Bias in the development of health and ecological assessments and potential solutions

The effectiveness and credibility of environmental decisions depend on the information provided by scientific assessments. However, the conflicting assessments provided by government agencies, industries, and environmental advocacy groups suggest that biases occur during assessment processes. Sources of bias include personal bias, regulatory capture, advocacy, reliance on volunteer assessors, biased stakeholder and peer review processes, literature searches, standardization of data, inappropriate standards of proof, misinterpretation, and ambiguity. Assessors can adopt practices to increase objectivity, transparency, and clarity. Decision-makers, managers of assessors, and institutions that commission assessments can adopt other practices that reduce pressures on assessors and reduce opportunities for expression of the personal biases of assessors. Environmental assessment should be recognized as a discipline with its own technical and ethical best practices.     

Direct electrochemical regeneration of NADH from NAD+ using cholesterol-modified gold amalgam electrode

The efficiency of the direct electrochemical regeneration of NADH from NAD+ was enhanced by applying a cholesterol-modified gold amalgam electrode. The modified electrode was prepared by immersing gold plate in mercury and casting few drops of cholesteryl oleate solution over the gold amalgam. Coenzymatically active NADH was formed from NAD+ directly at the cholesterol-modified gold amalgam electrode which is supposed to hinder the dimerization of the NAD radicals on its membrane surface. The direct electrochemical NAD+ reduction process was used favorably to drive an enzymatic reduction of pyruvate to d-lactate. d-Lactate of 18.2 mm was obtained from pyruvate of 25.3 mm at 21 h of total reaction time in the electrolysis of 50 cm3 solution with the electrode of 6 cm2area. The turnover number for NAD+ was estimated as 1400.     

Finding A Niche for Soil Microbial Toxicity Tests in Ecological Risk Assessment

Soil microbial toxicity tests are seldom used in ecological risk assessments or in the development of regulatory criteria in the U.S. The primary reason is the lack of an explicit connection between these tests and assessment end-points. Soil microorganisms have three potential roles with respect to ecological assessment endpoints: properties of microbial communities may be end-points; microbial responses may be used to estimate effects on plant production; and microbial responses may be used as surrogates for responses of higher organisms. Rates of microbial processes are important to ecosystem function, and thus should be valued by regulatory agencies. However, the definition of the microbial assessment endpoint is often an impediment to its use in risk assessment. Decreases in rates are not always undesirable. Processes in a nutrient cycle are particularly difficult to define as endpoints, because what constitutes an adverse effect on a process is dependent on the rates of others. Microbial tests may be used as evidence in an assessment of plant production, but the dependence of plants on microbial processes is rarely considered. As assessment endpoints are better defined in the future, microbial ecologists and toxicologists should be provided with more direction for developing appropriate microbial tests.     

Aggregation of amphipathic peptides at an aqueous–organic interface using coarse-grained simulations

The effect of an aqueous/organic interface on the folding and aggregation of amphipathic peptides is examined by applying discontinuous molecular dynamics (DMD) simulations combined with an intermediate resolution protein model, PRIME20, to a peptide/interface system. The systems contain 48 (KLLK)₄ peptides in random coil or α-helical conformations interacting with both strong and weak interfaces. In the absence of an interface, most of the oligomers form helical bundles, a small fraction of which convert to β-sheets when the temperature is above the folding transition. Adding a weak interface decreases oligomer formation above the folding temperature and increases it below. Little monolayer formation is observed at the weak interface; instead reversible adsorption increases the local peptide concentration near the interface, promoting helical bundle formation in the aqueous phase below the folding temperature and β-sheet formation above the folding temperature. Introducing a strong interface leads to irreversible adsorption, promoting formation of helical monolayers below the folding temperature and mixed β-sheet/amorphous monolayers above the folding temperature. The (KLLK)₄ peptide is more likely to adsorb to the interface when it is in an α-helical conformation, as opposed to a random coil, because of its larger hydrophobic moment.     

Cortisol stress response and histopathological alteration index in Clarias gariepinus exposed to sublethal concentrations of Qua Iboe crude oil and rig wash

The histological effect on and stress response of post juvenile Clarias gariepinus exposed to Qua Iboe crude oil and rig wash were investigated. Fish weighing 60–90 g and measuring 16–18 cm were exposed for 7–28 days to 8.00 ml^?1 Qua Iboe crude oil and 0.0018 ml^–1 rig wash, both being 0.1 of the 96 hr LC₅₀. Blood samples of C. gariepinus were collected every seven days and evaluated for stress by measuring cortisol concentration. The gills and liver were studied and scored for Gill Alteration Index (GAI) and Hepatic Alteration Index (HAI), respectively. There was an increase in cortisol level up to the 7th and 14th day among the group exposed to Qua Iboe crude oil, with a decrease on the 21st and 28th day. The rig wash group increased in cortisol level up to the 7th day and decreased slightly on the 14th day, after which the trend became irregular. The toxic effects of the Qua Iboe crude oil and rig wash were time dependent, as shown by the histopathological alteration index (HAI) of gill and liver. After 28 days of exposure, the gills had irreparable damage due to high frequency of cellular necrosis and degeneration, whereas the liver had from moderate to severe damage due to the high frequency of cellular degeneration and inflammation. Qua Iboe crude oil and rig wash are both toxic to C. gariepinus, therefore their indiscriminate discharge to the environment must be discouraged.     

Exploring the linkage between cell culture process parameters and downstream processing utilizing a plackett‐burman design for a model monoclonal antibody

Linkage of upstream cell culture with downstream processing and purification is an aspect of Quality by Design crucial for efficient and consistent production of high quality biopharmaceutical proteins. In a previous Plackett‐Burman screening study of parallel bioreactor cultures we evaluated main effects of 11 process variables, such as agitation, sparge rate, feeding regimens, dissolved oxygen set point, inoculation density, supplement addition, temperature, and pH shifts. In this follow‐up study, we observed linkages between cell culture process parameters and downstream capture chromatography performance and subsequent antibody attributes. In depth analysis of the capture chromatography purification of harvested cell culture fluid yielded significant effects of upstream process parameters on host cell protein abundance and behavior. A variety of methods were used to characterize the antibody both after purification and buffer formulation. This analysis provided insight in to the significant impacts of upstream process parameters on aggregate formation, impurities, and protein structure. This report highlights the utility of linkage studies in identifying how changes in upstream parameters can impact downstream critical quality attributes. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:163–170, 2017     

Mechanisms driving understory evergreen herb distributions across slope aspects: as derived from landscape position

In the Northern Hemisphere, the surface of south-facing slopes orients toward the sun and thus receives a greater duration and intensity of solar irradiation, resulting in a relatively warmer, drier microclimate and seasonal environmental extremes. This creates potentially detrimental conditions for evergreen plants which must endure the full gamut of conditions. I hypothesize that (1) increased southerly aspect will correlate negatively with evergreen understory plant distributions; (2) derived environmental variables (summer and winter light and heat load) will predict variance in evergreen distributions as well as topographic position (aspect, slope, and elevation) and (3) winter light will best predict evergreen understory plant distributions. In order to test these hypotheses, survey data were collected characterizing 10 evergreen understory herb distributions (presence, abundance, and reproduction) as well as the corresponding topographical information across north- and south-facing slopes in the North Carolina mountains and Georgia piedmont. The best predictive models were selected using AIC, and Bayesian hierarchical generalized linear models were used to estimate the strength of the retained coefficients. As predicted, evergreen understory herbs occurred and reproduced less on south-facing than north-facing slopes, though slope and elevation also had robust predictive power, and both discriminated well between evergreen species. While the landscape variables explained where the plants occurred, winter light and heat load provided the best explanation why they were there. Evergreen plants likely are limited on south-facing slopes by low soil moisture combined with high temperatures in summer and high irradiance combined with lower temperatures in winter. The robust negative response of the understory evergreen herbs to increased winter light also suggested that the winter rather than the summer (or growing season) environment provided the best predictive power for understory evergreen distributions, which has substantive implications for predicting responses to global climate change.     

Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors

Discovery and optimization of potency and selectivity of a non-Zn-chelating MMP-13 inhibitor with the aid of protein co-crystal structural information is reported. This inhibitor was observed to have a binding mode distinct from previously published MMP-13 inhibitors. Potency and selectivity were improved by extending the hit structure out from the active site into the S1′ pocket.     

Enzyme immobilization via silaffin‐mediated autoencapsulation in a biosilica support

Enzymes and other biomolecules are often immobilized in a matrix to improve their stability or to improve their ability to be reused. Performing a polycondensation reaction in the presence of a biomolecule of interest relies on random entrapment events during polymerization and may not ensure efficient, homogeneous, or complete biomolecule encapsulation. To overcome these limitations, we have developed a method of incorporating autosilification activity into proteins without affecting enzymatic functionality. The unmodified R5 silaffin peptide from Cylindrotheca fusiformis is capable of initiating silica polycondensation in vitro at ambient temperatures and pressures in aqueous solution. In this study, translational fusion proteins between R5 and various functional proteins (phosphodiesterase, organophosphate hydrolase, and green fluorescent protein) were produced in Escherichia coli. Each of the fusion proteins initiated silica polycondensation, and enzymatic activity (or fluorescence) was retained in the resulting silica spheres. Under certain circumstances, the enzymatically‐active biosilica displayed improved stability relative to free enzyme at elevated temperatures. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009