Changes in Toxicity and Mobility Resulting from Bioremediation Processes

Bioremediation is a commonly used process for the remediation of soils and sludges containing hydrocarbon compounds. The extent of chemical concentration reduction that occurs in bioremediation processes and the concentration of residual chemicals varies widely for different soils and sludges and for different processes. Along with changes in chemical concentration, measures of toxicity and chemical mobility are important information as site remediation decisions are increasingly being made within a risk-based corrective action framework.

This review article presents illustrative data from studies that evaluated the effectiveness of bioremediation processes and that contained information about changes in chemical mobility and soil or sludge toxicity. The weight-of-evidence data presented indicated that, as part of the bioremediation process, there is a reduction of the apparent toxicity of the soils and sludges that were treated. In addition, remaining chemical constituents generally were less mobile. The patterns were consistent for both laboratory and field-scale bioremediation studies.     

A CHROMATOGRAPHIC INVESTIGATION OF INTERSPECIFIC RELATIONSHIPS IN PINUS (SUBSECTION SYLVESTRES)

The foliage polyphenols of 16 Pinus species were compared by two-dimensional paper chromatography. The general patterns of chemical similarity were correlated with the geographic distributions of the species; sympatric species generally had greater chemical affinity than did allotropic species. This relationship did not always correspond to hybridization patterns and morphological similarities. The distinctive chromatographic patterns of the Southeast Asian species (P. insularis, P. luchuensis, P. merkusii) and their generally low affinities with species of Europe and the Asian mainland suggest that further investigation of the morphological relationships and the genetic compatibility of these species with other Sylvestres species is warranted. The chemical relationships of P. halepensis and P. heldreichii to other Sylvestres species were also unclear. The qualitative differences in polyphenols among species are consistent and of sufficient magnitude to enable the application of chromatographic analysis to studies of interspecific hybridization in Pinus.     

Negentropy and the evolution of chemical recruitment in ants (Hymenoptera: Formicidae)

The applicability of the concept of negentropy to the study of evolution is tested by tracing the phylogeny of the information content of the communication systems used for recruitment in the Formicidae. Data from the literature is reviewed and ordered around theoretical evolutionary routes based on increasing negentropy of the chemical communication systems used. One pathway presupposes the development of chemical orientation prior to chemical attraction, i.e. signalling the presence of food; whereas the others begin with the chemical attraction of nestmates without orientation with chemical cues to the food. The results suggest that the Myrmicinae, Ponerinae, Dolichoderinae, Pseudomyrmycinae and possibly Dorylinae evolved chemical recruitment via chemical attraction, whereas the Formicinae evolved chemical recruitment via chemical orientation. These alternative patterns permit the establishment of phyletic trends based on glandular evolution for chemical recruitment. The results are compared with phylogenetic studies based on morphological and chemical characters, and it emerges that the recruitment behaviour proves to be a particularly conservative characteristic, in that it is evident in the same form in a wider range of species. The conclusion is reached that the negentropy content of living systems is a powerful tool in phylogenetic studies, even of small taxonomic groups.     

Social behavior and pheromonal communication in reptiles

The role of pheromones in orchestrating social behaviors in reptiles is reviewed. Although all reptile orders are examined, the vast majority of the literature has dealt only with squamates, primarily snakes and lizards. The literature is surprisingly large, but most studies have explored relatively few behaviors. The evolution of chemical signaling in reptiles is discussed along with behaviors governed by pheromones including conspecific trailing, male-male agonistic interactions, sex recognition and sex pheromones, and reptilian predator recognition. Nonreptilian prey recognition by chemical cues was not reviewed. The recent literature has focused on two model systems where extensive chemical ecology studies have been conducted: the reproductive ecology of garter snakes and the behavioral ecology of Iberian lacertid lizards. In these two systems, enough is known about the chemical constituents that mediate behaviors to explore the evolution of chemical signaling mechanisms that affect life history patterns. In addition, these models illuminate natural and sexual selection processes which have lead to complex chemical signals whose different components and concentrations provide essential information about individuals to conspecifics. Reptiles provide excellent candidates for further studies in this regard not only in squamates, but also in the orders where little experimental work has been conducted to date.     

Interpretation of nonlinear steady state enzyme kinetics—Cyclic and mathematical properties of cooperative,second-site and random pathway models

Nonlinear steady state kinetic patterns are frequently encountered in enzyme studies. Consequently, there is a need to develop procedures for systematically interpreting such data. This paper contributes to this development by identifying a common feature in nonlinear systems and by showing that quite different models commonly in use give very similar mathematical functions.Identical or similar cycles can result from quite different chemical events in enzyme mechanisms, cooperativity, second sites and random pathways. Such cycles can account for many of the observed nonlinear patterns, i.e., power functions, substrate activation and inhibition. Therefore nonlinear steady state kinetics generally requires the presence of a cycle(s) in the mechanism without specifying the underlying chemical events giving rise to that cycle(s).Rate equations for cooperative, second-site and random pathway models are derived and shown to yield virtually identical mathematical functions. Thus empirical equations composed of these functions can be used to represent nonlinear kinetic data without specifying the underlying chemical events.     

Biochemical and chemical studies on Bacteroides multiacidus and Bacteroides hypermegas

Biochemical and chemical studies were performed on representative strains of Bacteroides hypermegas and Bact. multiacidus in an attempt to clarify their taxonomy. The results of the present and earlier studies indicate that Bact. hypermegas and Bact. multiacidus are distinct species. On the basis of DNA base composition, enzyme patterns and lipid criteria it is suggested that both species should be excluded from the genus Bacteroides.     

Metabolomics: a tool for early detection of toxicological effects and an opportunity for biology based grouping of chemicals-from QSAR to QBAR

BASF has developed a Metabolomics database (MetaMap(?) Tox) containing approximately 500 data rich chemicals, agrochemicals and drugs. This metabolome-database has been built based upon 28-day studies in rats (adapted to OECD 407 guideline) with blood sampling and metabolic profiling after 7, 14 and 28 days of test substance treatment. Numerous metabolome patterns have been established for different toxicological targets (liver, kidney, thyroid, testes, blood, nervous system and endocrine system) which are specific for different toxicological modes of action. With these patterns early detection of toxicological effects and the underlying mechanism can now be obtained from routine studies. Early recognition of toxicological mode of action will help to develop new compounds with a more favourable toxicological profile and will also help to reduce the number of animal studies necessary to do so. Thus this technology contributes to animal welfare by means of reduction through refinement (2R), but also has potential as a replacement method by analyzing samples from in vitro studies. With respect to the REACH legislation for which a large number of animal studies will need to be performed, one of the most promising methods to reduce the number of animal experiments is grouping of chemicals and read-across to those which are data rich. So far mostly chemical similarity or QSAR models are driving the selection process of chemical grouping. However, "omics" technologies such as metabolomics may help to optimize the chemical grouping process by providing biologically based criteria for toxicological equivalence. "From QSAR to QBAR" (quantitative biological activity relationship).     

Engineering chromatin states: Chemical and synthetic biology approaches to investigate histone modification function

Patterns of histone post-translational modifications (PTMs) and DNA modifications establish a landscape of chromatin states with regulatory impact on gene expression, cell differentiation and development. These diverse modifications are read out by effector protein complexes, which ultimately determine their functional outcome by modulating the activity state of underlying genes. From genome-wide studies employing high-throughput ChIP-Seq methods as well as proteomic mass spectrometry studies, a large number of PTMs are known and their coexistence patterns and associations with genomic regions have been mapped in a large number of different cell types. Conversely, the molecular interplay between chromatin effector proteins and modified chromatin regions as well as their resulting biological output is less well understood on a molecular level. Within the last decade a host of chemical approaches has been developed with the goal to produce synthetic chromatin with a defined arrangement of PTMs. These methods now permit systematic functional studies of individual histone and DNA modifications, and additionally provide a discovery platform to identify further interacting nuclear proteins. Complementary chemical- and synthetic-biology methods have emerged to directly observe and modulate the modification landscape in living cells and to readily probe the effect of altered PTM patterns on biological processes. Herein, we review current methodologies allowing chemical and synthetic biological engineering of distinct chromatin states in vitro and in vivo with the aim of obtaining a molecular understanding of histone and DNA modification function. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.     

Differences in Metabolism of Chemical Carcinogens in Cultured Human Epithelial Tissues and Cells

The metabolism of chemical carcinogens has been studied in cultured human bronchus, colon, duodenum, pancreatic duct, and esophagus. Metabolite patterns and carcinogen-DNA adducts are generally qualitatively similar among animal species, individuals within a species, and tissues within an individual. However, wide quantitative differences are observed between individuals in out-bred animal species, including humans. These interindividual differences in amounts of carcinogen-DNA adducts and in activities of enzymes that are important in the metabolism of chemical carcinogens are similar in magnitude (10-to 150-fold) to those observed in pharmacogenetic studies of drug metabolism. The role of these differences as risk factors in human cancer is being investigated.     

The flavin environment in old yellow enzyme. An evaluation of insights from spectroscopic and artificial flavin studies

Spectroscopic and chemical modification studies of modified flavins bound to old yellow enzyme have led to predictions about the flavin environment of this enzyme. These studies analyzed solvent accessibility and hydrogen bonding patterns of particular flavin atoms, in addition to suggesting amino acid residues that are in close proximity to those atoms. Here, these studies are evaluated in the light of the crystal structure of old yellow enzyme to reveal that the spectroscopic and modified flavin results are generally consistent with the crystal structure. This highlights the fact that these are useful methods for studying flavin binding site structure. Although several of the inferred properties of the flavin environment are not consistent with the crystal structure, these discrepancies occurred in cases where an incorrect choice was made from among multiple plausible explanations for an experimental result. We conclude that modified flavin studies are powerful probes of flavin environment; however, it is risky to specify details of interactions, especially because of uncertainties due to induced charge delocalization in the flavin.     

Chemo-orientation responses in hymenopteran parasitoids induced by substrate-borne semiochemicals

Hymenopteran parasitoids can utilize substrate-borne semiochemicals released by conspecifics or by their hosts, increasing the likelihood of successful mating and host location. According to the literature, two substrate-borne chemo-orientation patterns can occur: (1) biased random searching, a non-directional reaction toward the chemicals (kinesis), and (2) trail-following searching, a directional response toward the source emitting the chemical compounds (taxis). These two different strategies can be adopted by parasitoids to locate hosts and mates. In host location, random searching is induced by allelochemicals indirectly associated with the host, whereas trail-following behavior is induced by allelochemicals directly emitted by the target organism. In mate finding, sex pheromones emitted by conspecifics can induce either the random searching or the trail-following behavior, although the spatial distribution of virgin conspecifics could be an important factor driving the evolution of substrate-borne chemo-orientation patterns. The chemical nature of substrate-borne semiochemicals has not yet been fully elucidated. Most studies have shown that crude extracts are biologically active for eliciting parasitoid arrestment response, but few studies have clearly characterized their chemical nature. However, experimental evidence indicates that cuticular lipids located in the external layer of insects’ bodies play a role in parasitoid–parasitoid and host–parasitoid communication. The ecological role of parasitoid chemo-orientation in host and mate location is discussed from a biological control perspective.     

A Mechanochemical Model for Embryonic Pattern Formation: Coupling Tissue Mechanics and Morphogen Expression

Motivated by recent experimental findings, we propose a novel mechanism of embryonic pattern formation based on coupling of tissue curvature with diffusive signaling by a chemical factor. We derive a new mathematical model using energy minimization approach and show that the model generates a variety of morphogen and curvature patterns agreeing with experimentally observed structures. The mechanism proposed transcends the classical Turing concept which requires interactions between two morphogens with a significantly different diffusivity. Our studies show how biomechanical forces may replace the elusive long-range inhibitor and lead to formation of stable spatially heterogeneous structures without existence of chemical prepatterns. We propose new experimental approaches to decisively test our central hypothesis that tissue curvature and morphogen expression are coupled in a positive feedback loop.     

Chemical variation within and among six northern willow species

Plant tissues typically contain a diverse complement of secondary metabolites that serve as protection against various biotic and abiotic hazards. Chemical similarities are commonly used to infer phylogenetic relationships among plant taxa, but the studies are typically based on the mean concentration of each compound in each study species, thus overlooking within-species variability. In order to investigate patterns of intra- and interspecific chemical variation in plants, we measured the concentrations of condensed tannins and 36 other phenolic compounds in 120 leaf samples representing six northern Salix species. Multivariate clustering and ordination analyses of the data show that: (1) Despite considerable within-species variation in chemical profiles, intraspecific variability is on average lower than the variation among species. (2) Interspecific similarities are sensitive to the data analysis methods used, and different chemical classes produce partly contradictory results. (3) Compounds within each biosynthetic class tend to behave in a correlated manner and, consequently, overall chemical similarities are weakly correlated with the phylogeny of the studied species. The conclusion is that chemical data are poorly suited for phylogenetic inference, unless methods for data analysis are improved to take into account the biosynthetic routes by which the compounds are produced.     

Role of hydrocarbons in egg recognition in the honeybee

Abstract. Despite worker‐laid and queen‐laid honeybee eggs having significantly different hydrocarbon profiles, bioassays and chemical supplementation studies show that changing the hydrocarbon profile does not affect egg identity. Furthermore, full‐sized eggs that are tested just before being laid or just after being laid have similar hydrocarbon patterns but are treated differently in egg‐discrimination bioassays with only the laid eggs surviving. This suggests that hydrocarbons play no role in the egg‐recognition system in honeybees.     

Development of Diagnostic Microscopic and Chemical Markers of Some Euphorbia Latexes

The latexes of the three Euphorbia species, namely E. antiquorum L., E. nerifolia L., and E. tirucalli L., are highly valued in the Indian system of medicine as purgatives, in addition to their specific and distinct therapeutic activities. In order to distinguish these latexes and develop their diagnostic microscopic and chemical markers, we performed extensive chemical and microscopic studies. The three latexes differ significantly in their microscopic features by exhibiting characteristic starch grain patterns. Although amoebic structures were found to be characteristic of E. antiquorum, dumb-bell and oval structures are characteristic of E. nerifolia and E. tirucalli, respectively. In addition, these latexes showed bone-shaped structures as a common feature, but these differed considerably in their length （10-60, 30-55, and 50-70 μm in length in E. antiquorum, E. nerifolia, and E. tirucalli, respectively）. The chemical markers nerifoliene and euphol were found to be common to both E. antiquorum and E. nerifolia, whereas euphol is the only marker for E. tirucalli. A reverse-phase high-performance thin-layer chromatographic （HPTLC） method was developed to distinguish these three latexes and to generate their standard fingerprinting patterns. Most significantly, the markers nerifoliene and euphol could be resolved by RP-18 F254s precoated aluminium plates and the latexes have been quantitatively estimated with respect to these markers. The developed microscopic, chemical and HPTLC patterns can be used to distinguish the three latexes.     

Phytochemical diversity and synergistic effects on herbivores

Synergistic effects of multiple plant secondary metabolites on upper trophic levels constitute an underexplored but potentially widespread component of coevolution and ecological interactions. Examples of plant secondary metabolites acting synergistically as insect deterrents are not common, and many studies focus on the pharmaceutical applications of natural products, where activity is serendipitous and not an evolved response. This review summarizes some systems that are ideal for testing synergistic plant defenses and utilizes a focused meta-analysis to examine studies that have tested effects of multiple compounds on insects. Due to a dearth of ecological synergy studies, one of the few patterns for synergy that we are able to report from the meta-analysis is that phytochemical mixtures have a larger overall effect on generalist herbivores than specialist herbivores. We recommend a focus on synergy in chemical ecology programs and suggest future hypothesis tests and methods. These approaches are not focused on techniques in molecular biology to examine mechanisms at the cellular level, rather we recommend uncovering the existence of synergy first, by combining the best methods in organic synthesis, isolation, chemical ecology, bioassays, and quantitative analyses. Data generated by our recommended methods should provide rigorous tests of important hypotheses on how intraclass and interclass compounds act synergistically to deter insects, disrupt the immune response, and ultimately contribute to diversification. Further synergy research should also contribute to determining if antiherbivore synergy is widespread among plant secondary metabolites, which would be consistent with the hypothesis that synergistic defenses are a key attribute of the evolved diverse chemical mixtures found in plants.     

Edaphic and Floristic Variation within a 1‐ha Plot of Lowland Amazonian Rain Forest1

Several studies in lowland tropical rain forests have documented effects of local‐scale topographic variation on plant species distribution and abundance patterns. Few studies have compared the distribution patterns of more than one plant group, however, and even fewer have related these to measured physical and chemical soil characteristics. Here, we document such soil characteristics within a square 1‐ha plot in Amazonian Ecuador, and compare them to the distribution patterns of terrestrial pteridophytes, angiosperm ground herbs, and palms. Substantial variation in soil properties was found within the plot. The three plant groups showed highly correlated floristic patterns within the 1‐ha plot even after the effect of geographical distances had been taken into account. Mantel tests yielded significant correlations between edaphic patterns, as measured by distances in various soil and topographic characteristics, and floristic patterns. For all three plant groups, differences in elevation within the plot were highly correlated with floristic distances, and for terrestrial pteridophytes and palms, distances in soil calcium content and sand content were also important. Our results resembled those obtained at wider spatial scales with the same plant groups, which indicates that soil factors may play an important role for distribution and beta diversity of plants, even at the local scale.