedo, which are dependent on agricultural management practices and soil colour in three soil zones, were derived from 10-day composite 250-m Moderate Resolution Imaging Spectroradiometer (MODIS) data. Using this information, we found an overall increase of surface albedo due to the conversion from summer fallowing to continuous cropping and from conventional tillage (CT) to either no-tillage (NT) or reduced tillage (RT). The increase was dependent on soil brightness, type of vegetation and snow cover. Using data from the Census of Agriculture and taking into consideration both albedo and soil carbon changes, we estimated that from 1981 to 2016, the total radiative forcing for the cropland area in the Canadian Prairies was -405 µW m-2 due to the conversion of CT to either NT or RT and about 70% was due to the change in albedo. During the same period, the total radiative forcing was -410 µW m-2 due to a reduction in the area under summer fallow and about 62% was due to the change in albedo. The equivalent atmospheric CO2 drawdown from these two management changes from albedo change was about 7.8 and 8.7 Tg CO2 yr-1, respectively. These results demonstrate that it is important to consider both the changes of soil carbon and surface albedo in evaluating climate change impacts due to agricultural management practices.

Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.

First Report of Damping-Off of Durum Wheat Caused by Arthrinium sacchari in the Semi-Arid Saskatchewan Fields.

Durum wheat (Triticum durum Desf.) is an important crop in western Canada. In 2005, Arthrinium sacchari was frequently isolated from soil and durum wheat plants of the semi-arid fields of Swift Current, Saskatchewan, Canada (50°16'N, 107°44'W). The susceptibility of durum wheat to damping-off caused by this fungus was evaluated. To our knowledge, this is the first report of A. sacchari in North America (1) and the first mention of its association with durum wheat. DNA was extracted (MoBio Isolation Kit, Carlsbad, CA) from 2-week-old A. sacchari isolates (FBC.3, FBC.45, and FBC.143) grown on PDA. The internal transcribed spacer (ITS) of the rDNA was amplified from each isolate and sequenced (Plant Biotechnology Institute, Saskatoon, SK, Canada) and similarity analyses were performed using the BLAST search algorithm in GenBank. All three sequences (Accession Nos. EF076710, EF076711, and EF076712A) showed 99% similarity with A. sacchari (Accession No. AF393679). An in vitro assay was performed by placing 1-cm2 agar plugs containing mycelia of A. sacchari (FBC.3, FBC.45, and FBC.143) onto surface-sterilized durum. Surface-sterilized seeds inoculated in the same way with Fusarium graminearum or F. avenaceum were used as negative controls, and noninoculated surface-sterilized seeds were used as a positive control. A second in vitro assay involved inoculating the same isolates onto seeds placed in sterilized sandy soil. In both assays, 10 seeds per petri plate and three plates per treatment were used and plates were incubated at 21°C for 1 week in darkness. All experiments were performed twice. On PDA, preemergence damping-off was found in 60% of A. sacchari FBC.3, 55% of A. sacchari FBC.45 and FBC.143, 50% of F. avenaceum, and 58% of F. graminearum inoculated seeds. In sterilized soil, the incidence of preemergence damping-off ranged from 43 to 30%. Subsequent incubation over a period of 3 weeks resulted in 100% postemergence damping-off in A. sacchari FBC.45 and FBC.3 as well as in both Fusarium spp. inoculated controls, 60% postemergence damping-off in A. sacchari FBC.143, and no damping-off in the noninoculated control. Arthrinium and Fusarium spp. were reisolated only from symptomatic plants, satisfying Koch's postulates. In conclusion, durum wheat is highly susceptible to damping-off caused by A. sacchari, showing characteristic dark brown or violet lesions in infected tissues. A. sacchari was previously reported to be present in South America and eastern Asia. In China, it is considered an important mycotoxigenic species (2). Thus, infection of durum wheat crops with A. sacchari could pose a significant threat to North American wheat production. References: (1) D. F. Farr et al. Fungal Databases. Systematic Botany and Mycology Laboratory. Online publication. ARS, USDA, 2006. (2) X. J. Liu et al. Acta Mycol. Sinica 7:221, 1988.

Systems level modeling of the cell cycle using budding yeast.

Proteins involved in the regulation of the cell cycle are highly conserved across all eukaryotes, and so a relatively simple eukaryote such as yeast can provide insight into a variety of cell cycle perturbations including those that occur in human cancer. To date, the budding yeast Saccharomyces cerevisiae has provided the largest amount of experimental and modeling data on the progression of the cell cycle, making it a logical choice for in-depth studies of this process. Moreover, the advent of methods for collection of high-throughput genome, transcriptome, and proteome data has provided a means to collect and precisely quantify simultaneous cell cycle gene transcript and protein levels, permitting modeling of the cell cycle on the systems level. With the appropriate mathematical framework and sufficient and accurate data on cell cycle components, it should be possible to create a model of the cell cycle that not only effectively describes its operation, but can also predict responses to perturbations such as variation in protein levels and responses to external stimuli including targeted inhibition by drugs. In this review, we summarize existing data on the yeast cell cycle, proteomics technologies for quantifying cell cycle proteins, and the mathematical frameworks that can integrate this data into representative and effective models. Systems level modeling of the cell cycle will require the integration of high-quality data with the appropriate mathematical framework, which can currently be attained through the combination of dynamic modeling based on proteomics data and using yeast as a model organism.

Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure.

MOTIVATION: Geometric representations of proteins and ligands, including atom volumes, atom-atom contacts and solvent accessible surfaces, can be used to characterize interactions between and within proteins, ligands and solvent. Voronoi algorithms permit quantification of these properties by dividing structures into cells with a one-to-one correspondence with constituent atoms. As there is no generally accepted measure of atom-atom contacts, a continuous analytical representation of inter-atomic contacts will be useful. Improved geometric algorithms will also be helpful in increasing the speed and accuracy of iterative modeling algorithms. RESULTS: We present computational methods based on the Voronoi procedure that provide rapid and exact solutions to solvent accessible surfaces, volumes, and atom contacts within macromolecules. Furthermore, we define a measure of atom-atom contact that is consistent with the calculation of solvent accessible surfaces, allowing the integration of solvent accessibility and inter-atomic contacts into a continuous measure. The speed and accuracy of the algorithm is compared to existing methods for calculating solvent accessible surfaces and volumes. The presented algorithm has a reduced execution time and greater accuracy compared to numerical and approximate analytical surface calculation algorithms, and a reduced execution time and similar accuracy to existing Voronoi procedures for calculating atomic surfaces and volumes.

Fractional simplex designs for interaction screening in complex mixtures.

In mixture experiments, one may be interested in estimating not only main effects but also some interactions. Main effects and significant interactions in a mixture may be estimated through appropriate mixture experiments, such as simplex-centroid designs. However, for mixtures with a large number of factors, the run size for these designs becomes impractically large. A subset of a full simplex-centroid design may be used, but the problem remains regarding which factor-level settings should be selected. In this paper, we propose a solution that considers design points with either one or p individual nonzero factor-level settings. These fractional simplex designs provide a means of screening for interactions and of investigating the behavior of many-component mixtures as a whole while greatly reducing the run size compared with full simplex-centroid designs. The means of construction of the design arrays is described, and designs for < or = 31 factors are presented. Some of the proposed methodology is illustrated using generated data.

Impacts of structural photomodification on the toxicity of environmental contaminants: anthracene photooxidation products.

The toxicity of polycyclic aromatic hydrocarbons (PHAs) is known to be enhanced by light via photosensitization reactions (production of active oxygen) and photomodification of the chemicals (e.g., oxidation) to more toxic compounds. Anthracene (ANT) toxicity in particular has been found to increase dramatically following photomodification. The objective of this study was to identify the photooxidation products of ANT and assess the toxicity of selected photoproducts. High performance liquid chromatography (HPLC) analysis of anthracene photooxidation revealed a complex array of oxidation products; prevalent among these were anthraquinone (ATQ) and hydroxy-anthraquinones (hATQs). Eleven of these compounds were tested for toxicity using growth inhibition of the duckweed Lemna gibba L. G-3. All but one of the compounds tested were found to be toxic, and when UV radiation was present in the light source toxicity was generally enhanced. The chemicals were also irradiated under SSR prior to toxicity testing. In about half the cases, the ATQ compounds were rapidly photooxidized and the resultant photoproducts were more toxic than the parent compounds. Interestingly, 2-hydroxyanthraquinone, which was not subject to photooxidation, was the most toxic of the compounds tested. As a light stable compound it presents the risk of a persistent environmental hazard.

Photoinduced toxicity of three polycyclic aromatic hydrocarbons (fluoranthene, pyrene, and naphthalene) to the duckweed Lemna gibba L. G-3.

The authors recently demonstrated that light dramatically enhances the hazards of three polycyclic aromatic hydrocarbons (PAHs), anthracene, phenanthrene, and benzo[a]pyrene, to the duckweed Lemna gibba L. G-3 (X.-D. Huang, D. G. Dixon, and B. M. Greenberg, 1993, Environ. Toxicol. Chem., 12, 1067-1077). To extend this research, growth and chlorosis were used as end points to assess the photoinduced toxicity of three additional PAHs, fluoranthene, pyrene, and naphthalene, to L. gibba in the presence of simulated solar radiation (a light source with a UV-B: UV-A:visible light ratio equivalent to that of sunlight). The phytotoxicity of these three PAHs was photoactivated, with ultraviolet radiation being the only spectral region that enhanced the harmful effects of the chemicals. Dose-response curves based on chemical concentration and light intensity revealed that the order of phytotoxic strength was fluoranthene > pyrene > naphthalene. To explore whether photomodification (in addition to photosensitization) of fluoranthene, pyrene, and naphthalene could contribute to photoinduced toxicity, the chemicals were irradiated prior to (as opposed to simultaneously with) application to the plans. The rates of photomodification of the three PAHs were rapid enough for the photooxidized compounds to contribute to toxicity, and the photomodified PAHs were more toxic than the parent compounds. As well, toxicity could be correlated to photomodification; impacts increased in parallel with the extent of photomodification.

Glomerulonephritis in rheumatoid arthritis.

We present data on 10 patients with RA who developed glomerulonephritis which was not related to gold or penicillamine therapy. Although two of these patients had received gold this had been discontinued 13 and 18 yr before the diagnosis of glomerulonephritis. Seven patients presented with nephrotic syndrome and three with proteinuria and microscopic haematuria. Renal histology showed a membranous nephropathy (five patients), mesangial IgA nephropathy (two patients), focal segmental necrotizing glomerulonephritis (two patients) and focal segmental glomerulosclerosis (one patient).

Disease-modifying antirheumatic drugs: gold, penicillamine, antimalarials, and sulfasalazine.

In the assessment of the effects of disease-modifying antirheumatic drugs, three or four clinical measurements supported by the erythrocyte sedimentation rate, and sometimes radiographs, are generally agreed to be correct. Some advocate functional assessments also, or even alternatively. Several studies compared gold, penicillamine, antimalarials, and sulfasalazine either with each other or with placebo, and occasionally with methotrexate. No important differences between the general performance of the four drugs were found. More work was reported on sulfasalazine than on the other three drugs; the data support that it has a place in our armamentarium. Several important contributions concerned strategies of treatment. It is considered that disease-modifying antirheumatic drugs should be used earlier and more aggressively in rheumatoid arthritis. This aspect was perhaps the key note of the 1990 literature on this topic. As part of the new strategies, combination therapy is urged by some rheumatologists, whereas others urge caution on the grounds that we do not yet know enough about the effects of combinations, or by how much the risks of adverse effects are increased in combination.

Chain breaking antioxidant status in rheumatoid arthritis: clinical and laboratory correlates.

The ability of fresh sera to resist attack by peroxyl radicals (TRAP) was found to be significantly lower in 20 patients with rheumatoid arthritis (RA) than in 20 healthy controls, consistent with the existence of a redox stress in RA imposed by inflammation. TRAP values in RA varied inversely with a combination of visual analogue pain scale, duration of early morning stiffness, grip strength, and articular index (reflecting inflammatory activity) using multiple linear regression analysis. The concentration of the antioxidant vitamin ascorbic acid was lower in RA plasma and the oxidation-reduction equilibrium of ascorbic acid was disturbed, giving further support to the existence of a redox stress. The major determinant of TRAP in vitro was found to be serum uric acid in RA and serum vitamin E in controls. Serum urate concentration in RA correlated inversely with oxidative changes in serum albumin and IgG. It is suggested that serum urate might have an antioxidant role under certain conditions by limiting free radical induced oxidative changes to protein during inflammation.

Clinical and laboratory effects of prolonged therapy with sulfasalazine, gold or penicillamine: the effects of disease duration on treatment response.

Serial observations for up to 5 years of clinical score (a subjective global assessment), serum C-reactive protein (CRP) and the erythrocyte sedimentation rate (ESR) were analyzed in 3 groups of patients with active rheumatoid arthritis (RA) requiring treatment with a second line drug. The groups comprised 315 patients (243 women, 72 men) who had sulfasalazine (SAS); 203 patients (141 women, 62 men) who had sodium aurothiomalate (gold) and 163 patients (131 women, 32 men) who had penicillamine. The groups matched in most respects but the gold group had a smaller proportion of women, a shorter median disease duration and a higher median CRP than the remaining 2 groups. The penicillamine group contained a higher proportion of seropositive patients. In each group there were significant improvements in clinical score, CRP and ESR for all time points from 6 to 30 months; these improvements were maintained for longer (up to 60 months for SAS) in the SAS and gold groups but the differences between the drugs after 30 months were probably a consequence of falling number of patients, not differing drug potencies. The mean ESR and CRP levels fell to about 30 mm/h and 20-30 mg/l, respectively. Response was defined as (1) treatment duration greater than 6 months, (2) clinical score improvement greater than 4 by 6 months, (3) ESR fall to less than 30 mm/h by 6 months. By these criteria 142 of 681 patients (20.9%) responded; the response rates were SAS 20.3%, gold 24.1%, penicillamine 17.8%.(ABSTRACT TRUNCATED AT 250 WORDS)

Measurement of conjugated diene lipids by derivative spectroscopy in heptane extracts of plasma.

A series of experiments are described which show that second derivative spectroscopy can be used to quantify conjugated lipid dienes as markers of lipid peroxidation in heptane extracts of plasma from patients with rheumatoid arthritis, osteoarthritis, and healthy controls. Results obtained by this method gave reasonable agreement with those derived from the measurement of simple absorbance in chloroform/methanol extracts. Two minima were observed in the derivative spectrum of plasma lipid extracts. These minima occurred at 233 and 241 nm and corresponded to absorbance maxima in the conventional UV spectrum. Using a combination of phospholipase hydrolysis, reverse phase high performance liquid chromatography (HPLC) and second derivative spectroscopy we confirmed that these two minima can be attributed to a single fatty acid (9 cis-, 11 trans-linoleic acid) shown previously to account for greater than 90% of diene conjugation in human plasma samples. When the biological isomer 9 cis-, 11 trans-linoleic acid was separated by reverse phase HPLC from the mixture of other plasma phospholipid-2-esterified fatty acids we observed a change in derivative spectroscopy minima from 233 and 241 nm to 228 and 237 nm. Minima at the latter two wavelengths were also seen with pure preparations of the Paint Research Isomer (9 trans-, 11 trans-linoleic acid) which eluted later than biological 9 cis-, 11 trans-linoleic acid using reverse phase HPLC, suggesting that the absorption spectra of these pure cis-, trans and trans, trans dienes are similar but can be altered by the presence of other fatty acids in the extract.

It is said that elevated erythrocyte sedimentation rate and the elevation of C-reactive protein (CRP) may be indicators of continuing joint destruction in rheumatoid arthritis. What then is the explanation for joint destruction in some patients in whom there is no such apparent elevation of either the sedimentation rate of CRP?

It is said that elevated erythrocyte sedimentation rate and the elevation of C-reactive protein (CRP) may be indicators of continuing joint destruction in rheumatoid arthritis. What then is the explanation for joint destruction in some patients in whom there is no such apparent elevation of either the sedimentation rate or CRP?