A Multi-biological Assay Approach to Assess Microbial Diversity in Arsenic (As) Contaminated Soils

Microbial genetic, structural and functional diversity was assessed in response to arsenic (As) pollution in a former gold mine soil. Ester-linked fatty acid methyl ester (EL-FAME), quantitative PCR (qPCR), denaturating gradient gel electrophoresis (DGGE), enzyme activities and MicroResp techniques were used.

Multivariate analysis showed that As bioavailability in soil was an important driver affecting microbial diversity. Microbial biomass assessed by EL-FAMEs and qPCR generally decreased under higher bioavailable As, as well as enzyme activities and C substrate utilization. Conversely, actinomycetes and fungal biomass increased along with total As content suggesting the selection of more resistant species.     

A Model-Based Approach to Assess Epidemic Risk

Statistics in Biosciences - We study how international flights can facilitate the spread of an epidemic to a worldwide scale. We combine an infrastructure network of flight connections with a...     

城市景观复写——从空间分析到设计途径

当代景观设计中价值取向的转变,包括设计行为从创造画面转向塑造场所,从创造新事物转向重现场地本质与原貌。依据景观设计中的空间特征和规划设计应用价值,将文本视角下的当代景观空间特征“复写”（palimpsest）定义为场地中各历史层次与当代层次的结合与共同显现。复写空间利用场地的潜力,实现了景观意义的传达,具有二元性、互文性及透明性的特点。复写既可以作为分析工具,也可以作为设计手段,其核心价值在于：多层空间结构得以平等呈现;历史信息积累而显现场地特质;设计创造诱发新的发展空间与场地产生关联。结合案例论述,研究与复写相关的分析方法与设计路径：呈现自治或在场地介入过程中建立互设关系,相关设计思想可回溯到埃森曼“人工开挖”（artificial excavation）的设计理念,以及文化景观及遗产保护中的“踪迹”（trace）概念。以场地空间特征出发,选择合适的设计方法,进而提出复写空间的多层建构是设计过程的关键部分。     

A Score Regression Approach to Assess Calibration of Continuous Probabilistic Predictions

Summary Calibration, the statistical consistency of forecast distributions and the observations, is a central requirement for probabilistic predictions. Calibration of continuous forecasts is typically assessed using the probability integral transform histogram. In this article, we propose significance tests based on scoring rules to assess calibration of continuous predictive distributions. For an ideal normal forecast we derive the first two moments of two commonly used scoring rules: the logarithmic and the continuous ranked probability score. This naturally leads to the construction of two unconditional tests for normal predictions. More generally, we propose a novel score regression approach, where the individual scores are regressed on suitable functions of the predictive variance. This conditional approach is applicable even for certain nonnormal predictions based on the Dawid–Sebastiani score. Two case studies illustrate that the score regression approach has typically more power in detecting miscalibrated forecasts than the other approaches considered, including a recently proposed technique based on conditional exceedance probability curves.     

A Population Accounting Approach to Assess Tourism Contributions to Conservation of IUCN-Redlisted Mammal Species

Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥5% for over half of the species where relevant data exist, ≥15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.     

Surface Energetics to Assess Microbial Adhesion onto Fluidized Chromatography Adsorbents

Cell‐to‐support interaction and cell‐to‐cell aggregation phenomena have been studied in a model system composed of intact yeast cells and agarose‐based chromatography adsorbent surfaces. Biomass components and beaded adsorbents were characterized by contact angle determinations with three diagnostic liquids and, complementarily, by zeta potential measurements. Such experimental characterization of the interacting surfaces has allowed the calculation of interfacial free energy of interaction in aqueous media vs. distance profiles. The extent of biomass adhesion was inferred from calculations performed assuming standard chromatographic conditions, but different adsorption modes. Several stationary support/mobile phase systems were considered, i.e., ion exchange, hydrophobic interaction, and pseudo‐affinity. The calculated interaction energy minima revealed marginal attraction between cells and cation exchangers or agarose‐matrix beads (U ≤ |10–20| kT) but strong attraction with anion exchangers (U ≥ |200–1000| kT). Other systems including hydrophobic interaction and chelating beads showed intermediate energy minimum values (U <$>\approx<$> |40–100| kT) for interaction with biological particles. However, the calculations also showed that working conditions in the presence of salt can promote cell aggregation apart from cell‐to‐support interaction. Predictions based on the application of the XDLVO approach were confirmed by independent experimental methods, e.g., biomass deposition experiments and laser diffraction spectroscopy. The understanding of biomass attachment onto chromatographic supports can help in alleviating process limitations normally encountered during direct (primary) sequestration of bioproducts.     

A Probabilistic Palimpsest Model of Visual Short-term Memory

Working memory plays a key role in cognition, and yet its mechanisms remain much debated. Human performance on memory tasks is severely limited; however, the two major classes of theory explaining the limits leave open questions about key issues such as how multiple simultaneously-represented items can be distinguished. We propose a palimpsest model, with the occurrent activity of a single population of neurons coding for several multi-featured items. Using a probabilistic approach to storage and recall, we show how this model can account for many qualitative aspects of existing experimental data. In our account, the underlying nature of a memory item depends entirely on the characteristics of the population representation, and we provide analytical and numerical insights into critical issues such as multiplicity and binding. We consider representations in which information about individual feature values is partially separate from the information about binding that creates single items out of multiple features. An appropriate balance between these two types of information is required to capture fully the different types of error seen in human experimental data. Our model provides the first principled account of misbinding errors. We also suggest a specific set of stimuli designed to elucidate the representations that subjects actually employ.     

Intact Phospholipid and Quinone Biomarkers to Assess Microbial Diversity and Redox State in Microbial Mats

Microbial mats are stratified microbial communities composed by highly inter-related populations and therefore are frequently chosen as model systems to study diversity and ecophysiological strategies. The present study describes an integrated approach to analyze microbial quinones and intact polar lipids (IPLs) in microbial mats within layers as thin as 500 μm by liquid chromatography–tandem mass spectrometry. Quinone profiles revealed important depth-related differences in community composition in two mat systems. The higher abundance of ubiquinones, compared to menaquinones, reflected the clear predominance of microorganisms belonging to aerobic α-, β-, and γ-Proteobacteria in Ebro delta estuarine mats. Hypersaline photosynthetic Camargue mats (France) showed a predominance of menaquinone-9 at the top of the mat, which is consistent with an important contribution of facultative aerobic or anaerobic bacteria in its photic zone. Quinone indices also indicated a higher diversity of non-phototrophs and a more anaerobic character in the hypersaline mats. Besides, the dissimilarity index suggested that the samples were greatly influenced by a depth-related redox state gradient. In the analysis of IPLs, there was a predominance of phosphatidylglycerols and sulfoquinovosyldiacylglycerols, the latter being an abundant biomarker of Cyanobacteria. This combined approach based on quinone and IPL analysis has proven to be a useful method to establish differences in the microbial diversity and redox state of highly structure microbial mat systems at a fine-scale level.     

A Method for Assessing the Level of Microbial Contamination in Surgical Materials

S ummary . A method is described which increases the efficiency of recovery of microorganisms from solid, fibrous and polymer materials. It is suitable for routine assessment of the microbial quality of various medical products.     

A Fuzzy Logic Approach to Assess,Manage, and Communicate Carcinogenic Risk

A prospective approach to addressing carcinogen risk assessment is presented. Fuzzy reasoning is used to assess carcinogenic risk, characterize it, and control it. The approach is inspired by fuzzy control inference that deploys linguistic intelligence as input to a system described numerically through membership functions. Fuzzy-based reasoning to estimate carcinogenic risk provides several advantages as discussed here. The fuzzy reasoning approach has more capabilities than traditional models in dealing with risk agents that are probably carcinogens, possibly carcinogens, not classifiable as carcinogens, and probably not carcinogens. Input–output surfaces are presented for each hazard group to enable fast inferencing. Then, a hypothetical example is given to compare the results of traditional methods and the fuzzy-based approach to estimating the risk of a carcinogen to a human population. Results show similarity in risk characterization with less input information to the fuzzy-based approach. Fuzzy reasoning characterizes risk in more explicit and easy to grasp terms. Two outputs of the inferencing system are risk characterization and risk control or remediation.     

A Methodological Approach to Assess Cross-scale Relations and Interactions in Agricultural Ecosystems of Argentina

Agronomists, environmentalists, land managers, policy makers and development agents who make decisions at different levels (plot, farm, ecosystem, landscape, ecoregion, country) increasingly demand scientific information to understand cross-level links and interactions in systems that behave hierarchically. The purpose of this work is to study cross-scale relations and interactions in agricultural ecosystems of the Argentine Pampas. Based on public censuses and surveys from 1960 to 1996, data on crops cultivation, fossil energy (FE) consumption and energy productivity were used for the analysis. The whole region was divided into eight increasing geographic scales, and the impact of one scale on the broader ones was assessed through a simple analysis of energy productivity. Regression analysis was used to identify cross-scale linear slopes and to determine cross-scale interactions. We assume that non-parallel slopes in different years are attributable to cross-scale interactions. Given that the results show highly significant differences among inter-year slopes, we must accept that cross-scale interactions have occurred. Beyond any random behavior, it seems quite possible that decisions made at smaller scales may have a demonstrable effect on broader scales. Specific research is needed to elucidate key cause–effect relationships among scales. In principle, the possible interaction between intensification factors (for example, FE consumption) and spatial scales is a plausible hypothesis to be tested in the study area.     

An Integrated Approach to Assess the Role of Chemical Exposure in Obesity

The evidence that developmental exposure of humans to chemicals plays a role in onset of obesity is convincing, yet controversial as it challenges traditional views on the etiology of obesity. OBELIX, one of the largest pan‐European studies researching the obesogen hypothesis, is accruing experimental and epidemiologic data on major classes of endocrine disrupting chemicals (EDCs) in both laboratory animal and prospective human cohort studies. Though still underway, this integrated and multidisciplinary project is adding new insights to the weight of evidence for effects of EDCs on obesity. Animal studies indicate divergent sex‐specific effects of perinatal exposure on the development of overweight. In vitro mechanistic studies have shown that EDCs enhance murine adipocyte differentiation, an effect that is accompanied by global DNA demethylation. Epidemiological studies have revealed an inverse relationship between prenatal polychlorinated biphenyl exposure and birth weight, and suggest differences in pre‐ and postnatal exposure on growth trajectories in children.     

A Multidisciplinary Approach to Assess the Welfare of Weaned Pigs During Transport at Three Space Allowances

Transport can be a stressful experience for pigs, especially in pigs simultaneously experiencing weaning stress. The objective of this study was to use a multidisciplinary approach to assess the welfare of weaned pigs during transport at 3 space allowances. A commercial semitrailer, fitted with compartments, provided 0.05, 0.06, and 0.07 m²/pig. The study recorded frequency of standing, lying, sitting, and standing-rearing on another pig during the entire duration of transport. Blood samples, body weights, and lesion scores were collected from a subset of pigs (n = 48 per space allowance) in each experimental compartment. Transport time for the pigs was 148.0 ± 10.0 min to the wean-to-finishing site. Total white blood cell counts, cortisol, and several blood chemistry values increased (p < .05) after transport regardless of space allowance. Glucose and body weight decreased (p < .05) after transport regardless of space allowance. Space allowance influenced stand-rearing, sitting, standing, and lying behaviors in pigs. Combining behavioral and physiological measures of stress provides a robust picture of piglet welfare during transport at different space allowances.     

How to Deal with PCR Contamination in Molecular Microbial Ecology

Microbial ecology studies often use broad-range PCR primers to obtain community profiles. Contaminant microbial DNA present in PCR reagents may therefore be amplified together with template DNA, resulting in unrepeatable data which may be difficult to interpret, especially when template DNA is present at low levels. One possible decontamination method consists in pre-treating PCR mixes with restriction enzymes before heat-inactivating those enzymes prior to the start of the PCR. However, this method has given contrasting results, including a reduction in PCR sensitivity. In this study, we tested the efficiency of two different enzymes (DNase 1 and Sau3AI) as well as the effect of dithiothreitol (DTT), a strong reducing agent, in the decontamination procedure. Our results indicate that enzymatic treatment does reduce contamination levels. However, DNase 1 caused substantial reductions in the bacterial richness found in communities, which we interpret as a result of its incomplete inactivation by heat treatment. DTT did help maintain bacterial richness in mixes treated with DNase 1. No such issues arose when using Sau3AI, which therefore seems a more appropriate enzyme. In our study, four operational taxonomic units (OTU) decreased in frequency and relative abundance after treatment with Sau3AI and hence are likely to represent contaminant bacterial DNA. We found higher within-sample similarity in community structure after treatment with Sau3AI, probably better reflecting the initial bacterial communities. We argue that the presence of contaminant bacterial DNA may have consequences in the interpretation of ecological data, especially when using low levels of template DNA from highly diverse communities. We advocate the use of such decontaminating approaches as a standard procedure in microbial ecology.     

A New Modeling Approach to the Effect of Antimicrobial Agents on Heterogeneous Microbial Populations

We develop a mathematical framework to model the dynamics of the effect of antimicrobial agents on heterogeneous microbial populations of distributed antimicrobial resistance. Our framework uses the concept of cumulants of a distribution. Simplifications that result in easily usable approximation tools are presented. A case study on experimental data exemplifies shortcomings of standard methods and the usefulness of the proposed approach. Suggestions for future development are made. Author to whom all correspondence should be addressed     

A Pragmatic Approach to Assess the Exposure of the Honey Bee (Apis mellifera) When Subjected to Pesticide Spray

Plant protection spray treatments may expose non-target organisms to pesticides. In the pesticide registration procedure, the honey bee represents one of the non-target model species for which the risk posed by pesticides must be assessed on the basis of the hazard quotient (HQ). The HQ is defined as the ratio between environmental exposure and toxicity. For the honey bee, the HQ calculation is not consistent because it corresponds to the ratio between the pesticide field rate (in mass of pesticide/ha) and LD₅₀ (in mass of pesticide/bee). Thus, in contrast to all other species, the HQ can only be interpreted empirically because it corresponds to a number of bees/ha. This type of HQ calculation is due to the difficulty in transforming pesticide field rates into doses to which bees are exposed. In this study, we used a pragmatic approach to determine the apparent exposure surface area of honey bees submitted to pesticide treatments by spraying with a Potter-type tower. The doses received by the bees were quantified by very efficient chemical analyses, which enabled us to determine an apparent surface area of 1.05 cm²/bee. The apparent surface area was used to calculate the exposure levels of bees submitted to pesticide sprays and then to revisit the HQ ratios with a calculation mode similar to that used for all other living species. X-tomography was used to assess the physical surface area of a bee, which was 3.27 cm²/bee, and showed that the apparent exposure surface was not overestimated. The control experiments showed that the toxicity induced by doses calculated with the exposure surface area was similar to that induced by treatments according to the European testing procedure. This new approach to measure risk is more accurate and could become a tool to aid the decision-making process in the risk assessment of pesticides.     

Identifying Metals Contamination in Soil: A Geochemical Approach

The geochemical evaluation methodology described in this paper is used to distinguish contaminated samples from those that contain only naturally occurring levels of inorganic constituents. Site-to-background comparisons of trace elements in soil based solely on statistical techniques are prone to high false positive indications. Trace element distributions in soil tend to span a wide range of concentrations and are highly right-skewed, approximating lognormal distributions, and background data sets are typically too small to capture this range. Geochemical correlations of trace versus major elements are predicated on the natural elemental associations in soil. Linear trends with positive slopes are expected for scatter plots of specific trace versus major elements in uncontaminated samples. Individual samples that may contain a component of contamination are identified by their positions off the trend formed by uncontaminated samples. In addition to pinpointing which samples may be contaminated, this technique provides mechanistic explanations for naturally elevated element concentrations, information that a purely statistical approach cannot provide. These geochemical evaluations have been successfully performed at numerous facilities across the United States. Removing naturally occurring constituents from consideration early in a site investigation reduces or eliminates unnecessary investigation and risk assessment, and focuses remediation efforts.     

A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields

Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal capabilities were not as important.     

Feathers as a Tool to Assess Mercury Contamination in Gentoo Penguins: Variations at the Individual Level

Feathers have been widely used to assess mercury contamination in birds as they reflect metal concentrations accumulated between successive moult periods: they are also easy to sample and have minimum impact on the study birds. Moult is considered the major pathway for mercury excretion in seabirds. Penguins are widely believed to undergo a complete, annual moult during which they do not feed. As penguins lose all their feathers, they are expected to have a low individual-variability in feather mercury concentration as all feathers are formed simultaneously from the same somatic reserves. This assumption is central to penguin studies that use feathers to examine the annual or among-individual variation in mercury concentrations in penguins. To test this assumption, we measured the mercury concentrations in 3–5 body feathers of 52 gentoo penguins (Pygoscelis papua) breeding at Bird Island, South Georgia (54°S 38°W). Twenty-five percent of the penguins studied showed substantial within-individual variation in the amount of mercury in their feathers (Coefficient of Variation: 34.7–96.7%). This variation may be caused by differences in moult patterns among individuals within the population leading to different interpretations in the overall population. Further investigation is now needed to fully understand individual variation in penguins’ moult.