Spreadsheet Method for Evaluation of Biochemical Reaction Rate Coefficients and Their Uncertainties by Weighted Nonlinear Least-Squares Analysis of the Integrated Monod Equation

A convenient method for evaluation of biochemical reaction rate coefficients and their uncertainties is described. The motivation for developing this method was the complexity of existing statistical methods for analysis of biochemical rate equations, as well as the shortcomings of linear approaches, such as Lineweaver-Burk plots. The nonlinear least-squares method provides accurate estimates of the rate coefficients and their uncertainties from experimental data. Linearized methods that involve inversion of data are unreliable since several important assumptions of linear regression are violated. Furthermore, when linearized methods are used, there is no basis for calculation of the uncertainties in the rate coefficients. Uncertainty estimates are crucial to studies involving comparisons of rates for different organisms or environmental conditions. The spreadsheet method uses weighted least-squares analysis to determine the best-fit values of the rate coefficients for the integrated Monod equation. Although the integrated Monod equation is an implicit expression of substrate concentration, weighted least-squares analysis can be employed to calculate approximate differences in substrate concentration between model predictions and data. An iterative search routine in a spreadsheet program is utilized to search for the best-fit values of the coefficients by minimizing the sum of squared weighted errors. The uncertainties in the best-fit values of the rate coefficients are calculated by an approximate method that can also be implemented in a spreadsheet. The uncertainty method can be used to calculate single-parameter (coefficient) confidence intervals, degrees of correlation between parameters, and joint confidence regions for two or more parameters. Example sets of calculations are presented for acetate utilization by a methanogenic mixed culture and trichloroethylene cometabolism by a methane-oxidizing mixed culture. An additional advantage of application of this method to the integrated Monod equation compared with application of linearized methods is the economy of obtaining rate coefficients from a single batch experiment or a few batch experiments rather than having to obtain large numbers of initial rate measurements. However, when initial rate measurements are used, this method can still be used with greater reliability than linearized approaches.     

A Test of Two Annual Cover Crops for Controlling Phalaris arundinacea Invasion in Restored Sedge Meadow Wetlands

Abstract Rapid establishment by aggressive plants such as Phalaris arundinacea (reed canarygrass) often interferes with sedge meadow establishment in restored prairie pothole wetlands in the mid‐continental United States. Introducing a cover crop during community establishment might suppress P. arundinacea invasion in restored prairie potholes by reducing resource availability. We evaluated two potential cover crops, Echinochloa crusgalli (barnyardgrass) and Polygonum lapathifolium (nodding smartweed), for suppressing P. arundinacea invasion in an experimental wetland using replacement series competition experiments. Further, we assessed the effects of E. crusgalli and P. lapathifolium on sedge meadow establishment by sowing Carex hystericina, a common wetland sedge, as a third species at a constant density in the replacement experiments. Echinochloa crusgalli, compared with no cover crop, reduced P. arundinacea biomass by more than 1,000 g/m² (65%) after two growing seasons. Polygonum lapathifolium did not affect P. arundinacea biomass. Dense E. crusgalli canopies in the first year and thick E. crusgalli thatch in the second year substantially reduced light availability for P. arundinacea establishment. Echinochloa crusgalli also reduced C. hystericina biomass by more than 1,800 g/m² (99%) after two growing seasons. Carex hystericina biomass was similar in plots sown with E. crusgalli to P. arundinacea monocultures. Neither E. crusgalli nor P. lapathifolium is likely to improve sedge meadow restoration success. These trends were not sensitive to initial sowing density or elevation above water level. Without methods to suppress P. arundinacea invasions, sedge meadow restorations may often fail. Thorough site preparation to remove P. arundinacea propagule sources before restoration is essential.     

QTL mapping of partial resistance in winter wheat to Stagonospora nodorum blotch.

Stagonospora nodorum blotch is an important foliar and glume disease in cereals. Inheritance of resistance in wheat appears to be quantitative. To date, breeding of partially resistant cultivars has been the only effective way to combat this pathogen. The partial resistance components, namely length of incubation period, disease severity, and length of latent period, were evaluated on a population of doubled haploids derived from a cross between the partially resistant Triticum aestivum 'Liwilla' and susceptible Triticum aestivum 'Begra'. Experiments were conducted in a controlled environment and the fifth leaf was examined. Molecular analyses were based on bulked segregant analyses using 240 microsatellite markers. Four QTLs were significantly associated with partial resistance components and were located on chromosomes 2B, 3B, 5B, and 5D. The percentage of phenotypic variance explained by a single QTL ranged from 14 to 21% for incubation period, from 16 to 37% for disease severity, and from 13 to 28% for latent period,     

Structural characterization of the lipopolysaccharide O-polysaccharide antigen produced by Flavobacterium columnare ATCC 43622.

The structure of the antigenic O-chain polysaccharide of Flavobacterium columnare ATCC 43622, a Gram-negative bacterium that causes columnaris disease in warm water fish, was determined by high-field 1D and 2D NMR techniques, MS, and chemical analyses. The O-chain was shown to be an unbranched linear polymer of a trisaccharide repeating unit composed of 2-acetamido-2-deoxy-d-glucuronic acid (d-GlcNAcA), 2-acetamidino-2,6-dideoxy-l-galactose (l-FucNAm) and 2-acetamido-2,6-dideoxy-d-xylo-hexos-4-ulose (d-Sug) (1 : 1 : 1), having the structure: [structure: see text].     

Structural analysis of the lipopolysaccharide from the nontypable Haemophilus influenzae strain SB 33.

The structure of the core region of the lipopolysaccharide (LPS) from the nontypable Haemophilus influenzae strain SB 33 was elucidated. The LPS was subjected to a variety of degradative procedures. The structures of the derived oligosaccharide products were established by monosaccharide and methylation analyses, NMR spectroscopy and mass spectrometry. These analyses revealed a series of related phosphocholine (PCho) containing structures differing in the number of hexose residues. The results pointed to each species containing a conserved phosphoethanolamine (PEtn) substituted heptose-containing trisaccharide inner-core moiety. The major LPS glycoforms were identified as 2-Hex, 3-Hex and 4-Hex species according to the number of hexose residues present.     

Osmoregulatory Responses of Fungi Inhabiting Standing Litter of the Freshwater Emergent Macrophyte Juncus effusus

Standing litter of emergent macrophytes often forms a major portion of the detrital mass in wetland habitats. Microbial assemblages inhabiting this detritus must adapt physiologically to daily fluctuations in temperature and water availability. We examined the effects of various environmental conditions on the concentrations of osmoregulatory solutes (polyols and trehalose) and the respiratory activities of fungal assemblages inhabiting standing litter of the freshwater emergent macrophyte Juncus effusus. Under field conditions, the concentrations of osmolytes (polyols plus trehalose) in fungal decomposers were negatively correlated with plant litter water potentials (r = −0.75, P < 0.001) and rates of microbial respiration (r = −0.66, P < 0.001). The highest concentration of osmolytes (polyols plus trehalose) occurred in standing litter exposed to desiccating conditions (range from wet to dry, 0.06 to 0.68 μmol · mg of fungal biomass⁻¹). Similar fluctuations in polyol and trehalose concentrations were observed in standing litter wetted and dried under laboratory conditions and for four predominant fungal decomposers of J. effusus grown individually on sterilized Juncus leaves. These studies suggest that fungal inhabitants associated with standing litter of emergent macrophytes can adjust their intracellular solute concentrations in response to daily fluctuations in water availability.     

EVect of the Entomopathogenic Nematodes, Steinernema feltiae and S. carpocapsae , on the Potato Cyst Nematode, Globodera rostochiensis , in Pot Trials

Two pot experiments, one in a glasshouse and the other in an outdoor sand plunge, were conducted to examine the influence of the entomopathogenic nematodes, Steinernema feltiae and S. carpocapsae , on the invasion and development of the potato cyst nematode, Globodera rostochiensis . Of a total of eight diVerent treatments with entomopathogenic nematodes in the glasshouse trial, three reduced the invasion of G. rostochiensis and one reduced the numbers of new cysts that were produced compared with controls. In the outdoor experiment, seven of the 12 treatments gave a reduction in invasion but none resulted in changes in the numbers of cysts found at plant senescence. In general, invasion of G. rostochiensis juveniles was reduced more eVectively by S. carpocapsae than by S. feltiae , and was greatest in the outdoor trial where larger inocula of entomopathogenic nematodes were used. Overall, the results indicated that use of S. feltiae and S. carpocapsae is unlikely to provide a viable control strategy for G. rostochiensis .     

Glucosylated N-acetyllactosamine O-antigen chain in the lipopolysaccharide from Helicobacter pylori strain UA861

The O-antigen chain from the lipopolysaccharide of Helicobacter pylori strain UA861 was determined to be composed of an elongated type 2 N - acetyllactosamine backbone, -[-->3)-beta-D-Gal-(1-->4)-beta-D-GlcNAc-(1- ]n-->, with approximately half of the GlcNAc units carrying a terminal alpha-d-Glc residue at the O -6 position. The O-chain of H.pylori UA861 was terminated by a N -acetyllactosamine [beta-D-Gal-(1-->4)-beta-D- GlcNAc] (LacNAc) epitope and did not express terminal Lewis X or Lewis Y blood-group determinants as previously found in other H.pylori strains. The absence of terminal Lewis X and Lewis Y blood-group epitopes and the replacement of Fuc by Glc as a side chain in the O- chain of H.pylori UA861 represents yet another type of lipopolysaccharide structure from H.pylori species. These structural differences in H.pylori lipopolysaccharide molecules carry implications with regard to possible different pathogenic events between strains and respective hosts.