Biopartitioning micellar chromatography: an alternative high-throughput method for assessing the ecotoxicity of anilines and phenols

An investigation of the use of the chromatographic retention (log k) as an in vitro approach for modelling the toxicity to Fathead Minnows of anilines and phenols is developed. A data set of 65 compounds with available experimental toxicity data was used. Log k data at three pH values were used for the compounds classification and two groups or 'MODEs' were identified. For one 'MODE' a quantitative retention-activity relationship (QRAR) model was calculated. Finally, it was used to estimate the toxicity to Fathead minnows of anilines and phenols for which experimental data are not available. These estimations were compared to those obtained from another toxicity (to Tetrahymena pyriformis) data set and those estimated from a U.S. EPA QSAR approach (ECOSAR software) to decide on the toxicity level according to the Directive 3/21/EEC.     

Correlation weighting of valence shells in QSAR analysis of toxicity

In the rainbow trout (Oncorhynchus mykiss), we studied the acute toxicity LC(50)-96 h of 274 organic pesticides with a wide variety of molecular structures. Optimization of correlation weights of local and global graph invariants (OCWLGI) gave quantitative structure-activity relationships (QSARs) for predicting toxicity. We used a labeled hydrogen-filled graph (LHFG) to elucidate the molecular structure. We also used the extended connectivity of zero ((0)EC(k)), first ((1)EC(k)), and second ((2)EC(k)) order, numbers of path lengths 2 (P2(k)) and 3 (P3(k)) starting from a given vertex in the LHFG, and valence shells of second order (S2(k)). S2(k) is the sum of the degree of vertices at distance 2 from a given vertex k. The presence of three-, five-, and six-member cycles and hydrogen bond indices suggested they might be used as global LHFG invariants. We applied this method to a broad set of pesticides, to predict toxicity for the trout. The best model used weighted S2(k) and global LHFG invariants. Statistical characteristics of this model are as follows: n=233, r(2)=0.7689, r(2)(pred)=0.7688, s=0.75, F=769 (training set); n=41, r(2)=0.6421, r(2)(pred)=0.4241, s=1.14, F=70 (test set).     

QRAR models for cardiovascular system drugs using biopartitioning micellar chromatography

The capability of biopartitioning micellar chromatography (BMC) to describe and estimate pharmacological parameters of cardiovascular system drugs has been studied. The retention of cardiovascular system drugs was studied using different pH of Brij-35 as micellar mobile phase in modified C(18) stationary phase. Quantitative retention-activity relationships (QRAR) in BMC were investigated for these compounds. An adequate correlation between the retention factors (log k) and the toxicity (LD(50)) of cardiovascular system drugs was obtained.     

Comparison of Two U.S. Environmental Protection Agency Species Sensitivity Distribution Methods for Calculating Ecological Risk Criteria

Two major methods used by the U. S. Environmental Protection Agency (USEPA) to calculate ecological risk criteria using “species sensitivity distributions” (SSD) are compared using identical datasets. One method is the current USEPA Office of Water method for deriving acute numeric water quality criteria (EPA-FAV method). The 95% protection level generated by this method is the Final Acute Value (FAV). The other method is the USEPA Office of Pesticide Programs log normal distribution regression method that uses all available toxicological data in performing ecological risk assessments (OPP-Ecorisk method). Of the 50 comparisons made, 38% of the 95% protection levels calculated by the OPP-Ecorisk method are within a factor of 1.5 of the EPA FAV, 68% are within a factor of 2.0, 86% are within a factor of 2.5 and 92% are within a factor of 3.5. For pollutants where the difference between the OPP-Ecorisk 95% protection level and the EPA FAV are greatest, the OPP-Ecorisk 95% protection level is more protective than the EPA FAV. Where there are major differences, an analysis of the toxicity data indicates that the majority of the differences can be attributed to outliers, especially on the least sensitive ends of the toxicity distribution. In the one example dataset presented with one very sensitive genus, the OPP-Ecorisk method gave a protection level that was much closer to the lowest GMAV than the EPA-FAV method.     

A protocol for conducting 7-day daily renewal tests with Lemna gibba

Lemna gibba (a duckweed) is a freshwater macrophyte commonly used in toxicity testing, and Lemna spp are currently the only aquatic higher plants required for evaluation of pesticides under the pesticide registration guidelines of the EPA. The methods currently available for toxicity testing by various organizations and agencies, including ASTM, OECD, EPA and Environment Canada, are largely static or semistatic tests with unspecified renewal intervals (OECD) and may not provide a consistent means of exposure owing to short toxicant half-life in aquatic media, uptake of chemical by plants and evaporation of nutrient media. The procedure outlined here details a simple and efficient 7-day daily static renewal procedure for conducting toxicity tests with L. gibba, the appropriate end points to assess, the statistical criteria necessary for analyzing the toxicity data, as well as the steps required to culture and maintain L. gibba. This protocol is based on a modified version of a widely accepted static method.     

The Value of Human Testing of Pesticides

Recently, the issue of using human volunteers as subjects for studying the potential toxicity of pesticides has received public attention through the media and subsequently in the regulatory arena. The debate has focused on whether such studies are ethical per se and if data from these investigations should be used for regulatory decisions. The precipitating event that prompted the current debate was the enactment of the Food Quality Protection Act (FQPA) of 1996. The FQPA, which amended the two laws governing the regulation of pesticides in the United States, requires the Environmental Protection Agency to reassess all of the nearly 10,000 tolerances (maximum allowable residues in food) and exemptions from tolerances that were in place when the law went into effect. When reassessing tolerances the U.S. Environmental Protection Agency (USEPA) reviews the data, including toxicology, available on each pesticide to determine if they are adequate to allow the Agency to make the necessary safety finding. Historically, it had been considered acceptable to conduct and use data from studies of exposure to chemicals (including pesticides) of human volunteers if these studies were conducted according to specific criteria as outlined in the Helsinki Declaration and Common Rule. Now this philosophy is being challenged and the USEPA is faced with answering the question of whether pesticides should be viewed as different, from an ethical standpoint, from other chemicals, and how such data should be used in the risk assessment process. The following paper makes an argument for the use of human volunteer testing of pesticides applying the logic that, if one wants to protect humans from the potential harm that may occur from eating foods containing pesticides, one must use the best possible data available. There can be little doubt that the best data for predicting the toxicity of a chemical in humans is to obtain and use human data, as long as it is obtained in an ethical manner.     

The Chesapeake Bay Program: An Example of Ecological Risk Assessment

Ecological risk assessment grew from earlier efforts of federalagencies to protect human health from chemical releases. Overthe past several years, the U.S. Environmental Protection Agency(U.S. EPA) adapted the human health paradigm for use in protectingecological end-points, including ecosystems such as the ChesapeakeBay. The Bay restoration effort may be seen as an ecologicalrisk assessment in the sense that the program participants followedthe paradigm developed by U.S. EPA. This analysis of the programand risk assessment process provides an additional perspectiveon the success and efficacy of the Bay restoration efforts.Early efforts to determine the problems in the Bay system targetedhypoxia, habitat deterioration and natural resource degradationfor corrective actions. Additional monitoring and data gatheringrefined and focused program efforts on hypoxia caused by nutrientenrichment. Thus far, the ecological risk paradigm has beeneffectively applied to the Bay clean-up in a general sense.Recent research demonstrates that detailed application of anarrow risk approach will likely fail to include important biologicaleffects or processes     

An algorithm for approximate tandem repeats.

A perfect single tandem repeat is defined as a nonempty string that can be divided into two identical substrings, e.g., abcabc. An approximate single tandem repeat is one in which the substrings are similar, but not identical, e.g., abcdaacd. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k differences). For a string S of length n and an integer k our algorithm reports all locally optimal approximate repeats, r = umacro ?, for which the Hamming distance of umacro and ? is at most k, in O(nk log (n/k)) time, or all those for which the edit distance of umacro and ? is at most k, in O(nk log k log (n/k)) time. This paper concentrates on a more general type of repeat called multiple tandem repeats. A multiple tandem repeat in a sequence S is a (periodic) substring r of S of the form r = u(a)u', where u is a prefix of r and u' is a prefix of u. An approximate multiple tandem repeat is a multiple repeat with errors; the repeated subsequences are similar but not identical. We precisely define approximate multiple repeats, and present an algorithm that finds all repeats that concur with our definition. The time complexity of the algorithm, when searching for repeats with up to k errors in a string S of length n, is O(nka log (n/k)) where a is the maximum number of periods in any reported repeat. We present some experimental results concerning the performance and sensitivity of our algorithm. The problem of finding repeats within a string is a computational problem with important applications in the field of molecular biology. Both exact and inexact repeats occur frequently in the genome, and certain repeats occurring in the genome are known to be related to diseases in the human.     

Studies of the enzymic mechanism of Candida tenuis xylose reductase (AKR 2B5): X-ray structure and catalytic reaction profile for the H113A mutant

Xylose reductase from the yeast Candida tenuis (CtXR) is a family 2 member of the aldo-keto reductase (AKR) superfamily of proteins and enzymes. Active site His-113 is conserved among AKRs, but a unified mechanism of how it affects catalytic activity is outstanding. We have replaced His-113 by alanine using site-directed mutagenesis, determined a 2.2 A structure of H113A mutant bound to NADP(+), and compared catalytic reaction profiles of NADH-dependent reduction of different aldehydes catalyzed by the wild type and the mutant. Deuterium kinetic isotope effects (KIEs) on k(cat) and k(cat)/K(m xylose) show that, relative to the wild type, the hydride transfer rate constant (k(7) approximately 0.16 s(-1)) has decreased about 1000-fold in H113A whereas xylose binding was not strongly affected. No solvent isotope effect was seen on k(cat) and k(cat)/K(m xylose) for H113A, suggesting that proton transfer has not become rate-limiting as a result of the mutation. The pH profiles of log(k(cat)/K(m xylose)) for the wild type and H113A decreased above apparent pK(a) values of 8.85 and 7.63, respectively. The DeltapK(a) of -1.2 pH units likely reflects a proximally disruptive character of the mutation, affecting the position of Asp-50. A steady-state kinetic analysis for H113A-catalyzed reduction of a homologous series of meta-substituted benzaldehyde derivatives was carried out, and quantitative structure-reactivity correlations were used to factor the observed kinetic substituent effect on k(cat) and k(cat)/K(m aldehyde) into an electronic effect and bonding effects (which are lacking in the wild type). Using the Hammett sigma scale, electronic parameter coefficients (rho) of +0.64 (k(cat)) and +0.78 (k(cat)/K(m aldehyde)) were calculated and clearly differ from rho(k(cat)/K(aldehyde)) and rho(k(cat)) values of +1.67 and approximately 0.0, respectively, for the wild-type enzyme. Hydride transfer rate constants of H113A, calculated from kinetic parameters and KIE data, display a substituent dependence not seen in the corresponding wild-type enzyme rate constants. An enzymic mechanism is proposed in which His-113, through a hydrogen bond from Nepsilon2 to aldehyde O1, assists in catalysis by optimizing the C=O bond charge separation and orbital alignment in the ternary complex.     

U.S. regulatory framework for genetic biocontrol of invasive fish

This paper provides an overview of the U.S. regulatory framework governing genetic biocontrol efforts for invasive fish. Genetic biocontrol refers to the intentional release of genetically modified organisms (GMOs) into the environment to control a target population of a non-native species. The terms “genetically modified” and “genetically engineered” are often used interchangeably, despite the scientific distinctions. A GMO is an organism that has had its genetic material altered or modified by humans through any method, including conventional breeding. Genetic engineering, as defined by the Food and Drug Administration (FDA), is the use of recombinant DNA techniques to introduce new characteristics or traits into an organism. GE organisms are therefore a subset of GMOs. As this paper will discuss, existing laws focus on GE organisms raising significant questions as to whether organisms modified without utilizing rDNA techniques fall within the jurisdiction of any federal agency. Under the 1986 Coordinated Framework for Regulation of Biotechnology, three federal agencies have primary responsibility over biotechnology—the Environmental Protection Agency (EPA), the U.S. Department of Agriculture, and the FDA. Because the EPA has exempted biological control agents from regulation as pesticides and no fish species are currently considered plant pests, the FDA is the agency responsible for approving the use of genetically engineered fish for biocontrol. FDA regulates genetically engineered animals through its New Animal Drug Application (NADA) process. The NADA process presents several challenges to effective and transparent regulation of genetic biocontrol, including the FDA’s focus on drug safety, secrecy provisions potentially limiting disclosure of the results of environmental reviews, and the secondary role of the Fish and Wildlife Service, the federal agency with the most experience with invasive species management. In addition, relying on the NADA process creates a significant regulatory gap as NADA approval is only required for GE organisms. The regulatory framework for GMOs created for genetic biocontrol without rDNA technology is unclear and primary responsibility may fall to the states. Given its extensive experience with hatcheries, invasive fish species control, and environmental reviews, the Fish and Wildlife Service (FWS) is the more appropriate agency to review applications for genetic biocontrol. Efforts should be undertaken now, while genetic biocontrol is still in the theoretical stages, to increase the role of the FWS in the permitting process either through formal regulations or more informal mechanisms such as memorandum of understanding.     

The role of rRNA bases in the interaction of peptidyltransferase inhibitors with bacterial ribosomes.

Synergism of streptogramins A (virginiamycin M, VM) and B (virginiamycin S, VS), peptidyltransferase inhibitors, was explored in EM4/pLC7-21 (wild type) and EM4/pERY (VS-resistant). These bacterial strains contained multicopy plasmids carrying an rrnH operon with wild type (pLC7-21) or mutated (A2058----U transversion) 23 S rRNA gene. Ribosomes with wild type and mutated rRNA were both present in EM4/pERY. The latter particles did not bind VS; in the presence of VM, however, high affinity VS binding occurred. As shown previously, VS protected against chemical reagents certain bases in domain V rRNA and VM in the stems flanking this loop. Differences between wild type and mutant ribosomes were observed: A2058, A2059, A2062, and G2505, protected by VS and ERY in EM4/pLC7-21, were unshielded in EM4/pERY. A2062 was shielded by VM in EM4/pERY, not in EM4/pLC7-21, and G2505 of mutant ribosomes became protected by VS when VM was simultaneously present. Induction by VM of a high affinity VS binding site in VS-sensitive and -resistant ribosomes indicates A2058 mutation to entail a conformational change of this site, which is counteracted by VM fixation. Accessibility of A2062 to chemical reagents (unlike behavior of EM4/pERY and EM4/pLC7-21 in the presence of VM) implies different conformations for wild type and mutant ribosomes.     

防治甘草萤叶甲生物源农药筛选及其对生物多样性的影响

为了筛选出防治甘草萤叶甲Diorhbda tarsalis Weise的生物药剂,采用多种生物源药剂,通过室内、田间试验,进行综合分析。室内毒力测定结果表明,甘草萤叶甲对0.5%黎芦碱SL的敏感性最高,LD50为0.139mg/L,0.3%印楝素EC、L2、1%苦参碱SL、L1依次递减,LD50分别为0.457,1.352,2.014和2.251mg/L,均高于其他药剂。田间防效结果表明,黎芦碱药后21d对甘草萤叶甲的防效最高,为100%,苦参碱、印楝素次之,均为86.67%,L2、L1的分别为66.67%和40%;对非靶标害虫小绿叶蝉也有较好的控制作用,药后21d防效L1较低,为56.67%,其他防效均高于68.89%;对田间天敌多异瓢虫和中华草蛉的安全性,除黎芦碱外,印楝素、苦参碱、L2、L1均较好,药后21d校正虫口减退率最高为57.14%;另外,苦参碱药后各期生物多样性指数平均最高,为2.93,印楝素次之,为2.88,藜芦碱、L1、L2依次递减,分别为2.45,2.43和2.07。因此,印楝素、苦参碱是防治甘草萤叶甲的理想药剂。     

Toxicity of N-substituted aromatics to acetoclastic methanogenic activity in granular sludge.

N-substituted aromatics are important priority pollutants entering the environment primarily through anthropogenic activities associated with the industrial production of dyes, explosives, pesticides, and pharmaceuticals. Anaerobic treatment of wastewaters discharged by these industries could potentially be problematical as a result of the high toxicity of N-substituted aromatics. The objective of this study was to examine the structure-toxicity relationships of N-substituted aromatic compounds to acetoclastic methanogenic bacteria. The toxicity was assayed in serum flasks by measuring methane production in granular sludge. Unacclimated cultures were used to minimize the biotransformation of the toxic organic chemicals during the test. The nature and the degree of the aromatic substitution were observed to have a profound effect on the toxicity of the test compound. Nitroaromatic compounds were, on the average, over 500-fold more toxic than their corresponding aromatic amines. Considering the facile reduction of nitro groups by anaerobic microorganisms, a dramatic detoxification of nitroaromatics towards methanogens can be expected to occur during anaerobic wastewater treatment. While the toxicity exerted by the N-substituted aromatic compounds was closely correlated with compound apolarity (log P), it was observed that at any given log P, N-substituted phenols had a toxicity that was 2 orders of magnitude higher than that of chlorophenols and alkylphenols. This indicates that toxicity due to the chemical reactivity of nitroaromatics is much more important than partitioning effects in bacterial membranes.     

Kinetic mechanisms of the nucleotide cofactor binding to the strong and weak nucleotide-binding site of the Escherichia coli PriA helicase. 2

Kinetics of the nucleotide binding to the strong (S) and weak (W) nucleotide-binding site of the Escherichia coli PriA helicase have been studied using the fluorescence stopped-flow technique. Experiments were performed with TNP-ADP and TNP-ATP analogues. Binding of the ADP analogue to the strong binding site is a four-step sequential reaction: (PriA)S + D (k1)<-->(k(-1)) + (S)1 (k2)<-->(k(-2)) (S)2 (k3)<-->(k(-3)) (S)3 (k4)<-->(k(-4)) (S)4. Association of TNP-ATP proceeds through an analogous three-step mechanism. The first two steps and intermediates are similar for both cofactors. However, the (S)3 intermediate is dramatically different for ADP and ATP analogues. Its emission is close to the emission of the free TNP-ADP, while it is by a factor of approximately 16 larger than the free TNP-ATP fluorescence. Thus, only the ADP analogue passes through an intermediate where it leaves the hydrophobic cleft of the site. This behavior corroborates with the fact that ADP leaves the ATPase site without undergoing a chemical change. The fast bimolecular step and the sequential mechanism indicate that the site is easily accessible to the cofactor, and it does not undergo an adjustment prior to binding. The subsequent step is also fast and stabilizes the complex. Magnesium profoundly affects the population of intermediates. The data indicate that the dominant (S)2 species is a part of the ATP catalytic cycle. ADP analogue binding to the weak nucleotide-binding site proceeds in a simpler two-step mechanism: (PriA)W + D (k1)<-->(k(-1)) (W)1 (k2)<-->(k(-2)) (W)2 with (W)1 being a dominant intermediate both in the presence and in the absence of Mg2+. The results indicate that the weak site is an allosteric control site in the functioning of the PriA helicase.     

Detailed dissection of a new mechanism for glycoside cleavage: alpha-1,4-glucan lyase

The unusual enzyme, Gracilariopsis alpha-1,4-glucan lyase of the sequence-related glycoside hydrolase family 31, cleaves the glycosidic bond of alpha-1,4-glucans via a beta-elimination reaction involving a covalent glycosyl-enzyme intermediate (Lee, S. S., Yu, S., and Withers, S. G. (2002) J. Am. Chem. Soc. 124, 4948-4949). The classical bell-shaped pH dependence of k(cat)/K(m) indicates two ionizable groups in the active site with apparent pK(a) values of 3.05 and 6.66. Br?nsted relationships of log k(cat) versus pK(a) and log(k(cat)/K(m)) versus pK(a) for a series of aryl glucosides both show a linear monotonic dependence on leaving group pK(a) with low beta(lg) values of 0.32 and 0.33, respectively. The combination of these low beta(lg) values with large secondary deuterium kinetic isotope effects (k(H)/k(D) = 1.16 - 1.19) on the first step indicate a glycosylation step with substantial glycosidic bond cleavage and proton donation to the leaving group oxygen at the transition state. Developed oxocarbenium ion character of the transition state is also suggested by the potent inhibition afforded by acarbose and 1-deoxynojirimycin (K(i) = 20 and 130 nM, respectively) and by the substantial rate reduction afforded by adjacent fluorine substitution. For only one substrate, 5-fluoro-alpha-D-glucopyranosyl fluoride, was the second elimination step shown to be rate-limiting. The large alpha-secondary deuterium kinetic isotope effect (k(H)/k(D) = 1.23) at C-1 and the small primary deuterium kinetic isotope effect (k(H)/k(D) = 1.92) at C-2 confirm an E2 mechanism with strong E1 character for this second step. This considerable structural and mechanistic similarity with retaining alpha-glucosidases is clear evidence for the evolution of an enzyme mechanism within the family.     

The Need for Multiple Lines of Evidence for Predicting Site-Specific Ecological Effects

The goal of this paper is to illustrate the value and importance of the “weight of evidence” approach (use of multiple lines of evidence from field and laboratory data) to assess the occurrence or absence of ecological impairment in the aquatic environment. Single species toxicity tests, microcosms, and community metric approaches such as the Index of Biotic Integrity (IBI) are discussed. Single species toxicity tests or other single lines of evidence are valuable first tier assessments that should be used as screening tools to identify potentially toxic conditions in a effluent or the ambient environment but these tests should not be used as the final quantitative indicator of absolute ecological impairment that may result in regulatory action. Both false positive and false negative predictions of ecological effects can occur due to the inherent variability of measurement endpoints such as survival, growth and reproduction used in single species toxicity tests. A comparison of single species ambient toxicity test results with field data showed that false positives are common and likely related to experimental variability or toxicity to selected test species without measureable effects on the ecosystem. Results from microcosm studies have consistently demonstrated that chemical exposures exceeding the acute or chronic toxicity concentrations for highly sensitive species may cause little or no ecologically significant damage to an aquatic ecosystem. Sources of uncertainty identified when extrapolating from single species tests to ecological effects were: variability in individual response to pesticide exposure; variation among species in sensitivity to pesticides; effects of time varying and repeated exposures; and extrapolation from individual to population-level endpoints. Data sets from the Chesapeake Bay area (Maryland) were used to show the importance of using “multiple lines of evidence” when assessing biological impact due to conflicting results reported from ambient water column and sediment toxicity tests and biological indices (benthic and fish IBIs). Results from water column and sediment toxicity tests with multiple species in tidal areas showed that no single species was consistently the most sensitive. There was also a high degree of disagreement between benthic and fish IBI data for the various stations. The lack of agreement for these biological community indices is not surprising due to the differences in exposure among habitats occupied by these different taxonomic assemblages. Data from a fish IBI, benthic IBI and Maryland Physical Habitat Index (MPHI) were compared for approximately 1100 first through third-order Maryland non-tidal streams to show the complexity of data interpretation and the incidence of conflicting lines of evidence. A key finding from this non-tidal data set was the need for using more than one biological indicator to increase the discriminatory power of identifying impaired streams and reduce the possibility of “false negative results”. Based on historical data, temporal variability associated with an IBI in undisturbed areas was reported to be lower than the variability associated with single species toxicity tests.     

Relationship between Cancer Slope Factor and Acute Toxicity in Rats and Fish

The purpose of this study was to examine bivariate relationships among cancer slope factor (CSF) and acute toxicity in rats and salmonid fish. Chemicals (n=43) were selected based on the availability of both oral CSF and acute toxicity data (rat oral median lethal dose [LD50] or salmonid median lethal concentration [LC50]). Rat oral LD50, salmonid LC50, and oral CSF data were log-transformed, and a Bonferroni-adjusted alpha level was set at 0.05 for subsequent correlation analysis. A significant correlation was observed between CSF and rat oral LD50 (r=?0.61) but not for CSF and salmonid LC50 (r=?0.29). Moreover, rat and fish acute toxicity were not significantly correlated (r=0.38). The significant correlation between CSF and rat oral LD50 compares favorably with published results reported in related studies. Accordingly, these results support prediction of carcinogenic potency, expressed as oral CSF, based in part on acute toxicity in rats.