Estimating Potency for Hierarchical Dichotomous Responses in an Aquatic Toxicology Study

Toxicants in aquatic organisms may impact a variety of responses including hatching, survival, growth, deformity, and reproduction. These responses have a hierarchical relationship since survival is only possible for hatched organisms and deformity is only possible if organisms survive. Linear models and generalized linear models have been widely used to analyze individual responses; however, an analysis that simultaneously considers the structure of all responses would allow a more comprehensive assessment of toxicity. Ignoring the hierarchy of these responses and applying separate modeling approaches could be misleading. Motivated by a study of hatching–survival–deformities in fish, we developed a method to model these responses simultaneously. In the present study, we propose a Bayesian multinomial regression model to analyze the hierarchical toxicity responses simultaneously and estimate the concentrations associated with a specified level of reproductive inhibition (RI _p ) on hatching success, post hatching survival and deformity, respectively. Simulation studies are conducted to compare the estimates from the hierarchical model with those from the response-specific separate models. The proposed model outperforms the separate model by producing more precise point estimates and interval estimates with better coverage probabilities. The proposed method is illustrated with data from a study of hatching–survival–deformities in fish. The proposed model captures the hierarchy in the multiple responses from animals in the toxicity test and hence improves the understanding of concentration–response relationships for these responses. It provides a useful template of modeling hierarchical dichotomous responses in the aquatic toxicity studies.     

Stress combination: When two negatives may become antagonistic,synergistic or additive for plants?

Plants in their natural environment are constantly subjected to various abiotic and biotic stressors and, therefore, have developed several defense mechanisms to maintain fitness. Stress responses are intricate and require various physiological, biochemical, and cellular changes in plants. The reaction mechanisms in plants subjected to drought, salinity, or heat stress alone have been explained in numerous studies. However, the field conditions are significantly different from the controlled lab...     

Exogenous application of vitamins as regulators for growth and development of plants — a review

A survey of the recent literature on plant responses to exogenous vitamin application yielded the following results:

• Vitamins have been applied by soaking seeds, dipping cuttings, by sprays or dusts and as drenches to soils.
• Substantial yield increases due to exogenous vitamin application have been reported by a number of researchers.
• Vitamins may cause morphogenetic responses in plants. Most pronounced is the stimulation of root formation and of flowering under non-inductive conditions.
• Certain vitamins protect plants against ozone and sulfur dioxide, two important agents of air pollution.

     

Molecular basis of the nitrogen response in plants

Nitrogen is an essential element for living organisms because it is a crucial constituent of biomolecules. Inadequate supply of usable nitrogen reduces plant growth and crop yield. The primary nitrogen sources for plants are nitrate and ammonium in soils, and plants have multiple layers of sensing and adaptive mechanisms that respond to the availability of these nutrients. The adaptive responses are called ‘nitrogen responses,’ which include morphological and physiological responses enabling plants to efficiently take up nitrogen and adapt to spatiotemporal fluctuations in nitrogen abundance in the field. In this review, we summarize the strategies that plants use to respond to changes in the nitrogen nutrient status in the soil and discuss different effects produced by nitrate and ammonium, emphasizing the important role of nitrate for plant growth. Recent studies revealed the molecular mechanism mediating the primary response to nitrate provision and the molecular mechanisms that coordinate the nitrogen response with responses to another macronutrient, phosphorus. We thus discuss these molecular mechanisms as well.     

Invasive Acacia longifolia induce changes in the microbial catabolic diversity of sand dunes

Acacia longifolia is one of the main plant species invading Portuguese dune ecosystems. Areas invaded by this exotic tree have reduced plant diversity and altered soil microbial processes and nutrient pools, but the impacts on microbial functional diversity in the soil have been little explored. Soil samples were collected in areas invaded by A. longifolia for more than 20 years, in areas invaded after 1995 and in non-invaded areas. Respiration responses to 20 different substrates were analysed, in order to assess the catabolic response profile (CRP) as a measure of microbial functional diversity. Five substrate groups were tested: amino acids, carbohydrates, carboxylic acids, plant litters, and plant polymers. CRP clearly discriminated between the three different areas. Respiratory responses to the individual substrates α-ketoglutaric acid, oxalic acid, starch, citric acid, and xylose and to the groups of amino acids and plant polymers were similar in both invaded areas and different in the non-invaded. The responses to tartaric acid, gallic acid, fumaric acid, Cistus litter, and Acacia litter were the same in long- and non-invaded areas, but different from recently invaded areas. The duration of invasion, carbon (C) content, nitrogen (N) content, C/N ratio, pH, and litter quantity explained 39.6% of the variance of catabolic responses. It is concluded that invasion by A. longifolia has substantial effects on the catabolic diversity of the soil microbial communities. These effects may have wider implications for nutrient cycling and ecosystem-level processes and for the invasibility of the system.     

Analysis of anthocyanins in red wine and fruit juice using MALDI-MS.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful new technique that will have a great impact on food analysis. This study is the first to demonstrate the applicability of MALDI-MS to perform both qualitative and quantitative analyses of anthocyanins in food. 2,4, 6-Trihydroxyacetophenone (THAP) was found to be a good matrix for analysis of anthocyanins, with the best spot-to-spot repeatability. After a simple sample preparation, the presence of anthocyanins as cations with molecular masses was found in ratios expected from their fruit sources. Quantification of anthocyanins should be possible by choosing appropriate internal standards. MALDI-MS responses were linear, groups of chemically similar anthocyanins had similar responses, and addition of an internal standard had no effect on relative responses of the other anthocyanins.     

Spectrophotometric determination of phenolic compounds by enzymatic and chemical methods--a comparison of structure--activity relationship

A spectrophotometric determination of phenolic compounds by a peroxidase-catalyzed enzymatic (PE) method and the Folin-Ciocalteu (FC) chemical method was compared for their structure-activity relationship. In the PE method, the reaction time of 19 phenolic compounds with different chemical structures was found to be within 15 min, with those having bulky substituents showing slower reactivity. The responses of the phenolic compounds toward the PE method in terms of molar absorbance were positively correlated with the nucleophilicity of their corresponding phenoxyl radicals. An increase in the nucleophilicity by substitution of methoxyl and hydroxyl (electron-donating) groups enhanced the responses; while a decrease in nucleophilicity by substitution of the allyl carboxylic (electron-withdrawing) groups lowered the responses of phenolic compounds toward the enzymatic assay. The responses of phenolic compounds to the enzymatic method were found to be independent of the degree of hydroxylation while those to the FC assay were affected by both the position and degree of hydroxylation. Interfering chemicals found in the FC assay, including vitamin C, 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (a vitamin E analogue), and tert-butylhydroquinone (a commercial antioxidant) were insensitive to the enzymatic assay. The PE method appears to have a higher specificity toward phenolic compounds and subject to less interferences from other antioxidants than the FC method.     

Heat-killed cells of lactobacilli skew the immune response toward T helper 1 polarization in mouse splenocytes and dendritic cell-treated T cells

It is believed that probiotics play an important role for the health of the host, including modulation of immune responses. Most studies have focused on the immunomodulatory effects of viable cells of lactic acid bacteria; however, we investigated those of heat-killed cells of lactic acid bacteria in this study. We first observed the effects on immune functions via stimulating splenocytes with three heat-killed Lactobacillus strains. Furthermore, we also investigated the effect of mouse dendritic cells (DCs) treated with these heat-killed Lactobacillus strains on T cell responses. The results showed that these Lactobacillus strains were able to stimulate cell proliferation and interleukin (IL)-10, IL-12 p70, and interferon (IFN)-gamma production but not transforming growth factor (TGF)-beta in splenocytes. In addition, these heat-killed Lactobacillus strains also stimulated high-level secretion of IL-12 p70 in DCs and switched T cells to T helper (Th) 1 immune responses, as evidenced by the elevated secretion of IFN-gamma but not IL-5, IL-13, and TGF-beta. These results showed that lactobacilli play a potentially important role in modulating immune responses and allergic reactions.     

Soil extracellular enzyme dynamics in a changing climate

Assays for extracellular enzyme activity (EEA) have become a common tool for studying soil microbial responses in climate change experiments. Nevertheless, measures of potential EEA, which are conducted under controlled conditions, often do not account for the direct effects of climate change on EEA that occur as a result of the temperature and moisture dependence of enzyme activity in situ. Likewise, the indirect effects of climate on EEA in the field, that occur via effects on microbial enzyme producers, must be assessed in the context of potential changes in plant and soil faunal communities. Here, EEA responses to warming and altered precipitation in field studies are reviewed, with the goal of evaluating the role of EEA in enhancing our understanding of soil and ecosystem responses to climate change. Seasonal and interannual variation in EEA responses to climate change treatments are examined, and potential interactions with elevated atmospheric CO₂, increased atmospheric N deposition and changes in disturbance regimes are also explored. It is demonstrated that in general, soil moisture manipulations in field studies have had a much greater influence on potential EEA than warming treatments. However, these results may simply reflect the low magnitude of soil warming achieved in many field experiments. In addition, changes in plant species composition over the longer term in response to warming could strongly affect EEA. Future challenges involve extending studies of potential EEA to address EEA responses to climate change in situ, and gaining further insights into the mechanisms, such as enzyme production, stabilization and turnover, that underlie EEA responses.     

Reprint of “Soil extracellular enzyme dynamics in a changing climate”

Assays for extracellular enzyme activity (EEA) have become a common tool for studying soil microbial responses in climate change experiments. Nevertheless, measures of potential EEA, which are conducted under controlled conditions, often do not account for the direct effects of climate change on EEA that occur as a result of the temperature and moisture dependence of enzyme activity in situ. Likewise, the indirect effects of climate on EEA in the field, that occur via effects on microbial enzyme producers, must be assessed in the context of potential changes in plant and soil faunal communities. Here, EEA responses to warming and altered precipitation in field studies are reviewed, with the goal of evaluating the role of EEA in enhancing our understanding of soil and ecosystem responses to climate change. Seasonal and interannual variation in EEA responses to climate change treatments are examined, and potential interactions with elevated atmospheric CO₂, increased atmospheric N deposition and changes in disturbance regimes are also explored. It is demonstrated that in general, soil moisture manipulations in field studies have had a much greater influence on potential EEA than warming treatments. However, these results may simply reflect the low magnitude of soil warming achieved in many field experiments. In addition, changes in plant species composition over the longer term in response to warming could strongly affect EEA. Future challenges involve extending studies of potential EEA to address EEA responses to climate change in situ, and gaining further insights into the mechanisms, such as enzyme production, stabilization and turnover, that underlie EEA responses.     

玉米的生理指标对土壤水分有效性的响应

Knowledge of plant responses to soil water availability is essential for the development of effcient irrigation strategies.However,notably different results have been obtained in the past on the responses of various physiological indices for different plants to soil water availability.In this study,the responses of various plant processes to soil water availability were compared with data from pot and field plot experiments conducted on maize(Zea mays L.).Consistent results were obtained between pot and field plot experiments for the responses of various relative plant indices to changes in the fraction of available soil water(FASW).A threshold value,where the relative plant indices began to decrease with soil drying,and a lower water limit,where the decline of relative plant indices changed to a very slow rate,were found.Evaporative demand not only influenced the transpiration rate over a daily scale but also determined the difference in transpirational response to soil water availability among the transient,daily and seasonal time scales.At the seasonal scale,cumulative transpiration decreased linearly with soil drying,but the decrease of transpiration from FASW = 1 in response to water deficits did not affect dry weight until FASW = 0.75.On the other hand,the decrease in dry weight was comparable with plant height and leaf area.Therefore,the plant responses to soil water availability were notably different among various plant indices of maize and were influenced by the weather conditions.     

How many common reptile species are fire specialists? A replicated natural experiment highlights the predictive weakness of a fire succession model

Species with strong preferences for early or late successional stages after fire may be extinction prone under current fire regimes. However, the extent of specialisation to time since fire is poorly understood, and, for reptiles, succession models for predicting responses are in the development phase. In this study we tested predictions of a reptile succession model, and identified species that may be fire specialists. Reptiles were sampled in five burnt and unburnt mallee Eucalyptus woodlands, Australia. Two, 400 m transects within each burn treatment were sampled using 11 pairs of pitfall-traps that were opened for five weeks over two summers. A habitat accommodation model of succession that was previously developed for mallee reptiles correctly predicted the observed responses of three of 16 common reptile species. A further four species showed non-significant trends in the predicted direction. However, eight other species showed unexpected responses. One species showed a strong interaction between burn age and location, requiring a two-dimensional successional model in contrast with the usual linear models explaining reptile responses to fire. One third of common species were not affected by fire and so may not have increased risks of extinction due to the fire suppression/incineration cycle. However, approximately half to two-thirds of common reptiles did have a fire response, so the risk of deterministic extinction in small fragments may be substantial. Further model development is needed to better predict fire responses and to assist the design of fire mosaics that can accommodate early and late successional fire specialists.     

Patterns of species change in anthropogenically disturbed forests of Madagascar

Five main conclusions arise from this review of the responses of species to anthropogenic disturbance in Madagascar: First, species’ reactions to anthropogenic disturbance are generally negative, but remain poorly known. Our knowledge is patchy among and within higher taxonomic groups; we are still largely gathering case studies. Second, taxonomic groups vary considerably in which proximate factors are most important. Third, several groups show differing responses within different ecoregions. Whether these differences are consistent across groups requires further testing. Fourth, related species often have divergent reactions to disturbance, even within lower taxonomic groupings (families or genera). Thus, we cannot rely on phylogenetic relatedness or even ecological similarity to infer similarity in responses. Finally, disturbance typically reduces species diversity (especially of native and/or endemic species), but also causes species turnover, typically with forest specialists replaced by grassland generalists, and endemics replaced by non-endemics (including invasives). Given these knowledge gaps, we stress the urgency of applied studies that assess species’ ecology, behaviour and health across disturbance gradients, including purely anthropogenic landscapes. Remaining natural vegetation and protected areas will be unable to preserve Madagascar’s biodiversity under the impact of climatic change; we must understand responses of plants and animals to disturbance in order to create buffer zones and corridors combining secondary, degraded and natural habitats.     

Soil faunal assemblage composition modifies root in-growth to plant litter patches

Local-scale heterogeneity in the spatial distribution of soil nutrients promotes a suite of physiological and morphological responses in plants. These responses influence the competitive ability of plants within communities and potentially plant primary productivity. There is a growing appreciation then for the need to study factors that may modulate these plant responses to soil nutrient heterogeneity. Soil fauna are potentially one such modulating factor. For example, through impacts on organic matter decomposition and distribution they may directly modify nutrient patches and therefore the stimulus plants are responding to. In addition they may modify plant root mass and architecture through processes such as herbivory, potentially altering the outcome of a plant's response to a nutrient patch. Using grassland microcosms, consisting of a multi-species plant assemblage, multiple soil horizons and a speciose soil biota, we tested whether soil faunal assemblage composition might modulate plant responses to nutrient patches represented by litterbags. We show that root proliferation into a nutrient patch, a variable which is positively related to a plant's success under conditions of interspecific competition in a nutrient-limited environment, is reduced by the presence of mesofauna, and even more so by the presence of mesofauna together with macrofauna. Reductions in this proliferation response when mesofauna were present without macrofauna appeared to be a function of reduced root density. When macrofauna were included, reduced root density, and higher rates of litter patch disappearance, together contributed to the reduction in proliferation but additional mechanisms must also have played a role. Our results suggest that the effects and interactions generated by soil fauna need to be explicitly considered in analyses of how plants forage for nutrients in a patchy environment.     

Characterization of benzyl isothiocyanate and phenyl acetonitrile from papayas by mass spectrometry

Two unidentified analytical responses in a papaya extract were structurally determined by mass spectrometry to be benzyl isothiocyanate and phenyl acetonitrile. Both these compounds have previously been shown to result from degradation of benzylglucosinolate that occurs naturally in the seeds of the fruit. Characterization by mass spectrometry has now provided a convenient mechanism to detect both these degradation compounds in extracts resulting from routine pesticide residue analysis.     

Influence of nitrogen and other nutrients on the growth of Agave deserti

Although agaves are commercially important worldwide and ecologically interesting, their nutrient responses have not been extensively studied under controlled conditions. Here, nutrient responses of seedlings and adult plants of Agave deserti were examined, with particular emphasis on nitrogen. Growth of seedlings in hydroponics was enhanced by increasing potassium, phosphate, and especially nitrate. Seedling growth in sand culture was also enhanced by adding nitrate, leading to just over 2% N by dry weight in the leaves. Seedlings had optimal growth in soil having about 0.1% N by dry weight and a pH between 6 and 8. In going from irrigation with no added nutrients to full‐strength Hoagland solution for mature plants in soil, leaf unfolding (a non‐destructive measure of productivity) approximately doubled. The rate of leaf unfolding in the field was also doubled by adding 100 kg N hectare^‐1, higher levels proving inhibitory.     

Italian marine reserve effectiveness: Does enforcement matter?

Marine protected areas (MPAs) have become popular tools worldwide for ecosystem conservation and fishery management. Fish assemblages can benefit from protection provided by MPAs, especially those that include fully no-take reserves. Fish response to protection can thus be used to evaluate the effectiveness of marine reserves. Most target fish are high-level predators and their overfishing may affect entire communities through trophic cascades. In the Mediterranean rocky sublittoral, marine reserves may allow fish predators of sea urchins to recover and thus whole communities to be restored from coralline barrens to macroalgae. Such direct and indirect reserve effects, however, are likely to be related to the enforcement implemented. In Italy, many MPAs that include no-take reserves have been declared, but little effort has been spent to enforce them. This is a worldwide phenomenon (although more common in some regions than others) that may cause MPAs and reserves to fail to meet their targets. We found that 3 of 15 Italian marine reserves investigated had adequate enforcement, and that patterns of recovery of target fish were related to enforcement. No responses were detected when all reserves were analyzed as a whole, suggesting enforcement as an important factor to be considered in future studies particularly to avoid that positive ecological responses in properly managed reserves can be masked by neutral/negative results in paper parks. Positive responses were observed for large piscivores (e.g. dusky groupers) and sea urchin predators at reserves where enforcement was effective. Those reserves with low or null enforcement did not differ from fished areas.     

Crop and Soil Responses to Fertilization with Distillers’ Grains–Derived Manure in a Saskatchewan Soil

A 2-year field trial was conducted to evaluate crop and soil responses to application of manure from cattle fed distillers’ grain (DGM) in comparison with manure from cattle fed regular barley grain (BGM). Manure addition in general promoted grain and straw yield and increased plant nitrogen (N) and phosphorus (P) uptake in both years by approximately 30–50%. In the first year, effect of manure type on crop responses was insignificant, which is consistent with the similar chemical composition of both manures. In the second year, P recovery was greater in DGM treatments, presumably related to a relatively greater P in DGM. Manure application in general increased soil residual nitrate nitrogen (NO₃^– N) and available P contents at 0–15 cm deep. The high background fertility of studied soil together with the excess moisture during the second year may have masked the significant effects of manure type on most crop and soil responses during this study.     

Salt effects on the soil microbial decomposer community and their role in organic carbon cycling: A review

Salinization of soil is recognised as one of the most pressing environmental challenges to resolve for the next century. We here conduct a synoptic review of the available research on how salt affects decomposer microbial communities and carbon (C) cycling in soil. After summarizing known physiological responses of microorganisms to salinity, we provide a brief overview and qualification of a selection of widely applied methods to assess microorganisms in soil to date. The dominant approaches to characterise microbial responses to salt exposure have so far been microbial biomass and respiration measurements. We compile datasets from a selection of studies and find that (1) microbial biomass-carbon (C) per C held in soil organic matter shows no consistent pattern with long-term (field gradients) or short-term (laboratory additions) soil salinity level, and (2) respiration per soil organic C is substantially inhibited by higher salt concentrations in soil, and consistently so for both short-term and long-term salinity levels. Patterns that emerge from extra-cellular enzyme assessments are more difficult to generalize, and appear to vary with the enzyme studied, and its context. Growth based assessments of microbial responses to salinization are largely lacking. Relating the established responses of microbial respiration to that of growth could provide an estimate for how the microbial C-use efficiency would be affected by salt exposure. This would be a valuable predictor for changes in soil C sequestration. A few studies have investigated the connection between microbial tolerance to salt and the soil salinity levels, but so far results have not been conclusive. We predict that more systematic inquiries including comprehensive ranges of soil salinities will substantiate a connection between soil salinity and microbial tolerance to salt. This would confirm that salinity has a direct effect on the composition of microbial communities. While salt has been identified as one of the most powerful environmental factors to structure microbial communities in aquatic environments, no up-to-date sequence based assessments currently exist from soil. Filling this gap should be a research priority. Moreover, linking sequencing based assessments of microbial communities to their tolerance to salt would have the potential to yield biomarker sets of microbial sequences. This could provide predictive power for, e.g., the sensitivity of agricultural soils to salt exposure, and, as such, a useful tool for soil resource management. We conclude that salt exposure has a powerful influence on soil microbial communities and processes. In addition to being one of the most pressing agricultural problems to solve, this influence could also be used as an experimental probe to better understand how microorganisms control the biogeochemistry in soil.     

Ungulate flight responses to human disturbance: A review and meta-analysis

As human recreation in natural areas increases, so does the potential for disturbance to wildlife, and many factors (environmental, disturbance type, experience with humans) influence the impact of disturbance. However, there exists no comprehensive examination of the effects of human disturbance on ungulate escape responses. I conducted a comprehensive review of studies measuring Artiodactyl escape responses (e.g., flight initiation distance, distance moved) to experimental harassment by humans and vehicles, and meta-analyses aimed at predictive questions about the impact of human disturbance on ungulate behavior under an optimization framework. I found evidence across studies that ungulates pay attention to approacher behavior, have greater perceptions of risk when disturbed in open habitats, and females or groups with young offspring show greater flight responses than adult groups. Increased group size and the presence of hunting showed weak but positive heterogeneous effects on flight behavior both between and within species. Humans on foot were more evocative than other stimuli (vehicles, noises). Populations in areas with higher levels of human traffic showed reduced wariness but a lack of alternative sites to move to may explain some of this effect. Hunted populations showed significantly greater flight responses than non-hunted populations. Finally, I suggest five factors to consider when forming predictive models of ungulate flight behavior: (1) how seasonal variation in reproductive status and body condition effects wariness, (2) the relative impacts of lethal and non-lethal human contact, and (3) unique natural history traits that may cause differences in flight behavior between populations, (4) the availability of alternative sites, and (5) shorter distances between feeding sites and refugia can reduce the impact of other factors on flight responses.