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Sample records for molecular contamination analysis

  1. Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis.

    Science.gov (United States)

    Greenstone, Matthew H; Weber, Donald C; Coudron, Thomas A; Payton, Mark E; Hu, Jing S

    2012-05-01

    Ecological research requires large samples for statistical validity, typically hundreds or thousands of individuals, which are most efficiently gathered by mass-collecting techniques. For the study of interspecific interactions, molecular gut-content analysis enables detection of arthropod predation with minimal disruption of community interactions. Field experiments have demonstrated that standard mass-collection methods, such as sweep netting, vacuum sampling and foliage beating, sometimes lead to contamination of predators with nontarget DNA, thereby compromising resultant gut-content data. We deliberately contaminated immature Coleomegilla maculata and Podisus maculiventris that had been fed larvae of Leptinotarsa decemlineata by topically applying homogenate of the alternate prey Leptinotarsa juncta. We then attempted to remove contaminating DNA by washing in ethanol or bleach. A 40-min wash with end-over-end rotation in 80% EtOH did not reliably reduce external DNA contamination. Identical treatment with 2.5% commercial bleach removed most externally contaminating DNA without affecting the detectability of the target prey DNA in the gut. Use of this bleaching protocol, perhaps with minor modifications tailored to different predator-prey systems, should reliably eliminate external DNA contamination, thereby alleviating concerns about this possible source of cross-contamination for mass-collected arthropod predators destined for molecular gut-content analysis. Published 2012. This article is a US Government work and is in the public domain in the USA.

  2. Field Analysis of Microbial Contamination Using Three Molecular Methods in Parallel

    Science.gov (United States)

    Morris, H.; Stimpson, E.; Schenk, A.; Kish, A.; Damon, M.; Monaco, L.; Wainwright, N.; Steele, A.

    2010-01-01

    Advanced technologies with the capability of detecting microbial contamination remain an integral tool for the next stage of space agency proposed exploration missions. To maintain a clean, operational spacecraft environment with minimal potential for forward contamination, such technology is a necessity, particularly, the ability to analyze samples near the point of collection and in real-time both for conducting biological scientific experiments and for performing routine monitoring operations. Multiple molecular methods for detecting microbial contamination are available, but many are either too large or not validated for use on spacecraft. Two methods, the adenosine- triphosphate (ATP) and Limulus Amebocyte Lysate (LAL) assays have been approved by the NASA Planetary Protection Office for the assessment of microbial contamination on spacecraft surfaces. We present the first parallel field analysis of microbial contamination pre- and post-cleaning using these two methods as well as universal primer-based polymerase chain reaction (PCR).

  3. Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis

    Science.gov (United States)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  4. Molecular contamination modeling with CTSP

    Science.gov (United States)

    Brieda, Lubos

    2016-11-01

    Spacecraft instruments and thermal control surfaces are generally highly sensitive to molecular and particulate contamination. Despite best efforts taken during assembly, integration, and test, it is impossible to completely eliminate all sources of contaminants. Contamination transport analysis then becomes of critical importance. It can be used to predict the end of life accumulation on critical surfaces from prescribed source rates. Conversely, given allowable deposition levels, contamination modeling can be used to determine the cleanliness requirements to be met prior to launch. This paper describes a recently developed code for modeling contamination transport. Unlike other tools used by the community, CTSP concurrently traces many simulation particles through small time steps. This allows the code to visualize contaminant partial pressures, and to also include aerodynamic, gravitation, or electrostatic forces. The code is demonstrated by simulating an outgassing characterization test in a bell jar.

  5. Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

    Energy Technology Data Exchange (ETDEWEB)

    N' Guessan, L.A.; Elifantz, H.; Nevin, K.P.; Mouser, P.J.; Methe, B.; Woodard, T. L.; Manley, K.; Williams, K. H.; Wilkins, M. J.; Larsen, J.T.; Long, P. E.; Lovley, D. R.

    2009-09-01

    Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified via microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU the most up-regulated. Quantitative PCR analysis of pstB and phoU transcript levels in G. sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve due to the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.

  6. Contamination Analysis Tools

    Science.gov (United States)

    Brieda, Lubos

    2015-01-01

    This talk presents 3 different tools developed recently for contamination analysis:HTML QCM analyzer: runs in a web browser, and allows for data analysis of QCM log filesJava RGA extractor: can load in multiple SRS.ana files and extract pressure vs. time dataC++ Contamination Simulation code: 3D particle tracing code for modeling transport of dust particulates and molecules. Uses residence time to determine if molecules stick. Particulates can be sampled from IEST-STD-1246 and be accelerated by aerodynamic forces.

  7. TRMM project contamination control using molecular adsorbers

    Energy Technology Data Exchange (ETDEWEB)

    Straka, S.; Chen, P.; Thomson, S. [NASA Goddard Space Flight Center, Greenbelt, Maryland 20771 (United States); Bettini, R.; Triolo, J.; Carosso, N. [Swales and Associates, Inc., 5050 Powder Mill Road, Beltsville, Maryland 20705 (United States)

    1996-03-01

    The Tropical Rainfall Measuring Mission (TRMM) is a spacecraft under development by the National Aeronautics and Space Administration (NASA) and the National Space Development Agency of Japan (NASDA) and is scheduled for launch in August 1997. The spacecraft design includes the use of numerous optical instruments and the thermal control surfaces. In addition to the inherent contamination sensitivities of the optical and thermal systems, TRMM has had the added challenge of designing systems to function at a relatively low altitude (350 km), with solar exposure. Under these conditions, high atomic oxygen densities and potentially high levels of backscattered contamination (self-contamination), as well as UV photopolymerization effects, all pose major threats to sensitive TRMM elements. In considering the various contamination control paths to follow, the TRMM project management has opted for pursuing a relatively new, but very promising technology for the TRMM spacecraft in order to lower the on-orbit contamination levels. TRMM will be incorporating Molecular Adsorbers as part of the basic spacecraft design. This paper will summarize the TRMM requirements, describe the Molecular Adsorbers being fabricated for the mission, and discuss the expected benefits of this method of on-orbit contamination control. {copyright} {ital 1996 American Institute of Physics.}

  8. Molecular Contamination Investigation Facility (MCIF) Capabilities

    Science.gov (United States)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  9. Non-hospital environment contamination with Staphylococcus aureus and methicillin-resistant Staphylococcus aureus: proportion meta-analysis and features of antibiotic resistance and molecular genetics.

    Science.gov (United States)

    Lin, Jialing; Lin, Dongxin; Xu, Ping; Zhang, Ting; Ou, Qianting; Bai, Chan; Yao, Zhenjiang

    2016-10-01

    Staphylococcus aureus (S. aureus), including methicillin-resistant Staphylococcus aureus (MRSA), survives in dry conditions and can persist for long periods on surfaces touched by humans. Studies that estimate the proportions and characteristics of S. aureus and MRSA contamination in non-hospital environments are lacking. Therefore, we conducted a proportion meta-analysis and reviewed the features of antibiotic resistance and molecular genetics. Articles published between January 2005 and December 2015 that studied proportions of S. aureus and MRSA contamination in non-hospital environments were retrieved from the Medline database, Ovid database and Science Direct database. All statistics were analyzed by STATA 14.1. Twenty-nine articles were included. The overall proportions of S. aureus and MRSA contamination were 41.1% (95%CI 29-54%) and 8.6% (95%CI 5-13%), respectively. The proportion of MRSA contamination increased over time. From the articles, the proportion of Panton-Valentine Leukociden (PVL) genes among MRSA isolates was 54.5%, and the proportion of the qac gene was 100.0%. Distribution of the multilocus sequence type (MLST) and pulsed-field gel electrophoresis (PFGE) of MRSA indicated that MRSA strains were from both hospitals and communities. The overall proportions of S. aureus and MRSA contamination in non-hospital environments were high. The outcomes of antibiotic resistance and high proportions of PVL genes indicated that the antibiotic resistance of S. aureus and MRSA were notable. According to the different distributions of MLST and SCCmec of MRSA, we can infer that cross-circulation is within hospitals, communities, and livestock. The results also show that the risk from the MRSA strains was cross-transmitted among the population. High proportions of the qac gene of MRSA might indicate that current disinfection of MRSA has not been achieved, and it might be better to further identify the efficiency of the sterilization processes in a non

  10. The use of molecular adsorbers for spacecraft contamination control

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, S.; Chen, P. [NASA Goddard Space Flight Center, Greenbelt, Maryland 20771 (United States); Triolo, J.; Carosso, N. [Swales and Associates, Inc., 5050 Powder Mill Road, Beltsville, Maryland 20705 (United States)

    1996-03-01

    In recent years, the technologies associated with contamination control in space environments have grown increasingly more sophisticated, due to the ever expanding need for improving and enhancing optical and thermal control systems for spacecraft. The presence of contaminants in optical and thermal control systems can cause serious degradation of performance and/or impact the lifetime of a spacecraft. It has been a goal of the global contamination community to develop new and more effective means for controlling contamination for spacecraft. This paper describes an innovative method for controlling molecular contaminants in space environments, via the utilization of Molecular Adsorbers. It has been found that the incorporation of appropriate molecular adsorbing materials within spacecraft volumes will decrease the overall contamination level within the cavity, thereby decreasing the potential for contaminants to migrate to more critical areas. In addition, it has been found that the placement of a Molecular Adsorber at a vent location actually serves as a molecular {open_quote}{open_quote}trap{close_quote}{close_quote} for the contaminants that would have otherwise been vented into the external spacecraft environment. This paper summarizes the theory, basic design, planned applications and significant results already obtained during the investigation of using Molecular Adsorbers for spacecraft contamination control purposes. {copyright} {ital 1996 American Institute of Physics.}

  11. Contaminant analysis automation demonstration proposal

    Energy Technology Data Exchange (ETDEWEB)

    Dodson, M.G.; Schur, A.; Heubach, J.G.

    1993-10-01

    The nation-wide and global need for environmental restoration and waste remediation (ER&WR) presents significant challenges to the analytical chemistry laboratory. The expansion of ER&WR programs forces an increase in the volume of samples processed and the demand for analysis data. To handle this expanding volume, productivity must be increased. However. The need for significantly increased productivity, faces contaminant analysis process which is costly in time, labor, equipment, and safety protection. Laboratory automation offers a cost effective approach to meeting current and future contaminant analytical laboratory needs. The proposed demonstration will present a proof-of-concept automated laboratory conducting varied sample preparations. This automated process also highlights a graphical user interface that provides supervisory, control and monitoring of the automated process. The demonstration provides affirming answers to the following questions about laboratory automation: Can preparation of contaminants be successfully automated?; Can a full-scale working proof-of-concept automated laboratory be developed that is capable of preparing contaminant and hazardous chemical samples?; Can the automated processes be seamlessly integrated and controlled?; Can the automated laboratory be customized through readily convertible design? and Can automated sample preparation concepts be extended to the other phases of the sample analysis process? To fully reap the benefits of automation, four human factors areas should be studied and the outputs used to increase the efficiency of laboratory automation. These areas include: (1) laboratory configuration, (2) procedures, (3) receptacles and fixtures, and (4) human-computer interface for the full automated system and complex laboratory information management systems.

  12. Contamination: concept analysis and nursing implications.

    Science.gov (United States)

    Green, Pauline M; Polk, Laura V

    2009-01-01

    To analyze the concept of contamination and discuss the implications for nursing practice, research, and education. Published research articles, official governmental publications, policy reports, and textbooks. Various attributes of contamination are described using the Walker and Avant method of concept analysis and include: (a) exposure to a contaminant, and (b) contaminant exists in a dose sufficient to cause adverse health effects. The major antecedents of contamination include the presence of a contaminant, dose, duration of exposure, route of exposure, and individual human differences. Major consequences of contamination include organ and systemic responses, and psychological, social, and economic effects. Contamination is an important concept and is essential to the discipline of nursing. The concept of contamination is separate from exposure. Precision in the use of diagnostic language describing contamination incidents will lead to greater accuracy in outcomes and interventions for individuals and groups experiencing overt or covert contamination resulting from accidental or intentional acts. Broad agreement on the definition, antecedents, and consequences of contamination will improve the likelihood of successful management of contamination events. The nursing profession makes an important contribution to the improvement of individual, community, and societal environmental health. Clarifying the concept of contamination is an important first step in building the nursing science that will lead to identifying sound nursing interventions.

  13. Anchoring novel molecular biomarker responses to traditional responses in fish exposed to environmental contamination

    Energy Technology Data Exchange (ETDEWEB)

    Nogueira, Patricia [CESAM and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Department of Biology and Environmental Science, University of Sussex, Falmer, Brighton BN1 9QJ (United Kingdom); Pacheco, Mario [CESAM and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Lourdes Pereira, M. [CICECO and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Mendo, Sonia [CESAM and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Rotchell, Jeanette M., E-mail: J.Rotchell@sussex.ac.u [Department of Biology and Environmental Science, University of Sussex, Falmer, Brighton BN1 9QJ (United Kingdom)

    2010-05-15

    The responses of Dicentrarchus labrax and Liza aurata to aquatic pollution were assessed in a contaminated coastal lagoon, using both traditional and novel biomarkers combined. DNA damage, assessed by comet assay, was higher in both fish species from the contaminated sites, whereas levels of cytochrome P450 1A1 gene expression were not significantly altered. The liver histopathological analysis also revealed significant lesions in fish from contaminated sites. Alterations in ras and xpf genes were analysed and additional pollutant-responsive genes were identified. While no alterations were found in ras gene, a downregulation of xpf gene was observed in D. labrax from a contaminated site. Suppression subtractive hybridization applied to D. labrax collected at a contaminated site, revealed altered expression in genes involved in energy metabolism, immune system activity and antioxidant response. The approach and results reported herein demonstrate the utility of anchoring traditional biomarker responses alongside novel biomarker responses. - Novel molecular biomarkers of aquatic environmental contamination in fish.

  14. Unnecessary roughness? Testing the hypothesis that predators destined for molecular gut-content analysis must be hand-collected to avoid cross-contamination

    Science.gov (United States)

    Molecular gut-content analysis enables direct detection of arthropod predation with minimal disruption of on-going ecosystem processes. Mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, could lead to regurgitation or even rupturing of predators along with uneaten ...

  15. Standardization of surface contamination analysis systems

    Science.gov (United States)

    Boothe, Richard E.

    1995-01-01

    Corrosion products, oils and greases can potentially degrade material bonding properties. The Marshall Space Flight Center (MSFC) Surface Contamination Analysis Team (SCAT) utilizes a variety of analytical equipment to detect identify and quantify contamination on metallic and non-metallic substrates. Analysis techniques include FT-IR Microscopy (FT-IR), Near Infrared Optical Fiber Spectrometry (NIR), Optically Stimulated Electron Emission (OSEE), Ultraviolet Fluorescence (UVF) and Ellipsometry. To insure that consistent qualitative and quantitative information are obtained, standards are required to develop analysis techniques, to establish instrument sensitivity to potential contaminants, and to develop calibration curves. This paper describes techniques for preparing and preserving contamination standards. Calibration of surface contamination analysis systems is discussed, and methods are presented for evaluating the effects of potential contaminants on bonding properties.

  16. In-Line Detection and Measurement of Molecular Contamination in Semiconductor Process Solutions

    Science.gov (United States)

    Wang, Jason; West, Michael; Han, Ye; McDonald, Robert C.; Yang, Wenjing; Ormond, Bob; Saini, Harmesh

    2005-09-01

    This paper discusses a fully automated metrology tool for detection and quantitative measurement of contamination, including cationic, anionic, metallic, organic, and molecular species present in semiconductor process solutions. The instrument is based on an electrospray ionization time-of-flight mass spectrometer (ESI-TOF/MS) platform. The tool can be used in diagnostic or analytical modes to understand process problems in addition to enabling routine metrology functions. Metrology functions include in-line contamination measurement with near real-time trend analysis. This paper discusses representative organic and molecular contamination measurement results in production process problem solving efforts. The examples include the analysis and identification of organic compounds in SC-1 pre-gate clean solution; urea, NMP (N-Methyl-2-pyrrolidone) and phosphoric acid contamination in UPW; and plasticizer and an organic sulfur-containing compound found in isopropyl alcohol (IPA). It is expected that these unique analytical and metrology capabilities will improve the understanding of the effect of organic and molecular contamination on device performance and yield. This will permit the development of quantitative correlations between contamination levels and process degradation. It is also expected that the ability to perform routine process chemistry metrology will lead to corresponding improvements in manufacturing process control and yield, the ability to avoid excursions and will improve the overall cost effectiveness of the semiconductor manufacturing process.

  17. Environmental analysis of contaminated sites

    National Research Council Canada - National Science Library

    Sunahara, G.I; Renoux, A; Thellen, C; Gaudet, C.L; Pilon, A

    2002-01-01

    .... Topics addressed include: the integration of terrestrial ecotoxicity testing with respect to a chemical's behaviour in soil, developments in contaminated soil risk assessment, and the use of advanced scientific data...

  18. Statistical Evaluation of Molecular Contamination During Spacecraft Thermal Vacuum Test

    Science.gov (United States)

    Chen, Philip; Hedgeland, Randy; Montoya, Alex; Roman-Velazquez, Juan; Dunn, Jamie; Colony, Joe; Petitto, Joseph

    1999-01-01

    The purpose of this paper is to evaluate the statistical molecular contamination data with a goal to improve spacecraft contamination control. The statistical data was generated in typical thermal vacuum tests at the National Aeronautics and Space Administration, Goddard Space Flight Center (GSFC). The magnitude of material outgassing was measured using a Quartz Crystal Microbalance (QCNO device during the test. A solvent rinse sample was taken at the conclusion of each test. Then detailed qualitative and quantitative measurements were obtained through chemical analyses. All data used in this study encompassed numerous spacecraft tests in recent years.

  19. Rutherford backscattering analysis of contaminants in PET

    Science.gov (United States)

    Pierce, D. E.; Pfeffer, R. L.; Sadler, G. D.

    1997-05-01

    Rutherford Backscattering Spectrometry (RBS) was used to understand the sorption and desorption of organic contaminants in the polymer Poly(ethylene terephthalate), or PET. Samples were exposed to a range of organics to simulate contamination of PET that can take place in the post-consumer waste stream. From RBS analysis, concentration depth profiles were shown to vary from a monolayer regime surface layer to a saturation level, depending on the contaminant. Heat treatments were also applied to contaminated polymer to simulate thermal processing steps in the recycling of PET. Heating caused a dramatic decrease in contaminants and in some cases a complete removal of contamination was achieved to the limit of RBS detectability.

  20. Molecular biomonitoring during rhizoremediation of oil-contaminated soil

    Energy Technology Data Exchange (ETDEWEB)

    Jussila, M.

    2006-07-01

    Rhizoremediation is the use of microbial populations present in the rhizosphere of plants for environmental cleanup. The idea of this work was that bacteria living in the rhizosphere of a nitrogen-fixing leguminous plant, goat's rue (Galega orientalis), could take part in the degradation of harmful monoaromatic hydrocarbons, such as benzene, toluene and xylene (BTEX), from oil-contaminated soils. In addition to chemical (e.g. pollutant concentration) and physical (e.g. soil structure) information, the knowledge of biological aspects (e.g. bacteria and their catabolic genes) is essential when developing the rhizoremediation into controlled and effective bioremediation practice. Therefore, the need for reliable biomonitoring methods is obvious. The main aims of this thesis were to evaluate the symbiotic G. orientalis - Rhizobium galegae system for rhizoremediation of oil-contaminated soils, to develop molecular methods for biomonitoring, and to apply these methods for studying the microbiology of rhizoremediation. In vitro, Galega plants and rhizobia remained viable in m-toluate concentrations up to 3000 mg/l. Plant growth and nodulation were inhibited in 500 mg/l m-toluate, but were restored when plants were transferred to clean medium. In the greenhouse, Galega showed good growth, nodulation and nitrogen fixation, and developed a strong rhizosphere in soils contaminated with oil or spiked with 2000 mg/l m-toluate. The high aromatic tolerance of R. galegae and the viability of Galega plants in oil-polluted soils proved this legume system to be a promising method for the rhizoremediation of oil-contaminated soils. Molecular biomonitoring methods were designed and/or developed further for bacteria and their degradation genes. A combination of genomic fingerprinting ((GTG)5-PCR), taxonomic ribotyping of 16S rRNA genes and partial 16S rRNA gene sequencing were chosen for molecular grouping of culturable, heterogeneous rhizosphere bacteria. PCR primers specific for

  1. Airborne molecular contamination: quality criterion for laser and optical components

    Science.gov (United States)

    Otto, Michael

    2015-02-01

    Airborne molecular contaminations (AMCs) have been recognized as a major problem in semiconductor fabrication. Enormous technical and financial efforts are made to remove or at least reduce these contaminations in production environments to increase yield and process stability. It can be shown that AMCs from various sources in laser devices have a negative impact on quality and lifetime of lasers and optical systems. Outgassing of organic compounds, especially condensable compounds were identified as the main source for deterioration of optics. These compounds can lead to hazing on surfaces of optics, degradation of coating, reducing the signal transmission or the laser signal itself and can enhance the probability of laser failure and damage. Sources of organic outgassing can be molding materials, resins, seals, circuit boards, cable insulation, coatings, paints and others. Critical compounds are siloxanes, aromatic amines and high boiling aromatic hydrocarbons like phthalates which are used as softeners in plastic materials. Nowadays all sensitive assembly steps are performed in controlled cleanroom environments to reduce risks of contamination. We will demonstrate a high efficient air filter concept to remove AMCs for production environments with special AMC filters and methods for the qualification and monitoring of these environments. Additionally, we show modern techniques and examples for the pre-qualification of materials. For assembled components, we provide sampling concepts for a routine measurement for process, component and product qualification. A careful selection of previously tested and certified materials and components is essential to guarantee the quality of lasers and optical devices.

  2. Optimized molecular resolution of cross-contamination alerts in clinical mycobacteriology laboratories

    Directory of Open Access Journals (Sweden)

    de Viedma Darío

    2008-02-01

    Full Text Available Abstract Background The phenomenon of misdiagnosing tuberculosis (TB by laboratory cross-contamination when culturing Mycobacterium tuberculosis (MTB has been widely reported and it has an obvious clinical, therapeutic and social impact. The final confirmation of a cross-contamination event requires the molecular identification of the same MTB strain cultured from both the potential source of the contamination and from the false-positive candidate. The molecular tool usually applied in this context is IS6110-RFLP which takes a long time to provide an answer, usually longer than is acceptable for microbiologists and clinicians to make decisions. Our purpose in this study is to evaluate a novel PCR-based method, MIRU-VNTR as an alternative to assure a rapid and optimized analysis of cross-contamination alerts. Results MIRU-VNTR was prospectively compared with IS6110-RFLP for clarifying 19 alerts of false positivity from other laboratories. MIRU-VNTR highly correlated with IS6110-RFLP, reduced the response time by 27 days and clarified six alerts unresolved by RFLP. Additionally, MIRU-VNTR revealed complex situations such as contamination events involving polyclonal isolates and a false-positive case due to the simultaneous cross-contamination from two independent sources. Conclusion Unlike standard RFLP-based genotyping, MIRU-VNTR i could help reduce the impact of a false positive diagnosis of TB, ii increased the number of events that could be solved and iii revealed the complexity of some cross-contamination events that could not be dissected by IS6110-RFLP.

  3. Economic analysis of recycling contaminated concrete

    Energy Technology Data Exchange (ETDEWEB)

    Stephen, A.; Ayers, K.W.; Boren, J.K.; Parker, F.L. [Vanderbilt Univ., Nashville, TN (United States)

    1997-02-01

    Decontamination and Decommissioning activities in the DOE complex generate large volumes of radioactively contaminated and uncontaminated concrete. Currently, this concrete is usually decontaminated, the contaminated waste is disposed of in a LLW facility and the decontaminated concrete is placed in C&D landfills. A number of alternatives to this practice are available including recycling of the concrete. Cost estimates for six alternatives were developed using a spreadsheet model. The results of this analysis show that recycling alternatives are at least as economical as current practice.

  4. [Molecular Identification and Toxicity of Pufferfish Juveniles Contaminating Whitebait Products].

    Science.gov (United States)

    Kiriake, Aya; Ohta, Akira; Okayama, Sakurako; Matsuura, Keiichi; Ishizaki, Shoichiro; Nagashima, Yuji

    2016-01-01

    Catches of whitebait, sardine fry, sometimes contains other marine animals, including fishes, mollusks, and crustaceans, and therefore boiled and dried whitebait products may contain these marine animals if sorting is incomplete. In September 2014, contamination of boiled and dried whitebait products with pufferfish juveniles became a serious food safety concern, as tiger pufferfish Takifugu rubripes juveniles are toxic and contain tetrodotoxin (TTX). The toxicity of the juveniles of other pufferfish species, however, is unclear. To evaluate the food safety of whitebait products contaminated with pufferfish juveniles, we identified the species and toxicity of pufferfish juveniles contaminating whitebait products processed between July and September, 2014. Nucleotide sequence analysis of 16S rRNA or cytochrome b gene fragments of the mitochondrial DNA indicated that partial sequences of the polymerase chain reaction products of 15 specimens were identical with those of Lagocephalus spadiceus, and partial sequence from 2 specimens were identical with those of Takifugu vermicularis. We analyzed TTX by liquid chromatography-tandem mass spectrometry. TTX was not detected in the L. spadiceus specimens and was below the quantification limits (30 ng/g) in a T. vermicularis specimen. Based on whitebait product manufacturer's research, 795 individuals and 27.2 g of pufferfish juveniles were detected in 8,245 kg whitebait product. Thus, the ratio of pufferfish to whitebait product was estimated to be 0.096 individual/kg whitebait product and 0.0033 g/kg whitebait product, respectively.

  5. Molecular Characterization and Expression Analysis of P38 MAPK Gene and Protein in Aquatic Midge, Chironomus riparius (Diptera: Chironomidae), Exposed to Environmental Contaminants.

    Science.gov (United States)

    Park, Sun-Young; Choi, Jinhee

    2017-04-01

    P38 Mitogen-activated protein kinase (MAPK), an important signaling protein involved in various cellular processes, including stress responses, has been well characterized in model organisms. P38 has been identified in a number of insects, including the genus Drosophila; however, its homologue in Chironomus riparius has not yet been identified. In this study, we identified and characterized p38 MAPK (Crp38) gene in C. riparius using a transcriptome database that was previously generated 454 GS-FLX pyrosequencing. Comparative and phylogenetic analyses were performed using the p38 homologue of other species, such as Drosophila melanogaster, Aedes aegypti, Bombyx mori, Caenorhabditis elegans, Homo sapiens, etc. Furthermore, to test its potential as a biomarker of environmental contamination, Crp38 gene expression was analyzed upon exposure to nonylphenol (NP), silver nanoparticles (AgNPs), and cadmium (Cd). Crp38 gene expression was up- or down-regulated depending on the concentration and exposure duration of chemicals. These results show the role of Crp38 gene in defense against environmental stresses, as well as its potential use as a biomarker for various environmental pollutants. We further synthesized p38 antibody based on the predicted amino acid sequence deduced from Crp38 cDNA and, using this customized antibody, examined p38 protein expression in Cd exposed C. riparius. Although transcriptional alteration was not translated to the protein level, this result showed the possible application of a protein level functional study using cDNA sequence information from next-generation sequencing database in nonmodel organisms.

  6. A study on EUV reticle surface molecular contamination under different storage conditions in a HVM foundry fab

    Science.gov (United States)

    Singh, SherJang; Yatzor, Brett; Taylor, Ron; Wood, Obert; Mangat, Pawitter

    2017-03-01

    The prospect of EUVL (Extreme Ultraviolet Lithography) insertion into HVM (High Volume Manufacturing) has never been this promising. As technology is prepared for "lab to fab" transition, it becomes important to comprehend challenges associated with integrating EUVL infrastructure within existing high volume chip fabrication processes in a foundry fab. The existing 193nm optical lithography process flow for reticle handling and storage in a fab atmosphere is well established and in-fab reticle contamination concerns are mitigated with the reticle pellicle. However EUVL reticle pellicle is still under development and if available, may only provide protection against particles but not molecular contamination. HVM fab atmosphere is known to be contaminated with trace amounts of AMC's (Atmospheric Molecular Contamination). If such contaminants are organic in nature and get absorbed on the reticle surface, EUV photon cause photo-dissociation resulting into carbon generation which is known to reduce multilayer reflectivity and also degrades exposure uniformity. Chemical diffusion and aggregation of other ions is also reported under the e-beam exposure of a EUV reticle which is known to cause haze issues in optical lithography. Therefore it becomes paramount to mitigate absorbed molecular contaminant concerns on EUVL reticle surface. In this paper, we have studied types of molecular contaminants that are absorbed on an EUVL reticle surface under HVM fab storage and handling conditions. Effect of storage conditions (gas purged vs atmospheric) in different storage pods (Dual pods, Reticle Clamshells) is evaluated. Absorption analysis is done both on ruthenium capping layer as well as TaBN absorber. Ru surface chemistry change as a result of storage is also studied. The efficacy of different reticle cleaning processes to remove absorbed contaminant is evaluated as well.

  7. Application of molecular fingerprinting for analysis of a PAH-contaminated soil microbiota growing in the presence of complex PAHs - DOI: 10.4025/actascibiolsci.v32i1.7575

    Directory of Open Access Journals (Sweden)

    Margaret Britz

    2009-12-01

    Full Text Available Polycyclic aromatic hydrocarbons (PAHs constitute a group of priority pollutants which are present at high concentrations in the soils of many industrial contaminated sites. Pollution by these compounds may stimulate growth of organisms able to live in these environments causing changes in the structure of the microbial community due to some cooperative process of metabolization of toxic compounds. A long-term PAH-contaminated soil was stored for several years and used to analyze the native microbiota regarding their ability to grow on pyrene, benzo[a]pyrene, as well as in mixtures of LMW- and HMW-PAHs. Molecular profiles of the microbial community was assessed by PCR-DGGE of 16S rRNA gene, and the number of bands observed in DGGE analyses was interpreted as dominant microbial members into the bacterial community. Results of PAH-contaminated soil microorganisms showed different profiles in the degradative dynamics when some nutrients were added. Predominant species may play a significative role while growing and surviving on PAHs, and some other metabolically active species have emerged to interact themselves in a cooperative catabolism of PAHs.

  8. Adsorption modeling for macroscopic contaminant dispersal analysis

    Energy Technology Data Exchange (ETDEWEB)

    Axley, J.W.

    1990-05-01

    Two families of macroscopic adsorption models are formulated, based on fundamental principles of adsorption science and technology, that may be used for macroscopic (such as whole-building) contaminant dispersal analysis. The first family of adsorption models - the Equilibrium Adsorption (EA) Models - are based upon the simple requirement of equilibrium between adsorbent and room air. The second family - the Boundary Layer Diffusion Controlled Adsorption (BLDC) Models - add to the equilibrium requirement a boundary layer model for diffusion of the adsorbate from the room air to the adsorbent surface. Two members of each of these families are explicitly discussed, one based on the linear adsorption isotherm model and the other on the Langmuir model. The linear variants of each family are applied to model the adsorption dynamics of formaldehyde in gypsum wall board and compared to measured data.

  9. Molecular contamination mitigation in EUVL by environmental control

    NARCIS (Netherlands)

    Koster, N.; Mertens, B.; Jansen, R.; van de Runstraat, A.; Stietz, F.; Wedowski, M.; Meiling, H.; Klein, R.; Gottwald, A.; Scholze, F.; Visser, M.; Kurt, R.; Zalm, P.; E. Louis,; Yakshin, A.

    2002-01-01

    EUVL tools operate under vacuum conditions to avoid absorption losses. Under these conditions, the MoSi multilayer mirrors are contaminated, resulting in reduced reflection and thus throughput. We report on experiments on MoSi mirrors exposed to EUV radiation from a synchrotron. To mimic the effects

  10. Molecular contamination mitigation in EUVL by environmental control

    NARCIS (Netherlands)

    Koster, N.; Mertens, B.; Jansen, R.; van de Runstraat, A.; Stietz, F.; Wedowski, M.; Meiling, H.; Klein, R.; Gottwald, A.; Scholze, F.; Visser, M.; Kurt, R.; Zalm, P.; E. Louis,; Yakshin, A.

    2002-01-01

    EUVL tools operate under vacuum conditions to avoid absorption losses. Under these conditions, the MoSi multilayer mirrors are contaminated, resulting in reduced reflection and thus throughput. We report on experiments on MoSi mirrors exposed to EUV radiation from a synchrotron. To mimic the effects

  11. Molecular detection of mycobiota and aflatoxin contamination of chili

    Directory of Open Access Journals (Sweden)

    Gherbawy Youssuf A.

    2015-01-01

    Full Text Available Capsicum annuum grows in warm areas. Pepper production conditions require the drying of fruits by sunlight. During the drying processes, the crop is exposed to contamination by microorganisms, especially fungi. In this article, the isolation of mycobiota from retail markets and food restaurants of Taif city was studied. Crushed chili showed a high fungal load compared to chili sauce and chili powder, while chili powder showed a high occurrence of total aflatoxins (AFs. Aspergillus, Eurotium and Penicillium were the most common genera isolated from chili samples. Thirty-four samples (out of 60 were naturally contaminated with AFs ranging from 20 to 200 ppb. The total aflatoxin potential of 35 isolates of A. flavus, A. parasiticus and A. tamarri were studied. Seventy percent of A. flavus isolates were aflatoxigenic. The frequencies of aflatoxin biosynthesis genes aflR, nor-1, ver-1 and omtA were studied in aflatoxigenic and non-aflatoxigenic isolates of Aspergillus species collected in this study. All aflatoxigenic isolates (21 and 1 non-aflatoxigenic isolate of A. flavus showed DNA fragments that correspond to the complete set of the targeted genes. In conclusion, the high co-occurrence of Aspergillus species capable of producing aflatoxins, particularly in chili samples, suggests the need for more efficient control during processing and storage to reduce fungal contamination.

  12. Application of computer-assisted molecular modeling (CAMM) for immunoassay of low molecular weight food contaminants: A review

    Science.gov (United States)

    Immunoassay for low molecular weight food contaminants, such as pesticides, veterinary drugs, and mycotoxins is now a well-established technique which meets the demands for a rapid, reliable, and cost-effective analytical method. However, due to limited understanding of the fundamental aspects of i...

  13. Molecular diversity of arbuscular mycorrhizal fungi in relation to soil chemical properties and heavy metal contamination

    Energy Technology Data Exchange (ETDEWEB)

    Zarei, Mehdi [Department of Soil Science, College of Agriculture, University of Shiraz, Shiraz (Iran, Islamic Republic of); Hempel, Stefan, E-mail: hempel.stefan@googlemail.co [UFZ Helmholtz Centre for Environmental Research Leipzig-Halle, Department of Soil Ecology, Theodor-Lieser-Strasse 4, 06120 Halle (Germany); Freie Universitaet Berlin, Institut fuer Biologie, Okologie der Pflanzen, Altensteinstrasse 6, 14195 Berlin (Germany); Wubet, Tesfaye; Schaefer, Tina [UFZ Helmholtz Centre for Environmental Research Leipzig-Halle, Department of Soil Ecology, Theodor-Lieser-Strasse 4, 06120 Halle (Germany); Savaghebi, Gholamreza [Department of Soil Science Engineering, University College of Agriculture and Natural Resources, University of Tehran, Karaj (Iran, Islamic Republic of); Jouzani, Gholamreza Salehi; Nekouei, Mojtaba Khayam [Agricultural Biotechnology Research Institute of Iran (ABRII), P.O. Box 31535-1897, Karaj (Iran, Islamic Republic of); Buscot, Francois [UFZ Helmholtz Centre for Environmental Research Leipzig-Halle, Department of Soil Ecology, Theodor-Lieser-Strasse 4, 06120 Halle (Germany)

    2010-08-15

    Abundance and diversity of arbuscular mycorrhizal fungi (AMF) associated with dominant plant species were studied along a transect from highly lead (Pb) and zinc (Zn) polluted to non-polluted soil at the Anguran open pit mine in Iran. Using an established primer set for AMF in the internal transcribed spacer (ITS) region of rDNA, nine different AMF sequence types were distinguished after phylogenetic analyses, showing remarkable differences in their distribution patterns along the transect. With decreasing Pb and Zn concentration, the number of AMF sequence types increased, however one sequence type was only found in the highly contaminated area. Multivariate statistical analysis revealed that further factors than HM soil concentration affect the AMF community at contaminated sites. Specifically, the soils' calcium carbonate equivalent and available P proved to be of importance, which illustrates that field studies on AMF distribution should also consider important environmental factors and their possible interactions. - The molecular diversity of AMF was found to be influenced by a combination of soil heavy metal and other soil chemical parameters.

  14. More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA

    DEFF Research Database (Denmark)

    Malmström, Helena; Svensson, Emma M; Gilbert, M Thomas P;

    2007-01-01

    the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing....... Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination...

  15. Modeling effects of common molecular contaminants on the Euclid infrared detectors

    Science.gov (United States)

    Holmes, W.; McKenney, C.; Barbier, R.; Cho, H.; Cillis, A.; Clemens, J.-C.; Dawson, O.; Delo, G.; Ealet, A.; Feizi, A.; Ferraro, N.; Foltz, R.; Goodsall, T.; Hickey, M.; Hwang, T.; Israelsson, U.; Jhabvala, M.; Kahle, D.; Kan, Em.; Kan, Er.; Lotkin, G.; Maciaszek, T.; McClure, S.; Miko, L.; Nguyen, L.; Pravdo, S.; Prieto, E.; Powers, T.; Seiffert, M.; Strada, P.; Tucker, C.; Turck, K.; Waczynski, A.; Wang, F.; Weber, C.; Williams, J.

    2016-07-01

    Cleanliness specifications for infrared detector arrays are usually so stringent that effects are neglibile. However, the specifications determine only the level of particulates and areal density of molecular layer on the surface, but the chemical composition of these contaminants are not specified. Here, we use a model to assess the impact on system quantum efficiency from possible contaminants that could accidentally transfer or cryopump to the detector during instrument or spacecraft testing and on orbit operation. Contaminant layers thin enough to meet typical specifications, < 0.5μgram/cm2, have a negligible effect on the net quantum efficiency of the detector, provided that the contaminant does not react with the detector surface, Performance impacts from these contaminant plating onto the surface become important for thicknesses 5 - 50μgram/cm2. Importantly, detectable change in the "ripple" of the anti reflection coating occurs at these coverages and can enhance the system quantum efficiency. This is a factor 10 less coverage for which loss from molecular absorption lines is important. Thus, should contamination be suspected during instrument test or flight, detailed modelling of the layer on the detector and response to very well known calibrations sources would be useful to determine the impact on detector performance.

  16. Surface contamination analysis technology team overview

    Science.gov (United States)

    Burns, H. Dewitt

    1995-01-01

    A team was established which consisted of representatives from NASA (Marshall Space Flight Center and Langley Research Center), Thiokol Corporation, the University of Alabama in Huntsville, AC Engineering, SAIC, Martin Marietta, and Aerojet. The team's purpose was to bring together the appropriate personnel to determine what surface inspection techniques were applicable to multiprogram bonding surface cleanliness inspection. In order to identify appropriate techniques and their sensitivity to various contaminant families, calibration standards were developed. Producing standards included development of consistent low level contamination application techniques. Oxidation was also considered for effect on inspection equipment response. Ellipsometry was used for oxidation characterization. Verification testing was then accomplished to show that selected inspection techniques could detect subject contaminants at levels found to be detrimental to critical bond systems of interest. Once feasibility of identified techniques was shown, selected techniques and instrumentation could then be incorporated into a multipurpose inspection head and integrated with a robot for critical surface inspection. Inspection techniques currently being evaluated include optically stimulated electron emission (OSEE); near infrared (NIR) spectroscopy utilizing fiber optics; Fourier transform infrared (FTIR) spectroscopy; and ultraviolet (UV) fluorescence. Current plans are to demonstrate an integrated system in MSFC's Productivity Enhancement Complex within five years from initiation of this effort in 1992 assuming appropriate funding levels are maintained. This paper gives an overview of work accomplished by the team and future plans.

  17. Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes

    Directory of Open Access Journals (Sweden)

    Yuting eLiang

    2016-02-01

    Full Text Available With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001. Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential keystone genes, defined as either hubs or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.

  18. Contaminant remediation decision analysis using information gap theory

    CERN Document Server

    Harp, Dylan R

    2011-01-01

    Decision making under severe lack of information is a ubiquitous situation in nearly every applied field of engineering, policy, and science. A severe lack of information precludes our ability to determine a frequency of occurrence of events or conditions that impact the decision; therefore, decision uncertainties due to a severe lack of information cannot be characterized probabilistically. To circumvent this problem, information gap (info-gap) theory has been developed to explicitly recognize and quantify the implications of information gaps in decision making. This paper presents a decision analysis based on info-gap theory developed for a contaminant remediation scenario. The analysis provides decision support in determining the fraction of contaminant mass to remove from the environment in the presence of a lack of information related to the contaminant mass flux into an aquifer. An info-gap uncertainty model is developed to characterize uncertainty due to a lack of information concerning the contaminant...

  19. Wastewater contamination in Antarctic melt-water streams evidenced by virological and organic molecular markers.

    Science.gov (United States)

    Tort, L F L; Iglesias, K; Bueno, C; Lizasoain, A; Salvo, M; Cristina, J; Kandratavicius, N; Pérez, L; Figueira, R; Bícego, M C; Taniguchi, S; Venturini, N; Brugnoli, E; Colina, R; Victoria, M

    2017-12-31

    Human activities in the Antarctica including tourism and scientific research have been raised substantially in the last century with the concomitant impact on the Antarctic ecosystems through the release of wastewater mainly from different scientific stations activities. The aim of this study was to assess the wastewater contamination of surface waters and sediments of three melt-water streams (11 sites) by leaking septic tanks located in the vicinity of the Uruguayan Scientific Station in the Fildes Peninsula, King George Island, Antarctica, during summer 2015. For this purpose, we combined the analysis of fecal steroids in sediments by using gas chromatography and six enteric viruses in surface waters by quantitative and qualitative PCR. Coprostanol concentrations (from 0.03 to 3.31μgg(-1)) and fecal steroids diagnostic ratios indicated that stations C7 and C8 located in the kitchen stream presented sewage contamination. Rotavirus was the only enteric virus detected in five sites with concentration ranging from 1.2×10(5)gcL(-)(1) to 5.1×10(5)gcL(-)(1) being three of them located downstream from the leaking AINA and Kitchen septic tanks. This study shows for the first time the presence of both virological and molecular biomarkers of wastewater pollution in surface waters and sediments of three melt-water streams in the vicinity of a scientific station in the Antarctica. These results highlight the importance of the complementation of these biomarkers in two different matrices (surface waters and sediments) to assess wastewater pollution in an Antarctic environment related to anthropogenic activities in the area. Copyright © 2017. Published by Elsevier B.V.

  20. Environmental Forensics: Using Compound-Specific Stable Carbon Isotope Analysis to Track Petroleum Contamination

    Science.gov (United States)

    Imfeld, A.; Ouellet, A.; Gelinas, Y.

    2016-12-01

    Crude oil and petroleum products are continually being introduced into the environment during transportation, production, consumption and storage. Source identification of these organic contaminants proves challenging due to a variety of factors; samples tend to be convoluted, compounds need to be separated from an unresolved complex mixtures of highly altered aliphatic and aromatic compounds, and chemical composition and biomarker distributions can be altered by weathering, aging, and degradation processes. The aim of our research is to optimize a molecular and isotopic (δ13C, δ2H) method to fingerprint and identify petroleum contaminants in soil and sediment matrices, and to trace the temporal and spatial extent of the contamination event. This method includes the extraction, separation and analysis of the petroleum derived hydrocarbons. Sample extraction and separation is achieved using sonication, column chromatography and urea adduction. Compound identification and molecular/isotopic fingerprinting is obtained by gas chromatography with flame ionization (GC-FID) and mass spectrometer (GC-MS) detection, as well as gas chromatography coupled to an isotope ratio mass spectrometer (GC-IRMS). This method will be used to assist the Centre d'Expertise en Analyse Environnementale du Québec to determine the nature, sources and timing of contamination events as well as for investigating the residual contamination involving petroleum products.

  1. Analysis of culturable and unculturable microbial community in bensulfuron-methyl contaminated paddy soils

    Institute of Scientific and Technical Information of China (English)

    LIN Xiaoyan; ZHAO Yuhua; FU Qinglin; M. L. Umashankara; FENG Zhihong

    2008-01-01

    To investigate the influence of bensulfuron-methyl (BSM) on culturable microbial quantities and unculturable microbial community structures, conventional and molecular biological methods were employed in five BSM treated soils with three replications, respectively. The results obtained with traditional culture-dependent methods showed that a low-level of BSM had slight and transient effects on culturable microorganisms; nevertheless, high concentration of BSM resulted in a dramatic decrease in bacterial colony forming units (cfus). The result obtained using denaturing gradient gel electrophoresis (DGGE) revealed that more than 17 bands were observed in low BSM contaminated soil samples and only 10 bands were detected in samples with high BSM contamination. In other words, the diversity of soil community structure is related to the concentration of BSM. Cluster analysis showed that the community structure under low level of contamination was more similar to that of the control, while heavy contaminated amendments were far away from the above group. In a sense, the cooperation of the traditional method and the molecular biological method is more powerful to study the soil microbial information in contaminated ecosystem.

  2. Anti-airborne-molecular-contamination technology in clean rooms; Kukichu no kagaku osen no teigen taisaku

    Energy Technology Data Exchange (ETDEWEB)

    Sakata, S.; Sato, K.; Takahashi, H.; Okada, T.

    1998-07-31

    As for, countermeasures for chemical contaminants in a cleanroom air, the technical development has progressed earnestly since T top phenomenon of photo-amplified resist with basic gas due to atmosphere was pointed out in 1991 by MacDonald. Airborne-Molecular-Contamination (AMC) is classified into acids, bases, condensables, and dopants. According to SEMATECH no 95052812A-TR, condensable are defined as silicones or hydrocarbons with a boiling point greater than or equal to 150 degC. Water-soluble gaseous contaminants in outdoor air coming into cleanrooms are removed with a water spray equipment. AMC originated from circulating air in cleanrooms are prevented using various chemical filters. Conventional chemical filters made of activated charcoal, however, have several defects. Ceramic chemical filters developed by the authors are nonflammable, and consist of inorganic materials without any volatile organic matters and without alkaline metal and so on, and they have high removal efficiencies of condensable. 15 refs., 12 figs., 3 tabs.

  3. Molecular characterization and lipase profiling of the yeasts isolated from environments contaminated with petroleum.

    Science.gov (United States)

    Yalçın, H Tansel; Corbacı, Cengiz; Uçar, Füsun B

    2014-07-01

    In the present study, 120 yeast isolates from different sources (active sludge, soil, and wastewater samples obtained from petroleum refinery and soil contaminated by petroleum) were obtained. The yeast isolates were screened for lipase production and twelve of the isolates (D3, D17, D24, D27, D30, D38, D40, D42, D44, D46, D56, and D57) exhibited lipase activity. Molecular characterization of the yeasts showing the lipase production was performed with RFLP of ITS1-5.8S-ITS2 and 18S rRNA and sequence analysis of D1/D2 domain of 26S rRNA. The 26S rRNA sequencing revealed that four new strains, D38, D40, D44 and D57 identified as Rhodotorula slooffiae, Candida davisiana, Cryptococcus diffluens, and Cryptococcus uzbekistanensis, respectively, are lipase producing yeast species. This study is the first report showed lipase production by these species. The other lipase producing strains identified as Candida parapsilosis (D3), Rhodotorula muciloginosa (D17 and D42), Cryptococcus albidus (D24, D27, D30, and D56), and Wickerhamomyces anomalus (D46). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. A global indicator as a tool to follow airborne molecular contamination in a controlled environment.

    Science.gov (United States)

    Cariou, Stéphane; Guillot, Jean-Michel; Pépin, Laurence; Kaluzny, Pascal; Faure, Louis-Paul

    2005-02-01

    The impact of pollutants on production quality in nanotechnology necessitates reduction of contaminant levels in cleanrooms. So, devising a global airborne-pollutant indicator (GAPI) for rapid determination of the level of pollution and its danger to the process is justified. This tool used relative impact weights of the different molecules to quantify the pollution. A calculation of impact weight is proposed in this paper. Impact weights could take into account several characteristics of the molecules (molecular volume, sticking coefficient, ...). They could also be combined to be as close as possible to reality. An example of calculations of the impact of molecular volumes on air quality is given.

  5. Forensic analysis of MTBE contamination using basic hydrogeologic concepts.

    Science.gov (United States)

    Boving, Thomas

    2014-07-01

    Contamination of groundwater with petroleum hydrocarbons and additives, such as methyl tert-butyl ether (MTBE), is often linked to the leaking product distribution system of gas stations. In very few cases is it know if and when a leak occurred and how much product was released to the environment. In the absence of direct evidence, a careful analysis of the available data, such as contaminant breakthrough at receptor wells or discrepancies in the product inventory data, may provide evidence about the nature of the release, its timing and magnitude. Using a MTBE contamination site in the formerly glaciated New England region as an example, two possible release scenarios (slow, long-term release vs. spill) were examined. Of the two scenarios, the slow release could be ruled out as the sole source even though there was no direct evidence for a spill. The analysis of hydraulic test results together with chemical data further permitted to estimate when such an undocumented spill might have occurred. Analyses of the data also allowed these results to be compared to that of a prior transport and fate modeling study. Good agreement and consistency for contaminant travel times was confirmed. This forensic analysis demonstrates that applying basic hydrogeologic principles can aide in the reconstruction of contamination events while providing more readily understandable and defendable evidence relative to complex models. Conceptually, the approach described herein is transferable to other sites with similar hydrogeologies.

  6. Molecular-Level Processes Governing the Interaction of Contaminants with Iron and Manganese Oxides - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Brown Jr., G. E.; Chambers, S. A.

    1999-10-31

    Many of the inorganic and organic contaminants present in sediments at DOE sites can be altered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on structurally and compositionally well-defined mineral surfaces will lead to: (i) improved models of contaminant fate and transport in geochemical systems, and (ii) optimized manipulation of these processes for remediation purposes. To contribute to this understanding, we will study, both experimentally and theoretically, redox processes involving three important contaminants - chromate ion, carbon tetrachloride, and trichloroethene TCE, on the following iron and manganese oxides - hematite, magnetite, maghemite, and pyrolusite. These oxides and their hydroxylated analogs commonly occur as coatings on minerals or as interfaces in the subsurface environment. Single-crystal surfaces of these oxides will be synthesized in carefully controlled fashion by molecular beam epitaxy. These surfaces, as well as high surface are powdered samples of these oxides, will be used in spectroscopic and kinetic experiments in both aqueous and gas phases. Our goal is to identify products and to determine the kinetics and mechanisms of surface-catalyzed redox reaction of Cr(VI) and CR(III), and the reductive dechlorination of carbon tetrachloride and TCE. The combination of theory and experiment will provide the base information needed to scale from the molecular level to the microscopic grain level minerals.

  7. MAVEN Contamination Venting and Outgassing Analysis

    Science.gov (United States)

    Petro, Elaine M.; Hughes, David W.; Secunda, Mark S.; Chen, Philip T.; Morrissey, James R.; Riegle, Catherine A.

    2014-01-01

    Mars Atmosphere and Volatile EvolutioN (MAVEN) is the first mission to focus its study on the Mars upper atmosphere. MAVEN will study the evolution of the Mars atmosphere and climate, by examining the conduit through which the atmosphere has to pass as it is lost to the upper atmosphere. An analysis was performed for the MAVEN mission to address two distinct concerns. The first goal of the analysis was to perform an outgassing study to determine where species outgassed from spacecraft materials would redistribute to and how much of the released material might accumulate on sensitive surfaces. The second portion of the analysis serves to predict what effect, if any, Mars atmospheric gases trapped within the spacecraft could have on instrument measurements when re-released through vents. The re-release of atmospheric gases is of interest to this mission because vented gases from a higher pressure spacecraft interior could bias instrument measurements of the Mars atmosphere depending on the flow rates and directions.

  8. Robust decision analysis for environmental management of groundwater contamination sites

    CERN Document Server

    Vesselinov, Velimir V; Katzman, Danny

    2013-01-01

    In contrast to many other engineering fields, the uncertainties in subsurface processes (e.g., fluid flow and contaminant transport in aquifers) and their parameters are notoriously difficult to observe, measure, and characterize. This causes severe uncertainties that need to be addressed in any decision analysis related to optimal management and remediation of groundwater contamination sites. Furthermore, decision analyses typically rely heavily on complex data analyses and/or model predictions, which are often poorly constrained as well. Recently, we have developed a model-driven decision-support framework (called MADS; http://mads.lanl.gov) for the management and remediation of subsurface contamination sites in which severe uncertainties and complex physics-based models are coupled to perform scientifically defensible decision analyses. The decision analyses are based on Information Gap Decision Theory (IGDT). We demonstrate the MADS capabilities by solving a decision problem related to optimal monitoring ...

  9. Analysis of a case of internal contamination with cobalt radioisotopes.

    Science.gov (United States)

    Vrba, T; Malatova, I; Jurochova, B

    2007-01-01

    Internal contamination by compounds of cobalt radioisotopes occurs time to time at nuclear power plants. Intakes and committed effective doses are estimated by biokinetic models described in ICRP publications. The paper deals with a case of internal contamination of a worker engaged in a maintenance task at NPP Dukovany. In this case significant discrepancy was observed between intakes based on various datasets (whole body counting, analysis of urine and faeces) when default model setting was used. The reason of this phenomenon was searched for. Three different least square methods of fits were used to find out possible effect of a fitting method. The measured data were fitted by set of biokinetic functions, which covered all intake ways (ingestion and inhalation) and types (M, S, different AMADs and different f1) of the contaminant. The biokinetic model of cobalt needs further improvements as to find better agreement between data fit from direct measurements and bioassay.

  10. Application of molecular fingerprinting for analysis of a PAH-contaminated soil microbiota growing in the presence of complex PAHs = Aplicação de técnica molecular para análise da microbiota de solo contaminado em misturas complexas de HPAs

    Directory of Open Access Journals (Sweden)

    Ísis Serrano Silva

    2010-01-01

    Full Text Available Polycyclic aromatic hydrocarbons (PAHs constitute a group of priority pollutants which are present at high concentrations in the soils of many industrial contaminated sites. Pollution by these compounds may stimulate growth of organisms able to live in these environments causing changes in the structure of the microbial community due to some cooperative process of metabolization of toxic compounds. A long-term PAH-contaminated soil was stored for several years and used to analyze the native microbiota regarding their ability to grow on pyrene, benzo[a]pyrene, as well as in mixtures of LMW- and HMW-PAHs. Molecular profiles of the microbial community was assessed by PCR-DGGE of 16S rRNA gene, and the number of bands observed in DGGE analyses was interpreted as dominant microbial members into the bacterial community. Results of PAH-contaminated soil microorganisms showed different profiles in the degradative dynamics when some nutrients were added. Predominant species may play a significative role while growing and surviving on PAHs, and some other metabolically active species have emerged to interact themselves in a cooperative catabolism of PAHs.Os hidrocarbonetos poliaromáticos (HPAs são considerados poluentes prioritários presentes em expressiva concentração no solo contaminado com derivados de petróleo. A poluição por esses compostos estimula o crescimento de microrganismos capazes de sobreviverem nestes ambientes contaminados, causando alterações na estrutura da comunidade microbiana do solo pelo processo de cooperação metabólica entre as populações. Um solo contaminado por um longo período de tempo foi coletado de uma área industrial (Port Melbourne, Austrália e utilizado para análise da capacidade da comunidade microbiana em crescer em HPAs isolados e/ou em misturas como únicas fontes de carbono e energia. Os perfis moleculares foram obtidos por PCR-DGGE do fragmento da subunidade 16S do DNA ribossomal, sendo o n

  11. 1H NMR Metabolomics: A New Molecular Level Tool for Assessment of Organic Contaminant Bioavailability to Earthworms in Soil

    Science.gov (United States)

    McKelvie, J. R.; Wolfe, D. M.; Celejewski, M. A.; Simpson, A. J.; Simpson, M. J.

    2009-05-01

    At contaminated field sites, the complete removal of polycyclic aromatic hydrocarbons (PAHs) is rarely achieved since a portion of these compounds remain tightly bound to the soil matrix. The concentration of PAHs in soil typically decreases until a plateau is reached, at which point the remaining contaminant is considered non- bioavailable. Numerous soil extraction techniques, including cyclodextrin extraction, have been developed to estimate contaminant bioavailability. However, these are indirect methods that do not directly measure the response of organisms to chemical exposure in soil. Earthworm metabolomics offers a promising new way to directly evaluate the bioavailability and toxicity of contaminants in soil. Metabolomics involves the measurement of changes in small-molecule metabolites, including sugars and amino acids, in living organisms due to an external stress, such as contaminant exposure. The objective of this study was to compare cyclodextrin extraction of soil (a bioavailability proxy) and 1H NMR metabolomic analysis of aqueous earthworm tissue extracts as indicators of contaminant bioavailability. A 30 day laboratory experiment was conducted using phenanthrene-spiked sphagnum peat soil and the OECD recommended earthworm species for toxicity testing, Eisenia fetida. The initial phenanthrene concentration in the soil was 320 mg/kg. Rapid biodegradation of phenanthrene occurred and concentrations decreased to 16 mg/kg within 15 days. After 15 days, phenanthrene biodegradation slowed and cyclodextrin extraction of the soil suggested that phenanthrene was no longer bioavailable. Multivariate statistical analysis of the 1H NMR spectra for E. fetida tissue extracts indicated that the metabolic profile of phenanthrene exposed earthworms differed from control earthworms throughout the 30 day experiment. This suggests that the residual phenanthrene remaining in the soil after 15 days continued to elicit a metabolic response, even though it was not

  12. Sample Analysis at Mars Organic Contaminants Library (SAM-OCL)

    Science.gov (United States)

    Garcia-Sanchez, Raul; Misra, Prabhakar; Canham, John; Mahaffy, Paul

    2013-04-01

    The Sample Analysis at Mars Organic Contaminants Library (SAM-OCL) was developed as one of several components for the Mars rover mission's Contamination Control Protocol. The purpose of SAM-OCL is to determine the Gas Chromatography-Mass Spectroscopy (GCMS) signals of different materials composing the Mars Science Laboratory rover. In turn, this allows us to determine which GCMS signals originate from terrestrial contamination or rover material outgassing. The GCMS spectral library has several supplemental components, of which its descriptor spreadsheets are the most important, aimed to make SAM-OCL easily and readily accessible to users in and out of the Mars rover mission. One spreadsheet describes the contaminants that can be found in each file, while the other describes the information regarding each file. The library, along with its supplemental materials, is useful from an organizational and practical sense. Through them we are able to organize large volumes of GCMS data while breaking down the components that each material sample is made off. This allows us easy and fast access to information that will be critical when doing analysis in the data that the SAM instrumentation will obtain.

  13. Detection of inter-species contaminations in a cell line collection using isoenzymes and molecular markers

    Directory of Open Access Journals (Sweden)

    M. Ferarri

    2011-03-01

    Full Text Available As in human research, also in livestock species the use of continuous cell cultures is an important tool for the study of physiological and tissue developmental processes, as well as for immunological, virological and toxicological assays. This widespread use of animal cell cultures needs that quality control tests are systematically performed in order to evaluate the authenticity of the cells used. Cell cross-contamination (CCC can occur with cells from other species (interspecies contamination or with unrelated cells from the same species (intraspecies contamination. Several methods have been used to identify inter- and intraspecies CCC: isoenzyme profile (Nims, 1998, cytogenetic analysis (Macville et al., 1996, DNA fingerprinting (Stacey et al., 1992, and, more recently, PCR-based methods (Matsuo et al., 1999. Amplified Fragment Length Polymorphism (AFLP technology is a PCR-based technique (Vos et al., 1995 able to reveal polymorphism, with no need of prior sequence information or probe isolation..........

  14. Generalized analysis of molecular variance.

    Directory of Open Access Journals (Sweden)

    Caroline M Nievergelt

    2007-04-01

    Full Text Available Many studies in the fields of genetic epidemiology and applied population genetics are predicated on, or require, an assessment of the genetic background diversity of the individuals chosen for study. A number of strategies have been developed for assessing genetic background diversity. These strategies typically focus on genotype data collected on the individuals in the study, based on a panel of DNA markers. However, many of these strategies are either rooted in cluster analysis techniques, and hence suffer from problems inherent to the assignment of the biological and statistical meaning to resulting clusters, or have formulations that do not permit easy and intuitive extensions. We describe a very general approach to the problem of assessing genetic background diversity that extends the analysis of molecular variance (AMOVA strategy introduced by Excoffier and colleagues some time ago. As in the original AMOVA strategy, the proposed approach, termed generalized AMOVA (GAMOVA, requires a genetic similarity matrix constructed from the allelic profiles of individuals under study and/or allele frequency summaries of the populations from which the individuals have been sampled. The proposed strategy can be used to either estimate the fraction of genetic variation explained by grouping factors such as country of origin, race, or ethnicity, or to quantify the strength of the relationship of the observed genetic background variation to quantitative measures collected on the subjects, such as blood pressure levels or anthropometric measures. Since the formulation of our test statistic is rooted in multivariate linear models, sets of variables can be related to genetic background in multiple regression-like contexts. GAMOVA can also be used to complement graphical representations of genetic diversity such as tree diagrams (dendrograms or heatmaps. We examine features, advantages, and power of the proposed procedure and showcase its flexibility by

  15. Molecular Contamination on Anodized Aluminum Components of the Genesis Science Canister

    Science.gov (United States)

    Burnett, D. S.; McNamara, K. M.; Jurewicz, A.; Woolum, D.

    2005-01-01

    Inspection of the interior of the Genesis science canister after recovery in Utah, and subsequently at JSC, revealed a darkening on the aluminum canister shield and other canister components. There has been no such observation of film contamination on the collector surfaces, and preliminary spectroscopic ellipsometry measurements support the theory that the films observed on the anodized aluminum components do not appear on the collectors to any significant extent. The Genesis Science Team has made an effort to characterize the thickness and composition of the brown stain and to determine if it is associated with molecular outgassing.Detailed examination of the surfaces within the Genesis science canister reveals that the brown contamination is observed to varying degrees, but only on surfaces exposed in space to the Sun and solar wind hydrogen. In addition, the materials affected are primarily composed of anodized aluminum. A sharp line separating the sun and shaded portion of the thermal closeout panel is shown. This piece was removed from a location near the gold foil collector within the canister. Future plans include a reassembly of the canister components to look for large-scale patterns of contamination within the canister to aid in revealing the root cause.

  16. Identification of molecular markers to follow up the bioremediation of sites contaminated with chlorinated compounds.

    Science.gov (United States)

    Marzorati, Massimo; Balloi, Annalisa; De Ferra, Francesca; Daffonchio, Daniele

    2010-01-01

    The use of microorganisms to clean up xenobiotics from polluted ecosystems (soil and water) represents an ecosustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and sensitive strategies for monitoring and identifying bacteria and catabolic genes involved in the degradation of xenobiotics. This chapter provides a description of recently developed molecular-biology-based techniques, such as PCR with degenerate primers set, real-time quantitative PCR (qPCR), reverse transcription PCR (RT-PCR), southern blot hybridization, and long-range PCR, used to give a picture of the catabolically relevant microorganisms and of the functional genes present in a polluted system. By using a case study of a groundwater aquifer contaminated with 1,2-dichloroethane (1,2-DCA), we describe the identification of microorganisms potentially involved in the 1,2-DCA dehalorespiration (Dehalobacter sp. and Desulfitobacterium sp.) and a complete new gene cluster encoding for a 1,2-DCA reductive dehalogenase. The application of these techniques to bioremediation can improve our understanding of the inner mechanisms to evaluate the feasibility of a given treatment and provide us with a method to follow up bacteria and catabolic genes involved in the degradation of contaminants during the activities in situ.

  17. Understanding molecular mechanisms for improving phytoremediation of heavy metal-contaminated soils.

    Science.gov (United States)

    Hong-Bo, Shao; Li-Ye, Chu; Cheng-Jiang, Ruan; Hua, Li; Dong-Gang, Guo; Wei-Xiang, Li

    2010-03-01

    Heavy metal pollution of soil is a significant environmental problem with a negative potential impact on human health and agriculture. Rhizosphere, as an important interface of soil and plants, plays a significant role in phytoremediation of contaminated soil by heavy metals, in which, microbial populations are known to affect heavy metal mobility and availability to the plant through release of chelating agents, acidification, phosphate solubilization and redox changes, and therefore, have potential to enhance phytoremediation processes. Phytoremediation strategies with appropriate heavy metal-adapted rhizobacteria or mycorrhizas have received more and more attention. In addition, some plants possess a range of potential mechanisms that may be involved in the detoxification of heavy metals, and they manage to survive under metal stresses. High tolerance to heavy metal toxicity could rely either on reduced uptake or increased plant internal sequestration, which is manifested by an interaction between a genotype and its environment.A coordinated network of molecular processes provides plants with multiple metal-detoxifying mechanisms and repair capabilities. The growing application of molecular genetic technologies has led to an increased understanding of mechanisms of heavy metal tolerance/accumulation in plants and, subsequently, many transgenic plants with increased heavy metal resistance, as well as increased uptake of heavy metals, have been developed for the purpose of phytoremediation. This article reviews advantages, possible mechanisms, current status and future direction of phytoremediation for heavy-metal-contaminated soils.

  18. Identification of UDP-linked murein precursors as contaminants in recombinant proteins of low molecular weight.

    Science.gov (United States)

    Ram, M K; Andrade, L J; Phillips, T B; van Schravendijk, M R

    1999-11-01

    The A(280)/A(260) ratio of a purified protein is frequently used as an indication of the purity of the preparation with respect to nucleic acids. We show here that for low-molecular-weight recombinant proteins purified from Escherichia coli, a low A(280)/A(260) ratio can also result from contamination with UDP-linked murein precursors derived from bacterial cell wall metabolism. Although these precursors are small molecules of molecular weight 1000-1200, they comigrate in gel filtration with recombinant human FKBP (MW 11,820). This gel filtration behavior, which is distinct from that of unmodified mononucleotides, does not reflect binding interactions with FKBP, but is an intrinsic property of these precursors. Therefore, these molecules would be expected to copurify with other low-molecular-weight proteins, especially in the abbreviated purification protocols made possible by freeze-thaw release of recombinant proteins from E. coli (Johnson, B. H., and Hecht, M. H. (1994) BioTechnology 12, 1357-1360). Several alternative strategies are discussed for integrating these findings into the design of improved purification procedures for low-molecular-weight recombinant proteins.

  19. Principal Component Analysis with Contaminated Data: The High Dimensional Case

    CERN Document Server

    Xu, Huan; Mannor, Shie

    2010-01-01

    We consider the dimensionality-reduction problem (finding a subspace approximation of observed data) for contaminated data in the high dimensional regime, where the number of observations is of the same magnitude as the number of variables of each observation, and the data set contains some (arbitrarily) corrupted observations. We propose a High-dimensional Robust Principal Component Analysis (HR-PCA) algorithm that is tractable, robust to contaminated points, and easily kernelizable. The resulting subspace has a bounded deviation from the desired one, achieves maximal robustness -- a breakdown point of 50% while all existing algorithms have a breakdown point of zero, and unlike ordinary PCA algorithms, achieves optimality in the limit case where the proportion of corrupted points goes to zero.

  20. Single aflatoxin contaminated corn kernel analysis with fluorescence hyperspectral image

    Science.gov (United States)

    Yao, Haibo; Hruska, Zuzana; Kincaid, Russell; Ononye, Ambrose; Brown, Robert L.; Cleveland, Thomas E.

    2010-04-01

    Aflatoxins are toxic secondary metabolites of the fungi Aspergillus flavus and Aspergillus parasiticus, among others. Aflatoxin contaminated corn is toxic to domestic animals when ingested in feed and is a known carcinogen associated with liver and lung cancer in humans. Consequently, aflatoxin levels in food and feed are regulated by the Food and Drug Administration (FDA) in the US, allowing 20 ppb (parts per billion) limits in food and 100 ppb in feed for interstate commerce. Currently, aflatoxin detection and quantification methods are based on analytical tests including thin-layer chromatography (TCL) and high performance liquid chromatography (HPLC). These analytical tests require the destruction of samples, and are costly and time consuming. Thus, the ability to detect aflatoxin in a rapid, nondestructive way is crucial to the grain industry, particularly to corn industry. Hyperspectral imaging technology offers a non-invasive approach toward screening for food safety inspection and quality control based on its spectral signature. The focus of this paper is to classify aflatoxin contaminated single corn kernels using fluorescence hyperspectral imagery. Field inoculated corn kernels were used in the study. Contaminated and control kernels under long wavelength ultraviolet excitation were imaged using a visible near-infrared (VNIR) hyperspectral camera. The imaged kernels were chemically analyzed to provide reference information for image analysis. This paper describes a procedure to process corn kernels located in different images for statistical training and classification. Two classification algorithms, Maximum Likelihood and Binary Encoding, were used to classify each corn kernel into "control" or "contaminated" through pixel classification. The Binary Encoding approach had a slightly better performance with accuracy equals to 87% or 88% when 20 ppb or 100 ppb was used as classification threshold, respectively.

  1. TXRF analysis of soils and sediments to assess environmental contamination.

    Science.gov (United States)

    Bilo, Fabjola; Borgese, Laura; Cazzago, Davide; Zacco, Annalisa; Bontempi, Elza; Guarneri, Rita; Bernardello, Marco; Attuati, Silvia; Lazo, Pranvera; Depero, Laura E

    2014-12-01

    Total reflection x-ray fluorescence spectroscopy (TXRF) is proposed for the elemental chemical analysis of crustal environmental samples, such as sediments and soils. A comparative study of TXRF with respect to flame atomic absorption spectroscopy and inductively coupled plasma optical emission spectroscopy was performed. Microwave acid digestion and suspension preparation methods are evaluated. A good agreement was found among the results obtained with different spectroscopic techniques and sample preparation methods for Cr, Mn, Fe, Ni, Cu, and Zn. We demonstrated that TXRF is suitable for the assessment of environmental contamination phenomena, even if the errors for Pb, As, V, and Ba are ingent.

  2. Culture and molecular identification of fungal contaminants in edible bird nests.

    Science.gov (United States)

    Chen, Jennifer Xiao Jing; Wong, Shew Fung; Lim, Patricia Kim Chooi; Mak, Joon Wah

    2015-01-01

    Widespread food poisoning due to microbial contamination has been a major concern for the food industry, consumers and governing authorities. This study is designed to determine the levels of fungal contamination in edible bird nests (EBNs) using culture and molecular techniques. Raw EBNs were collected from five house farms, and commercial EBNs were purchased from five Chinese traditional medicine shops (companies A-E) in Peninsular Malaysia. The fungal contents in the raw and commercial EBNs, and boiled and unboiled EBNs were determined. Culturable fungi were isolated and identified. In this study, the use of these methods revealed that all EBNs had fungal colony-forming units (CFUs) that exceeded the limit set by Standards and Industrial Research Institute of Malaysia (SIRIM) for yeast and moulds in EBNs. There was a significant difference (p 0.05). The types of fungi isolated from the unboiled raw EBNs were mainly soil, plant and environmental fungi, while the types of fungi isolated from the boiled raw EBNs, unboiled and boiled commercial EBNs were mainly environmental fungi. Aspergillus sp., Candida sp., Cladosporium sp., Neurospora sp. and Penicillum sp. were the most common fungi isolated from the unboiled and boiled raw and commercial EBNs. Some of these fungi are mycotoxin producers and cause opportunistic infections in humans. Further studies to determine the mycotoxin levels and methods to prevent or remove these contaminations from EBNs for safe consumption are necessary. The establishment and implementation of stringent regulations for the standards of EBNs should be regularly updated and monitored to improve the quality of the EBNs and consumer safety.

  3. Soft X-ray-assisted detection method for airborne molecular contaminations (AMCs)

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Changhyuk; Zuo, Zhili [University of Minnesota, Department of Mechanical Engineering (United States); Finger, Hartmut; Haep, Stefan; Asbach, Christof; Fissan, Heinz [Institute of Energy and Environmental Technology (IUTA e. V.) (Germany); Pui, David Y. H., E-mail: dyhpui@umn.edu [University of Minnesota, Department of Mechanical Engineering (United States)

    2015-03-15

    Airborne molecular contaminations (AMCs) represent a wide range of gaseous contaminants in cleanrooms. Due to the unintentional nanoparticle or haze formation as well as doping caused by AMCs, improved monitoring and controlling methods for AMCs are urgent in the semiconductor industry. However, measuring ultra-low concentrations of AMCs in cleanrooms is difficult, especially, behind a gas filter. In this study, a novel detection method for AMCs, which is on-line, economical, and applicable for diverse AMCs, was developed by employing gas-to-particle conversion with soft X-ray, and then measuring the generated nanoparticles. Feasibility study of this method was conducted through the evaluations of granular-activated carbons (GACs), which are widely used AMC filter media. Sulfur dioxide (SO{sub 2}) was used as an AMC for the feasibility study. Using this method, the ultra-low concentrations of SO{sub 2} behind GACs were determined in terms of concentrations of generated sulfuric acid (H{sub 2}SO{sub 4}) nanoparticles. By calculating SO{sub 2} concentrations from the nanoparticle concentrations using empirical correlation equations between them, remarkable sensitivity of this method to SO{sub 2} was shown, down to parts-per-trillions, which are too low to detect using commercial gas sensors. Also, the calculated SO{sub 2} concentrations showed good agreement with those measured simultaneously by a commercial SO{sub 2} monitor at parts-per-billions.

  4. Signal analysis of behavioral and molecular cycles

    Directory of Open Access Journals (Sweden)

    Dowse Harold B

    2002-01-01

    Full Text Available Abstract Background Circadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities. Results We demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase. Conclusion Using data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed.

  5. Analysis And Assessment Of The Security Method Against Incidental Contamination In The Collective Water Supply System

    Directory of Open Access Journals (Sweden)

    Szpak Dawid

    2015-09-01

    Full Text Available The paper presents the main types of surface water incidental contaminations and the security method against incidental contamination in water sources. Analysis and assessment the collective water supply system (CWSS protection against incidental contamination was conducted. Failure Mode and Effects Analysis (FMEA was used. The FMEA method allow to use the product or process analysis, identification of weak points, and implementation the corrections and new solutions for eliminating the source of undesirable events. The developed methodology was shown in application case. It was found that the risk of water contamination in water-pipe network of the analyzed CWSS caused by water source incidental contamination is at controlled level.

  6. Selective removal of diclofenac from contaminated water using molecularly imprinted polymer microspheres

    Energy Technology Data Exchange (ETDEWEB)

    Dai Chaomeng [State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092 (China); Department of Environmental Technology, Chair of Environmental Process Engineering, Technical University of Berlin, Berlin (Germany); Geissen, Sven-Uwe, E-mail: sven.geissen@tu-berlin.de [Department of Environmental Technology, Chair of Environmental Process Engineering, Technical University of Berlin, Berlin (Germany); Zhang Yalei, E-mail: zhangyalei@tongji.edu.cn [State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092 (China); Zhang Yongjun [Department of Environmental Technology, Chair of Environmental Process Engineering, Technical University of Berlin, Berlin (Germany); Zhou Xuefei [State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092 (China)

    2011-06-15

    A molecularly imprinted polymer (MIP) was synthesized by precipitation polymerization using diclofenac (DFC) as a template. Binding characteristics of the MIP were evaluated using equilibrium binding experiments. Compared to the non-imprinted polymer (NIP), the MIP showed an outstanding affinity towards DFC in an aqueous solution with a binding site capacity (Q{sub max}) of 324.8 mg/g and a dissociation constant (K{sub d}) of 3.99 mg/L. The feasibility of removing DFC from natural water by the MIP was demonstrated by using river water spiked with DFC. Effects of pH and humic acid on the selectivity and adsorption capacity of MIP were evaluated in detail. MIP had better selectivity and higher adsorption efficiency for DFC as compared to that of powdered activated carbon (PAC). In addition, MIP reusability was demonstrated for at least 12 repeated cycles without significant loss in performance, which is a definite advantage over single-use activated carbon. - Highlights: > A MIP was synthesized by precipitation polymerization using DFC as template. > The MIP had better selectivity and higher adsorption efficiency for DFC. > The MIP is an effective method for selective removal of DFC from complex water. > MIP reusability is a definite advantage over single-use activated carbon. - A diclofenac molecularly imprinted polymer synthesized by precipitation polymerization was used for the selective removal of diclofenac from contaminated water.

  7. Development of transmissometer system for evaluating molecular contamination effects and the preliminary results

    Science.gov (United States)

    Itoh, Nobunari; Katoh, Masahiro; Okano, Nobuaki

    2005-01-01

    The presence of propagated molecular gas is one of the most probable causes of on-orbit degradation. The performance of optical sensors would be affected seriously if the strong absorption bands of the contaminants exist in the region of our interest and phase transition of adsorption gas on optical surfaces would induce not only absorption but also scatter. Although there are amount of trials to predict spectral degradation with model calculations, experimental approaches are also necessary to clarify degradation processes occurred in orbit and to improve the on-board calibration reliability. We built up the measurement system in order to evaluate transmittance degradation with various kinds of gases under different temperature and vacuum conditions. In our system, an optical glass, the site of adsorption, is set inside a cryostat and then a certain amount of molecular gas is injected. The amount of injected gas adsorption onto the optical surface is controlled by adjusting the sample surface temperature. Our systems have the capability to control vacuum within the range from 10-3Pa to 102Pa and temperature from 150K to 423K. As for the measurement of transmittance change, we adopted commercially available spectrophotometer and FTIR. The optical spectrophotometer covers the wavelength range from 300nm to 2.5um and the FTIR covers from 2um to 25um. We would present the details of our system and discuss about measurement accuracy and preliminary results of our measurements.

  8. Metagenomic analysis of microbial community in uranium-contaminated soil.

    Science.gov (United States)

    Yan, Xun; Luo, Xuegang; Zhao, Min

    2016-01-01

    Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.

  9. Tissue Microarray Technology for Molecular Applications: Investigation of Cross-Contamination between Tissue Samples Obtained from the Same Punching Device.

    Science.gov (United States)

    Vassella, Erik; Galván, José A; Zlobec, Inti

    2015-04-02

    Tissue microarray (TMA) technology allows rapid visualization of molecular markers by immunohistochemistry and in situ hybridization. In addition, TMA instrumentation has the potential to assist in other applications: punches taken from donor blocks can be placed directly into tubes and used for nucleic acid analysis by PCR approaches. However, the question of possible cross-contamination between samples punched with the same device has frequently been raised but never addressed. Two experiments were performed. (1) A block from mycobacterium tuberculosis (TB) positive tissue and a second from an uninfected patient were aligned side-by-side in an automated tissue microarrayer. Four 0.6 mm punches were cored from each sample and placed inside their corresponding tube. Between coring of each donor block, a mechanical cleaning step was performed by insertion of the puncher into a paraffin block. This sequence of coring and cleaning was repeated three times, alternating between positive and negative blocks. A fragment from the 6110 insertion sequence specific for mycobacterium tuberculosis was analyzed; (2) Four 0.6 mm punches were cored from three KRAS mutated colorectal cancer blocks, alternating with three different wild-type tissues using the same TMA instrument (sequence of coring: G12D, WT, G12V, WT, G13D and WT). Mechanical cleaning of the device between each donor block was made. Mutation analysis by pyrosequencing was carried out. This sequence of coring was repeated manually without any cleaning step between blocks. In both analyses, all alternating samples showed the expected result (samples 1, 3 and 5: positive or mutated, samples 2, 4 and 6: negative or wild-type). Similar results were obtained without cleaning step. These findings suggest that no cross-contamination of tissue samples occurs when donor blocks are punched using the same device, however a cleaning step is nonetheless recommended. Our result supports the use of TMA technology as an accessory

  10. Tissue Microarray Technology for Molecular Applications: Investigation of Cross-Contamination between Tissue Samples Obtained from the Same Punching Device

    Directory of Open Access Journals (Sweden)

    Erik Vassella

    2015-04-01

    Full Text Available Background: Tissue microarray (TMA technology allows rapid visualization of molecular markers by immunohistochemistry and in situ hybridization. In addition, TMA instrumentation has the potential to assist in other applications: punches taken from donor blocks can be placed directly into tubes and used for nucleic acid analysis by PCR approaches. However, the question of possible cross-contamination between samples punched with the same device has frequently been raised but never addressed. Methods: Two experiments were performed. (1 A block from mycobacterium tuberculosis (TB positive tissue and a second from an uninfected patient were aligned side-by-side in an automated tissue microarrayer. Four 0.6 mm punches were cored from each sample and placed inside their corresponding tube. Between coring of each donor block, a mechanical cleaning step was performed by insertion of the puncher into a paraffin block. This sequence of coring and cleaning was repeated three times, alternating between positive and negative blocks. A fragment from the 6110 insertion sequence specific for mycobacterium tuberculosis was analyzed; (2 Four 0.6 mm punches were cored from three KRAS mutated colorectal cancer blocks, alternating with three different wild-type tissues using the same TMA instrument (sequence of coring: G12D, WT, G12V, WT, G13D and WT. Mechanical cleaning of the device between each donor block was made. Mutation analysis by pyrosequencing was carried out. This sequence of coring was repeated manually without any cleaning step between blocks. Results/Discussion: In both analyses, all alternating samples showed the expected result (samples 1, 3 and 5: positive or mutated, samples 2, 4 and 6: negative or wild-type. Similar results were obtained without cleaning step. These findings suggest that no cross-contamination of tissue samples occurs when donor blocks are punched using the same device, however a cleaning step is nonetheless recommended. Our

  11. Removing external DNA decontamination from arthropod predators destined for molecular gut-content analysis

    Science.gov (United States)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  12. White Oak Creek Embayment site characterization and contaminant screening analysis

    Energy Technology Data Exchange (ETDEWEB)

    Blaylock, B.G.; Ford, C.J.; Frank, M.L.; Hoffman, F.O.; Hook, L.A.

    1993-01-01

    Analyses of sediment samples collected near the mouth of White Oak Creek during the summer of 1990 revealed [sup 137]Cs concentrations [> 10[sup 6] Bq/kg dry wt (> 10[sup 4] pCi/g dry wt)] near the sediment surface. Available evidence indicates that these relatively high concentrations of [sup 137]Cs now at the sediment surface were released from White Oak Dam in the mid-1950s and had accumulated at depositionalsites in the embayment. These accumulated sediments are being eroded and transported downstream primarily during winter low-water levels by flood events and by a combination of normal downstream flow and the water turbulence created by the release of water from Melton Hill Dam during hydropower generation cycles. This report provides a more thorough characterization of the extent of contamination in WOCE than was previously available. Environmental samples collected from WOCE were analyzed for organic, inorganic, and radiological contaminants in fish, water, and sediment. These results were used to conduct a human health effects screening analysis. Walkover radiation surveys conducted inside the fenced area surrounding the WOCE at summer-pool (741 ft MSL) and at winter-pool (733 ft MSL) level, indicated a maximum exposure rate of 3 mR h[sup 1] 1 m above the soil surface.

  13. The JCMT Gould Belt Survey: the effect of molecular contamination in SCUBA-2 observations of Orion A

    Science.gov (United States)

    Coudé, S.; Bastien, P.; Kirk, H.; Johnstone, D.; Drabek-Maunder, E.; Graves, S.; Hatchell, J.; Chapin, E. L.; Gibb, A. G.; Matthews, B.; JCMT Gould Belt Survey Team

    2016-04-01

    Thermal emission from cold dust grains in giant molecular clouds can be used to probe the physical properties, such as density, temperature and emissivity in star-forming regions. We present the Submillimetre Common-User Bolometer Array (SCUBA-2) shared-risk observations at 450 and 850 μm of the Orion A molecular cloud complex taken at the James Clerk Maxwell Telescope (JCMT). Previous studies showed that molecular emission lines can contribute significantly to the measured fluxes in those continuum bands. We use the Heterodyne Array Receiver Programme 12CO J = 3-2 integrated intensity map for Orion A in order to evaluate the molecular line contamination and its effects on the SCUBA-2 maps. With the corrected fluxes, we have obtained a new spectral index α map for the thermal emission of dust in the well-known integral-shaped filament. Furthermore, we compare a sample of 33 sources, selected over the Orion A molecular cloud complex for their high 12CO J = 3-2 line contamination, to 27 previously identified clumps in OMC 4. This allows us to quantify the effect of line contamination on the ratio of 850-450 μm flux densities and how it modifies the deduced spectral index of emissivity β for the dust grains. We also show that at least one Spitzer-identified protostellar core in OMC 5 has a 12CO J = 3-2 contamination level of 16 per cent. Furthermore, we find the strongest contamination level (44 per cent) towards a young star with disc near OMC 2. This work is part of the JCMT Gould Belt Legacy Survey.

  14. Heisenberg coupling constant predicted for molecular magnets with pairwise spin-contamination correction

    Energy Technology Data Exchange (ETDEWEB)

    Masunov, Artëm E., E-mail: amasunov@ucf.edu [NanoScience Technology Center, Department of Chemistry, and Department of Physics, University of Central Florida, Orlando, FL 32826 (United States); Photochemistry Center RAS, ul. Novatorov 7a, Moscow 119421 (Russian Federation); Gangopadhyay, Shruba [Department of Physics, University of California, Davis, CA 95616 (United States); IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120 (United States)

    2015-12-15

    New method to eliminate the spin-contamination in broken symmetry density functional theory (BS DFT) calculations is introduced. Unlike conventional spin-purification correction, this method is based on canonical Natural Orbitals (NO) for each high/low spin coupled electron pair. We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher spin state built on these bonding and antibonding NOs (not self-consistent Kohn–Sham orbitals of the high spin state). Compared to the other spin-contamination correction schemes, spin-correction is applied to each correlated electron pair individually. We investigate two binuclear Mn(IV) molecular magnets using this pairwise correction. While one of the molecules is described by magnetic orbitals strongly localized on the metal centers, and spin gap is accurately predicted by Noodleman and Yamaguchi schemes, for the other one the gap is predicted poorly by these schemes due to strong delocalization of the magnetic orbitals onto the ligands. We show our new correction to yield more accurate results in both cases. - Highlights: • Magnetic orbitails obtained for high and low spin states are not related. • Spin-purification correction becomes inaccurate for delocalized magnetic orbitals. • We use the natural orbitals of the broken symmetry state to build high spin state. • This new correction is made separately for each electron pair. • Our spin-purification correction is more accurate for delocalised magnetic orbitals.

  15. Microfluidic Sample Preparation Methods for the Analysis of Milk Contaminants

    Directory of Open Access Journals (Sweden)

    Andrea Adami

    2016-01-01

    Full Text Available In systems for food analysis, one of the major challenges is related to the quantification of specific species into the complex chemical and physical composition of foods, that is, the effect of “matrix”; the sample preparation is often the key to a successful application of biosensors to real measurements but little attention is traditionally paid to such aspects in sensor research. In this critical review, we discuss several microfluidic concepts that can play a significant role in sample preparation, highlighting the importance of sample preparation for efficient detection of food contamination. As a case study, we focus on the challenges related to the detection of aflatoxin M1 in milk and we evaluate possible approaches based on inertial microfluidics, electrophoresis, and acoustic separation, compared with traditional laboratory and industrial methods for phase separation as a baseline of thrust and well-established techniques.

  16. Spatial control of groundwater contamination, using principal component analysis

    Indian Academy of Sciences (India)

    N Subba Rao

    2014-06-01

    A study on the geochemistry of groundwater was carried out in a river basin of Andhra Pradesh to probe into the spatial controlling processes of groundwater contamination, using principal component analysis (PCA). The PCA transforms the chemical variables, pH, EC, Ca2+, Mg2+, Na+, K+, HCO$^{−}_{3}$, Cl−, SO$^{2−}_{4}$, NO$^{−}_{3}$ and F−, into two orthogonal principal components (PC1 and PC2), accounting for 75% of the total variance of the data matrix. PC1 has high positive loadings of EC, Na+, Cl−, SO$^{2−}_{4}$, Mg2+ and Ca2+, representing a salinity controlled process of geogenic (mineral dissolution, ion exchange, and evaporation), anthropogenic (agricultural activities and domestic wastewaters), and marine (marine clay) origin. The PC2 loadings are highly positive for HCO$^{−}_{3}$, F−, pH and NO$^{−}_{3}$, attributing to the alkalinity and pollution controlled processes of geogenic and anthropogenic origins. The PC scores reflect the change of groundwater quality of geogenic origin from upstream to downstream area with an increase in concentration of chemical variables, which is due to anthropogenic and marine origins with varying topography, soil type, depth of water levels, and water usage. Thus, the groundwater quality shows a variation of chemical facies from Na+ > Ca2+ > Mg2+ > K+: HCO$^{−}_{3}$ > Cl− > SO$^{2−}_{4}$ > NO$^{−}_{3}$ > F− at high topography to Na+ > Mg2+ > Ca2+ > K+: Cl− > HCO$^{−}_{3}$ > SO$^{2−}_{4}$ > NO$^{−}_{3}$ > F− at low topography. With PCA, an effective tool for the spatial controlling processes of groundwater contamination, a subset of explored wells is indexed for continuous monitoring to optimize the expensive effort.

  17. Accidental surface contamination - The effect on trace element analysis

    Energy Technology Data Exchange (ETDEWEB)

    Franklyn, C.B. E-mail: franklyn@aec.co.za; Ueckermann, H.; Merkle, R.K.W

    2001-07-01

    We discuss the accidental contamination of samples during a micro-PIXE study of Rh, Pd and Pt partition coefficients in the Fe-S and Ni-S systems. Trace amounts of Ni and Cu, mounted separately in epoxy as markers, were found to be present in various phases in the sections, sometimes selectively in specific mineral phases. This contamination is believed to result from polishing during preparation. Further surface contamination from conductive Ag paste was also observed.

  18. The Use of the Molecular Adsorber Coating Technology to Mitigate Vacuum Chamber Contamination During Pathfinder Testing for the James Webb Space Telescope

    Science.gov (United States)

    Abraham, Nithin S.; Hasegawa, Mark M.; Wooldridge, Eve M.; Henderson-Nelson, Kelly A.

    2016-01-01

    As a coating made of highly porous zeolite materials, the Molecular Adsorber Coating (MAC) was developed to capture outgassed molecular contaminants, such as hydrocarbons and silicones. For spaceflight applications, the adsorptive capabilities of the coating can alleviate on-orbit outgassing concerns on or near sensitive surfaces and instruments within the spacecraft. Similarly, this sprayable paint technology has proven to be significantly beneficial for ground based space applications, in particular, for vacuum chamber environments. This paper describes the recent use of the MAC technology during Pathfinder testing of the Optical Ground Support Equipment (OGSE) for the James Webb Space Telescope (JWST) at NASA Johnson Space Center (JSC). The coating was used as a mitigation tool to entrap persistent outgassed contaminants, specifically silicone based diffusion pump oil, from within JSC's cryogenic optical vacuum chamber test facility called Chamber A. This paper summarizes the sample fabrication, installation, laboratory testing, post-test chemical analysis results, and future plans for the MAC technology, which was effectively used to protect the JWST test equipment from vacuum chamber contamination.

  19. Molecular line contamination in the SCUBA-2 450 {\\mu}m and 850 {\\mu}m continuum data

    CERN Document Server

    Drabek, E; Friberg, P; Richer, J; Graves, S; Buckle, J V; Nutter, D; Johnstone, D; Di Francesco, J

    2012-01-01

    Observations of the dust emission using millimetre/submillimetre bolometer arrays can be contaminated by molecular line flux, such as flux from 12CO. As the brightest molecular line in the submillimetre, it is important to quantify the contribution of CO flux to the dust continuum bands. Conversion factors were used to convert molecular line integrated intensities to flux detected by bolometer arrays in mJy per beam. These factors were calculated for 12CO line integrated intensities to the SCUBA-2 850 {\\mu}m and 450 {\\mu}m bands. The conversion factors were then applied to HARP 12CO 3-2 maps of NGC 1333 in the Perseus complex and NGC 2071 and NGC 2024 in the Orion B molecular cloud complex to quantify the respective 12CO flux contribution to the 850 {\\mu}m dust continuum emission. Sources with high molecular line contamination were analysed in further detail for molecular outflows and heating by nearby stars to determine the cause of the 12CO contribution. The majority of sources had a 12CO 3-2 flux contribut...

  20. FINGERPRINT ANALYSIS OF CONTAMINANT DATA: A FORENSIC TOOL FOR EVALUATING ENVIRONMENTAL CONTAMINATION

    Science.gov (United States)

    Several studies have been conducted on behalf of the U .S. Environmental Protection Agency (EPA) to identify detection monitoring parameters for specific industries.1,2,3,4,5 One outcome of these studies was the evolution of an empirical multi-variant contaminant fingerprinting p...

  1. Cleaning Genesis Solar Wind Collectors with Ultrapure Water: Residual Contaminant Particle Analysis

    Science.gov (United States)

    Allton, J. H.; Wentworth, S. J.; Rodriquez, M. C.; Calaway, M. J.

    2008-01-01

    Additional experience has been gained in removing contaminant particles from the surface of Genesis solar wind collectors fragments by using megasonically activated ultrapure water (UPW)[1]. The curatorial facility has cleaned six of the eight array collector material types to date: silicon (Si), sapphire (SAP), silicon-on-sapphire (SOS), diamond-like carbon-on-silicon (DOS), gold-on-sapphire (AuOS), and germanium (Ge). Here we make estimates of cleaning effectiveness using image analysis of particle size distributions and an SEM/EDS reconnaissance of particle chemistry on the surface of UPW-cleaned silicon fragments (Fig. 1). Other particle removal techniques are reported by [2] and initial assessment of molecular film removal is reported by [3].

  2. Cross-contamination of a UROtsa stock with T24 cells--molecular comparison of different cell lines and stocks.

    Directory of Open Access Journals (Sweden)

    Georg Johnen

    Full Text Available BACKGROUND: UROtsa is an authentic, immortalized human urothelial cell line that is used to study the effects of metals and other toxic substances, mostly in the context of bladder cancer carcinogenesis. Unusual properties on the molecular level of a provided UROtsa cell line stock prompted us to verify its identity. METHODS: UROtsa cell line stocks from different sources were tested on several molecular levels and compared with other cell lines. MicroRNA and mRNA expression was determined by Real-Time PCR. Chromosome numbers were checked and PCR of different regions of the large T-antigen was performed. DNA methylation of RARB, PGR, RASSF1, CDH1, FHIT, ESR1, C1QTNF6, PTGS2, SOCS3, MGMT, and LINE1 was analyzed by pyrosequencing and compared with results from the cell lines RT4, T24, HeLa, BEAS-2B, and HepG2. Finally, short tandem repeat (STR profiling was applied. RESULTS: All tested UROtsa cell line stocks lacked large T-antigen. STR analysis unequivocally identified our main UROtsa stock as the bladder cancer cell line T24, which was different from two authentic UROtsa stocks that served as controls. Analysis of DNA methylation patterns and RNA expression confirmed their differences. Methylation pattern and mRNA expression of the contaminating T24 cell line showed moderate changes even after long-term culture of up to 56 weeks, whereas miRNAs and chromosome numbers varied markedly. CONCLUSIONS: It is important to check the identity of cell lines, especially those that are not distributed by major cell banks. However, for some cell lines STR profiles are not available. Therefore, new cell lines should either be submitted to cell banks or at least their STR profile determined and published as part of their initial characterization. Our results should help to improve the identification of UROtsa and other cells on different molecular levels and provide information on the use of urothelial cells for long-term experiments.

  3. Interferences in Prompt γ Analysis of corrosive contaminants in concrete

    Science.gov (United States)

    Naqvi, A. A.; Nagadi, M. M.; Al-Amoudi, O. S. B.

    2006-12-01

    An accelerator-based Prompt Gamma Neutron Activation Analysis (PGNAA) setup has been developed to measure the concentration of corrosive chloride and sulfate contaminants in concrete. The Minimum Detectable Concentration (MDC) limit of chlorine and sulfur in the concrete depends upon the γ-ray used for elemental analysis. For more interfering γ-rays, the MDC limit is higher than that for less interfering γ-rays. The MDC limit of sulfur in concrete measured for the KFUPM PGNAA setup was calculated to be 0.60±0.19 wt%. The MDC limit is equal to the upper limit of sulfur concentration in concrete set by the British Standards. The MDC limit of chlorine in concrete for the KFUPM PGNAA setup, which was calculated for less interfering 1.165 MeV γ-rays, was found to be 0.075±0.025 wt%. The lower limits of the MDC of chlorine in concrete was 73% higher than the limit set by American Concrete Institute. The limit of the MDC can be improved to the desired standard by increasing the intensity of neutron source. For moreinterfering 5.715 and 6.110 MeV chlorine γ-rays the MDC limit was found to be 2-3 times larger than that of 1.165 MeV γ-rays. When normalized to the same intensity of the neutron source, the MDC limits of chlorine and sulfur in concrete from the KFUPM PGNAA setup are better than MDC limits of chlorine in concrete obtained with the 241Am-Be source-based PGNAA setup. This study has shown that an accelerator-based PGNAA setup can be used in chlorine and sulfur analysis of concrete samples.

  4. The JCMT Gould Belt Survey: the effect of molecular contamination in SCUBA-2 observations of Orion A

    CERN Document Server

    Coudé, S; Kirk, H; Johnstone, D; Drabek-Maunder, E; Graves, S; Hatchell, J; Chapin, E L; Gibb, A G; Matthews, B

    2016-01-01

    Thermal emission from cold dust grains in giant molecular clouds can be used to probe the physical properties, such as density, temperature and emissivity in star-forming regions. We present the SCUBA-2 shared-risk observations at 450 $\\mu$m and 850 $\\mu$m of the Orion A molecular cloud complex taken at the James Clerk Maxwell Telescope (JCMT). Previous studies showed that molecular emission lines can contribute significantly to the measured fluxes in those continuum bands. We use the HARP $^{12}$CO J=3-2 integrated intensity map for Orion A in order to evaluate the molecular line contamination and its effects on the SCUBA-2 maps. With the corrected fluxes, we have obtained a new spectral index $\\alpha$ map for the thermal emission of dust in the well-known integral-shaped filament. Furthermore, we compare a sample of 33 sources, selected over the Orion A molecular cloud complex for their high $^{12}$CO J=3-2 line contamination, to 27 previously identified clumps in OMC-4. This allows us to quantify the effec...

  5. Random Matrix Theory in molecular dynamics analysis.

    Science.gov (United States)

    Palese, Luigi Leonardo

    2015-01-01

    It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.

  6. Structural Analysis of Molecular Clouds: Dendrograms

    CERN Document Server

    Rosolowsky, E W; Kauffmann, J; Goodman, A A

    2008-01-01

    We demonstrate the utility of dendrograms at representing the essential features of the hierarchical structure of the isosurfaces for molecular line data cubes. The dendrogram of a data cube is an abstraction of the changing topology of the isosurfaces as a function of contour level. The ability to track hierarchical structure over a range of scales makes this analysis philosophically different from local segmentation algorithms like CLUMPFIND. Points in the dendrogram structure correspond to specific volumes in data cubes defined by their bounding isosurfaces. We further refine the technique by measuring the properties associated with each isosurface in the analysis allowing for a multiscale calculation of molecular gas properties. Using COMPLETE 13CO(1-0) data from the L1448 region in Perseus and mock observations of a simulated data cube, we identify regions that have a significant contribution by self-gravity to their energetics on a range of scales. We find evidence for self-gravitation on all spatial sc...

  7. A Comprehensive Analysis of Organic Contaminant Adsorption by Clays

    Science.gov (United States)

    Macroscopic studies of nonionic organic contaminant (NOC) sorption by clays have revealed many important clues regarding factors that influence sorption affinity, and enabled the development of structural hypotheses for operative adsorption mechanisms. Integrating this understanding with knowledge g...

  8. Inventory of sea turtle eggs for contaminant analysis

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is an inventory of the bags of sea turtle eggs/hatchlings collected on St. Vincent NWR in 1996 and transferred to the Panama City Field Office for contaminants...

  9. Dental diagnostics: molecular analysis of oral biofilms.

    Science.gov (United States)

    Hiyari, Sarah; Bennett, Katie M

    2011-01-01

    Dental biofilms are complex, multi-species bacterial communities that colonize the mouth in the form of plaque and are known to cause dental caries and periodontal disease. Biofilms are unique from planktonic bacteria in that they are mutualistic communities with a 3-dimensional structure and complex nutritional and communication pathways. The homeostasis within the biofilm colony can be disrupted, causing a shift in the bacterial composition of the colony and resulting in proliferation of pathogenic species. Because of this dynamic lifestyle, traditional microbiological techniques are inadequate for the study of biofilms. Many of the bacteria present in the oral cavity are viable but not culturable, which severely limits laboratory analysis. However, with the advent of new molecular techniques, the microbial makeup of oral biofilms can be better identified. Some of these techniques include DNA-DNA hybridization, 16S rRNA gene sequencing, denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, denaturing high-performance liquid chromatography and pyrosequencing. This review provides an overview of biofilm formation and examines the major molecular techniques currently used in oral biofilm analysis. Future applications of the molecular analysis of oral biofilms in the diagnosis and treatment of caries and periodontal disease are also discussed.

  10. Molecular identification and potential of an isolate of white rot fungi in bioremediation of petroleum contaminated soils

    Directory of Open Access Journals (Sweden)

    Maryam Mohammadi-sichani

    2017-06-01

    Full Text Available Introduction:Elimination or reduction of petroleum hydrocarbons from natural resources such as water and soil is a serious problem of countries, particularly oil-rich countries of the world. Using white rotting fungi compost for bioremediation of soils contaminated by petroleum hydrocarbons is effective. The aim of this study is molecular identification and potential of anisolate of white rot fungi in bioremediation of petroleum contaminated soils. Materials and methods: Spent compost of white rotting fungi was inoculated with petroleum contaminated soil into 3%, 5% and 10% (w/w. Treatments were incubated at 25-23 °C for 3 months. Reduction of petroleum hydrocarbons in treated soil was determined by gas chromatography. Ecotoxicity of soil was evaluated by seed germination test. Results: Based on the genome sequence of 18s rRNA, it is revealed that this isolate is Ganoderma lucidum and this isolate is deposited as accession KX525204 in the Gene Bank database. Reduction of petroleum hydrocarbons in soil treated with compost (3, 5 and 10% ranged from 42% to 71%. The germination index (% in ecotoxicity tests ranged from 20.8% to 70.8%. Gas chromatography results also showed a decrease in soil Hydrocarbons compounds. Discussion and conclusion: The compost of Ganoderma lucidum, a white rot fungus, has a potential ability to remove petroleum hydrocarbons in contaminated soil. Removal of hydrocarbons was increased with increase in compost mixed with contaminated soil. Petroleum contaminated soil amended with spent compost of G.lucidum 10% during three months is appropriate to remove this pollutant.

  11. Analysis of predictors related to soil contamination in recreational areas of Romania.

    Science.gov (United States)

    Gagiu, C; Pica, E M; Querol, X; Botezan, C S

    2015-12-01

    Soil contamination in recreational areas can considerably affect children's health, as they are the segment of the population most sensitive to anthropogenic contamination. Soil contamination in recreational areas is influenced by a number of factors such as type and age of the recreational area, nearby traffic intensity, proximity to industrial areas, presence of vegetation, level of usage, treated wood structures, and the extent of maintenance operations carried out in the area. These can most often be observed during a simple site visit. The purpose of the present research is to analyze to which extent the presence of these factors can trigger an alarm signal, highlighting soil contamination in urban recreational areas. In this regard, soil contamination was scaled using the integrated pollution index applied on nine distinctive contaminants (As, Cu, Cd, Zn, Pb, Hg, Co, Ni, Mg) identified using inductively coupled plasma mass spectrometry (ICP-MS). Multiple linear regression analysis was performed in order to assess predictors of soil contamination. The research was carried out in a number of 88 recreational areas, parks, and playgrounds from 19 Romanian cities, revealing the fact that proximity to industrial areas and intensive traffic had statistically significant effects on soil contamination. Furthermore, it was observed that in 78 out of the 88 analyzed locations, the concentrations of contaminants exceeded the guidelines established through national legislation, thus confirming the presumption that high concentrations of contaminants exist in the parks and playgrounds of Romania.

  12. Case study sensitivity analysis of transmission spectra for water contaminant monitoring

    Science.gov (United States)

    Lambrakos, S. G.; Yapijakis, C.; Aiken, D.; Shabaev, A.; Ramsey, S.; Peak, J.

    2016-05-01

    Monitoring of contaminants associated with specific water resources using transmission spectra, with respect to types and relative concentrations, requires tracking statistical profiles of water contaminants in terms of spatial-temporal distributions of electromagnetic absorption spectra ranging from the ultraviolet to infrared. For this purpose, correlation between spectral signatures and types of contaminants within specific water resources must be made, as well as correlation of spectral signatures with results of processes for removal of contaminants, such as ozonation. Correlation between absorption spectra and changes in chemical and physical characteristics of contaminants, within a volume of sampled solution, requires sufficient sensitivity. The present study examines the sensitivity of transmission spectra with respect to general characteristics of water contaminants for spectral analysis of water samples.

  13. Molecular tools to understand the bioremediation effect of plants and earthworms on contaminated marine sediments.

    Science.gov (United States)

    Moreno, Beatriz; Cañizares, Rosa; Macci, Cristina; Doni, Serena; Masciandaro, Grazia; Benitez, Emilio

    2015-12-30

    A meso-scale pilot plant was set up to test the efficiency of a bioremediation scheme applied to marine sediments contaminated by heavy metals and hydrocarbons. The experiment was implemented for three years in two stages using two remediation agents: plants (Paspalum vaginatum and Tamarix gallica) and earthworms (Eisenia fetida). DNA and RNA-based methodologies were applied to elucidate the dynamics of the bacterial population and were related to improving biological and chemical conditions of the sediments. Bioremediation strategies were successful in removing pollutants from the contaminated sediments and specialization within the bacterial community related to the type of contamination present was detected in the different stages of the process. The highest response of Gram-positive PAH-degraders to the contamination was detected at the beginning and after the first stage of the experiment, corresponding to the uppermost values of degradation.

  14. Oncological image analysis: medical and molecular image analysis

    Science.gov (United States)

    Brady, Michael

    2007-03-01

    This paper summarises the work we have been doing on joint projects with GE Healthcare on colorectal and liver cancer, and with Siemens Molecular Imaging on dynamic PET. First, we recall the salient facts about cancer and oncological image analysis. Then we introduce some of the work that we have done on analysing clinical MRI images of colorectal and liver cancer, specifically the detection of lymph nodes and segmentation of the circumferential resection margin. In the second part of the paper, we shift attention to the complementary aspect of molecular image analysis, illustrating our approach with some recent work on: tumour acidosis, tumour hypoxia, and multiply drug resistant tumours.

  15. Molecular mechanics conformational analysis of tylosin

    Science.gov (United States)

    Ivanov, Petko M.

    1998-01-01

    The conformations of the 16-membered macrolide antibiotic tylosin were studied with molecular mechanics (AMBER∗ force field) including modelling of the effect of the solvent on the conformational preferences (GB/SA). A Monte Carlo conformational search procedure was used for finding the most probable low-energy conformations. The present study provides complementary data to recently reported analysis of the conformations of tylosin based on NMR techniques. A search for the low-energy conformations of protynolide, a 16-membered lactone containing the same aglycone as tylosin, was also carried out, and the results were compared with the observed conformation in the crystal as well as with the most probable conformations of the macrocyclic ring of tylosin. The dependence of the results on force field was also studied by utilizing the MM3 force field. Some particular conformations were computed with the semiempirical molecular orbital methods AM1 and PM3.

  16. Contamination analysis of radioactive samples in focused ion beam instruments.

    Science.gov (United States)

    Evelan, Audrey Ruth; Brey, Richard R

    2013-02-01

    The use of Focused Ion Beam (FIB) instrument's to analyze and prepare samples that are radioactive requires attentiveness to the materials that are dislodged and free inside the chamber. Radioactive sputtered material must be understood even when observed at trace concentrations. Measurements using liquid scintillation counting and high purity germanium detectors were used to evaluate contamination on accessible surfaces inside a focused ion beam chamber that was used in the preparation of samples that were radioactive. The maximum removable contamination found was 0.27 0.4 Bq cm(-2), on the focused ion beam wall with 0.24 0.019 Bq cm(-2) on the door. Although these magnitudes of removable contamination are inconsequential for activation products, these same magnitudes of actinides, for example 239Pu, would represent 3.2% of an Annual Limit of Intake. This might be considered significant if one examines the relatively infrequent use of this device for the preparation of radioactive samples. Predicted activities of sputtered material were found using the software Transport of Ions in Matter, estimating that 0.003% of a radioactive samples activity is released into the FIB chamber. A used secondary electron detector's activity was measured to be 383.7 8.1 Bq. Preferential build-up of sputtered materials due to temperature or static charge gradients was considered. No temperature gradients were observed. Static charge gradients were measured inside the chamber varying between 0.057% below the mean to 34% higher than the mean. However, the magnitudes of contamination measured did not correlate to static charge gradients. Deposition in the chamber appears to have no mechanical cause but rather is sporadic however, measureable. Experience to date has been limited to samples of low activity; nevertheless, contamination inside the chamber was observed. Users should anticipate higher levels of readily dispersible radioactive contamination within the FIB as sample activity

  17. JV Task 99-Integrated Risk Analysis and Contaminant Reduction, Watford City, North Dakota

    Energy Technology Data Exchange (ETDEWEB)

    Jaroslav Solc; Barry W. Botnen

    2007-05-31

    The Energy & Environmental Research Center (EERC) conducted a limited site investigation and risk analyses for hydrocarbon-contaminated soils and groundwater at a Construction Services, Inc., site in Watford City, North Dakota. Site investigation confirmed the presence of free product and high concentrations of residual gasoline-based contaminants in several wells, the presence of 1,2-dichloroethane, and extremely high levels of electrical conductivity indicative of brine residuals in the tank area south of the facility. The risk analysis was based on compilation of information from the site-specific geotechnical investigation, including multiphase extraction pilot test, laser induced fluorescence probing, evaluation of contaminant properties, receptor survey, capture zone analysis and evaluation of well head protection area for municipal well field. The project results indicate that the risks associated with contaminant occurrence at the Construction Services, Inc. site are low and, under current conditions, there is no direct or indirect exposure pathway between the contaminated groundwater and soils and potential receptors.

  18. Molecular characterization of microbial contaminants isolated from Umbilical Cord Blood Units for transplant

    Directory of Open Access Journals (Sweden)

    Juan Manuel Bello-López

    2015-12-01

    Full Text Available ABSTRACT Disposal of Umbilical Cord Blood Units due to microbial contamination is a major problem in Cord Blood Banks worldwide as it reduces the number of units available for transplantation. Additionally, economic losses are generated as result of resources and infrastructure used to obtain such units. Umbilical Cord Blood Units that showed initial microbial contamination were subject to strains isolation, identification, and characterization by sequencing the 16S rRNA gene and Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR. Moreover, tests of antimicrobial resistance/sensitivity and phenotypic activities that may play an important role in microbial infection were performed. Microbial contamination was detected in 120 Umbilical Cord Blood Units (2.31% in the period from 2003 to 2013. The most frequently isolated strains were Enterococcus faecium, followed by Staphylococcus epidermidis, Escherichia coli, Enterococcus faecalis, Staphylococcus haemoliticus, Klebsiella pneumoniae, Enterococcus durans, Lactobacillus helveticus, Enterococcus hiriae and Roseomonas genomospecies 5. The ERIC-PCR assays revealed a wide genetic diversity in some strains although belonging to the same genus and specie, indicating different sources of contamination. Broad-spectrum penicillins, third generation cephalosporins, aminoglycosides, and fluoroquinolones showed lower inhibitory activity on the tested strains. All strains were proteolytic, 67.69% were amylase-positive, 27.6% hemolysis-positive, and 34.71% nuclease-positive. The most common sources of contamination were: vaginal flora, digestive tract, and skin flora, highlighting the need for staff training in good manufacturing practices in collection SCU since all contaminants identified are part of the microbial flora of the donors. Implications and consequences in the therapeutic use of Umbilical Cord Blood Units for transplantation contaminated by multiresistant bacteria in immunocompromised

  19. A 3D model for carbon monoxide molecular line emission as a potential cosmic microwave background polarization contaminant

    Science.gov (United States)

    Puglisi, G.; Fabbian, G.; Baccigalupi, C.

    2017-08-01

    We present a model for simulating carbon monoxide (CO) rotational line emission in molecular clouds, taking account of their 3D spatial distribution in galaxies with different geometrical properties. The model implemented is based on recent results in the literature and has been designed for performing Monte Carlo (MC) simulations of this emission. We compare the simulations produced with this model and calibrate them, both on the map and the power spectrum levels, using the second release of data from the Planck satellite for the Galactic plane, where the signal-to-noise ratio is highest. We use the calibrated model to extrapolate the CO power spectrum at low Galactic latitudes where no high sensitivity observations are available yet. We then forecast the level of unresolved polarized emission from CO molecular clouds which could contaminate the power spectrum of cosmic microwave background polarization B modes away from the Galactic plane. Assuming realistic levels of the polarization fraction, we show that the level of contamination is equivalent to a cosmological signal with r ≲ 0.02. The MC MOlecular Line Emission (mcmole3d) python package, which implements this model, is being made publicly available.

  20. Advancements and application of immunosensors in the analysis of food contaminants

    Directory of Open Access Journals (Sweden)

    MD. SHOFIUL AZAM

    2014-11-01

    Full Text Available Azam MS, Rahman MRT, Lou Z, Tang Y, Raqib SM, Jothi JS. 2014. Advancements and application of immunosensors in the analysis of food contaminants. Nusantara Bioscience 6: 186-195. Immunosensors are affinity ligand-based biosensor solid-state devices in which the immunochemical reaction is coupled to a transducer. The fundamental basis of all immunosensors is the specificity of the molecular recognition of antigens by antibodies to form a stable complex. This is similar to the immunoassay methodology. Immunosensors can be categorized based on the detection principle applied. The main developments are electrochemical, optical, and microgravimetric immunosensors. In contrast to immunoassay, modern transducer technology enables the label-free detection and quantification of the immune complex. The analysis of trace substances in environmental science, pharmaceutical and food industries is a challenge since many of these applications demand a continuous monitoring mode. The use of immunosensors in these applications is most appropriate. Food chemists should take advantage of immunosensors in food and clinical diagnostics. There are many recent developments in the immunosensor field which have potential impacts. The future role of this technique in intra-laboratory, as well as bedside testing, will become even more important as the food laboratory is faced with increasing pressure to contain costs. Objective of this paper is to give a general overview of the possible application of immunosensors to the food analysis field.

  1. Thermogravimetric and differential thermal analysis of potassium bicarbonate contaminated cellulose

    Science.gov (United States)

    A. Broido

    1966-01-01

    When samples undergo a complicated set of simultaneous and sequential reactions, as cellulose does on heating, results of thermogravimetric and differential thermal analyses are difficult to interpret. Nevertheless, careful comparison of pure and contaminated samples, pyrolyzed under identical conditions, can yield useful information. In these experiments TGA and DTA...

  2. A Metagenomic Analysis of Microbial Contamination in Aviation Fuels

    Science.gov (United States)

    2009-03-01

    microbial growth at phase interfaces (liquid-liquid, liquid-solid, liquid-gas, and so forth) (ASTM, 1999). Biosurfactant , n. — A surface-active...toxic and biodegradable. Biosurfactants enhance the emulsification of hydrocarbons, have the potential to solubilize hydrocarbon contaminants and...utilize secreted biosurfactants to solubilize the alkanes prior to metabolizing them (Rauch, 2008). Unfortunately, the biosurfactants have deleterious

  3. Microbial communities of the Costa Rica Margin: contamination controls and community analysis

    Science.gov (United States)

    Martino, A. J.; Biddle, J.; House, C. H.

    2013-12-01

    Most microbiology work in marine subsurface sediments has been focused in the upper 100-200 meters of sediment, as the switchover from advanced piston coring (APC) to extended core barrel coring (XCB) generally occurs around this depth. This leads to large increases in drilling-induced contamination and interferes in molecular studies. Here, we utilized deep 16S rRNA sequencing of DNA from both the subsurface sediments and the drilling fluid as a strategy for separating sequence information originating from drill-fluid contamination from that which represents the indigenous microbial communities of the sediments. This permitted a characterization of both sediment microbial communities and drilling-fluid communities that was thorough enough to confidently show the differences in the communities. Examination of the results suggests that sequences originating from drilling fluid may be only a minor portion of the data obtained from even the deepest XCB cores examined, and further that the different community composition of the drilling fluid should permit the subtraction of contaminating lineages from the analysis. As part of this work, we also show an extensive community composition analysis of multiple samples from two drilling sites of IODP Expedition 334, on the upper plate of the subduction zone between the Cocos plate and the Caribbean plate, off the Costa Rica Margin. Preliminary analysis of the sequence data suggests that the bacterial communities at both the upper slope site (1379) and the mid-slope site (1378) are dominated by Chloroflexi, Nitrospirae, Actinobacteria, Planctomycetes, and Proteobacteria, while Archaeal communities are dominated by the Miscellaneous Crenarchaeotal Group. Using universal primers revealed that the relative dominance of Bacteria to Archaea differs between the two sites, and the trends of increasing and decreasing abundance with depth are nearly opposite between the sites. At site 1379, the Bacterial to Archaeal relationship seems

  4. Elimination and molecular identification of endophytic bacterial contaminants during in vitro propagation of Bambusa balcooa.

    Science.gov (United States)

    Ray, Syandan Sinha; Ali, Md Nasim; Mukherjee, Shibasis; Chatterjee, Gautam; Banerjee, Maitreyi

    2017-02-01

    Bambusa balcooa is an economically important, multipurpose bamboo species, decidedly used in construction industry. Availability of natural bamboo is depleting very rapidly due to accelerated deforestation and its unrestrained use. The large number and timely supply of saplings are the need of the hour for the restoration of bamboo stands. Micropropagation, being the potent alternative for season independent rapid regeneration, is restricted in bamboo because of endophytic contamination. An in vitro attempt has been taken to overcome the endophytic contamination by using broad spectrum antibiotics as surface sterilant as well as a media component. Ampicillin sodium salt (5 mg/ml for 30 min) as a surface sterilant was found as the best treatment for high bud breaking (80%) coupled with high branching and low contamination (20%) but it was found ineffective to control the contamination during multiplication stage. Then, two endophytes were isolated and minimum inhibitory concentration was determined through antibiotic susceptibility test for successful eradication at multiplication stage. Finally, contamination free cultures were obtained when streptocycline (100 μg/ml) and gentamicin sulphate (75 μg/ml) were added into the medium. The two isolated endophytes, BB1 and BB2, were identified through 16S rDNA techniques and NCBI-BLAST algorithm with 99% sequence similarity with those of Janibacter sp. (KX423734) and Serratia marcescens strain (KX423735). To our knowledge, this is the first report for B. balcooa where antibiotics were used as surface sterilant as well as medium component, to control endophytic bacterial contaminants, followed by their identification.

  5. [Applications of molecular biology techniques for the control of aflatoxin contamination].

    Science.gov (United States)

    Sanchis, V

    1993-02-01

    Aflatoxins are mycotoxins produced by species of Aspergillus flavus group. These toxins have received increased attention from the food industry and the general public because they shown a high toxicity against humans and animal. Different methods are applying to control the aflatoxin contamination. But these conventional methods do not seem to resolve the problem. So, new methods using techniques in biotechnology are now being developed: a) Inhibit the biosynthetic and secretory process responsible for aflatoxin contamination. b) Using biocompetitive agents that replace aflatoxigenic strains with non aflatoxigenic strains in the field. c) Using genetic engineering techniques to incorporate antifungal genes into specific plant species.

  6. Analysis of Food Contaminants, Residues, and Chemical Constituents of Concern

    Science.gov (United States)

    Ismail, Baraem; Reuhs, Bradley L.; Nielsen, S. Suzanne

    The food chain that starts with farmers and ends with consumers can be complex, involving multiple stages of production and distribution (planting, harvesting, breeding, transporting, storing, importing, processing, packaging, distributing to retail markets, and shelf storing) (Fig. 18.1). Various practices can be employed at each stage in the food chain, which may include pesticide treatment, agricultural bioengineering, veterinary drug administration, environmental and storage conditions, processing applications, economic gain practices, use of food additives, choice of packaging material, etc. Each of these practices can play a major role in food quality and safety, due to the possibility of contamination with or introduction (intentionally and nonintentionally) of hazardous substances or constituents. Legislation and regulation to ensure food quality and safety are in place and continue to develop to protect the stakeholders, namely farmers, consumers, and industry. [Refer to reference (1) for information on regulations of food contaminants and residues.

  7. Analysis of contaminated field failure data for repairable systems

    OpenAIRE

    Hansen, Christian Kornerup; Thyregod, Poul

    1991-01-01

    A simple model for electronic systems with repair, and a method for analyzing recorded field failure data for such systems are presented. The work performed has resulted in analytical results that may be used for assessing the product reliability. The method was originally developed for use under ideal circumstances, but it has been adapted for use with contaminated data (i.e., data where the failure times are observed embedded by noise). A simple model for the noise that enables an analytica...

  8. MOLECULAR TRACKING FECAL CONTAMINATION IN SURFACE WATERS: 16S RDNA VERSUS METAGENOMICS APPROACHES

    Science.gov (United States)

    Microbial source tracking methods need to be sensitive and exhibit temporal and geographic stability in order to provide meaningful data in field studies. The objective of this study was to use a combination of PCR-based methods to track cow fecal contamination in two watersheds....

  9. MOLECULAR TRACKING FECAL CONTAMINATION IN SURFACE WATERS: 16S RDNA VERSUS METAGENOMICS APPROACHES

    Science.gov (United States)

    Microbial source tracking methods need to be sensitive and exhibit temporal and geographic stability in order to provide meaningful data in field studies. The objective of this study was to use a combination of PCR-based methods to track cow fecal contamination in two watersheds....

  10. Contamination Sources Effects Analysis (CSEA) - A Tool to Balance Cost/Schedule While Managing Facility Availability

    Science.gov (United States)

    Wilcox, Margaret

    2008-01-01

    A CSEA is similar to a Failure Modes Effects Analysis (FMEA). A CSEA tracks risk, deterrence, and occurrence of sources of contamination and their mitigation plans. Documentation is provided spanning mechanical and electrical assembly, precision cleaning, thermal vacuum bake-out, and thermal vacuum testing. These facilities all may play a role in contamination budgeting and reduction ultimately affecting test and flight. With a CSEA, visibility can be given to availability of these facilities, test sequencing and trade-offs. A cross-functional team including specialty engineering, contamination control, electrostatic dissipation, manufacturing, testing, and material engineering participate in an exercise that identifies contaminants and minimizes the complexity of scheduling these facilities considering their volatile schedules. Care can be taken in an efficient manner to insure correct cleaning processes are employed. The result is reduction in cycle time ("schedule hits"), reduced cost due to rework, reduced risk and improved communication and quality while achieving adherence to the Contamination Control Plan.

  11. Study of Arcobacter spp. contamination in fresh lettuces detected by different cultural and molecular methods.

    Science.gov (United States)

    González, Ana; Ferrús, Maria Antonia

    2011-01-31

    Arcobacters are considered potential emerging food and waterborne pathogens. However, there is no data on the presence of Arcobacter spp. in fresh vegetables. Therefore the objective of this research was to study the presence of Arcobacter spp. in fresh lettuces. Fifty fresh lettuces purchased from different local shops in Valencia (Spain) were analyzed. The assay was performed simultaneously by cultural and molecular methods. Isolates were identified by real-time, multiplex PCR and restriction fragment length polymorphism analysis of PCR-amplified DNA fragment (PCR-RFLP). Finally, all the isolates were genotyped using the randomly amplified polymorphic DNA (RAPD-PCR) method. Arcobacter sp. was detected in 10 of the 50 samples (20%) by real-time PCR, being A. butzleri the unique detected species by mPCR. The detection levels obtained by conventional PCR (7 samples/50, 14%) were slightly lower. These seven samples were found to be positive also by culture isolation. All 19 obtained isolates were identified as A. butzleri by multiplex PCR and PCR-RFLP. Great genetic heterogeneity among the isolates was observed by RAPD-PCR profiling. To our knowledge, this is the first study in which Arcobacter spp. is detected in fresh vegetables such as lettuces. Although these foods are generally considered safe, given the large quantities consumed and the fact that further cooking is absent, lettuce could be a source of Arcobacters of public health concern.

  12. Quantification of organic pollutant degradation in contaminated aquifers using compound specific stable isotope analysis – Review of recent developments

    NARCIS (Netherlands)

    Thullner, M.; Centler, F.; Richnow, H.-H.; Fischer, A.

    2012-01-01

    Compound specific stable isotope analysis (CSIA) has been established as a viable tool for proving, characterizing and assessing degradation of organic pollutants within contaminated aquifers. The fractionation of stable isotopes during contaminant degradation leads to observable shifts in stable is

  13. Theory analysis and experimental research on on-line contamination detecting technology in hydraulic oil

    Institute of Scientific and Technical Information of China (English)

    YAO Cheng-yu; ZHAO Jing-yi; ZHANG Qi-sheng

    2006-01-01

    A system of on-line contamination detecting in hydraulic oil based on silting principle is accomplished, where, metal filter membrane as detector, solenoid as active force to propel piston to blotter and gain differential pressure, step motor drives the membrane to filtrate and counter-flush, LabVIEW as detecting software platform, oil's contamination detecting indirectly by gauging differential pressure. Based on theory analysis, accomplished is relation between contamination level and differential pressure, realizing polynomial curve fitting, and calibration experiment. Field experiment is simulated in the condition of experimental laboratory, has credible precision and real-time performance, which can popularize to the field of production.

  14. Widespread Environmental Contamination with Mycobacterium tuberculosis Complex Revealed by a Molecular Detection Protocol.

    Science.gov (United States)

    Santos, Nuno; Santos, Catarina; Valente, Teresa; Gortázar, Christian; Almeida, Virgílio; Correia-Neves, Margarida

    2015-01-01

    Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70-0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area.

  15. Propagation Modeling and Analysis of Molecular Motors in Molecular Communication.

    Science.gov (United States)

    Chahibi, Youssef; Akyildiz, Ian F; Balasingham, Ilangko

    2016-12-01

    Molecular motor networks (MMNs) are networks constructed from molecular motors to enable nanomachines to perform coordinated tasks of sensing, computing, and actuation at the nano- and micro- scales. Living cells are naturally enabled with this same mechanism to establish point-to-point communication between different locations inside the cell. Similar to a railway system, the cytoplasm contains an intricate infrastructure of tracks, named microtubules, interconnecting different internal components of the cell. Motor proteins, such as kinesin and dynein, are able to travel along these tracks directionally, carrying with them large molecules that would otherwise be unreliably transported across the cytoplasm using free diffusion. Molecular communication has been previously proposed for the design and study of MMNs. However, the topological aspects of MMNs, including the effects of branches, have been ignored in the existing studies. In this paper, a physical end-to-end model for MMNs is developed, considering the location of the transmitter node, the network topology, and the receiver nodes. The end-to-end gain and group delay are considered as the performance measures, and analytical expressions for them are derived. The analytical model is validated by Monte-Carlo simulations and the performance of MMNs is analyzed numerically. It is shown that, depending on their nature and position, MMN nodes create impedance effects that are critical for the overall performance. This model could be applied to assist the design of artificial MMNs and to study cargo transport in neurofilaments to elucidate brain diseases related to microtubule jamming.

  16. Microbial community analysis of soils contaminated with lead, chromium and petroleum hydrocarbons.

    Science.gov (United States)

    Joynt, Janet; Bischoff, Marianne; Turco, Ron; Konopka, Allan; Nakatsu, Cindy H

    2006-02-01

    The impact on the microbial community of long-term environmental exposure to metal and organic contamination was investigated. Twenty-four soil samples were collected along a transect dug in soils contaminated with road paint and paint solvents, mainly toluene. Chemical analysis along the transect revealed a range from high to low concentrations of metals (lead and chromium) and organic solvent compounds. Principal components analysis of microbial community structure based on denaturing gradient gel electrophoresis of the V3 region of the 16S rRNA gene and fatty acid methyl esters derived from phospholipids (phospholipid fatty acid analysis) showing samples with similar fingerprints also had similar contaminant concentrations. There was also a weak positive correlation between microbial biomass and the organic carbon concentration. Results indicated that microbial populations are present despite some extreme contaminant levels in this mixed-waste contaminated site. Nucleotide sequence determination of the 16S rRNA gene indicated the presence of phylogenetically diverse bacteria belonging to the alpha-, beta-, gamma-, and delta-Proteobacteria, the high and low G + C Gram-positive bacteria, green nonsulfur, OP8, and others that did not group within a described division. This indicates that soils contaminated with both heavy metals and hydrocarbons for several decades have undergone changes in community composition, but still contain a phylogenetically diverse group of bacteria (including novel phylotypes) that warrant further investigation.

  17. Recent Advances and Uses of Monolithic Columns for the Analysis of Residues and Contaminants in Food

    Directory of Open Access Journals (Sweden)

    Mónica Díaz-Bao

    2015-02-01

    Full Text Available Monolithic columns are gaining interest as excellent substitutes to conventional particle-packed columns. These columns show higher permeability and lower flow resistance than conventional liquid chromatography columns, providing high-throughput performance, resolution and separation in short run times. Monoliths possess also great potential for the clean-up and preparation of complex mixtures. In situ polymerization inside appropriate supports allows the development of several microextraction formats, such as in-tube solid-phase and pipette tip-based extractions. These techniques using porous monoliths offer several advantages, including miniaturization and on-line coupling with analytical instruments. Additionally, monoliths are ideal support media for imprinting template-specific sites, resulting in the so-called molecularly-imprinted monoliths, with ultra-high selectivity. In this review, time-saving LC columns and preparative applications applied to the analysis of residues and contaminants in food in 2010–2014 are described, focusing on recent improvements in design and with emphasis in automated on-line systems and innovative materials and formats.

  18. First comparative analysis concerning the plasma platelet contamination during MNC collection.

    Science.gov (United States)

    Pfeiffer, Hella; Achenbach, Susanne; Strobel, Julian; Zimmermann, Robert; Eckstein, Reinhold; Strasser, Erwin F

    2017-07-13

    Monocytes can be cultured into dendritic cells with addition of autologous plasma, which is highly prone to platelet contamination due to the apheresis process. Since platelets affect the maturation process of monocytes into dendritic cells and might even lead to a diminished harvest of dendritic cells, it is very important to reduce the platelet contamination. A new collection device (Spectra Optia) was analyzed, compared to two established devices (COM.TEC, Cobe Spectra) and evaluated regarding the potential generation of source plasma. Concurrent plasma collected during leukapheresis was analyzed for residual cell contamination in a prospective study with the new Spectra Optia apheresis device (n=24) and was compared with COM.TEC and Cobe Spectra data (retrospective analysis, n=72). Donor pre-donation counts of platelets were analyzed for their predictive value of contaminating PLTs in plasma harvests. The newest apheresis device showed the lowest residual platelet count of the collected concurrent plasma (median 3.50×10(9)/l) independent of pre-donation counts. The other two devices and sets had a higher platelet contamination. The contamination of the plasma with leukocytes was very low (only 2.0% were higher than 0.5×10(9)/l). This study showed a significant reduction of platelet contamination of the concurrent plasma collected with the new Spectra Optia device. This plasma product with low residual platelets and leukocytes might also be used as plasma for fractionation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Molecular analysis of holoprosencephaly in South America

    Directory of Open Access Journals (Sweden)

    Clarice Pagani Savastano

    2014-01-01

    Full Text Available Holoprosencephaly (HPE is a spectrum of brain and facial malformations primarily reflecting genetic factors, such as chromosomal abnormalities and gene mutations. Here, we present a clinical and molecular analysis of 195 probands with HPE or microforms; approximately 72% of the patients were derived from the Latin American Collaborative Study of Congenital Malformations (ECLAMC, and 82% of the patients were newborns. Alobar HPE was the predominant brain defect in almost all facial defect categories, except for patients without oral cleft and median or lateral oral clefts. Ethmocephaly, cebocephaly, and premaxillary agenesis were primarily observed among female patients. Premaxillary agenesis occurred in six of the nine diabetic mothers. Recurrence of HPE or microform was approximately 19%. The frequency of microdeletions, detected using Multiplex Ligation-dependant Probe Amplification (MLPA was 17% in patients with a normal karyotype. Cytogenetics or QF-PCR analyses revealed chromosomal anomalies in 27% of the probands. Mutational analyses in genes SHH, ZIC2, SIX3 and TGIF were performed in 119 patients, revealing eight mutations in SHH, two mutations in SIX3 and two mutations in ZIC2. Thus, a detailed clinical description of new HPE cases with identified genetic anomalies might establish genotypic and phenotypic correlations and contribute to the development of additional strategies for the analysis of new cases.

  20. Molecular forensic science analysis of nuclear materials

    Science.gov (United States)

    Reilly, Dallas David

    Concerns over the proliferation and instances of nuclear material in the environment have increased interest in the expansion of nuclear forensics analysis and attribution programs. A new related field, molecular forensic science (MFS) has helped meet this expansion by applying common scientific analyses to nuclear forensics scenarios. In this work, MFS was applied to three scenarios related to nuclear forensics analysis. In the first, uranium dioxide was synthesized and aged at four sets of static environmental conditions and studied for changes in chemical speciation. The second highlighted the importance of bulk versus particle characterizations by analyzing a heterogeneous industrially prepared sample with similar techniques. In the third, mixed uranium/plutonium hot particles were collected from the McGuire Air Force Base BOMARC Site and analyzed for chemical speciation and elemental surface composition. This work has identified new signatures and has indicated unexpected chemical behavior under various conditions. These findings have lead to an expansion of basic actinide understanding, proof of MFS as a tool for nuclear forensic science, and new areas for expansion in these fields.

  1. Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

    Science.gov (United States)

    Izunobi, Josephat U.; Higginbotham, Clement L.

    2011-01-01

    The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…

  2. Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

    Science.gov (United States)

    Izunobi, Josephat U.; Higginbotham, Clement L.

    2011-01-01

    The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…

  3. Molecular toxicity of earthworms induced by cadmium contaminated soil and biomarkers screening

    Institute of Scientific and Technical Information of China (English)

    Xiaohui MO; Yuhui Qiao; Zhenjun Sun; Xiaofei Sun; Yang Li

    2012-01-01

    Earthworms(Eiseniafetida)were used to study the impact of low-dose cadmium in treated artificial soil(0,0.6,3,6,15,30 mg/kg)and contaminated natural soil(1.46 mg/kg).The changes of earthworms' physiological related gene expressions of metallothionein (MT),annetocin,calreticulin and antimicrobial peptides were detected using real-time PCR after a 70-day incubation period.The results showed that low doses of cadmium could up regulate earthworms' MT and down regulate armetocin gene expression and show a significant positive and negative correlation respectively.The expression of two other genes,calreticulin and anti-microbial peptides,was induced at low doses of cadmium(highest gene expression at 0.6 mg/kg for calreticulin and 6 mg/kg for anti-microbial peptides)and inhibited at high doses.No significant correlation was found for these two genes.This study shows that MT and annetocin genes expression found in earthworms in contaminated soil have the potential to be developed as biomarkers of soil cadmium pollution.

  4. Molecular identification and nanoremediation of microbial contaminants in algal systems using untreated wastewater.

    Science.gov (United States)

    Limayem, Alya; Gonzalez, Francisco; Micciche, Andrew; Haller, Edward; Nayak, Bina; Mohapatra, Shyam

    2016-12-01

    Wastewater-algal biomass is a promising option to biofuel production. However, microbial contaminants constitute a substantial barrier to algal biofuel yield. A series of algal strains, Nannochloris oculata and Chlorella vulgaris samples (n = 30), were purchased from the University of Texas, and were used for both stock flask cultures and flat-panel vertical bioreactors. A number of media were used for isolation and differentiation of potential contaminants according to laboratory standards (CLSI). Conventional PCR amplification was performed followed by 16S rDNA sequencing to identify isolates at the species level. Nanotherapeutics involving a nanomicellar combination of natural chitosan and zinc oxide (CZNPs) were tested against the microbial lytic groups through Minimum Inhibitory Concentration (MIC) tests and Transmission Electronic Microscopy (TEM). Results indicated the presence of Pseudomonas spp., Bacillus pumilus/ safensis, Cellulosimicrobium cellulans, Micrococcus luteus and Staphylococcus epidermidis strains at a substantial level in the wastewater-fed algal reactors. TEM confirmed the effectiveness of CZNPs on the lytic group while the average MICs (mg/mL) detected for the strains, Pseudomonas spp, Micrococcus luteus, and Bacillus pumilus were 0.417, 3.33, and 1.458, respectively. Conclusively, CZNP antimicrobials proved to be effective as inhibitory agents against currently identified lytic microbial group, did not impact algae cells, and shows promise for in situ interventions.

  5. Flow cytometric analysis of microbial contamination in food industry technological lines – initial study

    Directory of Open Access Journals (Sweden)

    Katarzyna Czaczyk

    2012-06-01

    Full Text Available Background. Flow cytometry constitutes an alternative for traditional methods of microorganisms identifi cation and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer may be analysed directly. This leads to a signifi cant reduction of time required for analysis allowing monitoring of production processes and immediate reaction in case of contamination or any disruption occurs. Apart from the analysis of raw materials or products on different stages of manufacturing process, the fl ow cytometry seems to constitute an ideal tool for the assessment of microbial contamination on the surface of technological lines. Material and methods. In the present work samples comprising smears from 3 different surfaces of technological lines from fruit and vegetable processing company from Greater Poland were analysed directly with fl ow cytometer. The measured parameters were forward and side scatter of laser light signals allowing the estimation of microbial cell contents in each sample. Results. Flow cytometric analysis of the surface of food industry production lines enable the preliminary evaluation of microbial contamination within few minutes from the moment of sample arrival without the need of sample pretreatment. Conclusions. The presented method of fl ow cytometric initial evaluation of microbial state of food industry technological lines demonstrated its potential for developing a robust, routine method for the rapid and laborsaving detection of microbial contamination in food industry.

  6. LMWOA (low molecular weight organic acid) exudation by salt marsh plants: Natural variation and response to Cu contamination

    Science.gov (United States)

    Mucha, Ana P.; Almeida, C. Marisa R.; Bordalo, Adriano A.; Vasconcelos, M. Teresa S. D.

    2010-06-01

    This work aimed to evaluate, in vitro, the capability of roots of two salt marsh plants to release low molecular weight organic acids (LMWOAs) and to ascertain whether Cu contamination would stimulate or not organic acids exudation. The sea rush Juncus maritimus and the sea-club rush Scirpus maritimus, both from the lower Douro river estuary (NW Portugal), were used. Plants were collected seasonally, four times a year in 2004, during low tide. After sampling, plant roots were washed for removal of adherent particles and immersed for 2 h in a solution that matched salinity (3) and pH (7.5) of the pore water from the same location to obtain plant exudates. In one of the seasons, similar experiments were carried out but spiking the solution with different amounts of Cu in order to embrace the range between 0 and 1600 nM. In the final solutions as well as in sediment pore water LMWOAs were determined by high performance liquid chromatography. Plants were able to release, in a short period of time, relatively high amounts of LMWOAs (oxalate, citrate, malate, malonate, and succinate). In the sediment pore water oxalate, succinate and acetate were also detected. Therefore, plant roots probably contributed to the presence of some of these organic compounds in pore water. Exudation differed between the plant species and also showed some seasonally variation, particularly for S. maritimus. The release of oxalate by J. maritimus increased with Cu increase in the media. However, exudation of the other LMWOAs did not seem to be stimulated by Cu contamination in the media. This fact is compatible with the existence of alternative internal mechanisms for Cu detoxification, as denoted by the fact that in media contaminated with Cu both plant species accumulated relatively high amounts (29-83%) of the initially dissolved Cu. This study expands our knowledge on the contribution of globally dominant salt marsh plants to the release of LMWOAs into the environment.

  7. Determining uranium speciation in contaminated soils by molecular spectroscopic methods: Examples from the Uranium in Soils Integrated Demonstration

    Energy Technology Data Exchange (ETDEWEB)

    Allen, P.G.; Berg, J.M.; Chisholm-Brause, C.J.; Conradson, S.D.; Donohoe, R.J.; Morris, D.E.; Musgrave, J.A.; Tait, C.D.

    1994-03-01

    The US Department of Energy`s former uranium production facility located at Fernald, OH (18 mi NW of Cincinnati) is the host site for an Integrated Demonstration for remediation of uranium-contaminated soils. A wide variety of source terms for uranium contamination have been identified reflecting the diversity of operations at the facility. Most of the uranium contamination is contained in the top {approximately}1/2 m of soil, but uranium has been found in perched waters indicating substantial migration. In support of the development of remediation technologies and risk assessment, we are conducting uranium speciation studies on untreated and treated soils using molecular spectroscopies. Untreated soils from five discrete sites have been analyzed. We have found that {approximately}80--90% of the uranium exists as hexavalent UO{sub 2}{sup 2+} species even though many source terms consisted of tetravalent uranium species such as UO{sub 2}. Much of the uranium exists as microcrystalline precipitates (secondary minerals). There is also clear evidence for variations in uranium species from the microscopic to the macroscopic scale. However, similarities in speciation at sites having different source terms suggest that soil and groundwater chemistry may be as important as source term in defining the uranium speciation in these soils. Characterization of treated soils has focused on materials from two sites that have undergone leaching using conventional extractants (e.g., carbonate, citrate) or novel chelators such as Tiron. Redox reagents have also been used to facilitate the leaching process. Three different classes of treated soils have been identified based on the speciation of uranium remaining in the soils. In general, the effective treatments decrease the total uranium while increasing the ratio of U(IV) to U(VI) species.

  8. An Application of Discriminant Analysis to Pattern Recognition of Selected Contaminated Soil Features in Thin Sections

    DEFF Research Database (Denmark)

    Ribeiro, Alexandra B.; Nielsen, Allan Aasbjerg

    1997-01-01

    qualitative microprobe results: present elements Al, Si, Cr, Fe, As (associated with others). Selected groups of calibrated images (same light conditions and magnification) submitted to discriminant analysis, in order to find a pattern of recognition in the soil features corresponding to contamination already...... in the soluble and exchangeable phase, these elements being associated primarily with amorphous-crystalline Fe-oxides, organic matter and/or resistant phases. The results obtained with sequential extraction were the prerequisite to the attempt to identify the Cr and As distribution in the solid phase. If high...... concentrations of contaminants are indicated by chemical wet analysis, these contaminants must occur directly in the solid phase. Thin sections of soil aggregates were scanned for Cu, Cr and As using an electron microprobe, and qualitative analysis was made on selected areas. Microphotographs of thin sections...

  9. Removal and destruction of endocrine disrupting contaminants by adsorption with molecularly imprinted polymers followed by simultaneous extraction and phototreatment

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Alvarez, Paula [Department of Biotechnology, Lund University, P.O. Box 124, 22100 Lund (Sweden); University of Santiago de Compostela, Department of Chemical Engineering, Instituto de Investigaciones Tecnologicas, C/Constantino Candeira, s/n. E-15782 Santiago de Compostela (Spain); Le Noir, Mathieu [Department of Biotechnology, Lund University, P.O. Box 124, 22100 Lund (Sweden); Guieysse, Benoit [Department of Biotechnology, Lund University, P.O. Box 124, 22100 Lund (Sweden); School of Civil and Environmental Engineering, Nanyang Technological University, Block N1, Nanyang Avenue, Singapore 639798 (Singapore)], E-mail: bjguieysse@ntu.edu.sg

    2009-04-30

    This study presents a method to regenerate molecularly imprinted polymers (MIPs) used for the selective removal of endocrine disrupting compounds from aqueous effluents. Regeneration was based on solvent extraction under UV irradiation to regenerate the polymer and the solvent while destroying the contaminants. Acetone was selected as the best solvent for irradiation of estrone (E1), 17{beta}-estradiol (E2) and ethinylestradiol (EE2) using either UVC (254 nm) or UV-vis. A MIP synthesized with E2 as template was then tested for the extraction of this compound from a 2 {mu}g/L loaded aqueous solution. E2 was recovered by 73 {+-} 11% and 46 {+-} 13% from the MIPs and a non-imprinted control polymer synthesized under the same conditions, respectively, after a single step elution with acetone. The irradiated polymers and acetone were reused for an additional extraction-regeneration cycle and showed no capacity decrease.

  10. Analysis of contaminating elements in tree rings in Santiago, Chile

    Energy Technology Data Exchange (ETDEWEB)

    Romo-Kroeger, C.M.; Avila, M.J.; Eaton, L.C.; Lopez, L.A. [Faculty of Sciences. Univ. of Chile, Santiago (Chile)

    1996-12-31

    Using the 22`` isochronous cyclotron at the University of Chile, we have performed PIXE analyses on a group of samples collected from trees of metropolitan parks in Santiago. Dendrochronology was performed on each sample, which was then sectioned for the PIXE and other analyses, neutron activation and electro-chemistry. Available samples are trunk sections or cores obtained by the use of a 4.0 mm stainless steel incremental corer. We took three cores from each tree with permission of the municipalities. For the PIXE we use infinitely thick targets, as wood slabs taken along the trunk radius, and thin targets obtained by acid digestion of wood pieces and deposition on Kapton foils. Self supporting thick targets were placed directly in the PIXE chamber in a position so as to allow the irradiation of a specific annual ring. Potassium and Calcium appear as the most abundant elements in wood. Other elements such as S, Cu, Zn, As, Br and Pb were detected in amounts above the natural background in wood, and can be attributed to environmental contamination. The K/Ca ratios appear to be different for each species of tree, and seem to be related to the physico-chemical properties of wood. Preliminary results show important amounts of As and Cu (supposedly from mining origin) with increasing presence in the recent years. Pb and Zn (supposedly from vehicle origin) are also higher in recent years. (author)

  11. Electrochemical Analysis of Heavy Metal Contaminants in Plant Matter

    Science.gov (United States)

    Burghard, C. J.; Atkinson, D. B.; Zhu, X.

    2016-12-01

    Cadmium and Lead are toxic heavy metals found in the aerosol phase that can cause cancer (Cd) or neurological and developmental problems (Pb). In October 2015 the Oregon DEQ and USFS performed a follow-up investigation after a 2013 USFS moss study in Portland, Oregon showed high levels of Cadmium and Lead in a neighborhood in the Southeast part of the city. Findings from the ODEQ study implicated emissions from the Bullseye Glass Factory, and to a lesser extent, the Uroboros Glass Studio in producing the elevated Cadmium and Lead. These facilities were ordered to stop production until particulate filtering systems could be installed. Once production had ceased, ambient Cadmium concentrations dropped from 29.4 ng/m3 (49 times higher than the 0.6 ng/m3 Oregon Benchmark) to 1.1 ng/m3 near one factory and 0.67 ng/m3 near the other. The emissions of these metals were highly concentrated in an approximate 0.5 kilometer radius around the Bullseye facility and contamination of edible produce from gardens in the area is of concern. A simple extraction method, paired with Anodic Stripping Voltammetry was used to determine the levels of the two metals in produce and other plants from the area. Preliminary findings indicate that low levels of lead and cadmium are detectable in the vegetation samples from the area.

  12. Molecular biomarkers to assess health risks due to environmental contaminants exposure.

    Science.gov (United States)

    Poblete-Naredo, Irais; Albores, Arnulfo

    2016-06-03

    Biomarkers, or bioindicators, are metric tools that, when compared with reference values, allow specialists to perform risk assessments and provide objective information to decision makers to design effective strategies to solve health or environmental problems by efficiently using the resources assigned. Health risk assessment is a multidisciplinary exercise, and molecular biology is a discipline that greatly contributes to these evaluations because the genome, transcriptome, proteome and metabolome could be affected by xenobiotics causing measurable changes that might be useful biomarkers. Such changes may greatly depend on individual genetic background; therefore, the polymorphic distribution of exposed populations becomes an essential feature for adequate data interpretation. The aim of this paper is to offer an up-to-date review of the role of different molecular biomarkers in health risk assessments.

  13. Classification of corn kernels contaminated with aflatoxins using fluorescence and reflectance hyperspectral images analysis

    Science.gov (United States)

    Zhu, Fengle; Yao, Haibo; Hruska, Zuzana; Kincaid, Russell; Brown, Robert; Bhatnagar, Deepak; Cleveland, Thomas

    2015-05-01

    Aflatoxins are secondary metabolites produced by certain fungal species of the Aspergillus genus. Aflatoxin contamination remains a problem in agricultural products due to its toxic and carcinogenic properties. Conventional chemical methods for aflatoxin detection are time-consuming and destructive. This study employed fluorescence and reflectance visible near-infrared (VNIR) hyperspectral images to classify aflatoxin contaminated corn kernels rapidly and non-destructively. Corn ears were artificially inoculated in the field with toxigenic A. flavus spores at the early dough stage of kernel development. After harvest, a total of 300 kernels were collected from the inoculated ears. Fluorescence hyperspectral imagery with UV excitation and reflectance hyperspectral imagery with halogen illumination were acquired on both endosperm and germ sides of kernels. All kernels were then subjected to chemical analysis individually to determine aflatoxin concentrations. A region of interest (ROI) was created for each kernel to extract averaged spectra. Compared with healthy kernels, fluorescence spectral peaks for contaminated kernels shifted to longer wavelengths with lower intensity, and reflectance values for contaminated kernels were lower with a different spectral shape in 700-800 nm region. Principal component analysis was applied for data compression before classifying kernels into contaminated and healthy based on a 20 ppb threshold utilizing the K-nearest neighbors algorithm. The best overall accuracy achieved was 92.67% for germ side in the fluorescence data analysis. The germ side generally performed better than endosperm side. Fluorescence and reflectance image data achieved similar accuracy.

  14. Use of stochastic multi-criteria decision analysis to support sustainable management of contaminated sediments.

    Science.gov (United States)

    Sparrevik, Magnus; Barton, David N; Bates, Mathew E; Linkov, Igor

    2012-02-01

    Sustainable management of contaminated sediments requires careful prioritization of available resources and focuses on efforts to optimize decisions that consider environmental, economic, and societal aspects simultaneously. This may be achieved by combining different analytical approaches such as risk analysis (RA), life cycle analysis (LCA), multicriteria decision analysis (MCDA), and economic valuation methods. We propose the use of stochastic MCDA based on outranking algorithms to implement integrative sustainability strategies for sediment management. In this paper we use the method to select the best sediment management alternatives for the dibenzo-p-dioxin and -furan (PCDD/F) contaminated Grenland fjord in Norway. In the analysis, the benefits of health risk reductions and socio-economic benefits from removing seafood health advisories are evaluated against the detriments of remedial costs and life cycle environmental impacts. A value-plural based weighing of criteria is compared to criteria weights mimicking traditional cost-effectiveness (CEA) and cost-benefit (CBA) analyses. Capping highly contaminated areas in the inner or outer fjord is identified as the most preferable remediation alternative under all criteria schemes and the results are confirmed by a probabilistic sensitivity analysis. The proposed methodology can serve as a flexible framework for future decision support and can be a step toward more sustainable decision making for contaminated sediment management. It may be applicable to the broader field of ecosystem restoration for trade-off analysis between ecosystem services and restoration costs.

  15. Phylogenic analysis in Acacia senegal using AFLP molecular ...

    African Journals Online (AJOL)

    Phylogenic analysis in Acacia senegal using AFLP molecular markers across ... belt were tested in comparison with samples of Acacia mellifera and Acacia leata. ... According to the cluster analysis two main clusters were obtained in which A.

  16. Mars Through the Looking Glass: an Interdisciplinary Analysis of Forward and Backward Contamination

    Science.gov (United States)

    Goh, G. M.; Kazeminejad, B.

    2004-08-01

    The exploration of the planet Mars represents a significant milestone in humanity's exploration of the Universe. In the quest to better explore and understand Mars, issues of forward and backward contamination are particularly pertinent. This paper provides an interdisciplinary analysis of forward and backward contamination. Its substantive material reflects the scientific and technical concerns through the looking glass of legal and policy issues, and vice versa. The paper critically surveys contamination issues of current, nascent and proposed Mars missions from a scientific viewpoint. It then makes a comparative review of legal and policy mechanisms designed to protect against such contamination. It draws cross-linkages between the sciences and the law in this area. The paper then delineates a suggested interdisciplinary framework to protect against forward and backward contamination. This framework is based on co-operation between the various nations undertaking Mars missions, as well as between the various fields of expertise. It highlights the importance of an interdisciplinary overview in the implementation of measures protecting against forward and backward contamination. Strategies on the implementation of these measures are also outlined.

  17. Organic adlayer on inorganic materials: XPS analysis selectivity to cope with adventitious contamination

    Science.gov (United States)

    Landoulsi, Jessem; Genet, Michel J.; Fleith, Sandrine; Touré, Yetioman; Liascukiene, Irma; Méthivier, Christophe; Rouxhet, Paul G.

    2016-10-01

    This work addresses the ubiquitous presence of organic contaminants at inorganic solid surfaces and the improvement of XPS analysis selectivity to cope with it. Water contact angle measurements showed that the adsorption of organic contaminants occurs readily in ambient air, and faster and more extensively under high vacuum. It is stronger on stainless steel (SS) compared to silica and is significantly reduced when SS is sterilized by autoclaving. The reliability of XPS data was evaluated (selectivity, precision, accuracy) by correlations between spectral data incorporating a large amount of results obtained with different XPS spectrometers on SS and glass samples cleaned in different ways and conditioned with several biomacromolecules. The methodology used allows a discrimination to be made between contaminants and deliberately adsorbed biomacromolecules, and offers perspectives for tracking the source of contamination. Furthermore, a discrimination can be made between oxygen from the organic adlayer and oxygen from the substrate, and the O 1s component above 532.0 eV observed for SS is shown to be due to organic contaminants rather than adsorbed water. This approach offers new perspectives to examine the interactions (displacement or not) between contaminants and compounds of interest, e.g. proteins, at the stage of the adsorption process.

  18. Analysis methodology and development of a statistical tool for biodistribution data from internal contamination with actinides.

    Science.gov (United States)

    Lamart, Stephanie; Griffiths, Nina M; Tchitchek, Nicolas; Angulo, Jaime F; Van der Meeren, Anne

    2017-03-01

    The aim of this work was to develop a computational tool that integrates several statistical analysis features for biodistribution data from internal contamination experiments. These data represent actinide levels in biological compartments as a function of time and are derived from activity measurements in tissues and excreta. These experiments aim at assessing the influence of different contamination conditions (e.g. intake route or radioelement) on the biological behavior of the contaminant. The ever increasing number of datasets and diversity of experimental conditions make the handling and analysis of biodistribution data difficult. This work sought to facilitate the statistical analysis of a large number of datasets and the comparison of results from diverse experimental conditions. Functional modules were developed using the open-source programming language R to facilitate specific operations: descriptive statistics, visual comparison, curve fitting, and implementation of biokinetic models. In addition, the structure of the datasets was harmonized using the same table format. Analysis outputs can be written in text files and updated data can be written in the consistent table format. Hence, a data repository is built progressively, which is essential for the optimal use of animal data. Graphical representations can be automatically generated and saved as image files. The resulting computational tool was applied using data derived from wound contamination experiments conducted under different conditions. In facilitating biodistribution data handling and statistical analyses, this computational tool ensures faster analyses and a better reproducibility compared with the use of multiple office software applications. Furthermore, re-analysis of archival data and comparison of data from different sources is made much easier. Hence this tool will help to understand better the influence of contamination characteristics on actinide biokinetics. Our approach can aid

  19. Contamination of cockroaches (Insecta: Blattaria) to medically fungi: A systematic review and meta-analysis.

    Science.gov (United States)

    Nasirian, H

    2017-05-11

    Fungal infections have emerged worldwide. Cockroaches have been proved vectors of medically fungi. A systematic meta-analysis review about cockroach fungal contamination was investigated. Relevant topics were collected between January 2016 and January 2017. After a preliminary review among 392 collected papers, 156 were selected to become part of the detailed systematic meta-analysis review. Cockroaches contaminated to 38 fungi species belonging to 19 families and 12 orders. About 38, 25 and 13 fungal species were recovered from the American, German and brown-banded cockroaches, respectively with a variety of medical importance. Except the fungi isolated from German and brown-banded cockroaches, 15 species have been isolated only from the American cockroaches. The global world mean and trend of cockroach fungal contamination were 84.1 and 50.6-100%, respectively in the human dwelling environments. There is a significant difference between cockroach fungal contamination in the urban and rural environments (P0.05). The external and internal cockroach fungal contamination is more dangerous than entire surfaces, while the internal is more dangerous than the external surface. The German and brown-banded cockroach fungal contamination are more dangerous than the American cockroaches in the hospital environments. The study indicates that globally cockroach fungal contamination has been increased recognizing as agents of human infections and associating with high morbidity and mortality in immune-compromised patients. These facts, along with insecticide resistance emergence and increasing globally cockroach infestation, reveal importance of cockroaches and need for their control more than ever. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  20. The geochemical evolution of low-molecular-weight organic acids derived from the degradation of petroleum contaminants in groundwater

    Science.gov (United States)

    Cozzarelli, I.M.; Baedecker, M.J.; Eganhouse, R.P.; Goerlitz, D.F.

    1994-01-01

    The geochemical evolution of low-molecular-weight organic acids in groundwater downgradient from a crude-oil spill near Bemidji, Minnesota, was studied over a five year period (1986-1990). The organic acids are metabolic intermediates of the degradation of components of the crude oil and are structurally related to hydrocarbon precursors. The concentrations of organic acids, particularly aliphatic acids, increase as the microbial alteration of hydrocarbons progresses. The organic-acid pool changes in composition and concentration over time and in space as the degradation processes shift from Fe(III) reduction to methanogenesis. Over time, the aquifer system evolves into one in which the groundwater contains more oxidized products of hydrocarbon degradation and the reduced forms of iron, manganese, and nitrogen. Laboratory microcosm experiments with aquifer material support the hypothesis that organic acids observed in the groundwater originate from the microbial degradation of aromatic hydrocarbons under anoxic conditions. The geochemistry of two other shallow aquifers in coastal plain sediments, one contaminated with creosote waste and the other with gasoline, were compared to the Bemidji site. The geochemical evolution of the low-molecular-weight organic acid pool in these systems is controlled, in part, by the presence of electron acceptors available for microbially mediated electron-transfer reactions. The depletion of electron acceptors in aquifers leads to the accumulation of aliphatic organic acids in anoxic groundwater. ?? 1994.

  1. Molecular characterization of conjugative plasmids in pesticide tolerant and multi-resistant bacterial isolates from contaminated alluvial soil.

    Science.gov (United States)

    Anjum, Reshma; Grohmann, Elisabeth; Malik, Abdul

    2011-06-01

    A total of 35 bacteria from contaminated soil (cultivated fields) near pesticide industry from Chinhat, Lucknow, (India) were isolated and tested for their tolerance/resistance to pesticides, heavy metals and antibiotics. Bacterial isolates were identified by 16S rDNA sequencing. Gas Chromatography analysis of the soil samples revealed the presence of lindane at a concentration of 547 ng g(-1) and α-endosulfan and β-endosulfan of 422 ng g(-1) and 421 ng g(-1) respectively. Atomic Absorption Spectrophotometry analysis of the test sample was done and Cr, Zn, Ni, Fe, Cu and Cd were detected at concentrations of 36.2, 42.5, 43.2, 241, 13.3 and 11.20 mg kg(-1) respectively. Minimum inhibitory concentrations of all the isolates were determined for pesticides and heavy metals. All the multi-resistant/tolerant bacterial isolates were also tested for the presence of incompatibility (Inc) group IncP, IncN, IncW, IncQ plasmids and for rolling circle plasmids of the pMV158-family by PCR. Total community DNA was extracted from pesticide contaminated soil. PCR amplification of the bacterial isolates and soil DNA revealed the presence of IncP-specific sequences (trfA2 and oriT) which was confirmed by dot blot hybridization with RP4-derived DIG-labelled probes. Plasmids belonging to IncN, IncW and IncQ group were neither detected in the bacterial isolates nor in total soil DNA. The presence of conjugative or mobilizable IncP plasmids in the isolates indicate that these bacteria have gene transfer capacity with implications for dissemination of heavy metal and antibiotic resistance genes. We propose that IncP plasmids are mainly responsible for the spread of multi-resistant bacteria in the contaminated soils.

  2. Monitoring acidic and basic molecular contamination in leading edge lithography and metrology applications: quantitative comparison of solid state and impinger-based sampling methods

    Science.gov (United States)

    Riddle Vogt, Sarah; Landoni, Cristian

    2010-03-01

    Assessing molecular contamination (MC) at part-per-billion (ppbV) or part-per-trillion volume (pptV) levels in cleanroom air and purge gas lines is essential to protect lithography and metrology tools optics and components. Current lithography and metrology tool manufacturer's specifications require testing of some contaminants down to single digit pptV levels. Ideally this analysis would be performed with an on-line analyzer (capable of providing almost instant results): the best analyzers currently available are only capable of providing 100 pptV detection. Liquid impinger sampling has been the dominant sample collection method for sub ppbV acidic and basic MC analysis. Impinger sampling suffers from some inherent problems that can dramatically reduce the collection efficiency such as analyte solubility and evaporative losses. An innovative solid-state trapping technology has been recently developed by SAES Pure Gas along with the CollectTorr sampling system. NIST traceable gas phase standards have been used to compare the collection efficiency of the traditional impinger technology to that of the solid state trapping method. Results varied greatly for the different acid gases with sulfur dioxide showing comparable collection efficiencies while hydrofluoric acid and hydrochloric acid showed much lower recoveries in the impingers than the solid-state traps. Ammonia collection efficiencies were slightly higher for the solid state traps and were improved in the impingers when an acidified solution was used as the collection media. The use of solid-state traps, besides being much simpler from both the handling and logistical stand point, eliminates the analyte solubility and evaporation problems frequently seen with the impinger sampling.

  3. A Molecular Mechanics Analysis of Molecular Recognition by Cyclodextrin Mimics of Alpha-Chymotrypsin

    Science.gov (United States)

    1989-05-26

    Clasification ) A Molecular Mechanics Analysis of Molecular Recognition By Cyclodextrin Mimics of Alpha-Chymotrypsin. 12. PERSONAL AUTHOR(S) C.A. Venanzil...Field Parameters The AMBER force field was developed by Kollmann and coworkers tc 28293 treat proteins and nucleic acids , as well as small molecules2 9

  4. Mass Balance Model, A study of contamination effects in AMS 14C sample analysis

    NARCIS (Netherlands)

    Prokopiou, Markella

    2010-01-01

    In this training thesis a background correction analysis, also known as mass balance model, was implemented to study the contamination effects in AMS 14C sample processing. A variety of backgrounds and standards with sizes ranging from 50 μg C to 1500 μg

  5. ECONOMICS ANALYSIS OF THE IMPLEMENTATION OF PERMEABLE REACTIVE BARRIERS FOR REMEDIATION OF CONTAMINATED GROUND WATER

    Science.gov (United States)

    This report presents an analysis of the cost of using permeable reactive barriers to remediate contaminated ground water. When possible, these costs are compared with the cost of pump-and-treat technology for similar situations. Permeable reactive barriers are no longer perceiv...

  6. Emerging organic contaminants in sludges. Analysis, fate and biological treatment

    Energy Technology Data Exchange (ETDEWEB)

    Vicent, Teresa [Univ. Autonoma de Barcelona, Bellaterra (Spain). Chemical Engineering Dept.; Eljarrat, Ethel [IDAEA-CSIC, Barcelona (Spain). Dept. of Environmental Chemistry; Caminal, Gloria [IQAC-CSIC, Barcelona (Spain). Grupo de biocatalisis Aplicada y biodegradacion; Barcelo, Damia (eds.) [IDAEA-CSIC, Barcelona (Spain). Dept. of Environmental Chemistry; Girona Univ. (Spain). Catalan Inst. for Water Research

    2013-07-01

    A comprehensive review. Written by experts. Richly illustrated. There are a growing number of new chemicals in the environment that represent an ascertained or potential risk. Many of them can be found in sewage sludge and are the subject of this volume. Experts in the field highlight their occurrence and fate, risks of biosolid use, advanced chemical analysis methods, and degradation techniques with a special focus on biodegradation using fungi. In the final chapter conclusions and trends are offered as a point of departure for future studies. The double-disciplinary approach combining environmental analysis and engineering makes the book a valuable and comprehensive source of information for a broad audience, such as environmental chemists and engineers, biotechnologists, ecotoxicologists and professionals responsible for waste and water management.

  7. An analysis of working days contamination in micropulsation measurements

    Directory of Open Access Journals (Sweden)

    M. Vellante

    1998-06-01

    Full Text Available A long term analysis of the power of geomagnetic variations in the micropulsations band at L'Aquila (Italy revealed a weekly variation represented by an increased level of power in the working days with respect to Sundays. The maximum increase, by a factor of ~1.2, occurs during morning hours in the 100-500 Hz band. A daily-light-saving time effect has been also identified. Some implications on a wider scientific context are discussed.

  8. Analysis of molecular interactions in solid dosage forms; challenge to molecular pharmaceutics.

    Science.gov (United States)

    Yamamoto, Keiji; Limwikrant, Waree; Moribe, Kunikazu

    2011-01-01

    The molecular states of active pharmaceutical ingredients (APIs) in pharmaceutical dosage forms strongly affect the properties and quality of a drug. Various important fundamental physicochemical studies were reviewed from the standpoint of molecular pharmaceutics. Mechanochemical effects were evaluated in mixtures of APIs and pharmaceutical additives. Amorphization, complex formation and nanoparticle formation are observed after grinding process depending on the combination of APIs and pharmaceutical additives. Sealed-heating method and mesoporous materials have been used to investigate drug molecular interactions in dosage forms. Molecular states have been investigated using powder X-ray diffraction, thermal analysis, IR, solid state fluorometry, and NMR.

  9. Bench-scale optimization of bioaugmentation strategies for treatment of soils contaminated with high molecular weight polyaromatic hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Straube, W.l.; Jones-Meehan, J.; Pritchard, P.H.; Jones, W.R. [University of Maryland Biotechnology Institute, Baltimore, MD (United States). Center of Marine Biotechnology

    1999-07-01

    The chemical composition of crude oil, creosote, and refined petroleum includes hundreds of different alkanes and aromatic hydrocarbons, among which are the carcinogenic polycyclic aromatic hydrocarbons (PAHs). Some compounds in hydrocarbon-contaminated soils are rapidly removed by the activities of autochthonous bacterial populations while other PAHs, especially those with four or more fused aromatic rings, are refractory to biodegradation. The persistence of high molecular weight of polyaromatic hydrocarbons (hPAHs) in soils implies either that their low solubility renders them poorly available to bacteria, or that autochthonous bacteria do not contain the metabolic or co-metabolic pathways required for their degradation or both. The rate and extent of PAH degradation in contaminated soil is not always predictable for standard biological treatment strategies. This study examines a matrix of treatments suitable for land farming in order to identify those that maximize the removal of hPAHs. The treatments include those intended to increase the bioavailability of hPAH, such as additions of biosurfactant-producing bacteria (i.e. Pseudomonas aeruginosa No. 64) and addition of light oils, as well as treatments intended to increase the metabolic potential of the bacterial community. The latter includes the addition of inorganic nutrients and bacterial strains capable of degrading hPAHs co-metabolically (i.e. Sphingomonas paucimobilis EPA 505). The efficacy of immobilizing PAH-degrading bacteria on vermiculite is also considered, as will be the monitoring of leachate for biodegradation of PAHs in a simulated land farming operation. 17 refs., 4 figs.

  10. Statistical analysis of molecular signal recording.

    Directory of Open Access Journals (Sweden)

    Joshua I Glaser

    Full Text Available A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a "molecular ticker tape", in which an engineered DNA polymerase (DNAP writes time-varying signals into DNA in the form of nucleotide misincorporation patterns. Here, we define a theoretical framework quantifying the expected capabilities of molecular ticker tapes as a function of experimental parameters. We present a decoding algorithm for estimating time-dependent input signals, and DNAP kinetic parameters, directly from misincorporation rates as determined by sequencing. We explore the requirements for accurate signal decoding, particularly the constraints on (1 the polymerase biochemical parameters, and (2 the amplitude, temporal resolution, and duration of the time-varying input signals. Our results suggest that molecular recording devices with kinetic properties similar to natural polymerases could be used to perform experiments in which neural activity is compared across several experimental conditions, and that devices engineered by combining favorable biochemical properties from multiple known polymerases could potentially measure faster phenomena such as slow synchronization of neuronal oscillations. Sophisticated engineering of DNAPs is likely required to achieve molecular recording of neuronal activity with single-spike temporal resolution over experimentally relevant timescales.

  11. Architecture and Performance Analysis of General Bio-Molecular Networks

    Science.gov (United States)

    2012-01-14

    General Bio -Molecular Networks Contract/Grant #: FA9550-10-1-0128 Table of Contents...14-10-2011 4. TITLE AND SUBTITLE Architecture and Performance Analysis of Bio -Molecular Network 5a. CONTRACT NUMBER FA9550-10-1-0128 5b...method is expected to be much better, in terms of the running time, for the system with more molecules. 15. SUBJECT TERMS Stochastic Bio -molecular

  12. Bioassessment of contaminant transport and distribution in aquatic ecosystems by chemical analysis of burrowing mayflies (Hexagenia)

    Science.gov (United States)

    Steingraeber, M.T.; Wiener, J.G.

    1995-01-01

    Burrowing mayfly nymphs (Ephemeroptera) inhabit and ingest fine-grained sediments and detritus that may be enriched with metals and persistent organic compounds. The burrowing nymphs can externally adsorb and internally assimilate these contaminants, providing a link for the food chain transfer of potentially toxic substances from sediments to organisms in higher trophic levels. The emergent adults are short-lived and do not feed, thus their gut contents do not contribute greatly to their total contaminant burden. These characteristics make Hexagenia spp. And certain other burrowing mayflies useful for assessing ecosystem contamination. General protocols are presented for the collection, processing and analysis of emergent mayflies to assess the spatial distribution and bioaccumulation of sediment-associated contaminants in aquatic ecosystems. Two essential components of this bioassessment approach are a network of on-site volunteers with the materials and instructions needed to correctly collect and store samples and quality assurance procedures to estimate the accuracy of chemical analyses. The utility of this approach is demonstrated with an example of its application to the Upper Mississippi River (USA). Determination of cadmium, mercury and polychlorinated biphenyl congeners in emergent Hexagenia bilineata from a 1250 km reach of this river revealed (1) several source areas of contaminants and (2) distinct patterns in the bioaccumulation (and apparent sediment-associated transport) of each residue on both small and large spatial scales.

  13. Molecular phylogenetic analysis of Petunia Juss. (Solanaceae).

    Science.gov (United States)

    Kulcheski, Franceli R; Muschner, Valéria C; Lorenz-Lemke, Aline P; Stehmann, João R; Bonatto, Sandro L; Salzano, Francisco M; Freitas, Loreta B

    2006-01-01

    Representatives from 11 Petunia Jussieu species in south and southeast Brazil were compared with two Calibrachoa La Llave & Lex., one Bouchetia Dunal, and two Nierembergia Ruiz & Pav. taxa in relation to DNA molecular variability. A total of 4532 base pairs related to one nuclear, five plastidial and one mitochondrial systems was investigated. Petunia and Calibrachoa, although separated among themselves, clearly differentiate from the two other genera. Despite the fact that the Petunia species do not show marked molecular differences, they can be separated in two complexes, in good agreement with altitude data. Petunia + Calibrachoa should have diverged from other clades at about 25 million years before present.

  14. Molecular and structural analysis of viscoelastic properties

    Science.gov (United States)

    Yapp, Rebecca D.; Kalyanam, Sureshkumar; Insana, Michael F.

    2007-03-01

    Elasticity imaging is emerging as an important tool for breast cancer detection and monitoring of treatment. Viscoelastic image contrast in breast lesions is generated by disease specific processes that modify the molecular structure of connective tissues. We showed previously that gelatin hydrogels exhibit mechanical behavior similar to native collagen found in breast tissue and therefore are suitable as phantoms for elasticity imaging. This paper summarizes our study of the viscoelastic properties of hydrogels designed to discover molecular-scale sources of elasticity image contrast.

  15. Selective removal of Cu(Ⅱ) from contaminated water using molecularly imprinted polymer

    Institute of Scientific and Technical Information of China (English)

    Jingyao QI; Xin LI; Ying LI; Jianhua ZHU; Liangsheng QIANG

    2008-01-01

    A synthetic molecularly imprinted polymer (MIP) was prepared by noncovalent imprinting technique for the selective removal of Cu2+ from aqueous solutions. In the preparation of imprinted polymer, Cu2+ was used as the template, oleic acid as the functional monomer and divinylbenzene as the cross-linker. The surface morphol-ogies and characteristics of the MIP were determined by BET, scanning electron microscopy (SEM), FTIR and energy dispersive X-ray spectrometer (EDS). The proper adsorption and selective recognition ability of the MIP were studied by an equilibrium-adsorption method. In general, the removal efficiency of Cu2+ increased rapidly with pH from 2 to 7 and decreased at a pH 8. The removal efficiency of Cu2+ increased with temperature from 25℃ to 50℃. Competitive adsorption studies showed that the coexisting cations have no obvious influence on the adsorption of Cu2+. In addition, the variation in the adsorption ability of the MIP that was repeatedly used was investigated, and it showed excellent reproducibility.

  16. Removal of probable human carcinogenic polycyclic aromatic hydrocarbons from contaminated water using molecularly imprinted polymer.

    Science.gov (United States)

    Krupadam, Reddithota J; Khan, Muntazir S; Wate, Satish R

    2010-02-01

    A molecularly imprinted polymer (MIP) adsorbent for carcinogenic polycyclic aromatic hydrocarbons (PAHs) was prepared using a non-covalent templating technique. MIP particles sized from 2 to 5 microm were synthesized in acetonitrile by using six PAHs mix as a template, methacrylic acid as the functional monomer, and ethylene glycol dimethacrylate as the cross-linker. When compared with the non-imprinted polymer (NIP), the MIP showed an excellent affinity towards PAHs in aqueous solution with binding capacity (B(max)) of 687 microg g(-1)MIP, imprinting effect of 6, and a dissociation constant of 24 microM. The MIP exhibited significant binding affinity towards PAHs even in the presence of environmental parameters such as dissolved organic matter (COD) and total dissolved inorganic solids (TDS), suggesting that this material may be appropriate for removal of carcinogenic PAHs. The feasibility of removing PAHs from water by the MIP demonstrated using groundwater spiked with PAHs. In addition, the MIP reusability without any deterioration in performance was demonstrated at least ten repeated cycles.

  17. Selective removal of diclofenac from contaminated water using molecularly imprinted polymer microspheres.

    Science.gov (United States)

    Dai, Chao-Meng; Geissen, Sven-Uwe; Zhang, Ya-Lei; Zhang, Yong-Jun; Zhou, Xue-Fei

    2011-06-01

    A molecularly imprinted polymer (MIP) was synthesized by precipitation polymerization using diclofenac (DFC) as a template. Binding characteristics of the MIP were evaluated using equilibrium binding experiments. Compared to the non-imprinted polymer (NIP), the MIP showed an outstanding affinity towards DFC in an aqueous solution with a binding site capacity (Q(max)) of 324.8 mg/g and a dissociation constant (K(d)) of 3.99 mg/L. The feasibility of removing DFC from natural water by the MIP was demonstrated by using river water spiked with DFC. Effects of pH and humic acid on the selectivity and adsorption capacity of MIP were evaluated in detail. MIP had better selectivity and higher adsorption efficiency for DFC as compared to that of powdered activated carbon (PAC). In addition, MIP reusability was demonstrated for at least 12 repeated cycles without significant loss in performance, which is a definite advantage over single-use activated carbon. Copyright © 2011. Published by Elsevier Ltd.

  18. Molecular cytogenetics and its applications to soft tissue tumor analysis.

    Science.gov (United States)

    D'Amato, L

    1995-01-01

    Cytogenetic analyses have demonstrated the association of specific chromosomal changes with particular types of soft tissue tumors. This work describes the molecular cytogenetic approaches to genetic analysis of these tumors. It illustrates how molecular cytogenetics may provide a rapid and sensitive method of diagnosis and can contribute to identify specific genes implied in the aetiology of soft tissue tumors.

  19. Molecular diagnostics and phylogenetic analysis of 'Candidatus ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-02

    Nov 2, 2009 ... on molecular diagnostics and validation of phytoplasma association with symptomatic ... Southern hybridization of banana phytoplasma 16SrRNA gene. The 16S rRNA gene ... Multi-Imager (Bio-Rad). Cloning and sequencing ...

  20. Advanced sample preparation for the molecular quantification of Staphylococcus aureus in artificially and naturally contaminated milk.

    Science.gov (United States)

    Aprodu, Iuliana; Walcher, Georg; Schelin, Jenny; Hein, Ingeborg; Norling, Börje; Rådström, Peter; Nicolau, Anca; Wagner, Martin

    2011-03-01

    Sample treatment is an essential element when using real-time PCR for quantification of pathogens directly on food samples. This study comparatively evaluated three different principles of sample treatment, i.e. immunomagnetic separation based on phage-derived cell wall binding molecules, matrix solubilization and flotation, in order to establish their suitability for quantifying low numbers of Staphylococcus aureus in milk. All three procedures succeeded to remove S. aureus from the milk matrix, either raw or pasteurized, and, as a result of the concentration of the target cells, minimized the effect of milk associated PCR inhibitors. Sample preparation based on immunomagnetic separation albeit of being user friendly, specific and rapid, failed to allow quantification of low and medium numbers (<10(4)CFU) of S. aureus. In a mastitic milk model cell wall binding domain (CBD)-based target cell extraction revealed results most closely matching those derived from culture-based quantification. Both matrix lysis and flotation allowed quantification of S. aureus at a level of 1-10 cells per ml. Both methods resulted in higher numbers of bacterial cell equivalents (bce) than plating could reveal. Since both methods harvest cells that have been subjected to either mechanical and chemical stresses before quantification, we concluded that the higher bce numbers resulted from a disaggregation of S. aureus clusters initially present in the inoculum. Conclusively, since likely each S. aureus cell of a toxigenic strain contributes to enterotoxin production, molecular quantification could provide an even more realistic impact assessment in outbreak investigations than plating does.

  1. Landfill leachate treatment by MBR: Performance and molecular weight distribution of organic contaminant

    Institute of Scientific and Technical Information of China (English)

    CHEN Shaohua; LIU Junxin

    2006-01-01

    A membrane bioreactor (MBR) with an air-lift bioreactor and gravity flow is applied to'treating landfill leachate. More than 99% of BOD5 (biochemical oxygen demand for five days) removal efficiency is achieved with less than 35 mg/L of BOD5 in the effluent at less than 1.71 kg BOD5/m3.d of BOD5 loading rate. When DO (dissolved oxygen) is maintained at the range of 2.3-2.8 mg/L and the loading rate of NH4+-N (ammonium nitrogen) is kept at 0.16-0.24 kg NH4+-N/m3.d, the NH4+-N in the effluent is less than 15 mg/L. However, compared with high removal rates of BOD5 and NH4+-N, the removal efficiency of soluble chemical oxygen demand (SCOD)varies between 70% and 96%. The investigation of molecular weight (MW) distribution has been carried out by the gel permeation chromatography (GPC) so as to understand the fate of organic matters in the MBR treating of landfill leachate. Results indicate that organic matters of the landfill leachate are composed of a high MW fraction (MW of the peak, MWp =11480-13182 Da) and a low MW fraction (MWp =158-275 Da). The high MW fraction is not biodegradable, but can be decreased with microfiltration membrane. The most of the low MW fraction is biodegradable, but the residue of the low MW fraction is able to permeate through the membrane, thus resulting in high SCOD in the effluent of the MBR.

  2. Identifying avian sources of faecal contamination using sterol analysis.

    Science.gov (United States)

    Devane, Megan L; Wood, David; Chappell, Andrew; Robson, Beth; Webster-Brown, Jenny; Gilpin, Brent J

    2015-10-01

    Discrimination of the source of faecal pollution in water bodies is an important step in the assessment and mitigation of public health risk. One tool for faecal source tracking is the analysis of faecal sterols which are present in faeces of animals in a range of distinctive ratios. Published ratios are able to discriminate between human and herbivore mammal faecal inputs but are of less value for identifying pollution from wildfowl, which can be a common cause of elevated bacterial indicators in rivers and streams. In this study, the sterol profiles of 50 avian-derived faecal specimens (seagulls, ducks and chickens) were examined alongside those of 57 ruminant faeces and previously published sterol profiles of human wastewater, chicken effluent and animal meatwork effluent. Two novel sterol ratios were identified as specific to avian faecal scats, which, when incorporated into a decision tree with human and herbivore mammal indicative ratios, were able to identify sterols from avian-polluted waterways. For samples where the sterol profile was not consistent with herbivore mammal or human pollution, avian pollution is indicated when the ratio of 24-ethylcholestanol/(24-ethylcholestanol + 24-ethylcoprostanol + 24-ethylepicoprostanol) is ≥0.4 (avian ratio 1) and the ratio of cholestanol/(cholestanol + coprostanol + epicoprostanol) is ≥0.5 (avian ratio 2). When avian pollution is indicated, further confirmation by targeted PCR specific markers can be employed if greater confidence in the pollution source is required. A 66% concordance between sterol ratios and current avian PCR markers was achieved when 56 water samples from polluted waterways were analysed.

  3. MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH

    Science.gov (United States)

    Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000Molecular Analysis of Human Spermatozoa: Potential for Infertility ResearchDavid Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...

  4. MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH

    Science.gov (United States)

    Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000Molecular Analysis of Human Spermatozoa: Potential for Infertility ResearchDavid Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...

  5. Physiological response, molecular analysis and water use efficiency ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... Molecular analysis of three hybrids revealed the possibility of introgressing the ...... complex and depends on both biophysical and economic ... Grant RF, Jackson BS, Kiniry KR, Arkin GF (1989) Water deficit timing effects on ...

  6. Combined effects of low-molecular-weight organic acids on mobilization of arsenic and lead from multi-contaminated soils.

    Science.gov (United States)

    Onireti, Olaronke O; Lin, Chuxia; Qin, Junhao

    2017-03-01

    A batch experiment was conducted to examine the combined effects of three common low-molecular-weight organic acids (LMWOAs) on the mobilization of arsenic and lead in different types of multi-contaminated soils. The capacity of individual LMWOAs (at a same molar concentration) to mobilize soil-borne As and Pb varied significantly. The combination of the organic acids did not make a marked "additive" effect on the mobilization of the investigated three elements. An "antagonistic" effect on element mobilization was clear in the treatments involving oxalic acid for some soils. The acid strength of a LMWOA did not play an important role in controlling the mobilization of elements. While the mobilization of As and Pb was closely associated with the dissolution of soil-borne Fe, soil properties such as original soil pH, organic matter contents and the total amount of the element relative to the total Fe markedly complicated the mobility of that element. Aging led to continual consumption of proton introduced from addition of LMWOAs and consequently caused dramatic changes in solution-borne Fe, which in turn resulted in change in As and Pb in the soil solution though different elements behaved differently.

  7. Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis

    CERN Document Server

    Zhu, Jinglong; Site, Luigi Delle

    2016-01-01

    Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in the way the change of molecular resolution is made in a buffer/transition region. In particular a central question concerns the possibility of the existence of a global Hamiltonian which, by describing the change of resolution, is at the same time physically consistent, mathematically well defined and numerically accurate. In this paper we present an asymptotic analysis of the adaptive process complemented by numerical results and show that under certain mathematical conditions a Hamiltonian, which is physically consistent and numerically accurate, may exist. \\blue{Such conditions show that molecular simulations in the current computational implementation require systems of large size and thus a Hamiltonian approach as the one proposed, at this stage, would not be practica...

  8. Gas flow analysis during thermal vacuum test of a spacecraft. [self contamination of IMP spacecraft

    Science.gov (United States)

    Scialdone, J. J.

    1974-01-01

    The self-contamination of the IMP-H spacecraft, while it was undergoing thermal and solar vacuum tests, has been investigated in conjunction with the outgassing evaluation and detection of molecular flow anomalies occurring in the test chamber. The pressures indicated by two tubulated ionization gauges were used to calculate flow kinetics in the vacuum chamber. The fluxes of emitted molecules and chamber wall reflected molecules were monitored during the entire test. Representative equations and graphs are presented. Test results indicate that from 3 to 9 of every 100 emitted molecules returned to the spacecraft surface; that self-contamination by noncondensable gases was more severe than that by condensable gases; and that outgassing of the spacecraft was approximately 1.18 x 0.01 g/s after 10 hours and 1.18 x 0.001 after 90 hours of vacuum exposure. Testing deficiencies have been identified, and the type and location of instruments required to measure the outgassing, the degree of contamination, and return flow are discussed.

  9. Formalizing the definition of meta-analysis in Molecular Ecology.

    Science.gov (United States)

    ArchMiller, Althea A; Bauer, Eric F; Koch, Rebecca E; Wijayawardena, Bhagya K; Anil, Ammu; Kottwitz, Jack J; Munsterman, Amelia S; Wilson, Alan E

    2015-08-01

    Meta-analysis, the statistical synthesis of pertinent literature to develop evidence-based conclusions, is relatively new to the field of molecular ecology, with the first meta-analysis published in the journal Molecular Ecology in 2003 (Slate & Phua 2003). The goal of this article is to formalize the definition of meta-analysis for the authors, editors, reviewers and readers of Molecular Ecology by completing a review of the meta-analyses previously published in this journal. We also provide a brief overview of the many components required for meta-analysis with a more specific discussion of the issues related to the field of molecular ecology, including the use and statistical considerations of Wright's FST and its related analogues as effect sizes in meta-analysis. We performed a literature review to identify articles published as 'meta-analyses' in Molecular Ecology, which were then evaluated by at least two reviewers. We specifically targeted Molecular Ecology publications because as a flagship journal in this field, meta-analyses published in Molecular Ecology have the potential to set the standard for meta-analyses in other journals. We found that while many of these reviewed articles were strong meta-analyses, others failed to follow standard meta-analytical techniques. One of these unsatisfactory meta-analyses was in fact a secondary analysis. Other studies attempted meta-analyses but lacked the fundamental statistics that are considered necessary for an effective and powerful meta-analysis. By drawing attention to the inconsistency of studies labelled as meta-analyses, we emphasize the importance of understanding the components of traditional meta-analyses to fully embrace the strengths of quantitative data synthesis in the field of molecular ecology. © 2015 John Wiley & Sons Ltd.

  10. Current Measures on Radioactive Contamination in Japan: A Policy Situation Analysis.

    Science.gov (United States)

    Gilmour, Stuart; Miyagawa, Shoji; Kasuga, Fumiko; Shibuya, Kenji

    2016-01-01

    The Great East Japan Earthquake on 11th March 2011 and the subsequent Fukushima Dai-ichi nuclear power plant disaster caused radioactive contamination in the surrounding environment. In the immediate aftermath of the accident the Government of Japan placed strict measures on radio-contamination of food, and enhanced radio-contamination monitoring activities. Japan is a pilot country in the WHO Foodborne Disease Burden Epidemiology Reference Group (FERG), and through this initiative has an opportunity to report on policy affecting chemicals and toxins in the food distribution network. Nuclear accidents are extremely rare, and a policy situation analysis of the Japanese government's response to the Fukushima Dai-ichi nuclear accident is a responsibility of Japanese scientists. This study aims to assess Japan government policies to reduce radio-contamination risk and to identify strategies to strengthen food policies to ensure the best possible response to possible future radiation accidents. We conducted a hand search of all publicly available policy documents issued by the Cabinet Office, the Food Safety Commission, the Ministry of Health, Labor and Welfare (MHLW), the Ministry of Agriculture, Forestry and Fishery (MAFF) and prefectural governments concerning food safety standards and changes to radiation and contamination standards since March 11th, 2011. We extracted information on food shipment and sales restrictions, allowable radio-contamination limits, monitoring activities and monitoring results. The standard for allowable radioactive cesium (Cs-134 and Cs-137) of 100 Bq/Kg in general food, 50 Bq/Kg in infant formula and all milk products, and 10 Bq/Kg in drinking water was enforced from April 2012 under the Food Sanitation Law, although a provisional standard on radio-contamination had been applied since the nuclear accident. Restrictions on the commercial sale and distribution of specific meat, vegetable and fish products were released for areas at risk of

  11. Quantitative FE-EPMA measurement of formation and inhibition of carbon contamination on Fe for trace carbon analysis.

    Science.gov (United States)

    Tanaka, Yuji; Yamashita, Takako; Nagoshi, Masayasu

    2017-04-01

    Hydrocarbon contamination introduced during point, line and map analyses in a field emission electron probe microanalysis (FE-EPMA) was investigated to enable reliable quantitative analysis of trace amounts of carbon in steels. The increment of contamination on pure iron in point analysis is proportional to the number of iterations of beam irradiation, but not to the accumulated irradiation time. A combination of a longer dwell time and single measurement with a liquid nitrogen (LN2) trap as an anti-contamination device (ACD) is sufficient for a quantitative point analysis. However, in line and map analyses, contamination increases with irradiation time in addition to the number of iterations, even though the LN2 trap and a plasma cleaner are used as ACDs. Thus, a shorter dwell time and single measurement are preferred for line and map analyses, although it is difficult to eliminate the influence of contamination. While ring-like contamination around the irradiation point grows during electron-beam irradiation, contamination at the irradiation point increases during blanking time after irradiation. This can explain the increment of contamination in iterative point analysis as well as in line and map analyses. Among the ACDs, which are tested in this study, specimen heating at 373 K has a significant contamination inhibition effect. This technique makes it possible to obtain line and map analysis data with minimum influence of contamination. The above-mentioned FE-EPMA data are presented and discussed in terms of the contamination-formation mechanisms and the preferable experimental conditions for the quantification of trace carbon in steels. © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Bioremediation of marine sediments contaminated by hydrocarbons: experimental analysis and kinetic modeling.

    Science.gov (United States)

    Beolchini, Francesca; Rocchetti, Laura; Regoli, Francesco; Dell'Anno, Antonio

    2010-10-15

    This work deals with bioremediation experiments on harbor sediments contaminated by aliphatic and polycyclic aromatic hydrocarbons (PAHs), investigating the effects of a continuous supply of inorganic nutrients and sand amendments on the kinetics of microbial growth and hydrocarbon degradation. Inorganic nutrients stimulated microbial growth and enhanced the biodegradation of low and high molecular weight hydrocarbons, whereas sand amendment increased only the removal of high molecular weight compounds. The simultaneous addition of inorganic nutrients and sand provided the highest biodegradation (>70% for aliphatic hydrocarbons and 40% for PAHs). A semi-empirical kinetic model was successfully fitted to experimental temporal changes of hydrocarbon residual concentrations and microbial abundances. The estimated values for parameters allowed to calculate a doubling time of 2.9 d and a yield coefficient biomass/hydrocarbons 0.39 g C biomass g-1C hydrocarbons, for the treatment with the highest hydrocarbon biodegradation yield. A comparison between the organic carbon demand and temporal profiles of hydrocarbons residual concentration allowed also to calculate the relative contribution of contaminants to carbon supply, in the range 5-32%. This suggests that C availability in the sediments, influencing prokaryotic metabolism, may have cascade effects on biodegradation rates of hydrocarbons. Even if these findings do not represent a general rule and site-specific studies are needed, the approach used here can be a relevant support tool when designing bioremediation strategies on site.

  13. Mathematical analysis and calculation of molecular surfaces

    Science.gov (United States)

    Quan, Chaoyu; Stamm, Benjamin

    2016-10-01

    In this article we derive a complete characterization of the Solvent Excluded Surface (SES) for molecular systems including a complete characterization of singularities of the surface. The theory is based on an implicit representation of the SES, which, in turn, is based on the signed distance function to the Solvent Accessible Surface (SAS). All proofs are constructive so that the theory allows for efficient algorithms in order to compute the area of the SES and the volume of the SES-cavity, or to visualize the surface. Further, we propose to refine the notion of SAS and SES in order to take inner holes in a solute molecule into account or not.

  14. Standard Practice for Processing Aerospace Liquid Samples for Particulate Contamination Analysis Using Membrane Filters

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2008-01-01

    1.1 This practice covers the processing of liquids in preparation for particulate contamination analysis using membrane filters and is limited only by the liquid-to-membrane filter compatibility. 1.2 The practice covers the procedure for filtering a measured volume of liquid through a membrane filter. When this practice is used, the particulate matter will be randomly distributed on the filter surface for subsequent contamination analysis methods. 1.3 The practice describes procedures to allow handling particles in the size range between 2 and 1000 μm with minimum losses during handling. 1.4 The values stated in SI units are to be regarded as standard. No other units of measurement are included in this standard.

  15. Analysis and Derivation of Allocations for Fiber Contaminants in Liquid Bipropellant Systems

    Science.gov (United States)

    Lowrey, N. M; ibrahim, K. Y.

    2012-01-01

    An analysis was performed to identify the engineering rationale for the existing particulate limits in MSFC-SPEC-164, Cleanliness of Components for Use in Oxygen, Fuel, and Pneumatic Systems, determine the applicability of this rationale to fibers, identify potential risks that may result from fiber contamination in liquid oxygen/fuel bipropellant systems, and bound each of these risks. The objective of this analysis was to determine whether fiber contamination exceeding the established quantitative limits for particulate can be tolerated in these systems and, if so, to derive and recommend quantitative allocations for fibers beyond the limits established for other particulate. Knowledge gaps were identified that limit a complete understanding of the risk of promoted ignition from an accumulation of fibers in a gaseous oxygen system.

  16. Thermal Analysis of Brazing Seal and Sterilizing Technique to Break Contamination Chain for Mars Sample Return

    Science.gov (United States)

    Bao, Xiaoqi; Badescu, Mircea; Bar-Cohen, Yoseph

    2015-01-01

    The potential to return Martian samples to Earth for extensive analysis is in great interest of the planetary science community. It is important to make sure the mission would securely contain any microbes that may possibly exist on Mars so that they would not be able to cause any adverse effects on Earth's environment. A brazing sealing and sterilizing technique has been proposed to break the Mars-to-Earth contamination chain. Thermal analysis of the brazing process was conducted for several conceptual designs that apply the technique. Control of the increase of the temperature of the Martian samples is a challenge. The temperature profiles of the Martian samples being sealed in the container were predicted by finite element thermal models. The results show that the sealing and sterilization process can be controlled such that the samples' temperature is maintained below the potentially required level, and that the brazing technique is a feasible approach to break the contamination chain.

  17. Multiple Factor Analysis and k-Means Clustering-Based Classification of the DOE Groundwater Contaminant Database

    Science.gov (United States)

    Faybishenko, B.; Hazen, T. C.

    2009-12-01

    A proper classification of the plume characteristics is critical for selecting the most suitable characterization, monitoring, and remediation technologies. To perform a statistical analysis of the different groundwater plume characteristics, we used the DOE Groundwater Database, including 221 groundwater plumes located at 60 DOE sites. To classify the plume characteristics, we used a multiple factor analysis (MFA), including a principal component analysis (PCA) of quantitative plume characteristics and a multiple correspondence analysis (MCA) of qualitative plume characteristics. The input parameters used for the statistical analysis are: the presence of eight types of contaminant groups—chlorinated hydrocarbons, fuels, explosives, sulfates, nitrates, metals, tritium, and radioisotopes; a number and associations of contaminant groups; a contamination severity index (based on the association of contaminant groups and complexity of remediation); contaminant mass and plume volumes; groundwater depth and velocities; and climatic conditions. The input variables are also partitioned into the active and supplementary plume characteristics. Statistical results include the evaluation of the correlation matrix between the groups of variables and individual plume characteristics. From the results of the MFA, the first four factors can be used to describe the variability of the basic plume characteristics. The contaminant severity index and the number of contaminant groups provide a major contribution to the 1st factor; the types of contaminant groups and carbon tetrachloride concentrations provide the major contribution to the 2nd factor. The contribution of the supplementary data (climate and plume depth and velocity) is insignificant. The presence of radioactive contaminants is mostly related to the 1st factor; the presence of sulfates, and to a lesser degree the presence of nitrates and metals, is related to the 2nd factor. The strongest relationship is, as expected

  18. Analysis of Pollution Hazard Intensity: A Spatial Epidemiology Case Study of Soil Pb Contamination

    Science.gov (United States)

    Ha, Hoehun; Rogerson, Peter A.; Olson, James R.; Han, Daikwon; Bian, Ling; Shao, Wanyun

    2016-01-01

    Heavy industrialization has resulted in the contamination of soil by metals from anthropogenic sources in Anniston, Alabama. This situation calls for increased public awareness of the soil contamination issue and better knowledge of the main factors contributing to the potential sources contaminating residential soil. The purpose of this spatial epidemiology research is to describe the effects of physical factors on the concentration of lead (Pb) in soil in Anniston AL, and to determine the socioeconomic and demographic characteristics of those residing in areas with higher soil contamination. Spatial regression models are used to account for spatial dependencies using these explanatory variables. After accounting for covariates and multicollinearity, results of the analysis indicate that lead concentration in soils varies markedly in the vicinity of a specific foundry (Foundry A), and that proximity to railroads explained a significant amount of spatial variation in soil lead concentration. Moreover, elevated soil lead levels were identified as a concern in industrial sites, neighborhoods with a high density of old housing, a high percentage of African American population, and a low percent of occupied housing units. The use of spatial modelling allows for better identification of significant factors that are correlated with soil lead concentrations. PMID:27649221

  19. Analysis of Pollution Hazard Intensity: A Spatial Epidemiology Case Study of Soil Pb Contamination

    Directory of Open Access Journals (Sweden)

    Hoehun Ha

    2016-09-01

    Full Text Available Heavy industrialization has resulted in the contamination of soil by metals from anthropogenic sources in Anniston, Alabama. This situation calls for increased public awareness of the soil contamination issue and better knowledge of the main factors contributing to the potential sources contaminating residential soil. The purpose of this spatial epidemiology research is to describe the effects of physical factors on the concentration of lead (Pb in soil in Anniston AL, and to determine the socioeconomic and demographic characteristics of those residing in areas with higher soil contamination. Spatial regression models are used to account for spatial dependencies using these explanatory variables. After accounting for covariates and multicollinearity, results of the analysis indicate that lead concentration in soils varies markedly in the vicinity of a specific foundry (Foundry A, and that proximity to railroads explained a significant amount of spatial variation in soil lead concentration. Moreover, elevated soil lead levels were identified as a concern in industrial sites, neighborhoods with a high density of old housing, a high percentage of African American population, and a low percent of occupied housing units. The use of spatial modelling allows for better identification of significant factors that are correlated with soil lead concentrations.

  20. Analysis of higher harmonic contamination with a modified approach using a grating analyser

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Rajkumar, E-mail: rkg@rract.gov.in; Modi, Mohammed H.; Lodha, G. S. [X-ray Optics Section, Indus Synchrotrons Utilization Division, Raja Ramanna Centre for Advanced Technology, Indore 452 013 (India); Kumar, M.; Chakera, J. A. [Laser Plasma Division, Raja Ramanna Centre for Advanced Technology, Indore 452 013 (India)

    2014-04-15

    Soft x-ray spectra of the toroidal grating monochromator (TGM) at the reflectivity beamline of Indus-1 synchrotron source are analyzed for higher harmonic contribution. A diffraction grating of central line spacing 1200 l/mm is used to disperse the monochromatic beam received from TGM to quantify the harmonic contents in the 50–360 Å wavelength range. In order to calculate the harmonic contamination, conventionally the intensity of higher order peak is divided by first order peak intensity of the desired wavelength. This approach is found to give wrong estimate as first order peak itself is overlapped by higher order peaks. In the present study, a modified approach has been proposed to calculate harmonic contamination where the intensity contributions of overlapping orders have been removed from the first order diffraction peak of the desired wavelength. It is found that the order contamination in the TGM spectra is less than 15% in the wavelength range of 90–180 Å. The total harmonic contribution increases from 6%–60% in the wavelength range of 150–260 Å. The critical wavelength of Indus-1 is 61 Å hence the harmonic contamination below 90 Å is significantly low. The results obtained with modified approach match well with those obtained by quantitative analysis of multilayer reflectivity data. The obtained higher harmonics data are used to fit the transmission of aluminum edge filter in the 120–360 Å wavelength range.

  1. Radionuclide contaminated soil: Laboratory study and economic analysis of soil washing. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fuhrmann, M.; Zhou, H.; Patel, B.; Bowerman, B.; Brower, J.

    1996-05-20

    The objective of the work discussed in this report is to determine if soil washing is a feasible method to remediate contaminated soils from the Hazardous Waste Management Facility (HWMF) at Brookhaven National Laboratory (BNL). The contaminants are predominantly Cs-137 and Sr-90. The authors have assumed that the target activity for Cs-137 is 50 pCi/g and that remediation is required for soils having greater activities. Cs-137 is the limiting contaminant because it is present in much greater quantities than Sr-90. This work was done in three parts, in which they: estimated the volume of contaminated soil as a function of Cs-137 content, determined if simple removal of the fine grained fraction of the soil (the material that is less than 0.063 mm) would effectively reduce the activity of the remaining soil to levels below the 50 pCi/g target, assessed the effectiveness of chemical and mechanical (as well as combinations of the two) methods of soil decontamination. From this analysis the authors were then able to develop a cost estimate for soil washing and for a baseline against which soil washing was compared.

  2. Thermodynamic analysis of the theoretical energy consumption in the removal of organic contaminants by physical methods

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The essential requirements for evaluating the sustainable development of a system and the thermodynamic framework of the energy conservation mechanism in the waste-removal process are proposed.A thermodynamic method of analysis based on the first and second laws of thermodynamics is suggested as a means to analyze the theoretical energy consumption for the removal of organic contaminants by physical methods.Moreover,the theoretical energy consumption for the removal by physical methods of different kinds of representative organic contaminants with different initial concentrations and amounts is investigated at 298.15 K and 1.01325 × 105 Pa.The results show that the waste treatment process has a high energy consumption and that the theoretical energy consumption for the removal of organic contaminants increases with the decrease of their initial concentrations in aqueous solutions.The theoretical energy consumption for the removal of different organic contaminants varies dramatically.Furthermore,the theoretical energy consumption increases greatly with the increase in the amount to be removed.

  3. Hierarchical Bayesian analysis of censored microbiological contamination data for use in risk assessment and mitigation.

    Science.gov (United States)

    Busschaert, P; Geeraerd, A H; Uyttendaele, M; Van Impe, J F

    2011-06-01

    Microbiological contamination data often is censored because of the presence of non-detects or because measurement outcomes are known only to be smaller than, greater than, or between certain boundary values imposed by the laboratory procedures. Therefore, it is not straightforward to fit distributions that summarize contamination data for use in quantitative microbiological risk assessment, especially when variability and uncertainty are to be characterized separately. In this paper, distributions are fit using Bayesian analysis, and results are compared to results obtained with a methodology based on maximum likelihood estimation and the non-parametric bootstrap method. The Bayesian model is also extended hierarchically to estimate the effects of the individual elements of a covariate such as, for example, on a national level, the food processing company where the analyzed food samples were processed, or, on an international level, the geographical origin of contamination data. Including this extra information allows a risk assessor to differentiate between several scenario's and increase the specificity of the estimate of risk of illness, or compare different scenario's to each other. Furthermore, inference is made on the predictive importance of several different covariates while taking into account uncertainty, allowing to indicate which covariates are influential factors determining contamination.

  4. Modelling suspended-sediment propagation and related heavy metal contamination in floodplains: a parameter sensitivity analysis

    Science.gov (United States)

    Hostache, R.; Hissler, C.; Matgen, P.; Guignard, C.; Bates, P.

    2014-09-01

    Fine sediments represent an important vector of pollutant diffusion in rivers. When deposited in floodplains and riverbeds, they can be responsible for soil pollution. In this context, this paper proposes a modelling exercise aimed at predicting transport and diffusion of fine sediments and dissolved pollutants. The model is based upon the Telemac hydro-informatic system (dynamical coupling Telemac-2D-Sysiphe). As empirical and semiempirical parameters need to be calibrated for such a modelling exercise, a sensitivity analysis is proposed. An innovative point in this study is the assessment of the usefulness of dissolved trace metal contamination information for model calibration. Moreover, for supporting the modelling exercise, an extensive database was set up during two flood events. It includes water surface elevation records, discharge measurements and geochemistry data such as time series of dissolved/particulate contaminants and suspended-sediment concentrations. The most sensitive parameters were found to be the hydraulic friction coefficients and the sediment particle settling velocity in water. It was also found that model calibration did not benefit from dissolved trace metal contamination information. Using the two monitored hydrological events as calibration and validation, it was found that the model is able to satisfyingly predict suspended sediment and dissolve pollutant transport in the river channel. In addition, a qualitative comparison between simulated sediment deposition in the floodplain and a soil contamination map shows that the preferential zones for deposition identified by the model are realistic.

  5. Analysis of Pollution Hazard Intensity: A Spatial Epidemiology Case Study of Soil Pb Contamination.

    Science.gov (United States)

    Ha, Hoehun; Rogerson, Peter A; Olson, James R; Han, Daikwon; Bian, Ling; Shao, Wanyun

    2016-09-14

    Heavy industrialization has resulted in the contamination of soil by metals from anthropogenic sources in Anniston, Alabama. This situation calls for increased public awareness of the soil contamination issue and better knowledge of the main factors contributing to the potential sources contaminating residential soil. The purpose of this spatial epidemiology research is to describe the effects of physical factors on the concentration of lead (Pb) in soil in Anniston AL, and to determine the socioeconomic and demographic characteristics of those residing in areas with higher soil contamination. Spatial regression models are used to account for spatial dependencies using these explanatory variables. After accounting for covariates and multicollinearity, results of the analysis indicate that lead concentration in soils varies markedly in the vicinity of a specific foundry (Foundry A), and that proximity to railroads explained a significant amount of spatial variation in soil lead concentration. Moreover, elevated soil lead levels were identified as a concern in industrial sites, neighborhoods with a high density of old housing, a high percentage of African American population, and a low percent of occupied housing units. The use of spatial modelling allows for better identification of significant factors that are correlated with soil lead concentrations.

  6. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  7. Mechanism Analysis and Propagation Model of Heavy Metals Contamination in Urban Topsoil

    OpenAIRE

    Zhao-wei Wang; Yuan-biao Zhang; Zi-yue Chen; Ke-jia Li; Jia-lin Hu; Yu-jie Liu

    2013-01-01

    In order to further research on the polluting condition and spreading features of heavy metals in urban surface soil, this study makes statistical analysis on indexes of 8 heavy metal concentrations. Then Are GIS geo-statistical analyst was used for Kriging interpolation of each kind of heavy metal concentration before figuring out the spatial distribution. Firstly, heavy metal contamination was analyzed by single-element pollution evaluation and multi-element pollution evaluation, before rat...

  8. Safety analysis report for packaging, onsite, long-length contaminated equipment transport system

    Energy Technology Data Exchange (ETDEWEB)

    McCormick, W.A.

    1997-05-09

    This safety analysis report for packaging describes the components of the long-length contaminated equipment (LLCE) transport system (TS) and provides the analyses, evaluations, and associated operational controls necessary for the safe use of the LLCE TS on the Hanford Site. The LLCE TS will provide a standardized, comprehensive approach for the disposal of approximately 98% of LLCE scheduled to be removed from the 200 Area waste tanks.

  9. Quantification of pressure sensitive adhesive, residual ink, and other colored process contaminants using dye and color image analysis

    Science.gov (United States)

    Roy R. Rosenberger; Carl J. Houtman

    2000-01-01

    The USPS Image Analysis (IA) protocol recommends the use of hydrophobic dyes to develop contrast between pressure sensitive adhesive (PSA) particles and cellulosic fibers before using a dirt counter to detect all contaminants that have contrast with the handsheet background. Unless the sample contains no contaminants other than those of interest, two measurement steps...

  10. Characterization of contaminated soil and groundwater surrounding an illegal landfill (S. Giuliano, Venice, Italy) by principal component analysis and kriging

    Energy Technology Data Exchange (ETDEWEB)

    Critto, Andrea; Carlon, Claudio; Marcomini, Antonio

    2003-04-01

    Information on soil and groundwater contamination was used to develop a site conceptual model and to identify exposure scenarios. - The characterization of a hydrologically complex contaminated site bordering the lagoon of Venice (Italy) was undertaken by investigating soils and groundwaters affected by the chemical contaminants originated by the wastes dumped into an illegal landfill. Statistical tools such as principal components analysis and geostatistical techniques were applied to obtain the spatial distribution of chemical contaminants. Dissolved organic carbon (DOC), SO{sub 4}{sup 2-} and Cl{sup -} were used to trace the migration of the contaminants from the top soil to the underlying groundwaters. The chemical and hydrogeological available information was assembled to obtain the schematic of the conceptual model of the contaminated site capable to support the formulation of major exposure scenarios, which are also provided.

  11. Molecular Identification and Subtype Analysis of Blastocystis.

    Science.gov (United States)

    Stensvold, C Rune; Clark, C Graham

    2016-11-18

    Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites. Recently, a publicly available online facility was developed for quick and standardized identification of subtypes (ribosomal lineages) and subtype alleles (variation within subtypes) based on sequence data obtained by barcoding PCR. Moreover, a modified barcoding approach is now available using nested PCR, which enables detection of mixed subtype infections. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

  12. Time series analysis of contaminant transport in the subsurface: applications to conservative tracer and engineered nanomaterials.

    Science.gov (United States)

    Bai, Chunmei; Li, Yusong

    2014-08-01

    Accurately predicting the transport of contaminants in the field is subject to multiple sources of uncertainty due to the variability of geological settings, the complexity of field measurements, and the scarcity of data. Such uncertainties can be amplified when modeling some emerging contaminants, such as engineered nanomaterials, when a fundamental understanding of their fate and transport is lacking. Typical field work includes collecting concentration at a certain location for an extended period of time, or measuring the movement of plume for an extended period time, which would result in a time series of observation data. This work presents an effort to evaluate the possibility of applying time series analysis, particularly, autoregressive integrated moving average (ARIMA) models, to forecast contaminant transport and distribution in the subsurface environment. ARIMA modeling was first assessed in terms of its capability to forecast tracer transport at two field sites, which had different levels of heterogeneity. After that, this study evaluated the applicability of ARIMA modeling to predict the transport of engineered nanomaterials at field sites, including field measured data of nanoscale zero valent iron and (nZVI) and numerically generated data for the transport of nano-fullerene aggregates (nC60). This proof-of-concept effort demonstrates the possibility of applying ARIMA to predict the contaminant transport in the subsurface environment. Like many other statistical models, ARIMA modeling is only descriptive and not explanatory. The limitation and the challenge associated with applying ARIMA modeling to contaminant transport in the subsurface are also discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Stable isotope fractionation analysis as a tool to monitor biodegradation in contaminated acquifers

    Science.gov (United States)

    Meckenstock, Rainer U.; Morasch, Barbara; Griebler, Christian; Richnow, Hans H.

    2004-12-01

    The assessment of biodegradation in contaminated aquifers has become an issue of increasing importance in the recent years. To some extent, this can be related to the acceptance of intrinsic bioremediation or monitored natural attenuation as a means to manage contaminated sites. Among the few existing methods to detect biodegradation in the subsurface, stable isotope fractionation analysis (SIFA) is one of the most promising approaches which is pronounced by the drastically increasing number of applications. This review covers the recent laboratory and field studies assessing biodegradation of contaminants via stable isotope analysis. Stable isotope enrichment factors have been found that vary from no fractionation for dioxygenase reactions converting aromatic hydrocarbons over moderate fractionation by monooxygenase reactions ( ɛ=-3‰) and some anaerobic studies on microbial degradation of aromatic hydrocarbons ( ɛ=-1.7‰) to larger fractionations by anaerobic dehalogenation reactions of chlorinated solvents ( ɛ=between -5‰ and -30‰). The different isotope enrichment factors can be related to the respective biochemical reactions. Based on that knowledge, we discuss under what circumstances SIFA can be used for a qualitative or even a quantitative assessment of biodegradation in the environment. In a steadily increasing number of cases, it was possible to explain biodegradation processes in the field based on isotope enrichment factors obtained from laboratory experiments with pure cultures and measured isotope values from the field. The review will focus on the aerobic and anaerobic degradation of aromatic hydrocarbons and chlorinated solvents as the major contaminants of groundwater. Advances in the instrumental development for stable isotope analysis are only mentioned if it is important for the understanding of the application.

  14. Compound-Specific Isotope Analysis of Nitroaromatic Contaminant Transformations by Nitroarene Dioxygenases

    Science.gov (United States)

    Pati, Sarah G.; Kohler, Hans-Peter E.; Hofstetter, Thomas B.

    2014-05-01

    Dioxygenation is an important biochemical reaction that often initiates the mineralization of recalcitrant organic contaminants such as nitroaromatic explosives, chlorinated benzenes, and polycyclic aromatic hydrocarbons. However, to assess the extent of dioxygenation in contaminated environments is difficult because of competing transformation processes and further reactions of the dioxygenation products. Compound-specific isotope analysis (CSIA) offers a new approach to reliably quantify biodegradation initiated by dioxygenation based on changes in stable isotope ratios of the pollutant. For CSIA it is essential to know the kinetic isotope effects (KIEs) pertinent to the dioxygenation mechanism of organic contaminants. Unfortunately, the range of KIEs of such reactions is poorly constrained although many dioxygenase enzymes with a broad substrate specificity have been reported. Dioxygenase enzymes usually exhibit complex reaction kinetics involving multiple substrates and substrate-specific binding modes which makes the determination of KIEs challenging. The goal of this study was to explore the magnitude and variability of 13C-, 2H-, and 15N-KIEs for the dioxygenation of one contaminant class, that is nitroaromatic contaminants (NACs). To this end, we investigated the C, H, and N isotope fractionation during the dioxygenation of nitrobenzene (NB), 2-nitrotoluene (2-NT), and 3-nitrotoluene (3-NT) by pure cultures, E. coli clones, cell extracts, and purified enzymes. From isotope fractionations measured in the substrates and reaction products, we determined dioxygenation KIEs for different combinations of the three substrates with nitrobenzene dioxygenase (NBDO) and 2-nitrotoluene dioxygenase (2NTDO). The 13C-, 2H-, and 15N-KIEs for the dioxygenation of NB by NBDO were consistent for all experimental systems considered (i.e., Comamonas sp. Strain JS765, E. coli clones, cell extracts of E. coli clones, and purified NBDO). This observation suggests that the isotope

  15. Different low-molecular-mass organic acids specifically control leaching of arsenic and lead from contaminated soil

    Science.gov (United States)

    Ash, Christopher; Tejnecký, Václav; Borůvka, Luboš; Drábek, Ondřej

    2016-04-01

    Low-molecular-mass organic acids (LMMOA) are of key importance for mobilisation and fate of metals in soil, by functioning as ligands that increase the amount of dissolved metal in solution or by dissociation of metal binding minerals. Column leaching experiments were performed on soil polluted with As and Pb, in order to determine the specificity of LMMOA related release for individual elements, at varying organic acid concentrations. Acetic, citric and oxalic acids were applied in 12 h leaching experiments over a concentration range (0.5-25 mM) to soil samples that represent organic and mineral horizons. The leaching of As followed the order: oxalic > citric > acetic acid in both soils. Arsenic leaching was attributed primarily to ligand-enhanced dissolution of mineral oxides followed by As released into solution, as shown by significant correlation between oxalic and citric acids and content of Al and Fe in leaching solutions. Results suggest that subsurface mineral soil layers are more vulnerable to As toxicity. Leaching of Pb from both soils followed the order: citric > oxalic > acetic acid. Mineral soil samples were shown to be more susceptible to leaching of Pb than samples characterised by a high content of organic matter. The leaching efficiency of citric acid was attributed to formation of stable complexes with Pb ions, which other acids are not capable of. Results obtained in the study are evidence that the extent of As and Pb leaching in contaminated surface and subsurface soil depends significantly on the types of carboxylic acid involved. The implications of the type of acid and the specific element that can be mobilised become increasingly significant where LMMOA concentrations are highest, such as in rhizosphere soil.

  16. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    Science.gov (United States)

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  17. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    Science.gov (United States)

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  18. Quantum Phase Analysis of Field-Free Molecular Alignment

    CERN Document Server

    Yun, Sang Jae; Lee, Jongmin; Nam, Chang Hee

    2015-01-01

    We present quantum mechanical explanations for unresolved phenomena observed in field-free molecular alignment by a femtosecond laser pulse. Quantum phase analysis of molecular rotational states reveals the physical origin of the following phenomena: strong alignment peaks appear periodically, and the temporal shape of each alignment peak changes in an orderly fashion depending on molecular species; the strongest alignment is not achieved at the first peak; the transition between aligned and anti-aligned states is very fast compared to the time scale of rotational dynamics. These features are understood in a unified way analogous to that describing a carrier-envelope-phase-stabilized mode-locked laser.

  19. In situ extraction and analysis of volatiles and simple molecules in interplanetary dust particles, contaminants, and silica aerogel

    Science.gov (United States)

    Hartmetz, C. P.; Gibson, E. K., Jr.; Blanford, G. E.

    1990-01-01

    Results are presented for the analyses of eight interplanetary dust particles (IDPs) for the volatile elements H, C, N, O, and S and their molecular species, as well as of the volatiles associated with contaminants (i.e., the compounds used during the collection and curation of IDPs), which were carried out using a laser microprobe interfaced with a quadrupole mass spectrometer. It was found that the volatile species from contaminants were always present in the spectra of IDPs. Despite the contamination problems, several indigenous molecular species could be identified, including OH, CO2 or C2H4, C and CS2, CO2 along with CO (possibly indicating the presence of carbonate), H2S, SO, COS, SO2, and CS2. In some cases, the sulfur components can be attributed to aerosols; however, in one of the IDPs, the presence of H2S, SO, COS, and SO2 indicates the possible presence of elemental sulfur.

  20. Analysis and evaluation methods for chemical contaminants in clean room air; Kagaku osen no bunseki hyokaho clean room kukichu no kagaku osen busshitsu ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Fujimoto, T.

    1998-07-31

    As for, chemical contamination in a cleanroom air has taken up as a important problem. As the main source is building materials, after construction the execution of countermeasures is difficult. Out-gas evaluation and selection in building materials, chemical filters for removing specific organic matter and so on, are a large technical theme in the future and analytical techniques corresponding them become necessary. In this paper, analytical methods of airborne molecular contaminants (AMCs) are introduced. Main samples are AMCs in cleanroom atmosphere, on silicon wafer surface and out-gas from raw materials for cleanroom construction materials such as sealant, plastics and so on. Analytical methods consist of quantification of inorganic compounds, organic compounds and identification of abnormal spot with local/surface analysis. Various interesting findings with analytical data are obtained and investigated. 22 refs., 6 figs., 5 tabs.

  1. Molecular analysis of cytoplasmic male sterility

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, M.R.

    1990-01-01

    The ultimate aims of the project are to understand the molecular mechanism of the disruption in pollen development which occurs in cytoplasmic male sterile plants and to understand the control of respiratory energy flow in the higher plant cell. A mitochondrial locus termed S-pcf segregates with sterility and with an alteration in respiration in Petunia. This cloned locus contains three genes, an abnormal fused gene termed pcf, a gene for a subunit of an NADH dehydrogenase complex, and a small ribosomal subunit protein. The pcf gene is comprised of partial sequences of ATPase subunit 9, cytochrome oxidase subunit II, and an unidentified reading frame. Components of the S-Pcf locus will be introduced into the nuclear of a fertile genotype under the control of appropriate regulatory signals, and polypeptide products of introduced genes will be directed to the mitochondrion with a transit peptide. By examining transgenic plants, we can determine what elements of the locus are critical for altered respiration or sterility. Such knowledge could explain how mitochondrial DNA affects pollen development in the large number of plant species which exhibit the agronomically important trait of male sterility. 10 refs., 3 figs.

  2. GC-MS ANALYSIS OF STICKY CONTAMINANTS IN A DEINKING PULPING LINE

    Directory of Open Access Journals (Sweden)

    Yang Gao,

    2012-04-01

    Full Text Available Pulps were sampled from three major points of a deinking pulping line and classified as fibers fraction, fines fraction, and aqueous phase, respectively, then extracted with tetrahydrofuran (THF or methyl tert-butyl ether (MTBE. Sticky contaminants in the extractives were examined by GC-MS analysis. The results showed that the contaminants can be grouped as adhesive substances, wood extractives, lignin-derivatives, and other organic acids, of which the adhesive substances were accounted as the major component. Contents of sticky components in each group and their removal were further evaluated according to the related unit operation. Adhesives remaining in fibers and fines fractions were removed by the post-flotation. Wood extractives and degraded residual lignins were also released to some extent from pulp fibers during heat-dispersing, and then removed during the post-flotation.

  3. Analysis of TQCM surface contamination adsorbed during the Spacelab I Mission

    Science.gov (United States)

    McKeown, D.; Fountain, J. A.; Cox, V. H.; Peterson, R. V.

    The Temperature-Controlled Quartz Crystal Microbalance (TQCM) system was flown on the Spacelab I Mission as part of the Induced Environment Contamination Monitor to monitor surface contamination (SC) in the payload bay. SC on the five sensors of the TQCM was analyzed by means of IR spectroscopy, scanning electron spectroscopy, and energy dispersive X-ray fluorescence. The amount of SC ranged from 1.4 micrograms/sq cm for the -Z sensor to 39.9 micrograms/sq cm for the +X sensor. The IR analysis showed strong CH2, CH3, and carbonyl absorption bands, indicative of ester and polyester compounds found in adhesives, plasticizers, and tape. The particulates (mostly ranging from 1 micron to 20 microns in size) were mainly composed of Mg, Al, Al2O3, and Si, and probably originated in the solid rocket firings.

  4. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

    Energy Technology Data Exchange (ETDEWEB)

    Waldron, P.J.; Wu, L.; Van Nostrand, J.D.; Schadt, C.W.; Watson, D.B.; Jardine, P.M.; Palumbo, A.V.; Hazen, T.C.; Zhou, J.

    2009-06-15

    To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.

  5. Are sweep net sampling and pitfall trapping compatible with molecular analysis of predation?

    Science.gov (United States)

    Harwood, James D

    2008-08-01

    Molecular analysis of predation enables accurate and reliable elucidation of trophic linkages in complex food webs, but identifying the strength of such interactions can be subject to error. Currently two techniques dominate: monoclonal antibody-based enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). Although the optimization and characterization of these systems ensures their sensitivity and specificity, predator collection protocols such as sweep-netting and vacuum sampling could overestimate feeding rates because of surface-level contamination, yielding positive reactivity or predation within the sampling device. Therefore, two sampling techniques (sweep-net sampling and hand collection) were compared within an alfalfa agroecosystem using a monoclonal antibody-based ELISA to test the hypothesis that cross-contamination is a source of error, i.e., significantly more predators (linyphiid spiders) would test positive for prey (Diptera) proteins. A concurrent study examining the viability of trapping predators into saline solution was also undertaken. No significant differences were found between the proportions of spiders screening positive for Diptera when collected by sweep-net versus hand collection, rejecting the hypothesis that sweep-netting predators for subsequent molecular gut content analysis overestimates predation frequency. ELISA was also capable of detecting prey proteins in predator guts from pitfall traps containing phosphate-buffered saline, indicating the suitability of this approach for the collection and analysis of epigeal predators. Although these results indicate that sweep netting and pitfall trapping into solution is appropriate in this predator-prey and ELISA analysis system, caution should be exercised with other interactions and PCR-based analysis. The likelihood for false-positive reactivity should therefore be considered on a case-by-case basis.

  6. Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation.

    Science.gov (United States)

    Kuppusamy, Saranya; Thavamani, Palanisami; Megharaj, Mallavarapu; Venkateswarlu, Kadiyala; Lee, Yong Bok; Naidu, Ravi

    2016-11-05

    Diversity, distribution and composition of bacterial community of soils contaminated long-term with both polycyclic aromatic hydrocarbons (PAHs) and heavy metals were explored for the first time following 454 pyrosequencing. Strikingly, the complete picture of the Gram positive (+ve) and Gram negative (-ve) bacterial profile obtained in our study illustrates novel postulates that include: (1) Metal-tolerant and PAH-degrading Gram -ves belonging to the class Alphaproteobacteria persist relatively more in the real contaminated sites compared to Gram +ves, (2) Gram +ves are not always resistant to heavy metal toxicity, (3) Stenotrophomonas followed by Burkholderia and Pseudomonas are the dominant genera of PAH degraders with high metabolic activity in long-term contaminated soils, (4) Actinobacteria is the predominant group among the Gram +ves in soils contaminated with high molecular weight PAHs that co-exist with toxic heavy metals like Pb, Cu and Zn, (5) Microbial communities are nutrient-driven in natural environments and (6) Catabolically potential Gram +/-ves with diverse applicability to remediate the real contaminated sites evolve eventually in the historically-polluted soils. Thus, the most promising indigenous Gram +/-ve strains from the long-term contaminated sites with increased catabolic potential, enzymatic activity and metal tolerance need to be harnessed for mixed contaminant cleanups.

  7. [DNA extraction methods of compost for molecular ecology analysis].

    Science.gov (United States)

    Yang, Zhao-Hui; Xiao, Yong; Zeng, Guang-Ming; Liu, Yun-Guo; Deng, Jiu-Hua

    2006-08-01

    Molecular ecology provides new techniques for studying compost microbes, and the DNA extraction is the basis of molecular techniques. Because of the contamination of humic acids, it turns to be more difficult for compost microbial DNA extraction. Three different approaches, named as lysozyme lysis, ultrasonic lysis and proteinase K lysis with CTAB, were used to extract the total DNA from compost. The detection performed on a nucleic acids and protein analyzer showed that all the three approaches produced high DNA yields. The agarose gel electrophoresis showed that the DNA fragments extracted from compost had a length of about 23 kb. A eubacterial 16S rRNA gene targeted primer pair (27F and 1 495R) was used for PCR amplification, and all the samples got almost the full length 16S rDNA sequence (about 1.5 kb). After digested by restriction endonucleases (Hae Ill and Alu I), the restriction map showed relatively identical microbial diversity in the DNA, which was extracted by the three different approaches. All the compost microbial DNA extracted by the three different approaches could be used for molecular ecological study, and researchers should choose the right approach for extracting microbial DNA from compost based on the facts.

  8. Genetic and Molecular Network Analysis of Behavior

    OpenAIRE

    Williams, Robert W.; Mulligan, Megan K.

    2012-01-01

    This chapter provides an introduction into the genetic control and analysis of behavioral variation using powerful online resources. We introduce you to the new field of systems genetics using "case studies" drawn from the world of behavioral genetics that exploit populations of genetically diverse lines of mice. These lines differ very widely in patterns of gene and protein expression in the brain and in patterns of behavior. In this chapter we address the following set of related questions:...

  9. Quantitative proteomics analysis reveals the tolerance of Mirabilis jalapa L. to petroleum contamination.

    Science.gov (United States)

    Chen, Shuisen; Ma, Hui; Guo, Zhifu; Feng, Yaping; Lin, Jingwei; Zhang, Menghua; Zhong, Ming

    2017-03-01

    Petroleum is not only an important energy resource but is also a major soil pollutant. To gain better insight into the adaptability mechanism of Mirabilis jalapa to petroleum-contaminated soil, the protein profiles of M. jalapa root were investigated using label-free quantitative proteomics technique. After exposing to petroleum-contaminated soil for 24 h, 34 proteins significantly changed their protein abundance and most of the proteins increased in protein abundance (91.18%). Combined with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as data from previous studies, our results revealed that M. jalapa enhanced tolerance to petroleum by changing antioxidation and detoxification, cell wall organization, amino acid and carbohydrate metabolism, transportation and protein process, and so on. These metabolism alterations could result in the production and secretion of low molecular carbohydrate, amino acid, and functional protein, which enhanced the bioavailability of petroleum and reducing the toxicity of the petroleum. Taken together, these results provided novel information for better understanding of the tolerance of M. jalapa to petroleum stress.

  10. Molecular characterization of antibiotic-resistant bacteria in contaminated chicken meat sold at supermarkets in Bangkok, Thailand.

    Science.gov (United States)

    Chaisatit, Chaiyaporn; Tribuddharat, Chanwit; Pulsrikarn, Chaiwat; Dejsirilert, Surang

    2012-01-01

    We assessed contamination by antibiotic-resistant bacteria in chicken meat obtained from supermarkets in Bangkok, Thailand. The prevalence of Salmonella enterica and Escherichia coli was 18.7% (14/75) and 53% (106/200), respectively. Most probable number (MPN) analysis showed that 56.7% of the samples (34/60) were in violation of the limit of allowable coliform bacteria in chicken meat, for which the maximum is 46,000 MPN/g. Multidrug-resistant phenotypes of both S. enterica and E. coli were found. The presence of class 1 integrons was demonstrated by polymerase chain reaction (PCR) and dot-blot hybridization. PCR showed that class 1 integrons were present in 42.9% (6/14) and 37.7% (40/106) of S. enterica and E. coli isolates, respectively. Resistance genes identified in this study were aadA2, aadA4, aadA22, and aadA23 (for aminoglycoside resistance); dfrA5 (for trimethoprim resistance), and lnuF (for lincosamide resistance). Four S. enterica isolates underwent multilocus sequence typing and the results were sequence type (ST) 50, ST 96, ST 1543, and ST 1549, which matched well with strains from many countries and reflected an international spread. Our study revealed that class 1 integrons have spread into community sources and might play an important role in horizontal antibiotic resistance gene transfer.

  11. The cost and benefit analysis of a contaminated area remediation: case study of dose level selection

    Energy Technology Data Exchange (ETDEWEB)

    Lauria, D.C. [Instituto de Radioproteccion e Dosimetria- IRD/CNEN, Av. Salvador Allende s/n, Barra de Tijuca, Rio de Janeiro- RJ (Brazil)]. e-mail: dejanira@ird.gov.br

    2006-07-01

    In recent years there has been an increasing awareness of the radiological impact of non-nuclear industries that extract and/or process ores and minerals containing naturally occurring radioactive material (NORM). Without radiological rules, these industrial activities may result in significant radioactive contamination of installations and sites. Depending on the potential hazardous to the environment and public health, the radioactive contaminated sites may require remediation. The extent of the site cleanup is a function of the size, localization, complexity, potential risks and on possible future uses envisioned for the site. Since worker and public health, public anxiety and economics factors are involved; the selection of an appropriate dose level can be quite complicated. This paper discusses the selection of a dose level criterion to remedy a site, which was contaminated by wastes from monazite processing. The site is located in the Sao Paulo city; the most densely populated Brazilian City. In its 60,000 square meters of area, a preliminary survey showed contaminated zones covering an area of 6,500 square meters. In some places, contamination was found below the superficial layer of the soil, being the radionuclide vertical distribution not uniform. The {sup 228} Ra soil activity concentration reached values up to 33,000 Bq/kg while those for {sup 226} Ra reached values up to 6,700 Bq/kg. Based on pathway analysis model and considering both the current land use and a hypothetical residential scenario, the residual contamination levels of radionuclides in soil have been derived for dose values of 10 mSv/y (dose level for intervention), 5 mSv/y, 3 mSv/y, 1 mSv/y (dose limit for practices) and 0.3 mSv/y (dose constraint for practices). An optimized value o f annual dose of about 5 mSv/y would be a good option for intervention level, but taking into account the public concern and anxiety, the site location and size, and the remediation costs, it is suggested

  12. Remediation of PCB-contaminated soils. Risk analysis of biological in situ processes

    Energy Technology Data Exchange (ETDEWEB)

    Rein, Arno

    2006-12-08

    Biological in situ measures can be efficient and cost effective options for the remediation of contaminated sites. However, the accepted application requires a detailed and reliable analysis of potential impacts. An important objective is to quantify the potential of contaminant degradation and metabolite formation. This thesis addresses a quantitative multimedia risk assessment. Methodologies and tools were developed for this objective and applied to evaluate in situ bioremediation of soils contaminated with polychlorinated biphenyls (PCBs). Soil bacteria in conjunction with plant roots were addressed (rhizoremediation) with a focus on the use of genetically modified microorganisms (GMOs). PCBs are known to be harmful compounds that are ubiquitously distributed in the environment. PCB contaminations in soil and groundwater were identified as important problems. 209 different congeners are sterically possible, but not all are of environmental significance. PCB congeners of concern were evaluated with respect to their potential toxicity, environmental occurrence and mobility. For this objective, congener specific data on the toxicity potential and the frequency in environmental matrices were collected. To quantify the mobility potential, multimedia modelling was performed applying deterministic and probabilistic procedures. 56 PCB congeners of concern were evaluated, and multimedia risk assessments of PCB-contaminated soils should concentrate on this group. Kinetics parameters were specified for degradation experiments with individual PCB congeners in solution and different bacterial strains. These laboratory assays were performed with wild-type Burkholderia sp. strain LB400 and the genetically modified Pseudomonas fluorescens strains F113pcb and F113L::1180. The F113 derivatives demonstrated a good survival ability in willow (Salix sp.) rhizosphere (mesocosm experiments). Therefore, and due to high depletion rates, rhizoremediation with F113L::1180 and willow

  13. Adaptive molecular resolution approach in Hamiltonian form: An asymptotic analysis

    Science.gov (United States)

    Zhu, Jinglong; Klein, Rupert; Delle Site, Luigi

    2016-10-01

    Adaptive molecular resolution approaches in molecular dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in the way the change of molecular resolution is made in a buffer (transition) region. In particular a central question concerns the possibility of the existence of a global Hamiltonian which, by describing the change of resolution, is at the same time physically consistent, mathematically well defined, and numerically accurate. In this paper we present an asymptotic analysis of the adaptive process complemented by numerical results and show that under certain mathematical conditions a Hamiltonian, which is physically consistent and numerically accurate, may exist. Such conditions show that molecular simulations in the current computational implementation require systems of large size, and thus a Hamiltonian approach such as the one proposed, at this stage, would not be practical from the numerical point of view. However, the Hamiltonian proposed provides the basis for a simplification and generalization of the numerical implementation of adaptive resolution algorithms to other molecular dynamics codes.

  14. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  15. Evaluating the feasibility of hydraulic and physical barriers at contaminated sites by means of multicriteria analysis

    Directory of Open Access Journals (Sweden)

    Andrea Gigliuto

    2014-06-01

    Full Text Available Controlling contaminant plumes in groundwater using pump and treat or hydraulic and physical barriers is a common practice to contain and reduce solute contaminants in remediation activities. Recent evolution in engineering techniques also allowed to extend the number of solutions that can be designed and set in practice. As such, the decision-making process assumes great importance in leading the selection of the best suitable technology for a certain case study. This process has to take into account technical, environmental and socioeconomic factors. This paper presents the results of a research project aimed at defining a multi-criteria procedure analysis to support the decision-making process in the barrier technology selection, taking into account technical, economic, social and environmental factors. A multi-criteria analysis methodology has been defined to provide a quantitative tool to guide the selection of the best suitable technology concerning a specific case. The methodology was applied to a real case, selected from many case studies based on data availability and quality, in order to verify the effectiveness of the procedure in evaluating the alternative selections and to highlight the differences between the results of the multi-criteria analysis and the real engineers choices. A sensitivity analysis was performed to analyze the influence of each criterion on the final result of the study. With this paper we aim to start a discussion to deepen the decision making process, in order to develop methodologies allowing to chose the best solution without subjective evaluations.

  16. GROWTH AND NUTRITIONAL ANALYSIS OF TREE SPECIES IN CONTAMINATED SUBSTRATE BY LEACHABLE HERBICIDES

    Directory of Open Access Journals (Sweden)

    Rebecca de Araújo Fiore

    Full Text Available ABSTRACT Ecosystems contamination by residues of pesticides requires special attention to the herbicides subject to leaching. The objective was to select tree species to rhizodegradation contaminated by residues of 2,4-D and atrazine and to recompose riparian areas to agricultural fields, then reducing the risk of contamination of water courses. A total of 36 treatments consisted of the combinations of forest species were evaluated [Inga marginata (Inga, Schizolobium parahyba (guapuruvu, Handroanthus serratifolius (ipê amarelo, Jacaranda puberula (carobinha, Cedrela fissilis (cedro, Calophyllum brasiliensis (landin, Psidium mirsinoides (goiabinha, Tibouchina glandulosa (quaresmeira, Caesalpinia férrea (pau-ferro, Caesalpinia pluviosa (sibipiruna, Terminalia argêntea (capitão and Schinopsis brasiliensis (braúna] and three solutions simulating leachate compound (atrazine, 2,4-D and water - control, with four replicates each. The characteristics measured were plant height, stem diameter, number of leaves, leaf area and dry biomass, and foliar nutrition. Forest species survived the herbicide application, and most showed an increase in macronutrients even under an herbicide application, and the Inga had the highest tolerance regarding growth analysis. It is recommended to use species that are more tolerant to Atrazine and 2,4-D in field experiments to confirm previous results of this simulation.

  17. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

    Directory of Open Access Journals (Sweden)

    Tom O. Delmont

    2016-03-01

    Full Text Available High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

  18. Analysis of diffusion-adsorption equivalency of landfill liner systems for organic contaminants.

    Science.gov (United States)

    Xie, Haijian; Chen, Yunmin; Ke, Han; Tang, Xiaowu; Chen, Renpeng

    2009-01-01

    The equivalence between multilayered barriers regarding diffusion and adsorption was studied. The bottom boundary of the liner system is defined by assuming concentration continuous and flux continuous conditions of the contaminant between the bottom liner layer and the underlying soil. Five different liner systems were compared in terms of solute breakthrough time. The results of the analysis showed that breakthrough time of the hydrophobic organic compounds for a 2-meter-thick compacted clay liner (CCL) could be 3-4 orders of magnitude is greater than the breakthrough time for a geosynthetic clay liner (GCL) composite liner. The GM/GCL and GM/CCL composite liner systems provide a better diffusion barrier for the hydrophilic organic compounds than that for the hydrophobic compounds due to their different Henry's coefficient. The calculated breakthrough times of the organic contaminants for the Chinese standard liner systems were found to be generally greater than those for the GCL alternatives, for the specific conditions examined. If the distribution coefficient increases to 2.8 for the hydrophobic compounds or 1.0 for the hydrophilic compounds, the thickness of the attenuation layer needed to achieve the same breakthrough time as the standard liner systems can be reduced by a factor of about 1.9-2.4. As far as diffusive and adsorption contaminant transport are concerned, GM or GCL is less effective than CCL.

  19. Analysis of diffusion-adsorption equivalency of landfill liner systems for organic contaminants

    Institute of Scientific and Technical Information of China (English)

    XIE Haijian; CHEN Yunmin; KE Han; TANG Xiaowu; CHEN Renpeng

    2009-01-01

    The equivalence between multilayered barriers regarding diffusion and adsorption is analyzed by means of an analytical method. The bottom boundary of the liner system is defined by assuming concentration continuous and flux continuous conditions of the contaminant between the bottom liner layer and the underlying soil. Five different liner systems were compared in terms of solute breakthrough time. The results of the analysis show that breakthrough time of the hydrophobic organic compounds for a 2-meter-thick compacted clay liner (CCL) can be 3-4 orders of magnitude greater than the breakthrough time for a geosynthetic clay liner (GCL) composite liner. The GM/GCL and GM/CCL composite liner systems provide a better diffusion barrier for the hydrophilic organic compounds than that for the hydrophobic compounds due to their different Henry's coefficient. The calculated breakthrough times of the organic contaminants for the Chinese standard liner systems were found to be generally greater than those for the GCL alternatives, for the specific conditions examined. If the distribution coefficient increases to 2.8 for the hydrophobic compounds or 1.0 for the hydrophilic compounds, the thickness of the attenuation layer needed to achieve the same breakthrough time as the standard liner systems can be reduced by a factor of about 1.9-2.4. As far as diffusive and adsorption contaminant transport are concerned, GM or GCL is less effective than CCL.

  20. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

    Science.gov (United States)

    Delmont, Tom O.

    2016-01-01

    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes. PMID:27069789

  1. Emerging contaminants in the environment: Risk-based analysis for better management.

    Science.gov (United States)

    Naidu, Ravi; Arias Espana, Victor Andres; Liu, Yanju; Jit, Joytishna

    2016-07-01

    Emerging contaminants (ECs) are chemicals of a synthetic origin or deriving from a natural source that has recently been discovered and for which environmental or public health risks are yet to be established. This is due to limited available information on their interaction and toxicological impacts on receptors. Several types of ECs exist such as antibiotics, pesticides, pharmaceuticals, personal care products, effluents, certain naturally occurring contaminants and more recently nanomaterials. ECs may derive from a known source, for example released directly to the aquatic environment from direct discharges such as those from wastewater treatment plants. Although in most instances the direct source cannot be identified, ECs have been detected in virtually every country's natural environment and as a consequence they represent a global problem. There is very limited information on the fate and transport of ECs in the environment and their toxicological impact. This lack of information can be attributed to limited financial resources and the lack of analytical techniques for detecting their effects on ecosystems and human health on their own or as mixture. We do not know how ECs interact with each other or various contaminants. This paper presents an overview of existing knowledge on ECs, their fate and transport and a risk-based analysis for ECs management and complementary strategies.

  2. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies.

    Science.gov (United States)

    Delmont, Tom O; Eren, A Murat

    2016-01-01

    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today's microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

  3. Comparative analysis of decision tree algorithms on quality of water contaminated with soil

    Directory of Open Access Journals (Sweden)

    Mara Andrea Dota

    2015-02-01

    Full Text Available Agriculture, roads, animal farms and other land uses may modify the water quality from rivers, dams and other surface freshwaters. In the control of the ecological process and for environmental management, it is necessary to quickly and accurately identify surface water contamination (in areas such as rivers and dams with contaminated runoff waters coming, for example, from cultivation and urban areas. This paper presents a comparative analysis of different classification algorithms applied to the data collected from a sample of soil-contaminated water aiming to identify if the water quality classification proposed in this research agrees with reality. The sample was part of a laboratory experiment, which began with a sample of treated water added with increasing fractions of soil. The results show that the proposed classification for water quality in this scenario is coherent, because different algorithms indicated a strong statistic relationship between the classes and their instances, that is, in the classes that qualify the water sample and the values which describe each class. The proposed water classification varies from excelling to very awful (12 classes

  4. Current Measures on Radioactive Contamination in Japan: A Policy Situation Analysis.

    Directory of Open Access Journals (Sweden)

    Stuart Gilmour

    Full Text Available The Great East Japan Earthquake on 11th March 2011 and the subsequent Fukushima Dai-ichi nuclear power plant disaster caused radioactive contamination in the surrounding environment. In the immediate aftermath of the accident the Government of Japan placed strict measures on radio-contamination of food, and enhanced radio-contamination monitoring activities. Japan is a pilot country in the WHO Foodborne Disease Burden Epidemiology Reference Group (FERG, and through this initiative has an opportunity to report on policy affecting chemicals and toxins in the food distribution network. Nuclear accidents are extremely rare, and a policy situation analysis of the Japanese government's response to the Fukushima Dai-ichi nuclear accident is a responsibility of Japanese scientists. This study aims to assess Japan government policies to reduce radio-contamination risk and to identify strategies to strengthen food policies to ensure the best possible response to possible future radiation accidents.We conducted a hand search of all publicly available policy documents issued by the Cabinet Office, the Food Safety Commission, the Ministry of Health, Labor and Welfare (MHLW, the Ministry of Agriculture, Forestry and Fishery (MAFF and prefectural governments concerning food safety standards and changes to radiation and contamination standards since March 11th, 2011. We extracted information on food shipment and sales restrictions, allowable radio-contamination limits, monitoring activities and monitoring results. The standard for allowable radioactive cesium (Cs-134 and Cs-137 of 100 Bq/Kg in general food, 50 Bq/Kg in infant formula and all milk products, and 10 Bq/Kg in drinking water was enforced from April 2012 under the Food Sanitation Law, although a provisional standard on radio-contamination had been applied since the nuclear accident. Restrictions on the commercial sale and distribution of specific meat, vegetable and fish products were released for

  5. Facile synthesis of N–F codoped and molecularly imprinted TiO{sub 2} for enhancing photocatalytic degradation of target contaminants

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yanyan; Dong, Yuming; Xia, Xiaofeng [The Laboratory of Food Colloids and Biotechnology, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122 (China); Liu, Xiang, E-mail: liuxiang@jiangnan.edu.cn [The Laboratory of Food Colloids and Biotechnology, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122 (China); Li, Hexing, E-mail: hexing-li@shnu.edu.cn [The Key Laboratory of the Chinese Ministry of Education in Resource Chemistry, Shanghai Normal University, Shanghai 200234 (China)

    2016-02-28

    Graphical abstract: N–F codoped and molecularly imprinted TiO{sub 2} were prepared by simple ethanol–water solvothermal method. Their mechanism of high adsorption capacity, preferable photocatalytic degradation activity, good selectivity and excellent reusability for target contaminants were identified and discussed. - Highlights: • Synthesis of N–F codoped and molecularly imprinted TiO{sub 2} (MIP-NFTs) is simple. • Molecular imprinting enhanced the adsorption capacity and selectivity of MIP-NFTs. • MIP-NFTs show high photocatalytic activity under simulated solar light. • MIP-NFTs exhibit excellent reusability due to their inorganic framework. - Abstract: N–F codoped and molecularly imprinted TiO{sub 2} (MIP-NFTs) were successfully prepared by simple ethanol–water solvothermal method using 2-nitrophenol (2NP) and 4-nitrophenol (4NP) as template molecules (target contaminants), respectively. The surface structure and properties of the catalysts were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), nitrogen adsorption/desorption measurements (BET), X-ray photoelectron spectroscopy (XPS) and UV–vis diffuse reflectance spectra (UV–vis DRS). In comparison with non-imprinted N–F codoped TiO{sub 2} nanocomposites (NIP-NFTs), MIP-NFTs show a higher adsorption, good selectivity and preferable degradation capacity toward the target contaminants. The adsorption amounts of 2NP and 4NP over the corresponding MIP-NFTs are about 1.78 and 2.21 times of that over NIP-NFTs, respectively. MIP-NFTs show a much higher adsorption capacity and selectivity for target contaminants in the mixed solution. Degradation selectivity experiments demonstrate that the selectivity coefficient (R) of degradation of 2NP relative to 4NP over 2NP/MIP-NFTs and 4NP relative to 2NP over 4NP/MIP-NFTs are 1.93 and 1.61, respectively. The enhancement about adsorption capacity and selectivity can be attributed to the chemical interaction and size matching

  6. Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for realtime, in-situ, highly sensitive and highly selective protein analysis, including the nonspecific or specific protein detection and separation, protein/DNA interaction studies, cell surface protein recognition, and antigen-antibody binding process-based bacteria assays. The introduction of molecular beacon probes and biofunctionalized nanoparticles into the protein analysis area would necessarily advance the proteomics research.

  7. Molecular analysis of the glucocerebrosidase gene locus

    Energy Technology Data Exchange (ETDEWEB)

    Winfield, S.L.; Martin, B.M.; Fandino, A. [Clinical Neuroscience Branch, Bethesda, MD (United States)] [and others

    1994-09-01

    Gaucher disease is due to a deficiency in the activity of the lysosomal enzyme glucocerebrosidase. Both the functional gene for this enzyme and a pseudogene are located in close proximity on chromosome 1q21. Analysis of the mutations present in patient samples has suggested interaction between the functional gene and the pseudogene in the origin of mutant genotypes. To investigate the involvement of regions flanking the functional gene and pseudogene in the origin of mutations found in Gaucher disease, a YAC clone containing DNA from this locus has been subcloned and characterized. The original YAC containing {approximately}360 kb was truncated with the use of fragmentation plasmids to about 85 kb. A lambda library derived from this YAC was screened to obtain clones containing glucocerebrosidase sequences. PCR amplification was used to identify subclones containing 5{prime}, central, or 3{prime} sequences of the functional gene or of the pseudogene. Clones spanning the entire distance from the last exon of the functional gene to intron 1 of the pseudogene, the 5{prime} end of the functional gene and 16 kb of 5{prime} flanking region and approximately 15 kb of 3{prime} flanking region of the pseudogene were sequenced. Sequence data from 48 kb of intergenic and flanking regions of the glucocerebrosidase gene and its pseudogene has been generated. A large number of Alu sequences and several simple repeats have been found. Two of these repeats exhibit fragment length polymorphism. There is almost 100% homology between the 3{prime} flanking regions of the functional gene and the pseudogene, extending to about 4 kb past the termination codons. A much lower degree of homology is observed in the 5{prime} flanking region. Patient samples are currently being screened for polymorphisms in these flanking regions.

  8. Remediation of PCB-contaminated soils. Risk analysis of biological in situ processes

    Energy Technology Data Exchange (ETDEWEB)

    Rein, Arno

    2006-12-08

    Biological in situ measures can be efficient and cost effective options for the remediation of contaminated sites. However, the accepted application requires a detailed and reliable analysis of potential impacts. An important objective is to quantify the potential of contaminant degradation and metabolite formation. This thesis addresses a quantitative multimedia risk assessment. Methodologies and tools were developed for this objective and applied to evaluate in situ bioremediation of soils contaminated with polychlorinated biphenyls (PCBs). Soil bacteria in conjunction with plant roots were addressed (rhizoremediation) with a focus on the use of genetically modified microorganisms (GMOs). PCBs are known to be harmful compounds that are ubiquitously distributed in the environment. PCB contaminations in soil and groundwater were identified as important problems. 209 different congeners are sterically possible, but not all are of environmental significance. PCB congeners of concern were evaluated with respect to their potential toxicity, environmental occurrence and mobility. For this objective, congener specific data on the toxicity potential and the frequency in environmental matrices were collected. To quantify the mobility potential, multimedia modelling was performed applying deterministic and probabilistic procedures. 56 PCB congeners of concern were evaluated, and multimedia risk assessments of PCB-contaminated soils should concentrate on this group. Kinetics parameters were specified for degradation experiments with individual PCB congeners in solution and different bacterial strains. These laboratory assays were performed with wild-type Burkholderia sp. strain LB400 and the genetically modified Pseudomonas fluorescens strains F113pcb and F113L::1180. The F113 derivatives demonstrated a good survival ability in willow (Salix sp.) rhizosphere (mesocosm experiments). Therefore, and due to high depletion rates, rhizoremediation with F113L::1180 and willow

  9. Molecular analysis of Ku redox regulation

    Directory of Open Access Journals (Sweden)

    Shatilla Andrea

    2009-08-01

    Full Text Available Abstract Background DNA double-strand breaks (DSBs can occur in response to ionizing radiation (IR, radiomimetic agents and from endogenous DNA-damaging reactive oxygen metabolites. Unrepaired or improperly repaired DSBs are potentially the most lethal form of DNA damage and can result in chromosomal translocations and contribute to the development of cancer. The principal mechanism for the repair of DSBs in humans is non-homologous end-joining (NHEJ. Ku is a key member of the NHEJ pathway and plays an important role in the recognition step when it binds to free DNA termini. Ku then stimulates the assembly and activation of other NHEJ components. DNA binding of Ku is regulated by redox conditions and evidence from our laboratory has demonstrated that Ku undergoes structural changes when oxidized that results in a reduction in DNA binding activity. The C-terminal domain and cysteine 493 of Ku80 were investigated for their contribution to redox regulation of Ku. Results We effectively removed the C-terminal domain of Ku80 generating a truncation mutant and co-expressed this variant with wild type Ku70 in an insect cell system to create a Ku70/80ΔC heterodimer. We also generated two single amino acid variants of Cys493, replacing this amino acid with either an alanine (C493A or a serine (C493S, and over-expressed the variant proteins in SF9 insect cells in complex with wild type Ku70. Neither the truncation nor the amino acid substitutions alters protein expression or stability as determined by SDS-PAGE and Western blot analysis. We show that the C493 mutations do not alter the ability of Ku to bind duplex DNA in vitro under reduced conditions while truncation of the Ku80 C-terminus slightly reduced DNA binding affinity. Diamide oxidation of cysteines was shown to inhibit DNA binding similarly for both the wild-type and all variant proteins. Interestingly, differential DNA binding activity following re-reduction was observed for the Ku70/80

  10. Pyrosequence analysis of bacterial communities in aerobic bioreactors treating polycyclic aromatic hydrocarbon-contaminated soil.

    Science.gov (United States)

    Singleton, David R; Richardson, Stephen D; Aitken, Michael D

    2011-11-01

    Two aerobic, lab-scale, slurry-phase bioreactors were used to examine the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and the associated bacterial communities. The two bioreactors were operated under semi-continuous (draw-and-fill) conditions at a residence time of 35 days, but one was fed weekly and the other monthly. Most of the quantified PAHs, including high-molecular-weight compounds, were removed to a greater extent in the weekly-fed bioreactor, which achieved total PAH removal of 76%. Molecular analyses, including pyrosequencing of 16S rRNA genes, revealed significant shifts in the soil bacterial communities after introduction to the bioreactors and differences in the abundance and types of bacteria in each of the bioreactors. The weekly-fed bioreactor displayed a more stable bacterial community with gradual changes over time, whereas the monthly-fed bioreactor community was less consistent and may have been more strongly influenced by the influx of untreated soil during feeding. Phylogenetic groups containing known PAH-degrading bacteria previously identified through stable-isotope probing of the untreated soil were differentially affected by bioreactor conditions. Sequences from members of the Acidovorax and Sphingomonas genera, as well as the uncultivated "Pyrene Group 2" were abundant in the bioreactors. However, the relative abundances of sequences from the Pseudomonas, Sphingobium, and Pseudoxanthomonas genera, as well as from a group of unclassified anthracene degraders, were much lower in the bioreactors compared to the untreated soil.

  11. Molecular Analysis Research at Community College of Philadelphia

    Science.gov (United States)

    2015-09-21

    Molecular Analysis Research at Community College of Philadelphia Report Title AXIMA Assurance mass spectrometer, Leica DMI-8 fluorescent microscope...lab research and analysis of data, a poster presentation and seminar will be created to communicate scientific findings at The 2016 American Society ...SECURITY CLASSIFICATION OF: AXIMA Assurance mass spectrometer, Leica DMI-8 fluorescent microscope and BioRad V3 Western Workflow were purchased

  12. Visual verification and analysis of cluster detection for molecular dynamics.

    Science.gov (United States)

    Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas

    2007-01-01

    A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented.

  13. Mineralogical analysis of attic dust samples for contamination source identification in an industrial area, Ajka, Hungary

    Science.gov (United States)

    Völgyesi, Péter; Jordan, Gyozo; Gosar, Mateja; Szabó, Csaba; Miler, Miloš; Kónya, Péter; Bartha, András

    2013-04-01

    The post-war centrally directed economy forced massive heavy industry in Hungary, producing huge amount of wastes and pollution. Long-term airborne emissions from mining, coal-fired power plants and alumina industry have left the legacy of widely distributed contamination around industrial areas and nearby settlements in the Ajka region. Recent research suggests that significant amount of airborne pollutants, deposited in the urban environment, can be efficiently studied by attic dust analysis. The sampling strategy followed a grid-based stratified random sampling design and 30 samples were collected in 27 houses (at least 30 years old) in a 8x8 grid of the 64 km2 project area. In order to determine the pollution potential of attic dust samples, geochemical and mineralogical analyses were performed. The main aim of the mineralogical analyses was to study the phase composition of the dust particles and to identify potential anthropogenic sources. The total concentrations of the toxic elements (As, Pb, Cd, Cu, Ni and Zn) were measured with ICP-OES and mercury content was analyzed with atomic absorption spectrometry. Phase analyses of the samples were carried out by the means of scanning electron microscopy (SEM) coupled with energy dispersive spectroscopy (EDS) and X-Ray diffraction (XRD) methods. Laser particle size analyzer was used to measure the grain size of attic dust particles. Results showed that the studied attic dust in the Ajka urban area was contaminated mostly by Hg, Pb and Zn with contents ranging between 0.1-2 ppm, 42.5-881 ppm and 90.2-954 ppm, respectively. However, the study of extreme data values (statistical outliers) has shown that at certain points airborne dust can be extremely contaminated also with Cd (0.4-11.7 ppm). The size of the attic dust particles varied between 0.2 and 113 µm. Based on the SEM/EDS and XRD analysis, the most frequently identified mineralogical phases were quartz, calcite, gypsum and Fe- and Al-bearing phases. Fe

  14. Spectral characterization of soil and coal contamination on snow reflectance using hyperspectral analysis

    Indian Academy of Sciences (India)

    S K Singh; A V Kulkarni; B S Chaudhary

    2011-04-01

    Snow is a highly reflecting object found naturally on the Earth and its albedo is highly influenced by the amount and type of contamination. In the present study, two major types of contaminants (soil and coal) have been used to understand their effects on snow reflectance in the Himalayan region. These contaminants were used in two categories quantitatively – addition in large quantity and addition in small quantity. Snow reflectance data were collected between 350 and 2500 nm spectral ranges and binned at 10 nm interval by averaging. The experiment was designed to gather the field information in controlled conditions, and radiometric observations were collected. First derivative, band absorption depth, asymmetry, percentage change in reflectance and albedo in optical region were selected to identify and discriminate the type of contamination. Band absorption depth has shown a subtle increasing pattern for soil contamination, however, it was significant for small amounts of coal contamination. The absorption peak asymmetry was not significant for soil contamination but showed a nature towards left asymmetry for coal. The width of absorption feature at 1025 nm was not significant for both the contaminations. The percentage change in reflectance was quite high for small amount of coal contamination rather than soil contamination, however, a shift of peak was observed in soil-contaminated snow which was not present in coal contamination. The albedo drops exponentially for coal contamination rather than soil contamination.

  15. Analysis and computational dissection of molecular signature multiplicity.

    Directory of Open Access Journals (Sweden)

    Alexander Statnikov

    2010-05-01

    Full Text Available Molecular signatures are computational or mathematical models created to diagnose disease and other phenotypes and to predict clinical outcomes and response to treatment. It is widely recognized that molecular signatures constitute one of the most important translational and basic science developments enabled by recent high-throughput molecular assays. A perplexing phenomenon that characterizes high-throughput data analysis is the ubiquitous multiplicity of molecular signatures. Multiplicity is a special form of data analysis instability in which different analysis methods used on the same data, or different samples from the same population lead to different but apparently maximally predictive signatures. This phenomenon has far-reaching implications for biological discovery and development of next generation patient diagnostics and personalized treatments. Currently the causes and interpretation of signature multiplicity are unknown, and several, often contradictory, conjectures have been made to explain it. We present a formal characterization of signature multiplicity and a new efficient algorithm that offers theoretical guarantees for extracting the set of maximally predictive and non-redundant signatures independent of distribution. The new algorithm identifies exactly the set of optimal signatures in controlled experiments and yields signatures with significantly better predictivity and reproducibility than previous algorithms in human microarray gene expression datasets. Our results shed light on the causes of signature multiplicity, provide computational tools for studying it empirically and introduce a framework for in silico bioequivalence of this important new class of diagnostic and personalized medicine modalities.

  16. A molecular epidemiological study of methicillin-resistant Staphylococci environmental contamination in railway stations and coach stations in Guangzhou of China.

    Science.gov (United States)

    Lin, J L; Peng, Y; Ou, Q T; Lin, D X; Li, Y; Ye, X H; Zhou, J L; Yao, Z J

    2017-02-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has caused a series of public health problems since it was first found in 1961. However, there are few research studies on the MRSA environmental contamination in railway stations and coach stations. Therefore, the aim of this study was to determine MRSA environmental contamination in public transport stations. Between December 2013 and January 2014, 380 surface samples from three railway stations (180) and four coach stations (200) in Guangzhou were collected to isolate and determine the prevalence and characteristics of Staphylococci strains. 39·21% of all samples were Staphylococci isolates, 1·58% of Staphylococci isolates were MRSA isolates, and 6·05% were methicillin-susceptible S. aureus. The proportion of multidrug resistant among 149 Staphylococci isolates was 75·84%. None of MRSA isolates was identified with the Panton-Valentine Leukocidin (PVL) genes, and one of them was identified with the qac gene. Four MRSA isolates were Staphylococcal Cassette Chromosome mec IVa, and the other two were nontypeable. Staphylococcus aureus isolates were classified into several sequence types (STs), and STs showed possible cross-transmissions of isolates from various sources. Methicillin-resistant Staphylococci contamination prevalence was high, and the environment of stations may be the vectors transmitting the Staphylococci to passengers. This is the first study to comprehensively report the prevalence, antibiotic resistance, and molecular characteristics of contamination of Staphylococci isolates in railway stations and coach stations of China. It will have great public health implications on infection control in community settings because of the serious hazard of Staphylococci, especially methicillin-resistant Staphylococci. Our findings have provided evidence for relevant departments to reduce the contamination of Staphylococci in environment of public transport stations. © 2016 The Society for Applied

  17. Analysis of the contaminants released from municipal solid waste landfill site: A case study.

    Science.gov (United States)

    Samadder, S R; Prabhakar, R; Khan, D; Kishan, D; Chauhan, M S

    2017-02-15

    Release and transport of leachate from municipal solid waste landfills pose a potential hazard to both surrounding ecosystems and human populations. In the present study, soil, groundwater, and surface water samples were collected from the periphery of a municipal solid waste landfill (located at Ranital of Jabalpur, Madhya Pradesh, India) for laboratory analysis to understand the release of contaminants. The landfill does not receive any solid wastes for dumping now as the same is under a landfill closure plan. Groundwater and soil samples were collected from the bore holes of 15m deep drilled along the periphery of the landfill and the surface water samples were collected from the existing surface water courses near the landfill. The landfill had neither any bottom liner nor any leachate collection and treatment system. Thus the leachate generated from the landfills finds paths into the groundwater and surrounding surface water courses. Concentrations of various physico-chemical parameters including some toxic metals (in collected groundwater, soil, and surface water samples) and microbiological parameters (in surface water samples) were determined. The analyzed data were integrated into ArcGIS environment and the spatial distribution of the metals and other physic- chemical parameter across the landfill was extrapolated to observe the distribution. The statistical analysis and spatial variations indicated the leaching of metals from the landfill to the groundwater aquifer system. The study will help the readers and the municipal engineers to understand the release of contaminants from landfills for better management of municipal solid wastes.

  18. PCR-DGGE analysis of nematode diversity in Cu-contaminated soil

    Institute of Scientific and Technical Information of China (English)

    WANG Shi-Bin; LI Qi; LIANG Wen-Ju; JIANG Yong; JIANG Si-Wei

    2008-01-01

    A wheat pot experiment was conducted under greenhouse conditions to assess the effect of copper contamination on soil nematode diversity by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method and morphological analysis.The soil was treated with CuSO4.5H2O at the following concentrations:0,50,100,200,400,and 800 mg kg-1 dry soil,and the soil samples were collected at wheat jointing and ripening stages.Nematode diversity index (H') from morphological analysis showed no difference between the control and the treated samples in either of the sampling dates.At the wheat ripening stage,nematode diversity obtained by the PCR-DGGE method decreased noticeably in the Cu800 treatment in comparison with the control.With optimization of the method of nematode DNA extraction,PCR-DGGE could give more information on nematode genera,and the intensity of the bands could reflect the abundance of nematode genera in the assemblage.The PCR-DGGE method proved promising in distinguishing nematode diversity in heavy metal contaminated soil.

  19. Application of PIXE analysis to investigation of plants cultivated with contaminated soil of Fukushima

    Energy Technology Data Exchange (ETDEWEB)

    Ishii, K., E-mail: keizo.ishii@qse.tohoku.ac.jp [Research Center for Remediation Engineering of Living Environments Contaminated with Radioisotopes, Department of Quantum Science and Energy Engineering, Tohoku University, 6-6 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Terakawa, A.; Matsuyama, S.; Ishizaki, A.; Arai, H.; Osada, N.; Sugai, H.; Takahashi, H. [Research Center for Remediation Engineering of Living Environments Contaminated with Radioisotopes, Department of Quantum Science and Energy Engineering, Tohoku University, 6-6 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Sera, K. [Cyclotron Research Center, Iwate Medical University, 348-58 Tomegamori, Takizawa, Iwate 020-0173 (Japan); Sasaki, H.; Sasaki, K.; Sawamura, T. [Sasaki Taro memorial PIXE Center, Asano-cho 5, Hakodate 040-0076 (Japan)

    2014-08-01

    We present a method to research low radioactive cesium contaminated plants by the use of PIXE analysis. Highly contaminated regions still remain in the Fukushima prefecture. We collected wild plants growing in this area, that is, Butterbur, Welsh onion, Alpine leek and White clover and measured their specific activities of {sup 137}Cs and {sup 40}K. We also measured {sup 137}Cs and {sup 40}K specific activities of soil under these plants. Soil-to-plant transfer factors of {sup 137}Cs were ∼0.02 for 4 wild plants and those of {sup 40}K were ∼0.5 except for White clover. Using PIXE analysis, we measured the concentration of mineral elements in these plants. Among mineral elements, we noted the concentrations of additional alkali metal elements such as Na, K and Rb. The experimental results showed that the concentration of Rb was proportional to the specific activities of {sup 137}Cs except for Welsh onion and other elements had no strong correlation with {sup 137}Cs. These results indicate that there may be correlations between the adsorption of Cs and Rb.

  20. Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.

    Science.gov (United States)

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2015-07-01

    Cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. Agricultural soil with extensive history of CM application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using PCR-DGGE of 16 S rRNA gene. DGGE analysis revealed that dominant members of CM enrichment culture were associated with α-proteobacteria followed by γ-proteobacteria, Firmicutes, and Actinobacteria. Three potential CM-degrading isolates identified as Ochrobactrum anthropi JCm1, Bacillus megaterium JCm2, and Rhodococcus sp. JCm5 degraded 86-100% of CM (100 mg L(-1) ) within 10 days. These isolates were also able to degrade other pyrethroids, carbofuran, and cypermethrin degradation products. Enzyme activity assays revealed that enzymes involved in CM-degradation were inducible and showed activity when strains were grown on cypermethrin. Degradation kinetics of cypermethrin (200 mg kg(-1)) in soils inoculated with isolates JCm1, JCm2, and JCm5 suggested time-dependent disappearance of cypermethrin with rate constants of 0.0516, 0.0425, and 0.0807 d(-1), respectively, following first order rate kinetics. The isolated bacterial strains were among dominant genera selected under CM enriched conditions and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  1. UNCERT: geostatistics, uncertainty analysis and visualization software applied to groundwater flow and contaminant transport modeling

    Science.gov (United States)

    Wingle, William L.; Poeter, Eileen P.; McKenna, Sean A.

    1999-05-01

    UNCERT is a 2D and 3D geostatistics, uncertainty analysis and visualization software package applied to ground water flow and contaminant transport modeling. It is a collection of modules that provides tools for linear regression, univariate statistics, semivariogram analysis, inverse-distance gridding, trend-surface analysis, simple and ordinary kriging and discrete conditional indicator simulation. Graphical user interfaces for MODFLOW and MT3D, ground water flow and contaminant transport models, are provided for streamlined data input and result analysis. Visualization tools are included for displaying data input and output. These include, but are not limited to, 2D and 3D scatter plots, histograms, box and whisker plots, 2D contour maps, surface renderings of 2D gridded data and 3D views of gridded data. By design, UNCERT's graphical user interface and visualization tools facilitate model design and analysis. There are few built in restrictions on data set sizes and each module (with two exceptions) can be run in either graphical or batch mode. UNCERT is in the public domain and is available from the World Wide Web with complete on-line and printable (PDF) documentation. UNCERT is written in ANSI-C with a small amount of FORTRAN77, for UNIX workstations running X-Windows and Motif (or Lesstif). This article discusses the features of each module and demonstrates how they can be used individually and in combination. The tools are applicable to a wide range of fields and are currently used by researchers in the ground water, mining, mathematics, chemistry and geophysics, to name a few disciplines.

  2. Meta-analysis of biochar potential for pollutant immobilization and stabilization in contaminated soils

    Science.gov (United States)

    Soja, Gerhard; Marsz, Aleksandra; Fristak, Vladimir

    2015-04-01

    Biochar is the pyrolysis product of biomass, preferably from agricultural and forestry residues and waste materials. Characterized by a polyaromatic structure rich in carbon, it offers a microporous structure with a high specific surface area and active functional groups as binding sites. Because of the high sorption capacity for organic and inorganic soil pollutants biochar is an interesting tool for in-situ soil remediation. Especially if the reduction of contaminant bioavailability and the protection of groundwater from pollutants in the vadose zone are the most relevant issues for remediating a polluted site without excavation and removal of the soil, an in-situ application of biochar may offer a promising remediation strategy. The resulting interest of deploying biochar as sorbent for soil contaminants has stimulated a wealth of studies to develop successful applications for environmental technology. However, the existing studies do not always agree on the efficacy for different pollutants and on the most relevant char and soil characteristics that determine the rate of success when using biochar as sorbent. This makes it necessary to apply advanced literature assessment techniques to allow for the recognition of the extent and the significance of the efficacy of a given pollutant treatment technique. A meta-analysis is a study assessment technique that allows extracting a harmonized answer to a specific research question that has been studied more often than one time, even if the results are partially conflicting. Such a technique also allows getting an overview about the degree of consensus or contradiction in the answers to the question if biochar can be applied successfully for immobilizing certain soil contaminants. The meta-analysis results can also be used to quantify the average extent of effects of a certain treatment, depending on the characteristics of the sorbent and on the application rate. By checking 104 published papers in the peer

  3. Suction sampling as a significant source of error in molecular analysis of predator diets.

    Science.gov (United States)

    King, R A; Davey, J S; Bell, J R; Read, D S; Bohan, D A; Symondson, W O C

    2012-06-01

    The molecular detection of predation is a fast growing field, allowing highly specific and sensitive detection of prey DNA within the gut contents or faeces of a predator. Like all molecular methods, this technique is prone to potential sources of error that can result in both false positive and false negative results. Here, we test the hypothesis that the use of suction samplers to collect predators from the field for later molecular analysis of predation will lead to high numbers of false positive results. We show that, contrary to previous published work, the use of suction samplers resulted in previously starved predators testing positive for aphid and collembolan DNA, either as a results of ectopic contamination or active predation in the collecting cup/bag. The contradictory evidence for false positive results, across different sampling protocols, sampling devices and different predator-prey systems, highlights the need for experimentation prior to mass field collections of predators to find techniques that minimise the risk of false positives.

  4. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.

    Science.gov (United States)

    Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem

    2015-02-13

    Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  5. Characterization and phylogenetic analysis of a phenanthrene-degrading strain isolated from oil-contaminated soil

    Institute of Scientific and Technical Information of China (English)

    XIA Ying; MIN Hang; LU Zhen-mei; YE Yang-fang

    2004-01-01

    Bacterium strain EVA17 was isolated from an oil-contaminated soil, and identified as Sphingononas sp.based on analysis of 16S rDNA sequence, cellular fatty acid composition and physiological-chemical tests. The salicylate hydroxylase and catechol 2, 3-dioxygenase (C23O) were detected in cell-free lysates, suggesting a pathway for phenanthrene catabolism via salicylate and catechol. Alignment showed that both of the C23O and GST genes of the strain EVA17 had high similarity with homologues of strains from genus Sphingomonas. The phylogenetic analysis based on 16S rDNA and C23O gene sequence indicated that EVA17 should be classified into genus Sphingomonas, although the two phylogenetic trees were slightly different from each other. The results of coamplification and sequence determination indicated that GST gene should be located upstream of the C23O gene.

  6. Engineering evaluation/cost analysis for the proposed removal of contaminated materials at the Elza Gate site, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    1991-06-01

    This engineering evaluation/cost analysis (EE/CA) has been prepared in support of the proposed removal action for cleanup of radioactive and chemically contaminated soil at the Elza Gate site in Oak Ridge, Tennessee. This property became contaminated as a result of storage of ore residues, equipment, and other materials for the US Atomic Energy Commission. The US Department of Energy is responsible for cleanup of portions of the site under its Formerly Utilized Sites Remedial Action Program. In December 1990 an area known as Pad 1 was abrasively scoured to remove surface contamination, and in March 1991 removal of Pad 1 contamination was begun under a separate EE/CA. This EE/CA is intended to cover the remaining portions of the site for which the Department of Energy has responsibility. It has been determined that an EE/CA report is appropriate documentation for the proposed removal action. This EE/CA covers removal of contaminated soils and contaminated concrete rubble from the Elza Gate site. The primary objectives of this EE/CA report are to identify and describe the preferred removal action, and to document the selection of response activities that will mitigate the potential for release of contaminants from the property into the environment and that will minimize the associated threats to human health or welfare and the environment. The preferred alternative is disposition on the Oak Ridge Reservation. 30 refs., 7 figs., 12 tabs.

  7. Analysis of the potential contamination risk of groundwater resources circulating in areas with anthropogenic activities

    Directory of Open Access Journals (Sweden)

    M. Spizzico

    2005-01-01

    Full Text Available The area investigated is located in the province of Brindisi (Italy. It is a generally flat area separated from the nearby carbonatic plateau of the Murgia by quite indistinct and high fault scarps. As regards the geological features, carbonatic basement rocks and post-cretaceous terrains made up of calabrian calcarenites and middle-upper Pleistocenic marine terraced deposits can be distinguished. In the examined area there are two different hydrogeological environments. The first is represented by deep groundwater, the main groundwater resource in Apulia. The second hydrogeological environment, now of lesser importance than the deep aquifer in terms of size and use, is made up of some small shallow groundwater systems situated in post-calabrian sands and located in the eastern area. During some sampling cycles carried out in the studied area, water was withdrawn from both the deep aquifer and from the shallow groundwater. For every sample, the necessary parameters were determined for the physical and chemical characterisation of two different hydrogeological environments. Moreover, some chemical parameters indicating anthropogenic activities were determined. Analysis of the aerial distribution of the measured parameters has shown some main areas subject to different conditions of contamination risk, in accordance with the hydrogeological and geological features of the investigated area. In the south-eastern part of the investigated area, the important action performed by the surface aquifer for protecting the deep groundwater from contamination of anthropogenic origin is clear. On the other hand, in the shallow groundwater, areas of nitrate and nitrite contamination have been identified, which result from the extensive use of fertilizers.

  8. Analysis of microbiological contamination in mixed pressed ham and cooked sausage in Korea.

    Science.gov (United States)

    Park, Myoung-Su; Wang, Jun; Park, Joong-Hyun; Forghani, Fereidoun; Moon, Jin-San; Oh, Deog-Hwan

    2014-03-01

    The objective of this study was to investigate the microbial contamination levels (aerobic bacteria plate count [APC], coliforms, Escherichia coli, Staphylococcus aureus, and Listeria monocytogenes) in mixed pressed ham and cooked sausage. A total of 180 samples were collected from factories with and without hazard analysis critical control point (HACCP) systems at four steps: after chopping (AC), after mixing (AM), cooling after the first heating process, and cooling after the second heating process. For ham, APCs and coliform and E. coli counts increased when ingredients were added to the meat at the AC step. Final product APC was 1.63 to 1.85 log CFU/g, and coliforms and E. coli were not detected. S. aureus and L. monocytogenes were found in nine (15.0%) and six (10.0%) samples, respectively, but only at the AC and AM steps and not in the final product. Sausage results were similar to those for ham. The final product APC was 1.52 to 3.85 log CFU/g, and coliforms and E. coli were not detected. S. aureus and L. monocytogenes were found in 29 (24.2%) and 25 (20.8%) samples at the AC and AM steps, respectively, but not in the final product. These results indicate that the temperature and time of the first and second heating are of extreme importance to ensure the microbiological safety of the final product regardless of whether a HACCP system is in place. Microorganism contamination must be monitored regularly and regulations regarding sanitization during processing should be improved. Education regarding employee personal hygiene, environmental hygiene, prevention of cross-contamination, ingredient control, and step-by-step process control is needed to reduce the risk of food poisoning.

  9. Using discriminant analysis to assess polycyclic aromatic hydrocarbons contamination in Yongding New River.

    Science.gov (United States)

    Wang, Xiaojing; Zou, Zhihong; Zou, Hui

    2013-10-01

    Yongding New River has been polluted by polycyclic aromatic hydrocarbons (PAHs) which are carcinogenic and mutagenic. In three periods (the abundant water period, mean water period, dry water period), ten sites (totally 30 samples) in Yongding New River were clustered into four categories by hierarchical cluster analysis (hierarchical CA). In the same cluster, the samples had the same approximate contamination situation. In order to eliminate the dimensional differences, the data in each sample, containing 16 kinds of PAHs, were standardized with normal standardization and maximum difference standardization. According to the results of the cubic clustering criterion, pseudo F, and pseudo t (2) (PST2), the proper number of clustering for the 30 samples is 4. Before conducting hierarchical CA and K-means cluster analysis on the samples, we used principal component analysis to obtain another group data set. This data set was composed of the principal component scores which are uncorrelated variables. Hierarchical CA and K-means cluster analysis were used to classify the two data sets into four categories. With the classification results of hierarchical CA and K-means cluster analysis, discriminant analysis is applied to determine which method was better for normalization of the original data and which one was proper to cluster the samples and establish discriminant functions so that a new sample can be grouped into the right categories.

  10. Numerical modeling and experimental analysis of volatile contaminant removal from vertical flow filters

    NARCIS (Netherlands)

    De Biase, C.

    2012-01-01

    Vertical flow filters (unplanted) and vertical flow constructed wetlands (planted), simple and inexpensive technologies to treat effectively volatile organic compounds (VOCs) contaminated water, consist of containers filled with granular material which is intermittently fed with contaminated water.

  11. Deciphering drought-induced response patterns at the biochemical and molecular level in maize related to aflatoxin contamination resistance

    Science.gov (United States)

    Drought stress influences crop growth, decreases yield, and exacerbates Aspergillus flavus infection and pre-harvest aflatoxin contamination. In order to dissect drought stress-induced responses in maize, genotypes with contrasting levels of drought tolerance were used to investigate the physiologic...

  12. ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

    KAUST Repository

    Hungler, Arnaud

    2016-11-02

    Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for \\'crystallization and preliminary X-ray analysis\\' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data. A web server, titled ContaMiner, has been established, which allows fast molecular-replacement-based screening of crystallographic data against a database (ContaBase) of currently 62 potential contaminants. ContaMiner enables systematic screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for \\'crystallization and preliminary X-ray analysis\\' publications. © Arnaud Hungler et al. 2016.

  13. Geoelectrical time-lapse analysis for improved interpretation of data in a contaminated area

    Science.gov (United States)

    Chitea, Florina; Serban, Adrian; Ioane, Dumitru; Georgescu, Paul

    2014-05-01

    Non invasive geoelectrical studies are useful in the preliminary assessment of areas suspected to be contaminated but also in the investigation stage. Correctly adapted to the site specific situation, they are used to detect and investigate buried sources of pollution, to characterize the geology of the area, to detect the contaminated plume or to study the attenuation of pollution in case the appliance of an site-specific remediation techniques. Despite the improved technological acquisition techniques and the optimized inversion data algorithms, interpretation of geoelectrical data in still a challenging task, especially in a contaminated hydrogeological context. Beside the soil physical properties (composition, porosity, texture, etc.), moisture content and chemical composition of the pollutant are also influencing the measured parameter. Apparent electrical resistivity method was use in an area located near an Oil Refinery. Electrical measurements performed on profiles (transverse and along the direction of water flow -according to hydrological data) revealed the presence of contaminants by means of high resistivity anomalies. Using the same acquisition technique (Schlumberger array, same VES points, injection - AB - and voltage - MN - lines extension), measurements were repeated during time, along the same profiles. On the resulted electrical sections from 2006 to 2013, a dynamic situation regarding the pollution plume was observed. Time - lapse analysis, based on the calculation of resistivity differences between sets of data acquired along the same profile was applied, and data interpretation was made using the resulted sections. Significant variation between data sets (> 17% of apparent resistivity normalized differences) observed along the main profile were mainly ranging from the near surface (1.5 m) to an approximated depth (AB/2) of 10m. Using the time-lapse method, changes in the lateral and in depth extension of polluted areas could be observed and

  14. Sampling and Analysis Instruction for Evaluation of Residual Chromium Contamination in the Subsurface Soil at 100-C-7

    Energy Technology Data Exchange (ETDEWEB)

    W. S. Thompson

    2007-02-15

    This sampling and analysis instruction (SAI) provides the requirements for sample collection and laboratory analysis to evaluate the extent of hexavalent chromium contamination present in the soil below the 100-C-7 and 100-C-7:1 remedial action waste site excavations.

  15. Monitoring of Fasciola Species Contamination in Water Dropwort by cox1 Mitochondrial and ITS-2 rDNA Sequencing Analysis.

    Science.gov (United States)

    Choi, In-Wook; Kim, Hwang-Yong; Quan, Juan-Hua; Ryu, Jae-Gee; Sun, Rubing; Lee, Young-Ha

    2015-10-01

    Fascioliasis, a food-borne trematode zoonosis, is a disease primarily in cattle and sheep and occasionally in humans. Water dropwort (Oenanthe javanica), an aquatic perennial herb, is a common second intermediate host of Fasciola, and the fresh stems and leaves are widely used as a seasoning in the Korean diet. However, no information regarding Fasciola species contamination in water dropwort is available. Here, we collected 500 samples of water dropwort in 3 areas in Korea during February and March 2015, and the water dropwort contamination of Fasciola species was monitored by DNA sequencing analysis of the Fasciola hepatica and Fasciola gigantica specific mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 500 samples assessed, the presence of F. hepatica cox1 and 1TS-2 markers were detected in 2 samples, and F. hepatica contamination was confirmed by sequencing analysis. The nucleotide sequences of cox1 PCR products from the 2 F. hepatica-contaminated samples were 96.5% identical to the F. hepatica cox1 sequences in GenBank, whereas F. gigantica cox1 sequences were 46.8% similar with the sequence detected from the cox1 positive samples. However, F. gigantica cox1 and ITS-2 markers were not detected by PCR in the 500 samples of water dropwort. Collectively, in this survey of the water dropwort contamination with Fasciola species, very low prevalence of F. hepatica contamination was detected in the samples.

  16. Comparative analysis of doses to aquatic biota in water bodies impacted by radioactive contamination.

    Science.gov (United States)

    Kryshev, A I; Sazykina, T G

    2012-06-01

    Comparative analysis of doses to the reference species of freshwater biota was performed for the following water bodies in Russia or former USSR: Chernobyl NPPs cooling pond, Lakes Uruskul and Berdenish located in the Eastern Urals Radioactive Trace, Techa River, Yenisei River. It was concluded that the doses to biota were considerably different in the acute and chronic periods of radioactive contamination. The most vulnerable part of all considered aquatic ecosystems was benthic trophic chain. A numerical scale on the "dose rate - effects" relationships for fish was formulated. Threshold dose rates above which radiation effects can be expected in fish were evaluated to be the following: 1 mGy d(-1) for appearance of the first morbidity effects in fish; 5 mGy d(-1) for the first negative effects on reproduction system; 10 mGy d(-1) for the first effects on life shortening of fish. The results of dose assessment to biota were compared with the scale "dose rate - effects" and the literature data on the radiobiological effects observed in the considered water bodies. It was shown that in the most contaminated water bodies the dose rates were high enough to cause the radiobiological effects in fish. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. White Oak Creek Embayment site characterization and contaminant screening analysis. Environmental Restoration Program

    Energy Technology Data Exchange (ETDEWEB)

    Blaylock, B.G.; Ford, C.J.; Frank, M.L.; Hoffman, F.O.; Hook, L.A.

    1993-01-01

    Analyses of sediment samples collected near the mouth of White Oak Creek during the summer of 1990 revealed {sup 137}Cs concentrations [> 10{sup 6} Bq/kg dry wt (> 10{sup 4} pCi/g dry wt)] near the sediment surface. Available evidence indicates that these relatively high concentrations of {sup 137}Cs now at the sediment surface were released from White Oak Dam in the mid-1950s and had accumulated at depositionalsites in the embayment. These accumulated sediments are being eroded and transported downstream primarily during winter low-water levels by flood events and by a combination of normal downstream flow and the water turbulence created by the release of water from Melton Hill Dam during hydropower generation cycles. This report provides a more thorough characterization of the extent of contamination in WOCE than was previously available. Environmental samples collected from WOCE were analyzed for organic, inorganic, and radiological contaminants in fish, water, and sediment. These results were used to conduct a human health effects screening analysis. Walkover radiation surveys conducted inside the fenced area surrounding the WOCE at summer-pool (741 ft MSL) and at winter-pool (733 ft MSL) level, indicated a maximum exposure rate of 3 mR h{sup 1} 1 m above the soil surface.

  18. White light phase shifting interferometry and color fringe analysis for the detection of contaminants in water

    Science.gov (United States)

    Dubey, Vishesh; Singh, Veena; Ahmad, Azeem; Singh, Gyanendra; Mehta, Dalip Singh

    2016-03-01

    We report white light phase shifting interferometry in conjunction with color fringe analysis for the detection of contaminants in water such as Escherichia coli (E.coli), Campylobacter coli and Bacillus cereus. The experimental setup is based on a common path interferometer using Mirau interferometric objective lens. White light interferograms are recorded using a 3-chip color CCD camera based on prism technology. The 3-chip color camera have lesser color cross talk and better spatial resolution in comparison to single chip CCD camera. A piezo-electric transducer (PZT) phase shifter is fixed with the Mirau objective and they are attached with a conventional microscope. Five phase shifted white light interferograms are recorded by the 3-chip color CCD camera and each phase shifted interferogram is decomposed into the red, green and blue constituent colors, thus making three sets of five phase shifted intererograms for three different colors from a single set of white light interferogram. This makes the system less time consuming and have lesser effect due to surrounding environment. Initially 3D phase maps of the bacteria are reconstructed for red, green and blue wavelengths from these interferograms using MATLAB, from these phase maps we determines the refractive index (RI) of the bacteria. Experimental results of 3D shape measurement and RI at multiple wavelengths will be presented. These results might find applications for detection of contaminants in water without using any chemical processing and fluorescent dyes.

  19. Distributed Channel Estimation and Pilot Contamination Analysis for Massive MIMO-OFDM Systems

    KAUST Repository

    Zaib, Alam

    2016-07-22

    By virtue of large antenna arrays, massive MIMO systems have a potential to yield higher spectral and energy efficiency in comparison with the conventional MIMO systems. This paper addresses uplink channel estimation in massive MIMO-OFDM systems with frequency selective channels. We propose an efficient distributed minimum mean square error (MMSE) algorithm that can achieve near optimal channel estimates at low complexity by exploiting the strong spatial correlation among antenna array elements. The proposed method involves solving a reduced dimensional MMSE problem at each antenna followed by a repetitive sharing of information through collaboration among neighboring array elements. To further enhance the channel estimates and/or reduce the number of reserved pilot tones, we propose a data-aided estimation technique that relies on finding a set of most reliable data carriers. Furthermore, we use stochastic geometry to quantify the pilot contamination, and in turn use this information to analyze the effect of pilot contamination on channel MSE. The simulation results validate our analysis and show near optimal performance of the proposed estimation algorithms.

  20. Application of molecularly imprinted and non-imprinted polymers for removal of emerging contaminants in water and wastewater treatment: a review.

    Science.gov (United States)

    Murray, Audrey; Ormeci, Banu

    2012-11-01

    Over the past decade, several studies have reported trace levels of endocrine disrupting compounds, pharmaceuticals, and personal care products in surface waters, drinking water, and wastewater effluents. There has also been an increased concern about the ecological and human health impact of these contaminants, and their removal from water and wastewater has become a priority. Traditional treatment processes are limited in their ability to remove emerging contaminants from water, and there is a need for new technologies that are effective and feasible. This paper presents a review on recent research results on molecularly imprinted (MIP) and non-imprinted (NIP) polymers and evaluates their potential as a treatment method for the removal of emerging contaminants from water and wastewater. It also discusses the relative benefits and limitations of using MIP or NIP for water and wastewater treatment. MIP, and in particular NIP, offer promising applications for wastewater treatment, but their toxicity and possible health effects should be carefully studied before they are considered for drinking water treatment. More research is also required to determine how best to incorporate MIP and NIP in treatment plants.

  1. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

    Directory of Open Access Journals (Sweden)

    von Haeseler Arndt

    2004-06-01

    Full Text Available Abstract Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004 are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

  2. [Inhibition of Low Molecular Organic Acids on the Activity of Acidithiobacillus Species and Its Effect on the Removal of Heavy Metals from Contaminated Soil].

    Science.gov (United States)

    Song, Yong-wei; Wang, He-rul; Cao, Yan-xiao; Li, Fei; Cui, Chun-hong; Zhou, Li

    2016-05-15

    Application of organic fertilizer can reduce the solubility and bioavailability of heavy metals in contaminated soil, but in the flooded anaerobic environment, organic fertilizer will be decomposed to produce a large number of low molecular organic acids, which can inhibit the biological activity of Acidithiobacillus species. Batch cultures studies showed that the monocarboxylic organic acids including formic acid, acetic acid, propionic acid, and butyric acid exhibited a marked toxicity to Acidithiobacillus species, as indicated by that 90% of inhibitory rate for Fe2 and So oxidation in 72 h were achieved at extremely low concentrations of 41.2 mg · L⁻¹, 78.3 mg · L⁻¹, 43.2 mg · L⁻¹, 123.4 mg · L⁻¹ and 81.9 mg 230. 4 mg · L⁻¹, 170.1 mg · L⁻¹, 123.4 mg · L⁻¹ respectively. Of these organic acids, formic acid was the most toxic one as indicated by that Fe2 and So oxidation was almost entirely inhibited at a low concentration. In addition, it was found that Acidithiobacillus ferrooxidans was more sensitive to low molecular organic acids than Acidithiobacillus thiooxidans. What's more, there was little effect on biological acidification process of heavy metal contaminated soil when organic acids were added at initial stage (Oh), but it was completely inhibited when these acids were added after 12 h of conventional biological acidification, thus decreasing the efficiency of heavy metals dissolution from soil.

  3. Atomistic modeling of peptide adsorption on rutile (100) in the presence of water and of contamination by low molecular weight alcohols.

    Science.gov (United States)

    Friedrichs, Wenke; Langel, Walter

    2014-09-01

    Previous models for the interface between titanium implants and biosystems take into account the oxide passivation layer and the hydroxylation, but omit the hydrocarbon contamination on air-exposed samples. The authors develop a consistent model for the contamination of the rutile (100) surface by small alcohols, which are known to be present in ambient atmosphere, and use this approach in molecular dynamics calculations. Contact angle evaluation reveals that hydrophobic surfaces can be generated. During molecular dynamics simulations with three peptides (RPRGFGMSRERQ, WFCLLGCDAGCW, and RKLPDA), polar side chains penetrate the hydrocarbons and become immobilized on the titanium dioxide. In the carbon layer, the peptide recognizes a hydrophobic environment, which was not present on the clean surface, and the authors attribute changes in the secondary structure in one case to this interaction. The authors further include the popular Matsui-Akaogi approach [M. Matsui and M. Akaogi, Mol. Simul. 6, 239 (1991)] into the frame of the AMBER force field and quote van der Waals parameters for fitting the original Buckingham part. With the new potential, the authors evaluated lattice parameters, thermal fluctuation, and bulk modulus. Translational diffusion coefficients and dipole autocorrelation functions of water on the surface are discussed in relation to surface properties, and it is shown that the water layers are more rigid than on earlier titanium dioxide models, and that contacts between peptide and surface are less direct.

  4. Status of cleanliness maintaining in target beam enclosures in SG III facilities and contamination sources analysis

    Science.gov (United States)

    Wang, Meicong; Wang, Baoxu; Miao, Xinxiang; Cheng, Xiaofeng; Wu, Wenkai

    2014-09-01

    In SGIII lasers there are large number of transport mirrors in target beam enclosures. Surface contaminations could easily introduce optical damage, and increase laser energy loss under high laser influence conditions. It is significant for lasers to control contamination and maintain cleanliness. In SGIII prototype, the target beam enclosures are test to be seriously contaminated after about two years of routine operations. Volume cleanliness in mirror boxes are monitored through 24 hours before, during and after a shot. Ingredients of particle and organics are tested. Reconstructions are performed on the mirror boxes to remove debris and keep cleanliness for upward facing surface of mirrors effectively. In SGIII facility some contaminations are found in beam enclosures and on the mirrors after several months of test running. Contaminations sources are analyzed to further know about the contamination mechanisms. Some engineering countermeasures are introduced for controlling contamination and keeping cleanliness for optics.

  5. An Atom Trap Trace Analysis System for Measuring Krypton Contamination in Xenon Dark Matter Detectors

    CERN Document Server

    Aprile, Elena; Loose, Andre; Goetzke, Luke W; Zelevinsky, Tanya

    2013-01-01

    We have developed an atom trap trace analysis (ATTA) system to measure Kr in Xe at the part per trillion (ppt) level, a prerequisite for the sensitivity achievable with liquid xenon dark matter detectors beyond the current generation. Since Ar and Kr have similar laser cooling wavelengths, the apparatus has been tested with Ar to avoid contamination prior to measuring Xe samples. A radio-frequency (RF) plasma discharge generates a beam of metastable Ar which is optically collimated, slowed, and trapped using standard magneto-optical techniques. We detect the fluorescence of single trapped $^{40}$Ar atoms with a signal to noise ratio of 5. The measured system efficiency of $3 \\times 10^{-9}$ for Ar corresponds to an expected Kr in Xe sensitivity at the ppt level.

  6. Probabilistic analysis of the efficiency of reference levels in the evaluation of ground contamination

    Directory of Open Access Journals (Sweden)

    A. Callaba de Roa

    2002-12-01

    Full Text Available The developing of regulations for contaminated soils in Spain is taking place under considerations of specific uses for soil and also taking in to account environmental risk. Based on basic principles of risk assessment, a methodology to derive threshold concentrations for substances in soil has been proposed by IGME (Spanish Geological Survey. Regard these threshold concentrations an instrumental issue is to assess their efficiency (trend to produce few false positives and negatives by using them in soil pollution assessment. A probabilistic analysis for efficiency of these screening concentrations has been done by means of a Monte Carlo simulation exercise. Taking into account simulation results, threshold values show a high efficiency with negligible probabilities to yield false positives and probabilities around 0.1 for false positives.

  7. Identification and evaluation of cyp1a transcript expression in fish as molecular biomarker for petroleum contamination in tropical fresh water ecosystems.

    Science.gov (United States)

    dos Anjos, Nislanha Ana; Schulze, Tobias; Brack, Werner; Val, Adalberto Luis; Schirmer, Kristin; Scholz, Stefan

    2011-05-01

    In order to monitor potential contamination deriving from exploration and transport of oil in the Urucu region (Brazil), there is a need to establish suitable biomarkers for native Amazonian fish. Therefore, the transcript expression of various potentially sensitive genes (ahr2(1), cyp1a, hmox1, hsp70, maft, mt, nfe212, gstp1 and nqo1) in fish exposed to water soluble fractions of oil (WSF) was compared. The analysis was first performed in an established laboratory model, the zebrafish embryo. The cyp1a gene proved to be the most sensitive and robust marker for oil contamination and, hence, was selected to study the effect of oil-derived contaminants in the Amazonian cichlid Astronotus ocellatus. Induction of cyp1a transcript expression was observed for ≥0.0061% (v/v) WSFs. In liver samples of fish, collected from different lakes in the Urucu oil mining area, no elevated expression of cyp1a transcripts was observed. The data demonstrate the high sensitivity of cyp1a as indicator of oil exposure; further studies should be considered to test its usefulness at known contaminated sites and to evaluate influential factors by, e.g. mesocosm experiments. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. A quantitative analysis of IRAS maps of molecular clouds

    Science.gov (United States)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  9. Deterministic sensitivity analysis for the numerical simulation of contaminants transport; Analyse de sensibilite deterministe pour la simulation numerique du transfert de contaminants

    Energy Technology Data Exchange (ETDEWEB)

    Marchand, E

    2007-12-15

    The questions of safety and uncertainty are central to feasibility studies for an underground nuclear waste storage site, in particular the evaluation of uncertainties about safety indicators which are due to uncertainties concerning properties of the subsoil or of the contaminants. The global approach through probabilistic Monte Carlo methods gives good results, but it requires a large number of simulations. The deterministic method investigated here is complementary. Based on the Singular Value Decomposition of the derivative of the model, it gives only local information, but it is much less demanding in computing time. The flow model follows Darcy's law and the transport of radionuclides around the storage site follows a linear convection-diffusion equation. Manual and automatic differentiation are compared for these models using direct and adjoint modes. A comparative study of both probabilistic and deterministic approaches for the sensitivity analysis of fluxes of contaminants through outlet channels with respect to variations of input parameters is carried out with realistic data provided by ANDRA. Generic tools for sensitivity analysis and code coupling are developed in the Caml language. The user of these generic platforms has only to provide the specific part of the application in any language of his choice. We also present a study about two-phase air/water partially saturated flows in hydrogeology concerning the limitations of the Richards approximation and of the global pressure formulation used in petroleum engineering. (author)

  10. Tailoring molecularly imprinted polymer beads for alternariol recognition and analysis by a screening with mycotoxin surrogates.

    Science.gov (United States)

    Abou-Hany, Rahma A G; Urraca, Javier L; Descalzo, Ana B; Gómez-Arribas, Lidia N; Moreno-Bondi, María C; Orellana, Guillermo

    2015-12-18

    Molecularly imprinted porous polymer microspheres have been prepared for selective binding of alternariol (AOH), a phenolic mycotoxin produced by Alternaria fungi. In order to lead the synthesis of recognition materials, four original AOH surrogates have been designed, prepared and characterized. They bear different number of phenol groups in various positions and different degree of O-methylation on the dibenzo[b,d]pyran-6-one skeleton. A comprehensive library of mixtures of basic, acidic or neutral monomers, with divinylbenzene or ethyleneglycol dimethacrylate as cross-linkers, were polymerized at a small scale in the presence of the four molecular mimics of the toxin molecule. This polymer screening has allowed selection of the optimal composition of the microbeads (N-(2-aminoethyl)methacrylamide, EAMA, and ethylene glycol dimethacrylate). The latter are able to bind AOH in water-acetonitrile (80:20, v/v) with an affinity constant of 109±10mM(-1) and a total number of binding sites of 35±2μmolg(-1), being alternariol monomethylether the only competitor species. Moreover, (1)H NMR titrations have unveiled a 1:2 surrogate-to-EAMA stoichiometry, the exact interaction sites and a binding constant of 1.5×10(4)M(-2). A molecularly imprinted solid phase extraction (MISPE) method has been optimized for selective isolation of the mycotoxin from aqueous samples upon a discriminating wash with 3mL of acetonitrile/water (20:80, v/v) followed by determination by HPLC with fluorescence detection. The method has been applied, in combination to ultrasound-assisted extraction, to the analysis of AOH in tomato samples fortified with the mycotoxin at five concentration levels (33-110μgkg(-1)), with recoveries in the range of 81-103% (RSD n=6). To the best of our knowledge, this is the first imprinted material capable of molecularly recognizing this widespread food contaminant.

  11. Forensic application of microbiological culture analysis to identify mail intentionally contaminated with Bacillus anthracis spores.

    Science.gov (United States)

    Beecher, Douglas J

    2006-08-01

    The discovery of a letter intentionally filled with dried Bacillus anthracis spores in the office of a United States senator prompted the collection and quarantine of all mail in congressional buildings. This mail was subsequently searched for additional intentionally contaminated letters. A microbiological sampling strategy was used to locate heavy contamination within the 642 separate plastic bags containing the mail. Swab sampling identified 20 bags for manual and visual examination. Air sampling within the 20 bags indicated that one bag was orders of magnitude more contaminated than all the others. This bag contained a letter addressed to Senator Patrick Leahy that had been loaded with dried B. anthracis spores. Microbiological sampling of compartmentalized batches of mail proved to be efficient and relatively safe. Efficiency was increased by inoculating culture media in the hot zone rather than transferring swab samples to a laboratory for inoculation. All mail sampling was complete within 4 days with minimal contamination of the sampling environment or personnel. However, physically handling the intentionally contaminated letter proved to be exceptionally hazardous, as did sorting of cross-contaminated mail, which resulted in generation of hazardous aerosol and extensive contamination of protective clothing. Nearly 8 x 10(6) CFU was removed from the most highly cross-contaminated piece of mail found. Tracking data indicated that this and other heavily contaminated envelopes had been processed through the same mail sorting equipment as, and within 1 s of, two intentionally contaminated letters.

  12. Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

    Science.gov (United States)

    Gilbert, Kathleen M.; Skawinski, William J.; Misra, Milind; Paris, Kristina A.; Naik, Neelam H.; Buono, Ronald A.; Deutsch, Howard M.; Venanzi, Carol A.

    2004-11-01

    Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl

  13. Molecular phylogenetic analysis of an endangered Mexican sparrow: Spizella wortheni.

    Science.gov (United States)

    Canales-del-Castillo, Ricardo; Klicka, John; Favela, Susana; González-Rojas, José I

    2010-12-01

    The Worthen's Sparrow (Spizella wortheni) is an endemic bird species of the Mexican Plateau that is protected by Mexican law. Considering its limited range (25 km(2)), small population size (100-120 individuals), and declining population, it is one of the most endangered avian species in North America. Although it has been assumed to be the sister taxon of the Field Sparrow (Spizella pusilla), the systematic and evolutionary relationships of Worthen's Sparrow have never been tested using modern molecular phylogenetic methods. We addressed the molecular phylogeny of S. wortheni analyzing six mitochondrial genes (3571 bp) from all of the natural members of the genus Spizella. Our maximum likelihood and Bayeasian analysis indicate that despite the superficial similarity, S. wortheni is not the sister taxon of S. pusilla, but is instead most closely related to the Brewer's Sparrow (Spizella breweri). Also new insights about the phylogenetics relationships of the Spizella genera are presented.

  14. Fetus in fetu: molecular analysis of a fetiform mass.

    Science.gov (United States)

    Hing, A; Corteville, J; Foglia, R P; Bliss, D P; Donis-Keller, H; Dowton, S B

    1993-09-01

    Fetus-in-fetu is a rare condition presenting as a calcified intra-abdominal mass in the newborn infant. Over 50 cases of fetus-in-fetu have been reported since 1800. Karyotype analysis in 8 cases and protein polymorphisms in 4 documented identical findings in the host and fetiform mass. We report a case of fetus-in-fetu in a newborn female including cytogenetic and molecular studies of both the host and mass. Genotypic information from 7 polymerase chain reaction (PCR) assays representing 4 chromosomes demonstrates heterozygous and identical alleles in the infant and fetus-in-fetu at all loci studied. A review of the literature is provided including a discussion regarding the impact of molecular data on present hypotheses of fetus-in-fetu pathogenesis.

  15. Mechanism Analysis and Propagation Model of Heavy Metals Contamination in Urban Topsoil

    Directory of Open Access Journals (Sweden)

    Zhao-wei Wang

    2013-02-01

    Full Text Available In order to further research on the polluting condition and spreading features of heavy metals in urban surface soil, this study makes statistical analysis on indexes of 8 heavy metal concentrations. Then Are GIS geo-statistical analyst was used for Kriging interpolation of each kind of heavy metal concentration before figuring out the spatial distribution. Firstly, heavy metal contamination was analyzed by single-element pollution evaluation and multi-element pollution evaluation, before rationality analysis. Then, correlation extents between heavy polluting metals were calculated in each region by rationality analysis, leading to the correlations between the heavy metals. Finally, based on propagating features of different heavy metals, propagation models in water and atmosphere were established. Additionally, according to heavy metal distribution map, distribution point of high concentration was searched. With the assumption of the number of pollution source, theoretical concentration of sample point could be figured out, after the superposition of pollution intensity using propagation model based on data of the distribution points. Thus, the optimization model was established for locating the pollution source by minimizing the difference between theoretical value and actual value.

  16. Analysis of radwaste management alternatives during dismantling of Ignalina NPP systems with low level contamination

    Energy Technology Data Exchange (ETDEWEB)

    Poskas, Gintautas [Lithuanian Energy Institute, Kaunas (Lithuania). Nuclear Engineering Lab.; Kaunas Univ. of Technology (Lithuania); Poskas, Povilas; Simonis, Audrius [Lithuanian Energy Institute, Kaunas (Lithuania). Nuclear Engineering Lab.

    2013-12-15

    Ignalina NPP was operating two RBMK-1500 reactors which are under decommissioning now. In this paper, analysis on radwaste management alternatives during the dismantling of systems with low level contamination and different types of components in buildings 117/1 and V1 are presented. After situation analysis and collection of the primary information related to components' physical and radiological characteristics, location and other data, two alternatives for radwaste management during the dismantling were formulated and evaluated: the first one (A1) when the decontamination of the dismantled components is performed (if it is reasonable), and the second one (A2) when no decontamination of the dismantled components is performed and after the dismantling, the components are routed to appropriate waste storage or disposal sites. To select the preferable alternative, MCDA method - AHP (Analytic Hierarchy Process) is applied. Hierarchical lists of decision criteria, necessary for assessment of alternatives performance, are formulated. Quantitative decision criteria values for these alternatives are calculated using software DECRAD, which was developed by Lithuanian Energy Institute Nuclear Engineering Laboratory. Qualitative decision criteria are evaluated using expert judgment. Analysis results show that alternative A1 has a preference against alternative A2. (orig.)

  17. Enantioselective stable isotope analysis (ESIA) — A new concept to evaluate the environmental fate of chiral organic contaminants

    Energy Technology Data Exchange (ETDEWEB)

    Badea, Silviu-Laurentiu, E-mail: badeasilviu@gmail.com [Department of Chemistry, Umeå University, SE-901 87 Umeå (Sweden); Danet, Andrei-Florin [Department of Analytical Chemistry, University of Bucharest, Faculty of Chemistry, 90-92 Panduri Str., Bucharest 050657 (Romania)

    2015-05-01

    Since 2011, the enantiospecific stable carbon isotope analysis (ESIA) has emerged as an innovative technique to assess the environmental fate of chiral emerging compounds by combining in one experimental technique both compound specific isotope analysis (CSIA) and enantioselective analysis. To date, the ESIA was applied for four classes of compounds: α-hexachlorocyclohexane (α-HCH), polar herbicides (phenoxy acids), synthetic polycyclic musk galaxolide (HHCB), and phenoxyalkanoic methyl herbicides. From an analytical point of view there are factors that are hindering the application of ESIA methods for the field samples: (i.e. amounts of target analyte, matrix effects, GC resolution) and overcoming these factors is challenging. While ESIA was shown as a mature technique for the first three abovementioned class of compounds, no isotope analysis of individual enantiomers could be performed for phenoxyalkanoic methyl herbicides. With respect to field studies, one study showed that ESIA might be a promising tool to distinguish between biotic and abiotic transformation pathways of chiral organic contaminants and even to differentiate between their aerobic and anaerobic biotransformation pathways. The development of ESIA methods for new chiral emerging contaminants in combination with development of multi-element isotope analysis will contribute to a better characterization of transformation pathways of chiral organic contaminants. - Highlights: • ESIA is an innovative technique to assess the environmental fate of chiral pollutants • Overcoming the analytical limitations of ESIA is challenging • Development of ESIA methods for new chiral emerging contaminants is needed.

  18. Environmental Analysis of Endocrine Disrupting Effects from Hydrocarbon Contaminants in the Ecosystem

    Energy Technology Data Exchange (ETDEWEB)

    McLachlan, John A.

    2000-06-01

    This annual report summarizes the progress of three years of a three-year grant awarded to the Center for Bioenvironmental Research (CBR) at Tulane and Xavier Universities. The objective of this project is to determine how environmental contaminants, namely hydrocarbons, can act as hormones or anti-hormones in different species present in aquatic ecosystems. The three major areas of research include (1) a biotechnology based screening system to identify potential hormone mimics and antagonists; (2) an animal screening system to identify biomarkers of endocrine effects; and (3) a literature review to identify compounds at various DOE sites that are potential endocrine disruptors. Species of particular focus in this study are those which can serve as sentinel species (e.g., amphibians) and, thus, provide early warning signals for more widespread impacts on an ecosystem and its wildlife and human inhabitants. The focus of the literature research was to provide an analysis of the contaminants located on or around various Department of Energy (DOE) sites that are or have the potential to function as endocrine disruptors and to correlate the need for studying endocrine disruptors to DOE's programmatic needs. Previous research within the Center for Bioenvironmental Research at Tulane and Xavier Universities has focused on understanding the effects of environmental agents on the human and wildlife health and disease. In particular this research has focused on how exogenous agents can function to mimic or disrupt normal endocrine signaling, i.e. estrogen, thyroid within various systems from whole animal studies with fish, amphibians and insects to human cancer cell lines. Significant work has focused on the estrogenic and anti-estrogenic action of both synthetic organochlorine chemicals and naturally produced phytochemicals. Recent projects have extended these research objectives to examination of these environmental agents on the symbiotic relationship between

  19. Trace Contaminant Control for the International Space Station's Node 1- Analysis, Design, and Verification

    Science.gov (United States)

    Perry, J. L.

    2017-01-01

    Trace chemical contaminant generation inside crewed spacecraft cabins is a technical and medical problem that must be continuously evaluated. Although passive control through materials selection and active control by adsorption and catalytic oxidation devices is employed during normal operations of a spacecraft, contaminant buildup can still become a problem. Buildup is particularly troublesome during the stages between the final closure of a spacecraft during ground processing and the time that a crewmember enters for the first time during the mission. Typically, the elapsed time between preflight closure and first entry on orbit for spacecraft such as Spacelab modules was 30 days. During that time, the active contamination control systems are not activated and contaminants can potentially build up to levels which exceed the spacecraft maximum allowable concentrations (SMACs) specified by NASA toxicology experts. To prevent excessively high contamination levels at crew entry, the Spacelab active contamination control system was operated for 53 hours just before launch.

  20. Mitochondrial proteomic analysis reveals the molecular mechanisms underlying reproductive toxicity of zearalenone in MLTC-1 cells.

    Science.gov (United States)

    Li, Yuzhe; Zhang, Boyang; Huang, Kunlun; He, Xiaoyun; Luo, YunBo; Liang, Rui; Luo, Haoshu; Shen, Xiao Li; Xu, Wentao

    2014-10-03

    Zearalenone (ZEA), a Fusarium mycotoxin that contaminates cereal crops worldwide, has been shown to affect the male reproductive system and trigger reactive oxygen species (ROS) generation. However, the mechanisms of its toxicity have not been fully understood. Because mitochondrion is a key organelle involved in producing ROS and generating metabolic intermediates for biosynthesis, an iTRAQ-based mitoproteomics approach was employed to identify the molecular mechanism of zearalenone toxicity using mitochondria of mouse Leydig tumor cells (MLTC-1). A total of 2014 nonredundant proteins were identified, among which 1401 proteins (69.56%) were overlapped. There were 52 differentially expressed proteins in response to ZEA, and they were primarily involved in energy metabolism, molecular transport and endocrine-related functions. Consistent with mitochondrial proteomic analysis, the ATP and intracellular Ca(2+) levels increased after ZEA treatment. The results suggest that lipid metabolism changed significantly after low-dose ZEA exposure, resulting in two alterations. One is the increase in energy production through promoted fatty acid uptake and β-oxidation, along with excessive oxidative stress; the other is an inhibition of steroidogenesis and esterification, possibly resulting in reduced hormone secretion. A hypothetical model of ZEA-induced mitochondrial damage is proposed to provide a framework for the mechanism of ZEA toxicity. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. Microbial and molecular techniques to evaluate and to implement in-situ biodegradation potential and activity at sites contaminated with aromatic and chlorinated hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Karg, F. [HPC Envirotec / France and HPC AG (Germany); Henkler, Ch. [Planreal (Switzerland)

    2005-07-01

    Intrinsic bio-remediation harnesses the ability of indigenous microorganisms to degrade contaminants that are present in soil and groundwater. Over the past decade many environmental regulatory agencies especially in Europe have come to recognize the importance of these natural processes in contaminant attenuation. In order to use in-situ bio-remediation to clean up a site successfully it is necessary to investigate the indigenous microbial population and its potential activity to degrade the contaminants of concern (COCs). The evaluation of naturally-occurring degradative activity in initial screening of soil and groundwater samples using recently developed molecular and microbial methods may allow for the implementation of a contaminant reduction and management program without the need for fully engineered remediation intervention. Limited engineering approaches (nutrient delivery etc.) can be implemented to support naturally-occurring bio-restoration processes to achieve a controlled, dynamic attenuation of COCs. Techniques for monitoring pollutant-degrading microorganisms were previously limited to standard culturing techniques. More recently, techniques based upon detection of genetic elements and metabolic activities have been developed in collaboration with university partners Europe, especially in France. The modern techniques are more sensitive for monitoring microbial populations, metabolic activity and the genetic potential to degrade the COCs, and avoid the need for cultivation of microbes under artificial conditions in the laboratory. Especially the application of PCR-Tests (Polymerase Chain Reaction) are able to quantify the Genetic Potential of Pollutant Microbiological Degradation on a contaminated site. This enables to use very economic in-situ site rehabilitation strategies as for example (Dynamic Natural Attenuation). For this modern application of these new strategies PLANREAL created with HPC Envirotec and together with a French University

  2. Isolation, molecular characterization and phylogenetic analysis of canine parvovirus.

    Science.gov (United States)

    Mohan Raj, J; Mukhopadhyay, H K; Thanislass, J; Antony, P X; Pillai, R M

    2010-12-01

    Canine parvovirus type 2 (CPV-2) causes acute haemorrhagic enteritis in dogs. Canine parvovirus is prone to genetic evolution and has undergone several mutations that produced different strains like CPV-2a, CPV-2b, New CPV-2a, New CPV-2b and CPV-2c in the past three decades. Mutations affecting the VP2 gene of CPV have been responsible for evolution of different antigenic variants. Sequence analysis of VP2 gene of the virus and subsequent characterization is important for molecular epidemiology. The present study was conducted to isolate and to characterize the virus by amplifying partial VP2 gene and further sequence analysis and also to estimate phylogenetic relationship of field virus with the reference strains. Out of 77 samples, 51 samples were found to be positive by PCR and all the 51 samples were subjected for virus isolation in CRFK cell line. Sixteen viruses could be isolated and 10 randomly selected isolates were subjected to sequence analysis along with four random clinical samples. All the 10 isolates and 4 clinical samples were characterized as New CPV-2a (CPV2a with 297-Ser→Ala). One of the field isolates was found to be phylogenetically closely related to New CPV-2a strains of Japan and India; another field isolates was found to share ancestral origins with New CPV-2a strains of Korea, USA, Italy, Brazil, Germany, Taiwan and Vietnam; rest other sequences had distinct lineage but shared molecular relationship with New CPV-2a reference strains.

  3. [Primary failure of eruption (PFE). Clinical and molecular genetics analysis].

    Science.gov (United States)

    Stellzig-Eisenhauer, Angelika; Decker, Eva; Meyer-Marcotty, Philipp; Rau, Christiane; Fiebig, Britta S; Kress, Wolfram; Saar, Kathrin; Rüschendorf, Franz; Hubner, Norbert; Grimm, Tiemo; Witt, Emil; Weber, Bernhard H F

    2013-09-01

    The term "primary failure of eruption" (PFE) refers to the complete or partial failure of a primary non-ankylosed tooth to erupt due to a disturbance of the eruption mechanism. Up to now, the molecular basis for this failure was unknown. Four families were studied in whom at least two members were affected by non-syndromic PFE as part of a clinical and molecular genetics study. Radiological diagnostics (OPTs) were carried out in all patients and their unaffected relatives (control group). The genetic analysis included a genomewide linkage analysis followed by direct DNA sequencing of positional candidate genes. Starting from the index patients, we were able to reconstruct pedigrees over two and/or three generations in the families that indicated an autosomal-dominant mode of inheritance of non-syndromic PFE. Fifteen patients were diagnosed with PFE. Gender distribution was nearly equal (7 female, 8 male). Molecular genetic analysis of the PTHR1 gene revealed three distinct heterozygous mutations (c.1050-3C>G; c.543 + 1G>A; c.463G>T). Unaffected persons exhibited no mutations. Knowledge of the genetic causes of non-syndromic PFE can now be used for the differential diagnosis of eruption failure. It permits affected family members to be identified early and may lead to new treatment possibilities in the long term. The genetically-verified diagnosis of "primary failure of eruption" can protect patients and orthodontists from years of futile treatment, because orthodontic treatment alone does not lead to success. Moreover, it has a negative influence on unaffected teeth and areas of the jaw. © EDP Sciences, SFODF, 2013.

  4. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident

    Energy Technology Data Exchange (ETDEWEB)

    Kasai, Y.; Kishira, H.; Syutsubo, K.; Harayama, S.

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, {alpha}-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10{sup 5} to 1.6 x 10{sup 6} bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation. (Author)

  5. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident.

    Science.gov (United States)

    Kasai, Y; Kishira, H; Syutsubo, K; Harayama, S

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, alpha-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10(5) to 1.6 x 10(6) bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation.

  6. Crosslinkable mixed matrix membranes with surface modified molecular sieves for natural gas purification: II. Performance characterization under contaminated feed conditions

    KAUST Repository

    Ward, Jason K.

    2011-07-01

    Mixed matrix membranes (MMMs) composed of the crosslinkable polyimide PDMC and surface modified (SM) SSZ-13 have recently been shown to enhance carbon dioxide permeability and carbon dioxide/methane selectivity versus neat PDMC films by as much as 47% and 13%, respectively (Part I). The previous film characterization, however, was performed using ideal, clean mixed gas feeds. In this paper, PDMC/SSZ-13 MMMs are further characterized using more realistic mixed gases containing low concentrations (500 or 1000. ppm) of toluene as a model contaminant. Mixed matrix membranes are shown to outperform pure PDMC films in the presence of toluene with 43% greater carbon dioxide permeability and 12% greater carbon dioxide/selectivity at 35 °C and 700 psia feed pressure. These results suggest that MMMs-in addition to exhibiting enhanced transport properties-may mitigate performance degradation due to antiplasticization effects. Moreover, the analyses presented here show that the reduction in separation performance by trace contaminant-accelerated physical aging can be suppressed greatly with MMMs. © 2011 Elsevier B.V.

  7. Probabilistic Round Trip Contamination Analysis of a Mars Sample Acquisition and Handling Process Using Markovian Decompositions

    Science.gov (United States)

    Hudson, Nicolas; Lin, Ying; Barengoltz, Jack

    2010-01-01

    A method for evaluating the probability of a Viable Earth Microorganism (VEM) contaminating a sample during the sample acquisition and handling (SAH) process of a potential future Mars Sample Return mission is developed. A scenario where multiple core samples would be acquired using a rotary percussive coring tool, deployed from an arm on a MER class rover is analyzed. The analysis is conducted in a structured way by decomposing sample acquisition and handling process into a series of discrete time steps, and breaking the physical system into a set of relevant components. At each discrete time step, two key functions are defined: The probability of a VEM being released from each component, and the transport matrix, which represents the probability of VEM transport from one component to another. By defining the expected the number of VEMs on each component at the start of the sampling process, these decompositions allow the expected number of VEMs on each component at each sampling step to be represented as a Markov chain. This formalism provides a rigorous mathematical framework in which to analyze the probability of a VEM entering the sample chain, as well as making the analysis tractable by breaking the process down into small analyzable steps.

  8. Transuranic-contaminated solid waste Treatment Development Facility. Final safety analysis report

    Energy Technology Data Exchange (ETDEWEB)

    Warner, C.L. (comp.)

    1979-07-01

    The Final Safety Analysis Report (FSAR) for the Transuranic-Contaminated Solid-Waste Treatment Facility has been prepared in compliance with the Department of Energy (DOE) Manual Chapter 0531, Safety of Nonreactor Nuclear Facilities. The Treatment Development Facility (TDF) at the Los Alamos Scientific Laboratory is a research and development facility dedicated to the study of radioactive-waste-management processes. This analysis addresses site assessment, facility design and construction, and the design and operating characteristics of the first study process, controlled air incineration and aqueous scrub off-gas treatment with respect to both normal and accident conditions. The credible accidents having potentially serious consequences relative to the operation of the facility and the first process have been analyzed and the consequences of each postulated credible accident are presented. Descriptions of the control systems, engineered safeguards, and administrative and operational features designed to prevent or mitigate the consequences of such accidents are presented. The essential features of the operating and emergency procedures, environmental protection and monitoring programs, as well as the health and safety, quality assurance, and employee training programs are described.

  9. Probabilistic Round Trip Contamination Analysis of a Mars Sample Acquisition and Handling Process Using Markovian Decompositions

    Science.gov (United States)

    Hudson, Nicolas; Lin, Ying; Barengoltz, Jack

    2010-01-01

    A method for evaluating the probability of a Viable Earth Microorganism (VEM) contaminating a sample during the sample acquisition and handling (SAH) process of a potential future Mars Sample Return mission is developed. A scenario where multiple core samples would be acquired using a rotary percussive coring tool, deployed from an arm on a MER class rover is analyzed. The analysis is conducted in a structured way by decomposing sample acquisition and handling process into a series of discrete time steps, and breaking the physical system into a set of relevant components. At each discrete time step, two key functions are defined: The probability of a VEM being released from each component, and the transport matrix, which represents the probability of VEM transport from one component to another. By defining the expected the number of VEMs on each component at the start of the sampling process, these decompositions allow the expected number of VEMs on each component at each sampling step to be represented as a Markov chain. This formalism provides a rigorous mathematical framework in which to analyze the probability of a VEM entering the sample chain, as well as making the analysis tractable by breaking the process down into small analyzable steps.

  10. Vadose Zone Contaminant Fate and Transport Analysis for the 216-B-26 Trench

    Energy Technology Data Exchange (ETDEWEB)

    Ward, Andy L.; Gee, Glendon W.; Zhang, Z. F.; Keller, Jason M.

    2004-10-14

    contaminant inventory and water content depth distributions of any complexity. However, the results are somewhat conservative in that the model does not take credit for stratification and its dimensionality effects. Transient analysis shows transport to be controlled by small-scale stratification that resulted in laterally movement of contaminants and their failure to reach the ground water. Multiple discharges quickly merged into a single plume that migrated beyond the domain boundaries. However, it appears that this very feature that was effective in mitigating deep transport of the contaminants for almost 50 years now functions to confound expected barrier effects. Simulations suggest that a barrier provides no additional protection above the no-action alternative. Although continuous layers are assumed, in reality, there may be discontinuities that could lead to vertical movement. Episodic recharge events could also be conducive to downward movement. As more data becomes available, the conceptual model will be revised. Based on the analyses, capping appears to be no better than the no-action alternative. Projected 99Tc concentrations reaching the groundwater suggest that alternate source control actions may be necessary to reach soil screening levels. The benefits of active remediation are therefore readily apparent. Because none of the alternatives reduce soil concentrations, they effect no active reduction in the groundwater concentrations therefore the residual risk will remain high.

  11. Application of accelerated solvent extraction in the analysis of organic contaminants, bioactive and nutritional compounds in food and feed.

    Science.gov (United States)

    Sun, Hanwen; Ge, Xusheng; Lv, Yunkai; Wang, Anbang

    2012-05-11

    Accelerated solvent extraction (ASE) has become a popular green extraction technology for different classes of organic contaminants present in numerous kinds of food and feed for food safety. The parameters affecting ASE efficiency and application advancement of ASE in the analysis of organic contaminants, natural toxins compounds as well as bioactive and nutritional compounds in animal origin food, plant origin food and animal feed are reviewed in detail. ASE is a fully automated and reliable extraction technique with many advantages over traditional extraction techniques, so it could be especially useful for routine analyses of pollutants in food and feed.

  12. Metal contamination budget at the river basin scale: a critical analysis based on the Seine River

    Directory of Open Access Journals (Sweden)

    L. Lestel

    2007-06-01

    Full Text Available Material flow analysis and environmental contamination analysis are merged into a flux-flow analysis (F2A as illustrated for the metal circulation in the Seine River catchment. F2A combines about 30 metal flows in the anthroposphere (14 million people and/or metal fluxes in the environment (atmosphere, soils, and aquatic system originating from two dozens of sources. The nature and quality of data is very heterogeneous going from downscaled national economic statistics to upscaled daily environmental surveys.

    A triple integration is performed: space integration over the catchment (65000 km2, time integration for the 1950–2000 trend analysed at 5 year resolution, and a conceptual integration resulting in two F2A indicators.

    Despite the various data sources an average metal circulation is established for the 1994–2003 period and illustrated for zinc: (i metal circulation in the anthroposphere is now two orders of magnitude higher than river outputs, (ii long term metal storage, and their potential leaks, in soils, wastedumps and structures is also orders of magnitude higher than present river fluxes. Trend analysis is made through two F2A indicators, the per capita excess load at the river outlet and the leakage ratio (excess fluxes/metal demand. From 1950 to 2000, they both show a ten fold improvement of metal recycling while the metal demand has increased by 2.5 to 5 for Cd, Cu, Cr, Pb and Zn, and the population by 50%.

  13. Analysis of environmental contamination resulting from catastrophic incidents: part 1. Building and sustaining capacity in laboratory networks.

    Science.gov (United States)

    Magnuson, Matthew; Ernst, Hiba; Griggs, John; Fitz-James, Schatzi; Mapp, Latisha; Mullins, Marissa; Nichols, Tonya; Shah, Sanjiv; Smith, Terry; Hedrick, Elizabeth

    2014-11-01

    Catastrophic incidents, such as natural disasters, terrorist attacks, and industrial accidents, can occur suddenly and have high impact. However, they often occur at such a low frequency and in unpredictable locations that planning for the management of the consequences of a catastrophe can be difficult. For those catastrophes that result in the release of contaminants, the ability to analyze environmental samples is critical and contributes to the resilience of affected communities. Analyses of environmental samples are needed to make appropriate decisions about the course of action to restore the area affected by the contamination. Environmental samples range from soil, water, and air to vegetation, building materials, and debris. In addition, processes used to decontaminate any of these matrices may also generate wastewater and other materials that require analyses to determine the best course for proper disposal. This paper summarizes activities and programs the United States Environmental Protection Agency (USEPA) has implemented to ensure capability and capacity for the analysis of contaminated environmental samples following catastrophic incidents. USEPA's focus has been on building capability for a wide variety of contaminant classes and on ensuring national laboratory capacity for potential surges in the numbers of samples that could quickly exhaust the resources of local communities. USEPA's efforts have been designed to ensure a strong and resilient laboratory infrastructure in the United States to support communities as they respond to contamination incidents of any magnitude. The efforts include not only addressing technical issues related to the best-available methods for chemical, biological, and radiological contaminants, but also include addressing the challenges of coordination and administration of an efficient and effective response. Laboratory networks designed for responding to large scale contamination incidents can be sustained by applying

  14. SNR analysis: molecular investigation of an anthrax epidemic

    Science.gov (United States)

    2010-01-01

    Background In Italy, anthrax is endemic but occurs sporadically. During the summer of 2004, in the Pollino National Park, Basilicata, Southern Italy, an anthrax epidemic consisting of 41 outbreaks occurred; it claimed the lives of 124 animals belonging to different mammal species. This study is a retrospective molecular epidemiological investigation carried out on 53 isolates collected during the epidemic. A 25-loci Multiple Locus VNTR Analysis (MLVA) MLVA was initially performed to define genetic relationships, followed by an investigation of genetic diversity between epidemic strains through Single Nucleotide Repeat (SNR) analysis. Results 53 Bacillus anthracis strains were isolated. The 25-loci MLVA analysis identified all of them as belonging to a single genotype, while the SNR analysis was able to detect the existence of five subgenotypes (SGTs), allowing a detailed epidemic investigation. SGT-1 was the most frequent (46/53); SGTs 2 (4/53), 3 (1/53) 4 (1/53) and 5 (1/53) were detected in the remaining seven isolates. Conclusions The analysis revealed the prevalent spread, during this epidemic, of a single anthrax clone. SGT-1 - widely distributed across the epidemic area and present throughout the period in question - may, thus, be the ancestral form. SGTs 2, 3 and 4 differed from SGT-1 at only one locus, suggesting that they could have evolved directly from the latter during the course of this epidemic. SGT-5 differed from the other SGTs at 2-3 loci. This isolate, thus, appears to be more distantly related to SGT-1 and may not be a direct descendant of the lineage responsible for the majority of cases in this epidemic. These data confirm the importance of molecular typing and subtyping methods for in-depth epidemiological analyses of anthrax epidemics. PMID:20187980

  15. Chiral Analysis of Isopulegol by Fourier Transform Molecular Rotational Spectroscopy

    Science.gov (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Chiral analysis on molecules with multiple chiral centers can be performed using pulsed-jet Fourier transform rotational spectroscopy. This analysis includes quantitative measurement of diastereomer products and, with the three wave mixing methods developed by Patterson, Schnell, and Doyle (Nature 497, 475-477 (2013)), quantitative determination of the enantiomeric excess of each diastereomer. The high resolution features enable to perform the analysis directly on complex samples without the need for chromatographic separation. Isopulegol has been chosen to show the capabilities of Fourier transform rotational spectroscopy for chiral analysis. Broadband rotational spectroscopy produces spectra with signal-to-noise ratio exceeding 1000:1. The ability to identify low-abundance (0.1-1%) diastereomers in the sample will be described. Methods to rapidly identify rotational spectra from isotopologues at natural abundance will be shown and the molecular structures obtained from this analysis will be compared to theory. The role that quantum chemistry calculations play in identifying structural minima and estimating their spectroscopic properties to aid spectral analysis will be described. Finally, the implementation of three wave mixing techniques to measure the enantiomeric excess of each diastereomer and determine the absolute configuration of the enantiomer in excess will be described.

  16. COMPARATIVE ANALYSIS OF APPROACHES TO ECOLOGICAL ASSESSMENT OF POLYELEMENT CONTAMINATION SOIL OF URBAN ECOSYSTEM BY HEAVY METALS

    Directory of Open Access Journals (Sweden)

    YAKOVYSHYNA T. F.

    2016-06-01

    Full Text Available Raising of problem. In modern conditions, anthropogenic impact to the soil urban ecosystems is fairly stable over time and space, is manifested in various forms, as the transformation of the soil profile, the change in direction of the soil-forming processes, contamination of the various pollutants, and, above all, heavy metals (HM – elements of the first class of the danger. Their sources of the income to the urban environment are industrial enterprises, transport, housing and communal services. Determination of the anthropogenic pressure to the urban soil is carried out by the environmental assessment of the HM polyelement contamination, which allows to establish not only the fact of pollution, but also limits of the possible load with considering regional background or sanitary standards – MPC. However, until now discussions arise regarding the index which will be carried out the valuation – the cornerstone of any methodological approach to the environmental assessment of the soil polyelement contamination by the HM of the urban ecosystems, which allows to establish not only the fact of contamination, but also limits the possible load, taking into account the regional background or sanitary norm – MPC. Purpose. Lies in the grounded selection of the environmental assessment indexes of the soil contamination by the HM of the urban ecosystems through a comparative analysis of the existing approaches, such as the determination of the summary contamination index (SCI, the index of the soil contamination (ISC, factor imbalance (Sd, taking into account environmental safety standards and binding to the specific conditions territory. Conclusion. In summary it should be noted that it is necessary to use a set of integrated indexes, including the SCI to determine the violation of the metals content with respect to the geochemical background of zonal soil, ISC – link the contamination level with health indexes of the environmental safety

  17. On-site analysis of heavy metal contaminated areas by means of total reflection X-ray fluorescence analysis (TXRF)

    Science.gov (United States)

    Stosnach, Hagen

    2006-11-01

    In this paper the possibilities and restriction for applying the low power TXRF spectrometer PicoTAX for the one-site analysis of heavy metal contaminated soils and sediments are evaluated. Basis for this evaluation is the Superfund Innovative Technology Evaluation (SITE) program, conducted by the U.S. Environmental Protection Protection Agency (US EPA). During a measurement campaign, performed under realistic conditions, 320 soil and sediment samples were analyzed. The task was the fast analysis of the main target elements antimony, arsenic, cadmium, chromium, copper, iron, lead, mercury, nickel, selenium, silver, vanadium, and zinc. These elements were present in wide ranging concentrations. Out of a set of seven primary and five secondary objectives the method detection limits, accuracy and precision of the TXRF measurements are discussed. In addition to the on-site measurements, the application of TXRF analysis for the analysis of soil- and sediment samples after complete microwave assisted acid digestion is reported. Recent instrument improvements have distinctly increased the quality of measurement results. A detailed description of these new developments and new measurement results are discussed

  18. Chemical and biological methods for the analysis and remediation of environmental contaminants frequently identified at superfund sites

    Energy Technology Data Exchange (ETDEWEB)

    Melinda Christine Wiles [Texas A& amp; M University, College Station, TX (United States). Department of Veterinary Anatomy & Public Health

    2004-08-15

    Substantial environmental contamination has occurred from coal tar creosote and pentachlorophenol (C5P) in wood preserving solutions. The present studies focused on the characterization and remediation of these contaminants. The first objective was to delineate a sequence of biological changes caused by chlorinated phenol (CP) exposure. The second study was to develop multi-functional sorbents to remediate CPs and other components of wood preserving waste from groundwater. Following water remediation, the final aim of this work was to explore the safety of the parent clay minerals as potential enterosorbents for contaminants ingested in water and food. Based on evaluations of toxicity and neutron activation analysis of tissues, no significant differences were observed between animals receiving clay supplements and control animals, with the exception of slightly decreased brain Rb in animals ingesting clay. Overall, the results suggest that neither clay mineral, at relatively high dietary concentrations, influences mineral uptake or utilization in the pregnant rat. 420 refs., 28 figs, 15 tabs.

  19. Extent of Fecal Contamination of Household Drinking Water in Nepal: Further Analysis of Nepal Multiple Indicator Cluster Survey 2014.

    Science.gov (United States)

    Kandel, Pragya; Kunwar, Ritu; Lamichhane, Prabhat; Karki, Surendra

    2017-02-08

    Water sources classified as "improved" may not necessarily provide safe drinking water for householders. We analyzed data from Nepal Multiple Indicator Cluster Survey 2014 to explore the extent of fecal contamination of household drinking water. Fecal contamination was detected in 81.2% (95% confidence interval [CI]: 77.9-84.2) household drinking water from improved sources and 89.6% (95% CI: 80.4-94.7) in water samples from unimproved sources. In adjusted analysis, there was no difference in odds of fecal contamination of household drinking water between improved and unimproved sources. We observed significantly lower odds of fecal contamination of drinking water in households in higher wealth quintiles, where soap and water were available for handwashing and in households employing water treatment. The extent of contamination of drinking water as observed in this study highlights the huge amount of effort required to ensure the provision of safely managed water in Nepal by 2030 as aimed in sustainable development goals.

  20. The use of cluster analysis for plant grouping by their tolerance to soil contamination with hydrocarbons at the germination stage.

    Science.gov (United States)

    Potashev, Konstantin; Sharonova, Natalia; Breus, Irina

    2014-07-01

    Clustering was employed for the analysis of obtained experimental data set (42 plants in total) on seed germination in leached chernozem contaminated with kerosene. Among investigated plants were 31 cultivated plants from 11 families (27 species and 20 varieties) and 11 wild plant species from 7 families, 23 annual and 19 perennial/biannual plant species, 11 monocotyledonous and 31 dicotyledonous plants. Two-dimensional (two-parameter) clustering approach, allowing the estimation of tolerance of germinating seeds using a pair of independent parameters (С75%, V7%) was found to be most effective. These parameters characterized the ability of seeds to both withstand high concentrations of contaminants without the significant reduction of the germination, and maintain high germination rate within certain contaminant concentrations. The performed clustering revealed a number of plant features, which define the relation of a particular plant to a particular tolerance cluster; it has also demonstrated the possibility of generalizing the kerosene results for n-tridecane, which is one of the typical kerosene components. In contrast to the "manual" plant ranking based on the assessment of germination at discrete concentrations of the contaminant, the proposed clustering approach allowed a generalized characterization of the seed tolerance/sensitivity to hydrocarbon contaminants. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Real-time detection of organic contamination events in water distribution systems by principal components analysis of ultraviolet spectral data.

    Science.gov (United States)

    Zhang, Jian; Hou, Dibo; Wang, Ke; Huang, Pingjie; Zhang, Guangxin; Loáiciga, Hugo

    2017-05-01

    The detection of organic contaminants in water distribution systems is essential to protect public health from potential harmful compounds resulting from accidental spills or intentional releases. Existing methods for detecting organic contaminants are based on quantitative analyses such as chemical testing and gas/liquid chromatography, which are time- and reagent-consuming and involve costly maintenance. This study proposes a novel procedure based on discrete wavelet transform and principal component analysis for detecting organic contamination events from ultraviolet spectral data. Firstly, the spectrum of each observation is transformed using discrete wavelet with a coiflet mother wavelet to capture the abrupt change along the wavelength. Principal component analysis is then employed to approximate the spectra based on capture and fusion features. The significant value of Hotelling's T(2) statistics is calculated and used to detect outliers. An alarm of contamination event is triggered by sequential Bayesian analysis when the outliers appear continuously in several observations. The effectiveness of the proposed procedure is tested on-line using a pilot-scale setup and experimental data.

  2. The health risk of the agricultural production in potentially contaminated sites: an environmental-health risk analysis

    Directory of Open Access Journals (Sweden)

    Giovanni Russo

    2012-12-01

    Full Text Available Rural areas are often interested by pollution phenomena generated by agricultural activities with a high use of pesticides and/or by anthropic activities, such as industrial plants or illegal waste disposal sites, which may cause even long-range contamination. The risk for human health from the pollutants present in the environment can be quantitatively evaluated by the environmental health risk analysis set out in the Italian Legislative Decree no. 152/2006 (Italian Regulation, 2006. This analysis is the best technical-normative tool to estimate the health risks linked to the pollutants present in the environment but it does not consider the specificity of agricultural soils or the contamination of agricultural products. This study aims to provide this missing technical-normative data by identifying and applying a suitable methodology to evaluate the health risk caused by the ingestion of agricultural products grown in contaminated soils. The risk analysis was applied to two contaminated areas in southern Italy using an innovative methodology based on widely accepted parameters for the determination of polycyclic aromatic hydrocarbons (PAHs soil-plant bio-transfer factor in the case of horticultural crops. In addition, some concentration limits of PAHs in agricultural soils are proposed that may be of help to the competent authorities (health agencies, local authorities in delineating the areas requiring strict health surveillance of the food products cultivated.

  3. Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-nitro-2-phenoxymethyl benzimidazole

    Science.gov (United States)

    Menon, Vidya V.; Foto, Egemen; Mary, Y. Sheena; Karatas, Esin; Panicker, C. Yohannan; Yalcin, Gözde; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Yildiz, Ilkay

    2017-02-01

    FT-IR and FT-Raman spectra of 5-nitro-2-phenoxymethylbenzimidazole were recorded and analyzed theoretically and experimentally. The splitting of Nsbnd H stretching mode in the IR spectrum with a red shift from the calculated value indicates the weakening of the NH bond. The theoretical calculations give the phenyl ring breathing modes at 999 cm-1 for mono substituted benzene ring and at 1040 cm-1 for tri-substituted benzene ring. The theoretical NMR chemical shifts are in agreement with the experimental chemical shifts. The most reactive sites for electrophilic and nucleophilic attack are predicted from the MEP analysis. HOMO of π nature is delocalized over the entire molecule whereas the LUMO is located over the complete molecule except mono-substituted phenyl ring and oxygen atom. Reactive sites of the title molecule have been located with the help of ALIE surfaces and Fukui functions. In order to determine locations prone to autoxidation and locations interesting for starting of degradation, bond dissociation energies have been calculated for all single acyclic bonds. For the determination of atoms with pronounced interactions with water we have calculated radial distribution functions obtained after molecular dynamics simulations. The calculated first hyperpolarizability of the title compound is 58.03 times that of standard nonlinear optical material urea. The substrate binding site interactions of the title compound with Topo II enzyme is reported by using molecular docking study. Biological activity studies show that the title compound can be leaded for developing new anticancer agents.

  4. Delineation of Chondroid Lipoma: An Immunohistochemical and Molecular Biological Analysis

    Directory of Open Access Journals (Sweden)

    Ronald S. A. de Vreeze

    2011-01-01

    Full Text Available Aims. Chondroid lipoma (CL is a benign tumor that mimics a variety of soft tissue tumors and is characterized by translocation t(11;16. Here, we analyze CL and its histological mimics. Methods. CL (n=4 was compared to a variety of histological mimics (n=83 for morphological aspects and immunohistochemical features including cyclinD1(CCND1. Using FISH analysis, CCND1 and FUS were investigated as potential translocation partners. Results. All CLs were strongly positive for CCND1. One of 4 myoepitheliomas, CCND1, was positive. In well-differentiated lipomatous tumors and in chondrosarcomas, CCND1 was frequently expressed, but all myxoid liposarcomas were negative. FISH analysis did not give support for direct involvement of CCND1 and FUS as translocation partners. Conclusions. Chondroid lipoma is extremely rare and has several and more prevalent histological mimics. The differential diagnosis of chondroid lipomas can be unraveled using immunohistochemical and molecular support.

  5. Cost analysis of strategies to reduce blood culture contamination in the emergency department: sterile collection kits and phlebotomy teams.

    Science.gov (United States)

    Self, Wesley H; Talbot, Thomas R; Paul, Barbara R; Collins, Sean P; Ward, Michael J

    2014-08-01

    Blood culture collection practices that reduce contamination, such as sterile blood culture collection kits and phlebotomy teams, increase up-front costs for collecting cultures but may lead to net savings by eliminating downstream costs associated with contamination. The study objective was to compare overall hospital costs associated with 3 collection strategies: usual care, sterile kits, and phlebotomy teams. Cost analysis. This analysis was conducted from the perspective of a hospital leadership team selecting a blood culture collection strategy for an adult emergency department (ED) with 8,000 cultures drawn annually. Total hospital costs associated with 3 strategies were compared: (1) usual care, with nurses collecting cultures without a standardized protocol; (2) sterile kits, with nurses using a dedicated sterile collection kit; and (3) phlebotomy teams, with cultures collected by laboratory-based phlebotomists. In the base case, contamination rates associated with usual care, sterile kits, and phlebotomy teams were assumed to be 4.34%, 1.68%, and 1.10%, respectively. Total hospital costs included costs of collecting cultures and hospitalization costs according to culture results (negative, true positive, and contaminated). Compared with usual care, annual net savings using the sterile kit and phlebotomy team strategies were $483,219 and $288,980, respectively. Both strategies remained less costly than usual care across a broad range of sensitivity analyses. EDs with high blood culture contamination rates should strongly consider evidence-based strategies to reduce contamination. In addition to improving quality, implementing a sterile collection kit or phlebotomy team strategy is likely to result in net cost savings.

  6. Implementation of force distribution analysis for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Seifert Christian

    2011-04-01

    Full Text Available Abstract Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA, a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.

  7. Food chain analysis of exposures and risks to wildlife at a metals-contaminated wetland.

    Science.gov (United States)

    Pascoe, G A; Blanchet, R J; Linder, G

    1996-03-01

    A food chain analysis of risks to wetland receptors was performed in support of a baseline ecological risk assessment at the Milltown Reservoir Sediments Superfund site in Montana. The study area consisted of over 450 acres of primarily palustrine wetland contaminated with metals from mining wastes transported from upstream sources (average of 465 mg/kg for Cu in sediments, and 585 mg/kg in soils). The food chain analysis focused on several species of terrestrial and semiaquatic animals indigenous to montane wetlands of the northern Rocky Mountains. Receptors consisted of mice, voles, muskrats, beaver, various waterfowl species, osprey, bald eagles, and deer. Samples of aquatic and terrestrial invertebrates, small mammal tissues, fish tissue, aquatic and terrestrial vegetation, soils, sediment, and surface water were collected and analyzed for As, Cd, Cu, and Zn. A linear multimedia food-chain model was constructed to estimate daily intakes of the metals for each receptor, with assumed values for ingestion of aquatic and terrestrial food items, ingestion of local surface water, and incidental ingestion of soils and/or sediments. Evaluation of health risks to the receptors was performed by comparison of exposures expressed as daily intakes to a suite of toxicity values. The range of values consisted of the lower end of chronic toxicity data found in toxicology databases or the literature for the same or similar species, modified to account for extrapolation uncertainties. Daily intakes of chemicals of concern were below or within the range of toxicity values for all receptors. The weight of evidence from the food chain analysis and earlier bioassessment and ecological studies suggest that the health of the wetland receptors is at minimal risk due to the presence of elevated metals in sediments, upland soils, water, or food items at the site.

  8. Could organic phosphorus compounds contaminate the analysis of phosphate oxygen isotopes in freshwater matrices?

    Science.gov (United States)

    Davies, Ceri; Surridge, Ben; Gooddy, Daren

    2014-05-01

    Variation in the stable isotope composition of oxygen within dissolved phosphate (δ18Op) represents a novel and potentially powerful environmental tracer, providing insights into the sources of phosphorus and the extent to which phosphorus from different sources is metabolised. The analysis of δ18Opwithin freshwater matrices requires isolation of the phosphate ion from possible sources of contaminant oxygen within the bulk matrix, prior to pyrolysis (usually of a silver phosphate precipitate) and analysis of the oxygen isotope composition. The majority of published research uses co-precipitation of phosphate with brucite (Mg(OH)2) as an initial step in the isolation of the phosphate ion. However, freshwater matrices also contain a wide range of organic phosphorus compounds, including adenosine 5'-triphosphate (ATP) and phosphonates such as 2-aminoethylphosphonic acid. In this paper, we initially examine the potential for co-precipitation of organic phosphorus compounds with brucite. Our data indicate that ATP, sodium pyrophosphate and inositol hexakisphosphate are almost entirely removed from solution through co-precipitation with brucite, whilst glucose-6-phosphate and 2-aminoethylphosphonic acid are less readily co-precipitated. Subsequently, we assessed the potential for acid-hydrolysis of organic phosphorus compounds during re-dissolution of the brucite precipitate, using a range of acid systems. Our data indicate that up to 17% of ATP and up to 5% of sodium pyrophosphate can be hydrolysed by concentrated acetic acid, yielding fresh phosphate ions in solution. Our findings have potentially significant implications for analysis of δ18Opbecause the fresh phosphate ions produced following acid hydrolysis will be subjected to inheritance and kinetic isotope fractionations, likely altering the bulk δ18Op within a freshwater sample.

  9. Molecular analysis of endocrine disruption in hornyhead turbot at wastewater outfalls in southern california using a second generation multi-species microarray.

    Directory of Open Access Journals (Sweden)

    Michael E Baker

    Full Text Available Sentinel fish hornyhead turbot (Pleuronichthysverticalis captured near wastewater outfalls are used for monitoring exposure to industrial and agricultural chemicals of ~ 20 million people living in coastal Southern California. Although analyses of hormones in blood and organ morphology and histology are useful for assessing contaminant exposure, there is a need for quantitative and sensitive molecular measurements, since contaminants of emerging concern are known to produce subtle effects. We developed a second generation multi-species microarray with expanded content and sensitivity to investigate endocrine disruption in turbot captured near wastewater outfalls in San Diego, Orange County and Los Angeles California. Analysis of expression of genes involved in hormone [e.g., estrogen, androgen, thyroid] responses and xenobiotic metabolism in turbot livers was correlated with a series of phenotypic end points. Molecular analyses of turbot livers uncovered altered expression of vitellogenin and zona pellucida protein, indicating exposure to one or more estrogenic chemicals, as well as, alterations in cytochrome P450 (CYP 1A, CYP3A and glutathione S-transferase-α indicating induction of the detoxification response. Molecular responses indicative of exposure to endocrine disruptors were observed in field-caught hornyhead turbot captured in Southern California demonstrating the utility of molecular methods for monitoring environmental chemicals in wastewater outfalls. Moreover, this approach can be adapted to monitor other sites for contaminants of emerging concern in other fish species for which there are few available gene sequences.

  10. Emerging contaminants from industrial and municipal waste. Pt. 1. Occurence, analysis and effects

    Energy Technology Data Exchange (ETDEWEB)

    Barcelo, Damia; Petrovic, Mira (eds.) [IIQAB - CSIC, Barcelona (Spain). Dept. of Environmental Chemistry

    2008-07-01

    The group of non-regulated contaminants termed 'emerging contaminants' mainly comprises products used in large quantities in everyday life, such as human and veterinary pharmaceuticals, personal care products, surfactants and surfactant residues, plasticizers and various industrial additives. The occurrence of 'emerging contaminants' in wastewaters, and their behavior during wastewater treatment and production of drinking water are key issues in the re-use of water resources. Emerging Contaminants from Industrial and Municipal Waste focuses on innovative treatment technologies for the elimination of emerging contaminants from wastewater and drinking water. The respective treatment processes, such as membrane bioreactors, photocatalysis, ozonation and advanced oxidation are dealt with in detail. The book also discusses sources and occurrence of emerging contaminants in municipal and industrial waste, giving a concise and critical overview of state-of-the-art analytical methods for their identification. Further important aspects covered by the book include the acute and chronic effects and overall impact of emerging contaminants on the environment. (orig.)

  11. Proteogenomic Analysis of Geobacter Populations in a low Nutrient Contaminated Aquifer Under Stimulated Conditions.

    Science.gov (United States)

    Wilkins, M. J.; Williams, K. H.; Verberkmoes, N. C.; Hettich, R. L.; Lipton, M. S.; Callister, S. J.; Long, P. E.; Banfield, J. F.

    2008-12-01

    Proteogenomic samples were obtained from a U(VI)-contaminated aquifer undergoing acetate-stimulated bioreduction at the U.S. Department of Energy Integrated Field Challenge (IFC) site in Western Colorado. Analysis of these samples using ICP-MS/MS indicated that they were dominated by Geobacter species, with over 2,500 proteins identified per sample. The detected proteins revealed a wealth of information about how Geobacter species are able to dominate subsurface environments under nutrient-poor conditions such as those at Rifle. The presence of nitrogenase proteins indicates that the Geobacter populations are fixing nitrogen, although the absence of other proteins indicative of nitrogen stress, such as the uridylylated version of the P-II regulatory protein and NtrB, suggests that low-level N2 fixation occurs without the community undergoing extreme nitrogen stress. The detection of a large number of proteins involved in two- component sensor and chemotaxis systems, along with flagella subunits, indicates that Geobacter species are able to rapidly detect and respond to chemical gradients in the environment. Pathways for the efficient utilization of the elevated acetate concentrations in the subsurface have also been elucidated, with an important role suggested for acetyl-CoA transferase in controlling flux between succinyl-CoA and succinate. Other proteins detected that are clearly important for growth in the subsurface include those involved in phosphate acquisition and heavy-metal efflux.

  12. Epistemology of Contaminants of Emerging Concern and Literature Meta-analysis

    Science.gov (United States)

    Halden, Rolf U.

    2014-01-01

    A meta-analysis was conducted to inform the epistemology, or theory of knowledge, of contaminants of emerging concern (CECs). The CEC terminology acknowledges the existence of harmful environmental agents whose identities, occurrences, hazards, and effects are not sufficiently understood. Here, data on publishing activity were analyzed for 12 CECs, revealing a common pattern of emergence, suitable for identifying past years of peak concern and forecasting future ones: dichlorodiphenyltrichloroethane (DDT; 1972, 2008), trichloroacetic acid (TCAA; 1972, 2009), nitrosodimethylamine (1984), methyl tert-butyl ether (2001), trichloroethylene (2005), perchlorate (2006), 1,4-dioxane (2009), prions (2009), triclocarban (2010), triclosan (2012), nanomaterials (by 2016), and microplastics (2022 ± 4). CECs were found to emerge from obscurity to the height of concern in 14.1 ± 3.6 years, and subside to a new baseline level of concern in 14.5 ± 4.5 years. CECs can emerge more than once (e.g., TCAA, DDT) and the multifactorial process of emergence may be driven by inception of novel scientific methods (e.g., ion chromatography, mass spectrometry and nanometrology), scientific paradigm shifts (discovery of infectious proteins), and the development, marketing and mass consumption of novel products (antimicrobial personal care products, microplastics and nanomaterials). Publishing activity and U.S. regulatory actions were correlated for several CECs investigated. PMID:25294779

  13. Multiresidue analysis of 59 nonallowed substances and other contaminants in cosmetics.

    Science.gov (United States)

    Zhan, Jia; Ni, Mei-lin; Zhao, Hai-ying; Ge, Xiao-ming; He, Xiao-yu; Yin, Ju-yi; Yu, Xue-jun; Fan, Yuan-mu; Huang, Zhi-qiang

    2014-12-01

    A method was developed for the determination of 59 glucocorticoids, sex hormones, nonsteroidal anti-inflammatory drugs, antibiotics, and other contaminants in cosmetics simultaneously by ultra high performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Acetonitrile was used to extract the sample, and the mixed sorbents were dispersed for purification. With the optimal conditions, the optimized pretreatment processes led to no significant interference on analysis from an extremely complicated sample matrix, and the linear ranges of 59 analytes were 0-480.0 μg/kg with the correlation coefficients above 0.99 and the limits of quantification (S/N≥10) were 5-40 μg/kg. Statistical evaluation revealed that the average recoveries were in the range of 61.2-131.2%, and relative standard deviations were in the range of 2.0-22.8%, meanwhile the interday precision ranged from 3.8 to 21.8%. This method is simple, fast, and credible, and it can be applied to simultaneous screening and determination of various classes of substances under investigations illegally presented in cosmetic products, covering a wide diversity of polarities, and pKa values.

  14. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

    2015-10-22

    Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  15. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  16. Multicriteria decision analysis to assess options for managing contaminated sediments: Application to Southern Busan Harbor, South Korea.

    Science.gov (United States)

    Kim, Jongbum; Kim, Suk Hyun; Hong, Gi Hoon; Suedel, Burton C; Clarke, Joan

    2010-01-01

    Many years of untreated effluent discharge from residential areas, a shipyard, a marina, and a large fish market resulted in substantial contamination of bottom sediment in Southern Busan Harbor, South Korea. Contaminants in these sediments include heavy metals and organic compounds. Newly introduced regulations for ocean disposal of dredged material in South Korea pose significant challenges, because the previous practice of offshore disposal of contaminated dredged material was no longer possible after August 2008. The South Korean government has mandated that such sediments be assessed in a way that identifies the most appropriate dredged material management alternative, addressing environmental, social, and cost objectives. An approach using multicriteria decision analysis (MCDA) in combination with comparative risk assessment was used as a systematic and transparent framework for prioritizing several dredged sediment management alternatives. We illustrate how MCDA can recognize the multiple goals of contaminated sediment management. Values used in weighting decision criteria were derived from surveys of stakeholders who were sediment management professionals, business owners, or government decision makers. The results of the analysis showed that land reclamation was the preferred alternative among cement-lock, sediment washing, 3 contained aquatic disposal alternatives (one in combination with a hopper dredge), geotextile tubes, solidification, and land reclamation after solidification treatment. Land reclamation was the preferred alternative, which performed well across all MCDA objectives, because of the availability of a near-shore confined disposal facility within a reasonable distance from the dredging area.

  17. Retrospective analysis of a listeria monocytogenes contamination episode in raw milk goat cheese using quantitative microbial risk assessment tools.

    Science.gov (United States)

    Delhalle, L; Ellouze, M; Yde, M; Clinquart, A; Daube, G; Korsak, N

    2012-12-01

    In 2005, the Belgian authorities reported a Listeria monocytogenes contamination episode in cheese made from raw goat's milk. The presence of an asymptomatic shedder goat in the herd caused this contamination. On the basis of data collected at the time of the episode, a retrospective study was performed using an exposure assessment model covering the production chain from the milking of goats up to delivery of cheese to the market. Predictive microbiology models were used to simulate the growth of L. monocytogenes during the cheese process in relation with temperature, pH, and water activity. The model showed significant growth of L. monocytogenes during chilling and storage of the milk collected the day before the cheese production (median increase of 2.2 log CFU/ml) and during the addition of starter and rennet to milk (median increase of 1.2 log CFU/ml). The L. monocytogenes concentration in the fresh unripened cheese was estimated to be 3.8 log CFU/g (median). This result is consistent with the number of L. monocytogenes in the fresh cheese (3.6 log CFU/g) reported during the cheese contamination episode. A variance-based method sensitivity analysis identified the most important factors impacting the cheese contamination, and a scenario analysis then evaluated several options for risk mitigation. Thus, by using quantitative microbial risk assessment tools, this study provides reliable information to identify and control critical steps in a local production chain of cheese made from raw goat's milk.

  18. NCI-Molecular Analysis for Therapy Choice (NCI-MATCH) Trial

    Science.gov (United States)

    NCI's gateway for information about the NCI-Molecular Analysis for Therapy Choice (NCI-MATCH) trial, in which patients with advanced cancer are assigned to treatment arms based on the molecular profiles of their disease.

  19. Deciphering heavy metal contamination zones in soils of a granitic terrain of southern India using factor analysis and GIS

    Indian Academy of Sciences (India)

    D Purushotham; Mahjoor Ahmad Lone; Mehnaz Rashid; A Narsing Rao; Shakeel Ahmed

    2012-08-01

    Soil contamination by heavy metals has been a major concern for last few decades due to increase in urbanization and industrialization. The main objective of this research was to identify the heavy metal contaminated zones in the study area. Twenty five soil samples collected throughout the agriculture, residential and industrial areas were analysed by X-ray Fluorescence Spectrometer (XRF) for trace metals and major oxides. These metals can affect the quality of soil and infiltrate through the soil, thereby causing groundwater pollution. Based on the chemical analysis of major oxides (SiO2, Al2O3, Fe2O3, MnO, MgO, CaO, Na2O, K2O, TiO2, and P2O5) and their distribution; it is observed that these soils are predominantly siliceous type with slight enrichment of alumina component in the study area. Correlation matrix (CM) and factor analysis (FA) is employed to the heavy metal variables, viz., Ba, Cr, Cu, Ni, Pb, Rb, Sr, V, Y, Zn and Zr of the soil to determine the dominant factors contributing to the soil contamination in the area. In the analysis, five factors emerged as significant contributors to the soil quality. The total contribution of these five factors is about 90%. The contribution of the first factor is about 45% and has significant positive loadings of Co, Cr, Cu, Ni and Zn. The contribution of second factor is 22% and has significant positive loadings of Rb, Sr and Y. The contribution of third, fourth and fifth factors is 10, 8 and 5% and show positive loadings for lead, molybdenum and barium respectively to the soil contamination. The spatial variation maps deciphering different zones of heavy metal concentration in the soil were generated in a GIS (geographic information system) based environment using ArcGIS 9.3.1. The results reveal that heavy metal contamination in the area is mainly due to anthropogenic activities.

  20. Molecular analysis of precursor lesions in familial pancreatic cancer.

    Directory of Open Access Journals (Sweden)

    Tatjana Crnogorac-Jurcevic

    Full Text Available BACKGROUND: With less than a 5% survival rate pancreatic adenocarcinoma (PDAC is almost uniformly lethal. In order to make a significant impact on survival of patients with this malignancy, it is necessary to diagnose the disease early, when curative surgery is still possible. Detailed knowledge of the natural history of the disease and molecular events leading to its progression is therefore critical. METHODS AND FINDINGS: We have analysed the precursor lesions, PanINs, from prophylactic pancreatectomy specimens of patients from four different kindreds with high risk of familial pancreatic cancer who were treated for histologically proven PanIN-2/3. Thus, the material was procured before pancreatic cancer has developed, rather than from PanINs in a tissue field that already contains cancer. Genome-wide transcriptional profiling using such unique specimens was performed. Bulk frozen sections displaying the most extensive but not microdissected PanIN-2/3 lesions were used in order to obtain the holistic view of both the precursor lesions and their microenvironment. A panel of 76 commonly dysregulated genes that underlie neoplastic progression from normal pancreas to PanINs and PDAC were identified. In addition to shared genes some differences between the PanINs of individual families as well as between the PanINs and PDACs were also seen. This was particularly pronounced in the stromal and immune responses. CONCLUSIONS: Our comprehensive analysis of precursor lesions without the invasive component provides the definitive molecular proof that PanIN lesions beget cancer from a molecular standpoint. We demonstrate the need for accumulation of transcriptomic changes during the progression of PanIN to PDAC, both in the epithelium and in the surrounding stroma. An identified 76-gene signature of PDAC progression presents a rich candidate pool for the development of early diagnostic and/or surveillance markers as well as potential novel preventive

  1. Analysis of Process Gases and Trace Contaminants in Membrane-Aerated Gaseous Effluent Streams.

    Science.gov (United States)

    Coutts, Janelle L.; Lunn, Griffin Michael; Meyer, Caitlin E.

    2015-01-01

    In membrane-aerated biofilm reactors (MABRs), hollow fibers are used to supply oxygen to the biofilms and bulk fluid. A pressure and concentration gradient between the inner volume of the fibers and the reactor reservoir drives oxygen mass transport across the fibers toward the bulk solution, providing the fiber-adhered biofilm with oxygen. Conversely, bacterial metabolic gases from the bulk liquid, as well as from the biofilm, move opposite to the flow of oxygen, entering the hollow fiber and out of the reactor. Metabolic gases are excellent indicators of biofilm vitality, and can aid in microbial identification. Certain gases can be indicative of system perturbations and control anomalies, or potentially unwanted biological processes occurring within the reactor. In confined environments, such as those found during spaceflight, it is important to understand what compounds are being stripped from the reactor and potentially released into the crew cabin to determine the appropriateness or the requirement for additional mitigation factors. Reactor effluent gas analysis focused on samples provided from Kennedy Space Center's sub-scale MABRs, as well as Johnson Space Center's full-scale MABRs, using infrared spectroscopy and gas chromatography techniques. Process gases, such as carbon dioxide, oxygen, nitrogen, nitrogen dioxide, and nitrous oxide, were quantified to monitor reactor operations. Solid Phase Microextraction (SPME) GC-MS analysis was used to identify trace volatile compounds. Compounds of interest were subsequently quantified. Reactor supply air was examined to establish target compound baseline concentrations. Concentration levels were compared to average ISS concentration values and/or Spacecraft Maximum Allowable Concentration (SMAC) levels where appropriate. Based on a review of to-date results, current trace contaminant control systems (TCCS) currently on board the ISS should be able to handle the added load from bioreactor systems without the need

  2. [Health risk analysis of VOC/SVOC contaminated soil in an abandoned chemical plant].

    Science.gov (United States)

    Guo, Guan-lin; Wang, Shi-jie; Shi, Lie-yan; Li, Hui-ying; Han, Chun-mei; Gu, Qing-bao; Cao, Yun-zhe; Li, Fa-sheng

    2010-02-01

    Environmental health risk of contaminated soil in a typical abandoned industry was analyzed based on the full field investigation according to the site assessment procedure of American Society for Testing and Material (ASTM). Parameters were modified with the combination of Chinese crowd character and site specifics. Results indicated that the site was mainly contaminated with volatile and semi-volatile organic compounds in soil profiles. And the contents of carbon tetrachloride, tetrachloroethylene, pentachloroethane, hexachlorobutadiene, hexachloroethane and hexachlorobenzene in soil samples were exceeded the national environmental standard. These contaminants ranked the carcinogenic risks and hazard quotients more than 10(-2) and 1 in some locations with the exposure by oral ingestion, dermal contact and inhalation. Contaminants in this site had resulted in the high health risks to the residents and surrounding communities. The risk should be reduced to the health acceptable level by the treatment and remediation before further development for residential and commercial utilization.

  3. Elemental Analysis of Variably Contaminated Cremains Using X-ray Fluorescence Spectrometry.

    Science.gov (United States)

    Gilpin, Megan; Christensen, Angi M

    2015-07-01

    Analyzing and identifying skeletal remains becomes increasingly difficult when remains have been cremated, especially in cases where the cremated material may have been intentionally contaminated with nonskeletal material. This study examined the potential of X-ray fluorescence spectrometry (XRF) to detect the presence of nonskeletal contaminants in samples of cremains. Eleven samples of cremains were variably combined with concrete mix and analyzed using XRF. Photon counts of elements in each sample were analyzed, and the coefficient of determination (R(2)) using unweighted linear regression as a function of percent cremains was calculated. Results showed that with changes in the proportion of skeletal material and contaminant, there were significant (R(2) > 0.90) changes in detected levels of phosphorus, potassium, zinc, aluminum, and sulfur. The use of XRF is concluded to be a valid approach in the identification of the presence of nonskeletal material in potentially contaminated cremains.

  4. Analysis of organic contaminants from silicon wafer and disk surfaces by thermal desorption-GC-MS

    Science.gov (United States)

    Camenzind, Mark J.; Ahmed, Latif; Kumar, Anurag

    1999-03-01

    Organic contaminants can affect semiconductor wafer processing including gate oxide integrity, polysilicon growth, deep ultraviolet photoresist line-width, and cleaning & etching steps. Organophosphates are known to counter dope silicon wafers. Organic contaminants in disk drives can cause failures due to stiction or buildup on the heads. Therefore, it is important to identify organic contaminants adsorbed on wafer or disk surfaces and find their sources so they can be either completely eliminated or at least controlled. Dynamic headspace TD-GC-MS (Thermal Desorption-Gas Chromatography-Mass Spectrometry) methods are very sensitive and can be used to identify organic contaminants on disks and wafers, in air, or outgassing from running drives or their individual components.

  5. Great Lakes Contaminant Impacts Study: Residue analysis report on selected PCB Isomers in common tern eggs

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The status of environmental contamination and its possible effects on living resources in the St. Lawrence River and Niagara River ecosystems has been the subject of...

  6. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants

    Energy Technology Data Exchange (ETDEWEB)

    Deary, Michael E., E-mail: michael.deary@northumbria.ac.uk [Department of Geography,Faculty of Engineering and Environment, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST (United Kingdom); Ekumankama, Chinedu C. [Department of Geography,Faculty of Engineering and Environment, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST (United Kingdom); Cummings, Stephen P. [Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle upon Tyne NE1 8ST (United Kingdom)

    2016-04-15

    Highlights: • 40 week study of the biodegradation of 16 US EPA priority PAHs in a soil with high organic matter. • Effects of cadmium, lead and mercury co-contaminants studied. • Novel kinetic approach developed. • Biodegradation of lower molecular weight PAHs relatively unaffected by Cd or Pb. • Soil organic matter plays a key role in the PAH removal mechanism. - Abstract: We report on the results of a 40 week study in which the biodegradation of 16 US EPA polycyclic aromatic hydrocarbons (PAHs) was followed in microcosms containing soil of high organic carbon content (11%) in the presence and absence of lead and cadmium co-contaminants. The total spiked PAH concentration was 2166 mg/kg. Mercury amendment was also made to give an abiotic control. A novel kinetic model has been developed to explain the observed biphasic nature of PAH degradation. The model assumes that PAHs are distributed across soil phases of varying degrees of bioaccessibility. The results of the analysis suggest that overall percentage PAH loss is dependent on the respective rates at which the PAHs (a) are biodegraded by soil microorganisms in pore water and bioaccessible soil phases and (b) migrate from bioaccessible to non-bioaccessible soil phases. In addition, migration of PAHs to non-bioaccessible and non-Soxhlet-extractable soil phases associated with the humin pores gives rise to an apparent removal process. The presence of metal co-contaminants shows a concentration dependent inhibition of the biological degradation processes that results in a reduction in overall degradation. Lead appears to have a marginally greater inhibitory effect than cadmium.

  7. Metagenomic and Cultivation-Based Analysis of Novel Microorganisms and Functions in Metal-Contaminated Environments

    OpenAIRE

    Yelton, Alexis Pepper

    2012-01-01

    Some bacteria and archaea have evolved metabolic strategies that enable them to live in environments contaminated by toxic metals. In fact, many bacteria and archaea take advantage of the redox sensitivity of these very same metals to gain energy via anaerobic respiration. Here, metagenomic techniques were developed and applied along with conventional physiological and ecological methods to elucidate multiple modes of adaptation of bacteria and archaea in metal-contaminated acid mine drainage...

  8. Molecularly Imprinted Polymers for Ochratoxin A Extraction and Analysis

    Directory of Open Access Journals (Sweden)

    Jorn C. C. Yu

    2010-06-01

    Full Text Available Molecularly imprinted polymers (MIPs are considered as polymeric materials that mimic the functionality of antibodies. MIPs have been utilized for a wide variety of applications in chromatography, solid phase extraction, immunoassays, and sensor recognition. In this article, recent advances of MIPs for the extraction and analysis of ochratoxins are discussed. Selection of functional monomers to bind ochratoxin A (OTA with high affinities, optimization of extraction procedures, and limitations of MIPs are compared from different reports. The most relevant examples in the literature are described to clearly show how useful these materials are. Strategies on MIP preparation and schemes of analytical methods are also reviewed in order to suggest the next step that would make better use of MIPs in the field of ochratoxin research. The review ends by outlining the remaining issues and impediments.

  9. Phosphoproteome Analysis Reveals the Molecular Mechanisms Underlying Deoxynivalenol-Induced Intestinal Toxicity in IPEC-J2 Cells

    Science.gov (United States)

    Zhang, Zhi-Qi; Wang, Song-Bo; Wang, Rui-Guo; Zhang, Wei; Wang, Pei-Long; Su, Xiao-Ou

    2016-01-01

    Deoxynivalenol (DON) is a widespread trichothecene mycotoxin that commonly contaminates cereal crops and has various toxic effects in animals and humans. DON primarily targets the gastrointestinal tract, the first barrier against ingested food contaminants. In this study, an isobaric tag for relative and absolute quantitation (iTRAQ)-based phosphoproteomic approach was employed to elucidate the molecular mechanisms underlying DON-mediated intestinal toxicity in porcine epithelial cells (IPEC-J2) exposed to 20 μM DON for 60 min. There were 4153 unique phosphopeptides, representing 389 phosphorylation sites, detected in 1821 phosphoproteins. We found that 289 phosphopeptides corresponding to 255 phosphoproteins were differentially phosphorylated in response to DON. Comprehensive Gene Ontology (GO) analysis combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that, in addition to previously well-characterized mitogen-activated protein kinase (MAPK) signaling, DON exposure altered phosphatidylinositol 3-kinase/Akt (PI3K/Akt) and Janus kinase/signal transducer, and activator of transcription (JAK/STAT) pathways. These pathways are involved in a wide range of biological processes, including apoptosis, the intestinal barrier, intestinal inflammation, and the intestinal absorption of glucose. DON-induced changes are likely to contribute to the intestinal dysfunction. Overall, identification of relevant signaling pathways yielded new insights into the molecular mechanisms underlying DON-induced intestinal toxicity, and might help in the development of improved mechanism-based risk assessments in animals and humans. PMID:27669298

  10. Phosphoproteome Analysis Reveals the Molecular Mechanisms Underlying Deoxynivalenol-Induced Intestinal Toxicity in IPEC-J2 Cells

    Directory of Open Access Journals (Sweden)

    Zhi-Qi Zhang

    2016-09-01

    Full Text Available Deoxynivalenol (DON is a widespread trichothecene mycotoxin that commonly contaminates cereal crops and has various toxic effects in animals and humans. DON primarily targets the gastrointestinal tract, the first barrier against ingested food contaminants. In this study, an isobaric tag for relative and absolute quantitation (iTRAQ-based phosphoproteomic approach was employed to elucidate the molecular mechanisms underlying DON-mediated intestinal toxicity in porcine epithelial cells (IPEC-J2 exposed to 20 μM DON for 60 min. There were 4153 unique phosphopeptides, representing 389 phosphorylation sites, detected in 1821 phosphoproteins. We found that 289 phosphopeptides corresponding to 255 phosphoproteins were differentially phosphorylated in response to DON. Comprehensive Gene Ontology (GO analysis combined with Kyoto Encyclopedia of Genes and Genomes (KEGG pathway enrichment revealed that, in addition to previously well-characterized mitogen-activated protein kinase (MAPK signaling, DON exposure altered phosphatidylinositol 3-kinase/Akt (PI3K/Akt and Janus kinase/signal transducer, and activator of transcription (JAK/STAT pathways. These pathways are involved in a wide range of biological processes, including apoptosis, the intestinal barrier, intestinal inflammation, and the intestinal absorption of glucose. DON-induced changes are likely to contribute to the intestinal dysfunction. Overall, identification of relevant signaling pathways yielded new insights into the molecular mechanisms underlying DON-induced intestinal toxicity, and might help in the development of improved mechanism-based risk assessments in animals and humans.

  11. A critical evaluation of the use of cluster analysis to identify contaminated sediments in the Ria de Vigo

    Energy Technology Data Exchange (ETDEWEB)

    Rubio, B; Nombela, M. A; Vilas, F [Departamento de Geociencias Marinas y Ordenacion del Territorio, Vigo, Espana (Spain)

    2001-06-01

    The indiscriminate use of cluster analysis to distinguish contaminated and non-contaminated sediments has led us to make a comparative evaluation of different cluster analysis procedures as applied to heavy metal concentrations in subtidal sediments from the Ria de Vigo, NW Spain. The use of different clusters algorithms and other transformations from the same departing set of data lead to the formation of different clusters with a clear inconclusive result about the contamination status of the sediments. The results show that this approach is better suited to identifying groups of samples differing in sedimentological characteristics, such as grain size, rather than in the degree of contamination. Our main aim is to call attention to these aspects in cluster analysis and to suggest that researches should be rigorous with this kind of analysis. Finally, the use of discriminate analysis allows us to find a discriminate function that separates the samples into two clearly differentiated groups, which should not be treated jointly. [Spanish] El uso indiscriminado del analisis cluster para distinguir sedimentos contaminados y no contaminados nos ha llevado a realizar una evaluacion comparativa entre los diferentes procedimientos de estos analisis aplicada a la concentracion de metales pesados en sedimentos submareales de la Ria de Vigo, NW de Espana. La utilizacion de distintos algoritmos de cluster, asi como otras transformaciones de la misma matriz de datos conduce a la formacion de diferentes clusters con un resultado inconcluso sobre el estado de contaminacion de los sedimentos. Los resultados muestran que esta aproximacion se ajusta mejor para identificar grupos de muestras que difieren en caracteristicas sedimentologicas, tal como el tamano de grano, mas que el grado de contaminacion. El principal objetivo es llamar la atencion sobre estos aspectos del analisis cluster y sugerir a los investigadores que sean rigurosos con este tipo de analisis. Finalmente el uso

  12. A bibliometric analysis of scientific production in cancer molecular epidemiology.

    Science.gov (United States)

    Ugolini, Donatella; Puntoni, Riccardo; Perera, Frederica P; Schulte, Paul A; Bonassi, Stefano

    2007-08-01

    The main purpose of this research was to compare the scientific production in the field of cancer molecular epidemiology among countries and to evaluate the publication trend between 1995 and 2004. A bibliometric study was carried out searching the PubMed database with a combined search strategy based on the keywords listed in the medical subject headings and a free text search. Only articles from a representative subset of 92 journals--accounting for 80% of papers identified--were selected for the analysis, and the resulting 13,240 abstracts were manually checked according to a list of basic inclusion criteria. The study evaluated the number of publications and the impact factor (mean and sum), absolute and normalized by country population and gross domestic product. A total of 3,842 citations were finally selected for the analysis. Thirty-seven percent came from the European Union (UK, Germany, Italy, France and Sweden ranking at the top), 31.6% from USA and 9.7% from Japan. The highest mean impact factor was reported for Canada (6.3), USA (5.9), Finland (5.8) and UK (5.2). Finland, Sweden and Israel had the best ratio between scientific production and available resources. 'Genetic polymorphism, glutathione transferase, breast neoplasm, risk factors, case-control studies and polymerase chain reaction' were the most used keywords in each of the subgroups evaluated, although inclusion criteria may have privileged studies dealing with exogenous carcinogens. Cancer molecular epidemiology is an expanding area attracting an increasing interest. The identification of an operative definition is a necessary condition to give to this discipline a unique scientific identity.

  13. Eucb: A C++ program for molecular dynamics trajectory analysis

    Science.gov (United States)

    Tsoulos, Ioannis G.; Stavrakoudis, Athanassios

    2011-03-01

    Eucb is a standalone program for geometrical analysis of molecular dynamics trajectories of protein systems. The program is written in GNU C++ and it can be installed in any operating system running a C++ compiler. The program performs its analytical tasks based on user supplied keywords. The source code is freely available from http://stavrakoudis.econ.uoi.gr/eucb under LGPL 3 license. Program summaryProgram title:Eucb Catalogue identifier: AEIC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 31 169 No. of bytes in distributed program, including test data, etc.: 297 364 Distribution format: tar.gz Programming language: GNU C++ Computer: The tool is designed and tested on GNU/Linux systems Operating system: Unix/Linux systems RAM: 2 MB Supplementary material: Sample data files are available Classification: 3 Nature of problem: Analysis of molecular dynamics trajectories. Solution method: The program finds all possible interactions according to input files and the user instructions. Then it reads all the trajectory frames and finds those frames in which these interactions occur, under certain geometrical criteria. This is a blind search, without a priori knowledge if a certain interaction occurs or not. The program exports time series of these quantities (distance, angles, etc.) and appropriate descriptive statistics. Running time: Depends on the input data and the required options.

  14. Genetic diversity analysis of common beans based on molecular markers.

    Science.gov (United States)

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  15. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  16. Genetic diversity analysis of common beans based on molecular markers

    Science.gov (United States)

    Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-01-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  17. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  18. Molecular gene profiling of Clostridium botulinum group III and its detection in naturally contaminated samples originating from various European countries.

    Science.gov (United States)

    Woudstra, Cedric; Le Maréchal, Caroline; Souillard, Rozenn; Bayon-Auboyer, Marie-Hélène; Anniballi, Fabrizio; Auricchio, Bruna; De Medici, Dario; Bano, Luca; Koene, Miriam; Sansonetti, Marie-Hélène; Desoutter, Denise; Hansbauer, Eva-Maria; Dorner, Martin B; Dorner, Brigitte G; Fach, Patrick

    2015-04-01

    We report the development of real-time PCR assays for genotyping Clostridium botulinum group III targeting the newly defined C. novyi sensu lato group; the nontoxic nonhemagglutinin (NTNH)-encoding gene ntnh; the botulinum neurotoxin (BoNT)-encoding genes bont/C, bont/C/D, bont/D, and bont/D/C; and the flagellin (fliC) gene. The genetic diversity of fliC among C. botulinum group III strains resulted in the definition of five major subgroups named fliC-I to fliC-V. Investigation of fliC subtypes in 560 samples, with various European origins, showed that fliC-I was predominant and found exclusively in samples contaminated by C. botulinum type C/D, fliC-II was rarely detected, no sample was recorded as fliC-III or fliC-V, and only C. botulinum type D/C samples tested positive for fliC-IV. The lack of genetic diversity of the flagellin gene of C. botulinum type C/D would support a clonal spread of type C/D strains in different geographical areas. fliC-I to fliC-III are genetically related (87% to 92% sequence identity), whereas fliC-IV from C. botulinum type D/C is more genetically distant from the other fliC types (with only 50% sequence identity). These findings suggest fliC-I to fliC-III have evolved in a common environment and support a different genetic evolution for fliC-IV. A combination of the C. novyi sensu lato, ntnh, bont, and fliC PCR assays developed in this study allowed better characterization of C. botulinum group III and showed the group to be less genetically diverse than C. botulinum groups I and II, supporting a slow genetic evolution of the strains belonging to C. botulinum group III.

  19. Molecular Gene Profiling of Clostridium botulinum Group III and Its Detection in Naturally Contaminated Samples Originating from Various European Countries

    Science.gov (United States)

    Woudstra, Cedric; Le Maréchal, Caroline; Souillard, Rozenn; Bayon-Auboyer, Marie-Hélène; Anniballi, Fabrizio; Auricchio, Bruna; De Medici, Dario; Bano, Luca; Koene, Miriam; Sansonetti, Marie-Hélène; Desoutter, Denise; Hansbauer, Eva-Maria; Dorner, Martin B.; Dorner, Brigitte G.

    2015-01-01

    We report the development of real-time PCR assays for genotyping Clostridium botulinum group III targeting the newly defined C. novyi sensu lato group; the nontoxic nonhemagglutinin (NTNH)-encoding gene ntnh; the botulinum neurotoxin (BoNT)-encoding genes bont/C, bont/C/D, bont/D, and bont/D/C; and the flagellin (fliC) gene. The genetic diversity of fliC among C. botulinum group III strains resulted in the definition of five major subgroups named fliC-I to fliC-V. Investigation of fliC subtypes in 560 samples, with various European origins, showed that fliC-I was predominant and found exclusively in samples contaminated by C. botulinum type C/D, fliC-II was rarely detected, no sample was recorded as fliC-III or fliC-V, and only C. botulinum type D/C samples tested positive for fliC-IV. The lack of genetic diversity of the flagellin gene of C. botulinum type C/D would support a clonal spread of type C/D strains in different geographical areas. fliC-I to fliC-III are genetically related (87% to 92% sequence identity), whereas fliC-IV from C. botulinum type D/C is more genetically distant from the other fliC types (with only 50% sequence identity). These findings suggest fliC-I to fliC-III have evolved in a common environment and support a different genetic evolution for fliC-IV. A combination of the C. novyi sensu lato, ntnh, bont, and fliC PCR assays developed in this study allowed better characterization of C. botulinum group III and showed the group to be less genetically diverse than C. botulinum groups I and II, supporting a slow genetic evolution of the strains belonging to C. botulinum group III. PMID:25636839

  20. Assessing potential impacts associated with contamination events in water distribution systems : a sensitivity analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Davis, M. J.; Janke, R.; Taxon, T. N. (Decision and Information Sciences); ( EVS); (EPA)

    2010-11-01

    An understanding of the nature of the adverse effects that could be associated with contamination events in water distribution systems is necessary for carrying out vulnerability analyses and designing contamination warning systems. This study examines the adverse effects of contamination events using models for 12 actual water systems that serve populations ranging from about 104 to over 106 persons. The measure of adverse effects that we use is the number of people who are exposed to a contaminant above some dose level due to ingestion of contaminated tap water. For this study the number of such people defines the impact associated with an event. We consider a wide range of dose levels in order to accommodate a wide range of potential contaminants. For a particular contaminant, dose level can be related to a health effects level. For example, a dose level could correspond to the median lethal dose, i.e., the dose that would be fatal to 50% of the exposed population. Highly toxic contaminants may be associated with a particular response at a very low dose level, whereas contaminants with low toxicity may only be associated with the same response at a much higher dose level. This report focuses on the sensitivity of impacts to five factors that either define the nature of a contamination event or involve assumptions that are used in assessing exposure to the contaminant: (1) duration of contaminant injection, (2) time of contaminant injection, (3) quantity or mass of contaminant injected, (4) population distribution in the water distribution system, and (5) the ingestion pattern of the potentially exposed population. For each of these factors, the sensitivities of impacts to injection location and contaminant toxicity are also examined. For all the factors considered, sensitivity tends to increase with dose level (i.e., decreasing toxicity) of the contaminant, with considerable inter-network variability. With the exception of the population distribution (factor 4

  1. Mesoamerican tree squirrels evolution (Rodentia: Sciuridae): a molecular phylogenetic analysis.

    Science.gov (United States)

    Villalobos, Federico; Gutierrez-Espeleta, Gustavo

    2014-06-01

    The tribe Sciurini comprehends the genera Sciurus, Syntheosiurus, Microsciurus, Tamiasciurus and Rheinthrosciurus. The phylogenetic relationships within Sciurus have been only partially done, and the relationship between Mesoamerican species remains unsolved. The phylogenetic relationships of the Mesoamerican tree squirrels were examined using molecular data. Sequence data publicly available (12S, 16S, CYTB mitochondrial genes and IRBP nuclear gene) and cytochrome B gene sequences of four previously not sampled Mesoamerican Sciurus species were analyzed under a Bayesian multispecies coalescence model. Phylogenetic analysis of the multilocus data set showed the neotropical tree squirrels as a monophyletic clade. The genus Sciurus was paraphyletic due to the inclusion of Microsciurus species (M. alfari and M. flaviventer). The South American species S. aestuans and S. stramineus showed a sister taxa relationship. Single locus analysis based on the most compact and complete data set (i.e. CYTB gene sequences), supported the monophyly of the South American species and recovered a Mesoamerican clade including S. aureogaster, S. granatensis and S. variegatoides. These results corroborated previous findings based on cladistic analysis of cranial and post-cranial characters. Our data support a close relationship between Mesoamerican Sciurus species and a sister relationship with South American species, and corroborates previous findings in relation to the polyphyly of Microsciurus and Syntheosciurus paraphyly.

  2. Actual measurement, hygrothermal response experiment and growth prediction analysis of microbial contamination of central air conditioning system in Dalian, China.

    Science.gov (United States)

    Lv, Yang; Hu, Guangyao; Wang, Chunyang; Yuan, Wenjie; Wei, Shanshan; Gao, Jiaoqi; Wang, Boyuan; Song, Fangchao

    2017-04-03

    The microbial contamination of central air conditioning system is one of the important factors that affect the indoor air quality. Actual measurement and analysis were carried out on microbial contamination in central air conditioning system at a venue in Dalian, China. Illumina miseq method was used and three fungal samples of two units were analysed by high throughput sequencing. Results showed that the predominant fungus in air conditioning unit A and B were Candida spp. and Cladosporium spp., and two fungus were further used in the hygrothermal response experiment. Based on the data of Cladosporium in hygrothermal response experiment, this paper used the logistic equation and the Gompertz equation to fit the growth predictive model of Cladosporium genera in different temperature and relative humidity conditions, and the square root model was fitted based on the two environmental factors. In addition, the models were carried on the analysis to verify the accuracy and feasibility of the established model equation.

  3. Determination of dominant biogeochemical processes in a contaminated aquifer-wetland system using multivariate statistical analysis

    Science.gov (United States)

    Baez-Cazull, S. E.; McGuire, J.T.; Cozzarelli, I.M.; Voytek, M.A.

    2008-01-01

    Determining the processes governing aqueous biogeochemistry in a wetland hydrologically linked to an underlying contaminated aquifer is challenging due to the complex exchange between the systems and their distinct responses to changes in precipitation, recharge, and biological activities. To evaluate temporal and spatial processes in the wetland-aquifer system, water samples were collected using cm-scale multichambered passive diffusion samplers (peepers) to span the wetland-aquifer interface over a period of 3 yr. Samples were analyzed for major cations and anions, methane, and a suite of organic acids resulting in a large dataset of over 8000 points, which was evaluated using multivariate statistics. Principal component analysis (PCA) was chosen with the purpose of exploring the sources of variation in the dataset to expose related variables and provide insight into the biogeochemical processes that control the water chemistry of the system. Factor scores computed from PCA were mapped by date and depth. Patterns observed suggest that (i) fermentation is the process controlling the greatest variability in the dataset and it peaks in May; (ii) iron and sulfate reduction were the dominant terminal electron-accepting processes in the system and were associated with fermentation but had more complex seasonal variability than fermentation; (iii) methanogenesis was also important and associated with bacterial utilization of minerals as a source of electron acceptors (e.g., barite BaSO4); and (iv) seasonal hydrological patterns (wet and dry periods) control the availability of electron acceptors through the reoxidation of reduced iron-sulfur species enhancing iron and sulfate reduction. Copyright ?? 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

  4. A Systematic Review and Meta-Analysis of Fecal Contamination and Inadequate Treatment of Packaged Water.

    Science.gov (United States)

    Williams, Ashley R; Bain, Robert E S; Fisher, Michael B; Cronk, Ryan; Kelly, Emma R; Bartram, Jamie

    2015-01-01

    Packaged water products provide an increasingly important source of water for consumption. However, recent studies raise concerns over their safety. To assess the microbial safety of packaged water, examine differences between regions, country incomes, packaged water types, and compare packaged water with other water sources. We performed a systematic review and meta-analysis. Articles published in English, French, Portuguese, Spanish and Turkish, with no date restrictions were identified from online databases and two previous reviews. Studies published before April 2014 that assessed packaged water for the presence of Escherichia coli, thermotolerant or total coliforms were included provided they tested at least ten samples or brands. A total of 170 studies were included in the review. The majority of studies did not detect fecal indicator bacteria in packaged water (78/141). Compared to packaged water from upper-middle and high-income countries, packaged water from low and lower-middle-income countries was 4.6 (95% CI: 2.6-8.1) and 13.6 (95% CI: 6.9-26.7) times more likely to contain fecal indicator bacteria and total coliforms, respectively. Compared to all other packaged water types, water from small bottles was less likely to be contaminated with fecal indicator bacteria (OR = 0.32, 95%CI: 0.17-0.58) and total coliforms (OR = 0.10, 95%CI: 0.05, 0.22). Packaged water was less likely to contain fecal indicator bacteria (OR = 0.35, 95%CI: 0.20, 0.62) compared to other water sources used for consumption. Policymakers and regulators should recognize the potential benefits of packaged water in providing safer water for consumption at and away from home, especially for those who are otherwise unlikely to gain access to a reliable, safe water supply in the near future. To improve the quality of packaged water products they should be integrated into regulatory and monitoring frameworks.

  5. A Systematic Review and Meta-Analysis of Fecal Contamination and Inadequate Treatment of Packaged Water.

    Directory of Open Access Journals (Sweden)

    Ashley R Williams

    Full Text Available Packaged water products provide an increasingly important source of water for consumption. However, recent studies raise concerns over their safety.To assess the microbial safety of packaged water, examine differences between regions, country incomes, packaged water types, and compare packaged water with other water sources.We performed a systematic review and meta-analysis. Articles published in English, French, Portuguese, Spanish and Turkish, with no date restrictions were identified from online databases and two previous reviews. Studies published before April 2014 that assessed packaged water for the presence of Escherichia coli, thermotolerant or total coliforms were included provided they tested at least ten samples or brands.A total of 170 studies were included in the review. The majority of studies did not detect fecal indicator bacteria in packaged water (78/141. Compared to packaged water from upper-middle and high-income countries, packaged water from low and lower-middle-income countries was 4.6 (95% CI: 2.6-8.1 and 13.6 (95% CI: 6.9-26.7 times more likely to contain fecal indicator bacteria and total coliforms, respectively. Compared to all other packaged water types, water from small bottles was less likely to be contaminated with fecal indicator bacteria (OR = 0.32, 95%CI: 0.17-0.58 and total coliforms (OR = 0.10, 95%CI: 0.05, 0.22. Packaged water was less likely to contain fecal indicator bacteria (OR = 0.35, 95%CI: 0.20, 0.62 compared to other water sources used for consumption.Policymakers and regulators should recognize the potential benefits of packaged water in providing safer water for consumption at and away from home, especially for those who are otherwise unlikely to gain access to a reliable, safe water supply in the near future. To improve the quality of packaged water products they should be integrated into regulatory and monitoring frameworks.

  6. Screening and degrading characteristics and community structure of a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterial consortium from contaminated soil

    Institute of Scientific and Technical Information of China (English)

    Run Sun; Jinghua Jin; Guangdong Sun; Ying Liu; Zhipei Liu

    2010-01-01

    Inoculation with efficient microbes had been proved to be the most important way for the bioremediation of polluted environments.For the treatment of abandoned site of Beijing Coking Chemical Plant contaminated with high level of high-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs),a bacterial consortium capable of degrading HMW-PAHs,designated 1-18-1,was enriched and screened from HMW-PAHs contaminated soil.Its degrading ability was analyzed by high performance liquid chromatography (HPLC),and the community structure was investigated by construction and analyses of the 16S rRNA gene clone libraries (A,B and F) at different transfers.The results indicated that 1-18-1 was able to utilize pyrene,fluoranthene and benzo[a]pyrene as sole carbon and energy source for growth.The degradation rate of pyrene and fluoranthene reached 82.8% and 96.2% after incubation for 8 days at 30℃,respectively;while the degradation rate of benzo[a]pyrene was only 65.1% after incubation for 28 days at 30℃.Totally,108,100 and 100 valid clones were randomly selected and sequenced from the libraries A,B,and E Phylogenetic analyses showed that all the clones could be divided into 5 groups,Bacteroidetes,α-Proteobacteria,Actinobacteria,β-Proteobacteria and γ-Proteobacteria.Sequence similarity analyses showed total 39 operational taxonomic units (OTUs) in the libraries.The predominant bacterial groups were α-Proteobacteria (19 OTUs,48.7%),γ-Proteobacteria (9 OTUs,23.1%) and β-Protcobacteria (8 OTUs,20.5%).During the transfer process,the proportions of α-Proteobacteria and β-Proteobacteria increased greatly (from 47% to 93%),while γ-Proteobacteria decreased from 32% (library A) to 6% (library F);and Bacteroidetes group disappeared in libraries B and F.

  7. Evaluation of surface analysis methods for characterization of trace metal surface contaminants found in silicon IC manufacturing

    Energy Technology Data Exchange (ETDEWEB)

    Diebold, A.C.; Maillot, P.; Gordon, M.; Baylis, J.; Chacon, J.; Witowski, R. (SEMATECH, Austin, TX (United States)); Arlinghaus, H. (Atom Sciences, Inc., Oak Ridge, TN (United States)); Knapp, J.A.; Doyle, B.L. (Sandia National Labs., Albuquerque, NM (United States))

    1991-01-01

    A major topic at recent silicon-based integrated circuit (IC) manufacturing symposia is the pursuit of decreased contamination levels. The aim is to remove contamination from both processes and materials. In conjunction with this effort, characterization methods are being pushed to lower and lower detection limits. In this paper, we evaluate surface analysis methods used to determine the concentration of inorganic contamination on unpatterned Si wafers. We compare sampling depths, detection limits, and applicability of each method for use in support of Si IC manufacturing. This comparison is further limited to Fe and Cu which are transition metal contaminants associated with manufacturing yield loss. The surface analysis methods included in this evaluation are: Total Reflection X-Ray Fluorescence (TXRF or TRXRF); Secondary Ion Mass Spectrometry (SIMS); two post-ionization'' methods Surface Analysis by Laser Ionization (SALI) and Sputter Initiated Resonant Ionization Spectroscopy (SIRIS); Heavy Ion Backscattering Spectroscopy (HIBS); and Vapor Phase Phase Decomposition (VPD) based methods Atomic Absorption (VPD-AA) along with VPD-TXRF. Sets of 6 in. Si wafers with concentration levels between 10{sup 9} atoms/cm{sup 2} and 10{sup 12} atoms/cm{sup 2} Fe and Cu were characterized by TXRF, SIMS, SIRIS, and HIBS. This data allows estimation of detection limits (DLs) and relative method accuracy. In Section 1 we describe each surface analysis method and the circumstance under which it would be used to support Si IC manufacturing. The equipment used for this comparison and the 150 mm Si wafer set are described in Section 2. Results from each method are contrasted in Section 3. Finally, a conclusion is presented in Section 4.

  8. Passive PE Sampling in Support of In Situ Remediation of Contaminated Sediments: Standard Operating Procedure for PE Analysis

    Science.gov (United States)

    2012-12-01

    biofilms and epiphytic growth on PE surfaces does not compromise their behavior in the field during deployment, these coatings can substantially...4.5 Food -grade aluminum foil 4.6 Stainless steel forceps 4.7 Single-edge razor blades 4.8 Teflon (or similar non-contaminating material) cutting...extracted using organic solvents prior to analysis by GC/MS. 7.1.1 The PE is inspected for surface biofilms , particles, mud, or oily coatings. Biofilm

  9. Statistical characterization of contaminated groundwater in the agricultural area by multivariative analysis and kriging

    Science.gov (United States)

    Kaown, D.; Hyun, Y.; Lee, K.

    2004-12-01

    The characterization of groundwater contamination at a hydrologically complex agricultural site in Youpori, Chooncheon (Korea) was undertaken by analyzing hydro-chemical data of groundwater within a statistical framework. The data show that high and correlated concentrations of Ca, Mg, and NO3 reflected the polluted nature of groundwater at the site. More than 39% of samples showed nitrate concentrations above the human affected value (3mg/L as NO3-N ), while about 25% samples exceeded the maximum acceptable level (10mg/L as NO3-N ) according to the EPA regulation. Multivariate analyses (factor and cluster analyses) were used to identify contaminant pathway, source and geochemical process. The geostatistical method was applied in order to delineate the spatial extent and variation of nitrate contamination. Factor and cluster analyses indicate that hydrochemical data can clearly characterize the non-point contamination over the area by agrochemical fertilizer as well as point-source pollution like manure spreading near barn or pigpen on groundwater. Nitrate-N, the critical species in the study area, was used to delineate the spatial spread of the contaminants using kriging in the study area.

  10. Biomarkers and molecular analysis to improve bloodstream infection diagnostics in an emergency care unit.

    Directory of Open Access Journals (Sweden)

    Anne J M Loonen

    Full Text Available Molecular pathogen detection from blood is still expensive and the exact clinical value remains to be determined. The use of biomarkers may assist in preselecting patients for immediate molecular testing besides blood culture. In this study, 140 patients with ≥ 2 SIRS criteria and clinical signs of infection presenting at the emergency department of our hospital were included. C-reactive protein (CRP, neutrophil-lymphocyte count ratio (NLCR, procalcitonin (PCT and soluble urokinase plasminogen activator receptor (suPAR levels were determined. One ml EDTA blood was obtained and selective pathogen DNA isolation was performed with MolYsis (Molzym. DNA samples were analysed for the presence of pathogens, using both the MagicPlex Sepsis Test (Seegene and SepsiTest (Molzym, and results were compared to blood cultures. Fifteen patients had to be excluded from the study, leaving 125 patients for further analysis. Of the 125 patient samples analysed, 27 presented with positive blood cultures of which 7 were considered to be contaminants. suPAR, PCT, and NLCR values were significantly higher in patients with positive blood cultures compared to patients without (p < 0.001. Receiver operating characteristic curves of the 4 biomarkers for differentiating bacteremia from non-bacteremia showed the highest area under the curve (AUC for PCT (0.806 (95% confidence interval 0.699-0.913. NLCR, suPAR and CRP resulted in an AUC of 0.770, 0.793, and 0.485, respectively. When compared to blood cultures, the sensitivity, specificity, positive predictive value (PPV, and negative predictive value (NPV for SepsiTest and MagicPlex Sepsis Test were 11%, 96%, 43%, 80%, and 37%, 77%, 30%, 82%, respectively. In conclusion, both molecular assays perform poorly when one ml whole blood is used from emergency care unit patients. NLCR is a cheap, fast, easy to determine, and rapidly available biomarker, and therefore seems most promising in differentiating BSI from non

  11. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

    Science.gov (United States)

    Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

    2011-07-30

    MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com.

  12. Molecular Characterization and Expression Analysis of Equine ( Gene in Horse (

    Directory of Open Access Journals (Sweden)

    Ki-Duk Song

    2014-05-01

    Full Text Available The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog, we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks and non-synonymous substitution ratios (Ka revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR and quantitative-polymerase chain reaction (qPCR showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

  13. Molecular Cytogenetic Analysis of Deschampsia antarctica Desv. (Poaceae), Maritime Antarctic.

    Science.gov (United States)

    Amosova, Alexandra V; Bolsheva, Nadezhda L; Samatadze, Tatiana E; Twardovska, Maryana O; Zoshchuk, Svyatoslav A; Andreev, Igor O; Badaeva, Ekaterina D; Kunakh, Viktor A; Muravenko, Olga V

    2015-01-01

    Deschampsia antarctica Desv. (Poaceae) (2n = 26) is one of the two vascular plants adapted to the harshest environment of the Antarctic. Although the species is a valuable model for study of environmental stress tolerance in plants, its karyotype is still poorly investigated. We firstly conducted a comprehensive molecular cytogenetic analysis of D. antarctica collected on four islands of the Maritime Antarctic. D. antarctica karyotypes were studied by Giemsa C- and DAPI/C-banding, Ag-NOR staining, multicolour fluorescence in situ hybridization with repeated DNA probes (pTa71, pTa794, telomere repeats, pSc119.2, pAs1) and the GAA simple sequence repeat probe. We also performed sequential rapid in situ hybridization with genomic DNA of D. caespitosa. Two chromosome pairs bearing transcriptionally active 45S rDNA loci and five pairs with 5S rDNA sites were detected. A weak intercalary site of telomere repeats was revealed on the largest chromosome in addition to telomere hybridization signals at terminal positions. This fact confirms indirectly the hypothesis that chromosome fusion might have been the cause of the unusual for cereals chromosome number in this species. Based on patterns of distribution of the examined molecular cytogenetic markers, all chromosomes in karyotypes were identified, and chromosome idiograms of D. antarctica were constructed. B chromosomes were found in most karyotypes of plants from Darboux Island. A mixoploid plant with mainly triploid cells bearing a Robertsonian rearrangement was detected among typical diploid specimens from Great Jalour Island. The karyotype variability found in D. antarctica is probably an expression of genome instability induced by environmental stress factors. The differences in C-banding patterns and in chromosome distribution of rDNA loci as well as homologous highly repeated DNA sequences detected between genomes of D. antarctica and its related species D. caespitosa indicate that genome reorganization involving

  14. Molecular analysis of microbial communities in endotracheal tube biofilms.

    Directory of Open Access Journals (Sweden)

    Scott Cairns

    Full Text Available BACKGROUND: Ventilator-associated pneumonia is the most prevalent acquired infection of patients on intensive care units and is associated with considerable morbidity and mortality. Evidence suggests that an improved understanding of the composition of the biofilm communities that form on endotracheal tubes may result in the development of improved preventative strategies for ventilator-associated pneumonia. METHODOLOGY/PRINCIPAL FINDINGS: The aim of this study was to characterise microbial biofilms on the inner luminal surface of extubated endotracheal tubes from ICU patients using PCR and molecular profiling. Twenty-four endotracheal tubes were obtained from twenty mechanically ventilated patients. Denaturing gradient gel electrophoresis (DGGE profiling of 16S rRNA gene amplicons was used to assess the diversity of the bacterial population, together with species specific PCR of key marker oral microorganisms and a quantitative assessment of culturable aerobic bacteria. Analysis of culturable aerobic bacteria revealed a range of colonisation from no growth to 2.1×10(8 colony forming units (cfu/cm(2 of endotracheal tube (mean 1.4×10(7 cfu/cm(2. PCR targeting of specific bacterial species detected the oral bacteria Streptococcus mutans (n = 5 and Porphyromonas gingivalis (n = 5. DGGE profiling of the endotracheal biofilms revealed complex banding patterns containing between 3 and 22 (mean 6 bands per tube, thus demonstrating the marked complexity of the constituent biofilms. Significant inter-patient diversity was evident. The number of DGGE bands detected was not related to total viable microbial counts or the duration of intubation. CONCLUSIONS/SIGNIFICANCE: Molecular profiling using DGGE demonstrated considerable biofilm compositional complexity and inter-patient diversity and provides a rapid method for the further study of biofilm composition in longitudinal and interventional studies. The presence of oral microorganisms in

  15. Relative expression analysis for molecular cancer diagnosis and prognosis.

    Science.gov (United States)

    Eddy, James A; Sung, Jaeyun; Geman, Donald; Price, Nathan D

    2010-04-01

    The enormous amount of biomolecule measurement data generated from high-throughput technologies has brought an increased need for computational tools in biological analyses. Such tools can enhance our understanding of human health and genetic diseases, such as cancer, by accurately classifying phenotypes, detecting the presence of disease, discriminating among cancer sub-types, predicting clinical outcomes, and characterizing disease progression. In the case of gene expression microarray data, standard statistical learning methods have been used to identify classifiers that can accurately distinguish disease phenotypes. However, these mathematical prediction rules are often highly complex, and they lack the convenience and simplicity desired for extracting underlying biological meaning or transitioning into the clinic. In this review, we survey a powerful collection of computational methods for analyzing transcriptomic microarray data that address these limitations. Relative Expression Analysis (RXA) is based only on the relative orderings among the expressions of a small number of genes. Specifically, we provide a description of the first and simplest example of RXA, the K-TSP classifier, which is based on _ pairs of genes; the case K = 1 is the TSP classifier. Given their simplicity and ease of biological interpretation, as well as their invariance to data normalization and parameter-fitting, these classifiers have been widely applied in aiding molecular diagnostics in a broad range of human cancers. We review several studies which demonstrate accurate classification of disease phenotypes (e.g., cancer vs. normal), cancer subclasses (e.g., AML vs. ALL, GIST vs. LMS), disease outcomes (e.g., metastasis, survival), and diverse human pathologies assayed through blood-borne leukocytes. The studies presented demonstrate that RXA-specifically the TSP and K-TSP classifiers-is a promising new class of computational methods for analyzing high-throughput data, and has the

  16. Molecular dynamics analysis on impact behavior of carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Seifoori, Sajjad, E-mail: sajjad.seifoori@vru.ac.ir

    2015-01-30

    Graphical abstract: - Highlights: • We present an analytical solution of impact based on two degree of freedom model. • The accuracy is verified by Molecular dynamics simulations. • The effects of the small-size effects on the dynamic deflections are investigated. • The relative motion is also accounted that is due to local indentation. - Abstract: Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler–Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.

  17. Environmental analysis of endocrine disrupting effects from hydrocarbon contaminants in the ecosystem. 1997 annual progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-01-01

    'The overall objective of the basic research grant is to characterize the potential of common hydrocarbon contaminants in ecosystems to act as endocrine disruptors. The three major lines of research include (1) a biotechnology based screening system to identify potential hormone mimics and antagonists; (2) an animal screening system to identify biomarkers of endocrine effects. and (3) a literature review to identify compounds at a variety of DOE sites that need to be examined for endocrine disrupting effects. By relating results obtained from this research project to contamination problems at various DOE sites. CBR will provide data and information on endocrine disrupting contaminants to DOE for consideration in risk analyses for determining clean-up levels and priorities needed at the sites.'

  18. Transcriptomic analysis of bottlenose dolphin (Tursiops truncatus) skin biopsies to assess the effects of emerging contaminants.

    Science.gov (United States)

    Lunardi, Denise; Abelli, Luigi; Panti, Cristina; Marsili, Letizia; Fossi, Maria Cristina; Mancia, Annalaura

    2016-03-01

    Chemicals discovered in water at levels that may be significantly different than expected are referred to as contaminants of emerging concern (CECs) because the risk to environmental health posed by their occurrence/frequency is still unknown. The worldwide distributed compounds perfluorooctanoic acid (PFOA) and bisphenol A (BPA) may fall into this category due to effects on endocrine receptors. We applied an ex vivo assay using small slices of bioptic skin from the bottlenose dolphin, Tursiops truncatus, cultured and treated for 24 h with different PFOA or BPA concentrations to analyze global gene expression. RNA was labeled and hybridized to a species-specific oligomicroarray. The skin transcriptome held information on the contaminant exposure, potentially predictive about long-term effects on health, being the genes affected involved in immunity modulation, response to stress, lipid homeostasis, and development. The transcriptomic signature of dolphin skin could be therefore relevant as classifier for a specific contaminant.

  19. Analysis on contaminants transport process through clay-solidified grouting curtain in MSW landfills

    Institute of Scientific and Technical Information of China (English)

    CHEN Yong-gui; ZHANG Ke-neng; HUANG Chang-bo

    2005-01-01

    Clay-solidified grouting curtains are commonly used for remediation by containment or pollution prevention, in addition to their use as a barrier to water flow in municipal solid waste(MSW) landfills. A hydrological model.of water flow and a hydrodynamic model of contaminant are presented to simulate the migration of leachate through clay-solidified grouting curtain in MSW landfills, with particular attention paid to the role of diffusive and adsorptive fluxes in contaminant transport. The models were applied to simulate the sensitivity of the curtain's behavior to changes in parameters, such as thickness, depth, permeability coefficient, diffusion coefficient,resistance coefficient and concentration, and also to demonstrate the contaminant distribution on the evolution of travel time and offset distance of clay-solidified grouting curtain in landfills. It is found that a part of leachate components stays or is retarded in clay-solidified grouting curtain by precipitate or exchange, the retention rate is closely related to composition of clay-solidified grouting curtain, more than 800%, and the maximum occurs at the cementclay ratio of 2: 4 under experimental conditions. Contamination distribution is variable on travel time and offset distance, the highest concentration takes place where the contamination intensity is nearest to the pollution resource or takes place at early middle period of transport, and the pollutant attenuates gradually. The results indicate that claysolidified grouting curtain with a proper thickness, a low permeability coefficient and a high resistance coefficient might serve as a sufficiently effective vertical barrier against leachate seepage and contamination migration in MSWlandfills.

  20. Real-time surrogate analysis for potential oil and gas contamination of drinking water resources

    Science.gov (United States)

    Son, Ji-Hee; Carlson, Kenneth H.

    2015-09-01

    Public concerns related to the fast-growing shale oil and gas industry have increased during recent years. The major concern regarding shale gas production is the potential of fracturing fluids being injected into the well or produced fluids flowing out of the well to contaminate drinking water resources such as surface water and groundwater. Fracturing fluids contain high total dissolved solids (TDS); thus, changes in TDS concentrations in groundwater might indicate influences of fracturing fluids. An increase of methane concentrations in groundwater could also potentially be due to hydraulic fracturing activities. To understand the possible contamination of groundwater by fracturing activities, real-time groundwater monitoring is being implemented in the Denver-Julesburg basin of northeast Colorado. A strategy of monitoring of surrogate parameters was chosen instead of measuring potential contaminants directly, an approach that is not cost effective or operationally practical. Contaminant surrogates of TDS and dissolved methane were proposed in this study, and were tested for correlation and data distribution with laboratory experiments. Correlations between TDS and electrical conductivity (EC), and between methane contamination and oxidation-reduction potential (ORP) were strong at low concentrations of contaminants (1 mg/L TDS and 0.3 mg/L CH4). Dissolved oxygen (DO) was only an effective surrogate at higher methane concentrations (≥2.5 mg/L). The results indicated that EC and ORP are effective surrogates for detecting concentration changes of TDS and methane, respectively, and that a strategy of monitoring for easy to measure parameters can be effective detecting real-time, anomalous behavior relative to a predetermined baseline.

  1. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    Science.gov (United States)

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2015-11-20

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments.

  2. Analysis of consumer complaints related to microbial contamination in soft drinks.

    Science.gov (United States)

    Hara-Kudo, Yukiko; Goto, Keiichi; Onoue, Youichi; Watanabe, Maiko; Lee, Ken-ichi; Kumagai, Susumu; Sugita-Konishi, Yoshiko; Ohnishi, Takahiro

    2009-12-01

    Surveillance of consumer complaints related to microbial contamination in soft drinks indicated that tea drinks, and juice and juice drinks were major soft drinks involved in complaints. The frequency of complaints about juice and juice drinks is relatively high in relation to the production amount. Damage to containers during distribution and inappropriate storage of soft drinks by consumers are major causes of complaints. Molds were predominantly associated with complaints and symptoms caused by intake of contaminated soft drinks. To reduce complaints, more support for small companies, and greater education for carriers, dealers and consumers are needed.

  3. Numerical analysis of ALADIN optics contamination due to outgassing of solar array materials

    Energy Technology Data Exchange (ETDEWEB)

    Markelov, G [Advanced Operations and Engineering Services (AOES) Group BV, Postbus 342, 2300 AH Leiden (Netherlands); Endemann, M [ESA-ESTEC/EOP-PAS, Postbus 299, 2200 AG Noordwijk (Netherlands); Wernham, D [ESA-ESTEC/EOP-PAQ, Postbus 299, 2200 AG Noordwijk (Netherlands)], E-mail: Gennady.Markelov@aoes.com

    2008-03-01

    ALADIN is the very first space-based lidar that will provide global wind profile and a special attention has been paid to contamination of ALADIN optics. The paper presents a numerical approach, which is based on the direct simulation Monte Carlo method. The method allows one to accurately compute collisions between various species, in the case under consideration, free-stream flow and outgassing from solar array materials. The collisions create a contamination flux onto the optics despite there is no line-of-sight from the solar arrays to the optics. Comparison of obtained results with a simple analytical model prediction shows that the analytical model underpredicts mass fluxes.

  4. Quantitative molecular diagnostic assays of grain washes for Claviceps purpurea are correlated with visual determinations of ergot contamination

    Science.gov (United States)

    Comte, Alexia; Gräfenhan, Tom; Links, Matthew G.; Hemmingsen, Sean M.

    2017-01-01

    We examined the epiphytic microbiome of cereal grain using the universal barcode chaperonin-60 (cpn60). Microbial community profiling of seed washes containing DNA extracts prepared from field-grown cereal grain detected sequences from a fungus identified only to Class Sordariomycetes. To identify the fungal sequence and to improve the reference database, we determined cpn60 sequences from field-collected and reference strains of the ergot fungus, Claviceps purpurea. These data allowed us to identify this fungal sequence as deriving from C. purpurea, and suggested that C. purpurea DNA is readily detectable on agricultural commodities, including those for which ergot was not identified as a grading factor. To get a sense of the prevalence and level of C. purpurea DNA in cereal grains, we developed a quantitative PCR assay based on the fungal internal transcribed spacer (ITS) and applied it to 137 samples from the 2014 crop year. The amount of Claviceps DNA quantified correlated strongly with the proportion of ergot sclerotia identified in each grain lot, although there was evidence that non-target organisms were responsible for some false positives with the ITS-based assay. We therefore developed a cpn60-targeted loop-mediated isothermal amplification assay and applied it to the same grain wash samples. The time to positive displayed a significant, inverse correlation to ergot levels determined by visual ratings. These results indicate that both laboratory-based and field-adaptable molecular diagnostic assays can be used to detect and quantify pathogen load in bulk commodities using cereal grain washes. PMID:28257512

  5. Quantitative molecular diagnostic assays of grain washes for Claviceps purpurea are correlated with visual determinations of ergot contamination.

    Science.gov (United States)

    Comte, Alexia; Gräfenhan, Tom; Links, Matthew G; Hemmingsen, Sean M; Dumonceaux, Tim J

    2017-01-01

    We examined the epiphytic microbiome of cereal grain using the universal barcode chaperonin-60 (cpn60). Microbial community profiling of seed washes containing DNA extracts prepared from field-grown cereal grain detected sequences from a fungus identified only to Class Sordariomycetes. To identify the fungal sequence and to improve the reference database, we determined cpn60 sequences from field-collected and reference strains of the ergot fungus, Claviceps purpurea. These data allowed us to identify this fungal sequence as deriving from C. purpurea, and suggested that C. purpurea DNA is readily detectable on agricultural commodities, including those for which ergot was not identified as a grading factor. To get a sense of the prevalence and level of C. purpurea DNA in cereal grains, we developed a quantitative PCR assay based on the fungal internal transcribed spacer (ITS) and applied it to 137 samples from the 2014 crop year. The amount of Claviceps DNA quantified correlated strongly with the proportion of ergot sclerotia identified in each grain lot, although there was evidence that non-target organisms were responsible for some false positives with the ITS-based assay. We therefore developed a cpn60-targeted loop-mediated isothermal amplification assay and applied it to the same grain wash samples. The time to positive displayed a significant, inverse correlation to ergot levels determined by visual ratings. These results indicate that both laboratory-based and field-adaptable molecular diagnostic assays can be used to detect and quantify pathogen load in bulk commodities using cereal grain washes.

  6. COMPARATIVE ANALYSIS OF INTER SIMPLE SEQUENCE REPEATS AND SIMPLE SEQUENCE REPEATS MARKERS: GENETIC ANALYSIS OF DESCHAMPSIA CESPITOSA POPULATIONS GROWING IN METAL CONTAMINATED REGIONS IN CANADA

    Directory of Open Access Journals (Sweden)

    K.K. Nkongolo

    2014-01-01

    Full Text Available Comparative studies conducted on the genetic variation of metal-tolerant populations and their non-metal-tolerant counterparts have been performed on numerous species using isozyme markers. Analysis of genetic differences among plant populations growing in heavy metal-contaminated and uncontaminated regions are limited. The main objectives of the present study were to compare ISSR and microsatellite markers in assessing genetic variation in D. cespitosa populations that colonized metal-contaminated and uncontaminated regions in Northern Ontario, Canada. Total genomic DNA from D. cespitosa samples were amplified with ISSR and SSR primers using optimized PCR conditions. The level of polymorphic loci varies from 46 to 74% for ISSR analysis. The level of observed heterozygosity was moderate to high ranging from 0.44 to 0.68 for the SSR primers used. But no significant difference in genetic variation levels was detected between metal contaminated and uncontaminated sites with SSR markers. There was a significant reduction of polymorphic loci in samples from highly metal-contaminated areas of the Cobalt region compared to the reference sites based on ISSR analysis. Use of a combination of different marker systems is recommended to analyse genetic variation in plant populations.

  7. Contamination Control for Thermal Engineers

    Science.gov (United States)

    Rivera, Rachel B.

    2015-01-01

    The presentation will be given at the 26th Annual Thermal Fluids Analysis Workshop (TFAWS 2015) hosted by the Goddard Spaceflight Center (GSFC) Thermal Engineering Branch (Code 545). This course will cover the basics of Contamination Control, including contamination control related failures, the effects of contamination on Flight Hardware, what contamination requirements translate to, design methodology, and implementing contamination control into Integration, Testing and Launch.

  8. An analysis of the composition and metal contamination of plastics from waste electrical and electronic equipment (WEEE)

    Energy Technology Data Exchange (ETDEWEB)

    Stenvall, Erik, E-mail: erik.stenvall@chalmers.se [Department of Materials and Manufacturing Technology, Chalmers University of Technology, 41296 Göteborg (Sweden); Tostar, Sandra [Department of Industrial Materials Recycling, Chalmers University of Technology, 41296 Göteborg (Sweden); Boldizar, Antal [Department of Materials and Manufacturing Technology, Chalmers University of Technology, 41296 Göteborg (Sweden); Foreman, Mark R.StJ. [Department of Industrial Materials Recycling, Chalmers University of Technology, 41296 Göteborg (Sweden); Möller, Kenneth [Chemistry and Materials Technology, SP, 50115 Borås (Sweden)

    2013-04-15

    The compositions of three WEEE plastic batches of different origin were investigated using infrared spectroscopy, and the metal content was determined with inductively coupled plasma. The composition analysis of the plastics was based mainly on 14 samples collected from a real waste stream, and showed that the major constituents were high impact polystyrene (42 wt%), acrylonitrile–butadiene–styrene copolymer (38 wt%) and polypropylene (10 wt%). Their respective standard deviations were 21.4%, 16.5% and 60.7%, indicating a considerable variation even within a single batch. The level of metal particle contamination was found to be low in all samples, whereas wood contamination and rubber contamination were found to be about 1 wt% each in most samples. In the metal content analysis, iron was detected at levels up to 700 ppm in the recyclable waste plastics fraction, which is of concern due to its potential to catalyse redox reactions during melt processing and thus accelerate the degradation of plastics during recycling. Toxic metals were found only at very low concentrations, with the exception of lead and cadmium which could be detected at 200 ppm and 70 ppm levels, respectively, but these values are below the current threshold limits of 1000 ppm and 100 ppm set by the Restriction of Hazardous Substances directive.

  9. An analysis of the composition and metal contamination of plastics from waste electrical and electronic equipment (WEEE).

    Science.gov (United States)

    Stenvall, Erik; Tostar, Sandra; Boldizar, Antal; Foreman, Mark R StJ; Möller, Kenneth

    2013-04-01

    The compositions of three WEEE plastic batches of different origin were investigated using infrared spectroscopy, and the metal content was determined with inductively coupled plasma. The composition analysis of the plastics was based mainly on 14 samples collected from a real waste stream, and showed that the major constituents were high impact polystyrene (42 wt%), acrylonitrile-butadiene-styrene copolymer (38 wt%) and polypropylene (10 wt%). Their respective standard deviations were 21.4%, 16.5% and 60.7%, indicating a considerable variation even within a single batch. The level of metal particle contamination was found to be low in all samples, whereas wood contamination and rubber contamination were found to be about 1 wt% each in most samples. In the metal content analysis, iron was detected at levels up to 700 ppm in the recyclable waste plastics fraction, which is of concern due to its potential to catalyse redox reactions during melt processing and thus accelerate the degradation of plastics during recycling. Toxic metals were found only at very low concentrations, with the exception of lead and cadmium which could be detected at 200 ppm and 70 ppm levels, respectively, but these values are below the current threshold limits of 1000 ppm and 100 ppm set by the Restriction of Hazardous Substances directive. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Network environmental analysis based ecological risk assessment of a naphthalene-contaminated groundwater ecosystem under varying remedial schemes

    Science.gov (United States)

    Wang, Zheng; He, Li; Lu, Hongwei; Ren, Lixia; Xu, Zongda

    2016-12-01

    Many of the existing ecological risk studies for groundwater ecosystems paid little attention to either small-scale regions (e.g., an industrial contamination site) or ignored anthropogenic activities (e.g., site remediation). This study presented a network environmental analysis based ecological risk assessment (ERA) framework to a naphthalene-contaminated groundwater remediation site. In the ERA, four components (vegetation, herbivore, soil micro-organism and carnivore) were selected, which are directly or indirectly exposed to the contaminated groundwater ecosystem. By incorporating both direct and indirect ecosystem interactions, the risk conditions of the whole ecosystem and its components were quantified and illustrated in the case study. Results indicate that despite there being no input risks for herbivores and carnivores, the respective integral risks increase to 0.0492 and 0.0410. For soil micro-organisms, 58.8% of the integral risk comes from the input risk, while the other 41.2% of the integral risk comes from the direct risk. Therefore, the risk flow within the components is a non-negligible risk origination for soil micro-organisms. However, the integral risk for vegetation was similar to the input risk, indicating no direct risk. The integral risk at the 5-year point after remediation was the highest for the four components. This risk then decreased at the 10-year point, and then again increased. Results from the sensitivity analysis also suggest that the proposed framework is robust enough to avoid disturbance by parameter uncertainty.

  11. Detection of water contamination from hydraulic fracturing wastewater: a μPAD for bromide analysis in natural waters.

    Science.gov (United States)

    Loh, Leslie J; Bandara, Gayan C; Weber, Genevieve L; Remcho, Vincent T

    2015-08-21

    Due to the rapid expansion in hydraulic fracturing (fracking), there is a need for robust, portable and specific water analysis techniques. Early detection of contamination is crucial for the prevention of lasting environmental damage. Bromide can potentially function as an early indicator of water contamination by fracking waste, because there is a high concentration of bromide ions in fracking wastewaters. To facilitate this, a microfluidic paper-based analytical device (μPAD) has been developed and optimized for the quantitative colorimetric detection of bromide in water using a smartphone. A paper microfluidic platform offers the advantages of inexpensive fabrication, elimination of unstable wet reagents, portability and high adaptability for widespread distribution. These features make this assay an attractive option for a new field test for on-site determination of bromide.

  12. Detection and Separation of Event-related Potentials from Multi-Artifacts Contaminated EEG by Means of Independent Component Analysis

    Institute of Scientific and Technical Information of China (English)

    WANGRong-chang; DUSi-dan; GAODun-tang

    2004-01-01

    Event-related potentials (ERP) is an important type of brain dynamics in human cognition research. However, ERP is often submerged by the spontaneous brain activity EEG, for its relatively tiny scale. Further more, the brain activities collected from scalp electrodes are often inevitably contaminated by several kinds of artifacts, such as blinks, eye movements, muscle noise and power line interference. A new approach to correct these disturbances is presented using independent component analysis (ICA). This technique can effectively detect and extract ERP components from the measured electrodes recordings even if they are heavily contaminated. The results compare favorably to those obtained by parametric modeling. Besides, auto--adaptive projection of decomposed results to ERP components was also given. Through experiments, ICA proves to be highly capable of ERP extraction and S/N ratio improving.

  13. Impacts on groundwater recharge areas of megacity pumping: analysis of potential contamination of Kolkata, India, water supply

    Science.gov (United States)

    Sahu, Paulami; Michael, Holly A.; Voss, Clifford I.; Sikdar, Pradip K.

    2013-01-01

    Water supply to the world's megacities is a problem of quantity and quality that will be a priority in the coming decades. Heavy pumping of groundwater beneath these urban centres, particularly in regions with low natural topographic gradients, such as deltas and floodplains, can fundamentally alter the hydrological system. These changes affect recharge area locations, which may shift closer to the city centre than before development, thereby increasing the potential for contamination. Hydrogeological simulation analysis allows evaluation of the impact on past, present and future pumping for the region of Kolkata, India, on recharge area locations in an aquifer that supplies water to over 13 million people. Relocated recharge areas are compared with known surface contamination sources, with a focus on sustainable management of this urban groundwater resource. The study highlights the impacts of pumping on water sources for long-term development of stressed city aquifers and for future water supply in deltaic and floodplain regions of the world.

  14. ANALYSIS OF SEASONAL VARIATION ON DEGREE OF CONTAMINATION WITH HEAVY METALS IN AARJATE VILLAGE, MOROCCO. AN INDEX APPROACH

    Directory of Open Access Journals (Sweden)

    FRANÇOIS X. NSHIMIYIMANA

    2015-02-01

    Full Text Available Water samples from wells and samples from soil nearby them were taken during dry (June-September 2013 and wet (December 2013, January - February 2014 seasons and concentrations of Cd, Cu, Mn, Ni, Pb and Zn were determined. Contamination Factor for each heavy metal and Nemerow pollution index were calculated showing a decrease in contamination degree from summer to winter for soil and an increase in case of groundwater. Vertical transfer of pollutants from top soil to groundwater was assessed using Hierarchical Cluster Analysis, significant correlations between concentrations and composition of soil being found. In case of Ni, the variables corresponding to the concentrations from soil and groundwater were part of the same cluster, in both seasons, the distribution maps of concentrations confirming the pattern of transfer.

  15. A Simplified Method for Sampling and Analysis of High Volume Surface Water for Organic Contaminants Using XAD-2

    Science.gov (United States)

    Datta, S.; Do, L.V.; Young, T.M.

    2004-01-01

    A simple compressed-gas driven system for field processing and extracting water for subsequent analyses of hydrophobic organic compounds is presented. The pumping device is a pneumatically driven pump and filtration system that can easily clarify at 4L/min. The extraction device uses compressed gas to drive filtered water through two parallel XAD-2 resin columns, at about 200 mL/min. No batteries or inverters are required for water collection or processing. Solvent extractions were performed directly in the XAD-2 glass columns. Final extracts are cleaned-up on Florisil cartridges without fractionation and contaminants analyzed by GC-MS. Method detection limits (MDLs) and recoveries for dissolved organic contaminants, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and pesticides are reported along with results of surface water analysis for the San Francisco Bay, CA.

  16. Material Cycles and Chemicals: Dynamic Material Flow Analysis of Contaminants in Paper Recycling

    DEFF Research Database (Denmark)

    Pivnenko, Kostyantyn; Laner, David; Astrup, Thomas Fruergaard

    2016-01-01

    This study provides a systematic approach for assessment of contaminants in materials for recycling. Paper recycling is used as an illustrative example. Three selected chemicals, bisphenol A (BPA), diethylhexyl phthalate (DEHP) and mineral oil hydrocarbons (MOHs), are evaluated within the paper...

  17. Diallel analysis of resistance to fusarium ear rot and fumonisin contamination in maize

    Science.gov (United States)

    The fungus Fusarium verticillioides infects maize ears and kernels, resulting in Fusarium ear rot disease, reduced grain yields, and contamination of grain with the mycotoxin fumonisin. Typical hybrid maize breeding programs involve selection for both favorable inbred and hybrid performance, and the...

  18. Spatially explicit risk analysis: a new solution to contamination problems in the Metropolitan Delta

    NARCIS (Netherlands)

    Brink, van den N.W.; Baveco, J.M.

    2004-01-01

    In the current paper a new conceptual outline for the ecological risk assessment of contamination will be adressed. In the first place risk assessment has to be spatially explicit, taking in account the spatial structure of the landscape (landscape ecotoxicology). Secondly the concept of SSRA

  19. Molecular profiling of microbial communities from contaminated sources: Use of substractive cloning methods and rDNA spacer sequences. 1997 annual progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-01

    'This project is to develop molecular methods for rapid characterization of microbial communities in contaminated ecosystems. The authors are exploring the use of {sup 16}s ribosomal DNA intergenic spacer regions (ISRs) to profile community composition. The choice proves to be a good one: there are 200--550 bases of 1 to 3 variable regions from which to choose species-specific probes, as well as 2--4 stretches of conserved sequence from which to develop universal PCR (polymerase chain reaction) primers. Preliminary community characterization is complete, and several types of arrays are under development to determine the types of bacteria present and the status of the ground water. Profiling the community composition of polluted groundwater will impact the broad field of microbial ecology as well as mixed-waste bioremediation. Results The samples the authors have been analysing were provided by Dr. Fred Brockman from Pacific Northwest Laboratory, and were collected at the US DOE Hanford site, Washington state. The samples were microbial filtrates from ground water polluted with 2 mg/L carbon tetrachloride and 250 mg/L nitrate and subjected to enrichment (acetate + nitrate) and recirculation. This project is described in some detail in PNNL-11113, Accelerated In Situ Bioremediation of Groundwater, by M.J. Truex, B.S. Hooker, and D.B. Anderson, July 1996.'

  20. Microorganisms of radionuclides-contaminated soils of Chernobyl: in depth analysis of diversity and study of uranium-bacteria interactions

    Energy Technology Data Exchange (ETDEWEB)

    Chapon, V.; Berthomieu, C. [LIPM-CEA-CNRS-Universite d' Aix Marseille (France); Theodorakopoulos, N. [CEA-CNRS-Universite d' Aix Marseille-IRSN (France); Christen, R. [CNRS-Universite de Nice (France); Vercouter, T. [CEA-DEN-LANIE (France); Coppin, F.; Fevrier, L. [IRSN-L2BT (France); Sergeant, C. [CENBG-CNRS-Universite de Bordeaux (France)

    2014-07-01

    In this study, we explored the microbial diversity of Bacteria and Archaea evolving since 25 years in a radioactive-waste repository trench located in the Chernobyl exclusion zone. To assess the effect of long-term RNs exposure on diversity, microbial assemblages of soil samples highly contaminated with radionuclides (RNs) such as {sup 137}Cs and uranium were compared with nearby controls using high throughput pyro-sequencing of 16S rRNA genes. The analysis of 690,023 sequences evidenced high diversity in all samples with 34 bacterial and 2 archaeal phylum represented. Chloroflexi, Acidobacteria, Proteobacteria and Verrucomicrobia were the most consistently detected phyla, representing 90% of all sequences.This result demonstrates that a long term exposure did not lead to the decrease of microbial diversity. Furthermore, principal component analysis of pyro-sequencing data showed that microbial communities of RNs contaminated samples differed significantly from that of controls, suggesting the presence of RNs adapted species in the contaminated samples. Several heterotrophic aerobic bacteria have been cultured from the contaminated samples. Among them, the strain Microbacterium sp. A9 exhibited high uranium tolerance. The interaction between this strain and uranium was investigated by a combination of spectroscopic (FTIR and TRLFS) and microscopic (TEM/EDX) approaches. Comparison of data obtained at 4 and 25 deg. C evidenced active and passive mechanisms of uranium uptake and release. We demonstrated that after a first step of uranium and phosphate release via an active efflux mechanism, Microbacterium sp. A9 accumulates U(VI) as intracellular needle-like structures composed of autunite. The functional groups involved in the interactions with uranium were identified. Document available in abstract form only. (authors)

  1. Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

    KAUST Repository

    Casas, Laura

    2016-10-17

    Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.

  2. Molecular analysis of Korean isolate of barley yellow mosaic virus.

    Science.gov (United States)

    Lee, Kui Jae; Choi, Min Kyung; Lee, Wang Hyu; Rajkumar, Mani

    2006-04-01

    The complete sequences of both RNAs of an isolate of barley yellow mosaic virus (BaYMV) from Haenam, Korea, were determined. RNA1 is 7639 nucleotides long [excluding the 3'-poly(A)], and codes for a 270 kDa polyprotein of 2411 amino acids which contains the capsid protein (CP) at the C terminus and seven putative non-structural proteins. RNA2 is 3582 nucleotides long and codes for a polyprotein of 890 amino acids, which contains a 28 kDa putative proteinase (P1) and a 73 kDa polypeptide (P2). The whole sequences of Korean isolate (BaYMV-K) closely resembled those of an isolate from Japan (BaYMV-J) (99.6 identical nucleotides for RNA1; 99.4 for RNA2) and china (BaYMV-C) (96.7 and 96.2%, respectively) than from Germany (BaYMV-G) (93.6 and 90.4%, respectively). The greatest differences between the BaYMV-K and BaYMV-J isolates were in the 3'-NCRs of RNA1 and 5' NCRs of RNA2 and there were also some other regions of difference in Nib Pro (RNA1) and P1 (RNA2). Further, the phylogenetic analysis of CP region showed that Asian and European isolates formed distinct clusters. However, molecular variations between isolates could not be linked to earlier results showing differences in cultivar response.

  3. [Phenotype analysis and the molecular mechanism of enamel hypoplasia].

    Science.gov (United States)

    Lv, Ping; Gao, Xue-jun

    2009-02-18

    Enamel hypoplasia is a surface defect of the tooth crown caused by a disturbance of enamel matrix secretion. Enamel hypoplasia may be inherited, or result from illness, malnutrition, trauma, or high concentrations of fluorides or strontium in the drinking water or food. Different types of enamel hypoplasia have been distinguished, such as pit-type, plane-type, and linear enamel hypoplasia. Hypoplasia has been related to the intensity and duration of stress events, the number of affected ameloblasts, and their position along the forming tooth crown. Amelogenesis imperfecta (AI) is a heterogeneous group of inherited defects in dental enamel formation, most teeth are affected in both the primary and permanent dentition. The malformed enamel can be unusually thin, soft, rough and stained. The strict definition of AI includes only those cases where enamel defects occur in the absence of other symptoms. Currently, there are seven candidate genes for AI: amelogenin, enamelin, ameloblastin, tuftelin, distal-less homeobox 3, enamelysin, and kallikrein 4. Since the enamel is formed according to a strict chronological sequence, and once formed, undergoes no repair or regeneration. Then the analysis the phenotype of enamel hypoplasia can provide insights of the severity of inherited or environmental stress and the molecular mechanism during the period of enamel formation.

  4. Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

    Science.gov (United States)

    Casas, Laura; Saborido-Rey, Fran; Ryu, Taewoo; Michell, Craig; Ravasi, Timothy; Irigoien, Xabier

    2016-01-01

    Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites. PMID:27748421

  5. Molecular and Enantiomeric Analysis of Organic Compounds in Carbonaceous Meteorites

    Science.gov (United States)

    Cooper, George

    2003-01-01

    Carbonaceous meteorites are relatively enriched in carbon. Much of this carbon is in the form of soluble organic compounds. The Murchison and Murray meteorites are the best-characterized carbonaceous meteorites with respect to organic chemistry. Their content of organic compounds has led to an initial understanding of early solar system organic chemistry as well as what compounds may have played a role in the origin of life (Cronin and Chang, 1993). Reported compounds include: amino acids, amides, carboxylic acids, sulfonic acids, and polyols. This talk will focus on the molecular and enantiomeric analysis of individual meteoritic compounds: polyol acids; and a newly identified class of meteorite compounds, keto acids, i.e., acetoacetic acid, levulinic acid, etc. Keto acids (including pyruvic) are critically important in all contemporary organisms. They are key intermediates in metabolism and processes such as the citric acid cycle. Using gas chromatography-mass spectrometry we identified individual meteoritic keto acids after derivatization to one or more of the following forms: isopropyl ester (ISP), trimethyIsiIy1 (TMS), tert-butyldimethylsilyl (BDMS). Ongoing analyses will determine if, in addition to certain amino acids from Murchison (Cronin and Pizzarello, 1997), other potentially important prebiotic compounds also contain enantiomeric excesses, i.e., excesses that could have contributed to the current homochirality of life.

  6. Acceleration of dynamic fluorescence molecular tomography with principal component analysis.

    Science.gov (United States)

    Zhang, Guanglei; He, Wei; Pu, Huangsheng; Liu, Fei; Chen, Maomao; Bai, Jing; Luo, Jianwen

    2015-06-01

    Dynamic fluorescence molecular tomography (FMT) is an attractive imaging technique for three-dimensionally resolving the metabolic process of fluorescent biomarkers in small animal. When combined with compartmental modeling, dynamic FMT can be used to obtain parametric images which can provide quantitative pharmacokinetic information for drug development and metabolic research. However, the computational burden of dynamic FMT is extremely huge due to its large data sets arising from the long measurement process and the densely sampling device. In this work, we propose to accelerate the reconstruction process of dynamic FMT based on principal component analysis (PCA). Taking advantage of the compression property of PCA, the dimension of the sub weight matrix used for solving the inverse problem is reduced by retaining only a few principal components which can retain most of the effective information of the sub weight matrix. Therefore, the reconstruction process of dynamic FMT can be accelerated by solving the smaller scale inverse problem. Numerical simulation and mouse experiment are performed to validate the performance of the proposed method. Results show that the proposed method can greatly accelerate the reconstruction of parametric images in dynamic FMT almost without degradation in image quality.

  7. Molecular analysis of mutants of the Neurospora adenylosuccinate synthetase locus

    Indian Academy of Sciences (India)

    A. Wiest; A. J. McCarthy; R. Schnittker; K. McCluskey

    2012-08-01

    The ad-8 gene of Neurospora crassa, in addition to being used for the study of purine biology, has been extensively studied as a model for gene structure, mutagenesis and intralocus recombination. Because of this there is an extensive collection of well-characterized N. crassa ad-8 mutants in the Fungal Genetics Stock Center collection. Among these are spontaneous mutants and mutants induced with X-ray, UV or chemical mutagens. The specific lesions in these mutants have been genetically mapped at high resolution. We have sequenced the ad-8 locus from 13 of these mutants and identified the molecular nature of the mutation in each strain. We compare the historical fine-structure map to the DNA and amino acid sequence of each allele. The placement of the individual lesions in the fine-structure map was more accurate at the 5′ end of the gene and no mutants were identified in the 3′ untranslated region of this gene. We additionally analysed ad-8+ alleles in 18 N. crassa strains subjected to whole-genome sequence analysis and describe the variability among Neurospora strains and among fungi and other organisms.

  8. Molecular electrostatic potential analysis of non-covalent complexes

    Indian Academy of Sciences (India)

    PADINJARE VEETIL BIJINA; CHERUMUTTATHU H SURESH

    2016-10-01

    Ab initio MP4/Aug-cc-pvDZ//MP2/6-311++g(d,p) level interaction energy (Eint) and molecular electrostatic potential analysis (MESP) of a large variety of non-covalent intermolecular complexes, viz. tetrel, chalcogen, pnicogen, halogen, hydrogen, dihydrogen and lithium bonded complexes have been reported. The electronic changes associated with the non-covalent complex formation is monitored in terms of MESP minimum (Vmin) in the free and complexed states of the donor and acceptor molecules as well as in terms ofMESP at the donor and acceptor atoms (Vn) of the free monomers and complexes. The change in Vmin or Vn on the donor molecule (ΔVmin(D) or ΔVn(D)) during complex formation is proportional to its electron donating ability while such a change on the acceptor molecule (ΔVmin(A) or ΔVn(A)) is proportional to its electron accepting ability. Further, the quantities ΔΔVmin = ΔVmin(D) −ΔVmin(A) and ΔΔVn = ΔVn(D) −ΔVn(A) have shown strong linear correlations with Eint of the complex (Eint values fall in the range 0.7 to 46.2 kcal/mol for 54 complexes) and suggest that the intermolecular non-covalent interactions in a wide variety of systems can be monitored and assessed in terms of change in MESP due to complex formation in the gas phase. With the incorporation of solvent effect in the calculation, charged systems showed significant deviations from the linear correlation. The MESP based analysis proposes that the large variety of intermolecular non-covalent complexes considered in this study can be grouped under the general category of electron donor-acceptor (eDA) complexes

  9. HCN hyperfine ratio analysis of massive molecular clumps

    Science.gov (United States)

    Schap, W. J.; Barnes, P. J.; Ordoñez, A.; Ginsburg, A.; Yonekura, Y.; Fukui, Y.

    2017-03-01

    We report a new analysis protocol for HCN hyperfine data, based on the PYSPECKIT package, and results of using this new protocol to analyse a sample area of seven massive molecular clumps from the Census of High- and Medium-mass Protostars (CHaMP) survey, in order to derive maps of column density for this species. There is a strong correlation between the HCN integrated intensity, IHCN, and previously reported I_HCO+ in the clumps, but I_N_{2H+} is not well correlated with either of these other two 'dense gas tracers'. The four fitted parameters from PYSPECKIT in this region fall in the range of VLSR = 8-10 km s-1, σV = 1.2-2.2 km s-1, Tex = 4-15 K, and τ = 0.2-2.5. These parameters allow us to derive a column density map of these clouds, without limiting assumptions about the excitation or opacity. A more traditional (linear) method of converting IHCN to total mass column gives much lower clump masses than our results based on the hyperfine analysis. This is primarily due to areas in the sample region of low I, low Tex, and high τ. We conclude that there may be more dense gas in these massive clumps not engaged in massive star formation than previously recognized. If this result holds for other clouds in the CHaMP sample, it would have dramatic consequences for the calibration of the Kennicutt-Schmidt star formation laws, including a large increase in the gas depletion time-scale in such regions.

  10. Detection and Monitoring of E-Waste Contamination through Remote Sensing and Image Analysis

    Science.gov (United States)

    Garb, Yaakov; Friedlander, Lonia

    2015-04-01

    Electronic waste (e-waste) is one of today's fastest growing waste streams, and also one of the more problematic, as this end-of-life product contains precious metals mixed with and embedded in a variety of low value and potentially harmful plastic and other materials. This combination creates a powerful incentive for informal value chains that transport, extract from, and dispose of e-waste materials in far-ranging and unregulated ways, and especially in settings where regulation and livelihood alternatives are sparse, most notably in areas of India, China, and Africa. E-waste processing is known to release a variety of contaminants, such as heavy metals and persistent organic pollutants, including flame retardants, dioxins and furans. In several sites, where the livelihoods of entire communities are dependent on e-waste processing, the resulting contaminants have been demonstrated to enter the hydrological system and food chain and have serious health and ecological effects. In this paper we demonstrate for the first time the usefulness of multi-spectral remote sensing imagery to detect and monitor the release and possibly the dispersal of heavy metal contaminants released in e-waste processing. While similar techniques have been used for prospecting or for studying heavy metal contamination from mining and large industrial facilities, we suggest that these techniques are of particular value in detecting contamination from the more dispersed, shifting, and ad-hoc kinds of release typical of e-waste processing. Given the increased resolution and decreased price of multi-spectral imagery, such techniques may offer a remarkably cost-effective and rapidly responsive means of assessing and monitoring this kind of contamination. We will describe the geochemical and multi-spectral image-processing principles underlying our approach, and show how we have applied these to an area in which we have a detailed, multi-temporal, spatially referenced, and ground

  11. Gene hunting : molecular analysis of the chicken genome

    NARCIS (Netherlands)

    Crooijmans, R.P.M.A.

    2000-01-01

    This dissertation describes the development of molecular tools to identify genes that are involved in production and health traits in poultry. To unravel the chicken genome, fluorescent molecular markers (microsatellite markers) were developed and optimized to perform high throughput screening of re

  12. SNPs ANALYSIS AS A TOOL IN MOLECULAR GENETICS DIAGNOSTICS

    Directory of Open Access Journals (Sweden)

    Dewi Rusnita

    2015-05-01

    arrays is its ability in detecting low level mosaicism which was unidentified by conventional cytogenetic examination. Nowadays, SNP arrays are included in IVF process to obtain a healthy baby. It can be done by detecting the absence or the presence of disease-causing single gene in an embryo before it implanted to the womb. SNP analysis with SNP array has many advantages over other SNP analysis methods and is therefore expected can be widely used in the future in the field of molecular diagnostic.

  13. Texture-Analysis-Incorporated Wind Parameters Extraction from Rain-Contaminated X-Band Nautical Radar Images

    Directory of Open Access Journals (Sweden)

    Weimin Huang

    2017-02-01

    Full Text Available In this paper, a method for extracting wind parameters from rain-contaminated X-band nautical radar images is presented. The texture of the radar image is first generated based on spatial variability analysis. Through this process, the rain clutter in an image can be removed while the wave echoes are retained. The number of rain-contaminated pixels in each azimuthal direction of the texture is estimated, and this is used to determine the azimuthal directions in which the rain-contamination is negligible. Then, the original image data in these directions are selected for wind direction and speed retrieval using the modified intensity-level-selection-based wind algorithm. The proposed method is applied to shipborne radar data collected from the east Coast of Canada. The comparison of the radar results with anemometer data shows that the standard deviations of wind direction and speed using the rain mitigation technique can be reduced by about 14.5° and 1.3 m/s, respectively.

  14. Isolation of Campylobacter spp. from a pig slaughterhouse and analysis of cross-contamination

    DEFF Research Database (Denmark)

    Malakauskas, M.; Jorgensen, K.; Nielsen, Elsa;

    2006-01-01

    herds during slaughtering. Identification of Campylobacter isolates was determined by the use of phase-contrast microscopy, hippurate hydrolysis, indoxyl acetate hydrolysis tests and PCR based restriction fragment length polymorphism method (PCR-RFLP). Pulsed-field gel electrophoresis (PFGE) typing...... sample and a total of 120 different isolates were collected. 23.4% (28 of 120) isolates were identified as C. jejuni (19 from carcasses and 9 from slaughter line surfaces) and 76.6% (92 of 120) isolates as C. coli (28 from faeces, 47 from carcasses and 17 from slaughter line surfaces). The typing results...... showed identity between isolates from successive flocks, different carcasses, and places in the slaughterhouse in contact with carcasses. The results suggest that cross-contamination originated in the gastro-intestinal tract ofthe slaughtered pigs and that cross-contamination happened during...

  15. Rapid Analysis of Eukaryotic Bioluminescence to Assess Potential Groundwater Contamination Events

    Directory of Open Access Journals (Sweden)

    Zacariah L. Hildenbrand

    2015-01-01

    Full Text Available Here we present data using a bioluminescent dinoflagellate, Pyrocystis lunula, in a toxicological bioassay to rapidly assess potential instances of groundwater contamination associated with natural gas extraction. P. lunula bioluminescence can be quantified using spectrophotometry as a measurement of organismal viability, with normal bioluminescent output declining with increasing concentration(s of aqueous toxicants. Glutaraldehyde and hydrochloric acid (HCl, components used in hydraulic fracturing and shale acidization, triggered significant toxicological responses in as little as 4 h. Conversely, P. lunula was not affected by the presence of arsenic, selenium, barium, and strontium, naturally occurring heavy metal ions potentially associated with unconventional drilling activities. If exogenous compounds, such as glutaraldehyde and HCl, are thought to have been introduced into groundwater, quantification of P. lunula bioluminescence after exposure to water samples can serve as a cost-effective detection and risk assessment tool to rapidly assess the impact of putative contamination events attributed to unconventional drilling activity.

  16. Tanpopo cosmic dust collector: Silica aerogel production and bacterial DNA contamination analysis

    CERN Document Server

    Tabata, Makoto; Yokobori, Shin-ichi; Kawai, Hideyuki; Takahashi, Jun-ichi; Yano, Hajime; Yamagishi, Akihiko

    2011-01-01

    Hydrophobic silica aerogels with ultra-low densities have been designed and developed as cosmic dust capture media for the Tanpopo mission which is proposed to be carried out on the International Space Station. Glass particles as a simulated cosmic dust with 30 \\mu m in diameter and 2.4 g/cm^3 in density were successfully captured by the novel aerogel at a velocity of 6 km/s. Background levels of contaminated DNA in the ultra-low density aerogel were lower than the detection limit of a polymerase chain reaction assay. These results show that the manufactured aerogel has good performance as a cosmic dust collector and sufficient quality in respect of DNA contamination. The aerogel is feasible for the biological analyses of captured cosmic dust particles in the astrobiological studies.

  17. Comprehensive Analysis of Migration Pathways (CAMP): Contaminant Migration Pathways at Confined Dredged Material Disposal Facilities

    Science.gov (United States)

    1990-09-01

    of water. If contaminants are water soluble, they may become con- centrated in such plants. Some plants possess oily cuticles and/or oil cells on...Oxford University Press, Oxford, Great Britain. Cerniglia, C. E., and Gibson, D. T. 1978. "Metabolism of Naphthalene by Cell Extracts of...Naphthalene by Cyanobacteria and Microalgae ," Journal of General Microbiology, Vol 116, pp 495-500. Chakrabarty, A. M. 1982. Biodegradation and

  18. CO2 Radiocarbon Analysis to Quantify Organic Contaminant Degradation, MNA, and Engineered Remediation Approaches

    Science.gov (United States)

    2014-12-18

    environmental cleanup in the United States. One must understand the interplay between contaminants and natural compounds in complex biogeochemical ...carbon through natural biogeochemical cycles. Only recently has commercially available accelerator mass spectrometry (AMS) allowed routine 14CO2...Soil gas CO2 was assayed for radiocarbon content and CO2 concentration (Fig. 3). Background wells ( circled area) had a CO2 age from ~15 to 25 pMC. This

  19. Feasibility Analysis for Mitigating the Contamination of POPs in Crops Through Inoculation with Functional Endophytic Bacteria

    Directory of Open Access Journals (Sweden)

    SUN Kai

    2017-08-01

    Full Text Available Contamination of food-crops with persistent organic pollutants(POPsposes a great concern to food safety because of their toxicity, persistence, long-range transport and potential to bioaccumulate. Thus, how to avoid the residual of POPs in food -crops grown in POPcontaminated areas is essential for ensuring the safety of agricultural products and human health. Plant-endophytic bacteria(EBsymbioses are ubiquitous and have attained increasing acceptance as viable cleanup technologies to remove POPs in planta due to its low cost and being environment-friendly. It has been indicated that functional EB can enhance plant growth, reduce plant disease, and stimulate plant resistance to harsh external environments. Notably, certain functional EB can also lessen POPs accumulation in plants. However, the information is limited regarding the impact of functional endophytic colonization on POPs biodegradation and biotransformation in food-crops. Aimed at the problems, this paper reviewed the situation of crop contaminated by POPs in agroecosystems and its regulatory role in the transformation of POPs. More importantly, the influence of endophytic colonization on the biodegradation and biotransformation of POPs in crop cells were systematically estimated. The effectiveness of POPs biodegradation mainly depended on the abundance and activity of inoculated functional EB in plant compartments. Additionally, the advances, challenges, and existing issues of functional EB for reducing the risk of food-crops POP contamination were also prospected. These findings can be applied for utilizing endophytes to treat POPs in food -crops at POP-contaminated matrices, with ultimate goal of protecting food security and human health.

  20. Analysis of grease contamination influence on the internal radial clearance of ball bearings by thermographic inspection

    Directory of Open Access Journals (Sweden)

    Mišković Žarko Z.

    2016-01-01

    Full Text Available One of the most important factors influencing ball bearings service life is its internal radial clearance. However, this parameter is also very complex because it depends on applied radial load and ball bearings dimensions, surface finish and manufacturing materials. Thermal condition of ball bearings also significantly affects internal radial clearance. Despite many researches performed in order to find out relevant facts about different aspects of ball bearings thermal behaviour, only few of them are dealing with the real working conditions, where high concentration of solid contaminant particles is present. That’s why the main goal of research presented in this paper was to establish statistically significant correlation between ball bearings temperatures, their working time and concentration of contaminant particles in their grease. Because of especially difficult working conditions, the typical conveyor idlers bearings were selected as representative test samples and appropriate solid particles from open pit coal mines were used as artificial contaminants. Applied experimental methodology included thermographic inspection, as well as usage of custom designed test rig for ball bearings service life testing. Finally, by obtained experimental data processing in advanced software, statistically significant mathematical correlation between mentioned bearings characteristics was determined and applied in commonly used internal radial clearance equation. That is the most important contribution of performed research - the new equation and methodology for ball bearings internal clearance determination which could be used for eventual improvement of existing bearings service life equations. [Projekat Ministarstva nauke Republike Srbije, br. TR35029 i br. TR14033

  1. Use of PCR analysis for detecting low levels of bacteria and mold contamination in pharmaceutical samples.

    Science.gov (United States)

    Jimenez, L; Smalls, S; Ignar, R

    2000-08-01

    PCR assays were developed and compared to standard methods for quality evaluation of pharmaceutical raw materials and finished products with low levels of microbial contamination. Samples were artificially contaminated with less than 10 CFU of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Aspergillus niger. Bacterial DNA was extracted from each enrichment broth by mild lysis in Tris-EDTA-Tween 20 buffer containing proteinase K while mold DNA was extracted by boiling samples in Tris-EDTA-SDS buffer for 1 h. A 10-microl aliquot of extracted DNA was added to Ready-To-Go PCR beads and specific primers for E. coli, S. aureus, and P. aeruginosa. However, 50-microl aliquots of extracted mold DNA were used for amplification of specific A. niger DNA sequences. Standard methods required 6-8 days while PCR detection of all microorganisms was completed within 27 h. Low levels of microbial contamination were detected in all raw materials and products using PCR assays. Rapid quality evaluation of pharmaceutical samples resulted in optimization of product manufacturing, quality control, and release of finished products.

  2. Integrated risk analysis of a heavy-metal-contaminated site in Taiwan

    Energy Technology Data Exchange (ETDEWEB)

    Ching-Tsan Tsai [China Medical College, Taichung (Taiwan, Province of China); Wang, J.H.C. [National Science Council, Taipei (Taiwan, Province of China)

    1996-12-31

    The Love Canal episode began the long battle on hazardous wastes in the United States. Obviously, the potential danger of hazardous wastes is one of the hottest issues among environmental professionals as well as the public. The problems of hazardous wastes in economically booming Taiwan are also alarming. Several farmlands in northern Taiwan were contaminated heavily by industrial effluents containing heavy metals (cadmium and lead) in the early 1980s. Regardless of the many studies that have been conducted about these polluted farmlands, there has not been any remediation - just a passive abandonment of farming activities with minimal compensation. This paper addresses a heavy-metal-contaminated fanning area. A pollution profile across time is delineated using information from the abundance of reports, and the contamination is modeled mathematically. The past, the present, and future exposures are also modeled. The results are presented in terms of societal impacts and health effects. Reasonable soil guidelines for cleanup are estimated, and recommendations for rational mitigation solutions are presented. The current strategies for cleanup actions are also described. 23 refs., 4 figs., 5 tabs.

  3. Solubility analysis and disposal options of combustion residues from plants grown on contaminated mining area.

    Science.gov (United States)

    Kovacs, Helga; Szemmelveisz, Katalin; Palotas, Arpad Bence

    2013-11-01

    Biomass, as a renewable energy source, is an excellent alternative for the partial replacement of fossil fuels in thermal and electric energy production. A new fuel type as biomass for energy utilisation includes ligneous plants with considerable heavy metal content. The combustion process must be controlled during the firing of significant quantities of contaminated biomass grown on brownfield lands. By implementing these measures, air pollution and further soil contamination caused by the disposal of the solid burning residue, the ash, can be prevented. For the test samples from ligneous plants grown on heavy metal-contaminated fields, an ore mine (already closed for 25 years) was chosen. With our focus on the determination of the heavy metal content, we have examined the composition of the soil, the biomass and the combustion by-products (ash, fly ash). Our results confirm that ash resulting from the combustion must be treated as toxic waste and its deposition must take place on hazardous waste disposal sites. Biomass of these characteristics can be burnt in special combustion facility that was equipped with means for the disposal of solid burning residues as well as air pollutants.

  4. Spectroscopic analysis of soil metal contamination around a derelict mine site in the Blue Mountains, Australia

    Science.gov (United States)

    Shamsoddini, A.; Raval, S.; Taplin, R.

    2014-09-01

    Abandoned mine sites pose the potential threat of the heavy metal pollution spread through streams and via runoff leading to contamination of soil and water in their surrounding areas. Regular monitoring of these areas is critical to minimise impacts on water resources, flora and fauna. Conventional ground based monitoring is expensive and sometimes impractical; spectroscopic methods have been emerged as a reliable alternative for this purpose. In this study, the capabilities of the spectroscopy method were examined for modelling soil contamination from around the abandoned silver-zinc mine located at Yerranderie, NSW Australia. The diagnostic characteristics of the original reflectance data were compared with models derived from first and second derivatives of the reflectance data. The results indicate that the models derived from the first derivative of the reflectance data estimate heavy metals significantly more accurately than model derived from the original reflectance. It was also found in this study that there is no need to use second derivative for modelling heavy metal soil contamination. Finally, the results indicate that estimates were of greater accuracy for arsenic and lead compared to other heavy metals, while the estimation for silver was found to be the most erroneous.

  5. Polymyxin B as inhibitor of LPS contamination of Schistosoma mansoni recombinant proteins in human cytokine analysis

    Directory of Open Access Journals (Sweden)

    Pacífico Lucila G

    2007-01-01

    Full Text Available Abstract Background Recombinant proteins expressed in Escherichia coli vectors are generally contaminated with endotoxin. In this study, we evaluated the ability of Polymyxin B to neutralize the effect of LPS present as contaminant on Schistosoma mansoni recombinant proteins produced in E. coli in inducing TNF-α and IL-10. Peripheral blood mononuclear cells from individuals chronically infected with S. mansoni were stimulated in vitro with recombinant Sm22.6, Sm14 and P24 antigens (10 μg/mL in the presence of Polymyxin B (10 μg/mL. Results The levels of cytokines were measured using ELISA. There was greater than 90 % reduction (p S. mansoni recombinant proteins in the presence of Polymyxin B, a reduction in the levels of TNF-α and IL-10 was also observed. However, the percentage of reduction was lower when compared to the cultures stimulated with LPS, probably because these proteins are able to induce the production of these cytokines by themselves. Conclusion This study showed that Polymyxin B was able to neutralize the effect of endotoxin, as contaminant in S. mansoni recombinant antigens produced in E. coli, in inducing TNF-α and IL-10 production.

  6. Assessment of heavy metal contamination in water and sediments of Trepça and Sitnica rivers, Kosovo, using pollution indicators and multivariate cluster analysis.

    Science.gov (United States)

    Ferati, Flora; Kerolli-Mustafa, Mihone; Kraja-Ylli, Arjana

    2015-06-01

    The concentrations of As, Cd, Cr, Co, Cu, Ni, Pb, and Zn in water and sediment samples from Trepça and Sitnica rivers were determined to assess the level of contamination. Six water and sediment samples were collected during the period from April to July 2014. Most of the water samples was found within the European and Kosovo permissible limits. The highest concentration of As, Cd, Pb, and Zn originates primarily from anthropogenic sources such discharge of industrial water from mining flotation and from the mine waste eroded from the river banks. Sediment contamination assessment was carried out using the pollution indicators such as contamination factor (CF), degree of contamination (Cd), modified degree of contamination (mCd), pollution load index (PLI), and geo-accumulation index (Igeo). The CF values for the investigated metals indicated a high contaminated nature of sediments, while the Cd values indicated a very high contamination degree of sediments. The mCd values indicate a high degree of contamination of Sitnica river sediment to ultrahigh degree of contamination of Trepça river sediment. The PLI values ranged from 1.89 to 14.1 which indicate that the heavy metal concentration levels in all investigated sites exceeded the background values and sediment quality guidelines. The average values of Igeo revealed the following ranking of intensity of heavy metal contamination of the Trepça and Sitnica river sediments: Cd > As > Pb > Zn > Cu > Co > Cr > Ni. Cluster analysis suggests that As, Cd, Cr, Co, Cu, Ni, Pb, and Zn are derived from anthropogenic sources, particularly discharges from mining flotation and erosion form waste from a zinc mine plant. In order to protect the sediments from further contamination, the designing of a monitoring network and reducing the anthropogenic discharges are suggested.

  7. JPL Contamination Control Engineering

    Science.gov (United States)

    Blakkolb, Brian

    2013-01-01

    JPL has extensive expertise fielding contamination sensitive missions-in house and with our NASA/industry/academic partners.t Development and implementation of performance-driven cleanliness requirements for a wide range missions and payloads - UV-Vis-IR: GALEX, Dawn, Juno, WFPC-II, AIRS, TES, et al - Propulsion, thermal control, robotic sample acquisition systems. Contamination control engineering across the mission life cycle: - System and payload requirements derivation, analysis, and contamination control implementation plans - Hardware Design, Risk trades, Requirements V-V - Assembly, Integration & Test planning and implementation - Launch site operations and launch vehicle/payload integration - Flight ops center dot Personnel on staff have expertise with space materials development and flight experiments. JPL has capabilities and expertise to successfully address contamination issues presented by space and habitable environments. JPL has extensive experience fielding and managing contamination sensitive missions. Excellent working relationship with the aerospace contamination control engineering community/.

  8. Molecular analysis of skeletal tuberculosis in an ancient Egyptian population.

    Science.gov (United States)

    Zink, A; Haas, C J; Reischl, U; Szeimies, U; Nerlich, A G

    2001-04-01

    A paleomicrobiological study was performed on 37 skeletal tissue specimens from cadavers in the necropolis of Thebes-West, Upper Egypt, (2120-500 BC) and four from the necropolis of Abydos (3000 BC). The subjects had typical macromorphological evidence of osseous tuberculosis (n = 3), morphological alterations that were not specific, but probably resulted from tuberculosis (n = 17), or were without morphological osseous changes (n = 21). DNA was extracted from these bone samples and amplified by PCR with a primer pair that recognised the Mycobacterium tuberculosis complex insertion sequence IS6110. To confirm specificity of the analysis, the amplification products of several samples were subjected to restriction enzyme digestion, or direct sequencing, or both. In 30 of the 41 cases analysed, ancient DNA was demonstrated by amplification by the presence of the human beta-actin or the amelogenin gene and nine of these cases were positive for M. tuberculosis DNA. The results were confirmed by restriction endonuclease digestion and sequencing. A positive result for M. tuberculosis DNA was seen in two of the three cases with typical morphological signs of tuberculosis and amplifiable DNA, in five of 13 non-specific, but probable cases (including two cases from c. 3000 BC), but also in two of 14 cases without pathological bone changes. These observations confirm that tuberculosis may be diagnosed unequivocally in skeletal material from ancient Egypt, even dating back to c. 3000 BC. As a positive molecular reaction was observed in most of the typical cases of skeletal tuberculosis, in about one-third of non-specific, but probable tuberculous osseous changes and, surprisingly, in about one-seventh of unremarkable samples, this suggests that infection with M. tuberculosis was relatively frequent in ancient Egypt.

  9. Quantitative data analysis of chemical contamination in the Venice lagoon. A risk management perspective

    Energy Technology Data Exchange (ETDEWEB)

    Miniero, R.; Domenico, A. di [Istituto Superiore di Sanita, Rome (Italy). Dept. Environment and Primary Prevention

    2004-09-15

    A comprehensive risk management for the contaminants present in bottom sediments of the Venice lagoon appears to be complicated by three issues: the past, present, and future influence of human pressure; the obvious sensitivity of a wetland like the lagoon; its extension. The actual situation can be viewed as typical of stressors at regional scale. The relationships between a coastal city and its environment are one of the central question addressed in Chapter 17 of Agenda 21, adopted at the United Nations Conference on Environment and Development (UNCED). In this chapter, the importance of coasts in a life-supporting system and the positive opportunity for sustainable development that coastal areas represent are stressed. However, in industrialized countries a practicable co-existence of environment and development will require mostly regulatory measures to regulate their relationships. The Venice lagoon is one of the leading shellfish production areas in Italy, harvesting several metric tons per year of the clam Tapes philippinarum and the mussel Mytilus galloprovincialis. A number of studies in recent years have characterized the chemical contamination of matrices like biota and sediment. The chemicals analyzed belong to different families including organic contaminants (such as polychlorinated dibenzodioxins (PCDDs) and dibenzofurans (PCDFs)), chlorinated pesticides, heavy metals, organometals, etc. The primary contamination sources have been clearly identified with Porto Marghera industrial settlement and the city of Venice with its canals, motorboats, and dense anthropogenic activity. The impacts of all these activities appear to be concentrated in the central basin although the industrial area be situated at the southern boundaries of the northern basin. From the studies on sediments, the following four impact types were identified in the lagoon: industrial, urban, ''not classifiable'', and lagoon background. In this paper, the PCDD

  10. Generalised linear mixed models analysis of risk factors for contamination of Danish broiler flocks with Salmonella typhimurium

    DEFF Research Database (Denmark)

    Chriél, Mariann; Stryhn, H.; Dauphin, G.

    1999-01-01

    of rearing, and the sampling method are significant. Epidemiological control would seem most efficient on starting at the top levels of the production hierarchy from which a major part of the ST contamination is derived. A secondary purpose of the study is to evaluate different statistical approaches...... and software for the analysis of a moderately-sized data set of veterinary origin. We compare the results from five analyses of the generalised linear mixed model (GLMM) type. The first observation is that the results agree reasonably well and lead to similar conclusions. A closer look reveals certain patterns...

  11. Genome wide molecular analysis of minimally differentiated acute myeloid leukemia

    NARCIS (Netherlands)

    Silva, Fernando P. G.; Almeida, Ines; Morolli, Bruno; Brouwer-Mandema, Geeske; Wessels, Hans; Vossen, Rolf; Vrieling, Harry; Marijt, Erik W. A.; Valk, Peter J. M.; Kluin-Nelemans, Hanneke C.; Sperr, Wolfgang R.; Ludwig, Wolf-Dieter; Giphart-Gassler, Micheline

    2009-01-01

    Background Minimally differentiated acute myeloid leukemia is heterogeneous in karyotype and is defined by immature morphological and molecular characteristics. This originally French-American-British classification is still used in the new World Health Organization classification when other

  12. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  13. Genome wide molecular analysis of minimally differentiated acute myeloid leukemia

    NARCIS (Netherlands)

    Silva, Fernando P. G.; Almeida, Ines; Morolli, Bruno; Brouwer-Mandema, Geeske; Wessels, Hans; Vossen, Rolf; Vrieling, Harry; Marijt, Erik W. A.; Valk, Peter J. M.; Kluin-Nelemans, Hanneke C.; Sperr, Wolfgang R.; Ludwig, Wolf-Dieter; Giphart-Gassler, Micheline

    2009-01-01

    Background Minimally differentiated acute myeloid leukemia is heterogeneous in karyotype and is defined by immature morphological and molecular characteristics. This originally French-American-British classification is still used in the new World Health Organization classification when other criteri

  14. XPS和TOF-SIMS在硬盘驱动器(HDD)磁头表面微污染分析中的应用%XPS AND TOF-SIMS ANALYSIS OF MICRO-CONTAMINATION ON THE SURFACE OF MAGNETIC HEAD

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    XPS和TOF-SIMS表面分析仪器联用分析磁头臂焊接位表面有机微污染物成分,找出 污染物的来源;XPS能够提供污染物中元素组成及价态信息,而TOF-SIMS能够提供其分子信息。试验证明两者联用是分析表面有机微污染物强有力的手段。%The analysis of micro organic contamination on the surface of magnetic head by XPS and TOFSIMS is described in this paper. The informations of the composing elements and their valency states are obtained by XPS, and of the molecular structures by TOF-SIMS. The analytical results obtained proved that the hyphenation of XPS and TOF-SIMS is a very effective method for the surface ro-contamination analysis and searching for the sources of the contamination in the data storage industry.

  15. Degradation of contaminants by Cu{sup +}-activated molecular oxygen in aqueous solutions: Evidence for cupryl species (Cu{sup 3+})

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yong, E-mail: fengy@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong); Lee, Po-Heng, E-mail: phlee@polyu.edu.hk [Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon (Hong Kong); Wu, Deli, E-mail: wudeli@tongji.edu.cn [State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science & Engineering, Tongji University, Shanghai 200092 (China); Zhou, Zhengyuan, E-mail: zzy247@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong); Li, Hangkong, E-mail: hangkong@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong); Shih, Kaimin, E-mail: kshih@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong)

    2017-06-05

    Highlights: • Sulfadiazine and methylene blue were nearly completely degraded by Cu{sup +}-O{sub 2} oxidation. • Reaction of Cu{sup +} and hydrogen peroxide produced Cu{sup 3+} as the major active species. • 5,5-dimethyl-2-hydroxypyrrolidine-N-oxyl (DMPO-OH) was found in the reaction process. • Benzoic acid and electron paramagnetic resonance are not capable to differentiate Cu{sup 3+} and ·OH. - Abstract: Copper ions (Cu{sup 2+} and Cu{sup +}) have shown potential as Fenton-like activators for the circumneutral removal of organic contaminants from aqueous solutions. However, the major active species (cupryl species (Cu{sup 3+}) versus hydroxyl radical (·OH)) produced during the activation of hydrogen peroxide by Cu{sup +} remain unclear. In this study, Cu{sup +}-O{sub 2} oxidation, in which hydrogen peroxide is produced via the activated decomposition of dissolved molecular oxygen, was used to degrade sulfadiazine, methylene blue, and benzoic acid. The results showed that both sulfadiazine and methylene blue could be efficiently degraded by Cu{sup +}-O{sub 2} oxidation in a wide effective pH range from 2.0 to 10.0. Quenching experiments with different alcohols and the effect of Br{sup −} suggested that Cu{sup 3+} rather than ·OH was the major active species. Electron paramagnetic resonance detected 5,5-dimethyl-2-hydroxypyrrolidine-N-oxyl (DMPO-OH), which was probably produced by the oxidation of DMPO by Cu{sup 3+} or ·OH formed as a product of Cu{sup 3+} decomposition. 4-hydroxybenzoic acid was produced during the degradation of benzoic acid by Cu{sup 3+}. The findings of this study may help to explain the inconsistency regarding the dominant active species produced by the interaction of Cu{sup +} and hydrogen peroxide.

  16. Modeling Contamination Migration on the Chandra X-Ray Observatory - III

    Science.gov (United States)

    O'Dell, Stephen L.; Swartz, Douglas A.; Tice, Neil W.; Plucinsky, Paul P.; Grant, Catherine E.; Marshall, Herman L.; Vikhlinin, Alexy A.; Tennant, Allyn F.; Dahmer, Matthew T.

    2015-01-01

    During its first 16 years of operation, the cold (about -60 C) optical blocking filter of the Advanced CCD Imaging Spectrometer (ACIS), aboard the Chandra X-ray Observatory, has accumulated a growing layer of molecular contamination that attenuates low-energy x rays. Over the past few years, the accumulation rate, spatial distribution, and composition have changed. This evolution has motivated further analysis of contamination migration within and near the ACIS cavity, in part to evaluate potential bake-out scenarios intended to reduce the level of contamination. Keywords: X-ray astronomy, CCDs, contamination, modeling and simulation, spacecraft operations

  17. Probabilistic Analysis of Earthquake-Led Water Contamination: A Case of Sichuan, China

    Science.gov (United States)

    Yang, Yan; Li, Lin; Benjamin Zhan, F.; Zhuang, Yanhua

    2016-06-01

    The objective of this paper is to evaluate seismic-led point source and non-point source water pollution, under the seismic hazard of 10 % probability of exceedance in 50 years, and with the minimum value of the water quality standard in Sichuan, China. The soil conservation service curve number method of calculating the runoff depth in the single rainfall event combined with the seismic damage index were applied to estimate the potential degree of non-point source water pollution. To estimate the potential impact of point source water pollution, a comprehensive water pollution evaluation framework is constructed using a combination of Water Quality Index and Seismic Damage Index methods. The four key findings of this paper are: (1) The water catchment that has the highest factory concentration does not have the highest risk of non-point source water contamination induced by the outbreak of potential earthquake. (2) The water catchment that has the highest numbers of cumulative water pollutants types are typically located in the south western parts of Sichuan where the main river basins in the regions flow through. (3) The most common pollutants in sample factories studied is COD and NH3-N which are found in all catchments. The least common pollutant is pathogen—found present in W1 catchment which has the best rating in the water quality index. (4) Using water quality index as a standardization parameter, parallel comparisons is made among the 16 water catchments. Only catchment W1 reaches level II water quality status which has the rating of moderately polluted in events of earthquake induced water contamination. All other areas suffer from severe water contamination with multiple pollution sources. The results from the data model are significant to urban planning commissions and businesses to strategically choose their factory locations in order to minimize potential hazardous impact during the outbreak of earthquake.

  18. Characterization of heavy-metal contamination in surface sediments of the Minho river estuary by way of factor analysis.

    Science.gov (United States)

    Mil-Homens, M; Costa, A M; Fonseca, S; Trancoso, M A; Lopes, C; Serrano, R; Sousa, R

    2013-05-01

    Surface sediments were collected in August 2009 from 49 sites along the Minho estuary (between Tui and Caminha) and analyzed for grain size, organic carbon (Corg) and total nitrogen (Ntot) contents, and major (silicon [Si], aluminum [Al], iron [Fe], calcium [Ca], magnesium [Mg], sodium [Na], potassium [K], titanium [Ti], and mangesese [Mn]) and trace element (arsenic [As], chromium [Cr], copper [Cu], mercury [Hg], lithium [Li], lead [Pb], rubidium [Rb], tin [Sn], and zinc [Zn]) concentrations. Factor analysis was used to decrease 22 selected variables into 4 factors accounting for 85.9 % of the total variance explained, suggesting distinct elemental sources or sediment components affecting their spatial distributions. Although factors 1 (detrital component; elements strongly associated with fine- [Na, Mg, Ti, Li, Cr, Cu, Fe, Al, Zn, Ca, and As] and coarse-grained sediments [Si, K, Rb; mean grain-size [MGS]) and 3 (Fe-Mn oxyhydroxide sediment component; Fe, Mn, As, fine fraction) are interpreted as reflecting predominance of natural contributions, factors 2 (urban and industrial contamination: sediment components [Pb, Hg, organic carbon [Corg], total nitrogen [Ntot] and 4 (components associated with contamination by nautical activities; the association of tin [Sn] and calcium [Ca]) seem to indicate anthropogenic contributions). Nevertheless, the influence of elemental contributions derived from tungsten (W)-Sn mineralizations and those resulting from mining activities can also contribute to the obtained geochemical associations and should be considered. Spatial distribution of dominant factor scores shows the dominance of factors 2 and 4 between Tui and Vila Nova de Cerveira, whereas samples dominated by factors 3 and 1 are found between Ilha da Boega and Seixas and in the Caminha areas, respectively. Despite the dominance of factor score 1 in the Caminha area, the distribution pattern of dominant factor scores shows samples dominated by other factor scores that can

  19. Analysis of the Reactive Power Compensation in Contaminated Systems with Harmonics

    Directory of Open Access Journals (Sweden)

    Secundino Marrero

    2010-05-01

    Full Text Available The article is given the evaluation obtained of an industrial network with the presence of harmonic contamination, where the non lineal loads correspond fundamentally to rectifiers and variators of speed. Where the typical harmonic generated by these loads settled down and allowed it to determine the levels of harmonic distortion of tension and current to analyze their influence in the selection of the bank of condensers during the compensation of the power it reactivates assisting to the behavior of thesystem before different load states.

  20. A Monte Carlo analysis of health risks from PCB-contaminated mineral oil transformer fires.

    Science.gov (United States)

    Eschenroeder, A Q; Faeder, E J

    1988-06-01

    The objective of this study is the estimation of health hazards due to the inhalation of combustion products from accidental mineral oil transformer fires. Calculations of production, dispersion, and subsequent human intake of polychlorinated dibenzofurans (PCDFs) provide us with exposure estimates. PCDFs are believed to be the principal toxic products of the pyrolysis of polychlorinated biphenyls (PCBs) sometimes found as contaminants in transformer mineral oil. Cancer burdens and birth defect hazard indices are estimated from population data and exposure statistics. Monte Carlo-derived variational factors emphasize the statistics of uncertainty in the estimates of risk parameters. Community health issues are addressed and risks are found to be insignificant.

  1. Cluster analysis of toxins profile pattern as a tool for tracing shellfish contaminated with PSP-toxins.

    Science.gov (United States)

    Wong, Chun-Kwan; Hung, Patricia; Ng, Henry C C; Lee, Siu-Yuen; Kam, Kai-Man

    2011-11-01

    Paralytic shellfish poisoning (PSP) is one of the most lethal biotoxin-induced diseases worldwide, which may pose serious public health threat and potential devastating economic damage on fisheries industry in the affected region(s). To prevent the importation of PSP contaminated shellfish to a community, detailed documentation on the supply chain and routine surveillance systems are, in principle, crucial measures to protect people from this intoxication. However, difficulties have always been encountered on the traceability of the source/origin of contaminated shellfish. In the present study, we reported the potential application of PSP-toxins profiles with similarity analysis that can be used to identify epidemiological linkage between shellfish samples collected from markets and patients during a PSP outbreak. PSP-toxins were identified and quantified by ion-pair chromatographic separation followed by post-column oxidation to fluorescent imino purine derivatives. Samples from a PSP incident and other surveillance samples collected in our past 7-year record were also compared for their similarity in PSP-toxins profiles patterns. Molar distributions (nmol%) of 10 PSP-toxins were analyzed by Unweighted Pair Group Method with Arithmetric averages (UPGMA). Three prominent clusters emerged with similarity levels reaching over 80% for each, suggesting that each group of samples probably originated from a same source/batch. The PSP-toxins profiles and toxicities determined from surveillance samples could provide premonitory clues on the occurrences of PSP incident and outbreak with corresponding toxin profiles in the later time. Due to species-specific characteristics of PSP-toxins composition and profile in shellfish under varieties of environmental and physiological conditions, PSP-toxins profile can be a specific and useful biochemical indicator for tracing PSP contaminated shellfish provided that spatio-temporal occurrence patterns of toxins profiles are available

  2. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants

    OpenAIRE

    Orre Lotta; Bergman Per; Elmberger Göran; Pernemalm Maria; De Petris Luigi; Lewensohn Rolf; Lehtiö Janne

    2010-01-01

    Abstract Background In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS) from six lung cancer cases (two ade...

  3. Assessing aquifer contamination risk using immunoassay: trace analysis of atrazine in unsaturated zone sediments

    Science.gov (United States)

    Juracek, K.E.; Thurman, E.M.

    1997-01-01

    The vulnerability of a shallow aquifer in south-central Kansas to contamination by atrazine (2-chloro-4-ethylamino-6-isopropylamines-triazine) was assessed by analyzing unsaturated zone soil and sediment samples from about 60 dryland and irrigated sites using an ultrasensitive immunoassay (detection level of 0.02 µg/kg) with verification by gas chromatography/mass spectrometry (GC/MS). Samples were collected at depths of 0 to 1.2 m (i.e., the root zone), 1.2 to 1.8 m, and 1.8 to 3.0 m during two time periods-prior to planting and after harvest of crops. About 75% of the samples contained detectable concentrations of parent atrazine. At the shallow sampling depth, atrazine concentrations ranged from 0.5 to approximately 12 µg/kg. Atrazine concentrations at the intermediate (1.2-1.8 m) depth generally were degradation of parent atrazine in the root zone. Likewise, atrazine concentrations front the deepest (1.8-3.0 m) depth ranged from atrazine use ranging from 1 to 5 or more years, there does not appear to he a significant buildup of parent compound below the root zone. Therefore, the unsaturated zone does not appear to be a major storage compartment of atrazine contamination for the underlying shallow aquifer.

  4. An analysis of a mixed convection associated with thermal heating in contaminated porous media.

    Science.gov (United States)

    Krol, Magdalena M; Johnson, Richard L; Sleep, Brent E

    2014-11-15

    The occurrence of subsurface buoyant flow during thermal remediation was investigated using a two dimensional electro-thermal model (ETM). The model incorporated electrical current flow associated with electrical resistance heating, energy and mass transport, and density dependent water flow. The model was used to examine the effects of heating on sixteen subsurface scenarios with different applied groundwater fluxes and soil permeabilities. The results were analyzed in terms of the ratio of Rayleigh to thermal Peclet numbers (the buoyancy ratio). It was found that when the buoyancy number was greater than unity and the soil permeability greater than 10(-12) m(2), buoyant flow and contaminant transport were significant. The effects of low permeability layers and electrode placement on heat and mass transport were also investigated. Heating under a clay layer led to flow stagnation zones resulting in the accumulation of contaminant mass and transport into the low permeability layer. The results of this study can be used to develop dimensionless number-based guidelines for site management during subsurface thermal activities.

  5. Expanded target-chemical analysis reveals extensive mixed-organic-contaminant exposure in USA streams

    Science.gov (United States)

    Bradley, Paul M.; Journey, Celeste; Romanok, Kristin; Barber, Larry B.; Buxton, Herbert T.; Foreman, William; Furlong, Edward T.; Glassmeyer, Susan T.; Hladik, Michelle; Iwanowicz, Luke R.; Jones, Daniel K.; Kolpin, Dana W.; Kuivila, Kathryn M.; Loftin, Keith A.; Mills, Marc A.; Meyer, Michael T.; Orlando, James L.; Reilly, Timothy J.; Smalling, Kelly L.; Villeneuve, Daniel L.

    2017-01-01

    Surface water from 38 streams nationwide was assessed using 14 target-organic methods (719 compounds). Designed-bioactive anthropogenic contaminants (biocides, pharmaceuticals) comprised 57% of 406 organics detected at least once. The 10 most-frequently detected anthropogenic-organics included eight pesticides (desulfinylfipronil, AMPA, chlorpyrifos, dieldrin, metolachlor, atrazine, CIAT, glyphosate) and two pharmaceuticals (caffeine, metformin) with detection frequencies ranging 66–84% of all sites. Detected contaminant concentrations varied from less than 1 ng L–1 to greater than 10 μg L–1, with 77 and 278 having median detected concentrations greater than 100 ng L–1 and 10 ng L–1, respectively. Cumulative detections and concentrations ranged 4–161 compounds (median 70) and 8.5–102 847 ng L–1, respectively, and correlated significantly with wastewater discharge, watershed development, and toxic release inventory metrics. Log10 concentrations of widely monitored HHCB, triclosan, and carbamazepine explained 71–82% of the variability in the total number of compounds detected (linear regression; p-values: direct environment application (pesticides), designed-bioactive organics (median 41 per site at μg L–1 cumulative concentrations) in developed watersheds present aquatic health concerns, given their acknowledged potential for sublethal effects to sensitive species and lifecycle stages at low ng L–1.

  6. Hair analysis, a reliable and non-invasive method to evaluate the contamination by clenbuterol.

    Science.gov (United States)

    Jia, Jing-Ying; Zhang, Lu-Nan; Lu, You-Li; Zhang, Meng-Qi; Liu, Gang-Yi; Liu, Yan-Mei; Lu, Chuan; Li, Shui-Jun; Lu, Yi; Zhang, Rui-Wen; Yu, Chen

    2013-07-01

    The illegal use of clenbuterol has been an increasingly serious issue in today's livestock products industry. It becomes an important project to develop a reliable approach to detect its content in food animals. A simple and sensitive LC-MS/MS method was developed to detect clenbuterol residue in hair, with the low limit of quantitation (LLOQ) about 0.5ng/g. Hogs fed with 340µg/day of clenbuterol for 2 weeks were found a high clenbuterol residue in their hair approximately at 1-2 months after withdrawal. There remained 3.31ng/g clenbuterol in hog hair approximately 5 months after the last administration, focused on the tip of the hair (mainly in hogs with dark hair). An extensive contamination was observed in twenty investigated market hogs whose dark hair obviously had a higher clenbuterol residue than the light ones (p=0.017, t test). Volunteers (60.3 percent) from Xuhui district (Shanghai) were found to have a detectable amount of clenbuterol in their hair (>0.5ng/g). In conclusion, hair residue detection is a reliable method to evaluate the clenbuterol contamination in animals and humans. Meat supply in the Xuhui district might have serious potential safety risks which should be further investigated and discussed to determine the safety range of clenbuterol residue.

  7. Polycyclic Aromatic Hydrocarbon Contamination in Nile Tilapia (Oreochromis Niloticus : Analysis in Liver and Bile

    Directory of Open Access Journals (Sweden)

    Voravit Cheevaporn

    2010-07-01

    Full Text Available Polycyclic aromatic hydrocarbons (PAHs, mainly from petroleum products, are a source of worldwide contamination, and it is in the present study, we exposed Nile Tilapia in aquaria to No-Observed-Effect-Levels (NOELs of naphthalene, phenanthrene and pyrene for periods up to 9 days in a continuous flow system. Additional studies were carried out on fish exposed to lubricating oil, gasoline and diesel oil. Two methods were used to measure the levels of these PAHs: determination of ethoxyresorufin-O-deethylase (EROD activity in liver extracts, and fixed wavelength fluorescence (FF of PAH in bile. Optimal excitation wavelengths for FF analyses were determined to 290, 260 and 341 nm for naphthalene, phenanthrene and pyrene, respectively. The optimal emission wavelengths were 335, 380 and 383 nm, respectively. EROD activity and fluorescence intensity increased with increasing PAH concentrations and increasing exposure times. Similar results were obtained after exposure to lubricating oil, gasoline, or diesel oil. There was a high and significant correlation between the two methods. In view of its higher accuracy, lower cost, and convenience FF offered better possibilities than EROD determination to monitor PAH contamination in fish.

  8. Radionuclide contaminant analysis of small mammels, plants and sediments within Mortandad Canyon, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, K.; Biggs, J.; Fresquez, P.

    1996-01-01

    Small mammals, plants and sediments were sampled at one upstream location (Site 1) and two downstream locations (Site 2 and Site 3) from the National Pollution Discharge Elimination System outfall {number_sign}051-051 in Mortandad Canyon, Los Alamos County, New Mexico. The purpose of the sampling was to identify radionuclides potentially present, to quantitatively estimate and compare the amount of radionuclide uptake at specific locations (Site 2 and Site 3) within Mortandad Canyon to an upstream site (Site 1), and to identify the primary mode (inhalation ingestion, or surface contact) of contamination to small mammals. Three composite samples of at least five animals per sample were collected at each site. Pelts and carcasses of each animal were separated and analyzed independently. In addition, three composite samples were also collected for plants and sediments at each site. Samples were analyzed for {sup 241}Am, {sup 90}Sr, {sup 238}Pu, {sup 239}Pu, and total U. With the exception of total U, all mean radionuclide concentrations in small mammal carcasses and sediments were significantly higher at Site 2 than Site 1 or Site 3. No differences were detected in the mean radionuclide concentration of plant samples between sites. However, some radionuclide concentrations found at all three sites were higher than regional background. No differences were found between mean carcass radionuclide concentrations and mean pelt radionuclide concentrations, indicating that the two primary modes of contamination may be equally occurring.

  9. Molecular Analysis of Tube Cement of the Biofouling Tubeworm Hydroides elegans

    Science.gov (United States)

    2016-03-08

    combination of advanced microscopy, transcriptomics, and molecular biology we will describe: (1) the major molecular components of the compounds...19b. TELEPHONE NUMBER (Include area code) 08/03/2016 Final 01/05/2012-30/09/2015 Molecular analysis of tube cement of the biofouling tubeworm Hydroides...mount in situ hybridizations to determine where highly expressed transcripts are expressed in the worms. Initial results show these transcripts are

  10. Irreversible thermodynamic analysis and application for molecular heat engines

    Science.gov (United States)

    Lucia, Umberto; Açıkkalp, Emin

    2017-09-01

    Is there a link between the macroscopic approach to irreversibility and microscopic behaviour of the systems? Consumption of free energy keeps the system away from a stable equilibrium. Entropy generation results from the redistribution of energy, momentum, mass and charge. This concept represents the essence of the thermodynamic approach to irreversibility. Irreversibility is the result of the interaction between systems and their environment. The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible thermodynamics approaches are applied for a quantum heat engine with -1/2 spin system. Finally, lost works are determined for considered system and results show that macro and molecular heat engines obey same limitations. Moreover, a quantum thermodynamic approach is suggested in order to explain the results previously obtained from an atomic viewpoint.

  11. Molecular rheological analysis on binary blends of perfluoropolyether lubricants

    Science.gov (United States)

    Seung Chung, Pil; Hari Vemuri, Sesha; Park, Sejoon; Jhon, Myung S.

    2014-05-01

    The molecular rheology of PFPE becomes critically important in designing optimal lubricants that control the friction/wear and air-bearing by tuning elastic or viscous shear/elongation deformations, which affect the performance and reliability of the hard disk drive. In this paper, we examine the rheological responses of nano blended PFPEs including storage (elastic) and loss (viscous) moduli (G' and G″), by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. By introducing binary blend of nonfunctional and functional PFPEs, we control the degree of liquid/solid-like behavior using the rheology as a complementary tool for design criteria by tuning molecular conformation and diffusion with nano blend ratio.

  12. A 3D FINITE ELEMENT ANALYSIS OF INCOMPRESSIBLE FLUID FLOW AND CONTAMINANT TRANSPORT THROUGH A POROUS LANDFILL

    Directory of Open Access Journals (Sweden)

    ADEGUN, I. K.

    2014-08-01

    Full Text Available The paper investigated the flow of incompressible fluid and contaminant transport through a Porous Landfill using a numerical technique. A threedimensional finite element analysis technique was adopted for the solution. The problem was based on the Darcy’s Law and the Advection-Dispersion equation. The solutions of the Darcy’s and Advection-Dispersion equations were generated using Finite Element Analysis Software known as COMSOL Multiphysics. This simulation tool tracked the contaminant transport in the Landfill for 360 days at 10 days interval. It first modeled steady-state fluid flow by employing the Darcy’s Law Application Mode and then followed up with a transient solute-transport simulation by employing the Solute-Transport Application Mode from the Earth Science Module of COMSOL. The solution results obtained from this model were found to be in close agreement with reallife data obtained at the 130- million ton Bukit Tagar Mega Sanitary Landfill site, Selangor near Kuala Lumpur, Malaysia. This showed that the model can effectively predict the trends in the distributions of pollutants from a Municipal Solid Waste Landfill into nearby land and water sources. The model is thus applicable to the issues of environmental protection and safety of groundwater.

  13. Effectiveness of practices to reduce blood culture contamination: a Laboratory Medicine Best Practices systematic review and meta-analysis.

    Science.gov (United States)

    Snyder, Susan R; Favoretto, Alessandra M; Baetz, Rich Ann; Derzon, James H; Madison, Bereneice M; Mass, Diana; Shaw, Colleen S; Layfield, Christopher D; Christenson, Robert H; Liebow, Edward B

    2012-09-01

    This article is a systematic review of the effectiveness of three practices for reducing blood culture contamination rates: venipuncture, phlebotomy teams, and prepackaged preparation/collection (prep) kits. The CDC-funded Laboratory Medicine Best Practices Initiative systematic review methods for quality improvement practices were used. Studies included as evidence were: 9 venipuncture (vs. versus intravenous catheter), 5 phlebotomy team; and 7 prep kit. All studies for venipuncture and phlebotomy teams favored these practices, with meta-analysis mean odds ratios for venipuncture of 2.69 and phlebotomy teams of 2.58. For prep kits 6 studies' effect sizes were not statistically significantly different from no effect (meta-analysis mean odds ratio 1.12). Venipuncture and the use of phlebotomy teams are effective practices for reducing blood culture contamination rates in diverse hospital settings and are recommended as evidence-based "best practices" with high overall strength of evidence and substantial effect size ratings. No recommendation is made for or against prep kits based on uncertain improvement. Copyright © 2012 The Canadian Society of Clinical Chemists. All rights reserved.

  14. Molecular analysis of childhood primitive neuroectodermal tumors defines markers associated with poor outcome

    DEFF Research Database (Denmark)

    Scheurlen, W G; Schwabe, G C; Joos, S

    1998-01-01

    PURPOSE: The diagnostic and prognostic significance of well-defined molecular markers was investigated in childhood primitive neuroectodermal tumors (PNET). MATERIALS AND METHODS: Using microsatellite analysis, Southern blot analysis, and fluorescence in situ hybridization (FISH), 30 primary tumors......: In our study, amplification of c-myc was a poor-prognosis marker in PNET. LOH of chromosome 17p was associated with metastatic disease. Molecular analysis of primary tumors using these markers may be useful for stratification of children with PNET in future prospective studies. The other aberrations...... investigated were not of significant prognostic value, but may provide an entry point for future large-scale molecular studies....

  15. Molecular analysis of myophosphorylase deficiency in Dutch patients with McArdle's disease.

    NARCIS (Netherlands)

    Martin, M.A.; Rubio, J.C.; Wevers, R.A.; Engelen, B.G.M. van; Steenbergen-Spanjers, G.C.H.; Diggelen, O.P. van; Visser, M. de; Die-Smulders, C.E.M. de; Blazquez, A.; Andreu, A.L.; Arenas, J.

    2004-01-01

    We report on 8 Dutch patients with McArdle's disease from 6 unrelated families. Molecular analysis revealed the presence of four previously described mutations: the common R49X mutation, the IVS14+1G>A mutation and the recently reported R269X and Y84X nonsense mutations; and two new molecular def

  16. Molecular Analysis of AFP and HSA Interactions with PTEN Protein.

    Science.gov (United States)

    Zhu, Mingyue; Lin, Bo; Zhou, Peng; Li, Mengsen

    2015-01-01

    Human cytoplasmic alpha-fetoprotein (AFP) has been classified as a member of the albuminoid gene family. The protein sequence of AFP has significant homology to that of human serum albumin (HSA), but its biological characteristics are vastly different from HSA. The AFP functions as a regulator in the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway, but HSA plays a key role as a transport protein. To probe their molecular mechanisms, we have applied colocalization, coimmunoprecipitation (co-IP), and molecular docking approaches to analyze the differences between AFP and HSA. The data from colocalization and co-IP displayed a strong interaction between AFP and PTEN (phosphatase and tensin homolog), demonstrating that AFP did bind to PTEN, but HSA did not. The molecular docking study further showed that the AFP domains I and III could contact with PTEN. In silicon substitutions of AFP binding site residues at position 490M/K and 105L/R corresponding to residues K490 and R105 in HSA resulted in steric clashes with PTEN residues R150 and K46, respectively. These steric clashes may explain the reason why HSA cannot bind to PTEN. Ultimately, the experimental results and the molecular modeling data from the interactions of AFP and HSA with PTEN will help us to identify targets for designing drugs and vaccines against human hepatocellular carcinoma.

  17. Molecular analysis of candidate probiotic effector molecules of Lactobacillus plantarum

    NARCIS (Netherlands)

    Remus, D.M.

    2012-01-01

    Probiotics are health-promoting microorganisms that exert their beneficial effects in several ways. While it is known that probiotic bacteria interact with cells of the host gastrointestinal tractand modulate cell-signaling responses by which they might promote health, the underlying molecular

  18. Molecular analysis of candidate probiotic effector molecules of Lactobacillus plantarum

    NARCIS (Netherlands)

    Remus, D.M.

    2012-01-01

    Probiotics are health-promoting microorganisms that exert their beneficial effects in several ways. While it is known that probiotic bacteria interact with cells of the host gastrointestinal tractand modulate cell-signaling responses by which they might promote health, the underlying molecular mecha

  19. Analysis of Molecular Genetics Content in Spanish Secondary School Textbooks

    Science.gov (United States)

    Martinez-Gracia, M. V.; Gil-Quilez, M. J.; Osada, J.

    2006-01-01

    The treatment of molecular biology in thirty-four Spanish high school biology textbooks has been analysed using a check-list made up of twenty-three items. The study showed a tendency to confuse the genetic code with genetic information. The treatment of DNA transcription, regulation of gene expression and translation were presented as masses of…

  20. Molecular Cloning and Characterization of a New Cold-active Extradiol Dioxygenase from a Metagenomic Library Derived from Polychlorinated Biphenyl-contaminated Soil

    Institute of Scientific and Technical Information of China (English)

    REN He-jun; LU Yang; ZHOU Rui; DAI Chun-yan; WANG Yan; ZHANG Lan-ying

    2012-01-01

    To find new extradiol dioxygenases(EDOs,EC 1.13.11.2),a metagenomics library was constructed from polychlorinated biphenyl-contaminated soil and was screened for some dioxygenase with aromatic ring cleavage activity.A novel EDO,designated as BphC_A,was identified and heterologously expressed in Escherichia coli.The deduced amino acid sequence of BphC_A exhibited a homology of less than 60% with other known EDOs.Phylogenetic analysis of BphC_A suggests that the protein is a novel member of the EDO family.The enzyme exhibits higher substrate affinity and catalytic efficiency toward 3-methylcatechol than toward 2,3-dihydroxybiphenyl or catechol,the preferred substrate of other known EDOs.The optimum activity of purified BphC_A occurred at pH=8.5 and 35 ℃,and BphC_A showed more than 40% of its initial activity at 5 ℃.The activity of purified BphC_A was significantly induced by Mn2+ and slightly reduced bv Al3+,Cu2+ and Zn2+.

  1. Method development for trace analysis of heteroaromatic compounds in contaminated groundwater

    DEFF Research Database (Denmark)

    Johansen, Sys Stybe; Hansen, Asger B.; Mosbæk, Hans

    1996-01-01

    Water analysis,environmental analysis,extraction methods,aromatic compounds,heteroaromatic compounds,creosote,dichloromethane,diethyl ether,pentane......Water analysis,environmental analysis,extraction methods,aromatic compounds,heteroaromatic compounds,creosote,dichloromethane,diethyl ether,pentane...

  2. Determination of natural versus laboratory human infection with Mayaro virus by molecular analysis.

    Science.gov (United States)

    Junt, T; Heraud, J M; Lelarge, J; Labeau, B; Talarmin, A

    1999-12-01

    A laboratory worker developed clinical signs of infection with Mayaro virus (Togaviridae), an arbovirus of South and Central America, 6 days after preparation of Mayaro viral antigen and 10 days after a trip to a rain forest. There was no evidence of skin lesions during the antigen preparation, and level 3 containment safety measures were followed. Therefore, molecular characterization of the virus was undertaken to identify the source of infection. RT-PCR and DNA sequence comparisons proved the infection was with the laboratory strain. Airborne Mayaro virus contamination is thus a hazard to laboratory personnel.

  3. METAL TOLERANCE ANALYSIS OF MICROFUNGI ISOLATED FROM METAL CONTAMINATED SOIL AND WASTE WATER

    Directory of Open Access Journals (Sweden)

    Mathan Jayaraman

    2014-08-01

    Full Text Available The influence of Cr6+, Pb2+, Cu2+, Ni2+, Zn2+ and Cd2+ on the development of 24 fungi was investigated for Metal Tolerance Index (MTI at 1mg ml-1 Cr6+, Pb2+, Cu2+, Ni2+, Zn2+ and Cd2+ concentrations and also for Minimum Inhibitory Concentration (MIC. The MIC ranged from 0.5 to 1.5 mg ml-1 depending on the isolate Aspergillus, Fusarium and Penicillium sp. were tested for their metal tolerance index. Out of these Aspergillus flavus (ED4 shows a better tolerance index of 0.80 Cr6+, 0.72 for Pb2+ , 0.63 for Cu2+, 0.58 for Ni2+, 0.46 for Zn2+ and 0.60 Cd2+ for MIC value for the removal of heavy metals from contaminated soil and wastewaters.

  4. Preparation to the CMB Planck analysis : contamination due to the polarized galactic emission

    CERN Document Server

    Fauvet, L

    2010-01-01

    The Planck satellite experiment, which was launched the 14th of may 2009, will give an accurate measurement of the anisotropies of the Cosmic Microwave Background (CMB) in temperature and polarization. This measurement is polluted by the presence of diffuse galactic polarized foreground emissions. In order to obtain the level of accuracy required for the Planck mission it is necessary to deal with these foregrounds. In order to do this, have develloped and implemented coherent 3D models of the two main galactic polarized emissions : the synchrotron and thermal dust emissions. We have optimized these models by comparing them to preexisting data : the K-band of the WMAP data, the ARCHEOPS data at 353 GHz and the 408 MHz all-sky continuum survey. By extrapolation of these models at the frequencies where the CMB is dominant, we are able to estimate the contamination to the CMB Planck signal due to these polarized galactic emissions.

  5. A comprehensive analysis of contaminant transport in the vadose zone beneath tank SX-109

    Energy Technology Data Exchange (ETDEWEB)

    Ward, A.L.; Gee, G.W.; White, M.D.

    1997-02-01

    The Vadose Zone Characterization Project is currently investigating the subsurface distribution of gamma-emitting radionuclides in S and SX Waste Management Area (WMA-S-SX) located in the 200 West Area of the US Department of Energy`s Hanford Site in southeastern Washington State. Spectral-gamma logging of boreholes has detected elevated {sup 137}Cs concentrations as deep as 38 m, a depth considered excessive based on the assumed geochemistry of {sup 137}Cs in Hanford sediments. Routine groundwater sampling under the Resource Conservation and Recovery Act (RCRA) have also detected elevated levels of site-specific contaminants downgradient of WMA-S-SX. The objective of this report is to explore the processes controlling the migration of {sup 137}Cs, {sup 99}Tc, and NO{sub 3} through the vadose zone of WMA-S-SX, particularly beneath tank SX-109.

  6. Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils.

    Directory of Open Access Journals (Sweden)

    Etienne Yergeau

    Full Text Available As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0 and one month after the start of the bioremediation treatment (t = 1m, when degradation rates were at their highest, but decreased after one year (t = 1y, when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons.

  7. Statistical significance of hair analysis of clenbuterol to discriminate therapeutic use from contamination.

    Science.gov (United States)

    Krumbholz, Aniko; Anielski, Patricia; Gfrerer, Lena; Graw, Matthias; Geyer, Hans; Schänzer, Wilhelm; Dvorak, Jiri; Thieme, Detlef

    2014-01-01

    Clenbuterol is a well-established β2-agonist, which is prohibited in sports and strictly regulated for use in the livestock industry. During the last few years clenbuterol-positive results in doping controls and in samples from residents or travellers from a high-risk country were suspected to be related the illegal use of clenbuterol for fattening. A sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed to detect low clenbuterol residues in hair with a detection limit of 0.02 pg/mg. A sub-therapeutic application study and a field study with volunteers, who have a high risk of contamination, were performed. For the application study, a total dosage of 30 µg clenbuterol was applied to 20 healthy volunteers on 5 subsequent days. One month after the beginning of the application, clenbuterol was detected in the proximal hair segment (0-1 cm) in concentrations between 0.43 and 4.76 pg/mg. For the second part, samples of 66 Mexican soccer players were analyzed. In 89% of these volunteers, clenbuterol was detectable in their hair at concentrations between 0.02 and 1.90 pg/mg. A comparison of both parts showed no statistical difference between sub-therapeutic application and contamination. In contrast, discrimination to a typical abuse of clenbuterol is apparently possible. Due to these findings results of real doping control samples can be evaluated. Copyright © 2014 John Wiley & Sons, Ltd.

  8. Computer System for Analysis of Molecular Evolution Modes (SAMEM): analysis of molecular evolution modes at deep inner branches of the phylogenetic tree.

    Science.gov (United States)

    Gunbin, Konstantin V; Suslov, Valentin V; Genaev, Mikhail A; Afonnikov, Dmitry A

    SAMEM (System for Analysis of Molecular Evolution Modes), a web-based pipeline system for inferring modes of molecular evolution in genes and proteins (http://pixie.bionet.nsc.ru/samem/), is presented. Pipeline 1 performs analyses of protein-coding gene evolution; pipeline 2 performs analyses of protein evolution; pipeline 3 prepares datasets of genes and/or proteins, performs their primary analysis, and builds BLOSUM matrices; pipeline 4 checks if these genes really are protein-coding. Pipeline 1 has an all-new feature, which allows the user to obtain K(R)/K(C) estimates using several different methods. An important feature of pipeline 2 is an original method for analyzing the rates of amino acid substitutions at the branches of a phylogenetic tree. The method is based on Markov modeling and a non-parametric permutation test, which compares expected and observed frequencies of amino acid substitutions, and infers the modes of molecular evolution at deep inner branches.

  9. Strategies for the detection of food pathogens and contaminants

    DEFF Research Database (Denmark)

    Hearty, Stephen; Leonard, Paul; Sheehan, Alfredo Darmanin

    molecules and once suitably high affinity antibodies have been isolated, it is relatively straightforward to design and optimise concentration-based assays using SPR. Recently we have investigated the potential of applying Biacore technology to routine food analysis. Our experiences have shown...... that molecular contaminants such as microbial toxins and drug/pesticide residues translate well onto Biacore-based assay formats. However, larger and more complex entities such as spores and whole bacterial cells represent an altogether more difficult challenge. Here, we present an overview of our experiences...... to date with using Biacore for analysis of food contaminants and in particular the challenges associated with large analyte detection...

  10. Evaluation of gas chromatographic isotope fractionation and process contamination by carbon in compound-specific radiocarbon analysis.

    Science.gov (United States)

    Zencak, Zdenek; Reddy, Christopher M; Teuten, Emma L; Xu, Li; McNichol, Ann P; Gustafsson, Orjan

    2007-03-01

    The relevance of both modern and fossil carbon contamination as well as isotope fractionation during preparative gas chromatography for compound-specific radiocarbon analysis (CSRA) was evaluated. Two independent laboratories investigated the influence of modern carbon contamination in the sample cleanup procedure and preparative capillary gas chromatography (pcGC) of a radiocarbon-dead 3,3',4,4',5,5'-hexachlorobiphenyl (PCB 169) reference. The isolated samples were analyzed for their 14C/12C ratio by accelerator mass spectrometry. Sample Delta14C values of -996 +/- 20 and -985 +/- 20 per thousand agreed with a Delta14C of -995 +/- 20 per thousand for the unprocessed PCB 169, suggesting that no significant contamination by nonfossil carbon was introduced during the sample preparation process at either laboratory. A reference compound containing a modern 14C/12C ratio (vanillin) was employed to evaluate process contamination from fossil C. No negative bias due to fossil C was observed (sample Delta14C value of 165 +/- 20 per thousand agreed with Delta14C of 155 +/- 12 per thousand for the unprocessed vanillin). The extent of isotopic fractionation that can be induced during pcGC was evaluated by partially collecting the vanillin model compound of modern 14C/12C abundance. A significant change in the delta13C and delta14C values was observed when only parts of the eluting peak were collected (delta13C values ranged from -15.75 to -49.91 per thousand and delta14C values from -82.4 to +4.71 per thousand). Delta14C values, which are normalized to a delta13C of -25 per thousand, did not deviate significantly (-58.9 to -5.8 per thousand, considering the uncertainty of approximately +/-20 per thousand). This means that normalization of radiocarbon results to a delta13C of -25 per thousand, normally performed to remove effects of environmental isotope fractionation on 14C-based age determinations, also cor-rects sufficiently for putative isotopic fractionation that may

  11. Environmental effects of dredging. Preliminary guidelines and conceptual framework for comprehensive analysis of migration pathways (CAMP) of contaminated dredged material. Technical notes

    Energy Technology Data Exchange (ETDEWEB)

    Myers, T.E.

    1990-01-01

    The purpose of this note is to present the conceptual groundwork for the Comprehensive Analysis of Migration Pathways (CAMP). The conceptualization process for CAMP is discussed and available techniques for implementing CAMP are examined. Disposal of contaminated dredged material in a confined disposal facility is used to benchmark conceptual development. Case studies that illustrate analysis of selected migration pathways are also described.

  12. High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism.

    Science.gov (United States)

    Bao, Yun-Juan; Xu, Zixiang; Li, Yang; Yao, Zhi; Sun, Jibin; Song, Hui

    2017-06-01

    The soil with petroleum contamination is one of the most studied soil ecosystems due to its rich microorganisms for hydrocarbon degradation and broad applications in bioremediation. However, our understanding of the genomic properties and functional traits of the soil microbiome is limited. In this study, we used high-throughput metagenomic sequencing to comprehensively study the microbial community from petroleum-contaminated soils near Tianjin Dagang oilfield in eastern China. The analysis reveals that the soil metagenome is characterized by high level of community diversity and metabolic versatility. The metageome community is predominated by γ-Proteobacteria and α-Proteobacteria, which are key players for petroleum hydrocarbon degradation. The functional study demonstrates over-represented enzyme groups and pathways involved in degradation of a broad set of xenobiotic aromatic compounds, including toluene, xylene, chlorobenzoate, aminobenzoate, DDT, methylnaphthalene, and bisphenol. A composite metabolic network is proposed for the identified pathways, thus consolidating our identification of the pathways. The overall data demonstrated the great potential of the studied soil microbiome in the xenobiotic aromatics degradation. The results not only establish a rich reservoir for novel enzyme discovery but also provide putative applications in bioremediation. Copyright © 2016. Published by Elsevier B.V.

  13. A mouse model of cytogenetic analysis to evaluate caesium137 radiation dose exposure and contamination level in lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Roch-Lefevre, Sandrine; Martin-Bodiot, Cecile; Gregoire, Eric; Roy, Laurence [Institut de Radioprotection et de Surete Nucleaire (IRSN), Laboratoire de Dosimetrie Biologique (PRP-HOM/SRBE/LDB), Fontenay aux Roses Cedex (France); Desbree, Aurelie [Institut de Radioprotection et de Surete Nucleaire (IRSN), PRP-HOM/SDI, Laboratoire d' Evaluation de la Dose Interne, Fontenay aux Roses Cedex (France); Barquinero, Joan Francesc [Institut de Radioprotection et de Surete Nucleaire (IRSN), Laboratoire de Dosimetrie Biologique (PRP-HOM/SRBE/LDB), Fontenay aux Roses Cedex (France); Universitat Autonoma de Barcelona, Unitat d' Antropologia Biologica, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Bellaterra (Spain)

    2016-03-15

    In case of external overexposure to ionizing radiation, an estimation of its genotoxic effects on exposed individuals can be made retrospectively by the measurement of radiation-induced chromosome aberrations on circulating lymphocytes. Compared with external irradiation, intakes of radionuclides may, however, lead to specific features influencing dose distribution at the scale of body, of tissue or even of cell. Therefore, in case of internal contamination by radionuclides, experimental studies, particularly using animal models, are required to better understand mechanisms of their genotoxic effects and to better estimate the absorbed dose. The present study was designed to evaluate a cytogenetic method in mouse peripheral blood lymphocytes that would allow determination of yields and complexities of chromosome aberrations after low-dose rate exposure to {sup 137}Cs delivered in vitro either by irradiation or by contamination. By using M-FISH analysis, we compared the low-dose rate responses observed in mouse to the high-dose rate responses observed both in mouse and in human. Promising similarities between the two species in the relative biological effect evaluation show that our cytogenetic model established in mouse might be useful to evaluate various radiation exposures, particularly relevant in case of intakes of radionuclides. (orig.)

  14. Molecular kinetic analysis of a local equilibrium Carnot cycle

    Science.gov (United States)

    Izumida, Yuki; Okuda, Koji

    2017-07-01

    We identify a velocity distribution function of ideal gas particles that is compatible with the local equilibrium assumption and the fundamental thermodynamic relation satisfying the endoreversibility. We find that this distribution is a Maxwell-Boltzmann distribution with a spatially uniform temperature and a spatially varying local center-of-mass velocity. We construct the local equilibrium Carnot cycle of an ideal gas, based on this distribution, and show that the efficiency of the present cycle is given by the endoreversible Carnot efficiency using the molecular kinetic temperatures of the gas. We also obtain an analytic expression of the efficiency at maximum power of our cycle under a small temperature difference. Our theory is also confirmed by a molecular dynamics simulation.

  15. A Modiifed Molecular Structure Mechanics Method for Analysis of Graphene

    Institute of Scientific and Technical Information of China (English)

    HUA Jun; LI Dongbo; ZHAO Dong; LIANG Shengwei; LIU Qinlong; JIA Ruiyan

    2015-01-01

    Based on molecular mechanics and the deformation characteristics of the atomic lattice structure of graphene, a modiifed molecular structure mechanics method was developed to improve the original one, that is, the semi-rigid connections were used to model the bond angle variations between the C-C bonds in graphene. The simulated results show that the equivalent space frame model with semi-rigid connections for graphene proposed in this article is a simple, efifcient, and accurate model to evaluate the equivalent elastic properties of graphene. Though the present computational model of the semi-rigid connected space frame is only applied to characterize the mechanical behaviors of the space lattices of graphene, it has more potential applications in the static and dynamic analyses of graphene and other nanomaterials.

  16. A molecular propeller effect for chiral separation and analysis

    Science.gov (United States)

    Clemens, Jonathon B.; Kibar, Osman; Chachisvilis, Mirianas

    2015-07-01

    Enantiomers share nearly identical physical properties but have different chiral geometries, making their identification and separation difficult. Here we show that when exposed to a rotating electric field, the left- and right-handed chiral molecules rotate with the field and act as microscopic propellers; moreover, owing to their opposite handedness, they propel along the axis of field rotation in opposite directions. We introduce a new molecular parameter called hydrodynamic chirality to characterize the coupling of rotational motion of a chiral molecule into its translational motion and quantify the direction and velocity of such motion. We demonstrate >80% enrichment level of counterpart enantiomers in solution without using chiral selectors or circularly polarized light. We expect our results to have an impact on multiple applications in drug discovery, analytical and chiral chemistry, including determination of absolute configuration, as well as in influencing the understanding of artificial and natural molecular systems where rotational motion of the molecules is involved.

  17. Quantum information analysis of electronic states at different molecular structures

    CERN Document Server

    Barcza, G; Marti, K H; Reiher, M

    2010-01-01

    We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We also discuss the application of the configuration interaction based dynamically extended active space procedure which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures to a great extent. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal orbital ordering and carry out efficient calculations on transition metal clusters. We propose a recipe to perform DMRG calculations in a black-box fashion and we point out the connections of our work to other tensor network state approaches.

  18. In vitro and in vivo models for analysis of resistance to anticancer molecular therapies.

    Science.gov (United States)

    Rosa, Roberta; Monteleone, Francesca; Zambrano, Nicola; Bianco, Roberto

    2014-01-01

    The efficacy of classical and molecular therapies in cancer is hampered by the occurrence of primary (intrinsic) and secondary (acquired) refractoriness of tumours to selected therapeutic regimens. Nevertheless, the increased knowledge of the genetic, molecular and metabolic mechanisms underlying cancer results in the generation of a correspondingly increasing number of druggable targets and molecular drugs. Thus, a current challenge in molecular oncology and medicinal chemistry is to cope with the increased need for modelling, both in cellular and animal systems, the genetic assets associated to cancer resistance to drugs. In this review, we summarize the current strategies for generation and analysis of in vitro and in vivo models, which may reveal useful to extract information on the molecular basis of intrinsic and acquired resistance to anticancer molecular agents.

  19. Molecular malaria diagnostics: A systematic review and meta-analysis.

    Science.gov (United States)

    Roth, Johanna M; Korevaar, Daniël A; Leeflang, Mariska M G; Mens, Pètra F

    2016-01-01

    Accurate diagnosis of malaria is essential for identification and subsequent treatment of the disease. Currently, microscopy and rapid diagnostic tests are the most commonly used diagnostics, next to treatment based on clinical signs only. These tests are easy to deploy, but have a relatively high detection limit. With declining prevalence in many areas, there is an increasing need for more sensitive diagnostics. Molecular tools may be a suitable alternative, although costs and technical requirements currently hamper their implementation in resource limited settings. A range of (near) point-of-care diagnostics is therefore under development, including simplifications in sample preparation, amplification and/or read-out of the test. Accuracy data, in combination with technical characteristics, are essential in determining which molecular test, if any, would be the most promising to be deployed. This review presents a comprehensive overview of the currently available molecular malaria diagnostics, ranging from well-known tests to platforms in early stages of evaluation, and systematically evaluates their published accuracy. No important difference in accuracy was found between the most commonly used PCR-based assays (conventional, nested and real-time PCR), with most of them having high sensitivity and specificity, implying that there are no reasons other than practical ones to choose one technique over the other. Loop-mediated isothermal amplification and other (novel) diagnostics appear to be highly accurate as well, with some offering potential to be used in resource-limited settings.

  20. DRILL WEAR DURING THE BORING OF PARTICLE BOARD: A MULTI-FACTOR ANALYSIS INCLUDING EFFECTS OF MINERAL CONTAMINANTS

    Directory of Open Access Journals (Sweden)

    Boleslaw Porankiewicz

    2008-05-01

    Full Text Available This paper evaluates and discusses multifactor non-linear, statistical dependencies of drill side-edges recession VBK and drill diameter recession DW on the cutting path length LC, the content of hard mineral contaminants CMC, the size of contaminant particles SMC, and the Mohs hardness MH. Significant influence of the cutting path LC, the content CMC of hard mineral contaminants (HMC, and the size of contaminant particles SMC was found, whereas the Mohs hardness MH of the contamination particles was less important.

  1. Molecular ions and protonated molecules observed in the atmospheric solids analysis probe analysis of steroids.

    Science.gov (United States)

    Ray, Andrew D; Hammond, Janet; Major, Hilary

    2010-01-01

    Atmospheric pressure chemical ionisation (APCI) has often been used to ionise steroids in mass spectrometry, usually when interfaced to high-performance liquid chromatography (HPLC). However, in positive ion mode, a dehydrated protonated molecule is often observed with a loss of structural information. The recently introduced technique of atmospheric solids analysis probe (ASAP) has the advantage that the sample can be analysed directly and does not need to be interfaced to HPLC. Existing ionisation sources such as direct analysis in real time (DART) and desorption electrospray ionisation (DESI) have shown the advantage of direct analysis techniques in a variety of applications. ASAP can be performed on commercial atmospheric pressure ionisation (API) mass spectrometers with only simple modifications to API sources. The samples are vaporised by hot nitrogen gas from the electrospray desolvation heater and ionised by a corona discharge. A range of commercially available steroids were analysed by ASAP to investigate the mechanism of ionisation. ASAP analysis of steroids generally results in the formation of the parent molecular ion as either the radical cation M+* or the protonated molecule MH+. The formation of the protonated molecule is a result of proton transfer from ionised water clusters in the source. However, if the source is dry, then formation of the radical cation is the primary ionisation mechanism.

  2. Surface desorption atmospheric pressure chemical ionization mass spectrometry for direct ambient sample analysis without toxic chemical contamination.

    Science.gov (United States)

    Chen, Huanwen; Zheng, Jian; Zhang, Xie; Luo, Mingbiao; Wang, Zhichang; Qiao, Xiaolin

    2007-08-01

    Ambient mass spectrometry, pioneered with desorption electrospray ionization (DESI) technique, is of increasing interest in recent years. In this study, a corona discharge ionization source is adapted for direct surface desorption chemical ionization of compounds on various surfaces at atmospheric pressure. Ambient air, with about 60% relative humidity, is used as a reagent to generate primary ions such as H(3)O(+), which is then directed to impact the sample surface for desorption and ionization. Under experimental conditions, protonated or deprotonated molecules of analytes present on various samples are observed using positive or negative corona discharge. Fast detection of trace amounts of analytes present in pharmaceutical preparations, viz foods, skins and clothes has been demonstrated without any sample pretreatment. Taking the advantage of the gasless setup, powder samples such as amino acids and mixtures of pharmaceutical preparations are rapidly analyzed. Impurities such as sudan dyes in tomato sauce are detected semiquantitatively. Molecular markers (e.g. putrescine) for meat spoilage are successfully identified from an artificially spoiled fish sample. Chemical warfare agent stimulants, explosives and herbicides are directly detected from the skin samples and clothing exposed to these compounds. This provides a detection limit of sub-pg (S/N > or = 3) range in MS2. Metabolites and consumed chemicals such as glucose are detected successfully from human skins. Conclusively, surface desorption atmospheric pressure chemical ionization (DAPCI) mass spectrometry, without toxic chemical contamination, detects various compounds in complex matrices, showing promising applications for analyses of human related samples.

  3. DEVELOPMENT OF SEPARATION SYSTEMS FOR POLYNUCLEAR AROMATIC HYDROCARBON ENVIRONMENTAL CONTAMINANTS USING MICELLAR ELECTROKINETIC CHROMATOGRAPHY WITH MOLECULAR MICELLES AND FREE ZONE ELECTROPHORESIS

    Science.gov (United States)

    Of four systems available from the literature, based on cyclodextrins, dioctylsulfosuccinate, bile salts, and molecular micelles consisting of oligomers of undecylenic acid, the most successful separation system in our hands is based on the molecular micelles, oligomers of sodiu...

  4. Integrated GIS and multivariate statistical analysis for regional scale assessment of heavy metal soil contamination: A critical review.

    Science.gov (United States)

    Hou, Deyi; O'Connor, David; Nathanail, Paul; Tian, Li; Ma, Yan

    2017-09-19

    Heavy metal soil contamination is associated with potential toxicity to humans or ecotoxicity. Scholars have increasingly used a combination of geographical information science (GIS) with geostatistical and multivariate statistical analysis techniques to examine the spatial distribution of heavy metals in soils at a regional scale. A review of such studies showed that most soil sampling programs were based on grid patterns and composite sampling methodologies. Many programs intended to characterize various soil types and land use types. The most often used sampling depth intervals were 0-0.10 m, or 0-0.20 m, below surface; and the sampling densities used ranged from 0.0004 to 6.1 samples per km(2), with a median of 0.4 samples per km(2). The most widely used spatial interpolators were inverse distance weighted interpolation and ordinary kriging; and the most often used multivariate statistical analysis techniques were principal component analysis and cluster analysis. The review also identified several determining and correlating factors in heavy metal distribution in soils, including soil type, soil pH, soil organic matter, land use type, Fe, Al, and heavy metal concentrations. The major natural and anthropogenic sources of heavy metals were found to derive from lithogenic origin, roadway and transportation, atmospheric deposition, wastewater and runoff from industrial and mining facilities, fertilizer application, livestock manure, and sewage sludge. This review argues that the full potential of integrated GIS and multivariate statistical analysis for assessing heavy metal distribution in soils on a regional scale has not yet been fully realized. It is proposed that future research be conducted to map multivariate results in GIS to pinpoint specific anthropogenic sources, to analyze temporal trends in addition to spatial patterns, to optimize modeling parameters, and to expand the use of different multivariate analysis tools beyond principal component analysis

  5. Numerical analysis on performance and contaminated failures of the miniature split Stirling cryocooler

    Science.gov (United States)

    He, Ya-Ling; Zhang, Dong-Wei; Yang, Wei-Wei; Gao, Fan

    2014-01-01

    A mathematical model based on thermodynamic theory of variable mass is developed for the split Stirling refrigerator, in which, the whole machine is considered by one-dimensional approach while the processes in the regenerator are simulated by two-dimensional approach. First, the influence of the ideal frost layer distributions on the flow and heat transfer in the regenerator and the performance of the Stirling cryocooler are simulated. Then, the distribution of the contaminated water vapor and its coagulated and deposited process is qualitatively analyzed. Finally, the lifetime of the refrigerator is evaluated based on the calculated data. The results show that when the refrigerator is operated at uniform distribution of the water vapor partial pressure in the regenerator, the cooling capacity is reduced over 10% at about 631 h, and the power consumption of compressor is increased over 20% at about 1168 h. However, for the linear distribution of water vapor partial pressure, the refrigerator can work properly because the frost never reaches the criterion of failure. Also, it is found that when the Stirling cryocooler restarts after a shutdown, the cooling capacity is reduced by 10% once the frost mass is over 7.05 mg, and there is no cooling capacity once the frost mass reaches 41.2 mg.

  6. Optimized Multiresidue Analysis of Organic Contaminants of Priority Concern in a Daily Consumed Fish (Grass Carp)

    Science.gov (United States)

    He, Wei; Chen, Yanru; Yang, Chen; Liu, Wenxiu; Kong, Xiangzhen; Qin, Ning; He, Qishuang

    2017-01-01

    The organic contaminants, including polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs), polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs), are of priority concern because of their persistence, toxicity, and long-distance transportation in global environment. Their residues in a daily consumed fish (grass carp) pose potential threat to human health and aquatic ecosystems. The present study optimized an analytical protocol of microwave-assisted extraction (MAE), lip-removal by gel permeation chromatography (GPC), cleanup by solid phase cartridge (SC) or adsorption chromatography column (CC), and gas chromatography-mass spectrometry (GC/MS). Besides traditional statistical parameters, some indicators were calculated to judge the performances of extraction by various methods. The optimization experiment showed that n-hexane/acetone was the best MEA extraction solvent; an optimal fraction time of 10–39 min could simultaneously elute all the target chemicals in a single GPC run. Both CC and SC showed good recoveries. However, CC performed better than SC (p manual filling, and operation by automated SPE system. PMID:28348919

  7. Optimized Multiresidue Analysis of Organic Contaminants of Priority Concern in a Daily Consumed Fish (Grass Carp

    Directory of Open Access Journals (Sweden)

    Wei He

    2017-01-01

    Full Text Available The organic contaminants, including polycyclic aromatic hydrocarbons (PAHs, organochlorine pesticides (OCPs, polybrominated diphenyl ethers (PBDEs, and polychlorinated biphenyls (PCBs, are of priority concern because of their persistence, toxicity, and long-distance transportation in global environment. Their residues in a daily consumed fish (grass carp pose potential threat to human health and aquatic ecosystems. The present study optimized an analytical protocol of microwave-assisted extraction (MAE, lip-removal by gel permeation chromatography (GPC, cleanup by solid phase cartridge (SC or adsorption chromatography column (CC, and gas chromatography-mass spectrometry (GC/MS. Besides traditional statistical parameters, some indicators were calculated to judge the performances of extraction by various methods. The optimization experiment showed that n-hexane/acetone was the best MEA extraction solvent; an optimal fraction time of 10–39 min could simultaneously elute all the target chemicals in a single GPC run. Both CC and SC showed good recoveries. However, CC performed better than SC (p<0.05 for OCPs, and SC performed better than CC for PBDEs (p<0.05. We also emphasized the limitations and advantages of SC and CC and finally proposed SC as the promising cleanup method because of its low-cost materials, time-saving steps, being free of manual filling, and operation by automated SPE system.

  8. Analysis of chemical contamination within a canal in a Mexican border colonia

    Energy Technology Data Exchange (ETDEWEB)

    Owens, Janel E. [Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX 78626 (United States); Niemeyer, Emily D. [Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX 78626 (United States)]. E-mail: niemeyee@southwestern.edu

    2006-04-15

    This study examines urban pollution within Derechos Humanos, a colonia popular in Matamoros, Tamaulipas, Mexico. General water quality indicators (coliform bacteria, total dissolved solids, ecologically relevant cations and anions), heavy metals (copper, lead, nickel, zinc, iron and cadmium), and volatile organic compounds (benzene, toluene, ethylbenzene, styrene, and dichlorobenzene and xylene isomers) were quantified within a wastewater canal running adjacent to the community. Water samples were collected at multiple sites along the banks of the canal and evidence of anthropogenic emissions existed at each sampling location. Sample site 2, approximately 10 m upstream of the colonia, contained both the widest range of hazardous pollutants and the greatest number exceeding US Environmental Protection Agency surface water standards. At each sampling location, high concentrations of total coliform (>10{sup 4} colonies/100 mL sample), lead (ranging from 0.05 to 0.40 mg/L), nickel (levels from 0.21 to 1.45 mg/L), and benzene (up to 9.80 mg/L) were noted. - This study quantifies widespread industrial and urban contamination within a canal located in a colonia (unplanned community) in Matamoros, Tamaulipas on the US-Mexico border.

  9. Contamination of DNase Preparations Confounds Analysis of the Role of DNA in Alum-Adjuvanted Vaccines.

    Science.gov (United States)

    Noges, Laura E; White, Janice; Cambier, John C; Kappler, John W; Marrack, Philippa

    2016-08-15

    Aluminum salt (alum) adjuvants have been used for many years as adjuvants for human vaccines because they are safe and effective. Despite its widespread use, the means by which alum acts as an adjuvant remains poorly understood. Recently, it was shown that injected alum is rapidly coated with host chromatin within mice. Experiments suggested that the host DNA in the coating chromatin contributed to alum's adjuvant activity. Some of the experiments used commercially purchased DNase and showed that coinjection of these DNase preparations with alum and Ag reduced the host's immune response to the vaccine. In this study, we report that some commercial DNase preparations are contaminated with proteases. These proteases are responsible for most of the ability of DNase preparations to inhibit alum's adjuvant activity. Nevertheless, DNase somewhat reduces responses to some Ags with alum. The effect of DNase is independent of its ability to cleave DNA, suggesting that alum improves CD4 responses to Ag via a pathway other than host DNA sensing. Copyright © 2016 by The American Association of Immunologists, Inc.

  10. Pteros: fast and easy to use open-source C++ library for molecular analysis.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2012-07-15

    An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/.

  11. Matrix effects in applying mono- and polyclonal ELISA systems to the analysis of weathered oils in contaminated soil.

    Science.gov (United States)

    Pollard, S J T; Farmer, J G; Knight, D M; Young, P J

    2002-01-01

    Commercial mono- and polyclonal enzyme-linked immunosorbent assay (ELISA) systems were applied to the on-site analysis of weathered hydrocarbon-contaminated soils at a former integrated steelworks. Comparisons were made between concentrations of solvent extractable matter (SEM) determined gravimetrically by Soxhlet (dichloromethane) extraction and those estimated immunologically by ELISA determination over a concentration range of 2000-330,000 mg SEM/kg soil dry weight. Both ELISA systems tinder-reported for the more weathered soil samples. Results suggest this is due to matrix effects in the sample rather than any inherent bias in the ELISA systems and it is concluded that, for weathered hydrocarbons typical of steelworks and coke production sites, the use of ELISA requires careful consideration as a field technique. Consideration of the target analyte relative to the composition of the hydrocarbon waste encountered appears critical.

  12. Determination of the depth of localized radioactive contamination by 137Cs and 60Co in sand with principal component analysis.

    Science.gov (United States)

    Adams, Jamie C; Mellor, Matthew; Joyce, Malcolm J

    2011-10-01

    A method to determine the depth of buried localized radioactive contamination nonintrusively and nondestructively using principal component analysis is described. The γ-ray spectra from two radionuclides, cesium-137 and cobalt-60, have been analyzed to derive the two principal components that change most significantly as a result of varying the depth of the sources in a bespoke sand-filled phantom. The relationship between depth (d) and the angle (θ) between the first two principal component coefficients has been derived for both cases, viz. d(Φ) = x + y log(e) Φ where x and y are constants dependent on the shielding material and the γ-ray energy spectrum of the radioactivity in question, and φ is a function of θ. The technique enables the depth of a localized radioactive source to be determined nonintrusively in the range 5 to 50 mm with an accuracy of ±1 mm.

  13. Elemental characterization of superficial waters contaminated by an abandoned sulfide-mining area, through neutron activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Canha, N.; Freitas, M.C.; Dionisio, I.; Anawar, H.M. [URSN-ITN, Sacavem (Portugal). Technological and Nuclear Inst.; Pacheco, A.M.G. [Technical Univ. of Lisbon (Portugal). CERENA-IST

    2011-07-01

    In this work, superficial waters of two small rivers flowing in the Sao Domingos' abandoned mining area were analyzed in order to infer on soil-water transfer of the elements determined. Instrumental neutron activation analysis was used for elemental concentration assessment. The following elements were found at the mg L{sup -1} level: As, Ba, Co, Cu, Fe, K, Na and Zn. The dry-mass residues varied between 70 mg and 1 g in 20-mL volumes. High enrichment relative to soil was found for most elements. Good statistical associations between Br and Na, between Cr and Sc, and between Ce, Co, Fe, Yb, and Zn, were found, suggesting a similar mechanism of soil-water, elemental transfer. Both the superficial waters' composition and their elemental levels indicate a potential risk of contamination of the underground waters and an actual health risk for the resident populations. (orig.)

  14. On the accurate molecular dynamics analysis of biological molecules

    Science.gov (United States)

    Yamashita, Takefumi

    2016-12-01

    As the evolution of computational technology has now enabled long molecular dynamics (MD) simulation, the evaluation of many physical properties shows improved convergence. Therefore, we can examine the detailed conditions of MD simulations and perform quantitative MD analyses. In this study, we address the quantitative and accuracy aspects of MD simulations using two example systems. First, it is found that several conditions of the MD simulations influence the area/lipid of the lipid bilayer. Second, we successfully detect the small but important differences in antibody motion between the antigen-bound and unbound states.

  15. Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

    Directory of Open Access Journals (Sweden)

    Javis Anyangwe Nwaboh

    2011-01-01

    Full Text Available We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS, quantum cascade laser absorption spectroscopy (QCLAS, and cavity ring down spectroscopy (CRDS, all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are in agreement with respective gravimetric values, showing that the TILSAM method is feasible with all different techniques. We emphasize the data quality objectives given by traceability issues and uncertainty analyses.

  16. Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

    DEFF Research Database (Denmark)

    Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing

    2007-01-01

    Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included......, Mol. Simul. 33 (4–5) (2007) 449–457.]. The new one has advantages for systems with data points at dilute conditions. Prediction of bubble point pressures using parameters from the two objective functions are compared with experimental data for the binary mixtures methyl acetate–n-pentane and methyl...

  17. Molecular characterization and RAPD analysis of Juniperus species from Iran.

    Science.gov (United States)

    Kasaian, J; Behravan, J; Hassany, M; Emami, S A; Shahriari, F; Khayyat, M H

    2011-06-07

    The genus Juniperus L. (Cupressaceae), an aromatic evergreen plant, consists of up to 68 species around the world. We classified five species of Juniperus found in Iran using molecular markers to provide a means for molecular identification of Iranian species. Plants were collected (three samples of each species) from two different provinces of Iran (Golestan and East Azarbayejan). The DNA was extracted from the leaves using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using 18 ten-mer RAPD primers. Genetic distances were estimated based on 187 RAPD bands to construct a dendrogram by means of unweighted pair group method of arithmetic means. It was found that J. communis and J. oblonga were differentiated from the other species. Genetic distance values ranged from 0.19 (J. communis and J. oblonga) to 0.68 (J. communis and J. excelsa). Juniperus foetidissima was found to be most similar to J. sabina. Juniperus excelsa subspecies excelsa and J. excelsa subspecies polycarpos formed a distinct group.

  18. Molecular basis of essential fructosuria: molecular cloning and mutational analysis of human ketohexokinase (fructokinase).

    Science.gov (United States)

    Bonthron, D T; Brady, N; Donaldson, I A; Steinmann, B

    1994-09-01

    Essential fructosuria is one of the oldest known inborn errors of metabolism. It is a benign condition which is believed to result from deficiency of hepatic fructokinase (ketohexokinase, KHK, E.C.2.7.1.3). This enzyme catalyses the first step of metabolism of dietary fructose, conversion of fructose to fructose-1-phosphate. Despite the early recognition of this disorder, the primary structure of human KHK and the molecular basis of essential fructosuria have not been previously defined. In this report, the isolation and sequencing of full-length cDNA clones encoding human ketohexokinase are described. Alternative mRNA species and alternative KHK isozymes are produced by alternative polyadenylation and splicing of the KHK gene. The KHK proteins show a high level of sequence conservation relative to rat KHK. Direct evidence that mutation of the KHK structural gene is the cause of essential fructosuria was also obtained. In a well-characterized family, in which three of eight siblings have fructosuria, all affected individuals are compound heterozygotes for two mutations Gly40Arg and Ala43Thr. Both mutations result from G-->A transitions, and each alters the same conserved region of the KHK protein. Neither mutation was seen in a sample of 52 unrelated control individuals. An additional conservative amino acid change (Val49IIe) was present on the KHK allele bearing Ala43Thr.

  19. Desorption electrospray ionization mass spectrometry in the analysis of chemical food contaminants in food

    NARCIS (Netherlands)

    Nielen, M.W.F.; Hooijerink, H.; Zomer, P.; Mol, J.G.J.

    2011-01-01

    Since its introduction, desorption electrospray ionization (DESI) mass spectrometry (MS) has been mainly applied in pharmaceutical and forensic analysis. We expect that DESI will find its way in many different fields, including food analysis. In this review, we summarize DESI developments aimed at

  20. Seasonal bacteriological analysis of Gola river water contaminated with pulp paper mill waste in Uttaranchal, India.

    Science.gov (United States)

    Chandra, Ram; Singh, Shail; Raj, Abhay

    2006-07-01

    The seasonal physico-chemical and microbial quality of Gola river water has been analyzed after confluence of pulp paper mill waste. The study revealed that it has enhanced 20-30 times pollution load of BOD, COD, TDS, TSS, sulphate, chloride, sodium, nitrate, potassium, lignin and phenol after mixing of pulp paper mill waste with river water in all season. Further, it induced the bacterial growth by increasing most probable number value of E. coli was 1.57 x 10(4), 1.6 x 10(4), 1.37 x 10(4) and SPC count was 1.68 x 10(4), 1.64 x 10(4), 1.67 x 10(4)/100 ml during summer, monsoon, winter respectively. While the most probable number value in river water before mixing of pulp paper mill waste was 1.4 x 10(2), 1.82 x 10(2), 1.5 x 10(2) and SPC count was 2.8 x 10(3), 2.89 x 10(3), 2.78 x 10(3)/100 ml during summer, monsoon and winter respectively. This indicated from 88-114 fold increase in most probable number value of E. coli and 56.55-60.0 times increase in SPC count of river water after mixing of effluent in summer, monsoon and winter. Moreover, the most probable number value in effluent itself before mixing was 3.4 x 10(2), 3.3 x 10(2), 2.8 x 10(2) and SPC count was 6 x 10(4), 6.5 x 10(4), 6 x 10(4)/100 ml during summer, monsoon, winter, respectively. Furthermore, it was revealed that the seasonal variation also regulated the bacterial population dynamics as per the physico-chemical quality, in which E. coli was found highest at the rate of (5.9 x 10(4)), E. aerogenes (5.3 x 10(4)), P. aeruginosa (1.3 x 10(4)), S. aureus (3.2 x 10(3)), K. pneumoniae (2.6 x 10(4)), Enteritidis (1.1 x 10(4)) on monsoon season and V. cholerae (7.4 x 10(2)), V. vulnificus (9.2 x 10(2))/100 ml in river water when contaminated with pulp paper mill waste in monsoon season. Thus, the monsoon season showed presence of FC and TC indicated the thermo-tolerant and disease causing group of bacterial population in effluent and its sequence was observed as monsoon>summer>winter. This indicated the