Perspectives on measurement of denitrification in the field including recommended protocols for acetylene based methods

Of the biogeochemical processes, denitrification has perhaps been the most difficult to study in the field because of the inability to measure the product of the process. The last decade of research, however, has provided both acetylene and¹⁵N based methods as well as undisturbed soil core andin situ soil cover sampling approaches to implementing these methods. All of these methods, if used appropriately, give comparable results. Thus, we now have several methods, each with advantages for particular sites or objectives, that accurately measure denitrification in nature. Because of the general usefulness of the acetylene methods, updated protocols for the following three methods are given: gas-phase recirculation soil cores; static soil cores; and the denitrifying enzyme assay also known as the phase 1 assay. Despite the availability of these and other methods, denitrification budgets remain difficult to accurately establish in most environments because of the high spatial and temporal variability inherent in denitrification. Appropriate analysis of those data includes a distribution analysis of the data, and if highly skewed as is typically the case, the most accurate method to estimate the mean and the population variance is the UMVUE method (uniformly minimum variance unbiased estimator). Geostatistical methods have also been employed to improve spatial and temporal estimates of denitrification. These have occasionally been successful for spatial analysis but in the attempt described here for temporal analysis the approach was not useful.Discussions of the importance of denitrification have always focused on quantifying the process and whether particular measured quantities are judged to be a significant amount of nitrogen. A second line of evidence discussed here is the extant genetic record that results from natural selection. These analysis lead to the conclusion that strong selection for denitrification must currently be occurring, which implies that the process is of general significance in soils.     

Kinetics of mineralization of organic compounds at low concentrations in soil.

The kinetics of mineralization of 14C-labeled phenol and aniline were measured at initial concentrations ranging from 0.32 to 5,000 ng and 0.30 ng to 500 micrograms/g of soil, respectively. Mineralization of phenol at concentrations less than or equal to 32 ng/g of soil and of aniline at all concentrations began immediately, and the curves for the evolution of labeled CO2 were biphasic. The patterns of mineralization of 4.0 ng of 2,4-dichlorophenol per g of soil and 20 ng of nitrilotriacetic acid per g of soil were similar to the patterns for phenol and aniline. The patterns of mineralization of 1.0 to 100 ng of p-nitrophenol and 6.0 ng of benzylamine per g of soil were also biphasic but after a short apparent lag period. The curves of CO2 evolution from higher concentrations of phenol and p-nitrophenol had increasing apparent lag phases and were S-shaped or linear. Cumulative plots of the percentage of substrate converted to CO2 were fit by nonlinear regression to first-order, integrated Monod, logistic, logarithmic, zero-order, three-half-order, and two-compartment models. None of the models of the Monod family provided the curve of best fit to any of the patterns of mineralization. The linear growth form of the three-half-order model provided the best fit for the mineralization of p-nitrophenol, with the exception of the lowest concentrations, and of benzylamine. The two-compartment model provided the best fit for the mineralization of concentrations of phenol below 100 ng/g, of several concentrations of aniline, and of nitrilotriacetic acid. It is concluded that models derived from the Monod equation, including the first-order model, do not adequately describe the kinetics of mineralization of low concentrations of chemicals added to soil.     

Numerical taxonomic analysis of cross-inoculation patterns of legumes and Rhizobium

Summary A survey was made of published results of tests of the capacity of Rhizobium derived from one legume genus to nodulate plants from other genera. The data were derived from more than 14,000 separate cross-inoculation trials involving species from 165 genera of legumes. Numerical taxonomic techniques were applied to 113 of the genera for which results of substantial cross-infection tests were available. The data were examined using mean character difference coefficients re-expressed as total and positive-only similarity coefficients. The resulting similarity matrices were clustered by the unweighted pair-group method using arithmetic averages. Eighteen affinity groups were defined at the 70% similarity level. With few exceptions, the physiological and cultural behavior of the rhizobia was consistent within the defined groups. Two broad categories were suggested in the numerical taxonomic analysis, and their validity is discussed in regard to the geographic, physiological and cultural characteristics of the legumes and their Rhizobium microsymbionts. The taxonomic and agronomic value of this approach and the new groupings are discussed.     

Nonlinear estimation of the parameters of Monod kinetics that best describe mineralization of several substrate concentrations by dissimilar bacterial densities

The kinetics of mineralization of a wide range of concentrations of benzoate, glucose, and benzylamine by Pseudomonas sp., Salmonella typhimurium, and microorganisms in acclimated sewage was studied. The treatment of initial substrate concentration and population density as independent variables in nonlinear regression analysis permitted the estimation of a single value for each of the parameters of Monod kinetics that best described the mineralization of substrate at each concentration by the pure cultures and the sewage microflora. One value for each of the parameters of Monod kinetics was used for each of the three compounds to produce theoretical curves which lay close to the observed data on mineralization. Statistically significant differences existed in the values of the parameters of Monod kinetics that best described mineralization in cultures differing only in initial substrate concentration and cell density. However, for the compounds tested, the variance left by analyses using one value for each parameter of Monod kinetics was less than double the unexplained variance left by individual analyses of the data from each treatment. Although significant, this increase is small compared with the amount of variance that could be explained using only one value for each parameter of Monod kinetics.     

Kinetics of mineralization of organic compounds at low concentrations in soil

The kinetics of mineralization of 14C-labeled phenol and aniline were measured at initial concentrations ranging from 0.32 to 5,000 ng and 0.30 ng to 500 micrograms/g of soil, respectively. Mineralization of phenol at concentrations less than or equal to 32 ng/g of soil and of aniline at all concentrations began immediately, and the curves for the evolution of labeled CO2 were biphasic. The patterns of mineralization of 4.0 ng of 2,4-dichlorophenol per g of soil and 20 ng of nitrilotriacetic acid per g of soil were similar to the patterns for phenol and aniline. The patterns of mineralization of 1.0 to 100 ng of p-nitrophenol and 6.0 ng of benzylamine per g of soil were also biphasic but after a short apparent lag period. The curves of CO2 evolution from higher concentrations of phenol and p-nitrophenol had increasing apparent lag phases and were S-shaped or linear. Cumulative plots of the percentage of substrate converted to CO2 were fit by nonlinear regression to first-order, integrated Monod, logistic, logarithmic, zero-order, three-half-order, and two-compartment models. None of the models of the Monod family provided the curve of best fit to any of the patterns of mineralization. The linear growth form of the three-half-order model provided the best fit for the mineralization of p-nitrophenol, with the exception of the lowest concentrations, and of benzylamine. The two-compartment model provided the best fit for the mineralization of concentrations of phenol below 100 ng/g, of several concentrations of aniline, and of nitrilotriacetic acid. It is concluded that models derived from the Monod equation, including the first-order model, do not adequately describe the kinetics of mineralization of low concentrations of chemicals added to soil.     

Controlled experiments of habitat fragmentation: a simple computer simulation and a test using small mammals

Habitat fragmentation involves a reduction in the effective area available to a population and the imposition of hard patch edges. Studies seeking to measure effects of habitat fragmentation have compared populations in fragments of different size to estimate and area effect but few have examined the effect of converting open populations to closed ones (an effect of edges). To do so requires a shift in spatial scope-from comparison of individual fragments to that of fragmented versus unfragmented landscapes. Here we note that large-scale, controlled studies of habitat fragmentation have rarely been performed and are needed. In making our case we develop a simple computer simulation model based on how individual animals with home ranges are affected by the imposition of habitat edges, and use it to predict population-level responses to habitat fragmentation. We then compare predictions of the model with results from a field experiment on Peromyscus and Microtus. Our model treats the case where home ranges/territories fall entirely within or partially overlap with that of sample areas in continuous landscapes, but are restricted to areas within habitat fragments in impacted landscapes. Results of the simulations demonstrate that the imposition of hard edges can produce different population abundances for similar-sized areas in continuous and fragmented landscapes. This edge effect is disproportionately greater in small than large fragments and for species with larger than smaller home ranges. These predictions were generally supported by our field experiment. We argue that large-scale studies of habitat fragmentation are sorely needed, and that control-experiment contrasts of fragmented and unfragmented microlandscapes provide a logical starting point.     

GSK-3β dysregulation contributes to parkinson's-like pathophysiology with associated region-specific phosphorylation and accumulation of tau and α-synuclein

Aberrant posttranslational modifications (PTMs) of proteins, namely phosphorylation, induce abnormalities in the biological properties of recipient proteins, underlying neurological diseases including Parkinson''s disease (PD). Genome-wide studies link genes encoding α-synuclein (α-Syn) and Tau as two of the most important in the genesis of PD. Although several kinases are known to phosphorylate α-Syn and Tau, we focused our analysis on GSK-3β because of its accepted role in phosphorylating Tau and to increasing evidence supporting a strong biophysical relationship between α-Syn and Tau in PD. Therefore, we investigated transgenic mice, which express a point mutant (S9A) of human GSK-3β. GSK-3β-S9A is capable of activation through endogenous natural signaling events, yet is unable to become inactivated through phosphorylation at serine-9. We used behavioral, biochemical, and in vitro analysis to assess the contributions of GSK-3β to both α-Syn and Tau phosphorylation. Behavioral studies revealed progressive age-dependent impairment of motor function, accompanied by loss of tyrosine hydroxylase-positive (TH+ DA-neurons) neurons and dopamine production in the oldest age group. Magnetic resonance imaging revealed deterioration of the substantia nigra in aged mice, a characteristic feature of PD patients. At the molecular level, kinase-active p-GSK-3β-Y216 was seen at all ages throughout the brain, yet elevated levels of p-α-Syn-S129 and p-Tau (S396/404) were found to increase with age exclusively in TH+ DA-neurons of the midbrain. p-GSK-3β-Y216 colocalized with p-Tau and p-α-Syn-S129. In vitro kinase assays showed that recombinant human GSK-3β directly phosphorylated α-Syn at a single site, Ser129, in addition to its known ability to phosphorylate Tau. Moreover, α-Syn and Tau together cooperated with one another to increase the magnitude or rate of phosphorylation of the other by GSK-3β. Together, these data establish a novel upstream role for GSK-3β as one of several kinases associated with PTMs of key proteins known to be causal in PD.After Alzheimer''s disease (AD), Parkinson''s disease (PD) is the second most prevalent neurodegenerative disease, characterized by selective loss of TH+ DA-neurons of substantia nigra (SN) with diminished production of dopamine (DA).¹ Genome-wide studies have identified SNCA and MAPT, genes encoding α-synuclein (α-Syn) and Tau, respectively, as having strong association to the genesis of PD.^{2, 3, 4} Although the precise etiology of PD remains a mystery, SNCA amplifications and mutations directly link α-Syn dysfunction to disease causation,^{5, 6} firmly establishing a role for α-Syn in sporadic and familial PD, respectively. α-Syn can be phosphorylated at several sites,⁷ and the predominance of α-Syn phosphorylated at serine 129 (S129) in Lewy bodies⁸ suggests its phosphorylation status at S129 has an important pathological role. Various PD models have shown that phosphorylation at S219 enhanced α-syn toxicity resulting in accelerated motor abnormalities and loss of DA-neurons.^{9, 10}Fewer studies have examined the role of Tau (or p-Tau) in PD, but interest in the field has grown since completion of several genome-wide association studies. p-Tau has been found to colocalize with α-Syn in tissue from sporadic PD and dementia with Lewy bodies.¹¹ We^{12, 13} and others^14,15 have also identified p-Tau in different brain regions of PD, dementia with Lewy bodies, and AD. High levels of p-Tau have also been observed in vivo in several toxin^{16, 17, 18} and transgenic α-Syn models of PD,^19,20 suggesting that p-Tau may be an important common factor in the neurodegeneration of not only tauopathies but also of synucleinopathies, such as PD.^{21, 22, 23, 24} Most studies to date have focused on the formation and accumulation of Tau and p-Tau in idiopathic PD. Yet several studies have provided evidence that leucine-rich repeat kinase-2 (LRRK2), a kinase, that when mutated is involved in familial forms of PD, can directly interact with, and activate GSK-3β, resulting in increased p-TAU formation.^25,26Among the kinases known to hyperphosphorylate Tau, glycogen synthase kinase-3β (GSK-3β) may be the most important given its ability to phosphorylate Tau at the majority of its serine/threonine sites that cause associated toxicities in AD.^27,28 The importance of GSK-3β is illustrated in that it is embryonically lethal when knocked out in mice. Regulation of GSK-3β is tightly controlled through a series of direct and indirect measures. Direct regulation occurs through autophosphorylation at Tyr216,^29,30 resulting in a kinase-active form, p-GSK-3β-Y216, whereas phosphorylation at Ser9 results in a kinase-inactive state.³¹ The activity of GSK-3β can also be controlled indirectly through binding to inhibitory complexes with other cytoplasmic proteins,^32,33 or through Wnt-mediated sequestration into multivesicular bodies³⁴ resulting in the physical separation of GSK-3β from its cytoplasmic targets. Control of GSK-3β in the normal state is therefore tightly regulated, with its dysregulation and ensuing aberrant phosphorylation of targets being a common occurrence in many diverse diseases. Several studies have shown that GSK-3β is an important mediator in the injury and repair processes of neurons during cross-talk between DA-neurons and reactive astrocytes.^35,36 These studies showed that astrocyte-derived Wnt1 was capable of blocking GSK-3β activation, allowing the nuclear accumulation of β-catenin and subsequent gene expression of β-catenin-dependent targets essential for neuron survival and repair during chemical or metabolic insults. The importance of regulating the active/inactive states of GSK-3β in regard to neuronal stability is further supported through the analysis of conditional (Tet-inducible) transgenic mice expressing a dominant-negative GSK-3β-K85R mutant or expressing the GSK-3β-S9A mutant.^37,38 In these studies, post-natal Tet-regulated expression of either GSK-3β-K85R or GSK-3β-S9A led to neurodegeneration in the cortex, striatum, and hippocampus. What separates our TG PD model from the tet-inducible GSK-3β models is the spatial patterns of transgene expression, which is influenced by the choice of promoters. The Tet-inducible GSK-3β models are expressed using a CAMKII promoter with our human(h) GSK-3β-S9A transgene being expressed under the Thy-1 promoter. CAMKII-driven expression is limited to neurons originating from the forebrain with Thy-1 promoter-driven expression restricted to neurons in all or most brain regions.^39,40 Although promoter choice effecting tissue expression ultimately decides which regions show degeneration, the important message is that both inactive and hyperactive states of GSK-3β reduce neuronal viability.In our past studies in various in vitro and in vivo models of PD and in postmortem PD tissues, we have consistently observed a positive correlation between increased α-Syn and p-Tau levels with increased GSK-3β-Y216 (the kinase-active form of GSK-3β).^{12, 13, 16, 19, 20} In in vitro studies of MPTP-treated SH-SY5Y cells, blockade of GSK-3β with lithium, or with the highly selective non-ATP competitive inhibitor, TDZD-8, prevented the induction of p-GSK-3β-Y216, abolished p-Tau formation, and reversed the accumulation and aggregation of both p-Tau and α-Syn, averting cell death.¹⁶ Other studies using Rotenone or MPTP/MPP+ in chemical PD models, have shown similar results of decreased neuronal viability during treatments accompanied by dose- and time-dependent increases in GSK-3β activation, with decreased cytotoxicity detected when GSK-3β was inhibited or knocked-down through the use of GSK-3β-specific small molecule inhibitors or through RNAi.^41,42 This suggested to us that p-GSK-3β-Y216 may have a contributory role in the pathogenesis of PD. Using a mouse model overexpressing hGSK-3β-S9A under the Thy-1 promoter together with in vitro kinase assays allowed us to discern the role GSK-3β has in the development of PD-like pathology.⁴³ Analysis of our hGSK-3β-S9A mouse model showed here for the first time that upon aging, these mice develop the cardinal features of parkinsonism, manifested as impaired motor behavior, with associated loss of TH+ neurons, reduced DA production, and shrinkage of SN. Invitro kinase assays confirmed that hGSK-3β was capable of phosphorylating α-Syn on Serine 129 together with the known ability to phosphorylate Tau. Remarkably, both α-Syn and Tau influenced the rate and magnitude of phosphorylation of the other by GSK-3β indicating that an intimate physical relationship exist between the trio of PD related proteins. Together, these data shown indicate the importance of GSK-3β activation, in the behavioral and physiological development of PD like pathology in a new mouse model.     

Exploiting the role of endogenous lymphoid-resident dendritic cells in the priming of NKT cells and CD8+ T cells to dendritic cell-based vaccines

Transfer of antigen between antigen-presenting cells (APCs) is potentially a physiologically relevant mechanism to spread antigen to cells with specialized stimulatory functions. Here we show that specific CD8+ T cell responses induced in response to intravenous administration of antigen-loaded bone marrow-derived dendritic cells (BM-DCs), were ablated in mice selectively depleted of endogenous lymphoid-resident langerin+ CD8α+ dendritic cells (DCs), suggesting that the antigen is transferred from the injected cells to resident APCs. In contrast, antigen-specific CD4+ T cells were primed predominantly by the injected BM-DCs, with only very weak contribution of resident APCs. Crucially, resident langerin+ CD8α+ DCs only contributed to the priming of CD8+ T cells in the presence of maturation stimuli such as intravenous injection of TLR ligands, or by loading the BM-DCs with the glycolipid α-galactosylceramide (α-GalCer) to recruit the adjuvant activity of activated invariant natural killer-like T (iNKT) cells. In fact, injection of α-GalCer-loaded CD1d-/- BM-DCs resulted in potent iNKT cell activation, suggesting that this glycolipid antigen can also be transferred to resident CD1d+ APCs. While iNKT cell activation per se was independent of langerin+ CD8α+ DCs, some iNKT cell-mediated activities were reduced, notably release of IL-12p70 and transactivation of NK cells. We conclude that both protein and glycolipid antigens can be exchanged between distinct DC species. These data suggest that the efficacy of DC-based vaccination strategies may be improved by the incorporation of a systemic maturation signal aimed to engage resident APCs in CD8+ T cell priming, and α-GalCer may be particularly well suited to this purpose.     

Restoration of endothelin-1-induced impairment in endothelium-dependent relaxation by interleukin-10 in murine aortic rings

Endothelin-1 (ET-1) is implicated in the development of endothelial dysfunction through the generation of reactive oxygen species by NADPH oxidase activation. Interleukin-10 (IL-10) is an antiinflammatory cytokine that stimulates nitric oxide production, decreases superoxide production, and restores endothelial integrity after vascular injury. In this study, we tested whether IL-10 attenuates ET-1-induced endothelial dysfunction by improving acetylcholine (ACh)-induced relaxation of cultured murine aortic rings. Aortic rings (2 mm long) of C57BL/6 mice were incubated in 2 mL DMEM containing 120 U/mL penicillin and 120 mug/mL streptomycin in the presence of one of 4 treatments: vehicle (deionized water), ET-1 (100 nmol/L), recombinant mouse IL-10 (300 ng/mL), or a combination of both ET-1 and IL-10. After incubation at 37 degrees C for either 1 or 6 h (short-term exposure) or 22 h (overnight exposure), rings were mounted in a wire myograph and stretched to a passive force of 5 mN. Endothelium-dependent vasorelaxation was assessed by constructing cumulative concentration-response curves to ACh (0.001-10 mumol/L) during 10 mumol/L phenylephrine (PE)-induced contraction. Short-term exposure of ET-1 did not result in an impairment of ACh-induced relaxation. Overnight exposure of aortic rings to ET-1 resulted in a statistically significant endothelial dysfunction characterized by a reduced maximal relaxation response to ACh compared with that of untreated rings (Emax 57% +/- 3% versus 82% +/- 4%). IL-10 treatment restored ACh-induced relaxation (Emax 77% +/- 3%). Western blotting showed decreased eNOS expression in response to ET-1, whereas vessels treated with a combination of ET-1 and IL-10 showed increased expression of eNOS. Immunohistochemical analysis showed decreased eNOS expression in ET-1-treated vessels compared with those treated with both ET-1 and IL-10. We conclude that, in murine aorta, the antiinflammatory cytokine IL-10 prevents impairment in endothelium-dependent relaxation induced in response to long-term incubation with ET-1 via normalization of eNOS expression.     

Outgassing Losses of Toluene and m-Xylene Evaluated by 14C-Based Mass Balances for Laboratory Bioventing Simulations

Mixtures of toluene, ethylbenzene, and the xylenes spiked with ¹⁴C-labeled toluene or m-xylene were added to bench-scale bioventing simulation columns filled with hydrocarbon-contaminated subsurface soils. After 2 to 4 weeks of incubation during which air was pumped through the column at rates of at least 2?ml·min^?1·kg^?1 between 54 and 84% of the radiolabel was recovered in traps as outgassed parent compound from four columns sterilized with gamma-irradiation. In contrast, seven nonsterilized but otherwise identically treated (except for inorganic nitrogen addition) columns lost less than 0.4% (and one column lost 0.7%) of the radiolabel through outgassing of the parent compound. Nonsterilized columns lost 40 to 61% of the radiolabel as ¹⁴CO₂, whereas gamma-irradiated columns usually lost only trace amounts of ¹⁴C in this form. Biologically active columns also retained much larger fractions than sterilized columns of the radiolabel in the subsoil in forms, possibly microbial biomass, from which it could be recovered by wet oxidation. Addition of 10 or 40?mg/kg of mineral nitrogen had no consistent effect on bioventing performance.