Development of analytical methods for NMR spectra and application to a 13C toxicology study

Metabolomics offers the potential to assess the effects of toxicants on metabolite levels. To fully realize this potential, a robust analytical workflow for identifying and quantifying treatment-elicited changes in metabolite levels by nuclear magnetic resonance (NMR) spectrometry has been developed that isolates and aligns spectral regions across treatment and vehicle groups to facilitate analytical comparisons. The method excludes noise regions from the resulting reduced spectra, significantly reducing data size. Principal components analysis (PCA) identifies data clusters associated with experimental parameters. Cluster-centroid scores, derived from the principal components that separate treatment from vehicle samples, are used to reconstruct the mean spectral estimates for each treatment and vehicle group. Peak amplitudes are determined by scanning the reconstructed mean spectral estimates. Confidence levels from Mann–Whitney order statistics and amplitude change ratios are used to identify treatment-related changes in peak amplitudes. As a demonstration of the method, analysis of ¹³C NMR data from hepatic lipid extracts of immature, ovariectomized C57BL/6 mice treated with 30 μg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or sesame oil vehicle, sacrificed at 72, 120, or 168 h, identified 152 salient peaks. PCA clustering showed a prominent treatment effect at all three time points studied, and very little difference between time points of treated animals. Phenotypic differences between two animal cohorts were also observed. Based on spectral peak identification, hepatic lipid extracts from treated animals exhibited redistribution of unsaturated fatty acids, cholesterols, and triacylglycerols. This method identified significant changes in peaks without the loss of information associated with spectral binning, increasing the likelihood of identifying treatment-elicited metabolite changes.     

Developmental response of <Emphasis Type="Italic">Euplectrus comstockii</Emphasis> to ascorbic acid in the diet of the larval host, <Emphasis Type="Italic">Heliothis virescens</Emphasis>

Recent developments in genetic engineering have paved the way for researchers to produce crops of high nutritional and yield value, in addition to being resistant to diseases and pests. Ascorbic acid content is one of the parameters researchers are trying to enhance in plants. This study investigated the effect of different levels of dietary ascorbic acid of a beneficial wasp, Euplectrus comstockii Howard (Hymenoptera: Eulophidae), by measuring life history parameters of the wasp when reared on lepidopteran larvae fed a basal diet containing low and high levels of ascorbic acid. Odds and odds ratio analyses showed that the probability of egg hatch and adult emergence for the wasp increased with the amount of ascorbic acid in the diet of the host, and that the rate of development and probability of female or male progeny was similar for most levels of ascorbic acid tested. This would indicate that as the ascorbic acid concentration increases in the pest insect the effectiveness of the wasp is likely to increase and when, by comparison with other published findings, the effectiveness of microbial pathogens is likely to decrease.     

A Neural Computational Model of Incentive Salience

Incentive salience is a motivational property with ‘magnet-like’ qualities. When attributed to reward-predicting stimuli (cues), incentive salience triggers a pulse of ‘wanting’ and an individual is pulled toward the cues and reward. A key computational question is how incentive salience is generated during a cue re-encounter, which combines both learning and the state of limbic brain mechanisms. Learning processes, such as temporal-difference models, provide one way for stimuli to acquire cached predictive values of rewards. However, empirical data show that subsequent incentive values are also modulated on the fly by dynamic fluctuation in physiological states, altering cached values in ways requiring additional motivation mechanisms. Dynamic modulation of incentive salience for a Pavlovian conditioned stimulus (CS or cue) occurs during certain states, without necessarily requiring (re)learning about the cue. In some cases, dynamic modulation of cue value occurs during states that are quite novel, never having been experienced before, and even prior to experience of the associated unconditioned reward in the new state. Such cases can include novel drug-induced mesolimbic activation and addictive incentive-sensitization, as well as natural appetite states such as salt appetite. Dynamic enhancement specifically raises the incentive salience of an appropriate CS, without necessarily changing that of other CSs. Here we suggest a new computational model that modulates incentive salience by integrating changing physiological states with prior learning. We support the model with behavioral and neurobiological data from empirical tests that demonstrate dynamic elevations in cue-triggered motivation (involving natural salt appetite, and drug-induced intoxication and sensitization). Our data call for a dynamic model of incentive salience, such as presented here. Computational models can adequately capture fluctuations in cue-triggered ‘wanting’ only by incorporating modulation of previously learned values by natural appetite and addiction-related states.     

Drug Guru: a computer software program for drug design using medicinal chemistry rules

Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.     

Syntheses of glucose analogues of E5564 as a highly potent anti-sepsis drug candidate

Glucose analogues 5 and 9 of E5564 were synthesized, and their LPS-antagonistic activities were measured. The inhibitory activities (IC50) on LPS-induced TNFalpha production of these two compounds towards human whole blood cells were 0.06 and 0.83 nM, respectively. Inhibitory doses (ID50) of compounds 5 and 9 on TNFalpha production induced by coinjection of galactosamine and LPS in C3H/HeN mice in vivo were measured and were 0.55 and <0.20 mg/kg, respectively. And also C3H/HeN mice preinjected with compounds 5 and 9 were protected from lethality induced by coinjection of galactosamine and LPS; out of eight mice preinjected with 1 mg/kg of the compounds, one-six and three of eight mice were protected, respectively.     

Estimation of feeding threshold for Homalodisca vitripennis (Hemiptera: Cicadellidae) and its application to prediction of overwintering mortality

The glassy-winged sharpshooter, Homalodisca vitripennis (Germar), vectors the bacterium Xylella fastidiosa that induces Pierce's disease of grape. This study determined the effect of temperature on the feeding activity of H. vitripennis adults and the resulting production of excreta. The Logan type I model described a nonlinear pattern that showed excreta production increased up to an optimal temperature (33.1°C), followed by an abrupt decline near an estimated upper threshold (36.4°C). A temperature threshold for feeding, at or below which adults cease feeding, was estimated to be 10°C using a linear regression model based on the percentage of adults producing excreta over a range of constant temperatures. A simulated winter-temperature experiment using fluctuating thermal cycles confirmed that a time period above the temperature threshold for feeding was a critical factor in determining adult survival. Using data from the simulated temperature study, a predictive model was constructed by quantifying the relationship between cumulative mortality and cooling degree-hours. In field validation experiments, the model accurately predicted the temporal pattern of overwintering mortality of H. vitripennis adults held under winter temperatures simulating conditions in Bakersfield and Riverside, California, in 2006-2007. Model prediction using winter temperature data from a Riverside weather station indicated that H. vitripennis adults would experience an average of 92% overwintering mortality before reproduction in the spring, but levels of mortality varied depending on winter temperatures. The potential for temperature-based indices to predict temporal and spatial dynamics of H. vitripennis overwintering is discussed.     

Oxygen tension differentially influences osteogenic differentiation of human adipose stem cells in 2D and 3D cultures

Skeletal defects commonly suffer from poor oxygen microenvironments resulting from compromised vascularization associated with injury or disease. Adipose stem cells (ASCs) represent a promising cell population for stimulating skeletal repair by differentiating toward the osteogenic lineage or by secreting trophic factors. However, the osteogenic or trophic response of ASCs to reduced oxygen microenvironments is poorly understood. Moreover, a direct comparison between 2D and 3D response of ASCs to hypoxia is lacking. Thus, we characterized the osteogenic and angiogenic potential of human ASCs under hypoxic (1%), normoxic (5%), and atmospheric (21%) oxygen tensions in both 2D and 3D over 4 weeks in culture. We detected greatest alkaline phosphatase activity and extracellular calcium deposition in cells cultured in both 2D and 3D under 21% oxygen, and reductions in enzyme activity corresponded to reductions in oxygen tension. ASCs cultured in 1% oxygen secreted more vascular endothelial growth factor (VEGF) over the 4‐week period than cells cultured in other conditions, with cells cultured in 2D secreting VEGF in a more sustained manner than those in 3D. Expression of osteogenic markers revealed temporal changes under different oxygen conditions with peak expression occurring earlier in 3D. In addition, the increase of most osteogenic markers was significantly higher in 2D compared to 3D cultures at 1% and 5% oxygen. These results suggest that oxygen, in conjunction with dimensionality, affects the timing of the differentiation program in ASCs. These findings offer new insights for the use of ASCs in bone repair while emphasizing the importance of the culture microenvironment. J. Cell. Biochem. 110: 87–96, 2010. © 2010 Wiley‐Liss, Inc.     

Microbial Community Structure and Denitrification in a Wetland Mitigation Bank

Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts.Wetlands provide more ecosystem services (e.g., flood control, water purification, nutrient cycling, and habitat for wildlife) per hectare than any other ecosystem (16). Riparian wetlands, in particular, are sites of intense biogeochemical activity and play an important role in improving water quality, recycling nutrients, and detoxifying chemicals (41). Changing patterns of land use over the last century have resulted in the loss of over half of the wetlands in the contiguous United States (17) and about 60% of wetlands in the Midwestern United States (82). The loss of ecosystem services through conversion of wetlands to alternative (primarily agricultural) land uses exacerbates nutrient pollution and eutrophication of downstream ecosystems (57). Declines in wetland acreage have continued despite a federal policy goal of no-net-loss of wetland acreage and function adopted in 1990 (7, 55). Wetland mitigation projects provide compensation for impacted wetlands and aim to replace the critical functions provided by wetlands. Despite decades of wetland mitigation, however, restoration efforts frequently fail to reestablish desired levels of ecosystem services. Restoration outcomes remain uncertain, and more information is necessary in order to improve monitoring and assessment of wetland development (13, 18, 50, 80).One approach to wetland compensation is through mitigation banks. These sites are areas that are restored, established, enhanced, or preserved for replacement of wetlands that will be affected by future land use change. Mitigation banks are considered “third-party” compensatory mitigation, where the permittee (e.g., developer planning to destroy a wetland) is responsible for purchasing wetland credits in acreage, but the wetland bank is established and managed by another party (24). Wetland mitigation banks have unique characteristics that distinguish them from smaller individual restoration projects (7, 69, 81). Due to their size, wetland mitigation banks are especially heterogeneous and may have a great deal of within-site variability in hydrology and nutrient status, making it challenging to implement a single restoration design. Thus, wetland mitigation banks require intense management and monitoring for improved success (7, 69, 81).Restoration efforts such as mitigation banks aim to replace chemical, physical, and biological ecosystem functions of wetlands that have been lost through anthropogenic disturbance (24). Monitoring of wetland mitigation sites has largely focused on measures of macro-scale community structure (e.g., vegetation surveys) (52) along with measures of hydrology and soil type (24). Measurement of vegetation is a common proxy for wetland performance but does not provide an accurate assessment of wetland function (6, 52). Quantitative assessment is achievable, however, for ecosystem services such as water quality improvement through nitrate removal, where well-characterized microbial mechanisms underlie denitrification processes.The link between microbial community structure and function in a restoration context is a topic of current interest (33). Relating microbial community composition and dynamics to chemical, physical, and biological variables can help to reveal important ecological drivers of microbial communities and their activities (26, 35, 42). Conserved bacterial functional genes related to specific biogeochemical transformations allow evaluation of the community structure of microbial populations directly involved in these processes (49, 60, 63, 77, 79). Assessing the diversity of microorganisms that are specifically involved in denitrification is possible through amplification of the nosZ gene, which encodes the catalytic subunit of nitrous oxide reductase, the enzyme responsible for the final step of denitrification (60, 63, 66). Phylogenetically diverse microorganisms can carry out denitrification though the majority of previously described denitrifiers belong to subphyla within the Proteobacteria (53, 56, 60, 61). Denitrification is a facultative process that occurs only under anaerobic conditions (53, 75). Complete denitrification to N₂ is more prevalent in anaerobic, saturated wetland ecosystems (14, 76), and incomplete denitrification to N₂O is the less desirable, more common endpoint of denitrification under more aerobic, drier conditions (14, 62). While the environmental factors (e.g., oxygen, carbon, nitrate, and pH) that influence bulk denitrification rates have been well characterized (31, 72), the influence of these factors on the composition of denitrifier communities, particularly in a restoration context, is unclear. Understanding the relationship between the microbial populations responsible for nitrogen transformations and easily measured environmental parameters (e.g., soil chemical and physical measures) could lead to assessment metrics that are linked directly to ecosystem functions such as denitrification and bridge the current gap in functional assessment methods (36, 60, 70).The objectives of this study were (i) to compare the microbial and plant community composition in restored wetlands to the composition in adjacent reference floodplain forest wetlands; (ii) to assess the relationship between microbial community composition (based on terminal restriction fragment length polymorphism [T-RFLP]) and potential denitrification activity throughout the mitigation bank; and (iii) to examine soil factors correlated with microbial community composition using both phylogenetic and functional gene markers. As soil environmental conditions affect microbial community structure and activity, we expected that sites where wetland hydrology and soil chemistry have been successfully restored would harbor microbial assemblages that are similar in composition and denitrification function to those observed in reference wetlands within this mitigation bank.