Multidimensional Mapping Method Using an Arrayed Sensing System for Cross-Reactivity Screening

When measuring chemical information in biological fluids, challenges of cross-reactivity arise, especially in sensing applications where no biological recognition elements exist. An understanding of the cross-reactions involved in these complex matrices is necessary to guide the design of appropriate sensing systems. This work presents a methodology for investigating cross-reactions in complex fluids. First, a systematic screening of matrix components is demonstrated in buffer-based solutions. Second, to account for the effect of the simultaneous presence of these species in complex samples, the responses of buffer-based simulated mixtures of these species were characterized using an arrayed sensing system. We demonstrate that the sensor array, consisting of electrochemical sensors with varying input parameters, generated differential responses that provide synergistic information of sample. By mapping the sensing array response onto multidimensional heat maps, characteristic signatures were compared across sensors in the array and across different matrices. Lastly, the arrayed sensing system was applied to complex biological samples to discern and match characteristic signatures between the simulated mixtures and the complex sample responses. As an example, this methodology was applied to screen interfering species relevant to the application of schizophrenia management. Specifically, blood serum measurement of antipsychotic clozapine and antioxidant species can provide useful information regarding therapeutic efficacy and psychiatric symptoms. This work proposes an investigational tool that can guide multi-analyte sensor design, chemometric modeling and biomarker discovery.     

Fate of Pesticides in the Environment and its Bioremediation

The present paper is an overview of the presence and fate of pesticides as persistent organic pollutants in the environment as well as of the potential for their detoxification, also combined with chemical and physical treatment. It contains information gathered from a range of currently available sources. The fate of pesticides in the environment is analyzed considering the processes that determine their persistence and mobility, grouped into transport, transfer and transformation processes. Few pesticide characteristics such as persistence, mobility and biodegradability are emphasized. The fate of a pesticide and the potential for its persistence and mobility from the site of application are considered to be affected by the chemical and physical properties of the pesticide, site characteristics such as soil and groundwater individuality, climate and local weather conditions, biological population, and the handling practices of the pesticide user. Bioremediation, as one of the most environmentally‐sound and cost‐effective methods for the decontamination and detoxification of a pesticide‐contaminated environment is discussed especially considering the factors affecting the biodegradability of pesticides such as biological factors and the characteristics of the chemical compounds. In situ and ex situ bioremediation as possible types of bioremediation activities are weighted up. Also, the paper includes some considerations for developing strategies regarding the choice of bioremediation technology, as well as advantages and disadvantages of the bioremediation of environmental components polluted with pesticides.     

PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes

Relating expression signatures from different sources such as cell lines, in vitro cultures from primary cells and biopsy material is an important task in drug development and translational medicine as well as for tracking of cell fate and disease progression. Especially the comparison of large scale gene expression changes to tissue or cell type specific signatures is of high interest for the tracking of cell fate in (trans-) differentiation experiments and for cancer research, which increasingly focuses on shared processes and the involvement of the microenvironment. These signature relation approaches require robust statistical methods to account for the high biological heterogeneity in clinical data and must cope with small sample sizes in lab experiments and common patterns of co-expression in ubiquitous cellular processes. We describe a novel method, called PhysioSpace, to position dynamics of time series data derived from cellular differentiation and disease progression in a genome-wide expression space. The PhysioSpace is defined by a compendium of publicly available gene expression signatures representing a large set of biological phenotypes. The mapping of gene expression changes onto the PhysioSpace leads to a robust ranking of physiologically relevant signatures, as rigorously evaluated via sample-label permutations. A spherical transformation of the data improves the performance, leading to stable results even in case of small sample sizes. Using PhysioSpace with clinical cancer datasets reveals that such data exhibits large heterogeneity in the number of significant signature associations. This behavior was closely associated with the classification endpoint and cancer type under consideration, indicating shared biological functionalities in disease associated processes. Even though the time series data of cell line differentiation exhibited responses in larger clusters covering several biologically related patterns, top scoring patterns were highly consistent with a priory known biological information and separated from the rest of response patterns.     

SoilCAM: soil contamination: advanced integrated characterisation and time-lapse monitoring

The SoilCAM project is aimed at improving current methods for monitoring contaminant distribution and biodegradation in the subsurface. Currently proven methods, based on invasive sampling of soil, soil water and gaseous phase, are unable to provide sufficiently accurate data with high enough resolution, resulting in inability to assess bioremediation progress and quantification of the processes involved in such bioremediation at field sites. Consequently, present assessment strategies to decide on optimal remediation approach, including design of monitoring systems, and evaluation of degradation progress, are severely flawed by uncertainty. Geophysical time-lapse measurements in combination with novel ground truthing methods give the possibility to determine contamination levels and their spatial spreading in a heterogeneous environment. Geophysical methods of data acquisition alone are presently unable to provide absolute levels of biodegradable contamination concentrations. We aim to test and develop fundamental constitutive relations between soil physical and degradation activity parameters and geophysically measurable parameters. Despite current improvements, there is a strong need to test these theories in practical field situations. The SoilCAM project is dedicated to improving both site contamination assessment and the monitoring of bioremediation processes, and changes in soil environmental conditions. We suggest combining improved conventional soil monitoring techniques with state-of-the-art geophysical approaches and modelling. Two European sites with mobile contaminants in a highly permeable subsurface are central in the project. Focus on practical field situations and strong communication with stake-holders and SMEs will ensure high relevance for society. This article is a research project funded under FP7 .     

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.     

Network based consensus gene signatures for biomarker discovery in breast cancer

Diagnostic and prognostic biomarkers for cancer based on gene expression profiles are viewed as a major step towards a better personalized medicine. Many studies using various computational approaches have been published in this direction during the last decade. However, when comparing different gene signatures for related clinical questions often only a small overlap is observed. This can have various reasons, such as technical differences of platforms, differences in biological samples or their treatment in lab, or statistical reasons because of the high dimensionality of the data combined with small sample size, leading to unstable selection of genes. In conclusion retrieved gene signatures are often hard to interpret from a biological point of view. We here demonstrate that it is possible to construct a consensus signature from a set of seemingly different gene signatures by mapping them on a protein interaction network. Common upstream proteins of close gene products, which we identified via our developed algorithm, show a very clear and significant functional interpretation in terms of overrepresented KEGG pathways, disease associated genes and known drug targets. Moreover, we show that such a consensus signature can serve as prior knowledge for predictive biomarker discovery in breast cancer. Evaluation on different datasets shows that signatures derived from the consensus signature reveal a much higher stability than signatures learned from all probesets on a microarray, while at the same time being at least as predictive. Furthermore, they are clearly interpretable in terms of enriched pathways, disease associated genes and known drug targets. In summary we thus believe that network based consensus signatures are not only a way to relate seemingly different gene signatures to each other in a functional manner, but also to establish prior knowledge for highly stable and interpretable predictive biomarkers.     

Genome-wide detection of selective signatures in Simmental cattle

Artificial selection has greatly improved the beef production performance and changed its genetic basis. High-density SNP markers provide a way to track these changes and use selective signatures to search for the genes associated with artificial selection. In this study, we performed extended haplotype homozygosity (EHH) tests based on Illumina BovineSNP50 (54 K) Chip data from 942 Simmental cattle to identify significant core regions containing selective signatures, then verified the biological significance of these identified regions based on some commonly used bioinformatics analyses. A total of 224 regions over the whole genome in Simmental cattle showing the highest significance and containing some important functional genes, such as GHSR, TG and CANCNA2D1 were chosen. We also observed some significant terms in the enrichment analyses of second GO terms and KEGG pathways, indicating that these genes are associated with economically relevant cattle traits. This is the first detection of selection signature in Simmental cattle. Our findings significantly expand the selection signature map of the cattle genome, and identify functional candidate genes under positive selection for future genetic research.     

Bioremediation of radioactive waste: radionuclide-microbe interactions in laboratory and field-scale studies

Given the scale of the contamination associated with 60 years of global nuclear activity, and the inherent high financial and environmental costs associated with invasive physical and chemical clean-up strategies, there is an unparalleled interest in new passive in situ bioremediation processes for sites contaminated with nuclear waste. Many of these processes rely on successfully harnessing newly discovered natural biogeochemical cycles for key radionuclides and fission products. Recent advances have been made in understanding the microbial colonization of radioactive environments and the biological basis of microbial transformations of radioactive waste in these settings.     

Assessment of sediment contamination at Great Lakes Areas of Concern: the ARCS Program Toxicity-Chemistry Work Group strategy

In response to a mandate in Section 118(c)(3) of the Water Quality Act of 1987, a program called Assessment and Remediation of Contaminated Sediments (ARCS) was established. Four technical work groups were formed. This paper details the research strategy of the Toxicity-Chemistry Work Group.The Work Group's general objectives are to develop survey methods and to map the degree of contamination and toxicity in bottom sediments at three study areas, which will serve as guidance for future surveys at other locations. A related objective is to use the data base that will be generated to calculate sediment quality concentrations by several methods. The information needed to achieve these goals will be collected in a series of field surveys at three areas: Saginaw Bay (MI), Grand Calumet River (IN), and Buffalo River (NY). Assessments of the extent of contamination and potential adverse effects of contaminants in sediment at each of these locations will be conducted by collecting samples for physical characterization, toxicity testing, mutagenicity testing, chemical analyses, and fish bioaccumulation assays. Fish populations will be assessed for tumors and external abnormalities, and benthic community structure will be analyzed. A mapping approach will use low-cost indicator parameters at a large number of stations, and will extrapolate by correlation from traditional chemical and biological studies at a smaller number of locations. Sediment toxicity testing includes elutriate, pore water and whole sediment bioassays in a three-tiered framework. In addition to the regular series of toxicity tests at primary mater stations, some stations are selected for a more extensive suite of tests.     

Biofilm formation by nontypeable Haemophilus influenzae: strain variability, outer membrane antigen expression and role of pili

Background

Detecting microbial life in extraterrestrial locations is a goal of space exploration because of ecological and health concerns about possible contamination of other planets with earthly organisms, and vice versa. Previously we suggested a method for life detection based on the fact that living entities require a continual input of energy accessed through coupled oxidations and reductions (an electron transport chain). We demonstrated using earthly soils that the identification of extracted components of electron transport chains is useful for remote detection of a chemical signature of life. The instrument package developed used supercritical carbon dioxide for soil extraction, followed by chromatography or electrophoresis to separate extracted compounds, with final detection by voltammetry and tandem mass-spectrometry.

Results

Here we used Earth-derived soils to develop a related life detection system based on direct observation of a biological redox signature. We measured the ability of soil microbial communities to reduce artificial electron acceptors. Living organisms in pure culture and those naturally found in soil were shown to reduce 2,3-dichlorophenol indophenol (DCIP) and the tetrazolium dye 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt (XTT). Uninoculated or sterilized controls did not reduce the dyes. A soil from Antarctica that was determined by chemical signature and DNA analysis to be sterile also did not reduce the dyes.

Conclusion

Observation of dye reduction, supplemented with extraction and identification of only a few specific signature redox-active biochemicals such as porphyrins or quinones, provides a simplified means to detect a signature of life in the soils of other planets or their moons.     

A suitable model to describe bioremediation of a petroleum-contaminated soil

A critical environmental impact of the petroleum industry is the spillage of oil and related products that causes severe soil contamination. Although biodegradation of petroleum hydrocarbons may be successfully conducted under controlled conditions, the bioremediation of large volumes of contaminated soils still presents some technical challenges, particularly when contamination occurs in soils of high clay content. The main objective of this work is to evaluate the bioremediation of petroleum-contaminated clay-soil by fixed bed experiments. They were conducted in agreement with the full factorial experimental design 2³. The processes employed were shown to be highly effective in decontaminating the soil, achieving removal rates of around 80%. The model chosen to represent the bioremediation process provided satisfactory results. The values calculated by the model were consistent with the experimental results.     

Laboratory study on the bioremediation of petrochemical sludge-contaminated soil

This study evaluated by biological and chemical analyses the effectiveness of bioremediation of sludge from the petrochemical industry in systems containing artificially contaminated soil. The sludge–soil systems were prepared with three different initial concentrations of sludge, and during bioremediation 86–95% of the hydrocarbons was eliminated. Simultaneously, soil bacterial populations and inhibition of seed germination by aqueous extracts increased in all sludge–soil systems during the first 180 days of treatment. After 1 year of bioremediation, a loss in the catabolic capacity of the Gram-negative bacterial population was observed, but was not dependent on the initial sludge concentration. Furthermore, residual levels of hydrocarbons and seed germination inhibitory effect decreased sharply, but some level of toxicity remained in the systems containing the highest initial sludge concentration. Independent of the initial sludge concentration, the contaminated soils did not re-establish their original features even when residual hydrocarbon concentrations suggested the end of the process.     

Microbial surfactant activities from a petrochemical landfarm in a humid tropical region of Brazil

The goal of this study was to assess the presence and surfactant potential of naturally occurring microbes from a tropical soil with petrochemical contamination. Microorganisms in a soil sample from a Brazilian landfarm were isolated and grown on petroleum as the sole carbon source. Of 60 isolates screened for petroleum-based growth, 7 demonstrated surfactant activities by the drop-collapse methodology over various types of oils. From their growth profiles in liquid culture during 132 h, all had their first detection of surfactant activity after 96 h. Little is currently known about biosurfactant-producing microorganisms in tropical environments contaminated by hydrophobic compounds, and the search for them is essential for bioremediation and for oil recovery enhanced by microbes. Our results indicate that different petroleum-grown microorganisms showing surfactant activity can be recovered from landfarm soil in a tropical environment.     

A suitable model to describe bioremediation of a petroleum-contaminated soil

A critical environmental impact of the petroleum industry is the spillage of oil and related products that causes severe soil contamination. Although biodegradation of petroleum hydrocarbons may be successfully conducted under controlled conditions, the bioremediation of large volumes of contaminated soils still presents some technical challenges, particularly when contamination occurs in soils of high clay content. The main objective of this work is to evaluate the bioremediation of petroleum-contaminated clay-soil by fixed bed experiments. They were conducted in agreement with the full factorial experimental design 2³. The processes employed were shown to be highly effective in decontaminating the soil, achieving removal rates of around 80%. The model chosen to represent the bioremediation process provided satisfactory results. The values calculated by the model were consistent with the experimental results.     

Biodegradation of aged diesel in diverse soil matrixes: impact of environmental conditions and bioavailability on microbial remediation capacity

While bioremediation of total petroleum hydrocarbons (TPH) is in general a robust technique, heterogeneity in terms of contaminant and environmental characteristics can impact the extent of biodegradation. The current study investigates the implications of different soil matrix types (anthropogenic fill layer, peat, clay, and sand) and bioavailability on bioremediation of an aged diesel contamination from a heterogeneous site. In addition to an uncontaminated sample for each soil type, samples representing two levels of contamination (high and low) were also used; initial TPH concentrations varied between 1.6 and 26.6 g TPH/kg and bioavailability between 36 and 100 %. While significant biodegradation occurred during 100 days of incubation under biostimulating conditions (64.4–100 % remediation efficiency), low bioavailability restricted full biodegradation, yielding a residual TPH concentration. Respiration levels, as well as the abundance of alkB, encoding mono-oxygenases pivotal for hydrocarbon metabolism, were positively correlated with TPH degradation, demonstrating their usefulness as a proxy for hydrocarbon biodegradation. However, absolute respiration and alkB presence were dependent on soil matrix type, indicating the sensitivity of results to initial environmental conditions. Through investigating biodegradation potential across a heterogeneous site, this research illuminates the interplay between soil matrix type, bioavailability, and bioremediation and the implications of these parameters for the effectiveness of an in situ treatment.     

Changes of chromium behavior in soil during phenanthrene removal by <Emphasis Type="Italic">Penicillium frequentans</Emphasis>

Soil contamination due to polycyclic aromatic hydrocarbons is often associated with the presence of high levels of potentially toxic metals. Bioremediation is an important option for the clean up of this type of contamination. Changes of chromium fluxes and concentrations during the phenanthrene removal by Penicillium frequentans in soil were investigated. During the bioremediation process, changes in chromium behavior were monitored by Diffusive Gradients in Thin-films (DGT) and by filtration in both sterilized and non-sterilized soils. DGT provided absolute data on fluxes from the solid phase and relative trends of concentrations of the most labile metal species. Filtration provided data on the concentrations of Cr in the solution phase. Together the data provided information about the physical and chemical metal behavior. Results showed that the highest phenanthrene removal was observed in non-sterilized soil (which included the autochthonous microorganisms and P. frequentans inoculum), with a phenanthrene removal of 73 ± 3.2%. However, in all cases microbial activity increased chromium fluxes and chromium soil solution concentration. The bioremediation of soil by P. frequentans increased the lability and mobility of chromium in soil, with potential consequences for plant uptake and for increased movement of metals into the human food chain. Published online December 2004     

The double vocal signature of crested penguins: is the identity coding system of rockhopper penguins Eudyptes chrysocome due to phylogeny or ecology?

Parent-offspring recognition systems are used in bird colonies to avoid misdirected parental care. In penguins, where the risk of confusion is particularly high, recognition is achieved by acoustic signals that constitute highly efficient vocal signatures. Comparisons between species from the Pygoscelis and Aptenodytes genera have revealed interspecific differences on the encoding of information within the signatures which correlate with the presence/absence of nests in the colonies. However a recent study of individual recognition in macaroni penguins Eudyptes chrysolophus revealed diversity within nest-building species. This paper investigates whether the original and intermediate signature system found in macaroni penguins is shared by another species of Eudyptes , the rockhopper penguin E. chrysocome . Vocal signatures of rockhopper penguins were analysed and compared to macaroni penguins'. We used a methodology derived from the theory of information to determine which parameters of the call were likely to encode individual identity. Playbacks of modified calls in the field complemented the analyses, and parent-chick reunions were compared between the two species. Our results reveal a similar double signature system within the Eudyptes genus, which integrates information simultaneously from the temporal and spectral domains. This double encoding is made through the tempo given by the successive syllables of the call and the harmonic content of the call. While it confirms the hypothesis that signatures are simpler in nest-building species, this result reveals differences in the efficacies of signatures within this category. This suggests that other parameters such as the mean distance recognition should be considered to account for the differences in the encoding of the vocal signatures and in their resulting efficacies.     

Cross-Platform Prediction of Gene Expression Signatures

Gene expression signatures can predict the activation of oncogenic pathways and other phenotypes of interest via quantitative models that combine the expression levels of multiple genes. However, as the number of platforms to measure genome-wide gene expression proliferates, there is an increasing need to develop models that can be ported across diverse platforms. Because of the range of technologies that measure gene expression, the resulting signal values can vary greatly. To understand how this variation can affect the prediction of gene expression signatures, we have investigated the ability of gene expression signatures to predict pathway activation across Affymetrix and Illumina microarrays. We hybridized the same RNA samples to both platforms and compared the resultant gene expression readings, as well as the signature predictions. Using a new approach to map probes across platforms, we found that the genes in the signatures from the two platforms were highly similar, and that the predictions they generated were also strongly correlated. This demonstrates that our method can map probes from Affymetrix and Illumina microarrays, and that this mapping can be used to predict gene expression signatures across platforms.     

县区生态系统服务分布图编制——以北京市延庆区土壤保持服务为例

地图是直观展示生态系统服务空间分布格局的手段,是确定重要生态保护目标和区域的主要方法。结合制图学理论方法及国家、行业相关制图规范,探讨生态系统服务分布图编制的目标、原则、流程和制图方法。以编制北京市延庆区1 ： 25万土壤保持服务分布图为例,分析了地理基础确定、地理要素取舍以及土壤保持服务分级等关键制图方法,提出了土壤保持服务分布图的编制规范。研究结果表明,编制的图件能够详尽的展示土壤保持服务的分布特征,精细的反映生态系统服务与自然、人文要素的关系。通过详实的图面信息可进一步判别土壤保持服务分布重要区域,这将为区域生态环境保护规划提供重要技术手段。     

基于秩和检验与SVM的基因特征选取与分类方法

研究了如何提取基因图谱信息的方法问题,提出一种新的基因"标签"提取方法.该方法采用秩和检验法选取基因"标签",得到不同显著性水平下基因"标签"的数目,然后将秩和检验法和分类信息指数相结合,在与基于SVM建立的分类模型比较后,提取最合适的基因"标签",再结合分类信息指数重复数次对这些基因"标签"选取主基因,最后用SVM检验主基因选取及分类的准确率,发现准确率有所提高,说明该方法的有效性.