A Comparison of Three Weight-of-Evidence Approaches for Integrating Sediment Contamination Data within and Across Lines of Evidence

Multiple lines of evidence (LOE) are often considered when examining the potential impact of contaminated sediment. Three strategies are explored for combining information within and/or among different LOE. One technique uses a multivariate strategy for clustering sites into groups of similar impact. A second method employs meta-analysis to pool empirically derived P-values. The third method uses a quantitative estimation of probability derived from odds ratios. These three strategies are compared with respect to a set of data describing reference conditions and a contaminated area in the Great Lakes. Common themes in these three strategies include the critical issue of defining an appropriate set of reference/control conditions, the definition of impact as a significant departure from the normal variation observed in the reference conditions, and the use of distance from the reference distribution to define any of the effect measures. Reasons for differences in results between the three approaches are explored and strategies for improving the approaches are suggested.     

Weight-of-Evidence Issues and Frameworks for Sediment Quality (And Other) Assessments

Weight of evidence (WOE) frameworks for integrating and interpreting multiple lines of evidence are discussed, focusing on sediment quality assessments, and introducing a series of ten papers on WOE. Approaches to WOE include individual lines of evidence (LOE) as well as combined LOE (indices, statistical summarization, logic systems, scoring systems, and best professional judgment [BPJ]). The application of WOE, based on multiple LOE, is discussed relative to the published literature. Fully implementing WOE requires consideration of six main LOE in sediment (or other assessments); these LOE generally correspond to other causality considerations including Koch's Postulates. However, the issue of sediment stability is an additional consideration, and the use of tabular decision matrices is recommended in a logic system to address LOE described by others as “analogy”, “plausibility”, or “logical and scientific sense.” Three examples of logic system WOE determinations based on the Sediment Quality Triad and using tabular decision matrices are provided. Key lessons from these examples include the: generally limited utility of sediment quality value (SQV)-based LOE; need for BPJ; importance of ecological relevance; importance of assessing background conditions; and, need for appropriately customizing study designs to suit sitespecific circumstances (rather than application of “boiler-plate” assessments). Overall, more quantitative approaches are needed that better define certainty elements of WOE in an open framework process, i.e., statistical summarization culminating in a logic system incorporating BPJ.     

SCGPred： A Score-based Method for Gene Structure Prediction by Combining Multiple Sources of Evidence

Predicting protein-coding genes still remains a significant challenge. Although a variety of computational programs that use commonly machine learning methods have emerged, the accuracy of predictions remains a low level when implementing in large genomic sequences. Moreover, computational gene finding in newly se- quenced genomes is especially a difficult task due to the absence of a training set of abundant validated genes. Here we present a new gene-finding program, SCGPred, to improve the accuracy of prediction by combining multiple sources of evidence. SCGPred can perform both supervised method in previously well-studied genomes and unsupervised one in novel genomes. By testing with datasets composed of large DNA sequences from human and a novel genome of Ustilago maydi, SCGPred gains a significant improvement in comparison to the popular ab initio gene predictors. We also demonstrate that SCGPred can significantly improve prediction in novel genomes by combining several foreign gene finders with similarity alignments, which is superior to other unsupervised methods. Therefore, SCGPred can serve as an alternative gene-finding tool for newly sequenced eukaryotic genomes. The program is freely available at http：//bio.scu.edu.cn/SCGPred/.     

Weight-of-Evidence (WOE): Quantitative Estimation of Probability of Impairment for Individual and Multiple Lines of Evidence

Environmental decision-making is complex and often based on multiple lines of evidence. Integrating the information from these multiple lines of evidence is rarely a simple process. We present a quantitative approach to the combination of multiple lines of evidence through calculation of weight-of-evidence, with reference conditions used to define a not impaired state. The approach is risk-based with measurement of risk computed as the probability of impairment. When data on reference conditions are available, there are a variety of methods for calculating this probability. Statistical theory and the use of odds ratios provide a method for combining the measures of risk from the different lines of evidence. The approach is illustrated using data from the Great Lakes to predict the risk at potentially contaminated sites.     

Lines of Evidence for Horizontal Gene Transfer of a Phenazine Producing Operon into Multiple Bacterial Species

Phenazines are secondary metabolites with broad-spectrum antibiotic activity against bacteria, fungi, and eukaryotes. In pseudomonad species, a conserved seven-gene phenazine operon (phzABCDEFG) is required for the conversion of chorismic acid to the broad-spectrum antibiotic phenazine-1-carboxylate. Previous analyses of genes involved in phenazine production from nonpseudomonad species uncovered a high degree of sequence similarity to pseudomonad homologues. The analyses undertaken in this study wished to eluciadate the evolutionary history of genes involved in the production of phenazines. Furthermore, I wanted to determine if the phenazine operon has been transferred through horizontal gene transfer. Analyses of GC content, codon usage patterns, frequency of 3:1 dinucleotides, sequence similarities, and phylogenetic reconstructions were undertaken to map the evolutionary history of phenazine genes from multiple bacterial species. Patchy phyletic distribution, high sequence similarities, and phylogenetic evidence infer that pseudomonad, Streptomyces cinnamonensis, Pantoea agglomerans, Burkholderia cepacia, Pectobacterium atrosepticum, Brevibacterium linens, and Mycobacterium abscessus species all contain a phenazine operon which has most likely been transferred among these species through horizontal gene transfer. The acquisition of an antibiotic-associated operon is significant, as it may increase the relative fitness of the recipient species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Procedure for Ecological Tiered Assessment of Risks (PETAR)

Several procedures for Ecological Risk Assessment (ERA) have been suggested. The use of these existing procedures often relies on availability of existing data and/or on large resources for acquisition of new ones. This paper presents a three-tiered procedure for retrospective evaluation of risks adapted to limited resources and scarce background information of relevance for risk assessments, such as in developing countries. The tiers require successively more detailed investigations. The approach assures that resources available for site-specific investigations are directed towards well-formulated questions raised during previous stages of the assessment. The first tier, the preliminary assessment, is a qualitative evaluation of existing information on anthropogenic stressors, sources of stressors and expected ecological effects. The second tier is a regional risk assessment; a semi-quantitative evaluation of ecological risks, over large geographical areas, which results in a ranking of sources and stressors having the greatest potential for ecological impact and ranking of subareas inside the study area more likely to be impacted. The final tier is a site-specific and quantitative risk assessment, at a smaller scale and requiring more resources, that incorporates methodologies for establishing causality between exposure to multiple stressors and effects on specific endpoints of ecological and societal relevance.     

A method for evaluating the impact of navigationally induced suspended sediments from the Upper Great Lakes Connecting Channels on the primary productivity

The impact of navigationally induced suspended sediments from the Upper Great Lakes Connecting Channels on the size-fractionated primary productivity was evaluated by the Carbon-14 technique. The method applied was on-site, rapid, sensitive, inexpensive, and provided dynamic-toxicological information essential for hazard assessment. Both enhancement and inhibition of the primary productivity was observed in various parts of the Upper Great Lakes Connecting Channels. These responses appear to depend on the type of natural plankton and their exposure to various contaminant/nutrient complexes generated by the disturbance of the bottom sediments during the passage of ships. Traditionally, only the inhibition of primary productivity has been monitored from a toxicity point of view, but it is important also to evaluate the implications of enhancement since it may result in increased eutrophication, propagation of nuisance blooms, and change of intricate food-web interactions. The procedure adopted in this study for the first time appears to possess considerable potential for a simple and rapid screening of environmental perturbations resulting from navigational activities.     

Comparative Toxicity of Three Organic Acids to Freshwater Organisms and Their Impact on Aquatic Ecosystems

The comparative toxicity of lactic acid, acetic acid, and benzoic acid to tilapia (Oreochromis mossambicus), cladoceran crustacea (Moina micrura), and oligochaete worm (Branchiura sowerbyi) were determined using static bioassay tests. Worms were found most sensitive to all the acids whereas the cladoceran was found most resistant to lactic acid and the fish most resistant to acetic acid and benzoic acid. The 96h LC₅₀ values of lactic acid, acetic acid, and benzoic acid, were, respectively, 257.73, 272.87, and 276.74 mg L^?1 for O. mossambicus; 329.12, 163.72, and 71.65 mg L^?1 for M. micrura and 50.82, 14.90, and 39.47 mg L^?1 for B. sowerbyi. Tilapia lost appetite at sub-lethal concentrations as low as 2.18 mg L^?1 lactic acid, 1.26 mg L^?1 acetic acid, and 13.84 mg L^{? 1} of benzoic acid. Growth and reproduction of the fish were affected following 90-day chronic exposure to sub-lethal concentrations of the acids. Minimum effective concentration of the acids that significantly reduced food conversion efficiency (FCE), percent increase of weight, specific growth rate, yield and fecundity of the fish were 2.18, 1.47, and 3.95 mg · L^?1 of lactic acid, acetic acid, and benzoic acid, respectively. Effects of acetic acid and benzoic acid on FCE, weight increase, and yield were not significantly different from each other whereas lactic acid produced different effects from acetic acid as well as benzoic acid. Mean values of dissolved oxygen, primary productivity, and plankton populations of the test medium significantly reduced from control at 16.94 mg L^?1 lactic acid, 16.79 mg L^?1 acetic acid, and 13.84 mg L^?1 benzoic acid.     

Estimating the Toxicity of Pesticide Mixtures to Aquatic Organisms: A Review

A major difficulty in addressing chemical mixtures through legislation or regulations revolves around our limited understanding of their potential impacts. This review provides an overview of recent research on pesticide mixture toxicity to aquatic biota and the methods employed to predict toxic effects. The most common approaches are to assume concentration-addition or independent action of chemicals in a mixture. There are a number of cases in the literature of interactions between pesticides. However, models accounting for possible interactions between mixture components are used infrequently. Although results are limited, studies investigating the effects of pesticide mixtures have not demonstrated significant synergism at environmentally relevant concentrations. Based on the results of our review, we conclude that the concentration-addition model is a generally conservative and practical first-tier model for the ecological assessment of pesticide mixtures in aquatic systems.     

Response of shape in vitro cultures of shape Nicotiana tabacum L. to copper stress and selection of plants from Cu-tolerant callus

In Nicotiana tabacum L. var. BEL W3 copper (Cu) at concentrations higher than 50 μM significantly inhibited callus growth and shoot regeneration. After 5–6 months of culture only a few morphogenic callus lines survived in the presence of 100 μM Cu. These calluses showed the capacity to grow and regenerate shoots through successive subcultures on medium containing 100 μM Cu. The 100 μM Cu-tolerant shoots, in comparison to regenerated control shoots, formed roots only when cultured in the presence of 100 μM Cu. From five independent Cu-tolerant callus lines in a culture period of 4–5 months more than 50 plants (defined ‘tolerant’) able to grow in presence of 100 μM Cu were obtained. These plants showed normal xylem tissue formation while control regenerated plants growing in normal Cu MS content (0.1 μM) had few xylem elements in the central cylinder. No difference as far chlorophyll content and chloroplast structure was found among Cu-tolerant and control plants. In Cu-tolerant plants, dry matter production was higher than in controls, particularly in roots. This revised version was published online in June 2006 with corrections to the Cover Date.     

A Method to Estimate Practical Radial Oxygen Loss of Wetland Plant Roots

The estimation of practical radial oxygen loss (ROL) of wetland plant roots was attempted in this study. We have devised a new method to measure ROL of wetland plant roots. The whole root system was bathed in an anoxic nutrient solution. Oxygen released from the root was removed immediately by introducing oxygen-free nitrogen gas (O₂ < 4 nmol L⁻¹) to mimic natural habitats where released oxygen is consumed rapidly due to chemical and biological oxidation processes. Oxygen removed from the root-bathing chamber was simultaneously detected colorimetrically by use of the highly oxygen-sensitive anthraquinone radical anion (AQ·⁻) in a cell outside the root-bathing chamber, which decolorized by a rapid reaction with oxygen. An emergent macrophyte Typha latifolia L. was incubated, and its ROL was measured by both the new method and one of the conventional methods, the closed chamber/electrode method, by which the ROL of Typha latifolia L. had not yet been measured. The new method succeeded in detecting the ROL, whereas the conventional method was not able to detect oxygen, due to the level being below the detection limit of the oxygen electrode. The oxygen supply via the seedlings of Typha latifolia L. was ca. 10 times higher compared with control measurements without plant. Light illumination significantly enhanced the ROL of Typha latifolia L. (0.33 nmol O₂ g⁻¹ root dry weight s⁻¹ under light and 0.18 nmol O₂ g⁻¹ root dry weight s⁻¹ in the dark). Theses values fall between those previously reported by the closed chamber/titanium citrate method and the open chamber/electrode method.     

A Competitive Microflora Increases the Resistance of Salmonella typhimurium to Inimical Processes: Evidence for a Suicide Response

The presence of a viable competitive microflora at cell densities of 10⁸ CFU ml⁻¹ protects an underlying population of 10⁵ CFU of Salmonella typhimurium ml⁻¹ against freeze injury. The mechanism of enhanced resistance was initially postulated to be via an RpoS-mediated adaptive response. By using an spvRA::luxCDABE reporter we have shown that although the onset of RpoS-mediated gene expression was brought forward by the addition of a competitive microflora, the time taken for induction was measured in hours. Since the protective effect of a competitive microflora is essentially instantaneous, the stationary-phase adaptive response is excluded as the physiological mechanism. The only instantaneous effect of the competitive microflora was a reduction in the percent saturation of oxygen from 100% to less than 10%. For both mild heat treatment (55°C) and freeze injury this change in oxygen tension affords Salmonella a substantive (2 orders of magnitude) enhancement in survival. By reducing the levels of dissolved oxygen through active respiration, a competitive microflora reduces oxidative damage to exponential-phase cells irrespective of the inimical treatment. These results have led us to propose a suicide hypothesis for the destruction of rapidly growing cells by inimical processes. In essence, the suicide hypothesis proposes that a mild inimical process leads to the growth arrest of exponential-phase cells and to the decoupling of anabolic and catabolic metabolism. The result of this is a free radical burst which is lethal to unadapted cells.     

内蒙古科尔沁沙地两种沙生植物冷蒿和差不嘎蒿竞争策略的生理生态学依据(英文)

Gas exchange, water relations and leaf chemical characteristics were examined of twodominant psammophytes: Artemisia frigida Willd and A halodendron Turcz. ex Bess in Horqin sandy land, NeiMongol, China under different water regimes. The measurements were conducted by submitting the plantsto five different irrigation levels. A. fTigida was characterized by lower photosynthetic rate (Pn), lowertranspiration rate ( TR and lower shoot water potential (ψuw) relative to A. halodendron. Foliage of A frigdahad higher values of relative water deficit (RWD), bound water content (BWC), ratio of bound water contentto free water content (BWC/FWC) and integrated drought-resistant index (DI than that of A. halodendron.Water relations differed significantly between two species in response to soil water availability. ψw, BWCand BWC/FWC ratio of A halodendron exhibited large variation with gradual decrease of soil moisture.However, in terms of these parameters, A. fRIGIDA was characterized by higher capacity of water holding anddrought tolerance relative to A halodendron. Proline and total soluble sugar contents of A frigida and Ahalodendron tended to increase with decrease of soil moisture and the former had a larger increaseamplitude than the latter. This shows that A frigida has a higher osmotic regulation ability than A halodendron.Under the extreme drought conditions, ψw, RWD, BWC and BWC/FWC of two species were approximate,but soluble proteins degraded largely. A large amount of accumulation of organic matter, proline and totalsoluble sugars were observed in both A halodendron and A frigida. The increase in proline and total solublesugar contents and soluble protein degradation of A frigida far exceeded those of A. halodendron. Webelieve that the accumulated materials at this moment are mostly of nutrient substances available for therecovery of plants after the drought. This is one of the reasons why A halodendron plants died while Afrigida plants survived under extremely drought condition. Our results suggest that these ecophysiologicalfeatures of A frigida are favorable to its growth in the fixed sandy land compared with A halodendron, whichoften lost its dominance due to weak competition for water sources under lower soil water availability andare major factors resulting in replacement of A. halodendron by A. frigida in the later stage of sandyvegetation succession in Horqin.     

Exposure and Multiple Lines of Evidence Assessment of Risk for PCBs Found in the Diets of Passerine Birds at the Kalamazoo River Superfund Site,Michigan

Dietary exposures of passerine birds at the Kalamazoo River, Michigan, were examined due to the presence of polychlorinated biphenyls (PCBs) in the terrestrial and aquatic food webs. Average potential daily doses in diets were 6- to 29-fold and 16- to 35-fold greater at a contaminated location than at a reference location for PCB exposures quantified as total PCBs and 2,3,7,8–tetrachlorodibenzo-p-dioxin equivalents (TEQs), respectively. Birds with diets comprised of primarily aquatic insects had greater dietary exposure than birds with diets of primarily terrestrial insects. Risk associated with dietary exposure varied with the selection of the threshold for effects including hazard quotients, which exceeded 1 in instances where the most conservative toxicity reference values were utilized. Risk based on concentrations of PCBs in the tissues indicated little risk to avian species, and co-located studies evaluating reproductive health did not suggest that observed incidences of diminished reproductive success were related to PCB exposure. Measures of risk based on comparison to toxicity reference values (TRVs) were consistent with direct measures of ecologically relevant endpoints of reproductive fitness, but uncertainty exists in the selection of threshold values for effects in these species especially based on TEQs. This is largely due to the absence of species-specific, dose-response relationships. Therefore, the best estimate of risk is through the application of multiple lines of evidence.     

A potential economical substrate for large-scale production of Bacillus thuringiensis var. kurstaki for caterpillar control

Bacillus thuringiensis var. kurstaki has been widely used in caterpillar control programs. Large-scale production of this bacterium is expensive because of the high cost of the raw materials used in the medium. In this study, we attempted to develop an economical medium, based on inexpensive, locally available raw materials using a 3-L fermenter. Parthenium hysterophorus L. extract based culture medium resulted in highest toxicity (LC₅₀ 14.628 µg mL–¹) against 7-day-old Spodoptera litura (Fab) larvae, spore count (4.1 × 10⁹ spores mL^–1) and biomass (4.9 g L^–1) within a short fermentation time of 36 h. It was 512 times cheaper than the nutrient broth (standard medium) used for B. thuringiensis production. Hence, this parthenium extract based culture medium was considered most economical with potential for the large-scale industrial production of B. thuringiensis.     

Evidence for the contribution of LTR retrotransposons to C. elegans gene evolution

LTR retrotransposons may be important contributors to host gene evolution because they contain regulatory and coding signals. In an effort to assess the possible contribution of LTR retrotransposons to C. elegans gene evolution, we searched upstream and downstream of LTR retrotransposon sequences for the presence of predicted genes. Sixty-three percent of LTR retrotransposon sequences (79/124) are located within 1 kb of a gene or within gene boundaries. Most gene-retrotransposon associations were located along the chromosome arms. Our results are consistent with the hypothesis that LTR retrotransposons have contributed to the structural and/or regulatory evolution of genes in C. elegans.     

A Strategy to Optimize the Oligo-Probes for Microarray-based Detection of Viruses

DNA microarrays have been acknowledged to represent a promising approach for the detection of viral pathogens. However, the probes designed for current arrays could cover only part of the given viral variants, that could result in false-negative or ambiguous data. If all the variants are to be covered, the requirement for more probes would render much higher spot density and thus higher cost of the arrays. Here we have developed a new strategy for oligonucleotide probe design. Using type I human immunodeficiency virus (HIV-1) tat gene as an example, we designed the array probes and validated the optimized parameters in silico. Results show that the oligo number is significantly reduced comparing with the existing methods, while specificity and hybridization efficiency remain intact. The adoption of this method in reducing the oligo numbers could increase the detection capacity for DNA microarrays, and would significantly lower the manufacturing cost for making array chips.     

初生根伸长对环境响应的数学模型

在根组织细胞分裂和细胞体积增大亚过程基础上,建立了一个综合根生长特征参数和环境影响在内的单根伸长的数学模型,同时实验观测了大豆根在不同的环境水势下的生长过程。模型计算结果与实验结果吻合较好。最后利用模型探讨了根伸长对环境因子变化的响应,以及根内水势分布。     

Evidence for a shift from IgD to IgA synthesis in the maturation of human B lymphocytes.

A case of chronic lymphatic leukemia (CLL) is described in which IgD and IgA are the copredominant membrane immunoglobulins. Since CLL represents malignant proliferations of B lymphocytes arrested at discrete points during maturation, the findings in this case suggest that at least some of the developing cells destined to synthesize IgA for secretion pass through a stage in which immunoglobulins D and A are present together on the cell membrane.