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Sample records for contamination marker selection

  1. Assessment of contamination of the Svitava and Svratka rivers in the Czech Republic using selected biochemical markers.

    Science.gov (United States)

    Blahová, Jana; Havelková, Marcela; Kruzíková, Kamila; Hilscherová, Klára; Halouzka, Roman; Modrá, Helena; Grabic, Roman; Halírová, Jarmila; Jurcíková, Jana; Ocelka, Tomás; Harustiaková, Danka; Svobodová, Zdenka

    2010-03-01

    The aim of the present study is to assess aquatic ecosystem contamination using selected biochemical markers: cytochrome P450, ethoxyresorufin-O-deethylase (EROD), glutathione S-transferase (GST), tripeptide glutathione, vitellogenin, and 11-ketotestosterone in chub (Leuciscus cephalus L.). Seven locations on the Svitava and Svratka rivers (in the Brno conurbation, Czech Republic) were assessed. The results were compared with the levels of the most important inductors of these biomarkers: organic pollutants hexachlorocyclohexane (HCH), hexachlorobenzene (HCB), DDT and its metabolites, polychlorinated biphenyls, and polycyclic aromatic hydrocarbons in bottom sediment, fish muscle, and semipermeable membrane devices (SPMDs) and metals in sediment. The highest levels of pollutants were observed at sites situated downstream from Brno, especially at Modrice and Rajhradice. Significant positive correlations (p < 0.05) were found between EROD activity and HCH concentration in SPMDs, and also between GST and EROD activity with HCB concentration in muscle, after adjusting for age.

  2. Pig Manure Contamination Marker Selection Based on the Influence of Biological Treatment on the Dominant Fecal Microbial Groups▿

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    Marti, Romain; Dabert, Patrick; Pourcher, Anne-Marie

    2009-01-01

    The objective of this study was to identify a microbial marker for pig manure contamination. We quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. The partial 16S rRNA genes of Bacteroides-Prevotella, Eubacterium-Clostridiaceae, Bacillus-Streptococcus-Lactobacillus (BSL), and Bifidobacterium group isolates were amplified and analyzed by capillary electrophoresis single-strand conformation polymorphism. The most dominant bacterial populations were identified by cloning and sequencing their 16S rRNA genes. The results showed that Bifidobacterium spp. and, to a lesser extent, members of the BSL group, were less affected by the aerobic treatment than either Eubacterium-Clostridiaceae or Bacteroides-Prevotella. Two Bifidobacterium species found in raw manure were still present in manure during land application, suggesting that they can survive outside the pig intestinal tract and also survive aerobic treatment. The 16S-23S rRNA internal transcribed spacer of one species, Bifidobacterium thermacidophilum subsp. porcinum, was sequenced, and a specific pair of primers was designed for its detection in the environment. With this nested PCR assay, this potential marker was not detected in samples from 30 bovine, 30 poultry, and 28 human fecal samples or in 15 urban wastewater effluents. As it was detected in runoff waters after spreading of pig manure, we propose this marker as a suitable microbial indicator of pig manure contamination. PMID:19525269

  3. Pig manure contamination marker selection based on the influence of biological treatment on the dominant fecal microbial groups.

    Science.gov (United States)

    Marti, Romain; Dabert, Patrick; Pourcher, Anne-Marie

    2009-08-01

    The objective of this study was to identify a microbial marker for pig manure contamination. We quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. The partial 16S rRNA genes of Bacteroides-Prevotella, Eubacterium-Clostridiaceae, Bacillus-Streptococcus-Lactobacillus (BSL), and Bifidobacterium group isolates were amplified and analyzed by capillary electrophoresis single-strand conformation polymorphism. The most dominant bacterial populations were identified by cloning and sequencing their 16S rRNA genes. The results showed that Bifidobacterium spp. and, to a lesser extent, members of the BSL group, were less affected by the aerobic treatment than either Eubacterium-Clostridiaceae or Bacteroides-Prevotella. Two Bifidobacterium species found in raw manure were still present in manure during land application, suggesting that they can survive outside the pig intestinal tract and also survive aerobic treatment. The 16S-23S rRNA internal transcribed spacer of one species, Bifidobacterium thermacidophilum subsp. porcinum, was sequenced, and a specific pair of primers was designed for its detection in the environment. With this nested PCR assay, this potential marker was not detected in samples from 30 bovine, 30 poultry, and 28 human fecal samples or in 15 urban wastewater effluents. As it was detected in runoff waters after spreading of pig manure, we propose this marker as a suitable microbial indicator of pig manure contamination.

  4. Biochemical Markers for Assessing Aquatic Contamination

    Directory of Open Access Journals (Sweden)

    Zdeňka Svobodová

    2007-11-01

    Full Text Available Biochemical markers, specifically enzymes of the first phase of xenobiotic transformation - cytochrome P450 and ethoxyresorufin-O-deethylase (EROD - were used to determine the quantities of persistent organic pollutants (POPs in fish muscle (PCB, HCB, HCH, OCS, DDT. Eight rivers were monitored (Orlice, Chrudimka, Cidlina, Jizera, Vltava, Ohře and Bílina; and the River Blanice was used as a control. The indicator species selected was the chub (Leuciscus cephalus L.. There were no significant differences in cytochrome P450 content between the locations monitored. The highest concentration of cytochrome P450 in fish liver was in the Vltava (0.241 nmol mg-1 protein, and the lowest was in the Orlice (0.120 nmol mg-1 protein. Analysis of EROD activity showed a significant difference between the Blanice and the Vltava (P< 0.05, and also between the Orlice and the Vltava (P< 0.01, the Orlice and the Bílina (P< 0.01, and the Orlice and the Ohře (P< 0.05. The highest EROD activity in fish liver was in the Vltava (576.4 pmol min-1 mg-1 protein, and the lowest was in the Orlice (63.05 pmol min-1 mg-1 protein. In individual locations, results of chemical monitoring and values of biochemical markers were compared. A significant correlation (P< 0.05 was found between biochemical markers and OCS, and PCB. Among the tributaries studied those that contaminated the Elbe most were the Vltava and the Bílina. These tributaries should not be considered the main sources of industrial contamination of the River Elbe, because the most important contamination sources were along the river Elbe itself.

  5. Biochemical markers for the assessment of aquatic environment contamination

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    Havelková, Marcela; Randák, Tomáš; Blahová, Jana; Slatinská, Iveta; Svobodová, Zdeňka

    2008-01-01

    The need for assessment of aquatic ecosystem contamination and of its impact on water dwelling organisms was developed in response to rising aquatic environmental pollution. In this field study, liver enzymes of phase I and phase II of xenobiotic transformation, namely cytochrome P450, ethoxyresorufin-O-deethylase, glutathione-S-transferase and tripeptide glutathione were used to assess the contamination of the aquatic environment at different rivers in the Czech Republic. The indicator species selected was the male chub (Leuciscus cephalus L.) and male brown trout (Salmo trutta fario). Chemical analyses included also the assessment of the most important inductors of previously mentioned biochemical markers. The major inductors of monitored biomarkers are industrial contaminants which belong to a large group of organic pollutants (PCB, PAH, PCDD/F, DDT, HCH, HCB and OCS), persistent in the environment. Four different groups of river basins were assessed: the River Tichá Orlice and its tributary the Kralický brook; important tributaries of the River Elbe (the rivers Orlice, Chrudimka, Cidlina, Jizera, Vltava, Ohře and Bílina); major rivers in the Czech Republic (the rivers Lužnice, Otava, Sázava, Berounka, Vltava, Labe, Ohře, Svratka, Dyje, Morava and Odra) and the River Vltava. The use of the biochemical markers together with chemical analyses seems to be an effective way to monitor the quality of aquatic environment. PMID:21218108

  6. Marker-assisted selection in forestry species

    International Nuclear Information System (INIS)

    Butcher, P.; Southerton, S.

    2007-01-01

    The primary goal of tree breeding is to increase the quantity and quality of wood products from plantations. Major gains have been achieved using recurrent selection in genetically diverse breeding populations to capture additive variation. However, the long generation times of trees, together with poor juvenile-mature trait correlations, have promoted interest in marker-assisted selection (MAS) to accelerate breeding through early selection. MAS relies on identifying DNA markers, which explain a high proportion of variation in phenotypic traits. Genetic linkage maps have been developed for most commercial tree species and these can be used to locate chromosomal regions where DNA markers co-segregate with quantitative traits (quantitative trait loci, QTL). MAS based on QTL is most likely to be used for within-family selection in a limited number of elite families that can be clonally propagated. Limitations of the approach include the low resolution of marker-trait associations, the small proportion of phenotypic variation explained by QTL and the low success rate in validating QTL in different genetic backgrounds and environments. This has led to a change in research focus towards association mapping to identify variation in the DNA sequence of genes directly controlling phenotypic variation (gene-assisted selection, GAS). The main advantages of GAS are the high resolution of marker-trait associations and the ability to transfer markers across families and even species. Association studies are being used to examine the adaptive significance of variation in genes controlling wood formation and quality, pathogen resistance, cold tolerance and drought tolerance. Single nucleotide polymorphisms (SNPs) in these gene sequences that are significantly associated with trait variation can then be used for early selection. Markers for SNPs can be transferred among individuals regardless of pedigree or family relationship, increasing opportunities for their application in

  7. Marker-assisted selection for quantitative traits

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    Ivan Schuster

    2011-01-01

    Full Text Available Although thousands of scientific articles have been published on the subject of marker-assisted selection (MAS andquantitative trait loci (QTL, the application of MAS for QTL in plant breeding has been restricted. Among the main causes for thislimited use are the low accuracy of QTL mapping and the high costs of genotyping thousands of plants with tens or hundreds ofmolecular markers in routine breeding programs. Recently, new large-scale genotyping technologies have resulted in a costreduction. Nevertheless, the MAS for QTL has so far been limited to selection programs using several generations per year, wherephenotypic selection cannot be performed in all generations, mainly in recurrent selection programs. Methods of MAS for QTL inbreeding programs using self-pollination have been developed.

  8. Marker-assisted selection in poultry

    International Nuclear Information System (INIS)

    Koning, D.-J. de; Hocking, P.M.

    2007-01-01

    Among livestock species, chicken has the most extensive genomics toolbox available for detection of quantitative trait loci (QTL) and marker-assisted selection (MAS). The uptake of MAS is therefore not limited by technical resources but mostly by the priorities and financial constraints of the few remaining poultry breeding companies. With the cost of genotyping decreasing rapidly, an increase in the use of direct trait- single nucleotide polymorphism (SNP)-associations in MAS can be predicted. (author)

  9. Organic Pollutant Contamination of the River Tichá Orlice as Assessed by Biochemical Markers

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    M. Havelková

    2008-01-01

    Full Text Available This study used biochemical markers to assess contamination at two contaminated sites (Králíky and Lichkov and one control site (Červená Voda on the River Tichá Orlice, a left-side tributary of the River Elbe. The brown trout (Salmo trutta fario was selected as an indicator species. Enzymes of the first stage of xenobiotic conversion, namely cytochrome P450 (CYP 450 and ethoxyresorufin-O-deethylase (EROD in the liver were selected as biochemical markers. Blood plasma vitellogenin concentrations were used to evaluate xenoestrogenic effects of contamination. Results were compared with the most important inductors of these markers, i.e. with organic pollutants (PCB, HCH, HCB, OCS and DDT and their metabolites in fish muscle and with PAH concentrations in bottom sediments. The highest contamination with organic pollutants was at Králíky, and this was reflected in increased cytochrome P450, EROD activity and vitellogenin concentrations. Significant differences were demonstrated in EROD activity and vitellogenin concentrations between Králíky and Červená Voda (P s = -0.964 between EROD activity and vitellogenin concentrations was demonstrated. This relationship was discussed from the point of view of a possible induction or inhibition of the assessed biomarkers at persistently highly contaminated sites.

  10. Marker-assisted selection in Eucalyptus

    International Nuclear Information System (INIS)

    Grattapaglia, D.

    2007-01-01

    Planted Eucalyptus occupies globally more than 18 million hectares and has become the most widely planted hardwood tree in the world, supplying high-quality woody biomass for several industrial applications. In this chapter an overview is presented on the status and perspectives of marker-assisted selection (MAS) in species of Eucalyptus. After an introduction to the main features of modern eucalypt breeding and clonal forestry, some applications of molecular markers in support to operational breeding are presented. By reviewing the status of quantitative trait locus (QTL) mapping in Eucalyptus, the challenges and some realistic prospects for the application of MAS to improve relevant traits are outlined. With the expected availability of more powerful genomic tools, including a draft of the Eucalyptus genome, the main challenges in implementing MAS will be in phenotyping trees accurately, analysing the overwhelming amount of genomic data available and translating this into truly useful molecular tools for breeding. (author)

  11. Marker-assisted selection in dairy cattle

    International Nuclear Information System (INIS)

    Weller, J.I.

    2007-01-01

    Considering the long generation interval, the high value of each individual, the very limited female fertility and the fact that nearly all economic traits are expressed only in females, it would seem that cattle should be a nearly ideal species for application of marker-assisted selection (MAS). As genetic gains are cumulative and eternal, application of new technologies that increase rates of genetic gain can be profitable even if the nominal annual costs are several times the value of the nominal additional annual genetic gain. Complete genome scans for quantitative trait loci (QTL) based on the granddaughter design have been completed for most commercial dairy cattle populations, and significant across-study effects for economic traits have been found on chromosomes 1, 3, 6, 9, 10, 14 and 20. Quantitative trait loci associated with trypanotolerance have been detected in a cross between the African N'Dama and the Boran breeds as the first step in the introgression of these genes into breeds susceptible to trypanosomosis. In dairy cattle, the actual DNA polymorphism has been determined twice, for QTL on BTA 6 and BTA 14. In both cases the polymorphism caused a non-conservative amino acid change, and both QTL chiefly affect fat and protein concentration. Most theoretical studies have estimated the expected gains that can be obtained by MAS to be in the range of a 5 to 20 percent increase in the rates of genetic gain obtained by traditional selection programmes. Applied MAS programmes have commenced for French and German Holsteins. In both programmes genetic evaluations including QTL effects are computed by variants of marker-assisted best linear unbiased prediction (MA-BLUP). (author)

  12. Chemical Contaminants as Stratigraphic Markers for the Anthropocene

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    Kruge, M. A.

    2012-12-01

    Thousands and even millions of years from now, widespread anthropogenic contaminants in sediments would likely persist, incorporated into the geological record. They would inadvertently preserve evidence of our present era (informally designated as the Anthropocene Epoch) characterized by large human populations engaged in intensive industrial and agricultural activities. Hypothetical geologists in the distant future would likely find unusually high concentrations of a wide variety of contaminants at stratigraphic levels corresponding to our present time, analogous to the iridium anomaly marking the bolide impact event at the close of the Cretaceous Period. These would include both organic and inorganic substances, such as industrially-derived heavy metals (e.g., Hg, Pb, Cr, Zn) and hydrocarbons, both petrogenic (derived directly from petroleum) and pyrogenic (combustion products). While there are natural sources for these materials, such as volcanic eruptions, wildfires, and oil seeps, their co-occurrence would provide a signature characteristic of human activity. Diagnostic assemblages of organic compounds would carry an anthropogenic imprint. The distribution of polycyclic aromatic hydrocarbons (PAHs) in a sediment sample could distinguish between natural and human sources. Stable isotopic signatures would provide additional evidence. Concentrations of contaminants in the sedimentary record would increase exponentially with increasing proximity to urban source areas, where at present billions of people are collectively consuming vast quantities of fossil fuels and generating large amounts of waste. Aolian and marine transport prior to deposition has been seen at present to globally redistribute detectable amounts of contaminants including Hg and PAHs, even at great distances from principal source areas. For organic contaminants, deposition in an anoxic sedimentary environment could insure their preservation, increasing the likelihood of their inclusion in the

  13. Plant breeding with marker-assisted selection in Brazil

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    Ney Sussumu Sakiyama

    2014-03-01

    Full Text Available Over the past three decades, molecular marker studies reached extraordinary advances, especially for sequencing and bioinformatics techniques. Marker-assisted selection became part of the breeding program routines of important seed companies, in order to accelerate and optimize the cultivar developing processes. Private seed companies increasingly use marker-assisted selection, especially for the species of great importance to the seed market, e.g. corn, soybean, cotton, and sunflower. In the Brazilian public institutions few breeding programs use it efficiently. The possible reasons are: lack of know-how, lack of appropriate laboratories, few validated markers, high cost, and lack of urgency in obtaining cultivars. In this article we analyze the use and the constraints of marker-assisted selection in plant breeding programs of Brazilian public institutes

  14. Algorithms for selecting informative marker panels for population assignment.

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    Rosenberg, Noah A

    2005-11-01

    Given a set of potential source populations, genotypes of an individual of unknown origin at a collection of markers can be used to predict the correct source population of the individual. For improved efficiency, informative markers can be chosen from a larger set of markers to maximize the accuracy of this prediction. However, selecting the loci that are individually most informative does not necessarily produce the optimal panel. Here, using genotypes from eight species--carp, cat, chicken, dog, fly, grayling, human, and maize--this univariate accumulation procedure is compared to new multivariate "greedy" and "maximin" algorithms for choosing marker panels. The procedures generally suggest similar panels, although the greedy method often recommends inclusion of loci that are not chosen by the other algorithms. In seven of the eight species, when applied to five or more markers, all methods achieve at least 94% assignment accuracy on simulated individuals, with one species--dog--producing this level of accuracy with only three markers, and the eighth species--human--requiring approximately 13-16 markers. The new algorithms produce substantial improvements over use of randomly selected markers; where differences among the methods are noticeable, the greedy algorithm leads to slightly higher probabilities of correct assignment. Although none of the approaches necessarily chooses the panel with optimal performance, the algorithms all likely select panels with performance near enough to the maximum that they all are suitable for practical use.

  15. Selection processes in a citrus hybrid population using RAPD markers

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    Oliveira Roberto Pedroso de

    2003-01-01

    Full Text Available The objective of this work was to evaluate the processes of selection in a citrus hybrid population using segregation analysis of RAPD markers. The segregation of 123 RAPD markers between 'Cravo' mandarin (Citrus reticulata Blanco and 'Pêra' sweet orange (C. sinensis (L. Osbeck was analysed in a F1 progeny of 94 hybrids. Genetic composition, diversity, heterozygosity, differences in chromosomal structure and the presence of deleterious recessive genes are discussed based on the segregation ratios obtained. A high percentage of markers had a skeweness of the 1:1 expected segregation ratio in the F1 population. Many markers showed a 3:1 segregation ratio in both varieties and 1:3 in 'Pêra' sweet orange, probably due to directional selection processes. The distribution analysis of the frequencies of the segregant markers in a hybrid population is a simple method which allows a better understanding of the genetics of citrus group.

  16. Blood Contamination in Saliva: Impact on the Measurement of Salivary Oxidative Stress Markers

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    Natália Kamodyová

    2015-01-01

    Full Text Available Salivary oxidative stress markers represent a promising tool for monitoring of oral diseases. Saliva can often be contaminated by blood, especially in patients with periodontitis. The aim of our study was to examine the impact of blood contamination on the measurement of salivary oxidative stress markers. Saliva samples were collected from 10 healthy volunteers and were artificially contaminated with blood (final concentration 0.001–10%. Next, saliva was collected from 12 gingivitis and 10 control patients before and after dental hygiene treatment. Markers of oxidative stress were measured in all collected saliva samples. Advanced oxidation protein products (AOPP, advanced glycation end products (AGEs, and antioxidant status were changed in 1% blood-contaminated saliva. Salivary AOPP were increased in control and patients after dental treatment (by 45.7% and 34.1%, p<0.01. Salivary AGEs were decreased in patients after microinjury (by 69.3%, p<0.001. Salivary antioxidant status markers were decreased in both control and patients after dental treatment (p<0.05 and p<0.01. One % blood contamination biased concentrations of salivary oxidative stress markers. Saliva samples with 1% blood contamination are visibly discolored and can be excluded from analyses without any specific biochemic detection of blood constituents. Salivary markers of oxidative stress were significantly altered in blood-contaminated saliva in control and patients with gingivitis after dental hygiene treatment.

  17. Selection Of Drought Resistant Mutants In Rice Using DNA Markers

    International Nuclear Information System (INIS)

    Nguyen Duc Thanh; Le Thi Bich Thuy; Dang Thi Minh Lua

    2008-01-01

    In recent years, the marker - assisted selection (MAS) strategy have been used for selection of traits that are difficult and costly performed measurement and score. Selection for a well-developed root system could improve the drought resistance of rice as the plant would avoid water stress by absorbing water from the soil. There were several reports on map construction and identification of the markers tightly linked to morphological and physiological traits related to drought resistance in rice, in particular, root traits in upland and lowland rice (Champoux et al., 1995; Ray et al., 1996; Price et al., 1997, 2000; Yadav et al., 1997). In this report, we present the results on selection of drought resistance mutants in rice using the DNA markers tightly linked to root traits favorable for drought resistance. The mutant rice lines were obtained from irradiated seeds and calluses by gamma ray. The selection was performed at M2 mutants using the DNA markers linked to maximum root length (MRL), root weight to shoot weight ratio (RW/SR), and weight of deep root to shoot weight ratio (DRW/SR). The obtained results showed that there were many lines possessed drought resistant markers. In addition, there is a number of lines have altered genome. Several lines having drought markers proved to be more resistant to drought in green-house test. These lines could be useful for further test and development of drought resistant varieties. (author)

  18. Identification of fecal contamination sources in water using host-associated markers.

    Science.gov (United States)

    Krentz, Corinne A; Prystajecky, Natalie; Isaac-Renton, Judith

    2013-03-01

    In British Columbia, Canada, drinking water is tested for total coliforms and Escherichia coli, but there is currently no routine follow-up testing to investigate fecal contamination sources in samples that test positive for indicator bacteria. Reliable microbial source tracking (MST) tools to rapidly test water samples for multiple fecal contamination markers simultaneously are currently lacking. The objectives of this study were (i) to develop a qualitative MST tool to identify fecal contamination from different host groups, and (ii) to evaluate the MST tool using water samples with evidence of fecal contamination. Singleplex and multiplex polymerase chain reaction (PCR) were used to test (i) water from polluted sites and (ii) raw and drinking water samples for presence of bacterial genetic markers associated with feces from humans, cattle, seagulls, pigs, chickens, and geese. The multiplex MST assay correctly identified suspected contamination sources in contaminated waterways, demonstrating that this test may have utility for heavily contaminated sites. Most raw and drinking water samples analyzed using singleplex PCR contained at least one host-associated marker. Singleplex PCR was capable of detecting host-associated markers in small sample volumes and is therefore a promising tool to further analyze water samples submitted for routine testing and provide information useful for water quality management.

  19. Accuracy of marker-assisted selection with auxiliary traits

    Indian Academy of Sciences (India)

    Unknown

    Genetic information on molecular markers is increasingly being used in plant and animal improvement programmes particularly as indirect means to improve a metric trait by selection either on an individual basis or on the basis of an index incorporating such information. This paper examines the utility of an index of ...

  20. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Lalit Kumar

    2013-04-03

    Apr 3, 2013 ... Microsatellite and amplified fragment length polymorphism (AFLP) markers were used to differentiate. Manjari Naveen, a clonal selection of Centennial Seedless variety of grape. Twenty one (21) microsatellite primers could not detect variation between parent variety and its clone. AFLP analysis.

  1. Possibilities for marker-assisted selection in aquaculture breeding schemes

    International Nuclear Information System (INIS)

    Sonesson, A.K.

    2007-01-01

    FAO estimates that there are around 200 species in aquaculture. However, only a few species have ongoing selective breeding programmes. Marker-assisted selection (MAS) is not used in any aquaculture breeding scheme today. The aim of this chapter, therefore, is to review briefly the current status of aquaculture breeding schemes and to evaluate the possibilities for MAS of aquaculture species. Genetic marker maps have been published for some species in culture. The marker density of these maps is, in general, rather low and the maps are composed of many amplified fragment length polymorphism (AFLP) markers anchored to few microsatellites. Some quantitative trait loci (QTL) have been identified for economically important traits, but they are not yet mapped at a high density. Computer simulations of within-family MAS schemes show a very high increase in genetic gain compared with conventional family-based breeding schemes, mainly due to the large family sizes that are typical for aquaculture breeding schemes. The use of genetic markers to identify individuals and their implications for breeding schemes with control of inbreeding are discussed. (author)

  2. Chemometric Analysis of Selected Organic Contaminants in Surface Water of Langat River Basin

    International Nuclear Information System (INIS)

    Mohamad Rafaie Mohamed Zubir; Rozita Osman; Norashikin Saim

    2016-01-01

    Chemometric techniques namely hierarchical agglomerative cluster analysis (HACA), discriminant analysis (DA), principal component analysis (PCA) and factor analysis (FA) were applied to the distribution of selected organic contaminants (polycyclic aromatic hydrocarbons (PAHs), sterols, pesticides (chloropyrifos), and phenol) to assess the potential of using these organic contaminants as chemical markers in Langat River Basin. Water samples were collected from February 2012 to January 2013 on a monthly basis for nine monitoring sites along Langat River Basin. HACA was able to classify the sampling sites into three clusters which can be correlated to the level of contamination (low, moderate and high contamination sites). DA was used to discriminate the sources of contamination using the selected organic contaminants and relate to the existing DOE local activities groupings. Forward and backward stepwise DA was able to discriminate two and five organic contaminants variables, respectively, from the original 13 selected variables. The five significant variables identified using backward stepwise DA were fluorene, pyrene, stigmastanol, stigmasterol and phenol. PCA and FA (varimax functionality) were used to identify the possible sources of each organic contaminant based on the inventory of local activities. Five principal components were obtained with 66.5 % of the total variation. Result from FA indicated that PAHs (pyrene, fluorene, acenaphthene, benzo[a]anthracene) originated from industrial activity and socio-economic activities; while sterols (coprostanol, stigmastanol and stigmasterol) were associated to domestic sewage and local socio-economic activities. The occurrence of chloropyrifos was correlated to agricultural activities, urban and domestic discharges. This study showed that the application of chemometrics on the distribution of selected organic contaminants was able to trace the sources of contamination in surface water. (author)

  3. Marker-assisted selection in common beans and cassava

    International Nuclear Information System (INIS)

    Blair, M.W.; Fregene, M.A.; Beebe, S.E.; Ceballos, H.

    2007-01-01

    Marker-assisted selection (MAS) in common beans (Phaseolus vulgaris L.) and cassava (Manihot esculenta) is reviewed in relation to the breeding system of each crop and the breeding goals of International Agricultural Research Centres (IARCs) and National Agricultural Research Systems (NARS). The importance of each crop is highlighted and examples of successful use of molecular markers within selection cycles and breeding programmes are given for each. For common beans, examples are given of gene tagging for several traits that are important for bean breeding for tropical environments and aspects considered that contribute to successful application of MAS. Simple traits that are tagged with easy-to-use markers are discussed first as they were the first traits prioritized for breeding at the International Center for Tropical Agriculture (CIAT) and with NARS partners in Central America, Colombia and eastern Africa. The specific genes for MAS selection were the bgm-1 gene for bean golden yellow mosaic virus (BGYMV) resistance and the bc-3 gene for bean common mosaic virus (BCMV) resistance. MAS was efficient for reducing breeding costs under both circumstances as land and labour savings resulted from eliminating susceptible individuals. The use of markers for other simply inherited traits in marker-assisted backcrossing and introgression across Andean and Mesoamerican gene pools is suggested. The possibility of using MAS for quantitative traits such as low soil phosphorus adaptation is also discussed as are the advantages and disadvantages of MAS in a breeding programme. For cassava, the use of multiple flanking markers for selection of a dominant gene, CMD2 for cassava mosaic virus (CMV) resistance at CIAT and the International Institute of Tropical Agriculture (IITA) as well as with NARS partners in the United Republic of Tanzania using a participatory plant breeding scheme are reviewed. MAS for the same gene is important during introgression of cassava green mite

  4. Sunflower Hybrid Breeding: From Markers to Genomic Selection.

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    Dimitrijevic, Aleksandra; Horn, Renate

    2017-01-01

    In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi , or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches

  5. Sunflower Hybrid Breeding: From Markers to Genomic Selection

    Science.gov (United States)

    Dimitrijevic, Aleksandra; Horn, Renate

    2018-01-01

    In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches

  6. Sunflower Hybrid Breeding: From Markers to Genomic Selection

    Directory of Open Access Journals (Sweden)

    Aleksandra Dimitrijevic

    2018-01-01

    Full Text Available In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare

  7. Marker-assisted selection in fish and shellfish breeding schemes

    International Nuclear Information System (INIS)

    Martinez, V.

    2007-01-01

    The main goals of breeding programmes for fish and shellfish are to increase the profitability and sustainability of aquaculture. Traditionally, these have been carried out successfully using pedigree information by selecting individuals based on breeding values predicted for traits measured on candidates using an 'animal model'. This methodology assumes that phenotypes are explained by a large number of genes with small effects and random environmental deviations. However, information on individual genes with medium or large effects cannot be used in this manner. In selective breeding programmes using pedigree information, molecular markers have been used primarily for parentage assignment when tagging individual fish is difficult and to avoid causing common environmental effects from rearing families in separate tanks. The use of these techniques in such conventional breeding programmes is discussed in detail. Exploiting the great biological diversity of many fish and shellfish species, different experimental designs may use either chromosomal manipulations or large family sizes to increase the likelihood of finding the loci affecting quantitative traits, the so-called QTL, by screening the segregation of molecular markers. Using information on identified loci in breeding schemes in aquaculture is expected to be cost-effective compared with traditional breeding methods only when the accuracy of predicting breeding values is rather low, e.g. for traits with low heritability such as disease resistance or carcass quality. One of the problems facing aquaculture is that some of the resources required to locate QTL accurately, such as dense linkage maps, are not yet available for the many species. Recently, however, information from expressed sequence tag (EST) databases has been used for developing molecular markers such as microsatellites and single nucleotide polymorphisms (SNPs). Marker-assisted selection (MAS) or genome-wide marker-assisted selection (G-MAS) using

  8. Improving selection of markers in nutrition research: evaluation of the criteria proposed by the ILSI Europe Marker Validation Initiative.

    Science.gov (United States)

    Calder, Philip C; Boobis, Alan; Braun, Deborah; Champ, Claire L; Dye, Louise; Einöther, Suzanne; Greyling, Arno; Matthys, Christophe; Putz, Peter; Wopereis, Suzan; Woodside, Jayne V; Antoine, Jean-Michel

    2017-06-01

    The conduct of high-quality nutrition research requires the selection of appropriate markers as outcomes, for example as indicators of food or nutrient intake, nutritional status, health status or disease risk. Such selection requires detailed knowledge of the markers, and consideration of the factors that may influence their measurement, other than the effects of nutritional change. A framework to guide selection of markers within nutrition research studies would be a valuable tool for researchers. A multidisciplinary Expert Group set out to test criteria designed to aid the evaluation of candidate markers for their usefulness in nutrition research and subsequently to develop a scoring system for markers. The proposed criteria were tested using thirteen markers selected from a broad range of nutrition research fields. The result of this testing was a modified list of criteria and a template for evaluating a potential marker against the criteria. Subsequently, a semi-quantitative system for scoring a marker and an associated template were developed. This system will enable the evaluation and comparison of different candidate markers within the same field of nutrition research in order to identify their relative usefulness. The ranking criteria of proven, strong, medium or low are likely to vary according to research setting, research field and the type of tool used to assess the marker and therefore the considerations for scoring need to be determined in a setting-, field- and tool-specific manner. A database of such markers, their interpretation and range of possible values would be valuable to nutrition researchers.

  9. Marker-assisted selection in wheat: Evolution, not revolution

    International Nuclear Information System (INIS)

    Koebner, R.; Summers, R.

    2007-01-01

    This chapter reviews the uptake of marker-assisted selection (MAS) in wheat in a European context. Although less intense than the scale of its application in maize, reflecting the fact that maize varieties are predominantly F 1 hybrids, the use of MAS in wheat has grown over the last few years. This growth has been encouraged by an increase in the number of amenable target traits, but more significantly by a combination of technological improvements, particularly in the areas of DNA acquisition, laboratory management systems and integration into the breeding cycle, which together have served to reduce the per unit cost of each data point. Microsatellites (simple sequence repeats [SSRs]) are, and will likely remain for some time, the marker of choice because of their flexibility and the knowledge base associated with them. Some current examples are provided of the use of MAS in a major United Kingdom commercial breeding programme. (author)

  10. Marker-assisted selection in sheep and goats

    International Nuclear Information System (INIS)

    Werf, H.J. van der

    2007-01-01

    Sheep and goats are often kept in low input production systems, often at subsistence levels. In such systems, the uptake of effective commercial breeding programmes is limited, let alone the uptake of more advanced technologies such as those needed for marker-assisted selection (MAS). However, effective breeding programmes exist in a number of countries, the largest ones in Australia and New Zealand aiming for genetic improvement of meat and wool characteristics as well as disease resistance and fecundity. Advances have been made in sheep gene mapping with the marker map consisting of more than 1 200 microsatellites, and a virtual genome sequence together with a very dense single nucleotide polymorphism (SNP) map are expected within a year. Significant research efforts into quantitative trait loci (QTL) are under way and a number of commercial sheep gene tests have already become available, mainly for single gene effects but some for muscularity and disease resistance. Gene mapping in goats is much less advanced with mainly some activity in dairy goats. Integration of genotypic information into commercial genetic evaluation and optimal selection strategies is a challenge that deserves more development. (author)

  11. Selective flotation for the removal of radionuclides from contaminated soil

    International Nuclear Information System (INIS)

    Miller, J.D.; Yu, Q.; Lu, Y.Q.

    1995-01-01

    Low-level radioactive contaminated soils (10--500 pci/gm) created by defense-related activities at certain Superfund sites, such as Nevada Test Site (NTS), is a current environmental concern. Many of these contaminated sites may require appropriate cleanup and restoration, which could cost billions of dollars and put tremendous pressure on limited financial resources. Therefore, the development of a selective flotation process to separate such radionuclides from contaminated soils should be considered. In this study, both a pure depleted UO 2 sample and three synthetic UO 2 /soil mixtures were used to evaluate surface chemistry features and to examine the possibility for the flotation of fine UO 2 particles from selected soils. It was intended that this model system would be a reasonable representation of contaminated soils such as those found the Nevada Test Site which are reported to be contaminated by PuO 2 fallout. The effect of reagent schedule, particle size distribution, and surface charge are discussed with respect to the flotation separation of the UO 2 /soil mixtures. It was found that both commercial fatty acids and reagent grade sodium oleate are effective collectors for UO 2 flotation provided the pH is adjusted to the range of pH 8--9. The bench-scale flotation results successfully demonstrated that froth flotation technology can be used to remove UO 2 from such model contaminated soils with appropriate flotation chemistry conditions which depend on the soil characteristics and other pretreatment procedures

  12. Selection of Highly Expressed Gene Variants in Escherichia coli Using Translationally Coupled Antibiotic Selection Markers

    DEFF Research Database (Denmark)

    Rennig, Maja; Daley, Daniel O.; Nørholm, Morten H. H.

    2018-01-01

    Strategies to select highly expressed variants of a protein coding sequence are usually based on trial-and-error approaches, which are time-consuming and expensive. We address this problem using translationally coupled antibiotic resistance markers. The system requires that the target gene can...

  13. Origin of fecal contamination in waters from contrasted areas: stanols as Microbial Source Tracking markers.

    Science.gov (United States)

    Derrien, M; Jardé, E; Gruau, G; Pourcher, A M; Gourmelon, M; Jadas-Hécart, A; Pierson Wickmann, A C

    2012-09-01

    Improving the microbiological quality of coastal and river waters relies on the development of reliable markers that are capable of determining sources of fecal pollution. Recently, a principal component analysis (PCA) method based on six stanol compounds (i.e. 5β-cholestan-3β-ol (coprostanol), 5β-cholestan-3α-ol (epicoprostanol), 24-methyl-5α-cholestan-3β-ol (campestanol), 24-ethyl-5α-cholestan-3β-ol (sitostanol), 24-ethyl-5β-cholestan-3β-ol (24-ethylcoprostanol) and 24-ethyl-5β-cholestan-3α-ol (24-ethylepicoprostanol)) was shown to be suitable for distinguishing between porcine and bovine feces. In this study, we tested if this PCA method, using the above six stanols, could be used as a tool in "Microbial Source Tracking (MST)" methods in water from areas of intensive agriculture where diffuse fecal contamination is often marked by the co-existence of human and animal sources. In particular, well-defined and stable clusters were found in PCA score plots clustering samples of "pure" human, bovine and porcine feces along with runoff and diluted waters in which the source of contamination is known. A good consistency was also observed between the source assignments made by the 6-stanol-based PCA method and the microbial markers for river waters contaminated by fecal matter of unknown origin. More generally, the tests conducted in this study argue for the addition of the PCA method based on six stanols in the MST toolbox to help identify fecal contamination sources. The data presented in this study show that this addition would improve the determination of fecal contamination sources when the contamination levels are low to moderate. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Development of a marker assisted selection program for cacao.

    Science.gov (United States)

    Schnell, R J; Kuhn, D N; Brown, J S; Olano, C T; Phillips-Mora, W; Amores, F M; Motamayor, J C

    2007-12-01

    ABSTRACT Production of cacao in tropical America has been severely affected by fungal pathogens causing diseases known as witches' broom (WB, caused by Moniliophthora perniciosa), frosty pod (FP, caused by M. roreri) and black pod (BP, caused by Phytophthora spp.). BP is pan-tropical and causes losses in all producing areas. WB is found in South America and parts of the Caribbean, while FP is found in Central America and parts of South America. Together, these diseases were responsible for over 700 million US dollars in losses in 2001 (4). Commercial cacao production in West Africa and South Asia are not yet affected by WB and FP, but cacao grown in these regions is susceptible to both. With the goal of providing new disease resistant cultivars the USDA-ARS and Mars, Inc. have developed a marker assisted selection (MAS) program. Quantitative trait loci have been identified for resistance to WB, FP, and BP. The potential usefulness of these markers in identifying resistant individuals has been confirmed in an experimental F(1) family in Ecuador.

  15. Internal radioactive contamination in selected groups of CRNL employees

    International Nuclear Information System (INIS)

    Evans, D.W.S.

    1975-10-01

    This report details the development and execution of a 30 month program designed to characterize the magnitude and distribution of internal radioactive contaminaton amongst selected groups of employees at Chalk River Nuclear Laboratories, using a shadow shield whole-body counter. The results show that the levels of contamination in these employees are very low, and no contaminant was present in amounts exceeding 10% of the maximum permissible body burden, with the exception of a medically administered radionuclide (selenium-75). Details of the time course of some of the body burdens are also furnished. (author)

  16. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood

    DEFF Research Database (Denmark)

    van Tilborg, Angela A G; Kompier, Lucie C; Lurkin, Irene

    2012-01-01

    . Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers...... with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined...

  17. The role of molecular markers and marker assisted selection in breeding for organic agriculture

    DEFF Research Database (Denmark)

    Lammerts van Bueren, E.T.; Backes, G.; de Vriend, H.

    2010-01-01

    markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture...... was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder’s perspectives and perspectives seen from the organic sector’s standpoint. Clear strengths were...

  18. Considerations of selection suggested for internal contamination monitoring in Cuba

    International Nuclear Information System (INIS)

    Cruz S, R.; Lopez B, G.; Placeres V, C.; Arado L, J.; Jova S, L.

    1996-01-01

    A method for calculating effective risk of radionuclide intake and hypothetical annual dose that will receive a person who works with unsealed sources is proposed. Calculated committed dose equivalent and metabolic characteristic of radionuclides permit to select the type of monitoring 'in vivo' and/or 'in vitro'. The method was applied to 396 workers from 28 institutions, where 20 radionuclides in 124 different products for 266 applications are used. From this study 62% of the workers had to be monitored for internal contamination, meanly by 'in vitro' monitoring. In practices of Nuclear Medicine and other medical uses 75% of the workers had to be monitored. These results permitted to corroborate the criteria for internal contamination monitoring program carried out by Center for Hygiene and Radiation Protection and permitted to identify needs for control of radionuclides intakes. (authors).5 refs., 3 figs

  19. Development of DArT-based PCR markers for selecting drought-tolerant spring barley.

    Science.gov (United States)

    Fiust, Anna; Rapacz, Marcin; Wójcik-Jagła, Magdalena; Tyrka, Mirosław

    2015-08-01

    The tolerance of spring barley (Hordeum vulgare L.) cultivars to spring drought is an important agronomic trait affecting crop yield and quality in Poland. Therefore, breeders require new molecular markers to select plants with lower spring drought susceptibility. With the advent of genomic selection technology, simple molecular tools may still be applicable to screen material for markers of the most important traits and in-depth genome scanning. In previous studies, diversity arrays technology (DArT)-based genetic maps were constructed for F2 populations of Polish fodder and malt barley elite breeding lines, and 15 and 18 quantitative trait loci (QTLs) related to spring drought tolerance were identified, respectively. In this paper, we show the results of a conversion of 30 DArT markers corresponding to 11 QTLs into simple sequence repeat (SSR) and sequence tagged site (STS) markers. Twenty-two polymorphic markers were obtained, including 13 DArT-based SSRs. Additionally, 31 SSR markers, located in close proximity to the DArT markers, were selected from the GrainGenes database and tested. Further analyses of 24 advanced breeding lines with different drought tolerances confirmed that five out of the 30 converted markers, as well as three out of the 31 additional SSR markers, were effective in marker-assisted selection for drought tolerance. The possible function of clones related to these markers in drought tolerance is discussed.

  20. Accuracy of marker-assisted selection with auxiliary traits

    Indian Academy of Sciences (India)

    Unknown

    Genetic information on molecular markers is increasingly being used in plant and ..... index gets enhanced over RLT. ..... indicated in LT, the sampling errors in the parameter es- .... problem can only be handled by simulation studies of the.

  1. Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality.

    Science.gov (United States)

    Li, Li; Tacke, Eckhard; Hofferbert, Hans-Reinhardt; Lübeck, Jens; Strahwald, Josef; Draffehn, Astrid M; Walkemeier, Birgit; Gebhardt, Christiane

    2013-04-01

    Tuber yield, starch content, starch yield and chip color are complex traits that are important for industrial uses and food processing of potato. Chip color depends on the quantity of reducing sugars glucose and fructose in the tubers, which are generated by starch degradation. Reducing sugars accumulate when tubers are stored at low temperatures. Early and efficient selection of cultivars with superior yield, starch yield and chip color is hampered by the fact that reliable phenotypic selection requires multiple year and location trials. Application of DNA-based markers early in the breeding cycle, which are diagnostic for superior alleles of genes that control natural variation of tuber quality, will reduce the number of clones to be evaluated in field trials. Association mapping using genes functional in carbohydrate metabolism as markers has discovered alleles of invertases and starch phosphorylases that are associated with tuber quality traits. Here, we report on new DNA variants at loci encoding ADP-glucose pyrophosphorylase and the invertase Pain-1, which are associated with positive or negative effect with chip color, tuber starch content and starch yield. Marker-assisted selection (MAS) and marker validation were performed in tetraploid breeding populations, using various combinations of 11 allele-specific markers associated with tuber quality traits. To facilitate MAS, user-friendly PCR assays were developed for specific candidate gene alleles. In a multi-parental population of advanced breeding clones, genotypes were selected for having different combinations of five positive and the corresponding negative marker alleles. Genotypes combining five positive marker alleles performed on average better than genotypes with four negative alleles and one positive allele. When tested individually, seven of eight markers showed an effect on at least one quality trait. The direction of effect was as expected. Combinations of two to three marker alleles were

  2. Pearl millet transformation system using the positive selectable marker gene phosphomannose isomerase

    CSIR Research Space (South Africa)

    O'Kennedy, MM

    2004-04-01

    Full Text Available of the transgene. Similar to results obtained from previous studies with maize and wheat, the manA gene was shown to be a superior selectable marker gene for improving transformation efficiencies when compared to antibiotic or herbicide selectable marker genes....

  3. Criteria for selection and application of molecular markers for clinical studies of osteoarthritis.

    Science.gov (United States)

    Otterness, I G; Swindell, A C

    2003-03-01

    To develop criteria for the selection and application of molecular markers for the study of osteoarthritis (OA). Statistical criteria for marker selection for OA are developed. After studying more than 20 different molecular markers for monitoring OA, procedures for choosing markers for clinical studies have been developed. For a particular study, the process starts with the markers showing 'face-validity' for monitoring OA. They are next required to successfully distinguish OA patients from controls. This necessitates definition of the distribution of marker values in OA patients and controls. So far, they have been consistently log-normal. The difference (Delta) in marker values between OA and controls defines the opportunity for marker improvement. The between-visit standard deviation (S) in patients puts limits on the detection of marker changes. The two variables can be combined to estimate the practicality of a marker using a modified power analysis. The number of patients (N*) required to observe a 50% improvement with an alpha level of P=0.05 and with 80% certainty is estimated as 50(S/Delta)(2). N*, S and Delta should be used to characterize and compare markers. Marker efficiency can be refined by regressing on secondary variables, such as age, sex, BMI, severity, etc. Finally, the use of two or more markers may be required to improve marker prediction of clinical outcome. Correlated markers can be used to reinforce conclusions by essentially adding replicative data. Independent, complementary markers can be used to develop associations with clinical parameters, and perhaps diagnose and monitor disease status, activities that so far have not been possible with single markers.

  4. Tagging of blast resistance gene(s) to DNA markers and marker-assisted selection (MAS) in rice improvement

    International Nuclear Information System (INIS)

    Zhuang, J.Y.; Lu, J.; Qian, H.R.; Lin, H.X.; Zheng, K.L.

    1998-01-01

    This paper reports progress made on the tagging of blast resistance gene(s) to DNA markers and on the initiation of marker-assisted selection (MAS) for blast resistance in rice improvement. A pair of near isogenic lines, K8OR and K79S, were developed using a Chinese landrace Hong-jiao-zhan as the resistance donor. Ten putatively positive markers were identified by screening 177 mapped DNA markers. Using the F 2 population of 143 plants and the derived F 3 lines, three Restriction Fragment Length Polymorphism (RFLP) markers (RG81, RG869 and RZ397) on chromosome 12 of rice were identified to be closely linked to the blast resistance gene Pi-12(t). The genetic distance between Pi-12(t) and the closest marker RG869 was 5.1 cM. By employing the bulk segregant analysis (BSA) procedure, six of 199 arbitrary primers were found to produce positive Randomly Amplified Polymorphic DNA (RAPD) bands. Tight linkage between Pi-12(t) and three RAPD bands, each from a different primer, was confirmed after amplification of DNA of all F 2 individuals. Two fragments were cloned and sequenced, and two sequence characterised amplified re-ion (SCAR) markers were established. In two other F 3 populations, Xian-feng I/Tetep and Xian-feng, 1/Hong-jiao-zhan, the blast resistance was found to be controlled by interactions of two or more genes. One resistance gene was located in the vicinity of RG81 in both populations. Work to identify other gene(s) is currently under way. Marker assisted selection for blast resistance was initiated. Crosses were made between elite varieties and blast resistance donors to develop populations for DNA marker-assisted selection of blast resistance. In addition, 48 varieties widely used in current rice breeding programs were provided by rice breeders. DNA marker-based polymorphism among, these varieties and resistance donors were analysed to produce a database for future MAS program. (author)

  5. Biological markers in animals can provide information on exposure and bioavailability of environmental contaminants

    International Nuclear Information System (INIS)

    Shugart, L.R.; Adams, S.M.; Jimenez, B.D.; Talmage, S.S.; McCarthy, J.F.

    1987-01-01

    Epidemiologic studies of agents present in the environment seek to identify the extent to which they contribute to the causation of a specific toxic, clinical, or pathological endpoint. The multifactorial nature of disease etiology, long latency periods and the complexity of exposure, all contribute to the difficulty of establishing associations and casual relationships between a specific exposure and an adverse outcome. These barriers to studies of exposures and subsequent risk assessment cannot generally be changed. However, the appropriate use of biological markers in animal species living in a contaminated habitat can provide a measure of potential damage from that exposure and, in some instances, act as a surrogate for human environmental exposures. Quantitative predictivity of the effect of exposure to environmental pollutants is being approached by employing an appropriate array of biological end points. 34 refs., 1 fig., 6 tabs

  6. Identification of the origin of faecal contamination in estuarine oysters using Bacteroidales and F-specific RNA bacteriophage markers.

    Science.gov (United States)

    Mieszkin, S; Caprais, M P; Le Mennec, C; Le Goff, M; Edge, T A; Gourmelon, M

    2013-09-01

    The aim of this study was to identify the origin of faecal pollution impacting the Elorn estuary (Brittany, France) by applying microbial source tracking (MST) markers in both oysters and estuarine waters. The MST markers used were as follows: (i) human-, ruminant- and pig-associated Bacteroidales markers by real-time PCR and (ii) human genogroup II and animal genogroup I of F-specific RNA bacteriophages (FRNAPH) by culture/genotyping and by direct real-time reverse-transcriptase PCR. The higher occurrence of the human genogroup II of F-specific RNA bacteriophages using a culture/genotyping method, and human-associated Bacteroidales marker by real-time PCR, allowed the identification of human faecal contamination as the predominant source of contamination in oysters (total of 18 oyster batches tested) and waters (total of 24 water samples tested). The importance of using the intravalvular liquids instead of digestive tissues, when applying host-associated Bacteroidales markers in oysters, was also revealed. This study has shown that the application of a MST toolbox of diverse bacterial and viral methods can provide multiple lines of evidence to identify the predominant source of faecal contamination in shellfish from an estuarine environment. Application of this MST toolbox is a useful approach to understand the origin of faecal contamination in shellfish harvesting areas in an estuarine setting. © 2013 The Society for Applied Microbiology.

  7. Guttation fluid as a physiological marker for selection of nitrogen ...

    African Journals Online (AJOL)

    Oryza sativa L.) genotypes. Hukum Singh, Amit Verma, Alok Shukla. Abstract. A field experiment was conducted during the rainy season of 2008 and 2009 to use guttation fluid as a physiological marker for the screening of more nitrogen efficient ...

  8. Two Catalysts for Selective Oxidation of Contaminant Gases

    Science.gov (United States)

    Wright, John D.

    2011-01-01

    Two catalysts for the selective oxidation of trace amounts of contaminant gases in air have been developed for use aboard the International Space Station. These catalysts might also be useful for reducing concentrations of fumes in terrestrial industrial facilities especially facilities that use halocarbons as solvents, refrigerant liquids, and foaming agents, as well as facilities that generate or utilize ammonia. The first catalyst is of the supported-precious-metal type. This catalyst is highly active for the oxidation of halocarbons, hydrocarbons, and oxygenates at low concentrations in air. This catalyst is more active for the oxidation of hydrocarbons and halocarbons than are competing catalysts developed in recent years. This catalyst completely converts these airborne contaminant gases to carbon dioxide, water, and mineral acids that can be easily removed from the air, and does not make any chlorine gas in the process. The catalyst is thermally stable and is not poisoned by chlorine or fluorine atoms produced on its surface during the destruction of a halocarbon. In addition, the catalyst can selectively oxidize ammonia to nitrogen at a temperature between 200 and 260 C, without making nitrogen oxides, which are toxic. The temperature of 260 C is higher than the operational temperature of any other precious-metal catalyst that can selectively oxidize ammonia. The purpose of the platinum in this catalyst is to oxidize hydrocarbons and to ensure that the oxidation of halocarbons goes to completion. However, the platinum exhibits little or no activity for initiating the destruction of halocarbons. Instead, the attack on the halocarbons is initiated by the support. The support also provides a high surface area for exposure of the platinum. Moreover, the support resists deactivation or destruction by halogens released during the destruction of halocarbons. The second catalyst is of the supported- metal-oxide type. This catalyst can selectively oxidize ammonia to

  9. Markers

    Science.gov (United States)

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  10. Marker-assisted selection for improving quantitative traits of forage crops

    International Nuclear Information System (INIS)

    Dolstra, O.; Denneboom, C.; Vos, Ab L.F. de; Loo, E.N. van

    2007-01-01

    This chapter provides an example of using marker-assisted selection (MAS) for breeding perennial ryegrass (Lolium perenne), a pasture species. A mapping study had shown the presence of quantitative trait loci (QTL) for seven component traits of nitrogen use efficiency (NUE). The NUE-related QTL clustered in five chromosomal regions. These QTL were validated through divergent marker selection in an F 2 population. The criterion used for plant selection was a summation index based on the number of positive QTL alleles. The evaluation studies showed a strong indirect response of marker selection on NUE. Marker selection using a summation index such as applied here proved to be very effective for difficult and complex quantitative traits such as NUE. The strategy is easily applicable in outbreeding crops to raise the frequency of several desirable alleles simultaneously. (author)

  11. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity.

    Directory of Open Access Journals (Sweden)

    Nicolas Heslot

    Full Text Available Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L. genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

  12. Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

    Science.gov (United States)

    Heslot, Nicolas; Rutkoski, Jessica; Poland, Jesse; Jannink, Jean-Luc; Sorrells, Mark E.

    2013-01-01

    Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis. PMID:24040295

  13. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.

    Directory of Open Access Journals (Sweden)

    Angela A G van Tilborg

    Full Text Available Microsatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in the genome. Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined. LOH of the markers was observed in 59/104 tumor DNAs. We then determined the sensitivity of the marker panel for detection of recurrent bladder cancer by assaying 102 urine samples of these patients. Sensitivity was 63% when patients were stratified for LOH in their primary tumors. We demonstrate that up-front selection of microsatellite markers obliterates the need for a corresponding blood sample. For diagnosis of bladder cancer recurrences in urine this significantly reduces costs. Moreover, this approach facilitates retrospective analysis of archival tumor samples for allelic imbalance.

  14. Selection enhanced estimates of marker effects on means and variances of beef tenderness

    Science.gov (United States)

    Genetic marker associations from surveys of industry cattle populations have low frequencies of rare homozygous animals. Selection for calpain (CAPN1) and calpastatin (CAST) genetic markers was replicated in two cattle populations (Angus and MARC III) at the U.S. Meat Animal Research Center. These...

  15. Marker-assisted-selection (MAS): A fast track to increase genetic ...

    African Journals Online (AJOL)

    Mapping and tagging of agriculturally important genes have been greatly facilitated by an array of molecular markers in crop plants. Marker-assisted selection (MAS) is gaining considerable importance as it would improve the efficiency of plant breeding through precise transfer of genomic regions of interest (foreground ...

  16. Recent Advances in the Use of Chemical Markers for  Tracing Wastewater Contamination in Aquatic  Environment: A Review

    Directory of Open Access Journals (Sweden)

    Fang Yee Lim

    2017-02-01

    Full Text Available There has been increasing research focus on the detection and occurrence of wastewater contamination in aquatic environment. Wastewater treatment plants receive effluents containing various chemical pollutants. These chemicals may not be fully removed during treatment and could potentially enter the receiving water bodies. Detection of these chemical pollutants and source identification could be a challenging research task due to the diversified chemical and functional groups, concentration levels and fate and transportation mechanisms of these pollutants in the environment. Chemical markers such as pharmaceuticals and personal care products, artificial sweeteners, fluorescent whitening agents, sterols and stanols, and nitrate and nitrogen isotopics have been widely used by most research as markers. These markers served as indicators of wastewater contamination to the receiving bodies due to their frequent usage, resistance to biodegradability and, more importantly, anthropogenic origin. These markers are commonly used in combination to identify the contaminant source of different origins. This article discusses the main chemical markers that are used to identify wastewater contamination in receiving bodies, the current trends, and approach to select suitable chemical markers.

  17. A selectable and excisable marker system for the rapid creation of recombinant poxviruses.

    Directory of Open Access Journals (Sweden)

    Julia L Rintoul

    Full Text Available Genetic manipulation of poxvirus genomes through attenuation, or insertion of therapeutic genes has led to a number of vector candidates for the treatment of a variety of human diseases. The development of recombinant poxviruses often involves the genomic insertion of a selectable marker for purification and selection purposes. The use of marker genes however inevitably results in a vector that contains unwanted genetic information of no therapeutic value.Here we describe an improved strategy that allows for the creation of marker-free recombinant poxviruses of any species. The Selectable and Excisable Marker (SEM system incorporates a unique fusion marker gene for the efficient selection of poxvirus recombinants and the Cre/loxP system to facilitate the subsequent removal of the marker. We have defined and characterized this new methodological tool by insertion of a foreign gene into vaccinia virus, with the subsequent removal of the selectable marker. We then analyzed the importance of loxP orientation during Cre recombination, and show that the SEM system can be used to introduce site-specific deletions or inversions into the viral genome. Finally, we demonstrate that the SEM strategy is amenable to other poxviruses, as demonstrated here with the creation of an ectromelia virus recombinant lacking the EVM002 gene.The system described here thus provides a faster, simpler and more efficient means to create clinic-ready recombinant poxviruses for therapeutic gene therapy applications.

  18. Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

    Science.gov (United States)

    Johnston, Christopher; Byappanahalli, Muruleedhara N.; Gibson, Jacqueline MacDonald; Ufnar, Jennifer A.; Whitman, Richard L.; Stewart, Jill R.

    2013-01-01

    Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

  19. Targeting the Sources of Fecal Contamination using Dog-, Human-, and Ruminant- Specific Markers in the Lake Herrick Watershed, Georgia.

    Science.gov (United States)

    Saintil, T.; Radcliffe, D. E.; Rasmussen, T. C.; Habteselassie, M.; Sowah, R.; Kannan, A.

    2016-12-01

    The Lake Herrick Watershed is about 1.5 km2 and covers portions of the University of Georgia's East campus, the Oconee Forest, residential and commercial landuse. Lake Herrick, a recreational site on the University of Georgia campus, was closed in 2002 due to fecal contamination. Subsequent monitoring confirmed persistent contamination, which led to a permanent closure to swimming, boating, and fishing. While fecal coliform abundance is a standard metric for determining human health risks, Geldreich (1970) showed that fecal abundance does not necessarily correlate with the presence of pathogens. Nor does it identify pollution sources, which are needed to mitigate health risks. Two inflow tributaries and the outlet stream were monitored for discharge, fecal coliform, forms of nitrogen and phosphorus and other water-quality data to quantify lake influent and effluent bacteria loads. Fecal sources were identified using the human HF183 genetic marker (Seurinck et al., 2005), the ruminant BacR marker (Reischer et al., 2006), and the dog mitochondrial DNA (mtDNA) marker (Tambalo et al., 2012). Preliminary results confirm high concentrations of E. coli and Enterococci, above the State's limit of 124 MPN/100 mL, in both baseflows and stormflows. The findings also suggest that the E. coli and Enterococci loads from the inlet tributaries are on average higher compared to the bacteria loads coming out of the outlet stream. The human markers were detectable at all three sites but most of the samples were not quantifiable. The ruminant markers were quantifiable at both inlets but no ruminant markers were found at the outlet. The dog markers were detectable but not quantifiable at both inlets and no dog markers were detected at the outlet. Statistical analyses will be used to establish relationships between the nutrients data, the fecal concentrations, and the gene-specific markers.

  20. Geochemical markers of soil anthropogenic contaminants in polar scientific stations nearby (Antarctica, King George Island).

    Science.gov (United States)

    Prus, Wojciech; Fabiańska, Monika J; Łabno, Radosław

    2015-06-15

    The organic contamination of Antarctic soils and terrestrial sediments from nearby of five polar scientific stations on King George Island (Antarctica) was investigated. Gas chromatography-mass spectrometry (GC-MS) was applied to find composition of dichloromethane extracts of soil and terrestrial sediments. The presence of geochemical markers, such as n-alkanes, steranes, pentacyclic triterpenoids, and alkyl PAHs, their distribution types, and values of their ratios indicates the predominating source of organic fossil fuels and products of their refining rather than from the natural Antarctic environment. Fossil fuel-originated compounds well survived in conditions of Antarctic climate over long times thus enabling to characterize geochemical features of source fossil fuel identified as petroleum expelled from kerogen II of algal/bacterial origins deposited in sub-oxic conditions and being in the middle of catagenesis. Both microbial activity and water leaching play an important role in degradation of terrestrial oil spills in the Antarctica climate, and petroleum alteration occurs lowly over long periods of time. Synthetic anthropogenic compounds found in terrestrial Antarctica sediments included diisopropylnaphthalenes, products of their sulfonates degradation in paper combustion, and organophosporus compounds used as retardants and plasticizers. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Integrated site-specific quantification of faecal bacteria and detection of DNA markers in faecal contamination source tracking as a microbial risk tracking tool in urban Lake ecosystems

    Science.gov (United States)

    Donde, Oscar Omondi; Tian, Cuicui; Xiao, Bangding

    2017-11-01

    The presence of feacal-derived pathogens in water is responsible for several infectious diseases and deaths worldwide. As a solution, sources of fecal pollution in waters must be accurately assessed, properly determined and strictly controlled. However, the exercise has remained challenging due to the existing overlapping characteristics by different members of faecal coliform bacteria and the inadequacy of information pertaining to the contribution of seasonality and weather condition on tracking the possible sources of pollution. There are continued efforts to improve the Faecal Contamination Source Tracking (FCST) techniques such as Microbial Source Tracking (MST). This study aimed to make contribution to MST by evaluating the efficacy of combining site specific quantification of faecal contamination indicator bacteria and detection of DNA markers while accounting for seasonality and weather conditions' effects in tracking the major sources of faecal contamination in a freshwater system (Donghu Lake, China). The results showed that the use of cyd gene in addition to lacZ and uidA genes differentiates E. coli from other closely related faecal bacteria. The use of selective media increases the pollution source tracking accuracy. BSA addition boosts PCR detection and increases FCST efficiency. Seasonality and weather variability also influence the detection limit for DNA markers.

  2. Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea Using QTL-seq Reveals Markers for Marker-Assisted Selection

    Directory of Open Access Journals (Sweden)

    Josh Clevenger

    2018-02-01

    Full Text Available Late leaf spot (LLS; Cercosporidium personatum is a major fungal disease of cultivated peanut (Arachis hypogaea. A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools.Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

  3. Engineering more stable, selectable marker-free autoluminescent mycobacteria by one step.

    Science.gov (United States)

    Yang, Feng; Njire, Moses M; Liu, Jia; Wu, Tian; Wang, Bangxing; Liu, Tianzhou; Cao, Yuanyuan; Liu, Zhiyong; Wan, Junting; Tu, Zhengchao; Tan, Yaoju; Tan, Shouyong; Zhang, Tianyu

    2015-01-01

    In our previous study, we demonstrated that the use of the autoluminescent Mycobacterium tuberculosis as a reporter strain had the potential to drastically reduce the time, effort, animals and costs consumed in evaluation of the activities of drugs and vaccines in live mice. However, the strains were relatively unstable and lost reporter with time without selection. The kanamycin selection marker used wasn't the best choice as it provides resistance to amino glycosides which are an important class of second line drugs used in tuberculosis treatment. In addition, the marker could limit utility of the strains for screening of new potential drugs or evaluating drug combinations for tuberculosis treatment. Limited selection marker genes for mycobacterial genetic manipulation is a major drawback for such a marker-containing strain in many research fields. Therefore, selectable marker-free, more stable autoluminescent mycobacteria are highly needed. After trying several strategies, we created such mycobacterial strains successfully by using an integrative vector and removing both the resistance maker and integrase genes by Xer site-specific recombination in one step. The corresponding plasmid vectors developed in this study could be very convenient in constructing other selectable marker-free, more stable reporter mycobacteria with diverse applications.

  4. Engineering more stable, selectable marker-free autoluminescent mycobacteria by one step.

    Directory of Open Access Journals (Sweden)

    Feng Yang

    Full Text Available In our previous study, we demonstrated that the use of the autoluminescent Mycobacterium tuberculosis as a reporter strain had the potential to drastically reduce the time, effort, animals and costs consumed in evaluation of the activities of drugs and vaccines in live mice. However, the strains were relatively unstable and lost reporter with time without selection. The kanamycin selection marker used wasn't the best choice as it provides resistance to amino glycosides which are an important class of second line drugs used in tuberculosis treatment. In addition, the marker could limit utility of the strains for screening of new potential drugs or evaluating drug combinations for tuberculosis treatment. Limited selection marker genes for mycobacterial genetic manipulation is a major drawback for such a marker-containing strain in many research fields. Therefore, selectable marker-free, more stable autoluminescent mycobacteria are highly needed. After trying several strategies, we created such mycobacterial strains successfully by using an integrative vector and removing both the resistance maker and integrase genes by Xer site-specific recombination in one step. The corresponding plasmid vectors developed in this study could be very convenient in constructing other selectable marker-free, more stable reporter mycobacteria with diverse applications.

  5. Comparing the predictive abilities of phenotypic and marker-assisted selection methods in a biparental lettuce population

    Science.gov (United States)

    Breeding and selection for the traits with polygenic inheritance is a challenging task that can be done by phenotypic selection, by marker-assisted selection or by genome wide selection. We tested predictive ability of four selection models in a biparental population genotyped with 95 SNP markers an...

  6. Potential of marker-assisted selection for Tobacco mosaic ...

    African Journals Online (AJOL)

    Tobacco mosaic tobamovirus (TMV) is one of the most destructive virus threatening worldwide tobacco production. Use of host resistance is the best method of control. The N-gene was introgressed into tobacco from Nicotiana glutinosa to confer hypersensitive resistance to TMV. Phenotypic selection of TMV resistant ...

  7. Markers of anthropogenic contamination: A validated method for quantification of pharmaceuticals, illicit drug metabolites, perfluorinated compounds, and plasticisers in sewage treatment effluent and rain runoff.

    Science.gov (United States)

    Wilkinson, John L; Swinden, Julian; Hooda, Peter S; Barker, James; Barton, Stephen

    2016-09-01

    An effective, specific and accurate method is presented for the quantification of 13 markers of anthropogenic contaminants in water using solid phase extraction (SPE) followed by high performance liquid chromatography (HPLC) tandem mass spectrometry (MS/MS). Validation was conducted according to the International Conference on Harmonisation (ICH) guidelines. Method recoveries ranged from 77 to 114% and limits of quantification between 0.75 and 4.91 ng/L. A study was undertaken to quantify the concentrations and loadings of the selected contaminants in 6 sewage treatment works (STW) effluent discharges as well as concentrations in 5 rain-driven street runoffs and field drainages. Detection frequencies in STW effluent ranged from 25% (ethinylestradiol) to 100% (benzoylecgonine, bisphenol-A (BPA), bisphenol-S (BPS) and diclofenac). Average concentrations of detected compounds in STW effluents ranged from 3.62 ng/L (ethinylestradiol) to 210 ng/L (BPA). Levels of perfluorinated compounds (PFCs) perfluorooctanoic acid (PFOA) and perfluorononanoic acid (PFNA) as well as the plasticiser BPA were found in street runoff at maximum levels of 1160 ng/L, 647 ng/L and 2405 ng/L respectively (8.52, 3.09 and 2.7 times more concentrated than maximum levels in STW effluents respectively). Rain-driven street runoff may have an effect on levels of PFCs and plasticisers in receiving rivers and should be further investigated. Together, this method with the 13 selected contaminants enables the quantification of various markers of anthropogenic pollutants: inter alia pharmaceuticals, illicit drugs and their metabolites from humans and improper disposal of drugs, while the plasticisers and perfluorinated compounds may also indicate contamination from industrial and transport activity (street runoff). Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Sustained and selective attention deficits as vulnerability markers to psychosis.

    Science.gov (United States)

    Mulet, B; Valero, J; Gutiérrez-Zotes, A; Montserrat, C; Cortés, M J; Jariod, M; Martorell, L; Vilella, E; Labad, A

    2007-04-01

    The first descriptions of schizophrenia emphasized attention problems patients with schizophrenia have but recent results evidence that other psychotic disorders share them. We compared the performance in sustained and selective attention between psychotic patients (P), their healthy first degree relatives (R) and healthy volunteers (C) to prove whether these alterations could be an endophenotype of vulnerability to psychosis. We also compared the performance of schizophrenic patients (SZP) and that of patients with other functional psychoses (OP) in order to prove whether these alterations are specific of any psychotic disorder. Seventy-six P, 70 R and 39 C were included in the study. A selective attention index, comprising TMT A and B and Stroop Test, and a sustained attention index comprising the Continuous Performance Test were calculated. We conducted an univariant general linear model to compare three group performances in these indexes, with age, sex and years of education as a covariables. We found significant differences between the indexes when we compared P, R and C. No differences in performance were found between SZP and OP. Our data showed that sustained and selective attention alterations could be a vulnerability factor to psychotic disorders in general, but they were not specific of schizophrenia.

  9. Assessment Of Depleted Uranium Contamination In Selective IRAQI Soils

    International Nuclear Information System (INIS)

    Mohammed, A.A.; Hussien, A.Sh.M.; Tawfiq, N.F.

    2008-01-01

    The aim of this research was to measure the radiation exposure rates in three selected Locations in southren part of Iraq (two in Nassireya, and one in Amara) resulted from the existence of depleted uranium in soil and metal pieces have been taken from destroyed tank and study mathmatically the concentration of Depleted Uranium by its dispersion from soil surface by winds and rains from 2003 to 2007. The exposure rates were measured using inspector device, while depleted uranium concentration in soil samples and tank's matal pieces were detected with Solid State Nuclear Track Detectors(SSNTDs). The wind and rain effects were considered in the calculation of dispersion effect on depleted uranium concentration in soil, where the wind effect were calculated with respect to the sites nature and soil conditions, and rain effect with respect to dispersive-convective equation for radionuclide in soil. The results obtained for the exposure rates were high near the penetrated surfac, moderate and low in soil and metal pices. The Depleted Uranium concentration in soil and metal pieces have the highest value in Nassireya. The results from dispersion calculation (wind & rain) showed that the depleted uranium concentration in 2008 will be less than the danger level and in allowable contamination range

  10. Concentrations of selected contaminants in cabin air of airbus aircrafts.

    Science.gov (United States)

    Dechow, M; Sohn, H; Steinhanses, J

    1997-07-01

    The concentrations of selected air quality parameters in aircraft cabins were investigated including particle numbers in cabin air compared to fresh air and recirculation air, the microbiological contamination and the concentration of volatile organic compounds (VOC). The Airbus types A310 of Swissair and A340 of Lufthansa were used for measurements. The particles were found to be mainly emitted by the passengers, especially by smokers. Depending on recirculation filter efficiency the recirculation air contained a lower or equal amount of particles compared to the fresh air, whereas the amount of bacteria exceeded reported concentrations within other indoor spaces. The detected species were mainly non-pathogenic, with droplet infection over short distances identified as the only health risk. The concentration of volatile organic compounds (VOC) were well below threshold values. Ethanol was identified as the compound with the highest amount in cabin air. Further organics were emitted by the passengers--as metabolic products or by smoking--and on ground as engine exhaust (bad airport air quality). Cleaning agents may be the source of further compounds.

  11. Selection of chemical markers for the quality control of medicinal plants of the genus Cecropia.

    Science.gov (United States)

    Rivera-Mondragón, Andrés; Ortíz, Orlando O; Bijttebier, Sebastiaan; Vlietinck, Arnold; Apers, Sandra; Pieters, Luc; Caballero-George, Catherina

    2017-12-01

    Several Cecropia (Cecropiaceae) species are traditionally used in Latin America for the treatment of a variety of diseases including diabetes, arterial hypertension, asthma, bronchitis, anxiety, and inflammation. At present, a number of commercial products based on these plants have been introduced into the market with very little information on methods for guaranteeing their quality and safety. This work proposes potential chemical markers for the quality control of the raw materials of Cecropia obtusifolia Bertol., Cecropia peltata L., Cecropia glaziovii Snethl., Cecropia pachystachya Trécul, and Cecropia hololeuca Miq. The Herbal Chemical Marker Ranking System (Herb MaRS) developed by the National Institute of Complementary Medicine (NICM) at the University of Western Sydney was used for selecting chemical markers for the quality control of selected medicinal species of Cecropia. This review covers the period from 1982 to 2016. Chlorogenic acid, flavonoidal glycosides (orientin, isoorientin, vitexin, isovitexin, and rutin), catechin, epicatechin, procyanidins (B2, B5, and C1), steroids (β-sitosterol), and triterpenoids (α-amyrin, pomolic, tormentic and ursolic acids) were selected as chemical markers for the quality control of the leaves. It is necessary to establish comprehensive standards for guaranteeing quality, safety and efficacy of herbal drugs. The selection of adequate chemical markers for quality control purposes requires a good knowledge about the chemical composition of medicinal plants and their associated biological properties. To the best of our knowledge this review article is the first to address the identification and quantitative determination of the chemical markers for the genus Cecropia.

  12. Marker Assisted Selection can Reduce True as well as Pedigree Estimated Inbreeding

    DEFF Research Database (Denmark)

    Pedersen, L D; Sørensen, A C; Berg, P

    2009-01-01

    This study investigated whether selection using genotype information reduced the rate and level of true inbreeding, that is, identity by descent, at a selectively neutral locus as well as a locus under selection compared with traditional BLUP selection. In addition, the founder representation...... each of 40 herds. Selection was performed using BLUP, marker-assisted, or gene-assisted selection for a trait with low heritability (h2 = 0.04) only expressed in females, mimicking a health trait. The simulated genome consisted of 2 chromosomes. One biallelic quantitative trait loci (QTL......) with an initial frequency of the favorable allele of 0.1, and initially explaining 25% of the genetic variance as well as 4 markers were simulated in linkage disequilibrium, all positioned at chromosome 1. Chromosome 2 was selectively neutral, and consisted of a single neutral locus. The results showed...

  13. Strategies, limitations and opportunities for marker-assisted selection in livestock

    International Nuclear Information System (INIS)

    Dekkers, J.C.M.; Werf, H.J. van der

    2007-01-01

    This chapter reviews the principles, opportunities and limitations for detection of quantitative trait loci (QTL) in livestock and for their use in genetic improvement programmes. Alternate strategies for QTL detection are discussed, as are methods for inclusion of marker and QTL information in genetic evaluation. Practical issues regarding implementation of marker-assisted selection (MAS) for selection in breed crosses and for selection within breeds are described, along with likely routes towards achieving that goal. Opportunities and challenges are also discussed for the use of molecular information for genetic improvement of livestock in developing countries. (author)

  14. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle

    Science.gov (United States)

    Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

  15. Molecular marker-assisted selection for resistance to pathogens in tomato

    International Nuclear Information System (INIS)

    Barone, A.; Frusciante, L.

    2007-01-01

    Since the 1980s, the use of molecular markers has been suggested to improve the efficiency of releasing resistant varieties, thus overcoming difficulties met with classical breeding. For tomato, a high-density molecular map is available in which more than 40 resistance genes are localized. Markers linked to these genes can be used to speed up gene transfer and pyramiding. Suitable PCR markers targeting resistance genes were constructed directly on the sequences of resistance genes or on restriction fragment length polymorphisms (RFLPs) tightly linked to them, and used to select resistant genotypes in backcross schemes. In some cases, the BC 5 generation was reached, and genotypes that cumulated two homozygous resistant genes were also obtained. These results supported the feasibility of using marker-assisted selection (MAS) in tomato and reinforcing the potential of this approach for other genes, which is today also driven by the development of new techniques and increasing knowledge about the tomato genome. (author)

  16. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  17. Height, selected genetic markers and prostate cancer risk

    DEFF Research Database (Denmark)

    Lophatananon, Artitaya; Stewart-Brown, Sarah; Kote-Jarai, Zsofia

    2017-01-01

    Background:Evidence on height and prostate cancer risk is mixed, however, recent studies with large data sets support a possible role for its association with the risk of aggressive prostate cancer.Methods:We analysed data from the PRACTICAL consortium consisting of 6207 prostate cancer cases...... and 6016 controls and a subset of high grade cases (2480 cases). We explored height, polymorphisms in genes related to growth processes as main effects and their possible interactions.Results:The results suggest that height is associated with high-grade prostate cancer risk. Men with height >180 cm...... are at a 22% increased risk as compared to men with height prostate cancer risk. The aggregate scores of the selected variants identified a significantly increased risk of overall prostate cancer...

  18. Marker-assisted selection of Fusarium wilt-resistant and gynoecious melon (Cucumis melo L.).

    Science.gov (United States)

    Gao, P; Liu, S; Zhu, Q L; Luan, F S

    2015-12-08

    In this study, molecular markers were designed based on the sex determination genes ACS7 (A) and WIP1 (G) and the domain in the Fusarium oxysporum-resistant gene Fom-2 (F) in order to achieve selection of F. oxysporum-resistant gynoecious melon plants. Markers of A and F are cleaved amplified polymorphic sequences that distinguish alleles according to restriction analysis. Twenty F1 and 1863 F2 plants derived from the crosses between the gynoecious line WI998 and the Fusarium wilt-resistant line MR-1 were genotyped based on the markers. The results showed that the polymerase chain reaction and enzyme digestion results could be effectively used to identify plants with the AAggFF genotype in F2 populations. In the F2 population, 35 gynoecious wilt-resistant plants were selected by marker-assisted selection and were confirmed by disease infection assays, demonstrating that these markers can be used in breeding to select F. oxysporum-resistant gynoecious melon plants.

  19. Hepatitis E virus infection as a marker for contaminated community drinking water sources in Tibetan villages.

    Science.gov (United States)

    Toole, Michael J; Claridge, Frances; Anderson, David A; Zhuang, Hui; Morgan, Christopher; Otto, Brad; Stewart, Tony

    2006-02-01

    In April-May 2001, a study was conducted to determine the prevalence of antibodies against hepatitis E virus (HEV) among 426 persons 8-49 years of age randomly selected from two groups of rural villages in central Tibet. Group 1 villages were assessed in 1998 as having poor quality water sources; new water systems were then constructed prior to this study. Group 2 villages had higher quality water and were not designated as priority villages for new systems prior to the study. No participants tested positive for IgM; only IgG was detected in the analyzed samples. Overall, 31% of the participants had ever been infected with HEV (95% confidence interval [CI] = 26.7-35.7%). The rate was higher in men (36.6%) than women (26.3%) and highest in those 30-39 years of age (49.1%). The rate of past infection was higher in group 1; the risk ratio was 2.77 (95% CI = 1.98-3.88). This difference is most likely the result of the poor quality of the original water sources in these villages. In resource-poor countries, HEV may be a useful health indicator reflecting the degree of contamination in village water sources. This may be especially important in rural areas (such as Tibet) where maternal mortality ratios are high because HEV may be an important cause of deaths during pregnancy in disease-endemic areas.

  20. Biosafety considerations for selectable and scorable markers used in cassava (Manihot esculenta Crantz) biotechnology.

    Science.gov (United States)

    Petersen, William; Umbeck, Paul; Hokanson, Karen; Halsey, Mark

    2005-01-01

    Cassava is an important subsistence crop grown only in the tropics, and represents a major source of calories for many people in developing countries. Improvements in the areas of resistance to insects and viral diseases, enhanced nutritional qualities, reduced cyanogenic content and modified starch characteristics are urgently needed. Traditional breeding is hampered by the nature of the crop, which has a high degree of heterozygosity, irregular flowering, and poor seed set. Biotechnology has the potential to enhance crop improvement efforts, and genetic engineering techniques for cassava have thus been developed over the past decade. Selectable and scorable markers are critical to efficient transformation technology, and must be evaluated for biosafety, as well as efficiency and cost-effectiveness. In order to facilitate research planning and regulatory submission, the literature on biosafety aspects of the selectable and scorable markers currently used in cassava biotechnology is surveyed. The source, mode of action and current use of each marker gene is described. The potential for toxicity, allergenicity, pleiotropic effects, horizontal gene transfer, and the impact of these on food or feed safety and environmental safety is evaluated. Based on extensive information, the selectable marker genes nptII, hpt, bar/pat, and manA, and the scorable marker gene uidA, all have little risk in terms of biosafety. These appear to represent the safest options for use in cassava biotechnology available at this time.

  1. A COMPARISON STUDY OF DIFFERENT MARKER SELECTION METHODS FOR SPECTRAL-SPATIAL CLASSIFICATION OF HYPERSPECTRAL IMAGES

    Directory of Open Access Journals (Sweden)

    D. Akbari

    2015-12-01

    Full Text Available An effective approach based on the Minimum Spanning Forest (MSF, grown from automatically selected markers using Support Vector Machines (SVM, has been proposed for spectral-spatial classification of hyperspectral images by Tarabalka et al. This paper aims at improving this approach by using image segmentation to integrate the spatial information into marker selection process. In this study, the markers are extracted from the classification maps, obtained by both SVM and segmentation algorithms, and then are used to build the MSF. The segmentation algorithms are the watershed, expectation maximization (EM and hierarchical clustering. These algorithms are used in parallel and independently to segment the image. Moreover, the pixels of each class, with the largest population in the classification map, are kept for each region of the segmentation map. Lastly, the most reliable classified pixels are chosen from among the exiting pixels as markers. Two benchmark urban hyperspectral datasets are used for evaluation: Washington DC Mall and Berlin. The results of our experiments indicate that, compared to the original MSF approach, the marker selection using segmentation algorithms leads in more accurate classification maps.

  2. Genotyping by sequencing (GBS, an ultimate marker-assisted selection (MAS tool to accelerate plant breeding

    Directory of Open Access Journals (Sweden)

    Jiangfeng eHe

    2014-09-01

    Full Text Available Marker-assisted selection (MAS refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP, have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping by sequencing (GBS has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS, genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection (GS under a large scale of plant breeding programs.

  3. [A Method for Selecting Self-Adoptive Chromaticity of the Projected Markers].

    Science.gov (United States)

    Zhao, Shou-bo; Zhang, Fu-min; Qu, Xing-hua; Zheng, Shi-wei; Chen, Zhe

    2015-04-01

    The authors designed a self-adaptive projection system which is composed of color camera, projector and PC. In detail, digital micro-mirror device (DMD) as a spatial light modulator for the projector was introduced in the optical path to modulate the illuminant spectrum based on red, green and blue light emitting diodes (LED). However, the color visibility of active markers is affected by the screen which has unknown reflective spectrum as well. Here active markers are projected spot array. And chromaticity feature of markers is sometimes submerged in similar spectral screen. In order to enhance the color visibility of active markers relative to screen, a method for selecting self-adaptive chromaticity of the projected markers in 3D scanning metrology is described. Color camera with 3 channels limits the accuracy of device characterization. For achieving interconversion of device-independent color space and device-dependent color space, high-dimensional linear model of reflective spectrum was built. Prior training samples provide additional constraints to yield high-dimensional linear model with more than three degrees of freedom. Meanwhile, spectral power distribution of ambient light was estimated. Subsequently, markers' chromaticity in CIE color spaces was selected via maximization principle of Euclidean distance. The setting values of RGB were easily estimated via inverse transform. Finally, we implemented a typical experiment to show the performance of the proposed approach. An 24 Munsell Color Checker was used as projective screen. Color difference in the chromaticity coordinates between the active marker and the color patch was utilized to evaluate the color visibility of active markers relative to the screen. The result comparison between self-adaptive projection system and traditional diode-laser light projector was listed and discussed to highlight advantage of our proposed method.

  4. Identification of pork contamination in meatball using genetic marker mitochondrial DNA cytochrome b gene by duplex-PCR

    Science.gov (United States)

    Novianty, E.; Kartikasari, L. R.; Lee, J. H.; Cahyadi, M.

    2017-04-01

    Meat based food products have a big opportunity to mix and adulterated with other meats. Muslim communities are prohibited to consume pork-containing product or other pig derivatives in food. Therefore, the high sensitivity, fast, cheap and accurate approach is needed to detect pig contamination in raw meat and meat-processed product such as meatball. The aim of this study was to identify pork contamination in meatball using genetic marker of mitochondrial DNA cytochrome b gene by duplex-PCR. Samples were prepared and designed by following the proportions 0, 1, 5, 10, 25% of pork in meatballs, respectively. The DNA genome was extracted from meatballs and polymerase chain reaction (PCR) was performed using species specific primer to isolate mt-DNA cytochrome b gene. The results showed that the DNA genome was successfully isolated from pork, beef, and contaminated meatballs. Furthermore, 2% agarose gels was able to visualize of duplex-PCR to identify pork contamination in meatballs up to very small proportion (1%). It can be concluded that duplex-PCR of mt-DNA cytochrome b gene was very sensitive to identify pork contamination in meatball with the presence of specific 398 bp DNA band.

  5. Ecotoxicity literature review of selected Hanford Site contaminants

    International Nuclear Information System (INIS)

    Driver, C.J.

    1994-03-01

    Available information on the toxicity, food chain transport, and bioconcentration of several Hanford Site contaminants were reviewed. The contaminants included cesium-137, cobalt-60, europium, nitrate, plutonium, strontium-90, technetium, tritium, uranium, and chromium (III and VI). Toxicity and mobility in both aquatic and terrestrial systems were considered. For aquatic systems, considerable information was available on the chemical and/or radiological toxicity of most of the contaminants in invertebrate animals and fish. Little information was available on aquatic macrophyte response to the contaminants. Terrestrial animals such as waterfowl and amphibians that have high exposure potential in aquatic systems were also largely unrepresented in the toxicity literature. The preponderance of toxicity data for terrestrial biota was for laboratory mammals. Bioconcentration factors and transfer coefficients were obtained for primary producers and consumers in representative aquatic and terrestrial systems; however, little data were available for upper trophic level transfer, particularly for terrestrial predators. Food chain transport and toxicity information for the contaminants were generally lacking for desert or sage brush-steppe organisms, particularly plants and reptiles

  6. CHEMICAL MARKERS OF HUMAN WASTE CONTAMINATION: ANALYSIS OF UROBILIN AND PHARMACEUTICALS IN SOURCE WATERS

    Science.gov (United States)

    Giving public water authorities another tool to monitor and measure levels of human waste contamination of waters simply and rapidly would enhance public protection. Most of the methods used today detect such contamination by quantifying microbes occurring in feces in high enough...

  7. Testing water-soluble carbohydrate QTL effects in perennial ryegrass (Lolium perenne L.) by marker selection

    NARCIS (Netherlands)

    Turner, L.B.; Farrell, M.; Humphreys, M.O.; Dolstra, O.

    2010-01-01

    Water-soluble carbohydrates (WSC) are an important factor determining the nutritional value of grass forage and development of genetic markers for selection of WSC traits in perennial ryegrass would benefit future breeding programmes. Quantitative trait loci (QTLs) for WSC have been published for an

  8. Sensitivity to selected contaminants in a biological early warning ...

    African Journals Online (AJOL)

    Several early warning systems for the monitoring of water quality are based on the assessment of valve opening/closing in bivalves. Tests were conducted to assess the sensitivity of the mussel Anodonta woodiana, installed on the Mosselmonitor, to seven contaminants and evaluate the usefulness of these sensors for ...

  9. Evaluating Mediterranean Soil Contamination Risks in Selected Hydrological Scenarios.

    NARCIS (Netherlands)

    Rosa, de la D.; Crompvoets, J.

    1997-01-01

    This paper reports an attempt of predicting the contamination risk of soils and water as they respond to hydrological changes in the agricultural lands of Sevilla province, Spain. Based on land evaluation methodologies, a semi-empirical model (named Pantanal, as module of the integrated package

  10. Chemical contaminants on DOE lands and selection of contaminant mixtures for subsurface science research

    Energy Technology Data Exchange (ETDEWEB)

    Riley, R.G.; Zachara, J.M. [Pacific Northwest Lab., Richland, WA (United States)

    1992-04-01

    This report identifies individual contaminants and contaminant mixtures that have been measured in the ground at 91 waste sites at 18 US Department of Energy (DOE) facilities within the weapons complex. The inventory of chemicals and mixtures was used to identify generic chemical mixtures to be used by DOE`s Subsurface Science Program in basic research on the subsurface geochemical and microbiological behavior of mixed contaminants (DOE 1990a and b). The generic mixtures contain specific radionuclides, metals, organic ligands, organic solvents, fuel hydrocarbons, and polychlorinated biphenyls (PCBs) in various binary and ternary combinations. The mixtures are representative of in-ground contaminant associations at DOE facilities that are likely to exhibit complex geochemical behavior as a result of intercontaminant reactions and/or microbiologic activity stimulated by organic substances. Use of the generic mixtures will focus research on important mixed contaminants that are likely to be long-term problems at DOE sites and that will require cleanup or remediation. The report provides information on the frequency of associations among different chemicals and compound classes at DOE waste sites that require remediation.

  11. Development and small-scale validation of a novel pigeon-associated mitochondrial DNA source tracking marker for the detection of fecal contamination in harvested rainwater.

    Science.gov (United States)

    Waso, M; Khan, S; Khan, W

    2018-02-15

    The current study was aimed at designing and validating (on a small-scale) a novel pigeon mitochondrial DNA (mtDNA) microbial source tracking (MST) marker for the detection of pigeon fecal matter in harvested rainwater. The pigeon mtDNA MST marker was designed to target the mtDNA Cytochrome b gene by employing mismatch amplification mutation assay kinetics. The pigeon marker was validated by screening 69 non-pigeon and 9 pigeon fecal samples. The host-sensitivity of the assay was determined as 1.00 while the host-specificity of the assay was 0.96. Harvested rainwater samples (n=60) were screened for the prevalence of the marker with the mtDNA Cytochrome b marker detected in 78% of the samples. Bayes' theorem was applied to calculate the conditional probability of the marker detecting true pigeon contamination and the marker subsequently displayed a 99% probability of detecting true pigeon contamination in the harvested rainwater samples. In addition, the mtDNA Cytochrome b marker displayed high concurrence frequencies versus heterotrophic bacteria (78.3%), E. coli (73.3%), total coliforms (71.1%) and fecal coliforms (66.7%). This study thus validates that targeting mtDNA for the design of source tracking markers may be a valuable tool to detect avian fecal contamination in environmental waters. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Use of DNA Markers for Investigating Sources of Bacteria in Contaminated Ground Water: Wooster Township, Wayne County, Ohio

    Science.gov (United States)

    Dumouchelle, Denise H.

    2006-01-01

    In 2004, a public-health nuisance was declared by the Wayne County Board of Health in the Scenic Heights Drive-Batdorf Road area of Wooster Township, Wayne County, Ohio, because of concerns about the safety of water from local wells. Repeated sampling had detected the presence of fecal-indicator bacteria and elevated nitrate concentrations. In June 2006, the U.S. Geological Survey (USGS), in cooperation with the Ohio Environmental Protection Agency (Ohio EPA), collected and analyzed samples from some of the affected wells to help investigate the possibility of human-origin bacterial contamination. Water samples from 12 wells and 5 home sewage-treatment systems (HSTS) were collected. Bromide concentrations were determined in samples from the 12 wells. Samples from 5 of the 12 wells were analyzed for wastewater compounds. Total coliform, enterococci and Escherichia coli (E. coli) bacteria concentrations were determined for samples from 8 of the 12 wells. In addition, two microbial source-tracking tools that employ DNA markers were used on samples from several wells and a composite sample of water from five septic tanks. The DNA markers from the Enterococcus faecium species and the order Bacteroidales are associated with specific sources, either human or ruminant sources. Bromide concentrations ranged from 0.04 to 0.18 milligrams per liter (mg/L). No wastewater compounds were detected at concentrations above the reporting limits. Samples from the 12 wells also were collected by Ohio EPA and analyzed for chloride and nitrate. Chloride concentrations ranged from 12.6 to 61.6 mg/L and nitrate concentrations ranged from 2.34 to 11.9 mg/L (as N). Total coliforms and enterococci were detected in samples from 8 wells, at concentrations from 2 to 200 colony-forming units per 100 milliliters (CFU/100 mL) and 0.5 to 17 CFU/100 mL, respectively. E. coli were detected in samples from three of the eight wells, at concentrations of 1 or 2 CFU/100 mL. Tests for the human

  13. A non-destructive genotyping system from a single seed for marker-assisted selection in watermelon.

    Science.gov (United States)

    Meru, G; McDowell, D; Waters, V; Seibel, A; Davis, J; McGregor, C

    2013-03-11

    Genomic tools for watermelon breeding are becoming increasingly available. A high throughput genotyping system would facilitate the use of DNA markers in marker-assisted selection. DNA extraction from leaf material requires prior seed germination and is often time-consuming and cost prohibitive. In an effort to develop a more efficient system, watermelon seeds of several genotypes and various seed sizes were sampled by removing ⅓ or ½ sections from the distal ends for DNA extraction, while germinating the remaining proximal parts of the seed. Removing ⅓ of the seed from the distal end had no effect on seed germination percentage or seedling vigor. Different DNA extraction protocols were tested to identify a method that could yield DNA of sufficient quality for amplification by polymerase chain reaction. A sodium dodecyl sulfate extraction protocol with 1% polyvinylpyrrolidone yielded DNA that could be amplified with microsatellite primers and was free of pericarp contamination. In this study, an efficient, non-destructive genotyping protocol for watermelon seed was developed.

  14. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

    OpenAIRE

    He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin

    2014-01-01

    Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broad...

  15. CMI Remedy Selection for HE- and Barium-Contaminated Vadose Zone and Alluvium at LANL

    Science.gov (United States)

    Hickmott, D.; Reid, K.; Pietz, J.; Ware, D.

    2008-12-01

    A high explosives (HE) machining building outfall at Los Alamos National Laboratory's Technical Area 16 discharged millions of gallons of HE- and barium-contaminated water into the Canon de Valle watershed. The effluent contaminated surface soils, the alluvial aquifer, vadose zone waters, and deep-perched and regional groundwaters with HE and barium, frequently at levels greater than regulatory standards. Site characterization studies began in 1995 and included extensive monitoring of surface water, groundwater, soils, and subsurface solid media. Hydrogeologic and geophysical studies were conducted to help understand contaminant transport mechanisms and pathways. Results from the characterization studies were used to develop a site conceptual model. In 2000 the principal source area was removed. The ongoing Corrective Measure Study (CMS) and Corrective Measure Implementation (CMI) focus on residual vadose zone contamination and on the contaminated alluvial system. Regulators recently selected a CMI remedy that combined: 1) augmented source removal; 2) grouting of an HE- contaminated surge bed; 3) deployment of Stormwater Management System (SMS) stormfilters in contaminated springs; and 4) permeable reactive barriers (PRBs) in contaminated alluvium. The hydrogeologic conceptual model for the vadose zone and alluvial system as well as the status of the canyon as habitat for the Mexican Spotted Owl were key factors in selection of these minimal-environmental-impact remedies. The heterogeneous vadose zone, characterized by flow and contaminant transport in fractures and in surge beds, requires contaminant treatment at a point of discharge. The canyon PRB is being installed to capture water and contaminants prior to infiltration into the vadose zone. Pilot-scale testing of the SMS and lab-scale batch and column tests of a range of media suggest that granular activated carbon, zeolite, and gypsum may be effective media for removal of HE and/or barium from contaminated

  16. A and MdMYB1 allele-specific markers controlling apple (Malus x domestica Borkh.) skin color and suitability for marker-assisted selection.

    Science.gov (United States)

    Zhang, X J; Wang, L X; Chen, X X; Liu, Y L; Meng, R; Wang, Y J; Zhao, Z Y

    2014-10-31

    Pre-selection for fruit skin color at the seedling stage would be highly advantageous, with marker-assisted selection offering a potential method for apple pre-selection. A and MdMYB1 alleles are allele-specific DNA markers that are potentially associated with apple skin color, and co-segregate with the Rf and Rni loci, respectively. Here, we assessed the potential application of these 2 alleles for marker-assisted breeding across 30 diverse cultivars and 2 apple seedling progenies. The red skin color phenotype was usually associated with the MdMYB1-1 allele and A(1) allele, respectively, while the 2 molecular markers provided approximately 91% predictability in the 'Fuji' x 'Cripps Pink' and 'Fuji' x 'Gala' progenies. The results obtained from the 30 cultivars and 2 progenies were consistent for the 2 molecular markers. Hence, the results supported that Rf and Rni could be located in a gene cluster, or even correspond to alleles of the same gene. Our results are consistent with the hypothesis that red/yellow dimorphism is controlled by a monogenic system, with the presence of the red anthocyanin pigmentation being dominant. In addition, our results supported that the practical utilization of the 2 function markers to efficiently and accurately select red-skinned apple cultivars in apple scion breeding programs.

  17. Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

    Science.gov (United States)

    Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

    2016-01-01

    Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

  18. Rapid and targeted introgression of genes into popular wheat cultivars using marker-assisted background selection.

    Directory of Open Access Journals (Sweden)

    Harpinder S Randhawa

    Full Text Available A marker-assisted background selection (MABS-based gene introgression approach in wheat (Triticum aestivum L. was optimized, where 97% or more of a recurrent parent genome (RPG can be recovered in just two backcross (BC generations. A four-step MABS method was developed based on 'Plabsim' computer simulations and wheat genome structure information. During empirical optimization of this method, double recombinants around the target gene were selected in a step-wise fashion during the two BC cycles followed by selection for recurrent parent genotype on non-carrier chromosomes. The average spacing between carrier chromosome markers was <4 cM. For non-carrier chromosome markers that flanked each of the 48 wheat gene-rich regions, this distance was approximately 12 cM. Employed to introgress seedling stripe rust (Puccinia striiformis f. sp. tritici resistance gene Yr15 into the spring wheat cultivar 'Zak', marker analysis of 2,187 backcross-derived progeny resulted in the recovery of a BC(2F(2ratio3 plant with 97% of the recurrent parent genome. In contrast, only 82% of the recurrent parent genome was recovered in phenotypically selected BC(4F(7 plants developed without MABS. Field evaluation results from 17 locations indicated that the MABS-derived line was either equal or superior to the recurrent parent for the tested agronomic characteristics. Based on these results, MABS is recommended as a strategy for rapidly introgressing a targeted gene into a wheat genotype in just two backcross generations while recovering 97% or more of the recurrent parent genotype.

  19. CHEMICAL MARKERS OF HUMAN WASTE CONTAMINATION IN SOURCE WATERS: A SIMPLIFIED ANALYTICAL APPROACH

    Science.gov (United States)

    Giving public water authorities a tool to monitor and measure levels of human waste contamination of waters simply and rapidly would enhance public protection. This methodology, using both urobilin and azithromycin (or any other human-use pharmaceutical) could be used to give pub...

  20. [Cloning goat producing human lactoferrin with genetically modified donor cells selected by single or dual markers].

    Science.gov (United States)

    An, Liyou; Yuan, Yuguo; Yu, Baoli; Yang, Tingjia; Cheng, Yong

    2012-12-01

    We compared the efficiency of cloning goat using human lactoferrin (hLF) with genetically modified donor cells marked by single (Neo(r)) or double (Neo(r)/GFP) markers. Single marker expression vector (pBLC14) or dual markers expression vector (pAPLM) was delivered to goat fetal fibroblasts (GFF), and then the transgenic GFF was used as donor cells to produce transgenic goats. Respectively, 58.8% (20/34) and 86.7% (26/30) resistant cell lines confirmed the transgenic integration by PCR. Moreover, pAPLM cells lines were subcultured with several passages, only 20% (6/30) cell lines was observed fluorescence from each cell during the cell passage. Somatic cell nuclear transfer using the donor cells harbouring pBLC14 or pAPLM construct, resulting in a total of 806 reconstructed embryos, a pregnancy rate at 35 d (53.8%, 39.1%) and 60 d (26.9%, 21.7%), and an offspring birth rate (1.9%, 1.4%) with 5 and 7 newborn cloned goats, respectively. Transgene was confirmed by PCR and southern-blot in all cloned offspring. There were no significant differences at the reconstructed embryo fusion rates, pregnancy rates and the birth rate (P > 0.05) between single and double markers groups. The Neo(r)/GFP double markers could improve the reliability for accurately and efficiently selecting the genetically modified donor cells. No adverse effect was observed on the efficiency of transgenic goat production by SCNT using somatic cells transfected with double (Neo(r)/GFP) markers vector.

  1. Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding

    Science.gov (United States)

    White, Stephen N.; Knowles, Donald P.

    2013-01-01

    Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions. PMID:23771240

  2. Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding

    Directory of Open Access Journals (Sweden)

    Donald P. Knowles

    2013-06-01

    Full Text Available Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus and goats (caprine arthritis encephalitis virus [CAEV]. Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions.

  3. The value of using DNA markers for beef bull selection in the seedstock sector.

    Science.gov (United States)

    Van Eenennaam, A L; van der Werf, J H J; Goddard, M E

    2011-02-01

    The objective of this study was to estimate the value derived from using DNA information to increase the accuracy of beef sire selection in a closed seedstock herd. Breeding objectives for commercial production systems targeting 2 diverse markets were examined using multiple-trait selection indexes developed for the Australian cattle industry. Indexes included those for both maternal (self-replacing) and terminal herds targeting either a domestic market, where steers are finished on pasture, or the export market, where steers are finished on concentrate rations in feedlots and marbling has a large value. Selection index theory was used to predict the response to conventional selection based on phenotypic performance records, and this was compared with including information from 2 hypothetical marker panels. In 1 case the marker panel explained a percentage of additive genetic variance equal to the heritability for all traits in the breeding objective and selection criteria, and in the other case to one-half of this amount. Discounted gene flow methodology was used to calculate the value derived from the use of superior bulls selected using DNA test information and performance recording over that derived from conventional selection using performance recording alone. Results were ultimately calculated as discounted returns per DNA test purchased by the seedstock operator. The DNA testing using these hypothetical marker panels increased the selection response between 29 to 158%. The value of this improvement above that obtained using traditional performance recording ranged from $89 to 565 per commercial bull, and $5,332 to 27,910 per stud bull. Assuming that the entire bull calf crop was tested to achieve these gains, the value of the genetic gain derived from DNA testing ranged from $204 to 1,119 per test. All values assumed that the benefits derived from using superior bulls were efficiently transferred along the production chain to the seedstock producer incurring

  4. Origin of fecal contamination in waters from contrasted areas: Stanols as Microbial Source Tracking markers

    OpenAIRE

    Derrien, M.; Jarde, E.; Gruau, G.; Pourcher, A. M.; Gourmelon, Michele; Jadas-hecart, Alain; Wickmann, A. C. Pierson

    2012-01-01

    Improving the microbiological quality of coastal and river waters relies on the development of reliable markers that are capable of determining sources of fecal pollution. Recently, a principal component analysis (PCA) method based on six stanol compounds (i.e. 5 beta-cholestan-3 beta-ol (coprostanol), 5 beta-cholestan-3 alpha-ol (epicoprostanol), 24-methyl-5 alpha-cholestan-3 beta-ol (campestanol), 24-ethyl-5 alpha-cholestan-3 beta-ol (sitostanol), 24-ethyl-5 beta-cholestan-3 beta-ol (24-eth...

  5. Attractiveness of food and avoidance from contamination as conflicting stimuli to habitat selection by fish.

    Science.gov (United States)

    Araújo, Cristiano V M; Rodríguez, Elizabeth N V; Salvatierra, David; Cedeño-Macias, Luis A; Vera-Vera, Victoria C; Moreira-Santos, Matilde; Ribeiro, Rui

    2016-11-01

    Habitat selection by fish is the outcome of a choice between different stimuli. Typically, the presence of food tends to attract organisms, while contamination triggers an avoidance response to prevent toxic effects. Given that both food and contaminants are not homogeneously distributed in the environment and that food can be available in contaminated zones, a key question has been put forward in the present study: does a higher availability of food in contaminated areas interfere in the avoidance response to contaminants regardless of the contamination level? Tilapia fry (Oreochromis sp.; 2.5-3.0 cm and 0.5-0.8 g) were exposed to two different effluent samples, diluted along a free-choice, non-forced exposure system simulating a contamination gradient. Initially, avoidance to the effluents was checked during a one hour exposure. Afterwards, food was added to the system so that the availability of food increased with the increase in the level of contamination, and the avoidance response to contamination was checked during another hour. Results clearly showed a concentration-dependent avoidance response for both effluents during the first hour (i.e., with no food). However, in presence of the food, the avoidance pattern was altered: organisms were propelled to intermittently move towards contaminated areas where food availability was higher. The incursions were taken regardless of the potential risk linked to the toxic effects. In conclusion, even when the risk of toxicity was imminent, tilapia fry were more intensively stimulated by the attractiveness of the food than by repulsion to the contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Selected biological markers in various vascular lesions of the head and neck

    Directory of Open Access Journals (Sweden)

    Zuzanna Gronkiewicz

    2014-10-01

    Full Text Available Vascular anomalies are divided according to the contemporary system of classification into two groups: tumors and malformations. However, there is no consensus on juvenile angiofibroma’s place in that system. The general characteristics of selected markers of angiogenesis and tissue remodeling are presented in the series in the context of current knowledge in the field of pathophysiology of vascular lesions. The mentioned markers are currently the subjects of multidirectional studies in oncology, as they take part in the process of neoangiogenesis and proliferation of tumors. Nevertheless, they have not been widely examined in vascular lesions. The indirect goal of that series is to indicate the possible research direction on vascular lesions to determine their molecular profile, to create a more specific system of classification, and above all to develop new diagnostic and treatment methods.

  7. Use of Biochemical Markers for the Assessment of Organic Pollutant Contamination of the Vltava river, Czech Republic

    Directory of Open Access Journals (Sweden)

    Marcela Havelková

    2009-01-01

    Full Text Available In this study, selected biochemical markers - cytochrome P450 (CYP 450, ethoxyresorufin-O-deethylase (EROD, glutathione S-transferase (GST and glutathione (GSH - were measured in chub (Leuciscus cephalus L. liver samples obtained from three locations on the Vltava river (Podolí, Podbaba and Vraňany and from a control location nmicals commonly known as their inducers. These include polychlorinated biphenyls, hexachlorobenzene and octachlorostyrene measured in chub muscle and polyaromatic hydrocarbons measured in bear Vodňany. The levels of selected biomarkers should correlate with the concentration of cheottom sediments obtained from the same locations. The highest EROD activity (median 101.37 pmol min-1 mg-1 protein, GST activity (median 42.82 nmol min-1 mg-1 protein, and GSH concentration (median 8.01 nmol mg-1 protein were found in fish liver from the Podbaba location. There were no significant differences in CYP P450 level or EROD activity among the different locations. In Podbaba, GST activity (P P < 0.001 were significantly higher than in the control location. The results of these analyses were correlated and a significant correlation was found between biochemical markers and their inducers. The results show that the use of biochemical markers in water quality assessment is a convenient method that can supplement classical chemical monitoring.

  8. HisB as novel selection marker for gene targeting approaches in Aspergillus niger.

    Science.gov (United States)

    Fiedler, Markus R M; Gensheimer, Tarek; Kubisch, Christin; Meyer, Vera

    2017-03-08

    For Aspergillus niger, a broad set of auxotrophic and dominant resistance markers is available. However, only few offer targeted modification of a gene of interest into or at a genomic locus of choice, which hampers functional genomics studies. We thus aimed to extend the available set by generating a histidine auxotrophic strain with a characterized hisB locus for targeted gene integration and deletion in A. niger. A histidine-auxotrophic strain was established via disruption of the A. niger hisB gene by using the counterselectable pyrG marker. After curing, a hisB - , pyrG - strain was obtained, which served as recipient strain for further studies. We show here that both hisB orthologs from A. nidulans and A. niger can be used to reestablish histidine prototrophy in this recipient strain. Whereas the hisB gene from A. nidulans was suitable for efficient gene targeting at different loci in A. niger, the hisB gene from A. niger allowed efficient integration of a Tet-on driven luciferase reporter construct at the endogenous non-functional hisB locus. Subsequent analysis of the luciferase activity revealed that the hisB locus is tight under non-inducing conditions and allows even higher luciferase expression levels compared to the pyrG integration locus. Taken together, we provide here an alternative selection marker for A. niger, hisB, which allows efficient homologous integration rates as well as high expression levels which compare favorably to the well-established pyrG selection marker.

  9. Fine mapping of the rice Bph1 gene, which confers resistance to the brown planthopper (Nilaparvata lugens stal), and development of STS markers for marker-assisted selection.

    Science.gov (United States)

    Cha, Young-Soon; Ji, Hyeonso; Yun, Doh-Won; Ahn, Byoung-Ohg; Lee, Myung Chul; Suh, Seok-Cheol; Lee, Chun Seok; Ahn, Eok Keun; Jeon, Yong-Hee; Jin, Il-Doo; Sohn, Jae-Keun; Koh, Hee-Jong; Eun, Moo-Young

    2008-08-31

    The brown planthopper (BPH) is a major insect pest in rice, and damages these plants by sucking phloem-sap and transmitting viral diseases. Many BPH resistance genes have been identified in indica varieties and wild rice accessions, but none has yet been cloned. In the present study we report fine mapping of the region containing the Bph1 locus, which enabled us to perform marker-aided selection (MAS). We used 273 F8 recombinant inbred lines (RILs) derived from a cross between Cheongcheongbyeo, an indica type variety harboring Bph1 from Mudgo, and Hwayeongbyeo, a BPH susceptible japonica variety. By random amplification of polymorphic DNA (RAPD) analysis using 656 random 10-mer primers, three RAPD markers (OPH09, OPA10 and OPA15) linked to Bph1 were identified and converted to SCAR (sequence characterized amplified region) markers. These markers were found to be contained in two BAC clones derived from chromosome 12: OPH09 on OSJNBa0011B18, and both OPA10 and OPA15 on OSJNBa0040E10. By sequence analysis of ten additional BAC clones evenly distributed between OSJNBa0011B18 and OSJNBa0040E10, we developed 15 STS markers. Of these, pBPH4 and pBPH14 flanked Bph1 at distances of 0.2 cM and 0.8 cM, respectively. The STS markers pBPH9, pBPH19, pBPH20, and pBPH21 co-segregated with Bph1. These markers were shown to be very useful for marker-assisted selection (MAS) in breeding populations of 32 F6 RILs from a cross between Andabyeo and IR71190, and 32 F5 RILs from a cross between Andabyeo and Suwon452.

  10. Gateway binary vectors with the bialaphos resistance gene, bar, as a selection marker for plant transformation.

    Science.gov (United States)

    Nakamura, Shinya; Mano, Shoji; Tanaka, Yuji; Ohnishi, Masato; Nakamori, Chihiro; Araki, Masami; Niwa, Tomoko; Nishimura, Mikio; Kaminaka, Hironori; Nakagawa, Tsuyoshi; Sato, Yutaka; Ishiguro, Sumie

    2010-01-01

    We constructed two series of Gateway binary vectors, pGWBs and R4pGWBs, possessing the bialaphos resistance gene (bar) as a selection marker for plant transformation. The reporters and tags employed in this system are sGFP, GUS, LUC, EYFP, ECFP, G3GFP, mRFP, TagRFP, 6xHis, FLAG, 3xHA, 4xMyc, 10xMyc, GST, T7 and TAP. Selection of Arabidopsis transformants with BASTA was successfully carried out using both plate-grown and soil-grown seedlings. Transformed rice calli and suspension-cultured tobacco cells were selected on plates containing BASTA or glufosinate-ammonium. These vectors are compatible with existing pGWB and R4pGWB vectors carrying kanamycin and hygromycin B resistance.

  11. Space-based visual attention: a marker of immature selective attention in toddlers?

    Science.gov (United States)

    Rivière, James; Brisson, Julie

    2014-11-01

    Various studies suggested that attentional difficulties cause toddlers' failure in some spatial search tasks. However, attention is not a unitary construct and this study investigated two attentional mechanisms: location selection (space-based attention) and object selection (object-based attention). We investigated how toddlers' attention is distributed in the visual field during a manual search task for objects moving out of sight, namely the moving boxes task. Results show that 2.5-year-olds who failed this task allocated more attention to the location of the relevant object than to the object itself. These findings suggest that in some manual search tasks the primacy of space-based attention over object-based attention could be a marker of immature selective attention in toddlers. © 2014 Wiley Periodicals, Inc.

  12. Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls.

    Science.gov (United States)

    Staley, Zachery R; Grabuski, Josey; Sverko, Ed; Edge, Thomas A

    2016-11-01

    Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log 10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log 10 CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log 10 CFU/100 ml, and 7.65 log 10 CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds. Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can

  13. Selection of discrimination marker from various propolis for mapping and identify anti Candida albicans activity

    Science.gov (United States)

    Mahadewi, Alfiani Guntari; Christina, Daisy; Hermansyah, Heri; Wijanarko, Anondho; Farida, Siti; Adawiyah, Robiatul; Rohmatin, Etin; Sahlan, Muhamad

    2018-02-01

    The increase in fungal resistance against antifungal drugs available in the market will reduce the effectiveness of treatment for Candidiasis. Propolis contains various compounds with antifungal properties Candida albicans, but the content of each type is very diverse. The sample used was Sulawesi propolis type smooth (taken from inside the nest), rough (taken from outside the hive) and mix (a combination of both). Anti-C. albicans molecule marker is a marker compound for selecting propolis with the ability to overcome Candidiasis. The initial step was to test the levels of flavonoids and phenolic by using UV-Vis spectrometry method. It was founded that each sample was not always superior to any substance, so propolis cannot be directly selected. In Phenolic content, mix propolis has the highest value than other 5.109%. In Flavonoid content, propolis smooth has the highest value than other, 16.38%. Furthermore, propolis selected by antifungal activity test with good diffusion method at the concentration propolis 5% either 7%, the inhibitory diameter zone propolis smooth and rough has same value 10 mm. Propolis mix has an advantage while propolis smooth and rough have the same capability range 12 mm and 13 mm. In this study, the phenolic content plays a major role in antifungal cases.

  14. Technology selection for remediation of lead and hydrocarbon contaminated soil

    International Nuclear Information System (INIS)

    Richardson, K.E.; Sparks, G.M.

    1993-01-01

    This paper presents a methodology for selection of a technology for remediation of 70,000 tons of lead and hydrocarbon impacted soil resulting from an excavation at the Mobil Torrance Refinery. This methodology resulted from over two years of extensive research and technology evaluation. Twelve technologies and combination of technologies were evaluated, which often included bench scale testing, to determine the most cost effective and technically feasible remediation option. The results of the studies for each technology are discussed and presented in tabular form. The technologies investigated include: fixation/stabilization, soil washing, solvent washing, heap leach extraction, froth flotation, bioremediation, thermal desorption, electrokinetic extraction, asphalt incorporation, vitrification, off-site treatment, and off-site disposal. The associated costs and technical feasibility of each of the remediation options evaluated are presented. Laboratory analyses of the excavated soil indicate hydrocarbons range from non-detect to 11,000 ppm with an average of 2,600 ppm, soluble lead (CA test-not TCLP) range from 1.4 ppm to 100 ppm with an average of 29 ppm, and low levels of organic lead are present. Average grain size of the soil ranges from number-sign 200 to number-sign 120 mesh, and permeability averages 10--4 cm/sec. Significant odors, likely caused by hydrogen sulfide and thiophenes, were detected when the soil was excavated and control of odors during the remediation phase is a critical concern

  15. Marker-assisted selection. Current status and future perspectives in crops, livestock, forestry and fish

    International Nuclear Information System (INIS)

    Guimaraes, E.P.; Ruane, J.; Scherf, B.D.; Sonnino, A.; Dargie, J.D.

    2007-01-01

    This book provides a comprehensive description and assessment of the use of marker-assisted selection for increasing the rate of genetic gain in crops, livestock, forestry and farmed fish, including the related policy, organizational and resource considerations. It continues FAO's tradition of dealing with issues of importance to agricultural and economic development in a multidisciplinary and cross-sectoral manner. As such it is hoped that the information and options presented and the suggestions made will provide valuable guidance to scientists and breeders in both the public and private sectors, as well as to government and institutional policy and decision-makers

  16. Research for role of official veterinary inspector in cross contamination of offal and carcass at slaughterline with use of marker microorganisms

    Directory of Open Access Journals (Sweden)

    Jankuloski Dean

    2009-05-01

    Full Text Available Red meat and poultry meat is subject of legislation presented in Annex IV of Regulation 852/2004/EEC. Regulation is based on principle of individual examination and if necessary, palpation and incision of lymph nodes, offal and where necessary carcass from slaughtered animals at the slaughter line. Potentially pathogenic agents present on the carcass and offal through physical contact (palpation and incision are source for contamination of the palms and equipment of meat examiner that pose risk for cross contamination. The role of official veterinarian (OV in transfer of contaminants is extremely important, having in mind that during his work he manipulates with large number of offal and carcasses. To estimate the role of OV in carcass contamination during meat examination in this study we use 12 cattle and 18 sheep sets of organs and afterwards we inoculate them with two laboratory marker microorganisms E. coli K12 and Pseudomonas fluorescens. Offal were divided in groups composed from 6 samples and they were numerated. Examination of the offal is performed from sample number 1 to sample 6 using three different procedures: 1 without washing of hands and knife sanitation between each sample; 2 with washing of hands and without sanitation of the knife between each individual sample; 3 with washing of the hands between each individual sample. After that from each set of offal the number of marker microorganisms were determined and swabs were taken from the equipment that have been used in examination and surface of the hands of OV before and after the examination. From achieved number of marker microorganisms it can be noticed that in procedure where sanitation is not performed there is highest transfer of contamination marker microorganisms, while in procedure where sanitation is performed transfer of contamination have been disrupted and isn’t going further. Swabs token from the equipment and hands of examiner after washing it can be noticed

  17. Prediction-Oriented Marker Selection (PROMISE): With Application to High-Dimensional Regression.

    Science.gov (United States)

    Kim, Soyeon; Baladandayuthapani, Veerabhadran; Lee, J Jack

    2017-06-01

    In personalized medicine, biomarkers are used to select therapies with the highest likelihood of success based on an individual patient's biomarker/genomic profile. Two goals are to choose important biomarkers that accurately predict treatment outcomes and to cull unimportant biomarkers to reduce the cost of biological and clinical verifications. These goals are challenging due to the high dimensionality of genomic data. Variable selection methods based on penalized regression (e.g., the lasso and elastic net) have yielded promising results. However, selecting the right amount of penalization is critical to simultaneously achieving these two goals. Standard approaches based on cross-validation (CV) typically provide high prediction accuracy with high true positive rates but at the cost of too many false positives. Alternatively, stability selection (SS) controls the number of false positives, but at the cost of yielding too few true positives. To circumvent these issues, we propose prediction-oriented marker selection (PROMISE), which combines SS with CV to conflate the advantages of both methods. Our application of PROMISE with the lasso and elastic net in data analysis shows that, compared to CV, PROMISE produces sparse solutions, few false positives, and small type I + type II error, and maintains good prediction accuracy, with a marginal decrease in the true positive rates. Compared to SS, PROMISE offers better prediction accuracy and true positive rates. In summary, PROMISE can be applied in many fields to select regularization parameters when the goals are to minimize false positives and maximize prediction accuracy.

  18. 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...

  19. A quick rhizobacterial selection tests for the remediation of copper contaminated soils.

    Science.gov (United States)

    Braud, A M; Hubert, M; Gaudin, P; Lebeau, T

    2015-08-01

    The main objective of the study is to develop and improve quick bacterial tests to select the best candidates for the bioaugmentation of metal-contaminated soil, coupled with phytoextraction. Bacteria isolates (181) were selected from a collection originated from a Cu-contaminated sediment, on the basis of several miniaturized biochemical tests adapted to the copper contamination. Amongst them, we used a growth soil based-medium to select metal-tolerant bacteria, and their ability to grow and mobilize metals by mean of metabolites (siderophores, organic acids) was also assessed. The result of the bacterial selection tests showed differences in presence or absence of copper, especially for phosphate-solubilizing strains which ability decreased by 53% in the presence of copper hydroxide phosphate as compared to the standard tricalcium phosphate test. A promising Pseudomonas putida was selected from the collection. The study underlined the importance of choosing significant selection tests regarding the nature of the metal occurring in the soil to be cleaned-up to assess the real potential of each bacterial strain for subsequent soil bioaugmentation purposes. © 2015 The Society for Applied Microbiology.

  20. Determination of heavy metal pollution in soils from selected potentially contaminated sites in Tema

    International Nuclear Information System (INIS)

    Nyaaba, A.K.L.

    2011-01-01

    The objective of the study was to assess the concentration and determine the level of pollution by harmful heavy metals in soils from selected potentially contaminated sites in Tema. The metals of interest include; mercury, lead, cadmium, cobalt zinc, arsenic, nickel, copper and chromium. A total of forty seven (47) samples comprising thirty eight sub-samples (38) and nine (9) composite samples were collected from nine (9) different locations. These included playgrounds, steel processing factories, used Lead Acid Battery (ULAB) recycling plant, mechanic workshops and the municipal waste disposal site. The samples were prepared after which the elemental concentrations were determined using energy dispersive X-ray fluorescence (EDXRF) with a secondary target excitation arrangement (5.9 keV). The analysis of the samples yielded the following mean heavy metal concentrations in mg/kg: 424.38 (Cr); 408.68 (Ni); 14427 (Cu); 4129.87 (Zn); 1580.68 (As); 647.48 (Hg); 73361.51 (Pb) and 1176.16 (Co). The mean concentrations of heavy metals in the soils were in the following order Pb>Zn>As>Co>Cu>Hg>Cr>Ni. Mercury was detected at only two of the sites. The average heavy metals in the soils from the sites were generally high since most of them exceeded the optimum and action values of the New Dutch List. The Enrichment Factor (EF) ratios show that the enrichment of the elements in the soils ranged from deficiently to extremely highly enriched. The contamination factor show that the contamination by the heavy metals were low at some of the sites and very high at others. The geoaccumulation indices indicated that the playground (PG) has not been contaminated by any of the metals, C8 is contaminated strongly by mercury only and the contamination at the remaining sites varied from moderately contaminated to extremely contaminated by the metals. The Igeo also indicated that the elements accounting for extreme contamination are lead, arsenic, copper, zinc mercury and chromium. Lead

  1. Selection of distribution coefficients for contaminant fate and transport calculations: Strontium as a case study

    International Nuclear Information System (INIS)

    Kaplan, D.I.; Krupka, K.M.; Serne, R.J.

    1997-01-01

    As part of an ongoing project funded by a cooperative effort involving the Office of Radiation and Indoor Air (ORIA) of the U.S. Environmental Protection Agency (EPA), the Office of Environmental Restoration (EM-40) of the Department of Energy (DOE), and the Nuclear Regulatory Agency (NRC), distribution coefficient (K d ) values are being compiled from the literature to develop provisional tables for cadmium, cesium, chromium, lead, plutonium, strontium, thorium, and uranium. The tables are organized according to important aqueous- and solid-phase parameters affecting the sorption of these contaminants. These parameters, which vary with contaminant, include pH and redox conditions; cation exchange capacity (CEC); presence of iron-oxide, aluminum-oxide, clay, and mica minerals; organic matter content; and solution concentrations of contaminants, competing ions, and complexing ligands. Sorption information compiled for strontium is used to illustrate our approach. The strontium data show how selected geochemical parameters (i.e., CEC, pH, and clay content) affect Strontium K d values and the selection of open-quote default close-quote K d values needed for modeling contaminant transport and risks at sites for which site specific data are lacking. Results of our evaluation may be used by site management and technical staff to assess contaminant fate, migration, and risk calculations in support of site remediation and waste management decisions

  2. The Feasibility of Tree Coring as a Screening Tool for Selected Contaminants in the Subsurface

    DEFF Research Database (Denmark)

    Nielsen, Mette Algreen

    Chemical release resulting from inadequate care in the handling and storage of compounds has ultimately led to a large number of contaminated sites worldwide. Frequently found contaminants in the terrestrial environment include BTEX (benzene, toluene, ethylbenzene, and xylenes), heavy metals, PAH...... sampling density. This, together with a relatively large soil volume represented by a tree core, has shown to reduce the risk of overlooking contaminated areas and is a valuable method for the identification of previously unknown source areas within a short time period....... (polycyclic aromatic hydrocarbons) and chlorinated solvents. The large number of contaminated sites has created a need for effective and reliable site investigations. In this PhD project the feasibility of tree coring as a screening tool for selected contaminants in the subsurface has been investigated...... to obtain more efficient site investigations. Trees have a natural ability to take up water and nutrients from the subsurface; consequently, contaminants can also enter the roots and be translocated to plant parts above ground where they will be absorbed, degraded or phytovolatilized depending...

  3. Wipe sampling for nicotine as a marker of thirdhand tobacco smoke contamination on surfaces in homes, cars, and hotels.

    Science.gov (United States)

    Quintana, Penelope J E; Matt, Georg E; Chatfield, Dale; Zakarian, Joy M; Fortmann, Addie L; Hoh, Eunha

    2013-09-01

    Secondhand smoke contains a mixture of pollutants that can persist in air, dust, and on surfaces for months or longer. This persistent residue is known as thirdhand smoke (THS). Here, we detail a simple method of wipe sampling for nicotine as a marker of accumulated THS on surfaces. We analyzed findings from 5 real-world studies to investigate the performance of wipe sampling for nicotine on surfaces in homes, cars, and hotels in relation to smoking behavior and smoking restrictions. The intraclass correlation coefficient for side-by-side samples was 0.91 (95% CI: 0.87-0.94). Wipe sampling for nicotine reliably distinguished between private homes, private cars, rental cars, and hotels with and without smoking bans and was significantly positively correlated with other measures of tobacco smoke contamination such as air and dust nicotine. The sensitivity and specificity of possible threshold values (0.1, 1, and 10 μg/m(2)) were evaluated for distinguishing between nonsmoking and smoking environments. Sensitivity was highest at a threshold of 0.1 μg/m(2), with 74%-100% of smoker environments showing nicotine levels above threshold. Specificity was highest at a threshold of 10 μg/m(2), with 81%-100% of nonsmoker environments showing nicotine levels below threshold. The optimal threshold will depend on the desired balance of sensitivity and specificity and on the types of smoking and nonsmoking environments. Surface wipe sampling for nicotine is a reliable, valid, and relatively simple collection method to quantify THS contamination on surfaces across a wide range of field settings and to distinguish between nonsmoking and smoking environments.

  4. Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei

    Science.gov (United States)

    Yu, Yang; Zhang, Xiaojun; Liu, Jingwen; Li, Fuhua; Huang, Hao; Li, Yijun; Liu, Xiaolin; Xiang, Jianhai

    2015-01-01

    Selective breeding of the Pacific white shrimp Litopenaeus vannamei during the last decade has produced new varieties exhibiting high growth rates and disease resistance. However, the identification of new varieties of shrimps from their phenotypic characters is difficult. This study introduces a new approach for identifying varieties of shrimps using molecular markers of microsatellites and mitochondrial control region sequences. The method was employed to identify a new selected variety, Kehai No. 1 (KH-1), from three representative stocks (control group): Zhengda; Tongwei; and a stock collected from Fujian Province, which is now cultured in mainland China. By pooled genotyping of KH-1 and the control group, five microsatellites showing differences between KH-1 and the control group were screened out. Individual genotyping data confirmed the results from pooled genotyping. The genotyping data for the five microsatellites were applied to the assignment analysis of the KH-1 group and the control group using the partial Bayesian assignment method in GENECLASS2. By sequencing the mitochondrial control regions of individuals from the KH-1 and control group, four haplotypes were observed in the KH-1 group, whereas 14 haplotypes were obtained in the control group. By combining the microsatellite assignment analysis with mitochondrial control region analysis, the average accuracy of identification of individuals in the KH-1 group and control group reached 89%. The five selected microsatellite loci and mitochondrial control region sequences were highly polymorphic and could be used to distinguish new selected varieties of L. vannamei from other populations cultured in China.

  5. Estimates of epistatic and pleiotropic effects of casein alpha s1 (CSN1S1) and thyroglobulin (TG) genetic markers on beef heifer performance traits enhanced by selection

    Science.gov (United States)

    Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for two years to equalize CSN1S1 and TG genetic marker frequencies to evaluate the epista...

  6. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding

    Directory of Open Access Journals (Sweden)

    Arindam Ghatak

    2017-06-01

    Full Text Available Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

  7. Embedding filtering criteria into a wrapper marker selection method for brain tumor classification: an application on metabolic peak area ratios

    International Nuclear Information System (INIS)

    Kounelakis, M G; Zervakis, M E; Giakos, G C; Postma, G J; Buydens, L M C; Kotsiakis, X

    2011-01-01

    The purpose of this study is to identify reliable sets of metabolic markers that provide accurate classification of complex brain tumors and facilitate the process of clinical diagnosis. Several ratios of metabolites are tested alone or in combination with imaging markers. A wrapper feature selection and classification methodology is studied, employing Fisher's criterion for ranking the markers. The set of extracted markers that express statistical significance is further studied in terms of biological behavior with respect to the brain tumor type and grade. The outcome of this study indicates that the proposed method by exploiting the intrinsic properties of data can actually reveal reliable and biologically relevant sets of metabolic markers, which form an important adjunct toward a more accurate type and grade discrimination of complex brain tumors

  8. Effect of selected spices on chemical and sensory markers in fortified rye-buckwheat cakes.

    Science.gov (United States)

    Przygodzka, Małgorzata; Zieliński, Henryk; Ciesarová, Zuzana; Kukurová, Kristina; Lamparski, Grzegorz

    2016-07-01

    The aim of this study was to find out the effect of selected spices on chemical and sensorial markers in cakes formulated on rye and light buckwheat flour fortified with spices. Among collection of spices, rye-buckwheat cakes fortified individually with cloves, nutmeg, allspice, cinnamon, vanilla, and spice mix revealed the highest sensory characteristics and overall quality. Cakes fortified with cloves, allspice, and spice mix showed the highest antioxidant capacity, total phenolics, rutin, and almost threefold higher available lysine contents. The reduced furosine content as well as free and total fluorescent intermediatory compounds were observed as compared to nonfortified cakes. The FAST index was significantly lowered in all cakes enriched with spices, especially with cloves, allspice, and mix. In contrast, browning index increased in compare to cakes without spices. It can be suggested that clove, allspice, vanilla, and spice mix should be used for production of safety and good quality cakes.

  9. The Development of Magnetic Molecules for the Selective Removal of Contaminants

    International Nuclear Information System (INIS)

    Bushart, S.P.; Bradbury, D.; Elder, G.; Duffield, J.; Pascual, I.; Ratcliffe, N.

    2006-01-01

    'Magnetic molecules' are a new type of decontaminant for removing dilute dissolved contaminants from solution. Magnetic molecules have a specific ion exchange function to selectively react with a particular type of ionic contamination in a liquid solution. The magnetic molecules also have a very small magnetic ferritin core (ferritin is an iron-III mammalian storage protein having about 10 nm diameter), which enables the magnetic molecule to be removed from solution by magnetic filtration. The ion exchange function is attached to the magnetic ferritin core by organic reaction sequences. The ion exchange function selectively bonds to a specific type of contaminant ion. For example, ion exchange functions can selectively target radioactive contaminant ions such as cobalt, cesium and plutonium. The procedure for decontamination is that the appropriate magnetic molecule (which targets the contaminant which it is desired to remove) is added to the solution and the solution is then passed through a magnetic filter. The contaminant binds to the magnetic molecule and is then removed by the magnetic filter. The magnetic molecule/contaminant can then be recovered from the magnetic filter by back-washing. Work has been undertaken towards the development of magnetic molecules for use as radioactive decontaminants for radioactive waste management purposes. Previously we have reported on the functionalization of ferritin with the chelating agent DTPA and have shown that this can be used to bind Ca(II) in solution and separate it from Na(I) ions by the process of equilibrium dialysis. Approximately 100 DTPA molecules could be bound to the surface of the ferritin molecule. Synthetic conditions have been optimised, and which will be reported here, ferritin has been functionalized with approximately 1200 DTPA molecules per mole of ferritin and used successfully to achieve a quantitative separation of Co(II) from Cs(I) ions by equilibrium dialysis. This separation has been carried

  10. Increased prediction accuracy in wheat breeding trials using a marker × environment interaction genomic selection model.

    Science.gov (United States)

    Lopez-Cruz, Marco; Crossa, Jose; Bonnett, David; Dreisigacker, Susanne; Poland, Jesse; Jannink, Jean-Luc; Singh, Ravi P; Autrique, Enrique; de los Campos, Gustavo

    2015-02-06

    Genomic selection (GS) models use genome-wide genetic information to predict genetic values of candidates of selection. Originally, these models were developed without considering genotype × environment interaction(G×E). Several authors have proposed extensions of the single-environment GS model that accommodate G×E using either covariance functions or environmental covariates. In this study, we model G×E using a marker × environment interaction (M×E) GS model; the approach is conceptually simple and can be implemented with existing GS software. We discuss how the model can be implemented by using an explicit regression of phenotypes on markers or using co-variance structures (a genomic best linear unbiased prediction-type model). We used the M×E model to analyze three CIMMYT wheat data sets (W1, W2, and W3), where more than 1000 lines were genotyped using genotyping-by-sequencing and evaluated at CIMMYT's research station in Ciudad Obregon, Mexico, under simulated environmental conditions that covered different irrigation levels, sowing dates and planting systems. We compared the M×E model with a stratified (i.e., within-environment) analysis and with a standard (across-environment) GS model that assumes that effects are constant across environments (i.e., ignoring G×E). The prediction accuracy of the M×E model was substantially greater of that of an across-environment analysis that ignores G×E. Depending on the prediction problem, the M×E model had either similar or greater levels of prediction accuracy than the stratified analyses. The M×E model decomposes marker effects and genomic values into components that are stable across environments (main effects) and others that are environment-specific (interactions). Therefore, in principle, the interaction model could shed light over which variants have effects that are stable across environments and which ones are responsible for G×E. The data set and the scripts required to reproduce the analysis are

  11. Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.).

    Science.gov (United States)

    Kwong, Qi Bin; Teh, Chee Keng; Ong, Ai Ling; Chew, Fook Tim; Mayes, Sean; Kulaveerasingam, Harikrishna; Tammi, Martti; Yeoh, Suat Hui; Appleton, David Ross; Harikrishna, Jennifer Ann

    2017-12-11

    Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals. This family is an important breeding source for developing new mother palms for superior oil yield and bunch characters. The traits of interest selected for this study were fruit-to-bunch (F/B), shell-to-fruit (S/F), kernel-to-fruit (K/F), mesocarp-to-fruit (M/F), oil per palm (O/P) and oil-to-dry mesocarp (O/DM). The marker systems evaluated were simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). RR-BLUP, Bayesian A, B, Cπ, LASSO, Ridge Regression and two machine learning methods (SVM and Random Forest) were used to evaluate GS accuracy of the traits. The kinship coefficient between individuals in this family ranged from 0.35 to 0.62. S/F and O/DM had the highest genomic heritability, whereas F/B and O/P had the lowest. The accuracies using 135 SSRs were low, with accuracies of the traits around 0.20. The average accuracy of machine learning methods was 0.24, as compared to 0.20 achieved by other methods. The trait with the highest mean accuracy was F/B (0.28), while the lowest were both M/F and O/P (0.18). By using whole genomic SNPs, the accuracies for all traits, especially for O/DM (0.43), S/F (0.39) and M/F (0.30) were improved. The average accuracy of machine learning methods was 0.32, compared to 0.31 achieved by other methods. Due to high genomic resolution, the use of whole-genome SNPs improved the efficiency of GS dramatically for oil palm and is recommended for dura breeding programs. Machine learning slightly

  12. Accumulation of mercury in selected plant species grown in soils contaminated with different mercury compounds

    International Nuclear Information System (INIS)

    Su, Yi; Han, Fengxiang; Shiyab, Safwan; Chen, Jian; Monts, David L.

    2007-01-01

    The objective of our research is to screen and search for suitable plant species for phyto-remediation of mercury-contaminated soil. Currently our effort is specifically focused on mercury removal from the U.S. Department of Energy (DOE) sites, where mercury contamination is a major concern. In order to cost effectively implement mercury remediation efforts, it is necessary now to obtain an improved understanding of biological means of removing mercury and mercury compounds.. Phyto-remediation is a technology that uses various plants to degrade, extract, contain, or immobilize contaminants from soil and water. In particular, phyto-extraction is the uptake of contaminants by plant roots and translocation within the plants to shoots or leaves. Contaminants are generally removed by harvesting the plants. We have investigated phyto-extraction of mercury from contaminated soil by using some of the known metal-accumulating plants since no natural plant species with mercury hyper-accumulating properties has yet been identified. Different natural plant species have been studied for mercury uptake, accumulation, toxicity and overall mercury removal efficiency. Various mercury compounds, such as HgS, HgCl 2 , and Hg(NO 3 ) 2 , were used as contaminant sources. Different types of soil were examined and chosen for phyto-remediation experiments. We have applied microscopy and diffuse reflectance spectrometry as well as conventional analytical chemistry to monitor the phyto-remediation processes of mercury uptake, translocation and accumulation, and the physiological impact of mercury contaminants on selected plant species. Our results indicate that certain plant species, such as beard grass (Polypogon monospeliensis), accumulated a very limited amount of mercury in the shoots ( 2 powder, respectively; no visual stress symptoms were observed. We also studied mercury phyto-remediation using aged soils that contained HgS, HgCl 2 , or Hg(NO 3 ) 2 . We have found that up to hundreds

  13. Marker-assisted-selection (MAS): A fast track to increase genetic ...

    African Journals Online (AJOL)

    Administrator

    2011-09-21

    Sep 21, 2011 ... protein maize (QPM) through marker-assisted transfer of a recessive mutant ... and number which collectively determine the yield poten- tial (Monforte et .... A wide gap appears to exist between tagging genes with markers and ...

  14. Use of the alr gene as a food-grade selection marker in lactic acid bacteria.

    Science.gov (United States)

    Bron, Peter A; Benchimol, Marcos G; Lambert, Jolanda; Palumbo, Emmanuelle; Deghorain, Marie; Delcour, Jean; De Vos, Willem M; Kleerebezem, Michiel; Hols, Pascal

    2002-11-01

    Both Lactococcus lactis and Lactobacillus plantarum contain a single alr gene, encoding an alanine racemase (EC 5.1.1.1), which catalyzes the interconversion of D-alanine and L-alanine. The alr genes of these lactic acid bacteria were investigated for their application as food-grade selection markers in a heterologous complementation approach. Since isogenic mutants of both species carrying an alr deletion (Deltaalr) showed auxotrophy for D-alanine, plasmids carrying a heterologous alr were constructed and could be selected, since they complemented D-alanine auxotrophy in the L. plantarum Deltaalr and L. lactis Deltaalr strains. Selection was found to be highly stringent, and plasmids were stably maintained over 200 generations of culturing. Moreover, the plasmids carrying the heterologous alr genes could be stably maintained in wild-type strains of L. plantarum and L. lactis by selection for resistance to D-cycloserine, a competitive inhibitor of Alr (600 and 200 micro g/ml, respectively). In addition, a plasmid carrying the L. plantarum alr gene under control of the regulated nisA promoter was constructed to demonstrate that D-cycloserine resistance of L. lactis is linearly correlated to the alr expression level. Finally, the L. lactis alr gene controlled by the nisA promoter, together with the nisin-regulatory genes nisRK, were integrated into the chromosome of L. plantarum Deltaalr. The resulting strain could grow in the absence of D-alanine only when expression of the alr gene was induced with nisin.

  15. Augmenting the Genetic Toolbox for Sulfolobus islandicus with a Stringent Positive Selectable Marker for Agmatine Prototrophy

    Science.gov (United States)

    Cooper, Tara E.; Krause, David J.

    2013-01-01

    Sulfolobus species have become the model organisms for studying the unique biology of the crenarchaeal division of the archaeal domain. In particular, Sulfolobus islandicus provides a powerful opportunity to explore natural variation via experimental functional genomics. To support these efforts, we further expanded genetic tools for S. islandicus by developing a stringent positive selection for agmatine prototrophs in strains in which the argD gene, encoding arginine decarboxylase, has been deleted. Strains with deletions in argD were shown to be auxotrophic for agmatine even in nutrient-rich medium, but growth could be restored by either supplementation of exogenous agmatine or reintroduction of a functional copy of the argD gene from S. solfataricus P2 into the ΔargD host. Using this stringent selection, a robust targeted gene knockout system was established via an improved next generation of the MID (marker insertion and unmarked target gene deletion) method. Application of this novel system was validated by targeted knockout of the upsEF genes involved in UV-inducible cell aggregation formation. PMID:23835176

  16. Development of aromatic giant-embryo rice by molecular marker-assisted selection

    Directory of Open Access Journals (Sweden)

    ZHU Yingdong

    2013-12-01

    Full Text Available Aromatic rice is loved for its distinctive aroma when cooking and eating.In this research,aromatic normal-embryo rice and non-aromatic giant-embryo rice,"Shangshida No.5",both bred by our laboratory,were selected as the parents for the hybridization.We used conventional breeding techniques as well as fragrance gene marker-assisted selection to derive new aromatic giant-embryo rice "Shangshida No.8".By comparing the agronomic and yield characters of "Shangshida No.5" and "Shangshida No.8",the average of filled grains per panicle of "Shangshida No.5" exceeds "Shangshida No.8" very significantly,while the average of effective panicles of "Shangshida No.8" is slightly more than "Shangshida No.5".Also,in the weight of thousand grains "Shangshida No.8" is slightly heavier than "Shangshida No.5".Thus,their grain weights per plant are close,29.10 g and 28.92 g respectively.By comparing the traits of rice embryo,there is no significant difference in embryo weight and volume.Also,there is no significant difference in weight ratio and volume ratio of embryo.This research has laid a solid foundation for further market development and application of aromatic giant-embryo rice.

  17. Potential biochemical markers for selection of disease resistance in Vigna radiata

    International Nuclear Information System (INIS)

    Badere, R.S.; Koche, D.K.; Choudhary, A.D.; Pawar, S.E.

    2001-01-01

    The Vigna radiata (L.) Wilczek (Green gram), a major pulse crop is prone to damaging diseases caused by Erysiphe polygoni, Cercospora canescens and Rhizoctonia sp. Therefore, the development of multiple resistance is a major breeding objective in green gram. Resistance to powdery mildew has already been developed, however, there are no reports on the development of resistance to Cercospora in green gram. Owing to limitation of conventional screening methods, the improvement for multiple disease resistance is inadequate, in this crop. It needs an efficient and quick selection method, for screening the plant population at an early stage. It is well established that the resistant interaction, in plants, involves accumulation of antibiotic compound phytoalexin (Genestein in Vigna radiata) and induction of enzymes such as β-1,3 gulcanase and Chitinases. These compounds are not only induced by pathogens but also pathogen-derived elicitors. These biochemical compounds can be used as resistance indicative biochemical markers for screening the natural or mutagen induced genetic diversity in populations of Vigna radiata in non-destructive manner. It, however, needs a systematic study of plant defense response. This paper deals with the response of resistant and susceptible cultivars of vigna radiata to Cercospora elicitor and development of non-destructive selection method for disease resistance. (author)

  18. Selected Cardiovascular Risk Markers in Vegetarians and Subjects of General Population.

    Science.gov (United States)

    Valachovičová, Martina; Príbojová, Jana; Urbánek, Vladimír; Bírošová, Lucia

    2017-12-01

    Besides genetic factors there are environmental effects including nutritional habits which can influence the risk of age-related diseases. The aim of the study was to assess the age dependence of selected cardiovascular risk markers in two groups of subjects with different nutritional pattern. In 470 long-term vegetarians and 478 subjects of general population the following indicators were measured: total cholesterol, HDL-cholesterol, triacylglycerol, glucose, insulin concentrations, LDL-cholesterol, atherogenic index and insulin resistance IR(HOMA) were also calculated in studied subjects. Obtained data were evaluated according to age decades. Vegetarian vs. non-vegetarian concentrations of total cholesterol, LDL-cholesterol, insulin, and values of atherogenic index and IR(HOMA) were significantly reduced in all age decades. Vegetarian vs. non-vegetarian triacalglycerol concentrations were significantly reduced from 4th–7th decade. Vegetarian average decade values of all lipid parameters were in reference range. In non-vegetarian group, the risk average values of total cholesterol (>5.2 mmol/l) were found from 5th–7th decade, LDL-cholesterol (>3.3 mmol/l) in 7th decade and atherogenic index (>4) in 6th–7th decade. In vegetarians vs. non-vegetarians were noted the average decade values for total cholesterol ranging from 4.01–4.59 vs. 4.48–5.67 mmol/l, for triacylglycerols 1.00–1.33 vs. 1.13–1.74 mmol/l, for LDL-cholesterol 2.03–2.58 vs. 2.43–3.49 mmol/l, for atherogenic index 2.72–3.31 vs. 3.05–4.21 and for IR(HOMA) 0.99–1.15 vs. 1.15–1.84. Our data show significantly reduced mean age decade values of lipid and non-lipid cardiovascular risk markers in all adult vegetarians. Smaller changes of markers between decades compared to non-vegetarians document a protective effect of vegetarian nutrition in prevention of cardiovascular disease. Copyright© by the National Institute of Public Health, Prague 2017

  19. The major Alternaria alternata allergen, Alt a 1: A reliable and specific marker of fungal contamination in citrus fruits.

    Science.gov (United States)

    Gabriel, M F; Uriel, N; Teifoori, F; Postigo, I; Suñén, E; Martínez, J

    2017-09-18

    The ubiquitously present spores of Alternaria alternata can spoil a wide variety of foodstuffs, including a variety of fruits belonging to the Citrus genus. The major allergenic protein of A. alternata, Alt a 1, is a species-specific molecular marker that has been strongly associated with allergenicity and phytopathogenicity of this fungal species. This study aimed to evaluate the potential of the detection of Alt a 1 as a reliable indicator of A. alternata contamination in citrus fruits. To accomplish this aim, sixty oranges were artificially infected with a spore suspension of A. alternata. Internal fruit material was collected at different incubation times (one, two and three weeks after the fungal inoculation) and used for both total RNA extraction and protein extraction. Alt a 1 detection was then performed by polymerase chain reaction (PCR) amplification using Alt a 1 specific primers and by enzyme-linked immunosorbent assay (ELISA). The experimental model presented in this work was effective to simulate the typical Alternaria black rot phenotype and its progression. Although both PCR and ELISA techniques have been successfully carried out for detecting Alt a 1 allergen in A. alternata infected oranges, the PCR method was found to be more sensitive than ELISA. Nevertheless, ELISA results were highly valuable to demonstrate that considerable amounts of Alt a 1 are produced during A. alternata fruit infection process, corroborating the recently proposed hypothesis that this protein plays a role in the pathogenicity and virulence of Alternaria species. Such evidence suggests that the detection of Alt a 1 by PCR-based assay may be used as a specific indicator of the presence of pathogenic and allergenic fungal species, A. alternata, in fruits. This knowledge can be employed to control the fungal infection and mitigate agricultural losses as well as human exposure to A. alternata allergens and toxins. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Three vibrio-resistance related EST-SSR markers revealed by selective genotyping in the clam Meretrix meretrix.

    Science.gov (United States)

    Nie, Qing; Yue, Xin; Chai, Xueliang; Wang, Hongxia; Liu, Baozhong

    2013-08-01

    The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker-trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P SSR markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Occurrence of Intestinal Parasitic Contamination in Select Consumed Local Raw Vegetables and Fruits in Kuantan, Pahang

    Science.gov (United States)

    Yusof, Afzan Mat; Mohammad, Mardhiah; Abdullahi, Muna Abshir; Mohamed, Zeehaida; Zakaria, Robaiza; Wahab, Ridhwan Abdul

    2017-01-01

    Intestinal parasitic infections are one of the most common causes of human diseases that result in serious health and economic issues in many developing and developed countries. Raw vegetables and fruits play an important role in transmitting parasites to humans. Hence, the aim of this study was to investigate the parasitological contamination of select commonly consumed local leafy vegetables and fruits in Kuantan, Malaysia. One kilogram of locally consumed raw vegetables and fruits were collected randomly from the Kuantan wet market (Pasar Tani) during the monsoon season (November 2014–January 2015) and the dry season (February 2015–April 2015). A standard wet mount procedure and modified Ziehl-Neelsen staining were used for the detection of parasites. In the present study, the examination of vegetables revealed five different parasite species. The vegetable samples collected from Kuantan’s wet market were positive for both helminthes and protozoa. However, the fruits samples were negative for parasitic contamination. Pegaga was the most contaminated leafy vegetable in this study, and Strongyloides was the parasite found most frequently. Furthermore, there was a high diversity in the type of parasites observed during the dry season compared to the monsoon season. Therefore, further action should be taken to reduce the occurrence of parasitic contamination in vegetables by implementing the principles of good agricultural practice and improving water treatment efficacy. PMID:28228914

  2. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding.

    Science.gov (United States)

    He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin

    2014-01-01

    Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.

  3. ISSR marker-assisted genetic diversity analysis of Dioscorea hispida and selection of the best variety for sustainable production.

    Science.gov (United States)

    Nudin, Nur Fatihah Hasan; Ali, Abdul Manaf; Ngah, Norhayati; Mazlan, Nor Zuhailah; Mat, Nashriyah; Ghani, Mohd Noor Abd; Alias, Nadiawati; Zakaria, Abd Jamil; Jahan, Md Sarwar

    2017-08-01

    Plant breeding is a way of selection of a particular individual for the production of the progeny by separating or combining desired characteristics. The objective of this study was to justify different characteristics of Dioscorea hispida (Ubi gadong) varieties using molecular techniques to select the best variety for sustainable production at the farmer's level. A total of 160 germplasms of Ubi gadong were collected from different locations at the Terengganu and Kelantan states of Malaysia. Forty eight (48) out of 160 germplasms were selected as "primary" selection based on yield and other qualitative characters. Selected collections were then grown and maintained for ISSR marker-assisted genetic diversity analysis. Overall plant growth and yield of tubers were also determined. A total of 12 ISSR markers were tested to justify the characteristics of Ubi gadong varieties among which three markers showed polymorphic bands and on average 57.3% polymorphism were observed representing the highest variation among germplasms. The ISSR marker based on UPGMA cluster analysis grouped all 48 D. hispida into 10 vital groups that proved a vast genetic variation among germplasm collections. Therefore, hybridization should be made between two distant populations. The D. hispida is already proved as the highest starch content tuber crops and very rich in vitamins with both micro and macro minerals. Considering all these criteria and results from marker-assisted diversity analysis, accessions that are far apart based on their genetic coefficient (like DH27 and DH71; DH30 and DH70; DH43 and DH62; DH45 and DH61; DH77 and DH61; DH78 and DH57) could be selected as parents for further breeding programs. This will bring about greater diversity, which will lead to high productive index in terms of increase in yield and overall quality and for the ultimate target of sustainable Ubi gadong production. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights

  4. Selected markers of cardiovascular disease in a population exposed to arsenic from drinking water.

    Science.gov (United States)

    Bošnjak, Zinka; Cavar, Suzana; Klapec, Tomislav; Milić, Marija; Klapec-Basar, Mirta; Toman, Miroslav

    2008-09-01

    This study examined prevalence and serum levels of selected markers of cardiovascular disease in 34 subjects from a Croatian rural population exposed to high levels of arsenic (As) from drinking water (611.89±10.06μg/l). The prevalences of overweight and obese subjects in the population were 32% and 35%. Half the subjects had hypertension, 29% had increased fasting serum glucose level and two were diabetic. Median total cholesterol (5.82mmol/l) and triglycerides (2.15mmol/l) were above the desirable margins. The median C-reactive protein level (1.20mg/l) was slightly higher than previously reported for healthy subjects. Serum Hsp70 level was significantly higher in nonsmokers. Total urinary As levels were positively correlated with age-adjusted serum levels of cobalamin. Near significance were also serum total bilirubin, antibodies to Hsp60 and folate. Tentative investigation of risk factors among subjects classified by tumor necrosis factor-α -308G/A and interleukin-6-174G/C gene polymorphisms was also performed. Collectively, the results are in agreement with the hypothesis of As-induced and/or compounded cardiovascular disease. Copyright © 2008 Elsevier B.V. All rights reserved.

  5. Inflammatory markers as selection criteria of hepatocellular carcinoma in living-donor liver transplantation.

    Science.gov (United States)

    Na, Gun Hyung; Kim, Dong Goo; Han, Jae Hyun; Kim, Eun Young; Lee, Soo Ho; Hong, Tae Ho; You, Young Kyoung

    2014-06-07

    To investigate that inflammatory markers can predict accurately the prognosis of hepatocelluar carcinoma (HCC) patients in living-donor liver transplantation (LDLT). From October 2000 to November 2011, 224 patients who underwent living donor liver transplantation for HCC at our institution were enrolled in this study. We analyzed disease-free survival (DFS) and overall survival (OS) after LT in patients with HCC and designed a new score model using pretransplant neutrophil-lymphocyte ratio (NLR) and C-reactive protein (CRP). The DFS and OS in patients with an NLR level ≥ 6.0 or CRP level ≥ 1.0 were significantly worse than those of patients with an NLR level < 6.0 or CRP level < 1.0 (P = 0.049, P = 0.003 for NLR and P = 0.010, P < 0.001 for CRP, respectively). Using a new score model using the pretransplant NLR and CRP, we can differentiate HCC patients beyond the Milan criteria with a good prognosis from those with a poor prognosis. Combined with the Milan criteria, new score model using NLR and CRP represent new selection criteria for LDLT candidates with HCC, especially beyond the Milan criteria.

  6. Selection of mercury accumulator plants for gold mine tailing contaminated soils

    Directory of Open Access Journals (Sweden)

    N Muddarisna

    2015-04-01

    Full Text Available Phytoremediation, which is more efficient with less side effects than conventional physical and chemical methods, is increasing in popularity as a remediation system. This paper provides a brief overview of developments in research and application of phytoremediation of soil contaminated with gold mine tailings containing mercury. Lindernia crustacea L., Digitaria radicosa Presl. Miq., Zingiber purpurium L, Paspalum conjugatum Berg., Cyperus kyllingia Endl., and Caladium bicolor Vent., that were selected for this study were planted in the planting media consisting of soil (70% and tailings (30% for 9 weeks. The results showed that after 9 weeks of planting, Paspalum conjugatum had growth rate, biomass production, Hg accumulation, and ratio of shoot Hg : root Hg higher than those of other plant species tested, both in the media consisted of amalgamation and cyanidation tailings. It can thus be concluded that Paspalum conjugatum is potential plant species for remediating mercury-contaminated soil.

  7. Evaluation and selection of test methods for assessment of contaminated sediments in the Baltic Sea

    DEFF Research Database (Denmark)

    Lehtonen, Kari; Ahvo, Aino; Berezina, Nadya

    The purpose of the CONTEST project (2014-15) is to test, develop, evaluate and select suitable biological methods to be applied in the quantitative and qualitative assessment of toxicity of anthropogenically contaminated sediments in the Baltic Sea marine region. Here is presented results from...... showed large variability in the sensitivity of the different biotests. Most of the tests applied showed concentration-dependent effects on the test organisms. New experiments will be carried out in 2015. The CONTEST project is funded by the Nordic Council of Ministers and the Finnish Ministry...... a set of pilot experiments, which were performed by the participating laboratories. Chemical analysis of the contaminated harbour sediment chosen as the test matrix confirmed the presence of high concentrations of polycyclic aromatic hydrocarbons, organotins and trace metals, and the sediment...

  8. Addition of chromic oxide to creep feed as a fecal marker for selection of creep feed-eating suckling pigs

    NARCIS (Netherlands)

    Kuller, W.I.; Beers-Schreurs, van H.M.G.; Soede, N.M.; Taverne, M.A.M.; Kemp, B.; Verheijden, J.H.M.

    2007-01-01

    Objective-To determine whether the addition of chromic oxide (Cr2O3) to creep feed could be used as a visual marker in feces for selection of creep feed-eating suckling pigs. Animals-20 suckling pigs. Procedures-Via syringe, 5 pigs (2 to 3 days old on day 0; 1 pig/treatment) from each of 4 litters

  9. Assessment of heavy metal contamination, levels in topsoil at selected auto-workshops in Accra, Ghana

    International Nuclear Information System (INIS)

    Ziblim, M. Y.

    2015-07-01

    The research was conducted to assess the levels of contamination of heavy metals in the topsoil at selected auto-workshops in Accra to determine the anthropogenic and crustal contributions and the human heath risk associated with them. Soil samples collected from four auto-workshops were analysed using Atomic Absorption Spectrometer. Eleven (11) elements: Co, Fe, Cu, Mn, Cr, As, Hg, Zn, Pb, Ni, and Cd were identified in each sample collected from the auto-workshops. Pollution indices; contamintion factor (Cf) index of geoaccumulation (Igeo) and pollution load index (PLI) were used to assess the contamination levels. It revealed the extent of contamination at the auto-workshops for most of the elements which range from low to considerate contamintion. Lead (Pb) recorded the greatest contamination levels at the auto-electrical location. The results from the index of geoccumulation showed no pollution to highly pollution indicting high variations of pollution levels at different locations. The results of the PLI in almost all locations ranged from moderately to extremely polluted. Noncancer effect on children and adults due to exposure to the topsoil were also estimated with some selected metal elements. The hazard quotient (HQ) evaluation, showed ingestion to be the route of exposure to soil dust that results in a higher risk for heavy metals, followed by dermal contact. The effect due to inhalation of resuspended dust particles through the mouth and nose is relatively low. It was observed that, the auto-workshops are generally polluted with heavy metals and therefore posing ill-health effect to the humans and the environment. (au)

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

    International Nuclear Information System (INIS)

    Lauria, D.C.

    2006-01-01

    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 228 Ra soil activity concentration reached values up to 33,000 Bq/kg while those for 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 the

  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. Development and Validation of Marker-Aided Selection Methods for Wood Property Traits in Loblolly Pine and Hybrid Poplar; FINAL

    International Nuclear Information System (INIS)

    Tuskan, G.A.

    2001-01-01

    Wood properties influence pulp and paper quality. Certainly, overall pulp yields are directly related to the cellulose content, changes in hemicellulose content are associated with changes in pulp cohesiveness, and pulping efficiency is related to lignin content. Despite the importance of wood properties on product quality, little progress has been made in improving such traits because current methods of assessing wood and fiber characteristics are time-consuming, expensive, and often imprecise. Genetic improvement of wood and fiber properties has been further hampered by the large size of trees, delayed reproductive maturity and long harvest cycles. Recent developments in molecular genetics will help overcome the physical, economic and biological constraints in assessing and improving wood properties. Genetic maps consisting of numerous molecular markers are now available for loblolly pine and hybrid poplar. Such markers/maps may be used as part of a marker-aided selection and breeding effort or to expedite the isolation and characterization of genes and/or promoters that directly control wood properties. The objectives of this project are: (1) to apply new and rapid analytical techniques for assessing component wood properties to segregating F(sub 2) progeny populations of loblolly pine and hybrid poplar, (2) to map quantitative trait loci and identify molecular markers associated with wood properties in each of the above species and (3) to validate marker-aided selection methods for wood properties in loblolly pine and hybrid poplar

  13. Development and Validation of Marker-Aided Selection Methods for Wood Property Traits in Loblolly Pine and Hybrid Poplar

    Energy Technology Data Exchange (ETDEWEB)

    Tuskan, G.A.

    2001-06-20

    Wood properties influence pulp and paper quality. Certainly, overall pulp yields are directly related to the cellulose content, changes in hemicellulose content are associated with changes in pulp cohesiveness, and pulping efficiency is related to lignin content. Despite the importance of wood properties on product quality, little progress has been made in improving such traits because current methods of assessing wood and fiber characteristics are time-consuming, expensive, and often imprecise. Genetic improvement of wood and fiber properties has been further hampered by the large size of trees, delayed reproductive maturity and long harvest cycles. Recent developments in molecular genetics will help overcome the physical, economic and biological constraints in assessing and improving wood properties. Genetic maps consisting of numerous molecular markers are now available for loblolly pine and hybrid poplar. Such markers/maps may be used as part of a marker-aided selection and breeding effort or to expedite the isolation and characterization of genes and/or promoters that directly control wood properties. The objectives of this project are: (1) to apply new and rapid analytical techniques for assessing component wood properties to segregating F2 progeny populations of loblolly pine and hybrid poplar, (2) to map quantitative trait loci and identify molecular markers associated with wood properties in each of the above species and (3) to validate marker-aided selection methods for wood properties in loblolly pine and hybrid poplar.

  14. Oral cancer prognosis based on clinicopathologic and genomic markers using a hybrid of feature selection and machine learning methods

    Science.gov (United States)

    2013-01-01

    Background Machine learning techniques are becoming useful as an alternative approach to conventional medical diagnosis or prognosis as they are good for handling noisy and incomplete data, and significant results can be attained despite a small sample size. Traditionally, clinicians make prognostic decisions based on clinicopathologic markers. However, it is not easy for the most skilful clinician to come out with an accurate prognosis by using these markers alone. Thus, there is a need to use genomic markers to improve the accuracy of prognosis. The main aim of this research is to apply a hybrid of feature selection and machine learning methods in oral cancer prognosis based on the parameters of the correlation of clinicopathologic and genomic markers. Results In the first stage of this research, five feature selection methods have been proposed and experimented on the oral cancer prognosis dataset. In the second stage, the model with the features selected from each feature selection methods are tested on the proposed classifiers. Four types of classifiers are chosen; these are namely, ANFIS, artificial neural network, support vector machine and logistic regression. A k-fold cross-validation is implemented on all types of classifiers due to the small sample size. The hybrid model of ReliefF-GA-ANFIS with 3-input features of drink, invasion and p63 achieved the best accuracy (accuracy = 93.81%; AUC = 0.90) for the oral cancer prognosis. Conclusions The results revealed that the prognosis is superior with the presence of both clinicopathologic and genomic markers. The selected features can be investigated further to validate the potential of becoming as significant prognostic signature in the oral cancer studies. PMID:23725313

  15. Criteria for the Selection of Reference Groups in the Statistical Evaluation of Tumor Markers

    Czech Academy of Sciences Publication Activity Database

    Holubec jr., L.; Topolčan, O.; Pikner, R.; Pecen, Ladislav; Holubec sen., L.

    2002-01-01

    Roč. 22, 1B (2002), s. 531 ISSN 0250-7005. [International Hamburg Symposium on Tumor Markers /11./. 27.01.2002-29.01.2002, Hamburg] Institutional research plan: AV0Z1030915 Keywords : reference groups * tumor markers Subject RIV: BA - General Mathematics

  16. The impact of sample size and marker selection on the study of haplotype structures

    Directory of Open Access Journals (Sweden)

    Sun Xiao

    2004-03-01

    Full Text Available Abstract Several studies of haplotype structures in the human genome in various populations have found that the human chromosomes are structured such that each chromosome can be divided into many blocks, within which there is limited haplotype diversity. In addition, only a few genetic markers in a putative block are needed to capture most of the diversity within a block. There has been no systematic empirical study of the effects of sample size and marker set on the identified block structures and representative marker sets, however. The purpose of this study was to conduct a detailed empirical study to examine such impacts. Towards this goal, we have analysed three representative autosomal regions from a large genome-wide study of haplotypes with samples consisting of African-Americans and samples consisting of Japanese and Chinese individuals. For both populations, we have found that the sample size and marker set have significant impact on the number of blocks and the total number of representative markers identified. The marker set in particular has very strong impacts, and our results indicate that the marker density in the original datasets may not be adequate to allow a meaningful characterisation of haplotype structures. In general, we conclude that we need a relatively large sample size and a very dense marker panel in the study of haplotype structures in human populations.

  17. Apparent discrepancy in contamination history of a sub-tropical estuary evaluated through 21Pb profile and chronostratigraphical markers

    International Nuclear Information System (INIS)

    Marques, Aguinaldo N. . E-mail amarques@vm.uff.br; Monna, Fabrice; Silva Filho, Emmanoel V. da; Fernex, Francois E.; Fernando Lamego Simoes Filho, F.

    2006-01-01

    Zn and Cd concentrations, stable lead isotopes and 21 Pb-derived chronology were determined in a sediment core sampled at Sepetiba Bay (South-eastern Brazil). During the last decades, the bay's watershed has been modified by the increase of industrial activities and human interventions. In particular, Zn and Cd ore treatment plants were built near the coast in 1960 and 1970, respectively, and water has been diverted from the adjacent Paraiba do Sul River watershed since 1950. The core collected at shallow depth near the industrial area exhibits four successive events: (i) at 50 cm depth, a change in the 206 Pb/ 207 Pb ratio from about 1.162 to more than 1.18 might be the result of the Sao Francisco Channel opening and water diversion from Paraiba do Sul river; (ii) at 40 cm depth, Zn concentration starts to increase (up to 0.8 mg g -1 ) (iii) above 30 cm depth, relatively high Cd concentrations (up to 1.6 μg g -1 ) are observed and (iv) at 16 cm depth, change in unsupported 21 Pb slope is probably related to a waste dam built to prevent strong metal contamination in the bay. Sediment accumulation rates evaluated by Zn and Cd profiles used as time-markers are higher than those calculated from 21 Pb-based chronology models. Using the constant initial concentration (CIC) model both events are supposed to date back to about 1884 and 1902, respectively, while using the constant rate of supply (CRS) model it shifts to about 1925 and 1935. Such discrepancies are probably assigned to the fact that these models do not take into account site-specific local sedimentation dynamics. In the study area, particles deposition seems to be controlled by enrichment with unsupported 21 Pb transported by runoff from a mangrove flat bank. Chronology derived from a model that assumes an exponential increase of the initial 21 Pb activity fits well with the estimated rates obtained from historical events

  18. Apparent discrepancy in contamination history of a sub-tropical estuary evaluated through {sup 21}Pb profile and chronostratigraphical markers

    Energy Technology Data Exchange (ETDEWEB)

    Marques, Aguinaldo N. [Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Outeiro Sao Joao Batista, s/n, Centro-Niteroi, Caixa Postal 100 644, 24 001-970, RJ (Brazil)]. E-mail amarques@vm.uff.br; Monna, Fabrice [Archeologie, Culture et Societes, Centre des Sciences de la Terre, UMR 5594 Universite de Bourgogne, CNRS, bld Gabriel, F-21000 Dijon (France); Silva Filho, Emmanoel V. da [Departamento de Geoquimica, Instituto de Quimica, Universidade Federal Fluminense, Niteroi, RJ (Brazil); Fernex, Francois E. [Departamento de Geoquimica, Instituto de Quimica, Universidade Federal Fluminense, Niteroi, RJ (Brazil); Departement des Sciences de la Terre, Universite de Nice, Valrose, 06108 Nice (France); Fernando Lamego Simoes Filho, F. [Instituto de Radioprotecao e Dosimetria, Rio de Janeiro 22780-160, RJ (Brazil)

    2006-05-15

    Zn and Cd concentrations, stable lead isotopes and {sup 21}Pb-derived chronology were determined in a sediment core sampled at Sepetiba Bay (South-eastern Brazil). During the last decades, the bay's watershed has been modified by the increase of industrial activities and human interventions. In particular, Zn and Cd ore treatment plants were built near the coast in 1960 and 1970, respectively, and water has been diverted from the adjacent Paraiba do Sul River watershed since 1950. The core collected at shallow depth near the industrial area exhibits four successive events: (i) at 50 cm depth, a change in the {sup 206}Pb/{sup 207}Pb ratio from about 1.162 to more than 1.18 might be the result of the Sao Francisco Channel opening and water diversion from Paraiba do Sul river; (ii) at 40 cm depth, Zn concentration starts to increase (up to 0.8 mg g{sup -1}) (iii) above 30 cm depth, relatively high Cd concentrations (up to 1.6 {mu}g g{sup -1}) are observed and (iv) at 16 cm depth, change in unsupported {sup 21}Pb slope is probably related to a waste dam built to prevent strong metal contamination in the bay. Sediment accumulation rates evaluated by Zn and Cd profiles used as time-markers are higher than those calculated from {sup 21}Pb-based chronology models. Using the constant initial concentration (CIC) model both events are supposed to date back to about 1884 and 1902, respectively, while using the constant rate of supply (CRS) model it shifts to about 1925 and 1935. Such discrepancies are probably assigned to the fact that these models do not take into account site-specific local sedimentation dynamics. In the study area, particles deposition seems to be controlled by enrichment with unsupported {sup 21}Pb transported by runoff from a mangrove flat bank. Chronology derived from a model that assumes an exponential increase of the initial {sup 21}Pb activity fits well with the estimated rates obtained from historical events.

  19. A HYBRID FILTER AND WRAPPER FEATURE SELECTION APPROACH FOR DETECTING CONTAMINATION IN DRINKING WATER MANAGEMENT SYSTEM

    Directory of Open Access Journals (Sweden)

    S. VISALAKSHI

    2017-07-01

    Full Text Available Feature selection is an important task in predictive models which helps to identify the irrelevant features in the high - dimensional dataset. In this case of water contamination detection dataset, the standard wrapper algorithm alone cannot be applied because of the complexity. To overcome this computational complexity problem and making it lighter, filter-wrapper based algorithm has been proposed. In this work, reducing the feature space is a significant component of water contamination. The main findings are as follows: (1 The main goal is speeding up the feature selection process, so the proposed filter - based feature pre-selection is applied and guarantees that useful data are improbable to be detached in the initial stage which discussed briefly in this paper. (2 The resulting features are again filtered by using the Genetic Algorithm coded with Support Vector Machine method, where it facilitates to nutshell the subset of features with high accuracy and decreases the expense. Experimental results show that the proposed methods trim down redundant features effectively and achieved better classification accuracy.

  20. Recyclable bio-reagent for rapid and selective extraction of contaminants from soil

    International Nuclear Information System (INIS)

    Lomasney, H.L.

    1997-01-01

    This Phase I Small Business Innovation Research program is confirming the effectiveness of a bio-reagent to cost-effectively and selectively extract a wide range of heavy metals and radionuclide contaminants from soil. This bioreagent solution, developed by ISOTRON reg-sign Corporation (New Orleans, LA), is flushed through the soil and recycled after flowing through an electrokinetic separation module, also developed by ISOTRON reg-sign. The process is ex situ, and the soil remains in its transport container through the decontamination process. The transport container can be a fiberglass box, or a bulk bag or open-quotes super sack.close quotes Rocks, vegetation, roots, etc. need not be removed. High clay content soils are accommodated. The process provides rapid injection of reagent solution, and when needed, sand is introduced to speed up the heap leach step. The concentrated waste form is eventually solidified. The bio-reagent is essentially a natural product, therefore any solubizer residual in soil is not expected to cause regulatory concern. The Phase I work will confirm the effectiveness of this bio-reagent on a wide range of contaminants, and the engineering parameters that are needed to carry out a full-scale demonstration of the process. ISOTRON reg-sign scientists will work with contaminated soil from Los Alamos National Laboratory. LANL is in the process of decontaminating and decommissioning more than 300 sites within its complex, many of which contain heavy metals or radionuclides; some are mixed wastes containing TCE, PCB, and metals

  1. Recyclable bio-reagent for rapid and selective extraction of contaminants from soil

    Energy Technology Data Exchange (ETDEWEB)

    Lomasney, H.L. [ISOTRON Corp., New Orleans, LA (United States)

    1997-10-01

    This Phase I Small Business Innovation Research program is confirming the effectiveness of a bio-reagent to cost-effectively and selectively extract a wide range of heavy metals and radionuclide contaminants from soil. This bioreagent solution, developed by ISOTRON{reg_sign} Corporation (New Orleans, LA), is flushed through the soil and recycled after flowing through an electrokinetic separation module, also developed by ISOTRON{reg_sign}. The process is ex situ, and the soil remains in its transport container through the decontamination process. The transport container can be a fiberglass box, or a bulk bag or {open_quotes}super sack.{close_quotes} Rocks, vegetation, roots, etc. need not be removed. High clay content soils are accommodated. The process provides rapid injection of reagent solution, and when needed, sand is introduced to speed up the heap leach step. The concentrated waste form is eventually solidified. The bio-reagent is essentially a natural product, therefore any solubizer residual in soil is not expected to cause regulatory concern. The Phase I work will confirm the effectiveness of this bio-reagent on a wide range of contaminants, and the engineering parameters that are needed to carry out a full-scale demonstration of the process. ISOTRON{reg_sign} scientists will work with contaminated soil from Los Alamos National Laboratory. LANL is in the process of decontaminating and decommissioning more than 300 sites within its complex, many of which contain heavy metals or radionuclides; some are mixed wastes containing TCE, PCB, and metals.

  2. Marker-assisted selection: Policy considerations and options for developing countries

    International Nuclear Information System (INIS)

    Dargie, J.D.

    2007-01-01

    Policy options for research, development and diffusion of the products of marker-assisted selection (MAS) depend on the development objectives and priorities of the agricultural sector, its various subsectors and cross-cutting activities dealing with science and technology (S and T), including biotechnology and the management of genetic resources. The policy agenda in each of these areas has shifted from the traditional focus of 'raising productivity' to a broader agenda of improving rural livelihoods in both economic and non-economic terms in support of the Millennium Development Goals (MDGs). Securing financial commitments from national governments and donors to invest in MAS and related molecular approaches requires more active engagement by national agricultural research and extension systems (NARES) in the processes of revising poverty reduction strategy papers (PRSPs), and in developing policies and strategies for agricultural development, S and T and genetic resources. Agriculture and agricultural S and T are undergoing rapid change but few developing countries have either agricultural S and T or biotechnology policies. They need to develop these to build coherence across the agricultural sector including delineating the roles of public and private sector entities, and as a means to strengthen accountability with respect to priority setting, monitoring and evaluating the outcomes and impacts of both research and practical applications of MAS. Options are provided for developing and implementing MAS programmes and projects, for setting priorities and evaluating outcomes and impacts. Given the uncertain nature of technical change and the long time frames that often characterize translation of the research and extension services provided by NARES into sustainable improvements in productivity and livelihoods through genetic enhancement, it is concluded that greater emphasis needs to be placed on research to analyse systematically the critical paths involved in

  3. Marker-assisted selection in maize: current status, potential, limitations and perspectives from the private and public sectors

    International Nuclear Information System (INIS)

    Ragot, M.; Lee, M.

    2007-01-01

    More than twenty-five years after the advent of DNA markers, marker-assisted selection (MAS) has become a routine component of some private maize breeding programmes. Line conversion has been one of the most productive applications of MAS in maize breeding, reducing time to market and resulting in countless numbers of commercial products. Recently, applications of MAS for forward breeding have been shown to increase significantly the rate of genetic gain when compared with conventional breeding. Costs associated with MAS are still very high. Further improvements in marker technologies, data handling and analysis, phenotyping and nursery operations are needed to realize the full benefits of MAS for private maize breeding programmes and to allow the transfer of proven approaches and protocols to public breeding programmes in developing countries. (author)

  4. Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

    Directory of Open Access Journals (Sweden)

    Y. H. Li

    2014-05-01

    Full Text Available The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates

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

    International Nuclear Information System (INIS)

    Dai Chaomeng; Geissen, Sven-Uwe; Zhang Yalei; Zhang Yongjun; Zhou Xuefei

    2011-01-01

    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. - 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.

  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. Potential of vetiver (vetiveria zizanioides l.) grass in removing selected pahs from diesel contaminated soil

    International Nuclear Information System (INIS)

    Nisa, W.U.; Rashid, A.

    2015-01-01

    Phytoremediation has been renowned as an encouraging technology for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soils, little is known about how plant species behave during the process of PAH phytoremediation. Therefore, the aim of this study was to investigate the effectiveness of vetiver (Vetiveria zizanioides L.) plant in PAH phytoremediation and extraction potential of Vetiveria zizanioides for selected PAHs from the diesel contaminated soil. The field soil samples were spiked with varying concentrations (0.5% and 1%) of diesel and used for pot experiment which was conducted in greenhouse. Vetiver grass was used as experimental plant. Physico-chemical analysis of soil was performed before and after the experiment. Concentration of selected PAHs i.e. phenanthrene, pyrene and benzo(a)pyrene in soil was determined using HPLC. Plant parameters such as root/shoot length and dry mass were compared after harvest. Concentrations of PAHs were also determined in plant material and in soils after harvesting. Result showed that initial concentration of phenanthrene was significantly different from final concentration in treatments in which soil was spiked with diesel. Initial and final concentration of pyrene in soil was also significantly different from each other in two treatments in which soil was spiked with 1% diesel. Pyrene concentration was significantly different in roots and shoots of plants while benzo(a)pyrene concentration in treatments in which soil was spiked with diesel was also significantly different from roots and shoots. Phenanthrene was less extracted by the plant in all the treatments and it was present in higher concentration in soil as compared to plant. Our results indicate that vetiver grass has effectively removed PAHs from soil consequently a significantly higher root and shoot uptake of PAHs was observed than control treatments. Study concludes Vetiveria zizanioides as potentially promising plant specie for the removal

  8. Remediation of cadmium contamination in paddy soils by washing with chemicals: Selection of washing chemicals

    International Nuclear Information System (INIS)

    Makino, Tomoyuki; Sugahara, Kazuo; Sakurai, Yasuhiro; Takano, Hiroyuki; Kamiya, Takashi; Sasaki, Kouta; Itou, Tadashi; Sekiya, Naoki

    2006-01-01

    The efficiencies of neutral salts, strong acids, and chelates were tested for extracting cadmium (Cd) from three paddy soils. The higher the selectivity of the cations of the added neutral salts toward soil adsorption sites, the lower the pH in the extracts and the more soil Cd could be extracted. In addition, soil carbon and nitrogen contents and mineral composition were closely associated with the amount of Cd extracted. Calcium chloride and iron(III) chloride were selected as wash chemicals to restore Cd-contaminated paddy soils in situ. Washing with calcium chloride led to the formation of Cd chloride complexes, enhancing Cd extraction from the soils. The washing also substantially decreased soil levels of exchangeable and acid-soluble Cd, which are the major forms of bioavailable Cd for rice (Oryza sativa L.). The optimum conditions for in situ soil washing were also determined for calcium chloride. - Calcium chloride and iron(III) chloride were useful for the in situ washing of Cd-contaminated paddy soils

  9. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    OpenAIRE

    Ariffin, Zulhairil; Md Sah, Muhammad Shafie; Idris, Salma; Hashim, Nuradni

    2015-01-01

    ISSR markers were employed to reveal genetic diversity and genetic relatedness among 28 Mangifera accessions collected from Yan (Kedah), Bukit Gantang (Perak), Sibuti (Sarawak), and Papar (Sabah). A total of 198 markers were generated using nine anchored primers and one nonanchored primer. Genetic variation among the 28 accessions of Mangifera species including wild relatives, landraces, and clonal varieties is high, with an average degree of polymorphism of 98% and mean Shannon index, H0=7.5...

  10. Cre/lox system to develop selectable marker free transgenic tobacco plants conferring resistance against sap sucking homopteran insect.

    Science.gov (United States)

    Chakraborti, Dipankar; Sarkar, Anindya; Mondal, Hossain A; Schuermann, David; Hohn, Barbara; Sarmah, Bidyut K; Das, Sampa

    2008-10-01

    A binary expression vector was constructed containing the insecticidal gene Allium sativum leaf agglutinin (ASAL), and a selectable nptII marker gene cassette, flanked by lox sites. Similarly, another binary vector was developed with the chimeric cre gene construct. Transformed tobacco plants were generated with these two independent vectors. Each of the T(0) lox plants was crossed with T(0) Cre plants. PCR analyses followed by the sequencing of the target T-DNA part of the hybrid T(1) plants demonstrated the excision of the nptII gene in highly precised manner in certain percentage of the T(1) hybrid lines. The frequency of such marker gene excision was calculated to be 19.2% in the hybrids. Marker free plants were able to express ASAL efficiently and reduce the survivability of Myzus persiceae, the deadly pest of tobacco significantly, compared to the control tobacco plants. Results of PCR and Southern blot analyses of some of the T(2) plants detected the absence of cre as well as nptII genes. Thus, the crossing strategy involving Cre/lox system for the excision of marker genes appears to be very effective and easy to execute. Documentation of such marker excision phenomenon in the transgenic plants expressing the important insecticidal protein for the first time has a great significance from agricultural and biotechnological points of view.

  11. Equilibrium Strategy Based Recycling Facility Site Selection towards Mitigating Coal Gangue Contamination

    Directory of Open Access Journals (Sweden)

    Jiuping Xu

    2017-02-01

    Full Text Available Environmental pollution caused by coal gangue has been a significant challenge for sustainable development; thus, many coal gangue reduction approaches have been proposed in recent years. In particular, coal gangue facility (CGF construction has been considered as an efficient method for the control and recycling of coal gangue. Meanwhile, the identification and selection of suitable CGF sites is a fundamental task for the government. Therefore, based on the equilibrium strategy, a site selection approach under a fuzzy environment is developed to mitigate coal gangue contamination, which integrates a geographical information system (GIS technique and a bi-level model to identify candidate CGF sites and to select the most suitable one. In this situation, the GIS technique used to identify potential feasible sites is able to integrate a great deal of geographical data tofitwithpracticalcircumstances;thebi-levelmodelusedtoscreentheappropriatesitecanreasonably dealwiththeconflictsbetweenthelocalauthorityandthecolliery. Moreover,aKarush–Kuhn–Tucker (KKT condition-based approach is used to find an optimal solution, and a case study is given to demonstrate the effectiveness of the proposed method. The results across different scenarios show that appropriate site selection can achieve coal gangue reduction targets and that a suitable excess stack level can realize an environmental-economic equilibrium. Finally, some propositions and management recommendations are given.

  12. Selection of innovative technologies for the remediation of soils contaminated with radioactive and mixed wastes

    International Nuclear Information System (INIS)

    Steude, J.; Tucker, B.

    1991-01-01

    The remediation of sites containing radioactive and mixed wastes is in a period of rapid growth. The state of the art of remediation is progressing to handle the shortcomings of conventional pump and treat or disposal technologies. The objective of this paper is to review the status of selected innovative technologies which treat soils contaminated with radioactive and mixed waste. Technologies are generally classified as innovative if they are fully developed, but lack sufficient cost or performance data for comparison with conventional technologies. The Environmental Protection Agency recommends inclusion of innovative technologies in the RI/FS screening process if there is reason to believe that they would offer advantages in performance, implementability, cost, etc. This paper serves as a compilation of the pertinent information necessary to gain an overview of the selected innovative technologies to aid in the RI/F'S screening process. The innovative technologies selected for evaluation are listed below. Bioremediation, although innovative, was not included due to the combination of the vast amount of literature on this subject and the limited scope of this project. 1. Soil washing and flushing; 2. Low temperature thermal treatment; 3. Electrokinetics; 4. Infrared incineration; 5. Ultrasound; 6. In situ vitrification; 7. Soil vapor extraction; 8. Plasma torch slagging; 9. In situ hot air/steam extraction; 10. Cyclone reactor treatment; 11. In situ radio frequency; 12. Vegetative radionuclide uptake; and 13. In situ soil heating. The information provided on each technology includes a technical description, status, summary of results including types of contaminants and soils treated, technical effectiveness, feasibility and estimated cost

  13. Radiographic markers - A reservoir for bacteria?

    International Nuclear Information System (INIS)

    Tugwell, Jenna; Maddison, Adele

    2011-01-01

    Introduction: Amongst the most frequently handled objects in the radiology department are radiographic markers. They are personal accessories used with every patient, and are kept in the radiographers pockets when not utilised. Upon enquiry it was discovered that many radiographers disregarded the potential of these accessories to become a vector for cross-contamination thus never or rarely clean them. The aims of this study were therefore to identify if radiographic markers are a reservoir for bacteria and to establish an effective cleaning method for decontaminating them. Methodology: 25 radiographers/student radiographers were selected for this study. Swabbing of their markers prior and post cleaning took place. The microbiology laboratory subsequently analyzed the results by quantifying and identifying the bacteria present. The participants also completed a closed questionnaire regarding their markers (e.g. frequency of cleaning and type of marker) to help specify the results gained from the swabbing procedure. Results: From the sample swabbed, 92% were contaminated with various organisms including Staphylococcus and Bacillus species, the amount of bacteria present ranged from 0 to >50 CFU. There were no significant differences between disinfectant wipes and alcohol gel in decontaminating the markers. Both successfully reduced their bacterial load, with 80% of the markers post cleaning having 0 CFU. Conclusion: The results indicated that radiographic markers can become highly contaminated with various organisms thus serve as a reservoir for bacteria. In addition, the markers need to be cleaned on a regular basis, with either disinfectant wipes or alcohol gel to reduce their bacterial load.

  14. Volume reduction of low-level contaminated metal waste by melting: selection of method and conceptual plan

    International Nuclear Information System (INIS)

    Copeland, G.L.; Heestand, R.L.; Mateer, R.S.

    1978-06-01

    A review of the literature and prior experience led to selection of induction melting as the most promising method for volume reduction of low-level transuranic contaminated metal waste. The literature indicates that melting with the appropriate slags significantly lowers the total contamination level of the metals by preferentially concentrating contaminants in the smaller volume of slag. Surface contamination not removed to the slag is diluted in the ingot and is contained uniformly in the metal. This dilution and decontamination offers the potential of lower cost disposal such as shallow burial rather than placement in a national repository. A processing plan is proposed as a model for economic analysis of the collection and volume reduction of contaminated metals. Further development is required to demonstrate feasibility of the plan

  15. Selective Removal of Uranium from the Washing Solution of Uranium-Contaminated Soil

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seung Soo; Han, G. S.; Kim, G. N.; Koo, D. S.; Jeong, J. W.; Choi, J. W. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    This study examined selective removal methods of uranium from the waste solution by ion exchange resins or solvent extraction methods to reduce amount of the 2{sup nd} waste. Alamine-336, known as an excellent extraction reagent of uranium from the leaching solution of uranium ore, did not remove uranium from the acidic washing solution of soil. Uranyl ions in the acidic waste solution were sorbed on ampholyte resin with a high sorption efficiency, and desorbed from the resin by a washing with 0.5 M Na{sub 2}CO{sub 3} solution at 60 .deg. C. However, the uranium dissolved in the sulfuric acid solution was not sorbed onto the strong anion exchanger resins. A great amount of uranium-contaminated (U-contaminated) soil had been generated from the decommissioning of a uranium conversion plant. Our group has developed a decontamination process with washing and electrokinetic methods to decrease the amount of waste to be disposed of. However, this process generates a large amount of waste solution containing various metal ions.

  16. Selective Extraction of Organic Contaminants from Soil Using Pressurised Liquid Extraction

    Directory of Open Access Journals (Sweden)

    Rozita Osman

    2013-01-01

    Full Text Available This study focuses on the application of sorbents in pressurised liquid extraction (PLE cell to establish a selective extraction of a variety of organic contaminants (polycyclic aromatic hydrocarbons (PAHs, chlorpyrifos, phenol, pentachlorophenol, and sterols from soil. The selectivity and efficiency of each sorbent depend on the properties of the material, extracting solvent, capacity factor, organic compounds of interest, and PLE operating parameters (temperature, pressure, and extraction time. Several sorbents (silica, alumina, and Florisil were evaluated and with the proper choice of solvents, polar and nonpolar compounds were successfully separated in two fractions. Nonpolar compounds (PAHs, chlorpyrifos, and pentachlorophenol were recovered in the first fraction using a polar sorbent such as Florisil or alumina, and n-hexane as eluting solvent, while more polar compounds (phenol and sterols were recovered in the second fraction using methanol. Silica (5 g was found to be effective for selective extraction with the satisfactory recoveries for all compounds (PAHs from 87.1–96.2%, chlorpyrifos 102.9%, sterols from 93.7–100.5%, phenol 91.9%, and pentachlorophenol 106.2%. The efficiency and precision of this extraction approach and the existing EPA Method 3545 were compared.

  17. Bioremediation of diesel fuel contaminated soil: effect of non ionic surfactants and selected bacteria addition.

    Science.gov (United States)

    Collina, Elena; Lasagni, Marina; Pitea, Demetrio; Franzetti, Andrea; Di Gennaro, Patrizia; Bestetti, Giuseppina

    2007-09-01

    Aim of this work was to evaluate influence of two commercial surfactants and inoculum of selected bacteria on biodegradation of diesel fuel in different systems. Among alkyl polyethossilates (Brij family) and sorbitan derivates (Tween family) a first selection of surfactants was performed by estimation of Koc and Dafnia magna EC50 with molecular descriptor and QSAR model. Further experiments were conducted to evaluate soil sorption, biodegradability and toxicity. In the second part of the research, the effect of Brij 56, Tween 80 and selected bacteria addition on biodegradation of diesel fuel was studied in liquid cultures and in slurry and solid phase systems. The latter experiments were performed with diesel contaminated soil in bench scale slurry phase bioreactor and solid phase columns. Tween 80 addition increased the biodegradation rate of hydrocarbons both in liquid and in slurry phase systems. Regarding the effect of inoculum, no enhancement of biodegradation rate was observed neither in surfactant added nor in experiments without addition. On the contrary, in solid phase experiments, inoculum addition resulted in enhanced biodegradation compared to surfactant addition.

  18. Bioremediation of Diesel Fuel Contaminated Soil: Effect of Non Ionic Surfactants and Selected Bacteria Addition

    International Nuclear Information System (INIS)

    Collina, E.; Lasagni, M.; Pitea, D.; Franzetti, A.; Di Gennaro, P.; Bestetti, G.

    2007-01-01

    Aim of this work was to evaluate influence of two commercial surfactants and inoculum of selected bacteria on biodegradation of diesel fuel in different systems. Among alkyl polyethossilates (Brij family) and sorbitan derivates (Tween family) a first selection of surfactants was performed by estimation of Koc and Dafnia magna EC 50 with molecular descriptor and QSAR model. Further experiments were conducted to evaluate soil sorption, biodegradability and toxicity. In the second part of the research, the effect of Brij 56, Tween 80 and selected bacteria addition on biodegradation of diesel fuel was studied in liquid cultures and in slurry and solid phase systems. The latter experiments were performed with diesel contaminated soil in bench scale slurry phase bioreactor and solid phase columns. Tween 80 addition increased the biodegradation rate of hydrocarbons both in liquid and in slurry phase systems. Regarding the effect of inoculum, no enhancement of biodegradation rate was observed neither in surfactant added nor in experiments without addition. On the contrary, in solid phase experiments, inoculum addition resulted in enhanced biodegradation compared to surfactant addition

  19. Analytical Evaluation to Determine Selected PAHs in a Contaminated Soil With Type II Fuel

    International Nuclear Information System (INIS)

    Garcia Alonso, S.; Perez Pastor, R. M.; Sevillano Castano, M. L.; Garcia Frutos, F. J.

    2010-01-01

    A study on the optimization of an ultrasonic extraction method for selected PAHs determination in soil contaminated by type II fuel and by using HPLC with fluorescence detector is presented. The main objective was optimize the analytical procedure, minimizing the volume of solvent and analysis time and avoiding possible loss by evaporation. This work was carried out as part of a project that investigated a remediation process of agricultural land affected by an accidental spillage of fuel (Plan Nacional I + D + i, CTM2007-64 537). The paper is structured as: Optimization of wavelengths in the chromatographic conditions to improve resolution in the analysis of fuel samples. Optimization of the main parameters affecting in the extraction process by sonication. Comparison of results with those obtained by accelerated solvent extraction. (Author) 3 refs.

  20. Cleanup and treatment of radioactively contaminated land including areas near nuclear facilities. A selected bibliography

    International Nuclear Information System (INIS)

    Fore, C.S.; Faust, R.A.; Brewster, R.H.

    1982-09-01

    This annotated bibliography of 337 references summarizes the literature published on the cleanup and treatment of radioactively contaminated land. Specifically, this bibliography focuses on literature concerned with the methods of cleanup and treatment being applied - chemical, physical, or vegetative stabilization; the types of equipment being used; and the influence of climatic conditions on the method selected for use. The emphasis in such literature is placed on hazardous site cleanup efforts that have been completed as well as those that are in progress and are being planned. Appendix A includes 135 additional references to literature identified but not included in the bibliography because of time and funding constraints. Appendix B consists of a table that identifies the cleanup and treatment research conducted at specific sites. All of the information included in this bibliography is stored in a computerized form that is readily available upon request

  1. Development of tools and strategies towards marker assisted selection and gene cloning

    NARCIS (Netherlands)

    Brugmans, B.W.

    2005-01-01

    In this thesis research is described aiming at alleviation of the perceived limitations in the standard protocol which encompasses: mapping a trait, followed by marker saturation, genetic resolution, and finally BAC landing and walking to span the physical distance between the

  2. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood

    NARCIS (Netherlands)

    A.A.G. van Tilborg (Angela); L.C. Kompier (Lucie); I. Lurkin (Irene); R. Poort (Ricardo); S. El Bouazzaoui (Samira); K.A. van der Keur (Kirstin); T.C.M. Zuiverloon (Tahlita); L. Dyrskjot (Lars); T.F. Orntoft (Torben); M.J. Roobol-Bouts (Monique); E.C. Zwarthoff (Ellen)

    2012-01-01

    textabstractMicrosatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in

  3. Use of different marker pre-selection methods based on single SNP regression in the estimation of Genomic-EBVs

    Directory of Open Access Journals (Sweden)

    Corrado Dimauro

    2010-01-01

    Full Text Available Two methods of SNPs pre-selection based on single marker regression for the estimation of genomic breeding values (G-EBVs were compared using simulated data provided by the XII QTL-MAS workshop: i Bonferroni correction of the significance threshold and ii Permutation test to obtain the reference distribution of the null hypothesis and identify significant markers at P<0.01 and P<0.001 significance thresholds. From the set of markers significant at P<0.001, random subsets of 50% and 25% markers were extracted, to evaluate the effect of further reducing the number of significant SNPs on G-EBV predictions. The Bonferroni correction method allowed the identification of 595 significant SNPs that gave the best G-EBV accuracies in prediction generations (82.80%. The permutation methods gave slightly lower G-EBV accuracies even if a larger number of SNPs resulted significant (2,053 and 1,352 for 0.01 and 0.001 significance thresholds, respectively. Interestingly, halving or dividing by four the number of SNPs significant at P<0.001 resulted in an only slightly decrease of G-EBV accuracies. The genetic structure of the simulated population with few QTL carrying large effects, might have favoured the Bonferroni method.

  4. Tissue-specifically regulated site-specific excision of selectable marker genes in bivalent insecticidal, genetically-modified rice.

    Science.gov (United States)

    Hu, Zhan; Ding, Xuezhi; Hu, Shengbiao; Sun, Yunjun; Xia, Liqiu

    2013-12-01

    Marker-free, genetically-modified rice was created by the tissue-specifically regulated Cre/loxP system, in which the Cre recombinase gene and hygromycin phosphotransferase gene (hpt) were flanked by two directly oriented loxP sites. Cre expression was activated by the tissue-specific promoter OsMADS45 in flower or napin in seed, resulting in simultaneous excision of the recombinase and marker genes. Segregation of T1 progeny was performed to select recombined plants. The excision was confirmed by PCR, Southern blot and sequence analyses indicating that efficiency varied from 10 to 53 % for OsMADS45 and from 12 to 36 % for napin. The expression of cry1Ac and vip3A was detected by RT-PCR analysis in marker-free transgenic rice. These results suggested that our tissue-specifically regulated Cre/loxP system could auto-excise marker genes from transgenic rice and alleviate public concerns about the security of GM crops.

  5. Development of Selectable Marker-Free Transgenic Rice Plants with Enhanced Seed Tocopherol Content through FLP/FRT-Mediated Spontaneous Auto-Excision.

    Directory of Open Access Journals (Sweden)

    Hee-Jong Woo

    Full Text Available Development of marker-free transgenic plants is a technical alternative for avoiding concerns about the safety of selectable marker genes used in genetically modified (GM crops. Here, we describe the construction of a spontaneous self-excision binary vector using an oxidative stress-inducible modified FLP/FRT system and its successful application to produce marker-free transgenic rice plants with enhanced seed tocopherol content. To generate selectable marker-free transgenic rice plants, we constructed a binary vector using the hpt selectable marker gene and the rice codon-optimized FLP (mFLP gene under the control of an oxidative stress-inducible promoter between two FRT sites, along with multiple cloning sites for convenient cloning of genes of interest. Using this pCMF binary vector with the NtTC gene, marker-free T1 transgenic rice plants expressing NtTC were produced by Agrobacterium-mediated stable transformation using hygromycin as a selective agent, followed by segregation of selectable marker genes. Furthermore, α-, γ-, and total tocopherol levels were significantly increased in seeds of the marker-free transgenic TC line compared with those of wild-type plants. Thus, this spontaneous auto-excision system, incorporating an oxidative stress-inducible mFLP/FRT system to eliminate the selectable marker gene, can be easily adopted and used to efficiently generate marker-free transgenic rice plants. Moreover, nutritional enhancement of rice seeds through elevation of tocopherol content coupled with this marker-free strategy may improve human health and public acceptance of GM rice.

  6. Development of Selectable Marker-Free Transgenic Rice Plants with Enhanced Seed Tocopherol Content through FLP/FRT-Mediated Spontaneous Auto-Excision.

    Science.gov (United States)

    Woo, Hee-Jong; Qin, Yang; Park, Soo-Yun; Park, Soon Ki; Cho, Yong-Gu; Shin, Kong-Sik; Lim, Myung-Ho; Cho, Hyun-Suk

    2015-01-01

    Development of marker-free transgenic plants is a technical alternative for avoiding concerns about the safety of selectable marker genes used in genetically modified (GM) crops. Here, we describe the construction of a spontaneous self-excision binary vector using an oxidative stress-inducible modified FLP/FRT system and its successful application to produce marker-free transgenic rice plants with enhanced seed tocopherol content. To generate selectable marker-free transgenic rice plants, we constructed a binary vector using the hpt selectable marker gene and the rice codon-optimized FLP (mFLP) gene under the control of an oxidative stress-inducible promoter between two FRT sites, along with multiple cloning sites for convenient cloning of genes of interest. Using this pCMF binary vector with the NtTC gene, marker-free T1 transgenic rice plants expressing NtTC were produced by Agrobacterium-mediated stable transformation using hygromycin as a selective agent, followed by segregation of selectable marker genes. Furthermore, α-, γ-, and total tocopherol levels were significantly increased in seeds of the marker-free transgenic TC line compared with those of wild-type plants. Thus, this spontaneous auto-excision system, incorporating an oxidative stress-inducible mFLP/FRT system to eliminate the selectable marker gene, can be easily adopted and used to efficiently generate marker-free transgenic rice plants. Moreover, nutritional enhancement of rice seeds through elevation of tocopherol content coupled with this marker-free strategy may improve human health and public acceptance of GM rice.

  7. The thrombopoietin receptor, c-Mpl, is a selective surface marker for human hematopoietic stem cells

    Directory of Open Access Journals (Sweden)

    Kerr William G

    2006-02-01

    from mid-fetal through adult life. This study extends our previous work documenting human B-lineage, myeloid and CD34+ cell repopulation by c-mpl+ progenitors to show that c-mpl+ HSC/PC are also capable of significant T-lineage reconstitution in vivo. These results suggest that c-mpl merits consideration as a selective surface marker for the identification and isolation of human HSC in both basic research and clinical settings.

  8. Insights into population ecology and sexual selection in snakes through the application of DNA-based genetic markers.

    Science.gov (United States)

    Gibbs, H L; Weatherhead, P J

    2001-01-01

    Hypervariable genetic markers have revolutionized studies of kinship, behavioral ecology, and population biology in vertebrate groups such as birds, but their use in snakes remains limited. To illustrate the value of such markers in snakes, we review studies that have used microsatellite DNA loci to analyze local population differentiation and parentage in snakes. Four ecologically distinct species of snakes all show evidence for differentiation at small spatial scales (2-15 km), but with substantial differences among species. This result highlights how genetic analysis can reveal hidden aspects of the natural history of difficult-to-observe taxa, and it raises important questions about the ecological factors that may contribute to restricted gene flow. A 3-year study of genetic parentage in marked populations of the northern water snake showed that (1) participation in mating aggregations was a poor predictor of genetic-based measures of reproductive success; (2) multiple paternity was high, yet there was no detectable fitness advantage to multiple mating by females; and (3) the opportunity for selection was far higher in males than in females due to a larger variance in male reproductive success, and yet this resulted in no detectable selection on morphological variation in males. Thus genetic markers have provided accurate measures of individual reproductive success in this species, an important step toward resolving the adaptive significance of key features including multiple paternity and reversed sexual size dimorphism. Overall these studies illustrate how genetic analyses of snakes provide previously unobtainable information of long-standing interest to behavioral ecologists.

  9. Genetic diversity of indigenous chickens from selected areas in Kenya using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Okoth Noah Okumu

    2017-12-01

    Full Text Available In this study, indigenous chickens were collected from eight different regions in Kenya and kept at InCIP-Egerton University. These were studied using eighteen microsatellite markers to determine genetic variation. Statistics related to genetic variation were estimated using GenALEx6. Mean percentage polymorphic loci (PPL was 96.71% and 4% genetic variance (p ≥ 0.003 was seen between the eight populations. MCW0123 marker had the highest genetic variance of 13% among populations (p ≥ 0.003 at 95% CI. Mean He ranged from 0.351 ± 0.031 (SIB to 0.434 ± 0.022 (BM with a grand mean He of 0.399 ± 0.011 across the populations using the microsatellite markers. Nei’s genetic distance ranged from 0.016 (SIB and WP to 0.126 (NR and SIB. DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. This study found a lot of genetic variation and relatedness within and among populations. Based on the phylogenetic tree result, it is concluded that the clustering of the chicken populations in the present study is not based on geographical proximity. The microsatellite markers used in this study were suitable for the measurement of the genetic biodiversity and relationship of Kenyan chicken populations. These results can therefore serve as an initial step to plan the conservation of indigenous chickens in Kenya.

  10. Growth Factors and Breast Tumors, Comparison of Selected Growth Factors with Traditional Tumor Markers

    Czech Academy of Sciences Publication Activity Database

    Kučera, R.; Černá, M.; Ňaršanská, A.; Svobodová, Š.; Straková, M.; Vrzalová, J.; Fuchsová, R.; Třešková, I.; Kydlíček, T.; Třeška, V.; Pecen, Ladislav; Topolčan, O.; Padziora, P.

    2011-01-01

    Roč. 31, č. 12 (2011), s. 4653-4656 ISSN 0250-7005 Grant - others:GA MZd(CZ) NS9727; GA MZd(CZ) NS10238; GA MZd(CZ) NS10253 Institutional research plan: CEZ:AV0Z10300504 Keywords : growth factor * breast cancer * tumor markers * CA 15-3 * CEA * IGF1 * EGF * HGF Subject RIV: FD - Oncology ; Hematology Impact factor: 1.725, year: 2011

  11. Association of molecular markers with polyphenol oxidase activity in selected wheat genotypes

    International Nuclear Information System (INIS)

    Abbas, Z.; Javad, B.; Majeed, N.; Naqvi, S.

    2016-01-01

    Wheat (Triticum aestivum L.), a major staple food for the people of Pakistan and other Asian countries, is used as bread, chapatti, porridge, noodles and many other. It is established that color quality of wheat products depend on chemical and enzymatic factors especially the polyphenol oxidases (PPOs). These are copper containing enzymes which induce browning in wheat-based products. Various procedures for determining PPO activity available and differences in PPO activity among wheat genotypes have been documented. In present study, an attempt was made to establish the association of molecular markers with polyphenol oxidase activity in wheat genotypes having very high or very low PPO activities. Twelve pairs of markers were used out of which only three primer pairs viz. PPO43, PPO30 and WP2-2 yielded specific pattern discriminating high and low PPO genotypes. Cluster analysis for all 12 markers revealed that all the low PPO lline share the same sub cluster, but high PPO lines were dispersed in different clusters. (author)

  12. Beyond Neuronal Activity Markers: Select Immediate Early Genes in Striatal Neuron Subtypes Functionally Mediate Psychostimulant Addiction

    Directory of Open Access Journals (Sweden)

    Ramesh Chandra

    2017-06-01

    Full Text Available Immediate early genes (IEGs were traditionally used as markers of neuronal activity in striatum in response to stimuli including drugs of abuse such as psychostimulants. Early studies using these neuronal activity markers led to important insights in striatal neuron subtype responsiveness to psychostimulants. Such studies have helped identify striatum as a critical brain center for motivational, reinforcement and habitual behaviors in psychostimulant addiction. While the use of IEGs as neuronal activity markers in response to psychostimulants and other stimuli persists today, the functional role and implications of these IEGs has often been neglected. Nonetheless, there is a subset of research that investigates the functional role of IEGs in molecular, cellular and behavioral alterations by psychostimulants through striatal medium spiny neuron (MSN subtypes, the two projection neuron subtypes in striatum. This review article will address and highlight the studies that provide a functional mechanism by which IEGs mediate psychostimulant molecular, cellular and behavioral plasticity through MSN subtypes. Insight into the functional role of IEGs in striatal MSN subtypes could provide improved understanding into addiction and neuropsychiatric diseases affecting striatum, such as affective disorders and compulsive disorders characterized by dysfunctional motivation and habitual behavior.

  13. Generation of Trichoderma atroviride mutants with constitutively activated G protein signaling by using geneticin resistance as selection marker

    Directory of Open Access Journals (Sweden)

    Gruber Sabine

    2012-11-01

    Full Text Available Abstract Background Species of the fungal genus Trichoderma are important industrial producers of cellulases and hemicellulases, but also widely used as biocontrol agents (BCAs in agriculture. In the latter function Trichoderma species stimulate plant growth, induce plant defense and directly antagonize plant pathogenic fungi through their mycoparasitic capabilities. The recent release of the genome sequences of four mycoparasitic Trichoderma species now forms the basis for large-scale genetic manipulations of these important BCAs. Thus far, only a limited number of dominant selection markers, including Hygromycin B resistance (hph and the acetamidase-encoding amdS gene, have been available for transformation of Trichoderma spp. For more extensive functional genomics studies the utilization of additional dominant markers will be essential. Results We established the Escherichia coli neomycin phosphotransferase II-encoding nptII gene as a novel selectable marker for the transformation of Trichoderma atroviride conferring geneticin resistance. The nptII marker cassette was stably integrated into the fungal genome and transformants exhibited unaltered phenotypes compared to the wild-type. Co-transformation of T. atroviride with nptII and a constitutively activated version of the Gα subunit-encoding tga3 gene (tga3Q207L resulted in a high number of mitotically stable, geneticin-resistant transformants. Further analyses revealed a co-transformation frequency of 68% with 15 transformants having additionally integrated tga3Q207L into their genome. Constitutive activation of the Tga3-mediated signaling pathway resulted in increased vegetative growth and an enhanced ability to antagonize plant pathogenic host fungi. Conclusion The neomycin phosphotransferase II-encoding nptII gene from Escherichia coli proved to be a valuable tool for conferring geneticin resistance to the filamentous fungus T. atroviride thereby contributing to an enhanced genetic

  14. GAP1, a novel selection and counter-selection marker for multiple gene disruptions in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Regenberg, Birgitte; Hansen, J.

    2000-01-01

    the GAP1 gene. This is caused by recombination between two Salmonella typuimurium hisG direct repeats embracing GAP1, and will result in a sub-population of gap1 cells. Such cells are selected on a medium containing D-histidine, and may subsequently be used for a second gene disruption. Hence, multiple...... flanked by short (60 bp) stretches of the gene in question. Through homologous recombination, the cassette will integrate into the target gene, which is thus replaced by GAP1, and mutants are selected for on minimal L-citrulline medium. When propagated under non-selective conditions, some cells will lose...... gene disruptions can be made fast, cheaply and easily in a gap1 strain, with two positive selection steps for each disruption. Copyright (C) 2000 John Wiley & Sons, Ltd....

  15. Illustrating sensitivity in environmental fate models using partitioning maps - application to selected contaminants

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, T.; Wania, F. [Univ. of Toronto at Scarborough - DPES, Toronto (Canada)

    2004-09-15

    Generic environmental multimedia fate models are important tools in the assessment of the impact of organic pollutants. Because of limited possibilities to evaluate generic models by comparison with measured data and the increasing regulatory use of such models, uncertainties of model input and output are of considerable concern. This led to a demand for sensitivity and uncertainty analyses for the outputs of environmental fate models. Usually, variations of model predictions of the environmental fate of organic contaminants are analyzed for only one or at most a few selected chemicals, even though parameter sensitivity and contribution to uncertainty are widely different for different chemicals. We recently presented a graphical method that allows for the comprehensive investigation of model sensitivity and uncertainty for all neutral organic chemicals simultaneously. This is achieved by defining a two-dimensional hypothetical ''chemical space'' as a function of the equilibrium partition coefficients between air, water, and octanol (K{sub OW}, K{sub AW}, K{sub OA}), and plotting sensitivity and/or uncertainty of a specific model result to each input parameter as function of this chemical space. Here we show how such sensitivity maps can be used to quickly identify the variables with the highest influence on the environmental fate of selected, chlorobenzenes, polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), hexachlorocyclohexanes (HCHs) and brominated flame retardents (BFRs).

  16. A System Dynamics Approach for the Selection of Contaminated Land Management Options

    Science.gov (United States)

    McKnight, U. S.; Kuebert, M.; Finkel, M.; Bieg, M.

    2006-12-01

    Large-scale contaminated land and groundwater is a widespread problem that can severely impact human health, the environment and the economy at many urban sites all over the world. Usually a considerable number of potential management solutions exist at each of these sites. A detailed investigation of all these options, however, is not economically feasible which makes streamlining of the planning and decision process a mandatory requirement. Decisions to be taken should be made as early as possible in order to reduce expenditures on site investigation. Therefore, a tiered decision-making procedure is required, including (i) identification and prioritization of focal areas of risks, (ii) feasibility screening of remediation targets and available management alternatives to narrow the range of possible options for (iii) subsequent detailed investigations of only a select group of preferable options. For each of these elements, tailored decision and investigation concepts are required. These concepts and applied methods should be specifically adapted to the type and scale of the particular decision to be taken- more target-oriented, cost-efficient investigation programs, as well as model-based assessment methods are needed (Ruegner et al. 2006). A gap exists within this framework with respect to preliminary assessment methodologies representing the first decision level. To fill this gap, a new system dynamics approach has been developed that represents the system of source- pathway-receptor sequences by means of a mass flux model. The dynamics are governed by the effects of possible remedial actions, which are described as mass flux change over time (Serapiglia et al. 2005). This approach has been implemented in the preliminary evaluation tool CARO-plus (Cost-efficiency Assessment of Remediation Options) that models the effects of potential remedial actions, including tackling the contaminant source and managing the groundwater plume. The model represents the causal

  17. Pesticide contamination of fruits and vegetables - A market basket survey from selected regions in Ghana

    International Nuclear Information System (INIS)

    Asiedu, Eric

    2013-07-01

    A market - basket survey was carried out with the aim of determining the concentration levels of pesticides, in lettuce, garden eggs, pineapple and mango from some selected regions in Ghana and to assess the potential health risk associated with exposure to the pesticide residues from fruits and vegetables consumption. A total of 192 fresh samples of fruits and vegetables were randomly collected under normal purchase conditions from 12 major towns and cities in the three regions of Ghana. The samples were extracted and analyzed for organophosphates, synthetic pyrethroids and organo chlorine pesticides. The percentage of samples of fruits and vegetables with pesticide residues in Lettuce, Garden eggs, Pineapple and Mango were 52%, 40%, 45%, 48% respectively and concentrations of pesticides did not vary significantly in samples as well as the sampling areas (p>0.05) even though there were differences in residual concentrations of pesticides . The differences in residual concentrations of pesticides could be due to different agricultural practices adopted by farmers and also accessibility of the pesticides. The average residue concentrations range from 0.01-0.45 mg/kg, 0.01-0.30 mg/kg and 0.01-1.27 mg/kg for organophosphates, synthetic pyrethroids and organo chlorine pesticides respectively. Lindane, chloropyrifos and cypermethrin were the most frequent organo chlorine, organophosphate and synthetic pyrethroid pesticides respectively while lettuce was the most frequently contaminated sample. Comparing the concentration levels of organo chlorine pesticides residue with the maximum residue limits (MRLs) adopted by the FAO/WHO Codex Alimentarious Commission shows that some of the fruits and vegetables sold on Ghanaian markets are contaminated even though the levels are generally low. Health risk analysis indicates that heptachlor in particular may be of public concern since its concentration levels exceeded the reference dose in all the four different types of samples

  18. Steroid markers to assess sewage and other sources of organic contaminants in surface sediments of Cienfuegos Bay, Cuba.

    Science.gov (United States)

    Tolosa, I; Mesa, M; Alonso-Hernandez, C M

    2014-09-15

    Analyses of faecal steroids in coastal sediments from Cienfuegos Bay Cuba indicate chronic sewage contamination at the main outfalls from the city, where concentrations of coprostanol up to 5400ngg(-)(1) (dry wt) were measured. In contrast, steroid concentrations and compositions from sites from the south part of the Bay are characteristic of uncontaminated sewage environments. The levels of coprostanol in the Cienfuegos sediments compares to the lower to mid-range of concentrations reported for coastal sediments on a world-wide basis, with sedimentary levels markedly below those previously reported for heavily impacted sites. This study delivers baseline data for further investigation of the effectiveness of the proposed sewerage plan promoted by the GEF project in Cienfuegos. Investigations on the correlations between faecal steroids and other organic contaminants confirmed that the major source of petroleum hydrocarbons within the bay was associated with the sewage effluents from the Cienfuegos city. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Vitellogenin, a Marker of Estrogen Mimicking Contaminants in Fishes: Characterization, Quantification and Interference by Anti-Estrogens

    OpenAIRE

    Palumbo, Amanda J.

    2008-01-01

    Vitellogenin (Vg), the estrogen inducible protein precursor to egg yolk, serves as an indicator of exposure to estrogen mimicking environmental contaminants. Vg was isolated by size exclusion and ion exchange chromatography from plasma of California halibut (Paralichthys californicus) treated with estrogen. MALDI TOF mass spectrometry (MS) analysis resulted in a molecular mass of 188 kDa. MS/MS de novo sequencing provided evidence that California halibut has more than one form of Vg. Similar ...

  20. Amygdala activation as a marker for selective attention toward neutral faces in a chronic traumatic brain injury population.

    Science.gov (United States)

    Young, Leanne R; Yu, Weikei; Holloway, Michael; Rodgers, Barry N; Chapman, Sandra B; Krawczyk, Daniel C

    2017-09-01

    There has been great interest in characterizing the response of the amygdala to emotional faces, especially in the context of social cognition. Although amygdala activation is most often associated with fearful or angry stimuli, there is considerable evidence that the response of the amygdala to neutral faces is both robust and reliable. This characteristic of amygdala function is of particular interest in the context of assessing populations with executive function deficits, such as traumatic brain injuries, which can be evaluated using fMRI attention modulation tasks that evaluate prefrontal control over representations, notably faces. The current study tested the hypothesis that the amygdala may serve as a marker of selective attention to neutral faces. Using fMRI, we gathered data within a chronic traumatic brain injury population. Blood Oxygenation Level Dependent (BOLD) signal change within the left and right amygdalae and fusiform face areas was measured while participants viewed neutral faces and scenes, under conditions requiring participants to (1) categorize pictures of faces and scenes, (2) selectively attend to either faces or scenes, or (3) attend to both faces and scenes. Findings revealed that the amygdala is an effective marker for selective attention to neutral faces and, furthermore, it was more face-specific than the fusiform face area. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. A New Selectable Marker System for Genetic Studies of Bacteria: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Parsons, D; Tolmasky, M; Chain, P; Segelke, B W

    2011-03-18

    Genetic manipulations in bacteria currently rely on the introduction of antibiotic resistance genes into a bacterial strain; for those organisms that will be used for commercial or industrial applications, the genetic cassette encoding the antibiotic resistance is sometimes removed after selection. it is clear that if alternative technologies could obviate the need to introduce antibiotic resistance into bacteria, they would most certainly become a standard tool in molecular micriobiology for commercial, industrial as well as research applications. Here, they present the development of a novel genetic engineering technology based on toxin-antitoxin systems to modify bacterial genomes without the use of antibiotic resistance in the mutagenesis process. The primary goal is to develop antibiotic-free selection for genetically altered select agent pathogens. They are adapting the toxinc-antitoxin system to enable gene replacement in select agent pathogens since the NIH restrictions introducing antibiotic resistance into select agent pathogens have hindered research with select agent pathogens.

  2. Somatostatin receptor scintigraphy in sarcoidosis: relation to selected clinical and laboratory markers.

    Science.gov (United States)

    Piotrowski, Wojciech J; Bieńkiewicz, Małgorzata; Frieske, Izabella; Marczak, Jerzy; Antczak, Adam; Górski, Paweł; Kuśmierek, Jacek; Płachcińska, Anna

    2012-01-01

    Discriminating between active and inactive sarcoidosis may be problematic in everyday clinical practice. There are numerous biochemical markers used in the diagnosis and monitoring of sarcoidosis. Somatostatin receptor (SR) scintigraphy with the use of 99mTc-octreotide may be used to estimate disease activity. The aim of the paper was to assess the value of traditional biomarkers (serum angiotensin-converting enzyme [SACE], C-reactive protein, markers of calcium metabolism, bronchoalveolar lavage fluid [BALF] lymphocytes) and a novel biomarker, 8-isoprostane (8-IP) in exhaled breath condensate (EBC), in the assessment of sarcoidosis activity in relation to somatostatin receptor scintigraphy. The study included 32 patients with sarcoidosis. Scintigraphy was performed using somatostatin analogue, 99mTc-HYNIC-TOC; planar and SPECT/CT images were recorded. The study group was divided into a subgroup with positive radiotracer uptake (n = 20) and without a visible uptake (n = 12). 8-IP levels were measured in EBC by an immunoenzymatic assay. RESULTS We observed a significantly higher EBC 8-IP levels in the subgroup with positive uptake compared with those with negative uptake (19.1 ± 19.8 vs. 5.4 ± 3.5 pg/ml, P = 0.02). The levels of SACE and the percentage of BALF lymphocytes were also nonsignificantly elevated. In the group of patients with positive scintigraphy results, a positive correlation was observed between the uptake ratio and SACE (r = 0.44, P = 0.041). The results indicate low value of biochemical markers in the assessment of disease activity. SR scintigraphy may have practical usefulness in the monitoring of sarcoidosis.

  3. Optimum location of external markers using feature selection algorithms for real-time tumor tracking in external-beam radiotherapy: a virtual phantom study.

    Science.gov (United States)

    Nankali, Saber; Torshabi, Ahmad Esmaili; Miandoab, Payam Samadi; Baghizadeh, Amin

    2016-01-08

    In external-beam radiotherapy, using external markers is one of the most reliable tools to predict tumor position, in clinical applications. The main challenge in this approach is tumor motion tracking with highest accuracy that depends heavily on external markers location, and this issue is the objective of this study. Four commercially available feature selection algorithms entitled 1) Correlation-based Feature Selection, 2) Classifier, 3) Principal Components, and 4) Relief were proposed to find optimum location of external markers in combination with two "Genetic" and "Ranker" searching procedures. The performance of these algorithms has been evaluated using four-dimensional extended cardiac-torso anthropomorphic phantom. Six tumors in lung, three tumors in liver, and 49 points on the thorax surface were taken into account to simulate internal and external motions, respectively. The root mean square error of an adaptive neuro-fuzzy inference system (ANFIS) as prediction model was considered as metric for quantitatively evaluating the performance of proposed feature selection algorithms. To do this, the thorax surface region was divided into nine smaller segments and predefined tumors motion was predicted by ANFIS using external motion data of given markers at each small segment, separately. Our comparative results showed that all feature selection algorithms can reasonably select specific external markers from those segments where the root mean square error of the ANFIS model is minimum. Moreover, the performance accuracy of proposed feature selection algorithms was compared, separately. For this, each tumor motion was predicted using motion data of those external markers selected by each feature selection algorithm. Duncan statistical test, followed by F-test, on final results reflected that all proposed feature selection algorithms have the same performance accuracy for lung tumors. But for liver tumors, a correlation-based feature selection algorithm, in

  4. Optimum location of external markers using feature selection algorithms for real‐time tumor tracking in external‐beam radiotherapy: a virtual phantom study

    Science.gov (United States)

    Nankali, Saber; Miandoab, Payam Samadi; Baghizadeh, Amin

    2016-01-01

    In external‐beam radiotherapy, using external markers is one of the most reliable tools to predict tumor position, in clinical applications. The main challenge in this approach is tumor motion tracking with highest accuracy that depends heavily on external markers location, and this issue is the objective of this study. Four commercially available feature selection algorithms entitled 1) Correlation‐based Feature Selection, 2) Classifier, 3) Principal Components, and 4) Relief were proposed to find optimum location of external markers in combination with two “Genetic” and “Ranker” searching procedures. The performance of these algorithms has been evaluated using four‐dimensional extended cardiac‐torso anthropomorphic phantom. Six tumors in lung, three tumors in liver, and 49 points on the thorax surface were taken into account to simulate internal and external motions, respectively. The root mean square error of an adaptive neuro‐fuzzy inference system (ANFIS) as prediction model was considered as metric for quantitatively evaluating the performance of proposed feature selection algorithms. To do this, the thorax surface region was divided into nine smaller segments and predefined tumors motion was predicted by ANFIS using external motion data of given markers at each small segment, separately. Our comparative results showed that all feature selection algorithms can reasonably select specific external markers from those segments where the root mean square error of the ANFIS model is minimum. Moreover, the performance accuracy of proposed feature selection algorithms was compared, separately. For this, each tumor motion was predicted using motion data of those external markers selected by each feature selection algorithm. Duncan statistical test, followed by F‐test, on final results reflected that all proposed feature selection algorithms have the same performance accuracy for lung tumors. But for liver tumors, a correlation‐based feature

  5. Marker-Assisted Selection for Recognizing Wheat Mutant Genotypes Carrying HMW Glutenin Alleles Related to Baking Quality

    OpenAIRE

    Zamani, Mohammad Javad; Bihamta, Mohammad Reza; Naserian Khiabani, Behnam; Tahernezhad, Zahra; Hallajian, Mohammad Taher; Shamsi, Marzieh Varasteh

    2014-01-01

    Allelic diversity of HMW glutenin loci in several studies revealed that allelic combinations affect dough quality. Dx5 + Dy10 subunits are related to good baking quality and Dx2 + Dy12 are related to undesirable baking quality. One of the most regular methods to evaluate the baking quality is SDS-PAGE which is used to improve baking quality labs. Marker-assisted selection is the method which can recognize the alleles related to baking quality and this method is based on polymerase chain reac...

  6. Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market.

    Science.gov (United States)

    Zhao, Jie; Li, Tingting; Zhu, Chao; Jiang, Xiaoling; Zhao, Yan; Xu, Zhenzhen; Yang, Shuming; Chen, Ailiang

    2018-06-01

    Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.

  7. IVF or IUI as first-line treatment in unexplained subfertility: the conundrum of treatment selection markers.

    Science.gov (United States)

    Tjon-Kon-Fat, R I; Tajik, P; Zafarmand, M H; Bensdorp, A J; Bossuyt, P M M; Oosterhuis, G J E; van Golde, R; Repping, S; Lambers, M D A; Slappendel, E; Perquin, D; Pelinck, M J; Gianotten, J; Maas, J W M; Eijkemans, M J C; van der Veen, F; Mol, B W; van Wely, M

    2017-05-01

    Are there treatment selection markers that could aid in identifying couples, with unexplained or mild male subfertility, who would have better chances of a healthy child with IVF with single embryo transfer (IVF-SET) than with IUI with ovarian stimulation (IUI-OS)? We did not find any treatment selection markers that were associated with better chances of a healthy child with IVF-SET instead of IUI-OS in couples with unexplained or mild male subfertility. A recent trial, comparing IVF-SET to IUI-OS, found no evidence of a difference between live birth rates and multiple pregnancy rates. It was suggested that IUI-OS should remain the first-line treatment instead of IVF-SET in couples with unexplained or mild male subfertility and female age between 18 and 38 years. The question remains whether there are some couples that may have higher pregnancy chances if treated with IVF-SET instead of IUI. We performed our analyses on data from the INeS trial, where couples with unexplained or mild male subfertility and an unfavourable prognosis for natural conception were randomly allocated to IVF-SET, IVF in a modified natural cycle or IUI-OS. In view of the aim of this study, we only used data of the comparison between IVF-SET (201 couples) and IUI-OS (207 couples). We pre-defined the following baseline characteristics as potential treatment selection markers: female age, ethnicity, smoking status, type of subfertility (primary/secondary), duration of subfertility, BMI, pre-wash total motile count and Hunault prediction score. For each potential treatment selection marker, we explored the association with the chances of a healthy child after IVF-SET and IUI-OS and tested if there was an interaction with treatment. Given the exploratory nature of our analysis, we used a P-value of 0.1. None of the markers were associated with higher chances of a healthy child from IVF-SET compared to IUI-OS (P-value for interaction >0.10). Since this is the first large study that looked at

  8. Assessment of ptxD gene as an alternative selectable marker for Agrobacterium-mediated maize transformation.

    Science.gov (United States)

    Nahampun, Hartinio N; López-Arredondo, Damar; Xu, Xing; Herrera-Estrella, Luis; Wang, Kan

    2016-05-01

    Bacterial phosphite oxidoreductase gene and chemical phosphite can be used as a selection system for Agrobacterium -mediated maize transformation. Application of phosphite (Phi) on plants can interfere the plant metabolic system leading to stunted growth and lethality. On the other hand, ectopic expression of the ptxD gene in tobacco and Arabidopsis allowed plants to grow in media with Phi as the sole phosphorous source. The phosphite oxidoreductase (PTXD) enzyme catalyzes the conversion of Phi into phosphate (Pi) that can then be metabolized by plants and utilized as their essential phosphorous source. Here we assess an alternative selectable marker based on a bacterial ptxD gene for Agrobacterium-mediated maize transformation. We compared the transformation frequencies of maize using either the ptxD/Phi selection system or a standard herbicide bar/bialaphos selection system. Two maize genotypes, a transformation amenable hybrid Hi II and an inbred B104, were tested. Transgene presence, insertion copy numbers, and ptxD transcript levels were analyzed and compared. This work demonstrates that the ptxD/Phi selection system can be used for Agrobacterium-mediated maize transformation of both type I and type II callus culture and achieve a comparable frequency as that of the herbicide bar/bialaphos selection system.

  9. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers

    Science.gov (United States)

    Dinarti, Diny; Susilo, Agung W.; Meinhardt, Lyndel W.; Ji, Kun; Motilal, Lambert A.; Mischke, Sue; Zhang, Dapeng

    2015-01-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. PMID:26719747

  10. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers.

    Science.gov (United States)

    Dinarti, Diny; Susilo, Agung W; Meinhardt, Lyndel W; Ji, Kun; Motilal, Lambert A; Mischke, Sue; Zhang, Dapeng

    2015-12-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers' fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi.

  11. Predicting impending death: inconsistency in speed is a selective and early marker.

    Science.gov (United States)

    Macdonald, Stuart W S; Hultsch, David F; Dixon, Roger A

    2008-09-01

    Among older adults, deficits in both level and variability of speeded performance are linked to neurological impairment. This study examined whether and when speed (rate), speed (inconsistency), and traditional accuracy-based markers of cognitive performance foreshadow terminal decline and impending death. Victoria Longitudinal Study data spanning 12 years (5 waves) of measurement were assembled for 707 adults aged 59 to 95 years. Whereas 442 survivors completed all waves and relevant measures, 265 decedents participated on at least 1 occasion and subsequently died. Four main results were observed. First, Cox regressions evaluating the 3 cognitive predictors of mortality replicated previous results for cognitive accuracy predictors. Second, level (rate) of speeded performance predicted survival independent of demographic indicators, cardiovascular health, and cognitive performance level. Third, inconsistency in speed predicted survival independent of all influences combined. Fourth, follow-up random-effects models revealed increases in inconsistency in speed per year closer to death, with advancing age further moderating the accelerated growth. Hierarchical prediction patterns support the view that inconsistency in speed is an early behavioral marker of neurological dysfunction associated with impending death. (c) 2008 APA, all rights reserved

  12. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    Directory of Open Access Journals (Sweden)

    Zulhairil Ariffin

    2015-01-01

    Full Text Available ISSR markers were employed to reveal genetic diversity and genetic relatedness among 28 Mangifera accessions collected from Yan (Kedah, Bukit Gantang (Perak, Sibuti (Sarawak, and Papar (Sabah. A total of 198 markers were generated using nine anchored primers and one nonanchored primer. Genetic variation among the 28 accessions of Mangifera species including wild relatives, landraces, and clonal varieties is high, with an average degree of polymorphism of 98% and mean Shannon index, H0=7.50. Analysis on 18 Mangifera indica accessions also showed high degree of polymorphism of 99% and mean Shannon index, H0=5.74. Dice index of genetic similarity ranged from 0.0938 to 0.8046 among the Mangifera species. The dendrogram showed that the Mangifera species were grouped into three main divergent clusters. Cluster 1 comprised 14 accessions from Kedah and Perak. Cluster II and cluster III comprised 14 accessions from Sarawak and Sabah. Meanwhile, the Dice index of genetic similarity for 18 accessions of Mangifera indica ranged from 0.2588 to 0.7742. The dendrogram also showed the 18 accessions of Mangifera indica were grouped into three main clusters. Cluster I comprised 10 landraces of Mangifera indica from Kedah. Cluster II comprised 7 landraces of Mangifera indica followed by Chokanan to form Cluster III.

  13. QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

    Science.gov (United States)

    Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

    2016-03-18

    The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

  14. Splenomegaly and tumor marker response following selective internal radiation therapy for non-resectable liver metastases from neuroendocrine tumor

    International Nuclear Information System (INIS)

    Shehata, M.; Yan, K.; Itoh, Seiji; King, J.; Glenn, D.; Quinn, R.; Morris, D.L.

    2009-01-01

    The aim of this study was to investigate changes in spleen size, the level of chromogranin A as a tumor marker, and the relationship between these two parameters before and 3 months after selective internal radiation therapy (SIRT) for non-resectable liver metastases from neuroendocrine tumor (NET). Our first serious adverse event with this relatively new treatment is also discussed. A retrospective review of a prospective database identified patients with non-resectable liver metastases from NET who underwent SIRT between 2003 and 2007. Patients who underwent CT scans before and 3 months after treatment were included. The patients were divided into two groups: those with and without a 20% or more increase in splenic volume on the CT scans. The percentages of patients showing a tumor marker response in the two groups were then compared. Fourteen patients were included in the present analysis. A tumor marker response was seen in 6 of 7 patients (85.7%) who showed an increase in splenic volume of >20%, and in 3 of 7 patients (42.9%) without an increase in splenic volume (p=0.266). There was one death as a result of oesophageal variceal bleeding due to portal hypertension at 9 months after treatment. Splenic enlargement after SIRT may be associated with tumor marker response, although this could not be confirmed statistically in this study due to the small number of patients. Long-term splenomegaly and portal hypertension may be important complications of SIRT. This issue needs to be investigated further using a larger number of patients and longer follow-up. (author)

  15. Markers for hepatitis B, C, D and G contamination in the population suffered of the Chernobyl accident

    International Nuclear Information System (INIS)

    Zhavoronok, S.V.; Kalinin, A.L.; Grimbaum, O.A.; Chernovetskij, M.A.; Babarykina, N.Eh.; Ospobat, Ya.M.

    1998-01-01

    The results received in the study of 2814 persons having taken part in the liquidation of the Chernobyl accident consequences, of people (adult and teenagers) migrated from the contaminated territories to Vitebsk region and of the control group consisted of 46773 donors are presented. Hepatitis B and C viruses have been revealed more frequently in people suffered of the Chernobyl accident. Hepatitis D and G viruses have defined. It allows to predict a larger number of death caused by hepato cirrhosis or primary carcinomas of the liver

  16. ERP markers of target selection discriminate children with high vs. low working memory capacity

    Directory of Open Access Journals (Sweden)

    Andria eShimi

    2015-11-01

    Full Text Available Selective attention enables enhancing a subset out of multiple competing items to maximize the capacity of our limited visual working memory (VWM system. Multiple behavioral and electrophysiological studies have revealed the cognitive and neural mechanisms supporting adults’ selective attention of visual percepts for encoding in VWM. However, research on children is more limited. What are the neural mechanisms involved in children’s selection of incoming percepts in service of VWM? Do these differ from the ones subserving adults’ selection? Ten-year-olds and adults used a spatial arrow cue to select a colored item for later recognition from an array of four colored items. The temporal dynamics of selection were investigated through EEG signals locked to the onset of the memory array. Both children and adults elicited significantly more negative activity over posterior scalp locations contralateral to the item to-be-selected for encoding (N2pc. However, this activity was elicited later and for longer in children compared to adults. Furthermore, although children as a group did not elicit a significant N2pc during the time-window in which N2pc was elicited in adults, the magnitude of N2pc during the adult time-window related to their behavioral performance during the later recognition phase of the task. This in turn highlights how children’s neural activity subserving attention during encoding relates to better subsequent VWM performance. Significant differences were observed when children were divided into groups of high vs. low VWM capacity as a function of cueing benefit. Children with large cue benefits in VWM capacity elicited an adult-like contralateral negativity following attentional selection of the to-be-encoded item, whereas children with low VWM capacity did not. These results corroborate the close coupling between selective attention and VWM from childhood and elucidate further the attentional mechanisms constraining VWM

  17. ERP markers of target selection discriminate children with high vs. low working memory capacity.

    Science.gov (United States)

    Shimi, Andria; Nobre, Anna Christina; Scerif, Gaia

    2015-01-01

    Selective attention enables enhancing a subset out of multiple competing items to maximize the capacity of our limited visual working memory (VWM) system. Multiple behavioral and electrophysiological studies have revealed the cognitive and neural mechanisms supporting adults' selective attention of visual percepts for encoding in VWM. However, research on children is more limited. What are the neural mechanisms involved in children's selection of incoming percepts in service of VWM? Do these differ from the ones subserving adults' selection? Ten-year-olds and adults used a spatial arrow cue to select a colored item for later recognition from an array of four colored items. The temporal dynamics of selection were investigated through EEG signals locked to the onset of the memory array. Both children and adults elicited significantly more negative activity over posterior scalp locations contralateral to the item to-be-selected for encoding (N2pc). However, this activity was elicited later and for longer in children compared to adults. Furthermore, although children as a group did not elicit a significant N2pc during the time-window in which N2pc was elicited in adults, the magnitude of N2pc during the "adult time-window" related to their behavioral performance during the later recognition phase of the task. This in turn highlights how children's neural activity subserving attention during encoding relates to better subsequent VWM performance. Significant differences were observed when children were divided into groups of high vs. low VWM capacity as a function of cueing benefit. Children with large cue benefits in VWM capacity elicited an adult-like contralateral negativity following attentional selection of the to-be-encoded item, whereas children with low VWM capacity did not. These results corroborate the close coupling between selective attention and VWM from childhood and elucidate further the attentional mechanisms constraining VWM performance in children.

  18. Microorganism selection and performance in bioslurry reactors treating PAH-contaminated soil.

    Science.gov (United States)

    Cassidy, D P; Hudak, A J

    2002-09-01

    A continuous-flow reactor (CSTR) and a soil slurry-sequencing batch reactor (SS-SBR) were operated in 81 vessels for 200 days to treat a soil contaminated with polycyclic aromatic hydrocarbons (PAH). Filtered slurry samples were used to quantify bulk biosurfactant concentrations and PAH emulsification. Concentrations of Corynebacterium aquaticum, Flavobacterium mizutaii, Mycobacterium gastri, Pseudomonas aeruginosa, and Pseudomonas putida were determined using fatty acid methyl ester (FAME) analysis. The CSTR and SS-SBR selected microbial consortia with markedly different surfactant-producing and PAH-degrading abilities. Biosurfactant levels in the SS-SBR reached 4 times the critical micelle concentration (CMC) that resulted in considerable emulsification of PAH. In contrast, CSTR operation resulted in nomeasurable biosurfactant production. Total PAH removal efficiency was 93% in the SS-SBR, compared with only 66% in the CSTR, and stripping of PAH was 3 times less in the SS-SBR. Reversing the mode of operation on day 100 caused a complete reversal in microbial consortia and in reactor performance by day 140. These results show that bioslurry reactor operation can be manipulated to control overall reactor performance.

  19. Bioremediation of selected contaminants in aquatic environments of the Mississippi River Basin

    International Nuclear Information System (INIS)

    Bhattacharya, S.; Bennett, J.; Englande, A.J.; Law, V.; Mullin, D.; Mielke, H.; Eckert, J.; Fulginiti, R.; Kamath, B.; Ross, J.

    1993-01-01

    Bioremediation is generally accepted as a long-term and economic treatment option. However, quantitative information on bioremediation and biosorption is required before this option can be adopted successfully. The primary goal of this on-going project is to determine the extent of natural biodegradation of hazardous organics and biosorption of hazardous organics and heavy metals by the consortia of bacteria, fungi, and plants. Methods to enhance the biodegradation process will be studied during the second and third years of this 3-year proposed project. The Devil's Swamp area near Baton Rouge and Bayou St. John in New Orleans have been selected as the first set of test sites. Some samples from Lake Pontchartrain, bordering New Orleans on the north, have also been analyzed. It is expected that many of the contaminants found at the test site(s) are present at other sites of DOE's interest. Further, technology resulting from the proposed research involving enhanced natural biodegradation processes should be transferable to other DOE sites

  20. Selected markers of endothelial dysfunction in patients with subclinical and overt hyperthyroidism

    International Nuclear Information System (INIS)

    Modzelewska, A.; Szelachowska, M.; Zonenberg, A.; Abdelrazek, S.; Nikolajuk, A.; Gorska, M.

    2006-01-01

    Introduction: There are many factors causing endothelial dysfunction. The aim was to observe chosen markers of endothelial function in patients with subclinical and overt hyperthyroidism. Material and methods: We studied 97 patients with hyperthyroidism: 51 with subclinical (44 F/7 M; mean age 49.3 ± 15.9 y) and 46 patients with overt (39 F/7 M, mean age 50.4 ± 13.2 y). The control comprised of 39 healthy volunteers (26 F/13 M, mean age 47.5 ± 11.8 y). Concentration of TSH, FT3, FT4 were measured by MEIA, TPO Ab, TG Ab, E-selectin, interleukin 6, VCAM-1, ICAM-1 by ELISA. Results: The goiter was found in 71 persons 63F/8M, mean age 49.9 ± 15.3 y, (42-subclinical, 29-overt). Morbus Graves--Basedow was diagnosed in 26 persons, 20 F/6 M, mean age 49.5 ± 12.8 y (9-subclinical, 17-overt). There were no significant differences serum concentration of E-selectin, IL-6, ICAM-1 in patients with subclinical and overt hyperthyroidism compared to the control. Statistically significant differences were shown between concentration of IL-6 in patients with Graves-Basedow compared with the control (p < 0.05). Significance of VCAM-1 values were found in the patients with subclinical and overt hyperthyroidism compared to the control (p < 0.001; p < 0.001, respectively). Conclusions: Among persons with overt and subclinical hyperthyroidism occurs endothelial dysfunction which doesn't depends on exciting cause of thyrotoxicosis but on degree of hyperthyroidism. Elevated concentrations of endothelial markers may confirm that persons with thyroid disorders are extremely exposed to the occurrence of the cardiovascular diseases. (author)

  1. A geoprocessing model for the selection of populations most affected by diffuse industrial contamination: the case of oil refinery plants

    Directory of Open Access Journals (Sweden)

    Roberto Pasetto

    2013-03-01

    Full Text Available INTRODUCTION. A method to select populations living in areas affected by diffuse environmental contamination is presented, with particular regard to oil refineries, in the Italian context. The reasons to use municipality instead of census tract populations for environment and health small-area studies of contaminated sites are discussed. METHODS. Populations most affected by diffuse environmental contamination are identified through a geoprocessing model. Data from the national census 2001 were used to estimate census tract level populations. A geodatabase was developed using the municipality and census tract layers provided by the Italian National Bureau of Statistics (ISTAT. The orthophotos of the Italian territory - year 2006 - available on the geographic information systems (GIS of the National Cartographic Portal, were considered. The area within 2 km from the plant border was used as an operational definition to identify the area at major contamination. RESULTS. The geoprocessing model architecture is presented. The results of its application to the selection of municipality populations in a case study are shown. CONCLUSIONS. The application of the proposed geoprocessing model, the availability of long time series of mortality and morbidity data, and a quali-quantitative estimate of contamination over time, could allow an appraisal of the health status of populations affected by oil refinery emissions.

  2. A Cercla-Based Decision Model to Support Remedy Selection for an Uncertain Volume of Contaminants at a DOE Facility

    Energy Technology Data Exchange (ETDEWEB)

    Christine E. Kerschus

    1999-03-31

    The Paducah Gaseous Diffusion Plant (PGDP) operated by the Department of Energy is challenged with selecting the appropriate remediation technology to cleanup contaminants at Waste Area Group (WAG) 6. This research utilizes value-focused thinking and multiattribute preference theory concepts to produce a decision analysis model designed to aid the decision makers in their selection process. The model is based on CERCLA's five primary balancing criteria, tailored specifically to WAG 6 and the contaminants of concern, utilizes expert opinion and the best available engineering, cost, and performance data, and accounts for uncertainty in contaminant volume. The model ranks 23 remediation technologies (trains) in their ability to achieve the CERCLA criteria at various contaminant volumes. A sensitivity analysis is performed to examine the effects of changes in expert opinion and uncertainty in volume. Further analysis reveals how volume uncertainty is expected to affect technology cost, time and ability to meet the CERCLA criteria. The model provides the decision makers with a CERCLA-based decision analysis methodology that is objective, traceable, and robust to support the WAG 6 Feasibility Study. In addition, the model can be adjusted to address other DOE contaminated sites.

  3. A Cercla-Based Decision Model to Support Remedy Selection for an Uncertain Volume of Contaminants at a DOE Facility

    International Nuclear Information System (INIS)

    Christine E. Kerschus

    1999-01-01

    The Paducah Gaseous Diffusion Plant (PGDP) operated by the Department of Energy is challenged with selecting the appropriate remediation technology to cleanup contaminants at Waste Area Group (WAG) 6. This research utilizes value-focused thinking and multiattribute preference theory concepts to produce a decision analysis model designed to aid the decision makers in their selection process. The model is based on CERCLA's five primary balancing criteria, tailored specifically to WAG 6 and the contaminants of concern, utilizes expert opinion and the best available engineering, cost, and performance data, and accounts for uncertainty in contaminant volume. The model ranks 23 remediation technologies (trains) in their ability to achieve the CERCLA criteria at various contaminant volumes. A sensitivity analysis is performed to examine the effects of changes in expert opinion and uncertainty in volume. Further analysis reveals how volume uncertainty is expected to affect technology cost, time and ability to meet the CERCLA criteria. The model provides the decision makers with a CERCLA-based decision analysis methodology that is objective, traceable, and robust to support the WAG 6 Feasibility Study. In addition, the model can be adjusted to address other DOE contaminated sites

  4. Selective Detection of Target Volatile Organic Compounds in Contaminated Humid Air Using a Sensor Array with Principal Component Analysis

    Science.gov (United States)

    Itoh, Toshio; Akamatsu, Takafumi; Tsuruta, Akihiro; Shin, Woosuck

    2017-01-01

    We investigated selective detection of the target volatile organic compounds (VOCs) nonanal, n-decane, and acetoin for lung cancer-related VOCs, and acetone and methyl i-butyl ketone for diabetes-related VOCs, in humid air with simulated VOC contamination (total concentration: 300 μg/m3). We used six “grain boundary-response type” sensors, including four commercially available sensors (TGS 2600, 2610, 2610, and 2620) and two Pt, Pd, and Au-loaded SnO2 sensors (Pt, Pd, Au/SnO2), and two “bulk-response type” sensors, including Zr-doped CeO2 (CeZr10), i.e., eight sensors in total. We then analyzed their sensor signals using principal component analysis (PCA). Although the six “grain boundary-response type” sensors were found to be insufficient for selective detection of the target gases in humid air, the addition of two “bulk-response type” sensors improved the selectivity, even with simulated VOC contamination. To further improve the discrimination, we selected appropriate sensors from the eight sensors based on the PCA results. The selectivity to each target gas was maintained and was not affected by contamination. PMID:28753948

  5. Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker

    Directory of Open Access Journals (Sweden)

    M. Mahfuza Khatun

    2012-06-01

    Full Text Available In order to develop specific genetic markers and determine the genetic diversity of Bangladeshi native cattle (Pabna, Red Chittagong and exotic breeds (Sahiwal, randomly amplified polymorphic DNA (RAPD analysis was performed using 12 primers. Genomic DNA was extracted from 20 cattle (local and exotic blood samples and extracted DNA was observed by gel electrophoresis. Among the random primers three were matched and found to be polymorphic. Genetic relations between cattle’s were determined by RAPD polymorphisms from a total of 66.67%. Statistical analysis of the data, estimating the genetic distances between cattle and sketching the cluster trees were estimated by using MEGA 5.05 software. Comparatively highest genetic distance (0.834 was found between RCC-82 and SL-623. The lowest genetic distance (0.031 was observed between M-1222 and M-5730. The genetic diversity of Red Chittagong and Sahiwal cattle was relatively higher for a prescribed breed. Adequate diversity in performance and adaptability can be exploited from the study results for actual improvement accruing to conservation and development of indigenous cattle resources.

  6. Use of the alr gene as a food-grade selection marker in lactic acid bacteria

    NARCIS (Netherlands)

    Bron, P.A.; Benchimol, M.G.; Lambert, J.; Palumbo, E.; Deghorain, M.; Delcour, J.; Vos, de W.M.; Kleerebezem, M.; Hols, P.

    2002-01-01

    Both Lactococcus lactis and Lactobacillus plantarum contain a single alr gene, encoding an alanine racemase (EC 5.1.1.1), which catalyzes the interconversion of D-alanine and L-alanine. The alr genes of these lactic acid bacteria were investigated for their application as food-grade selection

  7. A bacterial haloalkane dehalogenase gene as a negative selectable marker in Arabidopsis

    DEFF Research Database (Denmark)

    Næsted, Henrik; Fennema, M.; Hao, L.

    1999-01-01

    , including Arabidopsis, tobacco, oil seed rape and rice, do not express detectable haloalkane dehalogenase activities, and that wild-type Arabidopsis grows in the presence of DCE. In contrast, DCE applied as a volatile can be used to select on plates or in soil transgenic Arabidopsis which express dhl...

  8. Selection of wild macrophytes for use in constructed wetlands for phytoremediation of contaminant mixtures.

    Science.gov (United States)

    Guittonny-Philippe, Anna; Petit, Marie-Eléonore; Masotti, Véronique; Monnier, Yogan; Malleret, Laure; Coulomb, Bruno; Combroux, Isabelle; Baumberger, Teddy; Viglione, Julien; Laffont-Schwob, Isabelle

    2015-01-01

    Constructed wetlands (CWs) offer an alternative to traditional industrial wastewater treatment systems that has been proved to be efficient, cost-effective and environmentally friendly. Most of the time, CWs are planted with proliferative species such as Phragmites australis or with plants originating from nurseries, both representing a risk for the natural biodiversity conservation of aquatic ecosystems located downstream of the CWs. For the removal of metals and organic pollutant mixtures present in industrial effluents, it is necessary to select tolerant plant species that are able to produce a high aboveground biomass and to develop a healthy belowground system. Wild plant species growing in aquatic bodies at industrial outfalls could constitute suitable tolerant species to use in CWs for industrial effluent treatment. To test this hypothesis, we assessed, under laboratory conditions (using an experimental design), the tolerance to mixtures of metals (Al, As, Cd, Cu, Cr, Fe, Mn, Ni, Pb, Sn, Zn) or/and organic pollutants (THC, PHE, PYR, LAS) of five European sub-cosmopolitan native macrophytes (Alisma lanceolatum, Carex cuprina, Epilobium hirsutum, Iris pseudacorus and Juncus inflexus) that had been collected in a polluted Mediterranean wetland, after a field study (crossing ecological relevés and analyses of contaminant concentrations in water and sediments). Our results demonstrated that research on phytoremediation of industrial effluents should focus much more on the use of native macrophytes growing at short distances from industrial discharges (such as C. cuprina in this study), and that root/shoot ratio, aerial height and proportion of green leaves are good and cost-effective indicators of plant tolerance to metals and organic pollutant mixtures in laboratory studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Impacts of intellectual property rights on marker-assisted selection research and application for agriculture in developing countries

    International Nuclear Information System (INIS)

    Henson-Apollonio, V.

    2007-01-01

    Although the impact of marker-assisted selection (MAS) in commercial and public sector breeding programmes in developing countries is to date limited to a few crops and traits, the potential benefits of using markers linked to genes of interest in breeding programmes for improving the productivity of crops, livestock, forest trees and farmed fish is substantial. While more recent methods associated with the use of MAS are technically demanding and often expensive, most applications of basic MAS were initially described in the literature, and thus will likely have very few intellectual property (IP) restrictions associated with their use, irrespective of the agricultural sector involved. For example, isolating DNA, amplifying specific gene sequences from that DNA (with most available primers), separating fragments using gel/polyacrylamide electrophoresis and imaging of fragments with standard techniques are likely to be available without restriction to scientists and breeders in the developing world, even as part of a commercial service. Problems arise when there is a need to use or develop high-throughput modes, which require more sophisticated technologies. For high-throughput use, a breeder will want to use the most efficient techniques that are currently available. This means that the more advanced processes/methods, reagents, software applications/simulations and equipment, which provide the most effective means to exploit MAS fully, are most likely covered by intellectual property rights (IPRs) such as patent rights, confidential information (trade secrets) and copyrights, both in industrialized countries and also in many developing countries such as Brazil, China and India. In situations where breeders wish to use cutting edge technologies and the most efficient markers, care must be taken to avoid activities that may infringe IPRs when using MAS methodologies. (author)

  10. The expression of selected molecular markers of immune tolerance in psoriatic patients.

    Science.gov (United States)

    Bartosińska, Joanna; Purkot, Joanna; Kowal, Małgorzata; Michalak-Stoma, Anna; Krasowska, Dorota; Chodorowska, Grażyna; Giannopoulos, Krzysztof

    2018-04-24

    Psoriasis is a chronic autoinflammatory disease whose underlying molecular mechanisms remain unclear. The disease is mediated by the cells and molecules of both the innate and adaptive immune systems. Some T cell surface molecules, including neuropilin-1 (NRP1), programmed death 1 (PD-1) and the human leukocyte antigen G (HLA-G), are known to play a role in the maintenance of immune tolerance. The aim of this study was to investigate HLA-G, NRP1 and programmed cell death gene (PDCD1) mRNA expression in psoriatic patients. The study included 72 psoriatic patients and 35 healthy individuals. Twentyone patients (29.17%) suffered from concomitant psoriatic arthritis. The mRNA expression of HLA-G, NRP1, and PDCD1 were determined using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The severity of skin lesions was assessed by means of the Psoriasis Area and Severity Index (PASI), Body Surface Area (BSA), the Patient Global Assessment (PGA), and the Dermatology Life Quality Index (DLQI). The median value of the PASI was 11.5, and of BSA was 15.8%. The expressions of NRP1 and PDCD1, but not HLA-G, were significantly lower in psoriatic patients in comparison with the control group. The expression of HLA-G, NRP1 and PDCD1 were not significantly different in the psoriatic arthritis and psoriasis vulgaris patients. The results of this study suggest that the molecular markers of immune tolerance, i.e., HLA-G, NRP1, and PD-1, may be involved in the immune response in psoriatic patients.

  11. Monitoring of selected essential elements and contaminants at sheep and cow farms in Eastern Slovakia

    Directory of Open Access Journals (Sweden)

    Martina TUNEGOVÁ

    2016-12-01

    Full Text Available The aim of this study was to determinate the actual contamination of selected area of Slovakia, in view of its environmental character referred both to the suitability or unsuitability of the use of milk from this area, to other food processing. This article deals with analysis of the content of selected compounds in soil, feed and milk, at the cow and sheep farms. Village in Eastern Slovakia, Tulčík, was the area of investigation. This area is characterized as an area with mild disturbance of environment. 11 compounds have been analyzed (calcium, selenium, cadmium, arsenic, polychlorinated biphenyls – congeners 138, 153, 180, and pesticides - p,p´ DDE, Endosulfan I., Beta-HCH, aflatoxin M1. Samples of soil were collected once a year (spring season, samples of feeds and milk were collected two-times a year (spring and autumn season. Analysis of samples was performed in Eurofins Bel/Novamann (Nové Zámky, Slovak Republic. Analyses were performed by routine methods, according to the valid methodologies. Levels of compounds were obtained and then results have been compared with the most acceptable limits in according to applicable legislation. At both farms, 73.08% (38 samples of analyzed compounds were below the limit of quantification (LOQ and 26.92% (14 samples of compounds were quantifiable. The most significant differences between monitored farms were recorded in soil (27 720 mg·kg-1 Ca, feed (27 620 mg·kg-1 Ca and milk (960 mg·kg-1 Ca. The high content of calcium in soil and feed did not affect the content of calcium in milk. The results showed that the content of toxic elements, polychorinated biphenyls, pesticides and aflatoxin M1 in analyzed area of Eastern Slovakia was very low and under the limit of quantification. It can be concluded, that the use of milk from this area for direct use or for dairy products is appropriate and poses no health risk to the consumers.

  12. Selected trace-element and organic contaminants in the streambed sediments of the Potomac River Basin, August 1992

    Science.gov (United States)

    Gerhart, James M.; Blomquist, Joel D.

    1995-01-01

    This report describes the occurrence and distribution of five selected contaminants in streambed sediments at 22 stream sites in the Potomac River Basin. Lead, mercury, and total DDT (dichlorodiphenyltrichloroethane) were detected at all sites, and chlordane and total PCB's (polychlorinated biphenyls) were detected at most sites. At six sites, streambed-sediment concentrations of contaminants were detected at levels with the potential to cause frequent adverse effects on aquatic organisms that live in the sediments. Chlordane was detected at these high levels at sampling sites on the Anacostia River, the North Branch Potomac River, Bull Run, and Accotink Creek; mercury was detected at these levels at sites on the South River and the South Fork Shenandoah River; and total PCB's were detected at these levels at the site on the South Fork Shenandoah River. The highest concentrations of all five contaminants generally occurred at sampling sites downstream from areas with industrial plants, urban centers, or orchard and agricultural activity. The occurrence of these contaminants in streambed sediments of the Potomac River Basin is of concern because the contaminants (1) are environmentally persistent, (2) are available for downstream transport during high streamflow periods, and (3) have the potential to cause adverse effects on the health of aquatic organisms and humans through bioaccumulation.

  13. Non-targeted detection of chemical contamination in carbonated soft drinks using NMR spectroscopy, variable selection and chemometrics

    Energy Technology Data Exchange (ETDEWEB)

    Charlton, Adrian J. [Department for Environment, Food and Rural Affairs, Central Science Laboratory, Sand Hutton, York YO41 1LZ (United Kingdom)], E-mail: adrian.charlton@csl.gov.uk; Robb, Paul; Donarski, James A.; Godward, John [Department for Environment, Food and Rural Affairs, Central Science Laboratory, Sand Hutton, York YO41 1LZ (United Kingdom)

    2008-06-23

    An efficient method for detecting malicious and accidental contamination of foods has been developed using a combined {sup 1}H nuclear magnetic resonance (NMR) and chemometrics approach. The method has been demonstrated using a commercially available carbonated soft drink, as being capable of identifying atypical products and to identify contaminant resonances. Soft-independent modelling of class analogy (SIMCA) was used to compare {sup 1}H NMR profiles of genuine products (obtained from the manufacturer) against retail products spiked in the laboratory with impurities. The benefits of using feature selection for extracting contaminant NMR frequencies were also assessed. Using example impurities (paraquat, p-cresol and glyphosate) NMR spectra were analysed using multivariate methods resulting in detection limits of approximately 0.075, 0.2, and 0.06 mM for p-cresol, paraquat and glyphosate, respectively. These detection limits are shown to be approximately 100-fold lower than the minimum lethal dose for paraquat. The methodology presented here is used to assess the composition of complex matrices for the presence of contaminating molecules without a priori knowledge of the nature of potential contaminants. The ability to detect if a sample does not fit into the expected profile without recourse to multiple targeted analyses is a valuable tool for incident detection and forensic applications.

  14. Non-targeted detection of chemical contamination in carbonated soft drinks using NMR spectroscopy, variable selection and chemometrics

    International Nuclear Information System (INIS)

    Charlton, Adrian J.; Robb, Paul; Donarski, James A.; Godward, John

    2008-01-01

    An efficient method for detecting malicious and accidental contamination of foods has been developed using a combined 1 H nuclear magnetic resonance (NMR) and chemometrics approach. The method has been demonstrated using a commercially available carbonated soft drink, as being capable of identifying atypical products and to identify contaminant resonances. Soft-independent modelling of class analogy (SIMCA) was used to compare 1 H NMR profiles of genuine products (obtained from the manufacturer) against retail products spiked in the laboratory with impurities. The benefits of using feature selection for extracting contaminant NMR frequencies were also assessed. Using example impurities (paraquat, p-cresol and glyphosate) NMR spectra were analysed using multivariate methods resulting in detection limits of approximately 0.075, 0.2, and 0.06 mM for p-cresol, paraquat and glyphosate, respectively. These detection limits are shown to be approximately 100-fold lower than the minimum lethal dose for paraquat. The methodology presented here is used to assess the composition of complex matrices for the presence of contaminating molecules without a priori knowledge of the nature of potential contaminants. The ability to detect if a sample does not fit into the expected profile without recourse to multiple targeted analyses is a valuable tool for incident detection and forensic applications

  15. Marker-Assisted Selection of Xa21 Conferring Resistance to Bacterial Leaf Blight in indica Rice Cultivar LT2

    Directory of Open Access Journals (Sweden)

    Hue Thi Nguyen

    2018-01-01

    Full Text Available Bacterial leaf blight of rice (BLB, caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive diseases in Asian rice fields. A high-quality rice variety, LT2, was used as the recipient parent. IRBB21, which carries the Xa21 gene, was used as the donor parent. The resistance gene Xa21 was introduced into LT2 by marker-assisted backcrossing. Three Xoo races were used to inoculate the improved lines following the clipping method. Eleven BC3F3 lines carrying Xa21 were obtained based on molecular markers and agronomic performance. The 11 lines were then inoculated with the three Xoo races. All the 11 improved lines showed better resistance to BLB than the recipient parent LT2. Based on the level of resistance to BLB and their agronomic performance, five lines (BC3F3 5.1.5.1, BC3F3 5.1.5.12, BC3F3 8.5.6.44, BC3F3 9.5.4.1 and BC3F3 9.5.4.23 were selected as the most promising for commercial release. These improved lines could contribute to rice production in terms of food security.

  16. Marker-assisted selection for recognizing wheat mutant genotypes carrying HMW glutenin alleles related to baking quality.

    Science.gov (United States)

    Zamani, Mohammad Javad; Bihamta, Mohammad Reza; Naserian Khiabani, Behnam; Tahernezhad, Zahra; Hallajian, Mohammad Taher; Shamsi, Marzieh Varasteh

    2014-01-01

    Allelic diversity of HMW glutenin loci in several studies revealed that allelic combinations affect dough quality. Dx5 + Dy10 subunits are related to good baking quality and Dx2 + Dy12 are related to undesirable baking quality. One of the most regular methods to evaluate the baking quality is SDS-PAGE which is used to improve baking quality labs. Marker-assisted selection is the method which can recognize the alleles related to baking quality and this method is based on polymerase chain reaction. 10 pairs of specific primers related to Dx2, Dx2.1, Dx5, Dy10, and Dy12 subunits were used for recognizing baking quality of some wheat varieties and some mutant genotypes. Only 5 pairs of them could show the specific bands. All subunits were recognized by the primers except Dx2.1. Some of the primers were extracted from previous studies and the others were designed based on D genome subunits of wheat. SDS-PAGE method accomplished having confidence in these marker's results. To realize the effect of mutation, seed storage proteins were measured. It showed that mutation had effect on the amount of seed storage protein on the mutant seeds (which showed polymorphism).

  17. Marker-assisted selection in crop and livestock improvement: how to strengthen national research capacity and international partnerships

    International Nuclear Information System (INIS)

    Lopes, M.A.

    2007-01-01

    It is generally recognized that marker-assisted selection (MAS) is a tool that breeders can use to accelerate the speed and precision of crop and livestock breeding in developing countries. However, its practical application has been more difficult than previously expected. Although advances in molecular marker technology have uncovered many possibilities for transferring genes into desired crops and livestock through MAS, more methodological development and better planning and implementation strategies will be needed for its successful and expeditious application to breeding programmes. Also, this technology should not be regarded as an end in itself, but as an interacting part of complex strategies and decision-making processes. An appropriate mix of technologies and capabilities together with effective approaches to networking must be viewed as key ingredients for its correct development and application to breeding programmes. This chapter describes some strategies to guide decisions about structures, methods and capacities that may contribute to enhancing the access and successful use of MAS in developing countries. (author)

  18. Marker-Assisted Selection of Xa21 Conferring Resistance to Bacterial Leaf Blight in indica Rice Cultivar LT2

    Institute of Scientific and Technical Information of China (English)

    Hue Thi NGUYEN; Trung Nguyen DINH; Nakano TOSHITSUGU; Liet Van VU; Quang Hong VU; Tan Van MAI; Thu Thi NGUYEN; Lam Duc VU; Tung Thanh NGUYEN; Long Viet NGUYEN; Hien Thu Thi VU; Hue Thi NONG

    2018-01-01

    Bacterial leaf blight of rice (BLB), caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive diseases in Asian rice fields. A high-quality rice variety, LT2, was used as the recipient parent. IRBB21, which carries the Xa21 gene, was used as the donor parent. The resistance gene Xa21 was introduced into LT2 by marker-assisted backcrossing. Three Xoo races were used to inoculate the improved lines following the clipping method. Eleven BC3F3lines carrying Xa21 were obtained based on molecular markers and agronomic performance. The 11 lines were then inoculated with the three Xoo races. All the 11 improved lines showed better resistance to BLB than the recipient parent LT2. Based on the level of resistance to BLB and their agronomic performance, five lines (BC3F35.1.5.1, BC3F35.1.5.12, BC3F38.5.6.44, BC3F3 9.5.4.1 and BC3F39.5.4.23) were selected as the most promising for commercial release. These improved lines could contribute to rice production in terms of food security.

  19. Genetics of radionuclide-contaminated mosquitofish populations and homology between Gambusia affinis and G. holbrooki

    International Nuclear Information System (INIS)

    Theodorakis, C.W.; Bickham, J.W.; Chesser, R.K.

    1998-01-01

    The effects of radionuclide contamination on genetic structure of eastern mosquitofish (Gambusia holbrooki) populations from the US Department of Energy's Savannah River Site (SRS) were investigated to develop methods of assessing ecological risk of chronic exposures to xenobiotics. Fish from two contaminated and two reference sites were examined by the randomly amplified polymorphic DNA (RAPD) technique, which revealed that the frequency of three markers was greater in the contaminated than the reference sites and that the frequency of two markers was greater in reference than in the contaminated sites. A previous study examined populations of western mosquitofish (G. affinis) from the Oak Ridge National Laboratory (ORNL) and found that certain RAPD markers were present in radionuclide-contaminated ORNL populations at a higher frequency than in reference populations. The contaminant-indicative markers observed in the SRS populations were the same size and amplified by the same polymerase chain reaction primers used in the ORNL study. Southern blot analysis revealed that the SRS G. holbrooki contaminant-indicative markers were homologous to the ORNL G. affinis contaminant-indicative markers. The observation that two species show similar patterns of band frequency shifts at two separate localities is consistent with the hypothesis that these DNA markers may originate from genetic elements that provide a selective advantage in contaminated habitats. Thus, the methodology used in these studies may prove to be useful to indicate population-level effects of environmental contamination

  20. Integrated chemical and biological assessment of contaminant impacts in selected European coastal and offshore marine areas

    NARCIS (Netherlands)

    Hylland, Ketil; Robinson, Craig D.; Burgeot, Thierry; Martínez-Gómez, Concepción; Lang, Thomas; Svavarsson, Jörundur; Thain, John E.; Vethaak, A. Dick; Gubbins, Mattew J.

    This paper reports a full assessment of results from ICON, an international workshop on marine integrated contaminant monitoring, encompassing different matrices (sediment, fish, mussels, gastropods), areas (Iceland, North Sea, Baltic, Wadden Sea, Seine estuary and the western Mediterranean) and

  1. Apparent discrepancy in contamination history of a sub-tropical estuary evaluated through 210Pb profile and chronostatigraphical markers

    International Nuclear Information System (INIS)

    Marques Junior, Aguinaldo N.

    2005-01-01

    Heavy metal concentrations (Zn, Cd, Cu and Pb), lead stable isotopes ( 204 Pb, 206 Pb, 207 Pb, and 208 Pb), and sediment chronology ( 210 Pb method) were determined in a core from Sepetiba Bay (southeastern coast of Brazil, 30 km west of Rio de Janeiro City). During last decades, this region has been modified by increase of industrial activities, population flows, and by human interventions in the watershed area of the bay. In particular, Zn and Cd emissions are well established to the bay, and inputs started during 1960 and 1970, respectively. The core was sampled in the more contaminated northern part of the bay, in the tidal flat in front of the Coroa Grande mangrove. This area is located near to the Sao Francisco Channel, which accounts for 86 % of the freshwater supply to the bay, and receive waters from the Paraiba do Sul River (another watershed) since 1950s. The proxies at the sediment core showed three successive events: at the depth of 50-52 cm, a marked change in the stable lead isotopic ratios; at 38-42 cm depth, the beginning of the Zn concentration upwards increase; and above 30 cm, relatively high Cd concentrations. Such records can easily be explained by the local metallurgic development history. However, sediment accumulation rates evaluated using these reference levels are higher than those calculated from the 210 Pb profile by using either the Constant Initial Concentration (CIC) or the Constant Rate of Supply (CRS) models. One possible interpretation can be provided by local hydrodynamics, which has been strongly influenced by deposition of particles transported by runoff in the core site. The main source of these particles may be the mangrove flat that experimented enrichment of unsupported 210 Pb by trapping it from the rain. A model, taking into account the exponential increase of the initial 210 Pb activity observed in the core allows the calculated rates to fit well with those evaluated from the 'historic' events. (author)

  2. Mapping and marker-assisted selection of a brown planthopper resistance gene bph2 in rice (Oryza sativa L.).

    Science.gov (United States)

    Sun, Li-Hong; Wang, Chun-Ming; Su, Chang-Chao; Liu, Yu-Qiang; Zhai, Hu-Qu; Wan, Jian-Min

    2006-08-01

    Nilaparvata lugens Stål (brown planthopper, BPH), is one of the major insect pests of rice (Oryza sativa L.) in the temperate rice-growing region. In this study, ASD7 harboring a BPH resistance gene bph2 was crossed to a susceptible cultivar C418, a japonica restorer line. BPH resistance was evaluated using 134 F2:3 lines derived from the cross between "ASD7" and "C418". SSR assay and linkage analysis were carried out to detect bph2. As a result, the resistant gene bph2 in ASD7 was successfully mapped between RM7102 and RM463 on the long arm of chromosome 12, with distances of 7.6 cM and 7.2 cM, respectively. Meanwhile, both phenotypic selection and marker-assisted selection (MAS) were conducted in the BC1F1 and BC2F1 populations. Selection efficiencies of RM7102 and RM463 were determined to be 89.9% and 91.2%, respectively. It would be very beneficial for BPH resistance improvement by using MAS of this gene.

  3. Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycine max).

    Science.gov (United States)

    Zhang, Jiaoping; Song, Qijian; Cregan, Perry B; Jiang, Guo-Liang

    2016-01-01

    Twenty-two loci for soybean SW and candidate genes conditioning seed development were identified; and prediction accuracies of GS and MAS were estimated through cross-validation and validation with unrelated populations. Soybean (Glycine max) is a major crop for plant protein and oil production, and seed weight (SW) is important for yield and quality in food/vegetable uses of soybean. However, our knowledge of genes controlling SW remains limited. To better understand the molecular mechanism underlying the trait and explore marker-based breeding approaches, we conducted a genome-wide association study in a population of 309 soybean germplasm accessions using 31,045 single nucleotide polymorphisms (SNPs), and estimated the prediction accuracy of genomic selection (GS) and marker-assisted selection (MAS) for SW. Twenty-two loci of minor effect associated with SW were identified, including hotspots on Gm04 and Gm19. The mixed model containing these loci explained 83.4% of phenotypic variation. Candidate genes with Arabidopsis orthologs conditioning SW were also proposed. The prediction accuracies of GS and MAS by cross-validation were 0.75-0.87 and 0.62-0.75, respectively, depending on the number of SNPs used and the size of training population. GS also outperformed MAS when the validation was performed using unrelated panels across a wide range of maturities, with an average prediction accuracy of 0.74 versus 0.53. This study convincingly demonstrated that soybean SW is controlled by numerous minor-effect loci. It greatly enhances our understanding of the genetic basis of SW in soybean and facilitates the identification of genes controlling the trait. It also suggests that GS holds promise for accelerating soybean breeding progress. The results are helpful for genetic improvement and genomic prediction of yield in soybean.

  4. Selective Inducible Nitric Oxide Synthase Inhibitor Reversed Zinc Chloride-Induced Spatial Memory Impairment via Increasing Cholinergic Marker Expression.

    Science.gov (United States)

    Tabrizian, Kaveh; Azami, Kian; Belaran, Maryam; Soodi, Maliheh; Abdi, Khosrou; Fanoudi, Sahar; Sanati, Mehdi; Mottaghi Dastjerdi, Negar; Soltany Rezaee-Rad, Mohammad; Sharifzadeh, Mohammad

    2016-10-01

    Zinc, an essential micronutrient and biochemical element of the human body, plays structural, catalytic, and regulatory roles in numerous physiological functions. In the current study, the effects of a pretraining oral administration of zinc chloride (10, 25, and 50 mg/kg) for 14 consecutive days and post-training bilateral intra-hippocampal infusion of 1400W as a selective inducible nitric oxide synthase (iNOS) inhibitor (10, 50, and 100 μM/side), alone and in combination, on the spatial memory retention in Morris water maze (MWM) were investigated. Animals were trained for 4 days and tested 48 h after completion of training. Also, the molecular effects of these compounds on the expression of choline acetyltransferase (ChAT), as a cholinergic marker in the CA1 region of the hippocampus and medial septal area (MSA), were evaluated. Behavioral and molecular findings of this study showed that a 2-week oral administration of zinc chloride (50 mg/kg) impaired spatial memory retention in MWM and decreased ChAT expression. Immunohistochemical analysis of post-training bilateral intra-hippocampal infusion of 1400W revealed a significant increase in ChAT immunoreactivity. Furthermore, post-training bilateral intra-hippocampal infusion of 1400W into the CA1 region of the hippocampus reversed zinc chloride-induced spatial memory impairment in MWM and significantly increased ChAT expression in comparison with zinc chloride-treated animals. Taken together, these results emphasize the role of selective iNOS inhibitors in reversing zinc chloride-induced spatial memory deficits via modulation of cholinergic marker expression.

  5. Functional molecular markers (EST-SSR) in the full-sib reciprocal recurrent selection program of maize (Zea mays L.).

    Science.gov (United States)

    Galvão, K S C; Ramos, H C C; Santos, P H A D; Entringer, G C; Vettorazzi, J C F; Pereira, M G

    2015-07-03

    This study aimed to improve grain yield in the full-sib reciprocal recurrent selection program of maize from the North Fluminense State University. In the current phase of the program, the goal is to maintain, or even increase, the genetic variability within and among populations, in order to increase heterosis of the 13th cycle of reciprocal recurrent selection. Microsatellite expressed sequence tags (EST-SSRs) were used as a tool to assist the maximization step of genetic variability, targeting the functional genome. Eighty S1 progenies of the 13th recur-rent selection cycle, 40 from each population (CIMMYT and Piranão), were analyzed using 20 EST-SSR loci. Genetic diversity, observed heterozygosity, information content of polymorphism, and inbreeding co-efficient were estimated. Subsequently, analysis of genetic dissimilarity, molecular variance, and a graphical dispersion of genotypes were conducted. The number of alleles in the CIMMYT population ranged from 1 to 6, while in the Piranão population the range was from 2 to 8, with a mean of 3.65 and 4.35, respectively. As evidenced by the number of alleles, the Shannon index showed greater diversity for the Piranão population (1.04) in relation to the CIMMYT population (0.89). The genic SSR markers were effective in clustering genotypes into their respective populations before selection and an increase in the variation between populations after selection was observed. The results indicate that the study populations have expressive genetic diversity, which cor-responds to the functional genome, indicating that this strategy may contribute to genetic gain, especially in association with the grain yield of future hybrids.

  6. Selection of Almond Vegetative Rootstocks for Water Stress Tolerance Based on the Morphological Markers

    Directory of Open Access Journals (Sweden)

    A.A. Shokouhian

    2016-02-01

    Full Text Available Introduction: One of the microbiological preparations used for this study was Effective Microorganisms (EM, being a commercial mixture of photosynthesizing bacteria, Actinomycetes, lactic acid bacteria, yeasts and fermenting fungi. The microbiological composition of the EM concentrateincludesStreptomyces albus, Propioni bacterium freudenreichil, Streptococcus lactis, Aspergillus oryzae, Mucor hiemalis, Saccharomycescerevisiae and Candida utilis. Moreover, EM also contains an unspecified amount of Lactobacillus sp. Rhodo pseudomonas sp. and Streptomyces griseus. Effective Microorganisms have a positive effect on the decomposition of organic matter, limiting putrefaction, increasing nitrogen content in the root medium of plants, phosphorus, improving soil fertility and as a result contributing to the growth and development of the root systems of plants. Selection of almond vegetative rootstocks for water stress tolerance is important for almond crop production in arid and semi-arid regions. The study of the eco-morphological characteristics that determine the success of a rootstock in a particular environment is a powerful tool for both agricultural management and breeding purposes. The aim of this work was to select the new rootstocks for water shortage tolerance, impact of water stress as well as Effective Microorganism (EM on morphological characteristics of almond rootstocks. Materials and Methods: In order to select the new rootstocks for water shortage tolerance, impact of water stress as well as EMonmorphologicalcharacteristics of almondrootstocks were studiedin thedepartment ofHorticulture, Ferdowsi University of Mashhad, in 2011-2012. The experiment was carried out with four replications in a completely random blockdesign to study the effects of two concentrations of EM (0 and 1%, three irrigation levels (normal irrigation 100%-control-and irrigation after depletion of 33 and 66% of available water, and four almond rootstocks including GF

  7. Apparent discrepancy in contamination history of a sub-tropical estuary evaluated through {sup 210}Pb profile and chronostatigraphical markers

    Energy Technology Data Exchange (ETDEWEB)

    Marques Junior, Aguinaldo N. [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Inst. de Biologia. Dept. de Biologia Marinha]. E-mail: amarques@vm.uff.br; Monna, Fabrice [Universite de Bourgogne, Dijon (France). Centre des Sciences de la Terre; Silva Filho, Emannoel V. da [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Inst. de Quimica. Dept. de Geoquimica; Fernex, Francois E. [Universite de Nice, Valrose (France). Dept. des Sciences de la Terre; Simoes Filho, Fernando Lamego [Instituto de Radioprotecao e Dosimetria (IRD), Rio de Janeiro, RJ (Brazil)]. E-mail: flamego@ird.gov.br

    2005-07-01

    Heavy metal concentrations (Zn, Cd, Cu and Pb), lead stable isotopes ({sup 204}Pb, {sup 206}Pb, {sup 207}Pb, and {sup 208}Pb), and sediment chronology ({sup 210}Pb method) were determined in a core from Sepetiba Bay (southeastern coast of Brazil, 30 km west of Rio de Janeiro City). During last decades, this region has been modified by increase of industrial activities, population flows, and by human interventions in the watershed area of the bay. In particular, Zn and Cd emissions are well established to the bay, and inputs started during 1960 and 1970, respectively. The core was sampled in the more contaminated northern part of the bay, in the tidal flat in front of the Coroa Grande mangrove. This area is located near to the Sao Francisco Channel, which accounts for 86 % of the freshwater supply to the bay, and receive waters from the Paraiba do Sul River (another watershed) since 1950s. The proxies at the sediment core showed three successive events: at the depth of 50-52 cm, a marked change in the stable lead isotopic ratios; at 38-42 cm depth, the beginning of the Zn concentration upwards increase; and above 30 cm, relatively high Cd concentrations. Such records can easily be explained by the local metallurgic development history. However, sediment accumulation rates evaluated using these reference levels are higher than those calculated from the {sup 210}Pb profile by using either the Constant Initial Concentration (CIC) or the Constant Rate of Supply (CRS) models. One possible interpretation can be provided by local hydrodynamics, which has been strongly influenced by deposition of particles transported by runoff in the core site. The main source of these particles may be the mangrove flat that experimented enrichment of unsupported {sup 210}Pb by trapping it from the rain. A model, taking into account the exponential increase of the initial {sup 210}Pb activity observed in the core allows the calculated rates to fit well with those evaluated from the &apos

  8. Marker-assisted selection as a potential tool for genetic improvement in developing countries: debating the issues

    International Nuclear Information System (INIS)

    Robinson, J.; Ruane, J.

    2007-01-01

    Marker-assisted selection (MAS) is a complementary technology, for use in conjunction with more established conventional methods of genetic selection, for plant and animal improvement. It has generated a good deal of expectations, many of which have yet to be realized. Although documentation is limited, the current impact of MAS on products delivered to farmers seems small. While the future possibilities and potential impacts of MAS are considerable, there are also obstacles to its use, particularly in developing countries. Principal among these are issues relating to current high costs of the technology and its appropriateness, given that publicly funded agricultural research in many developing countries is suboptimal and development priorities do not necessarily include genetic improvement programmes. Other potential obstacles to the uptake of MAS in developing countries include limited infrastructure, the absence of conventional selection and breeding programmes, poor private sector involvement and lack of research on specific crops of importance in developing countries. Intellectual property rights may also be an important constraint to development and uptake of MAS in the developing world. It is hoped that through partnerships between developing and developed country institutions and individuals, including public-private sector collaboration, MAS costs can be reduced, resources pooled and shared and capacity developed. With the assistance of the Consultative Group on International Agricultural Research (CGIAR) and international organizations such as FAO, developing countries can benefit more from MAS. These were some of the outcomes of a moderated e-mail conference, entitled 'Molecular Marker- Assisted Selection as a Potential Tool for Genetic Improvement of Crops, Forest Trees, Livestock and Fish in Developing Countries', that FAO hosted at the end of 2003. During the four-week conference, 627 people subscribed and 85 messages were posted, about 60 percent

  9. Treatment of Fukushima contaminated waters TEPCO selected Areva and Veolia solution

    International Nuclear Information System (INIS)

    Seberac, Philippe; Paillard, Herve; Thierry, Jean-Marie; Bae, Ho-Il; Prevost, Thierry; Piot, Gregoire; Bertrand Ytournel

    2012-09-01

    The Actiflo-Rad TM system successfully contributed to treat the contaminated wastewaters from the damaged Fukushima Daiichi nuclear power plant. The decontamination system jointly designed by AREVA and Veolia Water treated about 77 500 m 3 of high activity wastewater (∼10 6 Bq/cm 3 ), combining radionuclides adsorbents developed by AREVA and the know-how of Veolia in water treatment for the settlement of the adsorbed radioactive elements, producing sludge with a weight concentration of 80 g/L. Both companies delivered the treatment facility quickly with an efficient joint organization - in a very complex environment. Assembled on Fukushima site - badly damaged by the tsunami following the earthquake of March 11 th - the system was designed, built and started in a record time of 2 month 1 / 2 , instead of several years in a classical nuclear engineering project. The Actiflo-Rad TM was a key equipment to achieve a stable situation of reactors, allowing treated water to be reused for core cooling. Commissioned with the on-site support of Veolia experts, the system reduced by 10 000 the Cs-activity of the wastewater even with significant salt content (seawater diluted twice) at a flow-rate slightly below the design value of 50 m 3 /hr. The implemented technologies are already used separately on AREVA sites (la Hague, fuel reprocessing plant) and for many water treatment projects by Veolia all over the world (Actiflo TM and Multiflo TM processes, using lamellar settling devices - in addition, the first one making use of micro-sand for a better floc quality). The complete treatment process selected by TEPCO features a physico-chemical treatment and water desalination, in five steps. After de-oiling, wastewater is primarily decontaminated through zeolite columns (Kurion process). This pre-decontaminated water is then treated on the AREVA-Veolia two stages system; at each stage, more than 30 minutes contact time with radionuclides adsorbents is needed, adsorbed

  10. Multi-generational imputation of single nucleotide polymorphism marker genotypes and accuracy of genomic selection.

    Science.gov (United States)

    Toghiani, S; Aggrey, S E; Rekaya, R

    2016-07-01

    Availability of high-density single nucleotide polymorphism (SNP) genotyping platforms provided unprecedented opportunities to enhance breeding programmes in livestock, poultry and plant species, and to better understand the genetic basis of complex traits. Using this genomic information, genomic breeding values (GEBVs), which are more accurate than conventional breeding values. The superiority of genomic selection is possible only when high-density SNP panels are used to track genes and QTLs affecting the trait. Unfortunately, even with the continuous decrease in genotyping costs, only a small fraction of the population has been genotyped with these high-density panels. It is often the case that a larger portion of the population is genotyped with low-density and low-cost SNP panels and then imputed to a higher density. Accuracy of SNP genotype imputation tends to be high when minimum requirements are met. Nevertheless, a certain rate of genotype imputation errors is unavoidable. Thus, it is reasonable to assume that the accuracy of GEBVs will be affected by imputation errors; especially, their cumulative effects over time. To evaluate the impact of multi-generational selection on the accuracy of SNP genotypes imputation and the reliability of resulting GEBVs, a simulation was carried out under varying updating of the reference population, distance between the reference and testing sets, and the approach used for the estimation of GEBVs. Using fixed reference populations, imputation accuracy decayed by about 0.5% per generation. In fact, after 25 generations, the accuracy was only 7% lower than the first generation. When the reference population was updated by either 1% or 5% of the top animals in the previous generations, decay of imputation accuracy was substantially reduced. These results indicate that low-density panels are useful, especially when the generational interval between reference and testing population is small. As the generational interval

  11. Expression of Selected Markers in Immunohistochemical Diagnosis of Canine and Human Testicular Tumours

    Directory of Open Access Journals (Sweden)

    Ciaputa Rafał

    2015-04-01

    Full Text Available Immunohistochemical profiles of the most common canine testicular tumours, including the Leydig cell tumours, seminomas, and Sertoli cell tumours were analysed, and the results were compared with those obtained in the corresponding types of human testicular neoplasms. The expressions of vimentin, von Willebrand factor (FVIII, chromogranin A, synaptophysin, and MCM3 were quantified. In the case of Sertoli cell tumours, only canine ones were analysed, since this type of tumour is very rarely diagnosed in men. The expression of the analysed proteins in the testicular tumours was similar. The von Willebrand factor exhibited the strongest expression in Leydig cell tumours in dogs and men, while vimentin was expressed more strongly in dogs (96.7% had an intensity at +++ than in men (62.5% had +++ in the Leydigioma. The immunoexpression of MCM3 in seminomas was high in both men and dogs – 90% +++ and 100% +++ respectively. The lack of chromogranin A and synaptophysin was observed in almost 100% of seminomas in men and dogs. This differed from the results obtained for Leydigioma, where chromogranin A was expressed in 70% of dogs at +++ and in 100% of men at ++++. The results may indicate that the antibodies were selected correctly. Their analysis and interpretation provides valuable information concerning the nature of the studied tumours.

  12. Relations between sinkhole density and anthropogenic contaminants in selected carbonate aquifers in the eastern United States

    Science.gov (United States)

    Lindsey, Bruce D.; Katz, Brian G.; Berndt, Marian P.; Ardis, Ann F.; Skach, Kenneth A.

    2009-01-01

    The relation between sinkhole density and water quality was investigated in seven selected carbonate aquifers in the eastern United States. Sinkhole density for these aquifers was grouped into high (>25 sinkholes/100 km2), medium (1–25 sinkholes/100 km2), or low (2) categories using a geographical information system that included four independent databases covering parts of Alabama, Florida, Missouri, Pennsylvania, and Tennessee. Field measurements and concentrations of major ions, nitrate, and selected pesticides in samples from 451 wells and 70 springs were included in the water-quality database. Data were collected as a part of the US Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program. Areas with high and medium sinkhole density had the greatest well depths and depths to water, the lowest concentrations of total dissolved solids and bicarbonate, the highest concentrations of dissolved oxygen, and the lowest partial pressure of CO2 compared to areas with low sinkhole density. These chemical indicators are consistent conceptually with a conduit-flow-dominated system in areas with a high density of sinkholes and a diffuse-flow-dominated system in areas with a low density of sinkholes. Higher cave density and spring discharge in Pennsylvania also support the concept that the high sinkhole density areas are dominated by conduit-flow systems. Concentrations of nitrate-N were significantly higher (p sinkhole density than in low sinkhole-density areas; when accounting for the variations in land use near the sampling sites, the high sinkhole-density area still had higher concentrations of nitrate-N than the low sinkhole-density area. Detection frequencies of atrazine, simazine, metolachlor, prometon, and the atrazine degradate deethylatrazine indicated a pattern similar to nitrate; highest pesticide detections were associated with high sinkhole-density areas. These patterns generally persisted when analyzing the detection frequency by land

  13. Depletion of selected polychlorodibenzodioxins and polychlorodibenzofurans in farmed trout exposed to contaminated feeds

    Energy Technology Data Exchange (ETDEWEB)

    Brambilla, G.; Dellatte, E.; Fochi, I.; Iacovella, N.; Domenico, A. di [Dept. Food Safety and Animal Health, Ist. Superiore di Sanita, Rome (Italy)]|[Dept. Environment and Primary Health Care, Ist. Superiore di Sanita, Rome (Italy)

    2004-09-15

    Farmed fish can bioaccumulate persistent toxic substances when fed on animal-based fat feeds. This fact has recently prompted a re-evaluation of the overall toxicological risk associated with contamination levels recorded in farmed vs. wild salmons. The bioaccumulation of polychlorinated dibenzodioxins (PCDDs) and dibenzofurans (PCDFs) in farmed trout has recently been described nevertheless, poor information is available about their depletion under controlled conditions. In this paper, the results of a 90-day depletion study in groups of trout exposed to three different levels of feed contamination for 30 days are reported. As a follow-up of a PCB depletion study the present paper aims at giving indications for risk management in fish farming practices, to prevent an unacceptable contamination of the produce intended for human consumption.

  14. A high efficiency gene disruption strategy using a positive-negative split selection marker and electroporation for Fusarium oxysporum.

    Science.gov (United States)

    Liang, Liqin; Li, Jianqiang; Cheng, Lin; Ling, Jian; Luo, Zhongqin; Bai, Miao; Xie, Bingyan

    2014-11-01

    The Fusarium oxysporum species complex consists of fungal pathogens that cause serial vascular wilt disease on more than 100 cultivated species throughout the world. Gene function analysis is rapidly becoming more and more important as the whole-genome sequences of various F. oxysporum strains are being completed. Gene-disruption techniques are a common molecular tool for studying gene function, yet are often a limiting step in gene function identification. In this study we have developed a F. oxysporum high-efficiency gene-disruption strategy based on split-marker homologous recombination cassettes with dual selection and electroporation transformation. The method was efficiently used to delete three RNA-dependent RNA polymerase (RdRP) genes. The gene-disruption cassettes of three genes can be constructed simultaneously within a short time using this technique. The optimal condition for electroporation is 10μF capacitance, 300Ω resistance, 4kV/cm field strength, with 1μg of DNA (gene-disruption cassettes). Under these optimal conditions, we were able to obtain 95 transformants per μg DNA. And after positive-negative selection, the transformants were efficiently screened by PCR, screening efficiency averaged 85%: 90% (RdRP1), 85% (RdRP2) and 77% (RdRP3). This gene-disruption strategy should pave the way for high throughout genetic analysis in F. oxysporum. Copyright © 2014 Elsevier GmbH. All rights reserved.

  15. Analysis of environmental contamination resulting from catastrophic incidents: part 2. Building laboratory capability by selecting and developing analytical methodologies.

    Science.gov (United States)

    Magnuson, Matthew; Campisano, Romy; Griggs, John; Fitz-James, Schatzi; Hall, Kathy; Mapp, Latisha; Mullins, Marissa; Nichols, Tonya; Shah, Sanjiv; Silvestri, Erin; Smith, Terry; Willison, Stuart; Ernst, Hiba

    2014-11-01

    Catastrophic incidents can generate a large number of samples of analytically diverse types, including forensic, clinical, environmental, food, and others. Environmental samples include water, wastewater, soil, air, urban building and infrastructure materials, and surface residue. Such samples may arise not only from contamination from the incident but also from the multitude of activities surrounding the response to the incident, including decontamination. This document summarizes a range of activities to help build laboratory capability in preparation for sample analysis following a catastrophic incident, including selection and development of fit-for-purpose analytical methods for chemical, biological, and radiological contaminants. Fit-for-purpose methods are those which have been selected to meet project specific data quality objectives. For example, methods could be fit for screening contamination in the early phases of investigation of contamination incidents because they are rapid and easily implemented, but those same methods may not be fit for the purpose of remediating the environment to acceptable levels when a more sensitive method is required. While the exact data quality objectives defining fitness-for-purpose can vary with each incident, a governing principle of the method selection and development process for environmental remediation and recovery is based on achieving high throughput while maintaining high quality analytical results. This paper illustrates the result of applying this principle, in the form of a compendium of analytical methods for contaminants of interest. The compendium is based on experience with actual incidents, where appropriate and available. This paper also discusses efforts aimed at adaptation of existing methods to increase fitness-for-purpose and development of innovative methods when necessary. The contaminants of interest are primarily those potentially released through catastrophes resulting from malicious activity

  16. ENVIRONMENTAL CONTAMINANTS AND POTENTIAL HUMAN RISK ASSOCIATED WITH SELECTED BOTANICAL DIETARY SUPPLEMENTS

    Science.gov (United States)

    Botanical dietary supplements have a long history of use in Europe and China and they are becoming increasingly popular in the United States. However, little data is available regarding environmental contaminants in botanical dietary supplements and the risk posed to those ingest...

  17. Waveband selection and algorithm development to distinguish fecal contamination using multispectral imaging with solar light

    Science.gov (United States)

    Fecal contamination in fresh produce fields caused by animals or livestock entering the fields can lead to outbreaks of foodbourne illnesses. E.coli O157:H7 originating in the intestines of animals can transfer onto leafy greens via fecal matter. Leafy greens are often eaten fresh without thermal tr...

  18. Awareness and Prevalence of Mycotoxin Contamination in Selected Nigerian Fermented Foods

    Science.gov (United States)

    Njobeh, Patrick; Obadina, Adewale

    2017-01-01

    Fermented food samples (n = 191) including maize gruel (ogi), sorghum gruel (ogi-baba), melon seed (ogiri), locust bean (iru) and African oil bean seed (ugba) from Southwest Nigeria were quantified for 23 mycotoxins, including aflatoxin B1 (AFB1), fumonisin B1 (FB1), and sterigmatocystin (STE) using liquid chromatography-tandem mass spectrometry. The practices, perceived understanding and health risks related to fungal and mycotoxin contamination amongst fermented food sellers was also established. Data obtained revealed that 82% of the samples had mycotoxins occurring singly or in combination. FB1 was present in 83% of ogi-baba samples, whereas 20% of ugba samples contained AFB1 (range: 3 to 36 µg/kg) and STE was present in 29% of the ogi samples. In terms of multi-mycotoxin contamination, FB1 + FB2 + FB3 + STE + AFB1 + alternariol + HT-2 co-occurred within one sample. The awareness study revealed that 98% of respondents were unaware of mycotoxin contamination, and their education level slightly correlated with their level of awareness (p contaminated these food commodities, coupled with the poor perception of the population under study on fungi and mycotoxins, justifies the need to enact fungal and mycotoxin mitigation strategies along the food chain. PMID:29117141

  19. The orotate transporter oroP from Lactococcus lactis can be used both as a very efficient, food-grade selection and counter-selection marker for strain construction in many different organisms

    DEFF Research Database (Denmark)

    Defoor, Els Marie Celine; Martinussen, Jan

    frame oroP on pDBORO necessary for the uptake of orotate was identified. A number of industrial important strains like Lactococcus lactis, Bacillus subtilus, and Bacillus licheniformis have been shown to be unable to metabolize orotate. If the oroP gene was introduced into these strains they acquired...... the ability to utilize orotate. If the strains had a pyrimidine requirement, the oroP gene could function as a selectable marker when growing in the presence of orotate as sole pyrimidine source. In an otherwise resistant strain, oroP was shown to sensitize the strain towards the analog 5-Fluoroorotate....... It was shown that strains who have lost the oroP gene could easily be selected in the presence of 5-Fluoroorotate, thus being an efficient counter-selection marker. pyrimidine-requiring strain (pyr B, C or D) orotate negative Counter-selection marker: wild-type strain! Fluoro-orotate resistant Functional...

  20. Evaluation of Nonpoint-Source Contamination, Wisconsin: Selected Topics for Water Year 1995

    Science.gov (United States)

    Owens, D.W.; Corsi, Steven R.; Rappold, K.F.

    1997-01-01

    The objective of the watershed-management evaluation monitoring program in Wisconsin is to evaluate the effectiveness of best-management practices (BMP's) for controlling nonpoint-source contamination in eight rural and four urban watersheds. This report, the fourth in an annual series of reports, presents a summary of the data collected for the program by the U.S. Geological Survey and the results of several detailed analyses of the data. To complement assessments of water quality, a land-use and BMP inventory is ongoing for 12 evaluation monitoring projects to track nonpoint sources of contamination in each watershed and to document implementation of BMP's that were designed to cause changes in the water quality of streams. Each year, updated information is gathered, mapped, and stored in a geographic-information-system data base. Summaries of land-use, BMP implementation, and water-quality data collected during water years 1989-95 are presented. Storm loads, snowmelt-period loads, and annual loads of suspended sediment and total phosphorus are summarized for eight rural sites. Storm-load data for suspended solids, total phosphorus, total recoverable lead, copper, zinc, and cadmium are summarized for four urban sites. Quality-assurance and quality-control (QA/QC) samples were collected at the eight rural sites to evaluate inorganic sample contamination and at one urban site to evaluate sample-collection and filtration techniques for polycyclic aromatic hydrocarbons (PAR's). Some suspended solids and fecal coliform contamination was detected at the rural sites. Corrective actions will be taken to address this contamination. Evaluation of PAR sample-collection techniques did not uncover any deficiencies, but the small amount of data collected was not sufficient to draw any definite conclusions. Evaluation of PAR filtration techniques indicate that water-sample filtration with O.7-um glass-fiber filters in an aluminum filter unit does not result in significant loss

  1. Off-Gas Treatment: Evaluation of Nano-structured Sorbents for Selective Removal of Contaminants

    Energy Technology Data Exchange (ETDEWEB)

    Utgikar, Vivek; Aston, D. Eric; Sabharwall, Piyush

    2018-03-30

    Reprocessing of used nuclear fuel (UNF) is expected to play an important role for sustainable development of nuclear energy by increasing the energy extracted from the fuel and reducing the generation of the high level waste (HLW). However, aqueous reprocessing of UNF is accompanied by emission of off-gas streams containing radioactive nuclides including iodine, krypton, xenon, carbon, and tritium. Volatile iodine (129I), and krypton (85Kr) are long lived isotopes which have adverse effects on the environment as well as human health. Development of methods for the capture and long-term storage of radioactive gases is of crucial importance in order to manage their emissions that are anticipated to increase significantly with the growth of nuclear energy. For more than 70 years, porous solid sorbents have been in the forefront of radioactive contaminant removal due to promising results and their advantages such as high removal efficiency, low maintenance cost, simple equipment design and operation over other techniques. The research conducted in this project has focused on development of a novel nanostructured sorbent and its application for the capture of the above two contaminants of interest. Nanostructured carbon polyhedrons supported on Engelhard Titanosilicate-10 sorbent was synthesized using hydrothermal methods and subjected to structural and compositional characterization using various techniques including electron microscopy, Raman, x-ray diffraction and BET surface area analysis. Dynamic sorption experiments conducted using a flow-through column setup yielded information on the thermodynamics and kinetics of sorption in single-contaminant and multi-contaminant streams. Parameters varied in the study included carbon loading, temperature, contact time, contaminant concentration and humidity. The behavior of the system was modeled using models available in literature as well as development of a mass-transfer model from fundamental principles. Experimental

  2. Environmental remediation through sequestration of airfall-derived metals contamination by selective revegetation strategies

    Science.gov (United States)

    Sahagian, D.; Peters, S.; Yasko, G.

    2006-12-01

    Industrial activities in the 20th century left a legacy of contaminated air, water, and soils. The relative environmental enlightenment of the 21st century has already led to reductions in pollution sources, and has improved air and surface water quality in many areas. However, the residence time of contaminants in soils can be lengthy, presenting a challenge to 21st century restoration of impacted ecosystems and communities. The present study is centered on the Borough of Palmerton, PA, and a broad region of adjacent communities that were affected by two zinc smelters that operated continuously for more than 80 years, emitting thousands of tons of heavy metals including zinc, cadmium, lead and arsenic. While the air quality has vastly improved since the closure of the zinc smelters, the community remains adversely affected by the ecological damage caused by the pollution. The north face of the Kittatiny ridge was completely denuded of vegetation from the high metals concentrations. The region suffers further due to the ongoing perception of contaminated soils and water, leaving the town and surrounding areas economically depressed. In this study, we are examining the impact of revegetation strategies, particularly those using warm season grasses to determine which species survive and indeed thrive in the metals-contaminated soils. Because of the large areal extent and locally steep slopes in the broad area of concern, removal of metals from the entire region is impractical. It is considered more effective to sequester the metals in the soil so that they do not leach into the rivers, or enter the food web. Vegetation that absorbs and transports the metals throughout its tissues would mobilize these pollutants into the food web as well as make the metals available to reach the river via leaves and other vegetative structures. In this study, we are monitoring the uptake of metals by test grasses and other plants that are colonizing the contaminated area, as well as

  3. Effect of soil contamination with oil substances on the growth of selected plants

    International Nuclear Information System (INIS)

    Sara, V.; Kult, L.; Vavra, J.

    1993-12-01

    The growth of barley, maize, wheat and alfalfa was studied in dependence on the level of soil pollution with crude oil. Attention was also paid to the effect of such contamination on the vanadium and nickel contents of the above-ground parts of the plants. Experiments revealed that, with the exception of alfalfa, the vanadium content of plants which had been grown in the contaminated soil was about one-half with respect to the values observed in plants grown in uncontaminated soil, and the nickel content was also lower than in control plants. Introduced into the soil by injection in concentrations of 180 to 500 ppm, crude oil was found to induce local damage in the plants, resulting in a smaller size of the plants and a delayed or missing earing phase, with repercussions on the grain size and quantity. (J.B.). 2 tabs., 6 figs

  4. Evaluation of fungal air contamination in selected wards of two tertiary hospitals in Tehran, Iran

    Directory of Open Access Journals (Sweden)

    Zahra Kamali Sarwestani

    2017-07-01

    Conclusion: According to the results of this study, the frequency and diversity of fungal spores in hospital wards were different. In addition, since the fungal contamination in the hospital environment are affected by various environmental factors and the efficiency of ventilation systems, some of these wards require better ventilation system as well as regular monitoring to remove these fungal bioaerosols in order to maintain the health of patients and health care workers.

  5. Selection of Mercury Accumulator Plants for Gold Mine Tailing Contaminated Soils

    OpenAIRE

    Muddarisna, N; Krisnayanti, B D

    2015-01-01

    Phytoremediation, which is more efficient with less side effects than conventional physical and chemical methods, is increasing in popularity as a remediation system. This paper provides a brief overview of developments in research and application of phytoremediation of soil contaminated with gold mine tailings containing mercury. Lindernia crustacea L., Digitaria radicosa Presl. Miq., Zingiber purpurium L, Paspalum conjugatum Berg., Cyperus kyllingia Endl., and Caladium bicolor Vent., that w...

  6. Treatment and Remediation of Petroleum-Contaminated Soils Using Selective Ornamental Plants

    OpenAIRE

    Liu, Rui; Jadeja, Rajendrasinh N.; Zhou, Qixing; Liu, Zhe

    2012-01-01

    Pot-culture experiments were carried out to assess the phytoremediation potential of 14 ornamental plants in weathered petroleum-contaminated soil, which was collected in the Shengli Oil Field, one of the biggest oil fields in China, by examining their impact on the degradation potential of total petroleum hydrocarbons (TPHs) and its composition. Results showed Gaillardia aristata, Echinacea purpurea, Fawn (Festuca arundinacea Schreb), Fire Phoenix (a combined F. arundinacea), and Medicago sa...

  7. The Relationships between Selection and Processing Food with Escherichia coli Contaminant on Food Stall Serving

    Directory of Open Access Journals (Sweden)

    Tris Eryando

    2014-04-01

    Full Text Available Escherichia coli in food stalls surrounding the X Campuss in Depok, year 2012. The research conducted to examine food safety, which were served in surrounding the campus X in Depok. Escherichia coli (E. coli existence was used to indicate the quality of hygiene and sanitation of the food that was served. Using the cross sectional method, the research examined the persons who served the food to be sold in the food stalls in the campus. There were 173 food servers chosen as the respondents from 10 different food stalls around the university. The existence of E. coli examined in the microbiology laboratory in the Faculty of Public Health. Using the most probable number (MPN method found that 59.54% of the food served in the campus were contaminated E. coli. Factors affecting the existence of E. coli were the raw materials (vegetables treated and the length of cooking of the materials (rice/beens. The improper treatment such as washing with no running water or even unwashed vegetables had 5 times risk of the E. coli contamination. Cooking less than 15 minutes was also more risky than cooking more than 15 minutes. As a result, this is very important to find a method to improve knowledge and to increase practical skills in food safety. Furthermore, in this research area may give contribution to avoid E. coli contamination which will prevent unnecessary illness among students in the campus.

  8. Marker-Assisted Selection for Recognizing Wheat Mutant Genotypes Carrying HMW Glutenin Alleles Related to Baking Quality

    Directory of Open Access Journals (Sweden)

    Mohammad Javad Zamani

    2014-01-01

    Full Text Available Allelic diversity of HMW glutenin loci in several studies revealed that allelic combinations affect dough quality. Dx5 + Dy10 subunits are related to good baking quality and Dx2 + Dy12 are related to undesirable baking quality. One of the most regular methods to evaluate the baking quality is SDS-PAGE which is used to improve baking quality labs. Marker-assisted selection is the method which can recognize the alleles related to baking quality and this method is based on polymerase chain reaction. 10 pairs of specific primers related to Dx2, Dx2.1, Dx5, Dy10, and Dy12 subunits were used for recognizing baking quality of some wheat varieties and some mutant genotypes. Only 5 pairs of them could show the specific bands. All subunits were recognized by the primers except Dx2.1. Some of the primers were extracted from previous studies and the others were designed based on D genome subunits of wheat. SDS-PAGE method accomplished having confidence in these marker’s results. To realize the effect of mutation, seed storage proteins were measured. It showed that mutation had effect on the amount of seed storage protein on the mutant seeds (which showed polymorphism.

  9. Development of a chromosome-plasmid balanced lethal system for Lactobacillus acidophilus with thyA gene as selective marker.

    Science.gov (United States)

    Fu, X; Xu, J G

    2000-01-01

    A chromosome-plasmid balanced lethal gene delivery system for Lactobacillus acidophilus based on the thyA gene was developed. The selected L. acidophilus DOM La strain carries a mutated thyA gene and has an obligate requirement for thymidine. This strain can be used as a host for the constructed shuttle vector pFXL03, lacking antibiotic-resistant markers but having the wild-type thyA gene from L. casei which complements the thyA chromosomal mutation. The vector also contains the replicon region from plasmid pUC19 and that of the Lactococcus plasmid pWV01, which allows the transfer between Escherichia coli, L. casei and L. acidophilus. Eight unique restriction sites (i.e., PstI, HindIII, SphI, SalI, AccI, XbaI, KpnI and SacI) are available for cloning. After 40-time transfers in modified MRS medium, no plasmid loss was observed. The vector pFXL03 is potentially useful as a food-grade vaccine delivery system for L. acidophilus.

  10. A potential food-grade cloning vector for Streptococcus thermophilus that uses cadmium resistance as the selectable marker.

    Science.gov (United States)

    Wong, Wing Yee; Su, Ping; Allison, Gwen E; Liu, Chun-Qiang; Dunn, Noel W

    2003-10-01

    A potential food-grade cloning vector, pND919, was constructed and transformed into S. thermophilus ST3-1, a plasmid-free strain. The vector contains DNAs from two different food-approved organisms, Streptococcus thermophilus and Lactococcus lactis. The 5.0-kb pND919 is a derivative of the cloning vector pND918 (9.3 kb) and was constructed by deletion of the 4.3-kb region of pND918 which contained DNA from non-food-approved organisms. pND919 carries a heterologous native cadmium resistance selectable marker from L. lactis M71 and expresses the Cd(r) phenotype in S. thermophilus transformants. With the S. thermophilus replicon derived from the shuttle vector pND913, pND919 is able to replicate in the two S. thermophilus industrial strains tested, ST3-1 and ST4-1. Its relatively high retention rate in S. thermophilus further indicates its usefulness as a potential food-grade cloning vector. To our knowledge, this is the first report of a replicative potential food-grade vector for the industrially important organism S. thermophilus.

  11. Survey of physicochemical characteristics and microbial contamination in selected food locally vended in Morogoro Municipality, Tanzania.

    Science.gov (United States)

    Nonga, Hezron Emmanuel; Ngowi, Helena Aminiel; Mdegela, Robinson Hammerthon; Mutakyawa, Eliud; Nyahinga, Gabriel Busungu; William, Robert; Mwadini, Mtumwa Mohd

    2015-11-26

    Raw milk, raw fruit juice and raw fish are enriched with essential nutrients for human diet but are prone to microbial contamination along the value chain. This cross sectional study was conducted to assess physicochemical characteristics and microbial quality of raw milk, fruit juice and fish from food vendors in Morogoro Municipality, Tanzania. The physicochemical assessment of food samples was done by smell, colour, presence of debris, turbidity, consistence, pH and clot on alcohol test. Hygiene of food containers, personnel and the vending environment was also assessed. Qualitative and quantitative microbial assessment of food was done using standard laboratory protocols as described by Tanzania Bureau of Standards and International Systems of Standards. Raw milk sold in Morogoro was of poor quality since was adulterated with water, contained sediments and clotted on alcohol test. Up to 63 % of the milk samples were contaminated with Escherichia coli and 60 % had higher total viable count (TVC) than the recommended values. Raw fruit juice was stored in dirty containers and sold under unhygienic environment. Seventy-three percent of juice samples had TVC beyond the recommendations while E. coli contamination rate was 63.3 %. The raw fish samples had started spoiling as depicted through sensory evaluation. E. coli contamination rate was 55 % and that of Campylobacter jejuni was 0.5 %. The mean TVC of raw fish was 8.1 (Log cfu/g) and 96.2 % of the fish samples had TVC beyond the recommended limits of 5.0 Log cfu/g. The physicochemical characteristics of food vended in Morogoro Municipality were of poor quality. The food had high bacterial contaminations. This situation poses health risks to the public and losses to food vendors due to spoilage. Stakeholders in food value chain should be educated on safe production and good hygienic practices. Routine quality and safety assessment of locally vended food, inspection of selling premises and regular health check-up of

  12. Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle

    Directory of Open Access Journals (Sweden)

    Northcutt Sally L

    2010-04-01

    Full Text Available Abstract Background Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. Results Results were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle. Conclusions This research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.

  13. A deterministic simulation study of embryo marker-assisted selection for age at first calving in Nellore ( Bos indicus) beef cattle

    NARCIS (Netherlands)

    Rosa, A.J.M.; Bijma, P.; Oliveira, H.N.; Lobo, R.B.; Arendonk, van J.A.M.

    2007-01-01

    We used deterministic simulation of four alternative multiple ovulation and embryo manipulation (MOET) closed nucleus schemes to investigate the benefits of using marker-assisted selection (MAS) of Nellore (Bos indicus) beef cattle embryos prior to transplantation to reduce the age at first calving

  14. Genetic Gains in Yield and Yield Related Traits under Drought Stress and Favorable Environments in a Maize Population Improved Using Marker Assisted Recurrent Selection

    Directory of Open Access Journals (Sweden)

    Folusho Bankole

    2017-05-01

    Full Text Available The objective of marker assisted recurrent selection (MARS is to increase the frequency of favorable marker alleles in a population before inbred line extraction. This approach was used to improve drought tolerance and grain yield (GY in a biparental cross of two elite drought tolerant lines. The testcrosses of randomly selected 50 S1 lines from each of the three selection cycles (C0, C1, C2 of the MARS population, parental testcrosses and the cross between the two parents (F1 were evaluated under drought stress (DS and well watered (WW well as under rainfed conditions to determine genetic gains in GY and other agronomic traits. Also, the S1 lines derived from each selection types were genotyped with single nucleotide polymorphism (SNP markers. Testcrosses derived from C2 produced significantly higher grain field under DS than those derived from C0 with a relative genetic gain of 7% per cycle. Also, the testcrosses of S1 lines from C2 showed an average genetic gain of 1% per cycle under WW condition and 3% per cycle under rainfed condition. Molecular analysis revealed that the frequency of favorable marker alleles increased from 0.510 at C0 to 0.515 at C2, while the effective number of alleles (Ne per locus decreased from C0 (1.93 to C2 (1.87. Our results underscore the effectiveness of MARS for improvement of GY under DS condition.

  15. Effect of pulse sequence parameter selection on signal strength in positive-contrast MRI markers for MRI-based prostate postimplant assessment

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Tze Yee [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 and The University of Texas at Houston Graduate School of Biomedical Sciences, 6767 Bertner Avenue, Houston, Texas 77030 (United States); Kudchadker, Rajat J., E-mail: rkudchad@mdanderson.org; Wang, Jihong; Ibbott, Geoffrey S. [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States); Stafford, R. Jason [Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States); MacLellan, Christopher [Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 and The University of Texas at Houston Graduate School of Biomedical Sciences, 6767 Bertner Avenue, Houston, Texas 77030 (United States); Rao, Arvind [Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States); Frank, Steven J. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States)

    2016-07-15

    Purpose: For postimplant dosimetric assessment, computed tomography (CT) is commonly used to identify prostate brachytherapy seeds, at the expense of accurate anatomical contouring. Magnetic resonance imaging (MRI) is superior to CT for anatomical delineation, but identification of the negative-contrast seeds is challenging. Positive-contrast MRI markers were proposed to replace spacers to assist seed localization on MRI images. Visualization of these markers under varying scan parameters was investigated. Methods: To simulate a clinical scenario, a prostate phantom was implanted with 66 markers and 86 seeds, and imaged on a 3.0T MRI scanner using a 3D fast radiofrequency-spoiled gradient recalled echo acquisition with various combinations of scan parameters. Scan parameters, including flip angle, number of excitations, bandwidth, field-of-view, slice thickness, and encoding steps were systematically varied to study their effects on signal, noise, scan time, image resolution, and artifacts. Results: The effects of pulse sequence parameter selection on the marker signal strength and image noise were characterized. The authors also examined the tradeoff between signal-to-noise ratio, scan time, and image artifacts, such as the wraparound artifact, susceptibility artifact, chemical shift artifact, and partial volume averaging artifact. Given reasonable scan time and managable artifacts, the authors recommended scan parameter combinations that can provide robust visualization of the MRI markers. Conclusions: The recommended MRI pulse sequence protocol allows for consistent visualization of the markers to assist seed localization, potentially enabling MRI-only prostate postimplant dosimetry.

  16. THE IMPACT OF THE ELEVATOR GUIDES CONTAMINATION ON THE BRAKING PROCESS DELAY FOR SELECTED PROGRESSIVE GEARS

    Directory of Open Access Journals (Sweden)

    Rafał Longwic

    2017-06-01

    Full Text Available The authors’ tests results on the impact of the guiding system (the guides contamination in the friction lift on the delay of progressive gears braking process are presented in this article. The tests were conducted using a free fall method and a test bench built for that purpose. In order to render all working conditions the guiding system of tested gears was lubricated with the most commonly used lubricating agents. Solid grease (SM, mineral oil (OL, the mixture of solid grease and quartz sand (S50 as well as the mixture of mineral oil and quartz sand (O50 were used.

  17. Mercury Speciation in Contaminated Soils from Old Mining Activities in Mexico Using a Chemical Selective Extraction

    OpenAIRE

    Gavilán-García, Irma; Santos-Santos, Elvira; Tovar-Gálvez, Luis R.; Gavilán-García, Arturo; Suárez, Sara; Olmos, Jesús

    2008-01-01

    Amalgamation was heavily used in mining since 1557 in Spanish Colonies. In Mexico and other parts of Latin-America, this process generated tailings which were left aside in the mine backyards. In the valley of Zacatecas, tailings were carried out of the mines due to the run-off from the mountains and contaminated most of the Zacatecan Valley which most important economic activity is agricultural (crop and livestock raising). The main concern in this area is the high level of total mercury fou...

  18. Selective principal component regression analysis of fluorescence hyperspectral image to assess aflatoxin contamination in corn

    Science.gov (United States)

    Selective principal component regression analysis (SPCR) uses a subset of the original image bands for principal component transformation and regression. For optimal band selection before the transformation, this paper used genetic algorithms (GA). In this case, the GA process used the regression co...

  19. Determination of different contaminants in selective drinking water samples collected from Peshawar valley area

    International Nuclear Information System (INIS)

    Ihsanullah; Khan, M.; Khattak, T.N.; Sattar, A.

    1999-01-01

    Among the pollutants carried through sewage, industrial effluents, fertilizers, pesticides; heavy metals and various pathogenic bacteria are directly related to human/animal diseases. Samples of drinking water were collected from different locations, in the Peshawar area. Cadmium, lead and copper levels in these samples were determined by potentiometric stripping analysis (PSA). The data indicated wide variation in the concentration of these heavy metals. Variation in results is discussed on the basis of some possible sources of contamination. The concentration of cadmium and lead in all the samples was higher compared to the values given in the guideline of World Health Organization (WHO) for drinking water. Copper was below the detection limit in majority of the samples. The values of Cd, Pb and Cu were in the range of 0.023-2.75, 0.025-1.88 and 0-0.67 mg/1 respectively. Various physical quality indices (ph, electrical conductivity and total solids) and pathogenic bacteria (E. coli and total coliforms) were also determined in water samples. Most of the drinking waters was found contaminated with higher levels of Cd and Pb and pathogenic bacteria and hence, considered unfit for drinking purposes. (author)

  20. Selection of biosurfactan/bioemulsifier-producing bacteria from hydrocarbon-contaminated soil

    Directory of Open Access Journals (Sweden)

    Sabina Viramontes-Ramos

    2010-10-01

    Full Text Available Petroleum-derived hydrocarbons are among the most persistent soil contaminants, and some hydrocarbon-degrading microorganisms can produce biosurfactants to increase bioavailability and degradation. The aim of this work was to identify biosurfactant-producing bacterial strains isolated from hydrocarbon-contaminated sites, and to evaluate their biosurfactant properties. The drop-collapse method and minimal agar added with a layer of combustoleo were used for screening, and positive strains were grown in liquid medium, and surface tension and emulsification index were determined in cell-free supernantant and cell suspension. A total of 324 bacterial strains were tested, and 17 were positive for the drop-collapse and hydrocarbon-layer agar methods. Most of the strains were Pseudomonas, except for three strains (Acinetobacter, Bacillus, Rhodococcus. Surface tension was similar in cell-free and cell suspension measurements, with values in the range of 58 to 26 (mN/m, and all formed stable emulsions with motor oil (76-93% E24. Considering the variety of molecular structures among microbial biosurfactants, they have different chemical properties that can be exploited commercially, for applications as diverse as bioremediation or degradable detergents.

  1. An investigation of selected chemical contaminants in commercial pet foods in Egypt.

    Science.gov (United States)

    Abd-Elhakim, Yasmina M; El Sharkawy, Nabela I; Moustafa, Gihan G

    2016-01-01

    Our study aimed to identify the levels of various contaminants in both wet and dry commercial pet foods in Egypt. A total of 20 local and imported pet food products (3 samples each) were screened for heavy metals by atomic absorption spectroscopy, for mycotoxins by enzyme-linked immunosorbent assay, and for nitrate and nitrite levels by nitrate-nitrite spectrophotometry. Cat food, on average, had greater concentrations of the metals cadmium, chromium, lead, and tin than dog food. Of the investigated metals, only tin concentration exceeded the safe level compared with the standards of the National Research Council and the European Commission for the dog and cat. According to the guidelines of the Association of American Feed Control Officials for canned pet foods, the nitrate and nitrite contents of examined foods greatly exceeded the recommended level. No total aflatoxins were detected in the surveyed samples. None of the samples analyzed had levels above international limits established by the Food and Agriculture Organization (FAO) of the United Nations for ochratoxin, and only 1 sample exceeded the level for aflatoxin B1. Of the 20 samples analyzed for zearalenone, 4 samples had higher levels than the FAO maximum tolerable levels. These results indicate that pet foods marketed in Egypt, especially cat foods, occasionally contain contaminants that could result in adverse effects in pets. © 2016 The Author(s).

  2. Assessment of heavy metal contamination of dust at some selected fuel filling stations in Accra

    International Nuclear Information System (INIS)

    Afrifa, C. G.

    2011-07-01

    Heavy metal contaminated dust particles of fuel filling stations can be re-suspended into the ambient air and serve as a source of atmospheric pollution since the fine particles are aerodynamic and have longer life time in ambient air. This can cause ill-health effect on the fuel attendants and residents within the neighbourhood especially infants and the aged who are more vulnerable. In spite of this, not much research has been done on heavy metal contamination of dust at fuel filling stations. In this study, 55 dust samples were collected from six fuel filling stations in the Ga-East district and Accra Metropolitan assembly, both in Accra, in order to assess the levels of contamination of heavy metals; their possible sources and the human health risk associated with them. The dust samples were divided into two parts with one part sieved into four fractions using metric mesh sizes 500 µm, 200µm, 100µm and 45 µm, and pulverised. Total concentrations of heavy metals (Si, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Ga, Br, Rb, Sr, Y, Zr and Pb) were determined in the dust samples using energy dispersive X-ray fluorescence analysis. The pollution indices; enrichment factors (EF), index of geoaccumulation (Igeo), contamination factor (CF) and pollution load index (PLI) were used to identify possible levels of pollution from anthropogenic sources. The possible sources of metals were also identified with principal component analysis. Noncancer effect of children and adults due to exposure to dust from these fuel filling stations were also estimated. For the three fuelling areas, the average concentrations of V, Cr, Ni and Cu exceeded the acceptable values in common soil in the <45 µm fraction. The average concentration of Zn however exceeded the acceptable value only at the mixed-fuel fuelling area whereas the average concentration of Pb was within the acceptable value for all three fuelling areas. The dust samples showed moderate to significant enrichments for V, Cu, Br

  3. Criteria determining the selection of slags for the melt decontamination of radioactively contaminated stainless steel by electroslag remelting

    International Nuclear Information System (INIS)

    Buckentin, J.M.R.; Damkroger, B.K.; Shelmidine, G.J.; Atteridge, D.G.

    1997-01-01

    Electroslag remelting is an excellent process choice for the melt decontamination of radioactively contaminated metals. ESR furnaces are easily enclosed and do not make use of refractories which could complicate thermochemical interactions between molten metal and slag. A variety of cleaning mechanisms are active during melting; radionuclides may be partitioned to the slag by means of thermochemical reaction, electrochemical reaction, or mechanical entrapment. At the completion of melting, the slag is removed from the furnace in solid form. The electroslag process as a whole is greatly affected by the chemical and physical properties of the slag used. When used as a melt decontamination scheme, the ESR process may be optimized by selection of the slag. In this research, stainless steel bars were coated with non-radioactive surrogate elements in order to simulate surface contamination. These bars were electroslag remelted using slags of various chemistries. The slags investigated were ternary mixtures of calcium fluoride, calcium oxide, and alumina. The final chemistries of the stainless steel ingots were compared with those predicted by the use of a Free Energy Minimization Modeling technique. Modeling also provided insight into the chemical mechanisms by which certain elements are captured by a slag. Slag selection was also shown to have an impact on the electrical efficiency of the process as well as the surface quality of the ingots produced

  4. Use of Both Cumulus Cells’ Transcriptomic Markers and Zona Pellucida Birefringence to Select Developmentally Competent Oocytes in Human Assisted Reproductive Technologies

    Science.gov (United States)

    2015-01-01

    Background Selection of the best oocyte for subsequent steps of fertilization and embryo transfer was shown to be the crucial step in human infertility treatment procedure. Oocyte selection using morphological criteria mainly Zona pellucida (ZP) has been the gold standard method in assisted reproductive technologies (ART) clinics, but this selection approach has limitations in terms of accuracy, objectivity and constancy. Recent studies using OMICs-based approaches have allowed the identification of key molecular markers that quantitatively and non-invasively predict the oocyte quality for higher pregnancy rates and efficient infertility treatment. These biomarkers are a valuable reinforcement of the morphological selection criteria widely used in in vitro fertilization (IVF) clinics. In this context, this study was designed to investigate the relationship between transcriptomic predictors of oocyte quality found by our group and the conventional morphological parameters of oocyte quality mainly the ZP birefringence. Results Microarray data revealed that 48 and 27 differentially expressed candidate genes in cumulus cells (CCs) were respectively overexpressed and underexpressed in the ZGP (Zona Good Pregnant) versus ZBNP (Zona Bad Non Pregnant) groups. More than 70% of previously reported transcriptomic biomarkers of oocyte developmental competence were confirmed in this study. The analysis of possible association between ZP birefringence versus molecular markers approach showed an absence of correlation between them using the current set of markers. Conclusions This study suggested a new integrative approach that matches morphological and molecular approaches used to select developmentally competent oocytes able to lead to successful pregnancy and the delivery of healthy baby. For each ZP birefringence score, oocytes displayed a particular CCs' gene expression pattern. However, no correlations were found between the 7 gene biomarkers of oocyte developmental

  5. Radiation protection. Clothing for protection against radioactive contamination. Design, selection, testing and use

    International Nuclear Information System (INIS)

    1987-09-01

    The present Standard gives the characteristics of clothing protecting the wearer against radioactive contamination brought about by contact with liquid or solid substances or by atmospheric pollutants, such as solid particles, mist, gases or vapours. The Standard applies to two types of clothing: firstly, ventilated-pressurized garments; secondly, unventilated-unpressurized garments. A test method according to which any new type of garment can be assigned a protection factor that makes it easier for the user to make a choice is described. The report also gives methods for measuring leak-tightness and air supply flow rates of ventilated-pressurized garments. For guidance purposes only, recommendations for choosing protective clothing are given. 5 figs, 2 tabs [fr

  6. Use of technical and economic analysis for optimizing technology selection and remedial design for contaminated sites

    International Nuclear Information System (INIS)

    Hardisty, P.E.; Brown, A.

    1996-01-01

    The decision to remediate a contaminated site can be seen from the macroeconomic and microeconomic viewpoints. Macroeconomics can be used to plan and account for the overall cost of pollution as part of a firm's production, and thus make overall decisions on the real cost of pollution and the level of clean-up which may be called for. Valuation of damaged resources, option values and intrinsic worth is an important part of this process. Once the decision to remediate has been taken, the question becomes how best to remediate. Microeconomic analysis deals with providing efficient allocative decisions for reaching specified goals. it is safe to say that cost is one of the single most important factors in site clean-up decision making. A basic rule of remediation is often taken to be the maximization of contaminant mass removed per dollar spent. However, remediation may also be governed by other objectives and constraints. In some situations, minimization of time, rather than cost, could be the constraint. Or perhaps the objective could be to achieve a set level of clean-up for the lowest possible cost, even if a large program would result in unit-cost reductions. Evaluation of the economics of a clean-up project is directly linked to the objectives of the site owner, and the constraints within which the remediation is to be performed. Economic analysis of remedial options for containment of a 350,000 L hydrocarbon spill migrating through fractured rock into a river in Alberta, Canada, clear direction to the site owner

  7. Selectable antibiotic resistance marker gene-free transgenic rice harbouring the garlic leaf lectin gene exhibits resistance to sap-sucking planthoppers.

    Science.gov (United States)

    Sengupta, Subhadipa; Chakraborti, Dipankar; Mondal, Hossain A; Das, Sampa

    2010-03-01

    Rice, the major food crop of world is severely affected by homopteran sucking pests. We introduced coding sequence of Allium sativum leaf agglutinin, ASAL, in rice cultivar IR64 to develop sustainable resistance against sap-sucking planthoppers as well as eliminated the selectable antibiotic-resistant marker gene hygromycin phosphotransferase (hpt) exploiting cre/lox site-specific recombination system. An expression vector was constructed containing the coding sequence of ASAL, a potent controlling agent against green leafhoppers (GLH, Nephotettix virescens) and brown planthopper (BPH, Nilaparvata lugens). The selectable marker (hpt) gene cassette was cloned within two lox sites of the same vector. Alongside, another vector was developed with chimeric cre recombinase gene cassette. Reciprocal crosses were performed between three single-copy T(0) plants with ASAL- lox-hpt-lox T-DNA and three single-copy T(0) plants with cre-bar T-DNA. Marker gene excisions were detected in T(1) hybrids through hygromycin sensitivity assay. Molecular analysis of T(1) plants exhibited 27.4% recombination efficiency. T(2) progenies of L03C04(1) hybrid parent showed 25% cre negative ASAL-expressing plants. Northern blot, western blot and ELISA showed significant level of ASAL expression in five marker-free T(2) progeny plants. In planta bioassay of GLH and BPH performed on these T(2) progenies exhibited radical reduction in survivability and fecundity compared with the untransformed control plants.

  8. Determination of extractable fluoride in contaminated soils with ion-selective electrode

    OpenAIRE

    Mirlean, Nicolai; Baraj, Besnik; Garcia, Marina Reback Domingues; Niencheski, Luis Felipe Hax; Baisch, Paulo Roberto Martins; Casartelli, Maria Regina de Oliveira; Robinson, Daniel

    2003-01-01

    In a factorial design study involving the determination of F- by ion-selective electrodes, a significant interference was demonstrated for Fe, with an even more pronounced interference for Al. The fluoride leaching procedure from polluted soil showed more reliable results using 0.5 M citric acid

  9. Selective leaching of uranium from uranium-contaminated soils: Progress report 1

    International Nuclear Information System (INIS)

    Francis, C.W.; Mattus, A.J.; Farr, L.L.; Elless, M.P.; Lee, S.Y.

    1993-02-01

    Three soils and a sediment contaminated with uranium were used to determine the effectiveness of sodium carbonate and citric acid leaching to decontaminated or remove uranium to acceptable regulatory levels. Two of the soils were surface soils from the DOE facility formerly called the Feed Materials Production Center (FMPC) at Fernald, Ohio. This facility is presently called the Femald Environmental Management Project (FEMP). Carbonate extractions generally removed from 70 to 90% of the uranium from the Fernald storage pad soil. Uranium was slightly more difficult to extract from the Fernald incinerator and the Y-12 landfarm soils. Very small amounts of uranium could be extracted from the storm sewer sediment. Extraction with carbonate at high solution-to-soil ratios were as effective as extractions at low solution-to-soil ratios, indicating attrition by the paddle mixer was not significantly different than that provided in a rotary extractor. Also, pretreatments such as milling or pulverizing the soil sample did not appear to increase extraction efficiency when carbonate extractions were carried out at elevated temperatures (60 degree C) or long extraction times (23 h). Adding KMnO 4 in the carbonate extraction appeared to increase extraction efficiency from the Fernald incinerator soil but not the Fernald storage pad soil. The most effective leaching rates (> 90 % from both Fernald soils) were obtained using a citrate/dithionite extraction procedure designed to remove amorphous (noncrystalline) iron/aluminum sesquioxides from surfaces of clay minerals. Citric acid also proved to be a very good extractant for uranium

  10. Relationship between biomarker responses and contaminant concentration in selected tissues of flounder (Platichthys flesus from the Polish coastal area of the Baltic Sea

    Directory of Open Access Journals (Sweden)

    Magdalena Podolska

    2008-09-01

    Full Text Available Previous studies in the Gulf of Gdańsk discussed the responses of selected enzymatic biomarkers to the contaminant gradient in fish and mussels. In the present study, flounder muscle and liver tissues were analyzed for polychlorinated biphenyls (PCB congeners: 28, 52, 101, 118, 138, 153 and 180, organochlorine pesticides (HCHs, HCB and DDTs, and trace metals (Pb, Cd, Zn, Cu, Hg, Cr. An attempt was made to identify the relationship between the measured enzymatic biomarker responses (cholinesterases, malic enzyme, isocitrate dehydrogenase, glutathione S-transferase and contaminant concentrations in selected flounder tissues. The observed differences in enzymatic biomarker levels suggest that chronic exposure to low-concentration mixtures of contaminants may be occurring in the studied area. However, no conclusive evidence was found of a clear link between the biomarker responses and contaminant concentrations in flounder tissues.

  11. Morphological markers to select populations of oocytes with different cultural needs for dedicated pre-maturation protocols

    Directory of Open Access Journals (Sweden)

    Cecilia Dieci

    2017-05-01

    Full Text Available Oocyte’s chromatin gradually becomes more compacted during the final stage of oocyte development and the level of chromatin compaction is considered a marker of oocyte differentiation [Luciano et al, 2014]. Moreover, several studies demonstrate that in vitro pre-maturation treatments (Pre-IVM, aimed to improve the developmental capability of immature oocytes, might behave differently depending on the oocyte metabolic status, when it is isolated from follicle [Luciano et al., 2011]. This study aims at identifying correlations between cumulus-oocyte complex (COC morphology and oocyte chromatin configuration and secondly at testing the hypothesis that only fully grown oocytes at earlier stages of differentiation with loosely compacted chromatin  (GV1 can benefit from Pre-IVM treatment.   COCs were collected from bovine 2-6mm ovarian follicles, and further divided in three groups according to their morphology (Class-1, 2 and 3 as previously described [Blondin & Sirard, 1995]. Analysis of chromatin configuration revealed that only Class-1 COC was enriched in GV1 oocyte, while Class-2 and 3 presented a similar distribution of GV1, GV2 and GV3 oocytes, where GV2 and 3 oocytes are characterized by increased chromatin compaction [Lodde et al., 2007]. Then COCs were divided into two groups, one containing Class-1 COCs and the other containing Class-2 and 3 COCs and subjected to pre-IVM for 6 hours in presence of cilostamide and 10-4 UI/ml rhFSH. Finally, COCs underwent standard in vitro maturation (IVM for 22 hours, in vitro fertilization and embryo culture. Blastocyst rate and embryos cell number were assessed at day 7. Pre-IVM positively affected developmental competences of Class-1, while in Classes 2 and 3 Pre-IVM had detrimental effects.In conclusion COCs morphology could be used as a non-invasive approach to select population of oocyte with different cultural needs. These data could be useful in setting-up dedicated IVM protocols considering

  12. The effects of copper oxy chloride waste contamination on selected soil biochemical properties at disposal site

    International Nuclear Information System (INIS)

    Masaka, J.; Muunganirwa, M.

    2007-01-01

    A study was carried out at a sanitary waste disposal site for Kutsaga Tobacco Research Station, Zimbabwe, which uses large amounts of copper oxy chloride for sterilization of recycled float trays in flooded bench tobacco seedling production systems. Soil samples randomly collected from six stream bank zones (bands up the valley slope) varying in their distance ranges from the centre of both the wastewater-free and wastewater-affected paths [0-5 m (B1); 6-10 m (B2); 11-15 m (B3); 16-20 m (B4); 21-25 m (B5) and 26-30 m (B6)] in two sample depths (0-15; 15-30 cm) were analysed for metal copper, organic matter contents, and soil pH and subjected to agarized incubation for microbial counts. Results suggest that the repeated disposals of copper oxy chloride waste from tobacco float tray sanitation sinks into a creek amplify metal copper loads in the soil by 500 fold. The greatest concentrations of copper in both the topsoil and upper subsoil were recorded in the B3, B4 and B5 stream bank zones of the wastewater path. The concentration of copper was significantly lower in the middle of the waste-affected creek than that in the stream bank zones. This trend in the copper concentration coincided with the lowest acidity of the soil. Overloading the soil with copper, surprisingly, enhances the content of soil organic matter. The repeated release of copper oxy chloride waste into a stream causes an accelerated build-up of metal copper and soil acidity in the stream bank on-site while contamination is translocated to either underground water reserve or surface stream water flow in the middle of the wastewater path

  13. HRAS1-selected chromosome transfer generates markers that colocalize aniridia- and genitourinary dysplasia-associated translocation breakpoints and the Wilms tumor gene within band 11p13.

    OpenAIRE

    Porteous, D J; Bickmore, W; Christie, S; Boyd, P A; Cranston, G; Fletcher, J M; Gosden, J R; Rout, D; Seawright, A; Simola, K O

    1987-01-01

    We show that chromosome-mediated gene transfer can provide an enriched source of DNA markers for predetermined, subchromosomal regions of the human genome. Forty-four human DNA recombinants isolated from a HRAS1-selected chromosome-mediated gene transformant map exclusively to chromosome 11, with several sublocalizing to the Wilms tumor region at 11p13. We present a detailed molecular map of the deletion chromosomes 11 from five WAGR (Wilms tumor/aniridia/genitourinary abnormalities/mental re...

  14. Estimation of Pig contaminations in catchment by real-time PCR using two pig-specific bacteroidales 16S rRNA genetic markers

    International Nuclear Information System (INIS)

    Mieszkin, S.; Furet, J. P.; Corthier, G.; Gournelon, M.

    2009-01-01

    The microbiological quality of coastal and river waters can be deteriorated by fecal contamination from human or animal activities. In Brittany, France, pig farming is one of the most important animal activities and can cause fecal contamination of surface water due to spreading of pig manure to agricultural soils and in a lesser extent with the use of lagoon surface water for irrigation. (Author)

  15. Technical, economic and policy considerations on marker-assisted selection in crops: lessons from the experience at an international agricultural research centre

    International Nuclear Information System (INIS)

    William, H.M.; Warburton, M.; Morris, M.; Hoisington, D.A.

    2007-01-01

    Molecular markers and related technologies have been used extensively in genetic characterization and identification of loci controlling traits of economic importance in many crop species. However, the application of such tools for crop improvement has not been extensive, at least in the public sector. Although there are clear advantages in using molecular markers as tools for indirect selection of traits of importance, available examples indicate that their use is restricted to traits with monogenic inheritance or when the inheritance is conditioned by a few genes with large effects. Another important limitation of large-scale marker applications is the cost involved in marker assays, which may be beyond the capacities of many public plant breeding enterprises. For an effective marker-assisted selection (MAS) activity to facilitate ongoing crop improvement programmes, especially in the context of the developing countries, laboratories with adequate capacity and adequately trained scientific personnel as well as operational resources are required. Although recent technological advances such as single nucleotide polymorphisms (SNPs) and associated assay protocols are likely to reduce assay costs significantly, for many of these operations, assay platforms with significant capital investments including computational capacity are required. Coupled with these limitations, private sector domination of biotechnology research with proprietary rights to important products and processes with immediate benefits to developing countries may further constrain the benefits these technologies may offer to resource-poor farmers. Policy-makers in different national programmes and international development and research agencies have a responsibility to sustain and augment the capacity of national public agricultural research organizations to ensure that biotechnology tools and processes are infused appropriately into national research efforts. They must also ensure that any

  16. Natural and bioremediated selective degradation of polycyclic aromatic alkyl isomers in oil-contaminated soils

    International Nuclear Information System (INIS)

    Sauer, T.C.; McCarthy, K.; Uhler, A.; Porta, A.

    1995-01-01

    In studies where 2- to 6-ring polycyclic aromatic hydrocarbons (PAHs) are determined as part of characterizing released oil constituents in environmental samples, the changes in composition of PAHs from weathering (e.g., evaporation, dissolution) and biodegradation are most often represented by PAH alkyl homologue distributions. Concentrations of PAH alkyl groups are the sum of individual PAH isomers of similar carbon number; such as for C2-naphthalenes, the C2 alkyl group consists of dimethyl and ethyl substitutions on the parent naphthalene. In weathering and degradation studies, the changes in relative concentration of the individual isomers within an alkyl group are rarely reported. In a field study of oiled soils, the authors looked at the selective losses, for a period of a year, of individual PAH alkyl isomers that occur both naturally by weathering processes and through the use of bioremediation technology. Results showed that decreases in alkyl group concentrations were not always represented by similar losses of each isomer in the alkyl group, but were often due to the preferential or selective loss of certain isomers in the group

  17. Selective removal of 2,4-dichlorophenol from contaminated water using non-covalent imprinted microspheres

    International Nuclear Information System (INIS)

    Li Ying; Li Xin; Li Yuqi; Qi Jingyao; Bian Jiang; Yuan Yixing

    2009-01-01

    A molecularly imprinted polymer (MIP) for selective removal of 2,4-dichlorophenol (2,4-DCP) in water was prepared as microspheres by the reverse microemulsion polymerization method based on the non-covalent interactions between 2,4-DCP, oleic acid, and divinylbenzene in acetonitrile. Microspheres have been characterized by Fourier transform infrared spectrometer (FTIR) and energy dispersive X-ray spectrometer (EDS) studies with evidence of 2,4-DCP linkage in polymer particles and scanning electron microscopy (SEM) to study their morphological properties. The proper adsorption and selective recognition ability of the MIP were studied by an equilibrium-adsorption method. The MIP showed outstanding affinity towards 2,4-DCP in aqueous solution and the optimum pH value for binding has been found around the neutral range. The molecular recognition of 2,4-DCP was analyzed in detail by using molecular modeling software. In addition, by investigating the variation in the adsorption ability of the MIP, it clearly showed excellent reproducibility. - Molecular imprinting has potential as a remediation technology in water treatment.

  18. The accuracy of prediction of genomic selection in elite hybrid rye populations surpasses the accuracy of marker-assisted selection and is equally augmented by multiple field evaluation locations and test years.

    Science.gov (United States)

    Wang, Yu; Mette, Michael Florian; Miedaner, Thomas; Gottwald, Marlen; Wilde, Peer; Reif, Jochen C; Zhao, Yusheng

    2014-07-04

    Marker-assisted selection (MAS) and genomic selection (GS) based on genome-wide marker data provide powerful tools to predict the genotypic value of selection material in plant breeding. However, case-to-case optimization of these approaches is required to achieve maximum accuracy of prediction with reasonable input. Based on extended field evaluation data for grain yield, plant height, starch content and total pentosan content of elite hybrid rye derived from testcrosses involving two bi-parental populations that were genotyped with 1048 molecular markers, we compared the accuracy of prediction of MAS and GS in a cross-validation approach. MAS delivered generally lower and in addition potentially over-estimated accuracies of prediction than GS by ridge regression best linear unbiased prediction (RR-BLUP). The grade of relatedness of the plant material included in the estimation and test sets clearly affected the accuracy of prediction of GS. Within each of the two bi-parental populations, accuracies differed depending on the relatedness of the respective parental lines. Across populations, accuracy increased when both populations contributed to estimation and test set. In contrast, accuracy of prediction based on an estimation set from one population to a test set from the other population was low despite that the two bi-parental segregating populations under scrutiny shared one parental line. Limiting the number of locations or years in field testing reduced the accuracy of prediction of GS equally, supporting the view that to establish robust GS calibration models a sufficient number of test locations is of similar importance as extended testing for more than one year. In hybrid rye, genomic selection is superior to marker-assisted selection. However, it achieves high accuracies of prediction only for selection candidates closely related to the plant material evaluated in field trials, resulting in a rather pessimistic prognosis for distantly related material

  19. Recent innovation in microbial source tracking using bacterial real-time PCR markers in shellfish

    International Nuclear Information System (INIS)

    Mauffret, A.; Mieszkin, S.; Morizur, M.; Alfiansah, Y.; Lozach, S.; Gourmelon, M.

    2013-01-01

    Highlights: ► DNA extraction from intravalvular liquid is promising for microbial source tracking in oysters. ► Host-associated bacterial markers in shellfish digestive tissues were difficult to assess with real-time PCR. ► DNA extracts from shellfish flesh appeared to have low inhibitor levels but low marker levels. ► Protocol transfer from one shellfish species to another does not appear possible. -- Abstract: We assessed the capacity of real-time PCR markers to identify the origin of contamination in shellfish. Oyster, cockles or clams were either contaminated with fecal materials and host-associated markers designed from Bacteroidales or Catellicoccus marimammalium 16S RNA genes were extracted from their intravalvular liquid, digestive tissues or shellfish flesh. Extraction of bacterial DNA from the oyster intravalvular liquid with FastDNA spin kit for soil enabled the selected markers to be quantified in 100% of artificially contaminated samples, and the source of contamination to be identified in 13 out of 38 naturally contaminated batches from European Class B and Class C areas. However, this protocol did not enable the origin of the contamination to be identified in cockle or clam samples. Although results are promising for extracts from intravalvular liquid in oyster, it is unlikely that a single protocol could be the best across all bacterial markers and types of shellfish

  20. Graphic products used in the evaluation of traditional and emerging remote sensing technologies for the detection of fugitive contamination at selected superfund hazardous waste sites

    Science.gov (United States)

    Slonecker, E. Terrence; Fisher, Gary B.

    2011-01-01

    This report presents the overhead imagery and field sampling results used to prepare U.S. Geological Survey Open-File Report 2011-1050, 'Evaluation of Traditional and Emerging Remote Sensing Technologies for the Detection of Fugitive Contamination at Selected Superfund Hazardous Waste Sites'. These graphic products were used in the evaluation of remote sensing technology in postclosure monitoring of hazardous waste sites and represent an ongoing research effort. Soil sampling results presented here were accomplished with field portable x-ray fluoresence (XRF) technology and are used as screening tools only representing the current conditions of metals and other contaminants at selected Superfund hazardous waste sites.

  1. Prediction of malting quality traits in barley based on genome-wide marker data to assess the potential of genomic selection.

    Science.gov (United States)

    Schmidt, Malthe; Kollers, Sonja; Maasberg-Prelle, Anja; Großer, Jörg; Schinkel, Burkhard; Tomerius, Alexandra; Graner, Andreas; Korzun, Viktor

    2016-02-01

    Genomic prediction of malting quality traits in barley shows the potential of applying genomic selection to improve selection for malting quality and speed up the breeding process. Genomic selection has been applied to various plant species, mostly for yield or yield-related traits such as grain dry matter yield or thousand kernel weight, and improvement of resistances against diseases. Quality traits have not been the main scope of analysis for genomic selection, but have rather been addressed by marker-assisted selection. In this study, the potential to apply genomic selection to twelve malting quality traits in two commercial breeding programs of spring and winter barley (Hordeum vulgare L.) was assessed. Phenotypic means were calculated combining multilocational field trial data from 3 or 4 years, depending on the trait investigated. Three to five locations were available in each of these years. Heritabilities for malting traits ranged between 0.50 and 0.98. Predictive abilities (PA), as derived from cross validation, ranged between 0.14 to 0.58 for spring barley and 0.40-0.80 for winter barley. Small training sets were shown to be sufficient to obtain useful PAs, possibly due to the narrow genetic base in this breeding material. Deployment of genomic selection in malting barley breeding clearly has the potential to reduce cost intensive phenotyping for quality traits, increase selection intensity and to shorten breeding cycles.

  2. Analysis of correlations between selected endothelial cell activation markers, disease activity, and nailfold capillaroscopy microvascular changes in systemic lupus erythematosus patients.

    Science.gov (United States)

    Ciołkiewicz, Mariusz; Kuryliszyn-Moskal, Anna; Klimiuk, Piotr Adrian

    2010-02-01

    The aim of the study was to evaluate the correlation between selected serum endothelial cell activation markers such as vascular endothelial growth factor (VEGF), endothelin-1 (ET-1), soluble thrombomodulin (sTM), soluble E-selectin (sE-selectin), disease activity, and microvascular changes determined by nailfold capillaroscopy in patients with systemic lupus erythematosus (SLE). Serum levels of VEGF, ET-1, sTM, and sE-selectin were determined by an enzyme-linked immunosorbent assay in 80 SLE patients. The disease activity was measured with Systemic Lupus Erythematosus Disease Activity Index score. Nailfold capillaroscopy was performed in all patients. Positive correlation was found between VEGF and both ET-1 (r = 0.294, p nailfold capillaroscopy (r = 0.458, p nailfold capillaroscopy. The relationship between changes in nailfold capillaroscopy, endothelial cell activation markers, and the clinical activity of SLE points to an important role of microvascular abnormalities in the clinical manifestation of the disease.

  3. Marker-assisted selection as a tool for genetic improvement of crops, livestock, forestry and fish in developing countries: an overview of the issues

    International Nuclear Information System (INIS)

    Ruane, R.; Sonnino, A.

    2007-01-01

    This chapter provides an overview of the techniques, current status and issues involved in using marker-assisted selection (MAS) for genetic improvement in developing countries. Molecular marker maps, the necessary framework for any MAS programme, have been constructed for the majority of agriculturally important species, although the density of the maps varies considerably among species. Despite the considerable resources that have been invested in this field and despite the enormous potential it still represents, with few exceptions, MAS has not yet delivered its expected benefits in commercial breeding programmes for crops, livestock, forest trees or farmed fish in the developed world. When evaluating the potential merits of applying MAS as a tool for genetic improvement in developing countries, some of the issues that should be considered are its economic costs and benefits, its potential benefits compared with conventional breeding or with application of other biotechnologies, and the potential impact of intellectual property rights (IPRs) on the development and application of MAS. (author)

  4. Petrographic and X-ray diffraction analyses of selected samples from Marker Bed 139 at the Waste Isolation Pilot Plant

    International Nuclear Information System (INIS)

    Fredrich, J.T.; Zeuch, D.H.

    1996-04-01

    The Waste Isolation Pilot Plant (WIPP) is located 660 m underground in the Salado Formation which consists of thick, horizontally bedded pure and impure salt and thin, laterally continuous clay and anhydrite interbeds. The Salado Two-Phase Flow Laboratory Program was established to provide site-specific-two-phase flow and other related rock properties to support performance assessment modeling of the WIPP repository. Owing to their potentially significant role in the hydrologic response of the repository, the program initially focused on the anhydrite interbeds, and in particular, on Marker Bed 139 (MB 139), which lies approximately 1 m below the planned waste storage rooms. This report synthesizes petrographic and X-ray powder diffraction studies performed to support the Salado Two-Phase Flow Laboratory Program. Experimental scoping activities in this area were performed in FY 1993 by three independent laboratories in order to: (1) quantify the mineral composition to support laboratory studies of hydrologic properties and facilitate correlation of transport properties with composition; (2) describe textures, including grain size; and (3) describe observed porosity. Samples from various depths were prepared from six 6-inch diameter cores which were obtained by drilling into the marker bed from the floor of two separate rooms. The petrographic analyses are augmented here with additional study of the original thin sections, and the pore structure observations are also examined in relation to an independent observational study of microcracks in Marker Bed 139 core samples performed in FY 1994 by the Geomechanics Department at Sandia National Laboratories

  5. Petrographic and X-ray diffraction analyses of selected samples from Marker Bed 139 at the Waste Isolation Pilot Plant

    Energy Technology Data Exchange (ETDEWEB)

    Fredrich, J.T.; Zeuch, D.H. [Sandia National Labs., Albuquerque, NM (United States). Geomechanics Dept.

    1996-04-01

    The Waste Isolation Pilot Plant (WIPP) is located 660 m underground in the Salado Formation which consists of thick, horizontally bedded pure and impure salt and thin, laterally continuous clay and anhydrite interbeds. The Salado Two-Phase Flow Laboratory Program was established to provide site-specific-two-phase flow and other related rock properties to support performance assessment modeling of the WIPP repository. Owing to their potentially significant role in the hydrologic response of the repository, the program initially focused on the anhydrite interbeds, and in particular, on Marker Bed 139 (MB 139), which lies approximately 1 m below the planned waste storage rooms. This report synthesizes petrographic and X-ray powder diffraction studies performed to support the Salado Two-Phase Flow Laboratory Program. Experimental scoping activities in this area were performed in FY 1993 by three independent laboratories in order to: (1) quantify the mineral composition to support laboratory studies of hydrologic properties and facilitate correlation of transport properties with composition; (2) describe textures, including grain size; and (3) describe observed porosity. Samples from various depths were prepared from six 6-inch diameter cores which were obtained by drilling into the marker bed from the floor of two separate rooms. The petrographic analyses are augmented here with additional study of the original thin sections, and the pore structure observations are also examined in relation to an independent observational study of microcracks in Marker Bed 139 core samples performed in FY 1994 by the Geomechanics Department at Sandia National Laboratories.

  6. Assessment of selected contaminants in streambed- and suspended-sediment samples collected in Bexar County, Texas, 2007-09

    Science.gov (United States)

    Wilson, Jennifer T.

    2011-01-01

    Elevated concentrations of sediment-associated contaminants are typically associated with urban areas such as San Antonio, Texas, in Bexar County, the seventh most populous city in the United States. This report describes an assessment of selected sediment-associated contaminants in samples collected in Bexar County from sites on the following streams: Medio Creek, Medina River, Elm Creek, Martinez Creek, Chupaderas Creek, Leon Creek, Salado Creek, and San Antonio River. During 2007-09, the U.S. Geological Survey periodically collected surficial streambed-sediment samples during base flow and suspended-sediment (large-volume suspended-sediment) samples from selected streams during stormwater runoff. All sediment samples were analyzed for major and trace elements and for organic compounds including halogenated organic compounds and polycyclic aromatic hydrocarbons (PAHs). Selected contaminants in streambed and suspended sediments in watersheds of the eight major streams in Bexar County were assessed by using a variety of methods—observations of occurrence and distribution, comparison to sediment-quality guidelines and data from previous studies, statistical analyses, and source indicators. Trace elements concentrations were low compared to the consensus-based sediment-quality guidelines threshold effect concentration (TEC) and probable effect concentration (PEC). Trace element concentrations were greater than the TEC in 28 percent of the samples and greater than the PEC in 1.5 percent of the samples. Chromium concentrations exceeded sediment-quality guidelines more frequently than concentrations of any other constituents analyzed in this study (greater than the TEC in 69 percent of samples and greater than the PEC in 8 percent of samples). Mean trace element concentrations generally are lower in Bexar County samples compared to concentrations in samples collected during previous studies in the Austin and Fort Worth, Texas, areas, but considering the relatively

  7. Purifying arsenic and fluoride-contaminated water by a novel graphene-based nanocomposite membrane of enhanced selectivity and sustained flux.

    Science.gov (United States)

    Pal, Madhubonti; Mondal, Mrinal Kanti; Paine, Tapan Kanti; Pal, Parimal

    2018-06-01

    A novel graphene-based nanocomposite membrane was synthesized by interfacial polymerization (IP) through chemical bonding of the graphene oxide (GO) layer to polyethersulfone surface. Detailed characterization of the composite membrane through AFM, SEM, ATR-FTIR, XRD analysis, and Raman spectroscopy indicates strong potential of the membrane in highly selective removal of the toxic contaminants like arsenic and fluoride while permeating the essential minerals like calcium and magnesium. This makes the membrane suitable for production of safe drinking water from contaminated water. The membrane applied in a flat-sheet cross-flow module succeeded in removal of more than 98% arsenic and around 80% fluoride from contaminated water while selectively retaining the useful calcium and magnesium minerals in drinking water. A sustained pure water flux of around 150 LMH (liter per square meter per hour) during operation over long hours (> 150 h) with only 3-5% drop in flux indicates antifouling character of the membrane module.

  8. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  9. Genomic selection and association mapping in rice (Oryza sativa: effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Directory of Open Access Journals (Sweden)

    Jennifer Spindel

    2015-02-01

    Full Text Available Genomic Selection (GS is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  10. Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R.

    2015-01-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273

  11. The dtd gene from Bacillus amyloliquefaciens encodes a putative D-tyrosyl-tRNATyr deacylase and is a selectable marker for Bacillus subtilis.

    Science.gov (United States)

    Geraskina, Natalia V; Butov, Ivan A; Yomantas, Yurgis A V; Stoynova, Nataliya V

    2015-02-01

    Genetically engineered microbes are of high practical importance due to their cost-effective production of valuable metabolites and enzymes, and the search for new selectable markers for genetic manipulation is of particular interest. Here, we revealed that the soil bacterium Bacillus amyloliquefaciens A50 is tolerant to the non-canonical amino acid D-tyrosine (D-Tyr), in contrast to the closely related Bacillus strain B. subtilis 168, which is a widely used "domesticated" laboratory strain. The gene responsible for resistance to D-Tyr was identified. The resistance was associated with the activity of a potential D-tyrosyl-tRNA(Tyr) deacylase. Orthologs of this enzyme are capable of hydrolyzing the ester bond and recycling misacetylated D-aminoacyl-tRNA molecules into free tRNAs and D-amino acids. This gene, yrvI (dtd), is applicable as a convenient, small selectable marker for non-antibiotic resistance selection in experiments aimed at genome editing of D-Tyr-sensitive microorganisms. Copyright © 2014 Elsevier GmbH. All rights reserved.

  12. Fate of selected microorganisms when introduced as cross-contamination inocula into simulated food trash compartment waste

    Science.gov (United States)

    Strayer, Richard; Hummerick, Mary; Richards, Jeffrey; Birmele, Michele; Roberts, Michael

    counts and general cultivation-based methods. Detection and enumeration of challenge microbes was accomplished by cultivation-based microbiological methods with specific selective media and by molecular methods using quantitative stocktickerPCR (qPCR) with stocktickerDNA primers specific for each challenge organism. stocktickerDNA was extracted and purified from residual wastes with a stocktickerDNA isolation kit (Mo Bio), and quantified (NanoDrop) from standard curves prepared from pure culture isolates of each challenge organism. QPCR was conducted on a Roche LightCycler 480 using the Roche stocktickerSYBR Green Master Mix Kit. The identity of all challenge microbes in recovered isolates was verified by stocktickerDNA sequencing (stocktickerABI 3130 Genetic Analyzer - Applied Biosystems). To date, concentrations of challenge microbial populations at concentrations ranging from ˜107 - 108 have been added to simulated food waste and extracted either immediately after mixing or after 1 week of storage. Cultivation-based counts indicated that 5 of 6 challenge microbes could be recovered from simulated food wastes after inoculation for both concentrations. Only S. enterica serovar typhimurium could not be detected at week 0 for the 107 inoculum. Between week 0 and 1, challenge microbes increased in density: S. aureus, E. coli, and P. aeruginosa increasing up to 4 orders of magnitude from the 107 inoculum. Molecular results for the week 0 and week 1 stored samples indicated that the relative concentrations of target stocktickerDNA for the challenge microbes had increased between 1 and 3 orders of magnitude. These preliminary studies demonstrate that potential problems regarding pathogens as cross-contaminants from other waste streams could develop during storage of space mission solid wastes. Ongoing studies are examining longer storage times up to 6 weeks. The results can be used to determine requirements and criteria for waste treatment prior to storage and provides a

  13. Illicit drugs and pharmaceuticals in the environment--forensic applications of environmental data, Part 2: Pharmaceuticals as chemical markers of faecal water contamination.

    Science.gov (United States)

    Kasprzyk-Hordern, Barbara; Dinsdale, Richard M; Guwy, Alan J

    2009-06-01

    This manuscript is part two of a two-part study aiming to provide a better understanding and application of environmental data not only for environmental aims but also to meet forensic objectives. In this paper pharmaceuticals were investigated as potential chemical indicators of water contamination with sewage. The monitoring program carried out in Wales revealed that some pharmaceuticals are particularly persistent and/or ubiquitous in contaminated river water and therefore might be considered as potential conservative or labile wastewater indicators. In particular, these include some anti-inflammatory/analgesics, antiepileptics, beta-blockers, some H2-receptor antagonists and antibacterial drugs.

  14. Highlighting the complexities of a groundwater pilot study during an avian influenza outbreak: Methods, lessons learned, and select contaminant results

    Science.gov (United States)

    Hubbard, Laura E.; Kolpin, Dana W.; Fields, Chad L.; Hladik, Michelle L.; Iwanowicz, Luke

    2017-01-01

    The highly pathogenic avian influenza (H5N2) outbreak in the Midwestern United States (US) in 2015 was historic due to the number of birds and poultry operations impacted and the corresponding economic loss to the poultry industry and was the largest animal health emergency in US history. The U.S. Geological Survey (USGS), with the assistance of several state and federal agencies, aided the response to the outbreak by developing a study to determine the extent of virus transport in the environment. The study goals were to: develop the appropriate sampling methods and protocols for measuring avian influenza virus (AIV) in groundwater, provide the first baseline data on AIV and outbreak- and poultry-related contaminant occurrence and movement into groundwater, and document climatological factors that may have affected both survival and transport of AIV to groundwater during the months of the 2015 outbreak. While site selection was expedient, there were often delays in sample response times due to both relationship building between agencies, groups, and producers and logistical time constraints. This study's design and sampling process highlights the unpredictable nature of disease outbreaks and the corresponding difficulty in environmental sampling of such events. The lessons learned, including field protocols and approaches, can be used to improve future research on AIV in the environment.

  15. Adsorption of selected emerging contaminants onto PAC and GAC: Equilibrium isotherms, kinetics, and effect of the water matrix.

    Science.gov (United States)

    Real, Francisco J; Benitez, F Javier; Acero, Juan L; Casas, Francisco

    2017-07-03

    The removal of three emerging contaminants (ECs) (amitriptyline hydrochloride (AH), methyl salicylate (MS) and 2-phenoxyethanol (PE)) dissolved in several water matrices by means of their adsorption onto powdered activated carbon (PAC) and granular activated carbon (GAC) has been investigated. When dissolved in ultrapure water, adsorption of the ECs followed the trend of AH > MS > PE, with a positive effect of the adsorbent dose. According to the analysis of the adsorption isotherms and adsorption kinetics, PAC showed strongly higher adsorption efficiency in both capacity and velocity of the adsorption, in agreement with its higher mesoporosity. Equilibrium isotherm data were fitted by Langmuir and Freundlich models. Pseudo-second order kinetics modeled very successfully the adsorption process. Finally, the effect of the presence of dissolved organic matter (DOM) in the water matrices (ultrapure water, surface water and two effluents from wastewater treatment plants) on the adsorption of the selected ECs onto PAC was established, as well as its performance on the removal of water quality parameters. Results show a negative effect of the DOM content on the adsorption efficiency. Over 50% of organic matter was removed with high PAC doses, revealing that adsorption onto PAC is an effective technology to remove both micro-pollutants and DOM from water matrices.

  16. Highlighting the complexities of a groundwater pilot study during an avian influenza outbreak: Methods, lessons learned, and select contaminant results.

    Science.gov (United States)

    Hubbard, Laura E; Kolpin, Dana W; Fields, Chad L; Hladik, Michelle L; Iwanowicz, Luke R

    2017-10-01

    The highly pathogenic avian influenza (H5N2) outbreak in the Midwestern United States (US) in 2015 was historic due to the number of birds and poultry operations impacted and the corresponding economic loss to the poultry industry and was the largest animal health emergency in US history. The U.S. Geological Survey (USGS), with the assistance of several state and federal agencies, aided the response to the outbreak by developing a study to determine the extent of virus transport in the environment. The study goals were to: develop the appropriate sampling methods and protocols for measuring avian influenza virus (AIV) in groundwater, provide the first baseline data on AIV and outbreak- and poultry-related contaminant occurrence and movement into groundwater, and document climatological factors that may have affected both survival and transport of AIV to groundwater during the months of the 2015 outbreak. While site selection was expedient, there were often delays in sample response times due to both relationship building between agencies, groups, and producers and logistical time constraints. This study's design and sampling process highlights the unpredictable nature of disease outbreaks and the corresponding difficulty in environmental sampling of such events. The lessons learned, including field protocols and approaches, can be used to improve future research on AIV in the environment. Published by Elsevier Inc.

  17. Selective extraction of emerging contaminants from water samples by dispersive liquid-liquid microextraction using functionalized ionic liquids.

    Science.gov (United States)

    Yao, Cong; Li, Tianhao; Twu, Pamela; Pitner, William R; Anderson, Jared L

    2011-03-25

    Functionalized ionic liquids containing the tris(pentafluoroethyl)trifluorophosphate (FAP) anion were used as extraction solvents in dispersive liquid-liquid microextraction (DLLME) for the extraction of 14 emerging contaminants from water samples. The extraction efficiencies and selectivities were compared to those of an in situ IL DLLME method which uses an in situ metathesis reaction to exchange 1-butyl-3-methylimidazolium chloride (BMIM-Cl) to 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide (BMIM-NTf(2)). Compounds containing tertiary amine functionality were extracted with high selectivity and sensitivity by the 1-(6-amino-hexyl)-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate (HNH(2)MPL-FAP) IL compared to other FAP-based ILs and the BMIM-NTf(2) IL. On the other hand, polar or acidic compounds without amine groups exhibited higher enrichment factors using the BMIM-NTf(2) IL. The detection limits for the studied analytes varied from 0.1 to 55.1 μg/L using the traditional IL DLLME method with the HNH(2)MPL-FAP IL as extraction solvent, and from 0.1 to 55.8 μg/L using in situ IL DLLME method with BMIM-Cl+LiNTf(2) as extraction solvent. A 93-fold decrease in the detection limit of caffeine was observed when using the HNH(2)MPL-FAP IL compared to that obtained using in situ IL DLLME method. Real water samples including tap water and creek water were analyzed with both IL DLLME methods and yielded recoveries ranging from 91% to 110%. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Assessment of Tools for Marker-Assisted Selection in a Marine Commercial Species: Significant Association between MSTN-1 Gene Polymorphism and Growth Traits

    Directory of Open Access Journals (Sweden)

    Irma Sánchez-Ramos

    2012-01-01

    Full Text Available Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL have been regarded as useful for marker-assisted selection in complex traits as growth. Polymorphisms have been studied in five candidate genes influencing growth in gilthead seabream (Sparus aurata: the growth hormone (GH, insulin-like growth factor-1 (IGF-1, myostatin (MSTN-1, prolactin (PRL, and somatolactin (SL genes. Specimens evaluated were from a commercial broodstock comprising 131 breeders (from which 36 males and 44 females contributed to the progeny. In all samples eleven gene fragments, covering more than 13,000 bp, generated by PCR-RFLP, were analyzed; tests were made for significant associations between these markers and growth traits. ANOVA results showed a significant association between MSTN-1 gene polymorphism and growth traits. Pairwise tests revealed several RFLPs in the MSTN-1 gene with significant heterogeneity of genotypes among size groups. PRL and MSTN-1 genes presented linkage disequilibrium. The MSTN-1 gene was mapped in the centromeric region of a medium-size acrocentric chromosome pair.

  19. Genetic mapping, marker assisted selection and allelic relationships for the Pu 6 gene conferring rust resistance in sunflower.

    Science.gov (United States)

    Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

    2014-09-01

    Rust resistance in the sunflower line P386 is controlled by Pu 6 , a gene which was reported to segregate independently from other rust resistant genes, such as R 4 . The objectives of this work were to map Pu 6 , to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu 6 and R 4 . Genetic mapping of Pu 6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu 6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu 6 and R 4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the R adv /R 4 /R 11 / R 13a /R 13b /Pu 6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene.

  20. A deterministic simulation study of embryo marker-assisted selection for age at first calving in Nellore (Bos indicus beef cattle

    Directory of Open Access Journals (Sweden)

    Artur J.M. Rosa

    2007-01-01

    Full Text Available We used deterministic simulation of four alternative multiple ovulation and embryo manipulation (MOET closed nucleus schemes to investigate the benefits of using marker-assisted selection (MAS of Nellore (Bos indicus beef cattle embryos prior to transplantation to reduce the age at first calving (AFC. We found that MAS resulted in increased genetic gain as compared to selection without AFC quantitative trait loci (AFC-QTL information. With single-stage selection the genetic response (GR increased as follows: GR = 0.68% when the AFC-QTL explained 0.02 of the AFC additive genetic variance (sigma2A; GR = 1.76% for AFC-QTL explaining 0.05 sigma2A; GR = 3.7% for AFC-QTL explaining 0.1 sigma2A; and GR = 55.76% for AFC-QTL explaining 0.95 sigma2A. At the same total selected proportion, two-stage selection resulted in less genetic gain than single stage MAS at two-years of age. A single stage selection responses of > 95% occurred with pre-selected proportions of 0.4 (0.1 sigma2A explained by AFC-QTL, 0.2 (0.3 sigma2A explained by AFC-QTL and 0.1 (0.5 sigma2A explained by AFC-QTL, indicating that the combined use of MAS and pre-selection can substantially reduce the cost of keeping recipient heifers in MOET breeding schemes. When the number of recipients was kept constant, the benefit of increasing embryo production was greater for the QTL explaining a higher proportion of the additive genetic variance. However this advantage had a diminishing return especially for QTL explaining a small proportion of the additive genetic variance. Thus, marker assisted selection of embryos can be used to achieve increased genetic gain or a similar genetic response at reduced expense by decreasing the number of recipient cows and number of offspring raised to two-years of age.

  1. Investigation the effect of ionizing radiation on the level of microbial contamination and usefulness of selected raw materials and cosmetics of new generation

    International Nuclear Information System (INIS)

    Migdal, W.; Owczarczyk, H.B.; Malec-Czechowska, K.

    1997-01-01

    The results of investigations the electron beam irradiation on the microbial contamination of selected new generation cosmetics and raw products used in cosmetic industry are reported. The radiation doses applied were not higher than 6.0 kGy. The levels of microbial contamination were determined in irradiated and non-irradiated samples by standard methods routinely used. The results obtained show that radiation can be successfully used for decontamination of cosmetics and some of their raw materials, without changing the quality and applicability of the product. (author)

  2. Environmental E.coli isolate characterization and selection as improved indicators for pathogens associated with produce contamination

    Science.gov (United States)

    Contamination of food and water by pathogens is a substantial public health issue in the United States. According to the Centers for Disease Control and Prevention, 49% of foodborne illness is caused by produce, and despite efforts to reduce produce contamination, these issues persist. Escherichia c...

  3. A Fluorescent Tile DNA Diagnocode System for In Situ Rapid and Selective Diagnosis of Cytosolic RNA Cancer Markers

    Science.gov (United States)

    Park, Kyung Soo; Shin, Seung Won; Jang, Min Su; Shin, Woojung; Yang, Kisuk; Min, Junhong; Cho, Seung-Woo; Oh, Byung-Keun; Bae, Jong Wook; Jung, Sunghwan; Choi, Jeong-Woo; Um, Soong Ho

    2015-01-01

    Accurate cancer diagnosis often requires extraction and purification of genetic materials from cells, and sophisticated instrumentations that follow. Otherwise in order to directly treat the diagnostic materials to cells, multiple steps to optimize dose concentration and treatment time are necessary due to diversity in cellular behaviors. These processes may offer high precision but hinder fast analysis of cancer, especially in clinical situations that need rapid detection and characterization of cancer. Here we present a novel fluorescent tile DNA nanostructure delivered to cancer cytosol by employing nanoparticle technology. Its structural anisotropicity offers easy manipulation for multifunctionalities, enabling the novel DNA nanostructure to detect intracellular cancer RNA markers with high specificity within 30 minutes post treatment, while the nanoparticle property bypasses the requirement of treatment optimization, effectively reducing the complexity of applying the system for cancer diagnosis. Altogether, the system offers a precise and rapid detection of cancer, suggesting the future use in the clinical fields. PMID:26678430

  4. Use of LCA as decision support for the selection of remedial strategies for remediation of contaminated soil and groundwater

    DEFF Research Database (Denmark)

    Lemming, Gitte; Hauschild, Michael Zwicky; Bjerg, Poul Løgstrup

    2009-01-01

    , there is a trade-off between obtaining local beneficial effects from the remediation and generating environmental impacts on the regional and global scale due to the remedial actions. Therefore there is a need for including the impact of soil contaminants that will potentially leach to the groundwater, e......Groundwater is the dominant source of drinking water in Denmark and the general policy is to maintain the groundwater as a clean source of drinking water. The risk of groundwater contamination is therefore often the prime reason for remediating a contaminated site. Chlorinated solvents are among...... the contaminants most frequently found to be threatening the groundwater quality in Denmark and worldwide. Life cycle assessment has recently been applied as part of decision support for contaminated site management and subsurface remediation techniques. Impacts in the groundwater compartment have only gained...

  5. Selection of antigenic markers on a GFP-Cκ fusion scaffold with high sensitivity by eukaryotic ribosome display

    International Nuclear Information System (INIS)

    Yang Yongmin; Barankiewicz, Teresa J.; He Mingyue; Taussig, Michael J.; Chen, Swey-Shen

    2007-01-01

    Ribosome display is a cell-free system permitting gene selection through the physical association of genetic material (mRNA) and its phenotypic (protein) product. While often used to select single-chain antibodies from large libraries by panning against immobilized antigens, we have adapted ribosome display for use in the 'reverse' format in order to select high affinity antigenic determinants against solid-phase antibody. To create an antigenic scaffold, DNA encoding green fluorescent protein (GFP) was fused to a light chain constant domain (Cκ) with stop codon deleted, and with 5' signals (T7 promoter, Kozak) enabling coupled transcription/translation in a eukaryotic cell-free system. Epitopes on either GFP (5') or Cκ (3') were selected by anti-GFP or anti-Cκ antibodies, respectively, coupled to magnetic beads. After selection, mRNA was amplified directly from protein-ribosome-mRNA (PRM) complexes by in situ PCR followed by internal amplification and reassembly PCR. As little as 10 fg of the 1 kb DNA construct, i.e. approximately 7500 molecules, could be recovered following a single round of interaction with solid-phase anti-GFP antibody. This platform is highly specific and sensitive for the antigen-antibody interaction and may permit selection and reshaping of high affinity antigenic variants of scaffold proteins

  6. Selection of antigenic markers on a GFP-C{kappa} fusion scaffold with high sensitivity by eukaryotic ribosome display

    Energy Technology Data Exchange (ETDEWEB)

    Yongmin, Yang [Institute of Genetics, San Diego, CA 92121-2233 (United States); IgE Therapeutics, Inc., San Diego, CA 92121-2233 (United States); Barankiewicz, Teresa J [Institute of Genetics, San Diego, CA 92121-2233 (United States); IgE Therapeutics, Inc., San Diego, CA 92121-2233 (United States); Mingyue, He [Babraham Institute, Cambridge CB2 4AT (United Kingdom); Taussig, Michael J [Babraham Institute, Cambridge CB2 4AT (United Kingdom); Chen, Swey-Shen [Institute of Genetics, San Diego, CA 92121-2233 (United States) and IgE Therapeutics, Inc., San Diego, CA 92121-2233 (United States)

    2007-07-27

    Ribosome display is a cell-free system permitting gene selection through the physical association of genetic material (mRNA) and its phenotypic (protein) product. While often used to select single-chain antibodies from large libraries by panning against immobilized antigens, we have adapted ribosome display for use in the 'reverse' format in order to select high affinity antigenic determinants against solid-phase antibody. To create an antigenic scaffold, DNA encoding green fluorescent protein (GFP) was fused to a light chain constant domain (C{kappa}) with stop codon deleted, and with 5' signals (T7 promoter, Kozak) enabling coupled transcription/translation in a eukaryotic cell-free system. Epitopes on either GFP (5') or C{kappa} (3') were selected by anti-GFP or anti-C{kappa} antibodies, respectively, coupled to magnetic beads. After selection, mRNA was amplified directly from protein-ribosome-mRNA (PRM) complexes by in situ PCR followed by internal amplification and reassembly PCR. As little as 10 fg of the 1 kb DNA construct, i.e. approximately 7500 molecules, could be recovered following a single round of interaction with solid-phase anti-GFP antibody. This platform is highly specific and sensitive for the antigen-antibody interaction and may permit selection and reshaping of high affinity antigenic variants of scaffold proteins.

  7. Improving Blast Resistance of a Thermo-Sensitive Genic Male Sterile Rice Line GD-8S by Molecular Marker-Assisted Selection

    Directory of Open Access Journals (Sweden)

    Wu-ge LIU

    2008-09-01

    Full Text Available The broad-spectrum blast resistance gene Pi-1, from donor line BL122, was introduced into a thermo-sensitive genic male sterile rice line GD-8S, which possessed good grain quality but high susceptibility to rice blast, by using backcross breeding and molecular marker-assisted selection. Five elite improved male sterile lines, RGD8S-1, RGD8S-2, RGD8S-3, RGD8S-4 and RGD8S-5, were selected based on the results of molecular marker analysis, spikelet sterility, recovery rate of genetic background and agronomic traits. Thirty-three representative blast isolates collected from Guangdong Province, China were used to inoculate the improved lines and the original line GD-8S artificially. The resistance frequencies of the improved lines ranged from 76.47% to 100%, much higher than that of the original line GD-8S (9.09%. On the agronomic characters, there were no significant differences between the improved lines and GD-8S except for flag leaf length and panicle number per plant. The improved lines could be used for breeding hybrid rice with high blast resistance.

  8. Expression of selected pathway-marker genes in human urothelial cells exposed chronically to a non-cytotoxic concentration of monomethylarsonous acid

    Directory of Open Access Journals (Sweden)

    Matthew Medeiros

    2014-01-01

    Full Text Available Bladder cancer has been associated with chronic arsenic exposure. Monomethylarsonous acid [MMA(III] is a metabolite of inorganic arsenic and has been shown to transform an immortalized urothelial cell line (UROtsa at concentrations 20-fold less than arsenite. MMA(III was used as a model arsenical to examine the mechanisms of arsenical-induced transformation of urothelium. A previous microarray analysis revealed only minor changes in gene expression at 1 and 2 months of chronic exposure to MMA(III, contrasting with substantial changes observed at 3 months of exposure. To address the lack of information between 2 and 3 months of exposure (the critical period of transformation, the expression of select pathway marker genes was measured by PCR array analysis on a weekly basis. Cell proliferation rate, anchorage-independent growth, and tumorigenicity in SCID mice were also assessed to determine the early, persistent phenotypic changes and their association with the changes in expression of these selected marker genes. A very similar pattern of alterations in these genes was observed when compared to the microarray results, and suggested that early perturbations in cell signaling cascades, immunological pathways, cytokine expression, and MAPK pathway are particularly important in driving malignant transformation. These results showed a strong association between the acquired phenotypic changes that occurred as early as 1–2 months of chronic MMA(III exposure, and the observed gene expression pattern that is indicative of the earliest stages in carcinogenesis.

  9. Illicit drugs and pharmaceuticals in the environment - Forensic applications of environmental data, Part 2: Pharmaceuticals as chemical markers of faecal water contamination

    International Nuclear Information System (INIS)

    Kasprzyk-Hordern, Barbara; Dinsdale, Richard M.; Guwy, Alan J.

    2009-01-01

    This manuscript is part two of a two-part study aiming to provide a better understanding and application of environmental data not only for environmental aims but also to meet forensic objectives. In this paper pharmaceuticals were investigated as potential chemical indicators of water contamination with sewage. The monitoring program carried out in Wales revealed that some pharmaceuticals are particularly persistent and/or ubiquitous in contaminated river water and therefore might be considered as potential conservative or labile wastewater indicators. In particular, these include some anti-inflammatory/analgesics, antiepileptics, beta-blockers, some H2-receptor antagonists and antibacterial drugs. - Wastewater as an indicative source of information can be used in forensic applications.

  10. Illicit drugs and pharmaceuticals in the environment - Forensic applications of environmental data, Part 2: Pharmaceuticals as chemical markers of faecal water contamination

    Energy Technology Data Exchange (ETDEWEB)

    Kasprzyk-Hordern, Barbara, E-mail: B.Kasprzyk-Hordern@hud.ac.u [University of Huddersfield, Department of Chemical and Biological Sciences, Queensgate, Huddersfield HD1 3DH (United Kingdom); University of Glamorgan, Sustainable Environment Research Centre, Faculty of Health, Sport and Science, Pontypridd CF37 1DL (United Kingdom); Dinsdale, Richard M.; Guwy, Alan J. [University of Glamorgan, Sustainable Environment Research Centre, Faculty of Health, Sport and Science, Pontypridd CF37 1DL (United Kingdom)

    2009-06-15

    This manuscript is part two of a two-part study aiming to provide a better understanding and application of environmental data not only for environmental aims but also to meet forensic objectives. In this paper pharmaceuticals were investigated as potential chemical indicators of water contamination with sewage. The monitoring program carried out in Wales revealed that some pharmaceuticals are particularly persistent and/or ubiquitous in contaminated river water and therefore might be considered as potential conservative or labile wastewater indicators. In particular, these include some anti-inflammatory/analgesics, antiepileptics, beta-blockers, some H2-receptor antagonists and antibacterial drugs. - Wastewater as an indicative source of information can be used in forensic applications.

  11. Morphological abnormalities in gall-forming aphids in a radiation-contaminated area near Fukushima Daiichi: selective impact of fallout?

    Science.gov (United States)

    Akimoto, Shin-ichi

    2014-01-01

    To evaluate the impact of fallout from the Fukushima Daiichi Nuclear Power Plant accident on organisms, this study compared the morphology and viability of gall-forming aphids between the Fukushima population and control populations from noncontaminated areas. This study, in particular, focused on the morphology of first-instar gall formers derived from the first sexual reproduction after the accident. Of 164 first instars from Tetraneura sorini galls collected 32 km from Fukushima Daiichi in spring 2012, 13.2% exhibited morphological abnormalities, including four conspicuously malformed individuals (2.4%). In contrast, in seven control areas, first instars with abnormal morphology accounted for 0.0–5.1% (on average, 3.8%). The proportions of abnormalities and mortality were significantly higher in Fukushima than in the control areas. Similarly, of 134 first instars from T. nigriabdominalis galls, 5.9% exhibited morphological abnormalities, with one highly malformed individual. However, of 543 second-generation larvae produced in T. sorini galls, only 0.37% had abnormalities, suggesting that abnormalities found in the first generation were not inherited by the next generation. Although investigation is limited to one study site, this result suggests that radioactive contamination had deleterious effects on embryogenesis in eggs deposited on the bark surface, but a negligible influence on the second generation produced in closed galls. Furthermore, analysis of both species samples collected in spring 2013 indicated that the viability and healthiness of the aphids were significantly improved compared to those in the 2012 samples. Thus, the results of this study suggest the possibility that a reduced level of radiation and/or selection for radiation tolerance may have led to the improved viability and healthiness of the Fukushima population. PMID:24634721

  12. Accumulation and selective maternal transfer of contaminants in the turtle Trachemys scripta associated with coal ash deposition

    Energy Technology Data Exchange (ETDEWEB)

    Nagle, R.D.; Rowe, C.L.; Congdon, J.D. [University of Georgia, Aiken, SC (USA). Savannah River Ecology Laboratory

    2001-07-01

    Coal combustion wastes are enriched in a number of potentially toxic compounds and may pose risks to biota exposed to the wastes. Slider turtles (Trachemys scripta) are common inhabitants of coal ash settling basins in South Carolina, USA, where they feed on contaminated prey items and accumulate high levels of potentially toxic compounds in their tissues. Furthermore, female sliders sometimes nest in contaminated spill piles and thus may expose embryos to contaminated soils. We examined two potential pathways by which female T. scripta may influence the survivorship and quality of their offspring in a contaminated habitat: (1) nesting in contaminated soil and (2) maternal transfer of pollutants. Eggs were collected from turtles captured in coal ash-polluted or unpolluted sites; individual clutches were incubated in both ash-contaminated and uncontaminated soil in outdoor, artificial nests. Incubation in contaminated soil was associated with reduced embryo survivorship. Adult females from the polluted site accumulated high levels of As, Cd, Cr, and Se in their tissues, yet Se was the only element transferred maternally to hatchlings at relatively high levels. Hatchlings from polluted-site females exhibited reduced O{sub 2} consumption rates compared to hatchlings from reference sites. Relatively high levels of Se transferred to hatchlings by females at the ash-polluted site might contribute to the observed differences in hatchling physiology.

  13. Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa

    Directory of Open Access Journals (Sweden)

    Rekiya O. Abdulmalik

    2017-05-01

    Full Text Available Marker-assisted recurrent selection (MARS is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S1 lines derived from the original (C0 and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS and well-watered (WW conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S1 lines each derived from the four cycles (C0, C1, C2, C3 were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga, improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S1 lines from 114 in C0 to 124 in C3. The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved

  14. Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa.

    Science.gov (United States)

    Abdulmalik, Rekiya O; Menkir, Abebe; Meseka, Silvestro K; Unachukwu, Nnanna; Ado, Shehu G; Olarewaju, Joseph D; Aba, Daniel A; Hearne, Sarah; Crossa, Jose; Gedil, Melaku

    2017-01-01

    Marker-assisted recurrent selection (MARS) is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S 1 lines derived from the original (C 0 ) and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS) and well-watered (WW) conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S 1 lines each derived from the four cycles (C 0 , C 1 , C 2 , C 3 ) were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga , improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S 1 lines from 114 in C 0 to 124 in C 3 . The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved

  15. Effects of natural and human factors on groundwater quality of basin-fill aquifers in the southwestern United States-conceptual models for selected contaminants

    Science.gov (United States)

    Bexfield, Laura M.; Thiros, Susan A.; Anning, David W.; Huntington, Jena M.; McKinney, Tim S.

    2011-01-01

    As part of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program, the Southwest Principal Aquifers (SWPA) study is building a better understanding of the factors that affect water quality in basin-fill aquifers in the Southwestern United States. The SWPA study area includes four principal aquifers of the United States: the Basin and Range basin-fill aquifers in California, Nevada, Utah, and Arizona; the Rio Grande aquifer system in New Mexico and Colorado; and the California Coastal Basin and Central Valley aquifer systems in California. Similarities in the hydrogeology, land- and water-use practices, and water-quality issues for alluvial basins within the study area allow for regional analysis through synthesis of the baseline knowledge of groundwater-quality conditions in basins previously studied by the NAWQA Program. Resulting improvements in the understanding of the sources, movement, and fate of contaminants are assisting in the development of tools used to assess aquifer susceptibility and vulnerability.This report synthesizes previously published information about the groundwater systems and water quality of 15 information-rich basin-fill aquifers (SWPA case-study basins) into conceptual models of the primary natural and human factors commonly affecting groundwater quality with respect to selected contaminants, thereby helping to build a regional understanding of the susceptibility and vulnerability of basin-fill aquifers to those contaminants. Four relatively common contaminants (dissolved solids, nitrate, arsenic, and uranium) and two contaminant classes (volatile organic compounds (VOCs) and pesticide compounds) were investigated for sources and controls affecting their occurrence and distribution above specified levels of concern in groundwater of the case-study basins. Conceptual models of factors that are important to aquifer vulnerability with respect to those contaminants and contaminant classes were subsequently formed. The

  16. Evaluation of distribution and sources of sewage molecular marker (LABs) in selected rivers and estuaries of Peninsular Malaysia.

    Science.gov (United States)

    Magam, Sami M; Zakaria, Mohamad Pauzi; Halimoon, Normala; Aris, Ahmad Zaharin; Kannan, Narayanan; Masood, Najat; Mustafa, Shuhaimi; Alkhadher, Sadeq; Keshavarzifard, Mehrzad; Vaezzadeh, Vahab; Sani, Muhamad S A; Latif, Mohd Talib

    2016-03-01

    This is the first extensive report on linear alkylbenzenes (LABs) as sewage molecular markers in surface sediments collected from the Perlis, Kedah, Merbok, Prai, and Perak Rivers and Estuaries in the west of Peninsular Malaysia. Sediment samples were extracted, fractionated, and analyzed using gas chromatography mass spectrometry (GC-MS). The concentrations of total LABs ranged from 68 to 154 (Perlis River), 103 to 314 (Kedah River), 242 to 1062 (Merbok River), 1985 to 2910 (Prai River), and 217 to 329 ng g(-1) (Perak River) dry weight (dw). The highest levels of LABs were found at PI3 (Prai Estuary) due to the rapid industrialization and population growth in this region, while the lowest concentrations of LABs were found at PS1 (upstream of Perlis River). The LABs ratio of internal to external isomers (I/E) in this study ranged from 0.56 at KH1 (upstream of Kedah River) to 1.35 at MK3 (Merbok Estuary) indicating that the rivers receive raw sewage and primary treatment effluents in the study area. In general, the results of this paper highlighted the necessity of continuation of water treatment system improvement in Malaysia.

  17. Blood Monocyte Subsets and Selected Cardiovascular Risk Markers in Rheumatoid Arthritis of Short Duration in relation to Disease Activity

    Directory of Open Access Journals (Sweden)

    Ewa Klimek

    2014-01-01

    Full Text Available Objectives. To evaluate blood monocyte subsets and functional monocyte properties in patients with rheumatoid arthritis (RA of short duration in the context of cardiovascular (CV risk and disease activity. Methods. We studied conventional markers of CV risk, intima media thickness (IMT, and blood monocyte subsets in 27 patients aged 41 ± 10 years with RA of short duration (median 12 months and 22 healthy controls. The RA subjects were divided into low (DAS28: 2.6–5.1 and high (DAS28 > 5.1 disease activity. Results. RA patients exhibited increased levels of intermediate (CD14++CD16+ monocytes with decreased CD45RA expression compared to controls, increased counts of classical (CD14++CD16− monocytes, and decreased percentages of nonclassical (CD14+CD16++ monocytes. Patients with high disease activity had lower HLA DR expression on classical monocytes compared to low disease activity patients. There were no differences in monocyte subsets between subjects with DAS > 5.1 and DAS ≤ 5.1. There were no significant intergroup differences in IMT and the majority of classical CV risk factors. Conclusions. Patients with RA of short duration show alteration in peripheral blood monocyte subsets despite the fact that there is no evidence of subclinical atherosclerosis. Disease activity assessed with DAS28 was associated with impaired functional properties but not with a shift in monocyte subpopulations.

  18. Selective extraction and determination of chlorogenic acids as combined quality markers in herbal medicines using molecularly imprinted polymers based on a mimic template.

    Science.gov (United States)

    Ji, Wenhua; Zhang, Mingming; Yan, Huijiao; Zhao, Hengqiang; Mu, Yan; Guo, Lanping; Wang, Xiao

    2017-12-01

    We describe a solid-phase extraction adsorbent based on molecularly imprinted polymers (MIPs), prepared with use of a mimic template. The MIPs were used for the selective extraction and determination of three chlorogenic acids as combined quality markers for Lonicera japonica and Lianhua qingwen granules. The morphologies and surface groups of the MIPs were assessed by scanning electron microscopy, Brunauer-Emmett-Teller surface area analysis, and Fourier transform infrared spectroscopy. The adsorption isotherms, kinetics, and selectivity of the MIPs were systematically compared with those of non-molecularly imprinted polymers. The MIPs showed high selectivity toward three structurally similar chlorogenic acids (chlorogenic acid, cryptochlorogenic acid, and neochlorogenic acid). A procedure using molecularly imprinted solid-phase extraction coupled with high-performance liquid chromatography was established for the determination of three chlorogenic acids from Lonicera japonica and Lianhua qingwen granules. The recoveries of the chlorogenic acids ranged from 93.1% to 101.4%. The limits of detection and limits of quantification for the three chlorogenic acids were 0.003 mg g -1 and 0.01 mg g -1 , respectively. The newly developed method is thus a promising technique for the enrichment and determination of chlorogenic acids from herbal medicines. Graphical Abstract Mimic molecularly imprinted polymers for the selective extraction of chlorogenic acids.

  19. A Bio-Economic Case Study of Canadian Honey Bee (Hymenoptera: Apidae) Colonies: Marker-Assisted Selection (MAS) in Queen Breeding Affects Beekeeper Profits

    Science.gov (United States)

    Baylis, Kathy; Hoover, Shelley E.; Currie, Rob W.; Melathopoulos, Andony P.; Pernal, Stephen F.; Foster, Leonard J.; Guarna, M. Marta

    2017-01-01

    Abstract Over the past decade in North America and Europe, winter losses of honey bee (Hymenoptera: Apidae) colonies have increased dramatically. Scientific consensus attributes these losses to multifactorial causes including altered parasite and pathogen profiles, lack of proper nutrition due to agricultural monocultures, exposure to pesticides, management, and weather. One method to reduce colony loss and increase productivity is through selective breeding of queens to produce disease-, pathogen-, and mite-resistant stock. Historically, the only method for identifying desirable traits in honey bees to improve breeding was through observation of bee behavior. A team of Canadian scientists have recently identified markers in bee antennae that correspond to behavioral traits in bees and can be tested for in a laboratory. These scientists have demonstrated that this marker-assisted selection (MAS) can be used to produce hygienic, pathogen-resistant honey bee colonies. Based on this research, we present a beekeeping case study where a beekeeper’s profit function is used to evaluate the economic impact of adopting colonies selected for hygienic behavior using MAS into an apiary. Our results show a net profit gain from an MAS colony of between 2% and 5% when Varroa mites are effectively treated. In the case of ineffective treatment, MAS generates a net profit benefit of between 9% and 96% depending on the Varroa load. When a Varroa mite population has developed some treatment resistance, we show that MAS colonies generate a net profit gain of between 8% and 112% depending on the Varroa load and degree of treatment resistance. PMID:28334400

  20. Quality changes of pasteurised mango juice during storage. Part I: Selecting shelf-life markers by integration of a targeted and untargeted multivariate approach.

    Science.gov (United States)

    Wibowo, Scheling; Grauwet, Tara; Gedefa, Getnet Belete; Hendrickx, Marc; Van Loey, Ann

    2015-12-01

    For the first time, a multivariate approach combining targeted and untargeted data was used to obtain insight into quality changes in pasteurised mango juice (cv. 'Totapuri') as a function of storage (42°C for 8weeks). Mango juice samples were formulated with addition of different potential precursors for different quality-related chemical reactions: ascorbic acid, citric acid and sugars. Control (diluted mango puree with water), ascorbic acid-enriched (AA 250 and AA 500 ), citric acid-enriched (CA, CA+AA 250 and CA+AA 500 ) and sugar-enriched (S) samples were characterised for a range of targeted quality parameters as well as for a volatile fingerprint (untargeted). Selection of shelf-life markers or quality parameters significantly changing during shelf-life was performed over all formulations as well as per mango juice formulation. Our study showed that a common trend over all formulations was observed for colour values (VID>│0.90│), while specific shelf-life markers were selected for each formulation. In acidified mango juice samples (CA, CA+AA 250 , CA+AA 500 ), more terpene oxides were selected compared to other formulations. In ascorbic acid-enriched samples (AA 250 , AA 500 , CA+AA 250 , CA+AA 500 ), furfural and ascorbic acid were significantly changing during shelf-life. It seems that the reaction pathways for compounds being formed or degraded upon shelf-life are clearly affected by the acidity level. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. A Bio-Economic Case Study of Canadian Honey Bee (Hymenoptera: Apidae) Colonies: Marker-Assisted Selection (MAS) in Queen Breeding Affects Beekeeper Profits.

    Science.gov (United States)

    Bixby, Miriam; Baylis, Kathy; Hoover, Shelley E; Currie, Rob W; Melathopoulos, Andony P; Pernal, Stephen F; Foster, Leonard J; Guarna, M Marta

    2017-06-01

    Over the past decade in North America and Europe, winter losses of honey bee (Hymenoptera: Apidae) colonies have increased dramatically. Scientific consensus attributes these losses to multifactorial causes including altered parasite and pathogen profiles, lack of proper nutrition due to agricultural monocultures, exposure to pesticides, management, and weather. One method to reduce colony loss and increase productivity is through selective breeding of queens to produce disease-, pathogen-, and mite-resistant stock. Historically, the only method for identifying desirable traits in honey bees to improve breeding was through observation of bee behavior. A team of Canadian scientists have recently identified markers in bee antennae that correspond to behavioral traits in bees and can be tested for in a laboratory. These scientists have demonstrated that this marker-assisted selection (MAS) can be used to produce hygienic, pathogen-resistant honey bee colonies. Based on this research, we present a beekeeping case study where a beekeeper's profit function is used to evaluate the economic impact of adopting colonies selected for hygienic behavior using MAS into an apiary. Our results show a net profit gain from an MAS colony of between 2% and 5% when Varroa mites are effectively treated. In the case of ineffective treatment, MAS generates a net profit benefit of between 9% and 96% depending on the Varroa load. When a Varroa mite population has developed some treatment resistance, we show that MAS colonies generate a net profit gain of between 8% and 112% depending on the Varroa load and degree of treatment resistance. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

  2. Pesticide and Water management alternatives to mitigate potential ground-water contamination for selected counties in Utah

    OpenAIRE

    Ehteshami, Majid; Requena, Antonio M.; Peralta, R. C.; Deer, Howard M.; Hill, Robert W.; Ranjha, Ahmad Yar

    1990-01-01

    Production of adequate supplies of food and fiber currently requires that pesticides be used to limit crop losses from insects, pathogens, weeds and other pests. Although pesticides are necessary in today's agriculture, they can be a serious problem if they reach and contaminate ground water, especially in places where drinking water needs are supplied from ground water. The relative reduction of potential ground-water contamination due to agricultural use of pesticides was analyzed for parti...

  3. A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

    Science.gov (United States)

    Jones, David B; Jerry, Dean R; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

    2013-11-20

    The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters. A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes. This high-density SNP genetic map is the first comprehensive linkage

  4. Parasitic contamination of raw vegetables and fruits collected from selected local markets in Arba Minch town, Southern Ethiopia.

    Science.gov (United States)

    Bekele, Fitsum; Tefera, Tamirat; Biresaw, Gelila; Yohannes, Tsegaye

    2017-03-07

    One way that people get infected with intestinal parasites is through the consumption of contaminated vegetables and fruits. This study aimed at determining the prevalence and predictors of parasitic contamination of fruits and vegetables collected from four local markets in Arba Minch town, Southern Ethiopia. A cross-sectional study was conducted from 1 to 21 September 2014 to determine the level of parasitic contamination of fruits and vegetables sold in Arba Minch town. A total of 360 samples of different types of fruits and vegetables were soaked in physiological saline, followed by vigorous shaking with the aid of a mechanical shaker for 15 minutes and then examined using the sedimentation concentration technique. Out of the 360 samples examined, 196 (54.4%) were contaminated with at least one type of parasite. Ascaris lumbricoides (20.83%) was the most frequently detected parasite and Isospora belli (3.06%) was the least frequently detected one. It was also observed that decreased parasitic contamination was significantly associated with washing the products before displaying it for selling (P parasitic infections from the consumption of raw vegetables and fruits in Arba Minch, Ethiopia. The authors believe that an effort should be made by the relevant bodies to reduce the rate of contamination of products with medically important parasites by educating the vendors and the community.

  5. Health risk assessment of pesticides and polychlorinated biphenyls contaminations in dairy products from selected farms in Greater Accra Region - Ghana

    International Nuclear Information System (INIS)

    Amoako, D.

    2013-07-01

    The residual concentrations of synthetic chemicals such as organochlorines pesticides (OCPs), pyrethroids and polychlorinated biphenyls (PCBs) in dairy products (milk, yoghurt, cheese) from selected farms in Greater Accra were analyzed using Gas Chromatography (GC). A total of 50 samples of dairy products (9 cheese, 25 cow milk and 16 yogourt) were analyzed for OCPs, prethroids and PCBs. Of the numerious pesticides evaluated, detectable levels of OCPs (β-HCH, endrin, heptachlor, endosulfan, p ' p-DDT and methoxchlor); synthetic prethroids (permathrin, allethrin, cypermethrin and deltamethrin) and PCBs (18, 28, 52, 101, 153, 138, and 180) were found in all the dairy product samples analysed. Milk samples were found to be the most contaminated with respect to the OCPs and the levels ranged between 0.0001µg/ml and 0.0407µg/ml. ß-HCH was the highest OCP with concentration of 0.0407µg/ml while cyfluthrin was the highest synthetic prethroids recorded in yoghurt sample (0.0318µg/ml). The highest PCB 18 (2,2,5-Trichlorobiphenyl) recorded (0.2668µg/ml) in yoghurt samples. (Data obtained from the field survey regarding safe use of pesticides, toxicity awareness and symptoms among farmers indicated that a very high proportion of animal farmers were at a high risk of pesticide poisoning from occupational exposure. More than 70% of farm workers did not practise safety precaution during pesticide mixing and application leading to considerable prevalence of pesticide related illness including nausea, vomiting, blurred vision, abdominal cramps, dizziness, diarrhoea and headaches in this agricultural community. The presence of pesticide residues in dairy products was of further concern because milk is the main protein diet for infants. The estimated dose for γ-chlordane(8.5x10 5 µ/ml), endrin(0.0114 µg/ml) p ' p ' -DDT(8.5x10 5 µg/ml), DDE(8.5x10 5 µg/ml),heptachlor(2.5x10 5 µg/ml), dieldrin(6.8x10 5 µg/ml) do not pose a direct hazard to human health, although present

  6. Epstein-Barr virus (EBV) recombinants: use of positive selection markers to rescue mutants in EBV-negative B-lymphoma cells.

    Science.gov (United States)

    Wang, F; Marchini, A; Kieff, E

    1991-04-01

    The objective of these experiments was to develop strategies for creation and identification of recombinant mutant Epstein-Barr viruses (EBV). EBV recombinant molecular genetics has been limited to mutations within a short DNA segment deleted from a nontransforming EBV and an underlying strategy which relies on growth transformation of primary B lymphocytes for identification of recombinants. Thus, mutations outside the deletion or mutations which affect transformation cannot be easily recovered. In these experiments we investigated whether a toxic drug resistance gene, guanine phosphoribosyltransferase or hygromycin phosphotransferase, driven by the simian virus 40 promoter can be recombined into the EBV genome and can function to identify B-lymphoma cells infected with recombinant virus. Two different strategies were used to recombine the drug resistance marker into the EBV genome. Both utilized transfection of partially permissive, EBV-infected B95-8 cells and positive selection for cells which had incorporated a functional drug resistance gene. In the first series of experiments, B95-8 clones were screened for transfected DNA that had recombined into the EBV genome. In the second series of experiments, the transfected drug resistance marker was linked to the plasmid and lytic EBV origins so that it was maintained as an episome and could recombine with the B95-8 EBV genome during virus replication. The recombinant EBV from either experiment could be recovered by infection and toxic drug selection of EBV-negative B-lymphoma cells. The EBV genome in these B-lymphoma cells is frequently an episome. Virus genes associated with latent infection of primary B lymphocytes are expressed. Expression of Epstein-Barr virus nuclear antigen 2 (EBNA-2) and the EBNA-3 genes is variable relative to that of EBNA-1, as is characteristic of some naturally infected Burkitt tumor cells. Moreover, the EBV-infected B-lymphoma cells are often partially permissive for early replicative

  7. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES

    Science.gov (United States)

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

  8. Modelling the impacts of pasture contamination and stocking rate for the development of targeted selective treatment strategies for Ostertagia ostertagi infection in calves

    OpenAIRE

    Berk, Zoe; Laurenson, Yan C.S.M.; Forbes, Andrew B.; Kyriazakis, Ilias

    2017-01-01

    A simulation study was carried out to assess whether variation in pasture contamination or stocking rate impact upon the optimal design of targeted selective treatment (TST) strategies. Two methods of TST implementation were considered: 1) treatment of a fixed percentage of a herd according to a given phenotypic trait, or 2) treatment of individuals that exceeded a threshold value for a given phenotypic trait. Four phenotypic traits, on which to base treatment were considered: 1) average dail...

  9. Characterisation of Triticum vavilovii-derived stripe rust resistance using genetic, cytogenetic and molecular analyses and its marker-assisted selection.

    Science.gov (United States)

    Bariana, H. S.; Brown, G. N.; Ahmed, N. U.; Khatkar, S.; Conner, R. L.; Wellings, C. R.; Haley, S.; Sharp, P. J.; Laroche, A.

    2002-02-01

    Stripe rust resistance was identified in Triticum vavilovii( T. vaviloviiAus22498)-derived Russian wheat aphid (RWA)-resistant germplasm. Inheritance studies indicated monogenic control of resistance. The resistance gene was tentatively designated as Yrvav and was located on chromosome 1B by monosomic analysis. A close association (1.5+/-0.9% recombination) of Yrvav with a T. vavilovii-derived gliadin allele ( Gli-B1vav) placed it in chromosome arm 1BS. Yrvavwas allelic with Yr10. Tests with Yr10 avirulent and virulent pathotypes showed that Yrvav and Yr10 possess identical pathogenic specificity. Yrvav and Yr10 showed close genetic associations with alternate alleles at the Xpsp3000(microsatellite marker), Gli-B1 and Rg1 loci. Based on these observations Yrvav was named as Yr10vav. The close association between Xpsp3000 and Gli-B1 was also confirmed. The Yr10vav-linked Xpsp3000 allele (285 bp) was not present in 65 Australian cultivars, whereas seven Australian wheats lacking Yr10 carried the same Xpsp3000 allele (260 bp) as Yr10carrying wheat cultivar Moro. Xpsp3000 and/or Gli-B1 could be used in marker-assisted selection for pyramiding Yr10vavor Yr10 with other stripe rust resistance genes. Yr10vav was inherited independently of the T. vavilovii-derived RWA resistance.

  10. Saccharomyces cerevisiae single-copy plasmids for auxotrophy compensation, multiple marker selection, and for designing metabolically cooperating communities [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Michael Mülleder

    2016-09-01

    Full Text Available Auxotrophic markers are useful tools in cloning and genome editing, enable a large spectrum of genetic techniques, as well as facilitate the study of metabolite exchange interactions in microbial communities. If unused background auxotrophies are left uncomplemented however, yeast cells need to be grown in nutrient supplemented or rich growth media compositions, which precludes the analysis of biosynthetic metabolism, and which leads to a profound impact on physiology and gene expression. Here we present a series of 23 centromeric plasmids designed to restore prototrophy in typical Saccharomyces cerevisiae laboratory strains. The 23 single-copy plasmids complement for deficiencies in HIS3, LEU2, URA3, MET17 or LYS2 genes and in their combinations, to match the auxotrophic background of the popular functional-genomic yeast libraries that are based on the S288c strain. The plasmids are further suitable for designing self-establishing metabolically cooperating (SeMeCo communities, and possess a uniform multiple cloning site to exploit multiple parallel selection markers in protein expression experiments.

  11. Rapid and selective detection of acetone using hierarchical ZnO gas sensor for hazardous odor markers application

    International Nuclear Information System (INIS)

    Jia, Qianqian; Ji, Huiming; Zhang, Ying; Chen, Yalu; Sun, Xiaohong; Jin, Zhengguo

    2014-01-01

    Highlights: • ZnO spheres fabricated via solvothermal method are with (0 0 2) polar facet exposed. • Response time of ZnO sensor for detecting 100 ppm acetone is as short as 3 s. • R a /R g toward 100 ppm acetone is 33 when operated at 230 °C. • ZnO sensor exhibits good selectivity against other toxic gases and water vapor. • Porous structure and exposure of polar facet contribute to good sensing properties. - Abstract: Hierarchical nanostructured ZnO dandelion-like spheres were synthesized via solvothermal reaction at 200 °C for 4 h. The products were pure hexagonal ZnO with large exposure of (0 0 2) polar facet. Side-heating gas sensor based on hierarchical ZnO spheres was prepared to evaluate the acetone gas sensing properties. The detection limit to acetone for the ZnO sensor is 0.25 ppm. The response (R a /R g ) toward 100 ppm acetone was 33 operated at 230 °C and the response time was as short as 3 s. The sensor exhibited remarkable acetone selectivity with negligible response toward other hazardous gases and water vapor. The high proportion of electron depletion region and oxygen vacancies contributed to high gas response sensitivity. The hollow and porous structure of dandelion-like ZnO spheres facilitated the diffusion of gas molecules, leading to a rapid response speed. The largely exposed (0 0 2) polar facets could adsorb acetone gas molecules easily and efficiently, resulting in a rapid response speed and good selectivity of hierarchical ZnO spheres gas sensor at low operating temperature

  12. Identification of Potential Metabolic Markers for the Selection of a High-Yield Clone of Quercus acutissima in Clonal Seed Orchard

    Directory of Open Access Journals (Sweden)

    Jun Won Kang

    2018-03-01

    Full Text Available Quercus acutissima Carruth. is one of the most economically important deciduous tree species in Korea. The acorns of Q. acutissima are used for both food and medicinal purposes in Korea and China. In this study, we analyzed plant hormones and metabolite profiles to identify their correlation with the yield production of Q. acutissima. The contents of sucrose and inositol in the leaves of high-yield clones were significantly higher (p < 0.05 than those of low-yield clones. In addition, high-yield clones have a higher content of phosphoric acid, succinic acid, malic acid, and butane-1,3-diol in stems compared with low-yield clones. Among the identified metabolites, zeatin-9-glucoside showed highly significant negative correlations with tree height, crown volume, and acorn production. It is considered that these metabolites could be useful metabolic markers for the selection of a high yield clone of Q. acutissima.

  13. Proteins in seed and seedlings of selected Austrian pine (Pinus nigra Arnold trees as genetic markers tolerant to drought

    Directory of Open Access Journals (Sweden)

    Mataruga Milan

    2007-01-01

    Full Text Available A precondition necessary for creation and selection of genotypes tolerant of stress conditions is a study of physiological, biochemical and molecular bases of their adaptive reaction to stress. The study includes 40 lines of free pollination originating from 5 provenances: Sutjeska, Višegrad, Tara, Teslić and Durmitor (B&H, Serbia and Montenegro. Two populations were selected from each provenance, i.e.: 5 lines of free pollination represent the population growing on the cliffs and 3 lines of free pollination represent the population growing at the best site of Austrian pine. Specific characteristics of the studied provenances, populations, and free pollination lines were confirmed by the analyses in the salt-soluble proteins. The identical protein composition was proved in a small number of cases in the replicates of the same free pollination line, which indicates a high intra-line variability, which can be the result of the effect of father, as well as of heterozygosity of mother trees. The analyses of protein composition of seed showed considerable differences at provenance level. Inter-line, population and provenance differences, and also, the interaction between the origin and drought factor, were recorded for 9-day-old seedlings germinated in induced drought conditions and in normal conditions.

  14. Rapid and selective detection of acetone using hierarchical ZnO gas sensor for hazardous odor markers application.

    Science.gov (United States)

    Jia, Qianqian; Ji, Huiming; Zhang, Ying; Chen, Yalu; Sun, Xiaohong; Jin, Zhengguo

    2014-07-15

    Hierarchical nanostructured ZnO dandelion-like spheres were synthesized via solvothermal reaction at 200°C for 4h. The products were pure hexagonal ZnO with large exposure of (002) polar facet. Side-heating gas sensor based on hierarchical ZnO spheres was prepared to evaluate the acetone gas sensing properties. The detection limit to acetone for the ZnO sensor is 0.25ppm. The response (Ra/Rg) toward 100ppm acetone was 33 operated at 230°C and the response time was as short as 3s. The sensor exhibited remarkable acetone selectivity with negligible response toward other hazardous gases and water vapor. The high proportion of electron depletion region and oxygen vacancies contributed to high gas response sensitivity. The hollow and porous structure of dandelion-like ZnO spheres facilitated the diffusion of gas molecules, leading to a rapid response speed. The largely exposed (002) polar facets could adsorb acetone gas molecules easily and efficiently, resulting in a rapid response speed and good selectivity of hierarchical ZnO spheres gas sensor at low operating temperature. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Selective modulation of endoplasmic reticulum stress markers in prostate cancer cells by a standardized mangosteen fruit extract.

    Directory of Open Access Journals (Sweden)

    Gongbo Li

    Full Text Available The increased proliferation of cancer cells is directly dependent on the increased activity of the endoplasmic reticulum (ER machinery which is responsible for protein folding, assembly, and transport. In fact, it is so critical that perturbations in the endoplasmic reticulum can lead to apoptosis. This carefully regulated organelle represents a unique target of cancer cells while sparing healthy cells. In this study, a standardized mangosteen fruit extract (MFE was evaluated for modulating ER stress proteins in prostate cancer. Two human prostate cancer cell lines, 22Rv1 and LNCaP, and prostate epithelial cells (PrECs procured from two patients undergoing radical prostatectomy were treated with MFE. Flow cytometry, MTT, BrdU and Western blot were used to evaluate cell apoptosis, viability, proliferation and ER stress. Next, we evaluated MFE for microsomal stability and anti-cancer activity in nude mice. MFE induced apoptosis, decreased viability and proliferation in prostate cancer cells. MFE increased the expression of ER stress proteins. Interestingly, MFE selectively promotes ER stress in prostate cancer cells while sparing PrECs. MFE suppressed tumor growth in a xenograft tumor model without obvious toxicity. Mangosteen fruit extract selectively promotes endoplasmic reticulum stress in cancer cells while sparing non-tumorigenic prostate epithelial cells. Furthermore, in an in vivo setting mangosteen fruit extract significantly reduces xenograft tumor formation.

  16. Selective modulation of endoplasmic reticulum stress markers in prostate cancer cells by a standardized mangosteen fruit extract.

    Science.gov (United States)

    Li, Gongbo; Petiwala, Sakina M; Pierce, Dana R; Nonn, Larisa; Johnson, Jeremy J

    2013-01-01

    The increased proliferation of cancer cells is directly dependent on the increased activity of the endoplasmic reticulum (ER) machinery which is responsible for protein folding, assembly, and transport. In fact, it is so critical that perturbations in the endoplasmic reticulum can lead to apoptosis. This carefully regulated organelle represents a unique target of cancer cells while sparing healthy cells. In this study, a standardized mangosteen fruit extract (MFE) was evaluated for modulating ER stress proteins in prostate cancer. Two human prostate cancer cell lines, 22Rv1 and LNCaP, and prostate epithelial cells (PrECs) procured from two patients undergoing radical prostatectomy were treated with MFE. Flow cytometry, MTT, BrdU and Western blot were used to evaluate cell apoptosis, viability, proliferation and ER stress. Next, we evaluated MFE for microsomal stability and anti-cancer activity in nude mice. MFE induced apoptosis, decreased viability and proliferation in prostate cancer cells. MFE increased the expression of ER stress proteins. Interestingly, MFE selectively promotes ER stress in prostate cancer cells while sparing PrECs. MFE suppressed tumor growth in a xenograft tumor model without obvious toxicity. Mangosteen fruit extract selectively promotes endoplasmic reticulum stress in cancer cells while sparing non-tumorigenic prostate epithelial cells. Furthermore, in an in vivo setting mangosteen fruit extract significantly reduces xenograft tumor formation.

  17. Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker-assisted selection.

    Science.gov (United States)

    Flachowsky, Henryk; Le Roux, Pierre-Marie; Peil, Andreas; Patocchi, Andrea; Richter, Klaus; Hanke, Magda-Viola

    2011-10-01

    Breeding of apple (Malus × domestica) remains a slow process because of protracted generation cycles. Shortening the juvenile phase to achieve the introgression of traits from wild species into prebreeding material within a reasonable time frame is a great challenge. In this study, we evaluated early flowering transgenic apple lines overexpressing the BpMADS4 gene of silver birch with regard to tree morphology in glasshouse conditions. Based on the results obtained, line T1190 was selected for further analysis and application to fast breeding. The DNA sequences flanking the T-DNA were isolated and the T-DNA integration site was mapped on linkage group 4. The inheritance and correctness of the T-DNA integration were confirmed after meiosis. A crossbred breeding programme was initiated by crossing T1190 with the fire blight-resistant wild species Malus fusca. Transgenic early flowering F(1) seedlings were selected and backcrossed with 'Regia' and 98/6-10 in order to introgress the apple scab Rvi2, Rvi4 and powdery mildew Pl-1, Pl-2 resistance genes and the fire blight resistance quantitative trait locus FB-F7 present in 'Regia'. Three transgenic BC'1 seedlings pyramiding Rvi2, Rvi4 and FB-F7, as well as three other BC'1 seedlings combining Pl-1 and Pl-2, were identified. Thus, the first transgenic early flowering-based apple breeding programme combined with marker-assisted selection was established. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

  18. Introgression of Blast Resistance Genes (Putative Pi-b and Pi-kh) into Elite Rice Cultivar MR219 through Marker-Assisted Selection

    Science.gov (United States)

    Tanweer, Fatah A.; Rafii, Mohd Y.; Sijam, Kamaruzaman; Rahim, Harun A.; Ahmed, Fahim; Ashkani, Sadegh; Latif, Mohammad A.

    2015-01-01

    Blast is the most common biotic stress leading to the reduction of rice yield in many rice-growing areas of the world, including Malaysia. Improvement of blast resistance of rice varieties cultivated in blast endemic areas is one of the most important objectives of rice breeding programs. In this study, the marker-assisted backcrossing strategy was applied to improve the blast resistance of the most popular Malaysian rice variety MR219 by introgressing blast resistance genes from the Pongsu Seribu 2 variety. Two blast resistance genes, Pi-b and Pi-kh, were pyramided into MR219. Foreground selection coupled with stringent phenotypic selection identified 15 plants homozygous for the Pi-b and Pi-kh genes, and background selection revealed more than 95% genome recovery of MR219 in advanced blast resistant lines. Phenotypic screening against blast disease indicated that advanced homozygous blast resistant lines were strongly resistant against pathotype P7.2 in the blast disease endemic areas. The morphological, yield, grain quality, and yield-contributing characteristics were significantly similar to those of MR219. The newly developed blast resistant improved lines will retain the high adoptability of MR219 by farmers. The present results will also play an important role in sustaining the rice production of Malaysia. PMID:26734013

  19. Transformation of apple (Malus × domestica) using mutants of apple acetolactate synthase as a selectable marker and analysis of the T-DNA integration sites.

    Science.gov (United States)

    Yao, Jia-Long; Tomes, Sumathi; Gleave, Andrew P

    2013-05-01

    Apple acetolactate synthase mutants were generated by site-specific mutagenesis and successfully used as selection marker in tobacco and apple transformation. T-DNA/Apple genome junctions were analysed using genome-walking PCR and sequencing. An Agrobacterium-mediated genetic transformation system was developed for apple (Malus × domestica), using mutants of apple acetolactate synthase (ALS) as a selectable marker. Four apple ALS mutants were generated by site-specific mutagenesis and subsequently cloned under the transcriptional control of the CaMV 35S promoter and ocs 3' terminator, in a pART27-derived plant transformation vector. Three of the four mutations were found to confer resistance to the herbicide Glean(®), containing the active agent chlorsulfuron, in tobacco (Nicotiana tabacum) transformation. In apple transformation, leaf explants infected with Agrobacterium tumefaciens EHA105 containing one of the three ALS mutants resulted in the production of shoots on medium containing 2-8 μg L(-1) Glean(®), whilst uninfected wild-type explants failed to regenerate shoots or survive on medium containing 1 and 3 μg L(-1) Glean(®), respectively. Glean(®)-resistant, regenerated shoots were further multiplied and rooted on medium containing 10 μg L(-1) Glean(®). The T-DNA and apple genome-DNA junctions from eight rooted transgenic apple plants were analysed using genome-walking PCR amplification and sequencing. This analysis confirmed T-DNA integration into the apple genome, identified the genome integration sites and revealed the extent of any vector backbone integration, T-DNA rearrangements and deletions of apple genome DNA at the sites of integration.

  20. Alanine racemase mutants of Burkholderia pseudomallei and Burkholderia mallei and use of alanine racemase as a non-antibiotic-based selectable marker.

    Directory of Open Access Journals (Sweden)

    Sheryl L W Zajdowicz

    Full Text Available Burkholderia pseudomallei and Burkholderia mallei are category B select agents and must be studied under BSL3 containment in the United States. They are typically resistant to multiple antibiotics, and the antibiotics used to treat B. pseudomallei or B. mallei infections may not be used as selective agents with the corresponding Burkholderia species. Here, we investigated alanine racemase deficient mutants of B. pseudomallei and B. mallei for development of non-antibiotic-based genetic selection methods and for attenuation of virulence. The genome of B. pseudomallei K96243 has two annotated alanine racemase genes (bpsl2179 and bpss0711, and B. mallei ATCC 23344 has one (bma1575. Each of these genes encodes a functional enzyme that can complement the alanine racemase deficiency of Escherichia coli strain ALA1. Herein, we show that B. pseudomallei with in-frame deletions in both bpsl2179 and bpss0711, or B. mallei with an in-frame deletion in bma1575, requires exogenous D-alanine for growth. Introduction of bpsl2179 on a multicopy plasmid into alanine racemase deficient variants of either Burkholderia species eliminated the requirement for D-alanine. During log phase growth without D-alanine, the viable counts of alanine racemase deficient mutants of B. pseudomallei and B. mallei decreased within 2 hours by about 1000-fold and 10-fold, respectively, and no viable bacteria were present at 24 hours. We constructed several genetic tools with bpsl2179 as a selectable genetic marker, and we used them without any antibiotic selection to construct an in-frame ΔflgK mutant in the alanine racemase deficient variant of B. pseudomallei K96243. In murine peritoneal macrophages, wild type B. mallei ATCC 23344 was killed much more rapidly than wild type B. pseudomallei K96243. In addition, the alanine racemase deficient mutant of B. pseudomallei K96243 exhibited attenuation versus its isogenic parental strain with respect to growth and survival in murine

  1. Alanine Racemase Mutants of Burkholderia pseudomallei and Burkholderia mallei and Use of Alanine Racemase as a Non-Antibiotic-Based Selectable Marker

    Science.gov (United States)

    Zajdowicz, Sheryl L. W.; Jones-Carson, Jessica; Vazquez-Torres, Andres; Jobling, Michael G.; Gill, Ronald E.; Holmes, Randall K.

    2011-01-01

    Burkholderia pseudomallei and Burkholderia mallei are category B select agents and must be studied under BSL3 containment in the United States. They are typically resistant to multiple antibiotics, and the antibiotics used to treat B. pseudomallei or B. mallei infections may not be used as selective agents with the corresponding Burkholderia species. Here, we investigated alanine racemase deficient mutants of B. pseudomallei and B. mallei for development of non-antibiotic-based genetic selection methods and for attenuation of virulence. The genome of B. pseudomallei K96243 has two annotated alanine racemase genes (bpsl2179 and bpss0711), and B. mallei ATCC 23344 has one (bma1575). Each of these genes encodes a functional enzyme that can complement the alanine racemase deficiency of Escherichia coli strain ALA1. Herein, we show that B. pseudomallei with in-frame deletions in both bpsl2179 and bpss0711, or B. mallei with an in-frame deletion in bma1575, requires exogenous d-alanine for growth. Introduction of bpsl2179 on a multicopy plasmid into alanine racemase deficient variants of either Burkholderia species eliminated the requirement for d-alanine. During log phase growth without d-alanine, the viable counts of alanine racemase deficient mutants of B. pseudomallei and B. mallei decreased within 2 hours by about 1000-fold and 10-fold, respectively, and no viable bacteria were present at 24 hours. We constructed several genetic tools with bpsl2179 as a selectable genetic marker, and we used them without any antibiotic selection to construct an in-frame ΔflgK mutant in the alanine racemase deficient variant of B. pseudomallei K96243. In murine peritoneal macrophages, wild type B. mallei ATCC 23344 was killed much more rapidly than wild type B. pseudomallei K96243. In addition, the alanine racemase deficient mutant of B. pseudomallei K96243 exhibited attenuation versus its isogenic parental strain with respect to growth and survival in murine peritoneal macrophages

  2. Evaluation of processing factors for selected organic contaminants during virgin olive oil production: Distribution of BTEXS during olives processing.

    Science.gov (United States)

    López-Blanco, Rafael; Gilbert-López, Bienvenida; Rojas-Jiménez, Rubén; Robles-Molina, José; Ramos-Martos, Natividad; García-Reyes, Juan F; Molina-Díaz, Antonio

    2016-05-15

    The presence of BTEXS (benzene, toluene, ethylbenzene, xylenes and styrene) in virgin olive oils can be attributed to environmental contamination, but also to biological processes during oil lipogenesis (styrene). In this work, the processing factor of BTEXS from olives to olive oil during its production was evaluated at lab-scale with an Abencor system. Benzene showed the lowest processing factor (15%), whereas toluene and xylenes showed an intermediate behavior (with 40-60% efficiency), and ethylbenzene and styrene were completely transferred (100%). In addition, an attempt to examine the contribution of potential sources to olives contamination with BTEXS was carried out for the first time. Two types of olives samples were classified according to their proximity to the contamination source (road). Although higher levels of BTEXS were found in samples close to roads, the concentrations were relatively low and do not constitute a major contribution to BTEXS usually detected in olive oil. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. The selection of hyperaccumulators for phytoremediation of uranium-contaminated soils and their uranium-accumulating characters

    International Nuclear Information System (INIS)

    Tang Li; Ren Yamin; Xu Jun; Yao Zhongwei; Xia Chuanqin; Bo Yun; Deng Dachao

    2009-01-01

    A pot experiment was conducted to investigate the possibility for phytoremediation of U-contaminated soils. The plants of cruciferae (8 species), malvaceae or compositae were planted for 55 days in the U-contaminated soils (100 mg·kg -1 ). The samples were analyzed using an inductively-coupled plasma atomic emission spectrometer (ICP-AES). The results showed that U concentration was the highest in shoots of Chinese mustard (var.Texuanzhacai, 1115 mg·kg -1 ), the highest U removal from U-contaminated soils to plants occurred in the shoots of Artemisia argyi(1113 μg per pot). For the Chinese mustard (var.Paoqingcai, var. Texuanzhacai), uranium concentration in shoots was higher than in roots, and bioaccumulation factors (BFs) and transfer factors (TFs) were more than one. They showed better suitability for phytoremediation of U than other plants due to their high U accumulation in the aboveground tissues. (authors)

  4. Effects of Wheat Naturally Contaminated with Fusarium Mycotoxins on Growth Performance and Selected Health Indices of Red Tilapia (Oreochromis niloticus × O. mossambicus

    Directory of Open Access Journals (Sweden)

    Siriporn Tola

    2015-05-01

    Full Text Available An 8-week feeding trial was conducted to examine effects of wheat naturally contaminated with Fusarium mycotoxins (deoxynivalenol, DON 41 mg·kg−1 on growth performance and selected health indices of red tilapia (Oreochromis niloticus × O. mossambicus; initial weight = 4.3 g/fish. Five experimental diets were formulated by replacement of clean wheat with naturally contaminated wheat resulting in graded levels of DON and zearalenone (ZEN (Diet 1 0.07/0.01, Diet 2 0.31/0.09, Diet 3 0.50/0.21, Diet 4 0.92/0.37 and Diet 5 1.15/0.98 mg·kg−1. Groups of 50 fish were randomly allocated into each of 20 aquaria and fed to near-satiety for eight weeks. Growth rate, feed intake and feed efficiency of fish fed the experimental diets decreased linearly with increasing levels of Fusarium mycotoxins (p < 0.05. Although growth depression was associated with feeding diets naturally contaminated with Fusarium mycotoxins, especially DON, no biochemical and histopathological parameters measured in blood and liver appeared affected by Fusarium mycotoxin concentrations of diets (p > 0.05. Though there was no clear evidence of overt DON toxicity to red tilapia, it is recommended that feed ingredients should be screened for Fusarium mycotoxin contamination to ensure optimal growth performance.

  5. Analysis of food contaminants

    National Research Council Canada - National Science Library

    Gilbert, John

    1984-01-01

    ... quantification methods used in the analysis of mycotoxins in foods - Confirmation and quantification of trace organic food contaminants by mass spectrometry-selected ion monitoring - Chemiluminescence...

  6. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.

    Science.gov (United States)

    Meglécz, Emese; Costedoat, Caroline; Dubut, Vincent; Gilles, André; Malausa, Thibaut; Pech, Nicolas; Martin, Jean-François

    2010-02-01

    QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input. The following tasks are completed by QDD: tag sorting, adapter/vector removal, elimination of redundant sequences, detection of possible genomic multicopies (duplicated loci or transposable elements), stringent selection of target microsatellites and customizable primer design. It can treat up to one million sequences of a few hundred base pairs in the tag-sorting step, and up to 50,000 sequences in a single input file for the steps involving estimation of sequence similarity. QDD is freely available under the GPL licence for Windows and Linux from the following web site: http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html. Supplementary data are available at Bioinformatics online.

  7. CONTENT OF SELECTED HEAVY METALS IN NI-CONTAMINATED SOIL FOLLOWING THE APPLICATION OF HALLOYSITE AND ZEOLITE

    Directory of Open Access Journals (Sweden)

    Maja Radziemska

    2016-07-01

    Full Text Available Nickel has been listed as a priory control pollutant by the United States Environmental Protection Agency (US EPA. Compared with other methods, the combination of vegetation and the addition of mineral sorbents to heavy metal-contaminated soils can be readily applied on a large scale because of the simplicity of technology and low cost. Halloysite and zeolite, among others, can be used for this purpose. A greenhouse study was performed to evaluate the feasibility of using natural zeolite, as well as raw and modified halloysite for the remediation of simulated Ni-contaminated soil. The soil was spiked with five doses of nickel, i.e. 0 (control, 80, 160, 240 and 320 mg Ni kg-1 soil. The average accumulation of heavy metals in nickel-contaminated soil was found to follow the decreasing order of Ni>Zn>Cr>Cu>Pb. The highest reduction of Pb content was observed in soil samples taken from pots containing 80 and 160 mg.kg-1 of Ni along with the addition of modified halloysite. The strongest effects were caused by natural zeolite, which significantly reduced the average content of chromium. Contamination at 320 mg Ni.kg-1 of soil led to the highest increases in the Ni, Pb and Cr contents of soil.

  8. Decreased chronic-stage cortical C-11-flumazenil binding after focal ischemia-reperfusion in baboons - A marker of selective neuronal loss?

    International Nuclear Information System (INIS)

    Giffard, C.; Landeau, B.; Kerrouche, N.; Young, A.R.; Giffard, C.; Landeau, B.; Kerrouche, N.; Young, A.R.; Giffard, C.; Landeau, B.; Baron, J.C.

    2008-01-01

    Background and Purpose - Although the penumbra can be saved by early reperfusion, in the rat it is consistently affected by selective neuronal loss. Mapping selective neuronal loss in the living primate would be desirable. Methods - Five young adult baboons underwent 15 O positron emission tomography for cerebral blood flow, cerebral oxygen consumption, and oxygen extraction fraction mapping at baseline and serially during and after 20-hours temporary middle cerebral artery occlusion. At approximately day 30, 11 C-flumazenil (FMZ), a potential positron emission tomography marker of selective neuronal loss, and structural magnetic resonance-based infarct mapping were obtained, and the brain was perfused-fixed. Reduced FMZ binding in non-infarcted cortical middle cerebral artery areas was searched voxel-wise, and specific binding was assessed using compartmental modeling of FMZ time-activity curves. Results - Visual inspection revealed reduced late FMZ uptake in the affected cortical territory, extending well beyond the infarct. Accordingly, the incidence of selected voxels was greater than chance, documenting mildly but significantly reduced FMZ uptake and specific binding. Serial 15 O positron emission tomography revealed moderately severe acute ischemia followed by reperfusion. Histopathology documented only mild neuronal changes in or near the affected areas. Conclusions - We document moderate but definite late FMZ binding decrements in non-infarcted cortical areas in the baboon, consistent with previous rat and human studies. These were acutely characterized by moderate ischemia followed by reperfusion, consistent with neuronal damage from ischemic or reperfusion injury in the salvaged at-risk tissue. Only mild histopathological changes subtended these FMZ alterations suggesting subtle processes such as isolated dendrite or synapse loss. Whether these changes impact on clinical outcome deserves studying because they may be targeted by specific neuro

  9. Chronic Exposure of Early Stages of Development of Japanese Oyster to Contaminants from the Industry in the English Channel. Stress Markers at Integrated and Molecular Level

    International Nuclear Information System (INIS)

    Devos, Alexandre

    2013-01-01

    This thesis explores the effects of pollutants from the industry in the English Channel, in particular radionuclides, on the early stages of development of the Japanese oyster Crassostrea gigas. Original experimental devices were designed to study in laboratory controlled conditions the growth of a large number of larvae and spats. Emphasis was given to a joint use of stress markers at integrated and molecular levels. First exposures to non-radioactive pollutants revealed a highly sensitive response of the growth of juveniles exposed to a metal (zinc). Thereafter, juveniles were exposed for several weeks to dose rates of ionizing radiation and radionuclide activities several orders of magnitude higher than the levels likely to be encountered in the marine environment. An eco-geno-toxicological approach contributed to the understanding of the effects of ionizing radiations on DNA. The results strongly suggest that biochemical mechanisms act efficiently against radio-induced damages as early as the first days of life of the Japanese oyster. It still remains a lack of information about the long-term effects of DNA damages to higher level of biological organization. (author) [fr

  10. Heavy metals bioaccumulation in selected tissues of red swamp crayfish: An easy tool for monitoring environmental contamination levels.

    Science.gov (United States)

    Goretti, E; Pallottini, M; Ricciarini, M I; Selvaggi, R; Cappelletti, D

    2016-07-15

    In this paper we explored the heavy metal bioaccumulation (Cd, Cu, Pb and Zn) in Procambarus clarkii, a crayfish recently suggested as a potential bioindicator for metals pollution in freshwater systems. The present study is focused on crayfishes populations caught in a heavily polluted industrial and in a reference sites (Central Italy), though the results are generalized with a thorough analysis of literature metadata. In agreement with the literature, the hepatopancreas (Hep, detoxification tissues) of the red swamp crayfish showed a higher concentration of heavy metals in comparison to the abdominal muscle (AbM, not detoxification tissues) in the sites under scrutiny. Hep/AbM concentration ratio was dependent on the specific metal investigated and on its sediment contamination level. Specifically we found that Hep/AbM ratio decreases as follows: Cd (11.7)>Cu (5.5)>Pb (3.6)>Zn (1.0) and Pb (4.34)>Cd (3.66)>Zn (1.69)>Cu (0.87) for the industrial and reference sites, respectively. The analysis of our bioaccumulation data as well as of literature metadata allowed to elaborate a specific contamination index (Toxic Contamination Index, TCI), dependent only on the bioaccumulation data of hepatopancreas and abdominal muscle. In the industrial site, TCI expressed values much higher than the unit for Cd and Cu, confirming that these metals were the main contaminants; in contrast for lower levels of heavy metals, as those observed in the reference site for Cu, Zn and Pb, the index provided values below unit. TCI is proposed as a useful and easy tool to assess the toxicity level of contaminated sites by heavy metals in the environmental management. Copyright © 2016. Published by Elsevier B.V.

  11. Determination of the Marker Diarylheptanoid Phytoestrogens in Curcuma comosa Rhizomes and Selected Herbal Medicinal Products by HPLC-DAD.

    Science.gov (United States)

    Yingngam, Bancha; Brantner, Adelheid; Jinarat, Damrongsak; Kaewamatawong, Rawiwun; Rungseevijitprapa, Wandee; Suksamrarn, Apichart; Piyachaturawat, Pawinee; Chokchaisiri, Ratchanaporn

    2018-01-01

    A method for quantification of diarylheptanoids in Curcuma comosa rhizomes and selected pharmaceutical preparations was established by using HPLC-diode array detector (DAD). The chromatographic separation of three diarylheptanoids [(3S)-1-(3,4-dihydroxy-phenyl)-7-phenyl-(6E)-6-hepten-3-ol (1), (3R)-1,7-diphenyl-(4E,6E)-4,6-heptadien-3-ol (2), and (3S)-1,7-diphenyl-(6E)-6-hepten-3-ol (3)] was performed on a Luna C 18 analytical column using gradient elution with 0.5% acetic acid in water and acetonitrile with a flow rate of 1 mL/min and a column temperature of 35°C. The calibration curves for the analytes showed good linearity (R 2 >0.999), high precision (relative standard deviation (RSD) <2%) and acceptable recovery (98.35-103.90%, RSD <2%). The limit of detection (LOD) and limit of quantification (LOQ) were 0.06-0.22 and 0.18-0.69 µg/mL, respectively. The results of all validated parameters were within the limits according to the International Conference on Harmonization (ICH) Guidelines. The established method was successfully applied for qualitative and quantitative determination of the three constituents in different samples of C. comosa and some commercial products in capsules. The simplicity, rapidity, and reliability of the method could be useful for the fingerprint analysis and standardization of diarylheptanoids, which are responsible for the estrogenic activity in raw materials and herbal medicinal products of C. comosa.

  12. Observed differentials in the levels of selected environmental contaminants among Mexican and other Hispanic American children, adolescents, adults, and senior citizens.

    Science.gov (United States)

    Jain, Ram B

    2018-02-01

    Starting with the 2007-2008 cycle, the National Health and Nutrition Examination Survey (NHANES) also oversampled Hispanics other than Mexicans (OHISP) making it possible to treat OHISP as a separate demographic group along with Mexican Americans (MAs), non-Hispanic whites (NHWs), and non-Hispanic blacks (NHBs). Yet, more often than not, OHISP have been merged with MA to form an all-Hispanic demographic group (HISP) thus limiting comparisons between NHW, NHB, and HISP. Consequently, for the first time, this study was undertaken to evaluate differences in the observed levels of selected environmental contaminants between MA and OHISP from five groups of environmental contaminants, namely, polycyclic aromatic hydrocarbons (PAHs), iodine uptake inhibitors (IUIs), environmental phenols (EPHs), priority pesticides (PPs), and perfluoroalkyl acids (PFAAs). Data for 2007-2010 from NHANES were used to conduct this study. OHISP children born in USA had higher levels of selected PAH metabolites than USA-born MA, and Mexican-born MA adolescents had higher levels of selected PAH metabolites than USA-born MA adolescents. USA-born adolescent MA had higher levels of selected parabens than USA-born adolescent OHISP, and OHISP adults born in another Spanish-speaking country had higher levels of selected parabens than USA-born OHISP adults. USA-born MA adults and seniors had higher levels of selected dichlorophenols than Mexico-born MA adults and seniors, respectively. Females had higher levels of selected PAH metabolites, EPHs, and PPs than males among children, adolescents, adults, and seniors, but the reverse was true for the levels of selected IUIs and PFAAs among adolescents and seniors. Smokers had higher levels of almost all PAH metabolites than non-smokers for adolescents, adults, and seniors. The same was true for urinary thiocynate for adolescents, adults, and seniors. OHISP is a multiracial multiethnic demographic group substantially different from MA with possibly

  13. Interactions between Glu-1 and Glu-3 loci and associations of selected molecular markers with quality traits in winter wheat (Triticum aestivum L.) DH lines.

    Science.gov (United States)

    Krystkowiak, Karolina; Langner, Monika; Adamski, Tadeusz; Salmanowicz, Bolesław P; Kaczmarek, Zygmunt; Krajewski, Paweł; Surma, Maria

    2017-02-01

    The quality of wheat depends on a large complex of genes and environmental factors. The objective of this study was to identify quantitative trait loci controlling technological quality traits and their stability across environments, and to assess the impact of interaction between alleles at loci Glu-1 and Glu-3 on grain quality. DH lines were evaluated in field experiments over a period of 4 years, and genotyped using simple sequence repeat markers. Lines were analysed for grain yield (GY), thousand grain weight (TGW), protein content (PC), starch content (SC), wet gluten content (WG), Zeleny sedimentation value (ZS), alveograph parameter W (APW), hectolitre weight (HW), and grain hardness (GH). A number of QTLs for these traits were identified in all chromosome groups. The Glu-D1 locus influenced TGW, PC, SC, WG, ZS, APW, GH, while locus Glu-B1 affected only PC, ZS, and WG. Most important marker-trait associations were found on chromosomes 1D and 5D. Significant effects of interaction between Glu-1 and Glu-3 loci on technological properties were recorded, and in all types of this interaction positive effects of Glu-D1 locus on grain quality were observed, whereas effects of Glu-B1 locus depended on alleles at Glu-3 loci. Effects of Glu-A3 and Glu-D3 loci per se were not significant, while their interaction with alleles present at other loci encoding HMW and LMW were important. These results indicate that selection of wheat genotypes with predicted good bread-making properties should be based on the allelic composition both in Glu-1 and Glu-3 loci, and confirm the predominant effect of Glu-D1d allele on technological properties of wheat grains.

  14. CDC Study Finds Fecal Contamination in Pools

    Science.gov (United States)

    ... Communication (404) 639-3286 CDC study finds fecal contamination in pools A study of public pools done ... The E. coli is a marker for fecal contamination. Finding a high percentage of E. coli-positive ...

  15. Evaluation of Physico-Chemical and Fungal Species Associated with Oil Contaminated Soil from Selected Automobile Garage in Sokoto Metropolis

    Directory of Open Access Journals (Sweden)

    Hassan Muhammad Maishanu

    2018-03-01

    Full Text Available This study was conducted with a view to evaluating the physicochemical and mycological properties of different oil contaminated soils collected from three different automobile garages in Sokoto Metropolis, and uncontaminated soil from the temporary site, Usmanu Danfodiyo University, Sokoto (UDUS was used as the control. The pH was determined using pH meter model Hanna (H1991301, quantity of mineral elements was evaluated in accordance with Murphy and Fungi were isolated from the three oil contaminated samples (A, B. and C and the uncontaminated (sample D as control, this was done by standard procedure using the method of P. Ren, T. Jankun & B. Leaderer. The physical, chemical, and mineral elements from the oil-contaminated soils of the three automobile garages and control. The results of particle soil analysis revealed the high content of sandy soil (96.2 to 87.3 and silt is the lowest with (2.5–0.6. Magnesium had the highest concentration of studied minerals, ranging from 193 to 649.2 mg/kg. while PH result revealed that the soil samples were pH value ranged from (16.85–16.20 in oil Contaminated samples, while the control had 15.90, and electrical conductivity ranged from 12.8–13.8 % and 28 % in control, four fungal isolates Aspergillus sp., Penicillum sp., Mucor sp. and Sporobolomyces sp. were identified based on colonial, sexual and morphological characteristics. These fungal strains can be used in bioremediation process and oil pollution reduction in aquatic ecosystems.

  16. Simultaneous removal of selected oxidized contaminants in groundwater using a continuously stirred hydrogen-based membrane biofilm reactor.

    Science.gov (United States)

    Xia, Siqing; Liang, Jun; Xu, Xiaoyin; Shen, Shuang

    2013-01-01

    A laboratory trial was conducted for evaluating the capability of a continuously stirred hydrogen-based membrane biofilm reactor to simultaneously reduce nitrate (NO(3-)-N), sulfate (SO4(2-)), bromate (BrO3-), hexavalent chromium (Cr(VI)) and parachloronitrobenzene (p-CNB). The reactor contained two bundles of hollow fiber membranes functioning as an autotrophic biofilm carrier and hydrogen pipe as well. On the condition that hydrogen was supplied as electron donor and diffused into water through membrane pores, autohydrogenotrophic bacteria were capable of reducing contaminants to forms with lower toxicity. Reduction occurred within 1 day and removal fluxes for NO(3-)-N, SO4(2-), BrO3-, Cr(VI), and p-CNB reached 0.641, 2.396, 0.008, 0.016 and 0.031 g/(day x m2), respectively after 112 days of continuous operation. Except for the fact that sulfate was 37% removed under high surface loading, the other four contaminants were reduced by over 95%. The removal flux comparison between phases varying in surface loading and H2 pressure showed that decreasing surface loading or increasing H2 pressure would promote removal flux. Competition for electrons occurred among the five contaminants. Electron-equivalent flux analysis showed that the amount of utilized hydrogen was mainly controlled by NO(3-)-N and SO4(2-) reduction, which accounted for over 99% of the electron flux altogether. It also indicated the electron acceptor order, showing that nitrate was the most prior electron acceptor while suIfate was the second of the five contaminants.

  17. Uptake and Effects of Six Rare Earth Elements (REEs on Selected Native and Crop Species Growing in Contaminated Soils.

    Directory of Open Access Journals (Sweden)

    David Carpenter

    Full Text Available Rare earth elements (REEs have become increasingly important metals used in modern technology. Processes including mining, oil refining, discarding of obsolete equipment containing REEs, and the use of REE-containing phosphate fertilizers may increase the likelihood of environmental contamination. However, there is a scarcity of information on the toxicity and accumulation of these metals to terrestrial primary producers in contaminated soils. The objective of this work was to assess the phytotoxicity and uptake from contaminated soil of six REEs (chloride forms of praseodymium, neodymium, samarium, terbium, dysprosium, and erbium on three native plants (Asclepias syriaca L., Desmodium canadense (L. DC., Panicum virgatum L. and two crop species (Raphanus sativus L., Solanum lycopersicum L. in separate dose-response experiments under growth chamber conditions. Limited effects of REEs were found on seed germination and speed of germination. Effects on aboveground and belowground biomass were more pronounced, especially for the three native species, which were always more sensitive than the crop species tested. Inhibition concentrations (IC25 and IC50 causing 25 or 50% reductions in plant biomass respectively, were measured. For the native species, the majority of aboveground biomass IC25s (11 out of 18 fell within 100 to 300 mg REE/kg dry soil. In comparison to the native species, IC25s for the crops were always greater than 400 mg REE/kg, with the majority of results (seven out of 12 falling above 700 mg REE/kg. IC50s were often not detected for the crops. Root biomass of native species was also affected at lower doses than in crops. REE uptake by plants was higher in the belowground parts than in the above-ground plant tissues. Results also revealed that chloride may have contributed to the sensitivity of the native species, Desmodium canadense, one of the most sensitive species studied. Nevertheless, these results demonstrated that

  18. Emerging contaminants in agricultural ecosystems: impact of selected pharmaceutical on water and soil ecology and pratical implications

    OpenAIRE

    Saccà, Maria Ludovica

    2010-01-01

    Pharmaceuticals are useful tools to prevent and treat human and animal diseases. Following administration, a significant fraction of pharmaceuticals is excreted unaltered into faeces and urine and may enter the aquatic ecosystem and agricultural soil through irrigation with recycled water, constituting a significant source of emerging contaminants into the environment. Understanding major factors influencing their environmental fate is consequently needed to value the risk, reduce contaminati...

  19. Accumulation of polycyclic aromatic hydrocarbons from creosote-contaminated soil in selected plants and the oligochaete worm Enchytraeus crypticus

    Energy Technology Data Exchange (ETDEWEB)

    Ann-Sofie Allard; Marianne Malmberg; Alasdair H. Neilson; Mikael Remberger [IVL, Stockholm (Sweden). Swedish Environmental Research Institute

    2005-07-01

    The accumulation of PAHs from a creosote-contaminated soil was examined in laboratory experiments using English ryegrass (Lolium perenne), white clover (Trifolium repens) and radish (Raphanus sativus), and the oligochaete worm Enchytraeus crypticus. Toxicity to the plants and the worms was assessed, and a soil sample mixed with calcined sand was used for accumulation experiments to avoid interference from toxicity in the soil. Accumulation of potentially carcinogenic PAHs varied among the plants, and there was a linear relation between concentrations of PAHs in the soil and in the plants. Correlations between values of the biota-soil accumulation factors and octanol-water partition coefficients, or water solubility varied among the plants and were rather weak, so that lipophilic character or water solubility of the PAHs alone cannot explain PAH accumulation. Accumulation of carcinogenic PAHs from the soil, in the presence of the other PAHs was greatest for Trifolium repens. PAHs were accumulated in the oligochaete worm (Enchytraeus crypticus), and biota-soil accumulation factors exceeded those for the plants. It is suggested that site-specific evaluation of contaminated sites should include not only chemical analysis and evaluation of toxicity but also accumulation of contaminants into biota such as plants and worms.

  20. MARCADORES RAPD PARA MAPEAMENTO GENÉTICO E SELEÇÃO DE HÍBRIDOS DE CITROS RAPD MARKERS TO GENETIC MAPPING AND SELECTION OF CITRUS HYBRIDS

    Directory of Open Access Journals (Sweden)

    ROBERTO PEDROSO DE OLIVEIRA

    2001-12-01

    Full Text Available Os marcadores moleculares apresentam várias aplicações no melhoramento de plantas, permitindo uma série de análises genéticas. Este trabalho foi realizado com o objetivo de estabelecer marcadores RAPD para serem utilizados em estudos de mapeamento genético e na seleção de híbridos entre tangerina-'Cravo' (Citrus reticulata Blanco e laranja-'Pêra' (C. sinensis (L. Osbeck. Extraiu-se DNA de folhas dos parentais e de seis híbridos F1. As reações de amplificação foram preparadas em 13 uL de solução, constituída por tampão 1x GIBCO BRL; soluções 1,54 mM de MgCl2 e 0,2 mM de cada dNTP; 15 ng de cada 'primer'; 1,5 unidade de 'Taq DNA Polymerase' e 15 ng de DNA genômico. As reações foram realizadas em termocicladores programados para 36 ciclos de 1 min a 92ºC, 1 min a 36ºC, 2 min a 72ºC e 10 min de extensão a 72ºC. Foram testados 'primers' decâmeros arbitrários dos 'kits' A, AB, AT, AV, B, C, D, E, G, H, M, N, P, Q, R e U da Operon, sendo selecionados 113 por apresentarem polimorfismo, com número de marcadores variando de 1 a 6 por 'primer'. Esses 'primers' amplificaram 201 (23,13% bandas polimórficas, aplicáveis no mapeamento genético e seleção de híbridos. A freqüência de 'primers' com 1; 2; 3; 4; 5 e 6 bandas polimórficas foi de 49,5%, 33,6%, 9,7%, 4,4%, 1,8% e 1,0%, respectivamente.Molecular markers have many applications in plant breeding, enabling some types of genetic analyses. The aim of this work was to establish RAPD markers to be used to genetic mapping studies and selection of hybrids between 'Cravo' tangerine (Citrus reticulata Blanco and 'Pêra' orange (C. sinensis (L. Osbeck. DNA of the parents and six hybrids F1 was isolated from the leaves. The amplification reactions were performed in volumes of 13 µL, composed by GIBCO BRL 1x buffer, 1,54 mM MgCl2, 0,2 mM of each dNTP, 15 ng of each primer, 1,5 unit of Taq DNA Polymerase and 15 ng of genomic DNA. These reactions were carried out in

  1. The orotate transporter oroP from Lactococcus lactis is required for orotate uptake and can be used both as a food-grade selection and counter-selection marker

    DEFF Research Database (Denmark)

    Defoor, Els Marie Celine; Martinussen, Jan

    The plasmid pDBORO conferred sensitivity of Lactococcus lactis towards 5´-Fluoroorotate. Moreover, by transformation, this plasmid was found to be essential for orotate dependent growth in a pyrimidine requiring strain. A single gene on pDBORO was required for growth on orotate, and was termed oro......P. Since the corresponding open reading frame, OroP showed the features of a membrane protein, OroP most likely is an orotate transporter. A number of strains like L. lactis and Bacillus subtilus have been shown to be unable to metabolize orotate. If the oroP gene was introduced into these strains......, they acquired the ability to utilize orotate. If the strains had a pyrimidine requirement, the oroP gene could function as a selectable marker when growing in the presence of orotate as sole pyrimidine source. In an otherwise resistant strain, oroP was shown to sensitize the strain towards the analog 5...

  2. The use of ion-selective membranes for the recovery of sulphuric acid out of contaminated solutions. Comparing electrodialysis, electro electrodialysis and diffusion dialysis

    International Nuclear Information System (INIS)

    Cattoir, S.

    1998-02-01

    The amount of waste arising from dismantled reactors is minimized by decontamination processes. These processes result in contaminated effluents, containing acid and metal salts. The quantity of final waste can be substantially reduced when the acid is extracted out of the decontamination effluents prior to neutralisation. This report discusses three membrane techniques for the displacement of acids out of mixed acid/salt solutions: electrodialysis (ED), electro electrodialysis (EED) and diffusion dialysis (DD). EED uses an electrical potential difference across an anion-selective membrane; DD uses a concentration difference across an anion-selective membrane; ED uses an electrical potential difference, across an anion- and a cation-selective membrane. EED can displace up to 90% of the sulphuric acid, the amount of metal ions in the displaced-acid solution is less than 1% of the ions in the original contaminated solution. Treatment costs are estimated to about 18 Belgian Francs per litre. In DD the purity of the displaced acid is comparable to EED. Treatment costs are about 21 Belgian Francs per litre. In ED 90% acid-displacement is easily reached, but 5% metal ions are also displaced. Treatment costs are about 6 Belgian Francs per litre. Therefore, in spite of the lower purity of the resulting acid, ED is economically speaking the best choice

  3. Effects of Wheat Naturally Contaminated with Fusarium Mycotoxins on Growth Performance and Selected Health Indices of Red Tilapia (Oreochromis niloticus × O. mossambicus)

    Science.gov (United States)

    Tola, Siriporn; Bureau, Dominique P.; Hooft, Jamie M.; Beamish, Frederick W. H.; Sulyok, Michael; Krska, Rudolf; Encarnação, Pedro; Petkam, Rakpong

    2015-01-01

    An 8-week feeding trial was conducted to examine effects of wheat naturally contaminated with Fusarium mycotoxins (deoxynivalenol, DON 41 mg·kg−1) on growth performance and selected health indices of red tilapia (Oreochromis niloticus × O. mossambicus; initial weight = 4.3 g/fish). Five experimental diets were formulated by replacement of clean wheat with naturally contaminated wheat resulting in graded levels of DON and zearalenone (ZEN) (Diet 1 0.07/0.01, Diet 2 0.31/0.09, Diet 3 0.50/0.21, Diet 4 0.92/0.37 and Diet 5 1.15/0.98 mg·kg−1). Groups of 50 fish were randomly allocated into each of 20 aquaria and fed to near-satiety for eight weeks. Growth rate, feed intake and feed efficiency of fish fed the experimental diets decreased linearly with increasing levels of Fusarium mycotoxins (p mycotoxins, especially DON, no biochemical and histopathological parameters measured in blood and liver appeared affected by Fusarium mycotoxin concentrations of diets (p > 0.05). Though there was no clear evidence of overt DON toxicity to red tilapia, it is recommended that feed ingredients should be screened for Fusarium mycotoxin contamination to ensure optimal growth performance. PMID:26035489

  4. Characterization of Carbon-Contaminated B4C-Coated Optics after Chemically Selective Cleaning with Low-Pressure RF Plasma.

    Science.gov (United States)

    Moreno Fernández, H; Rogler, D; Sauthier, G; Thomasset, M; Dietsch, R; Carlino, V; Pellegrin, E

    2018-01-22

    Boron carbide (B 4 C) is one of the few materials that is expected to be most resilient with respect to the extremely high brilliance of the photon beam generated by free electron lasers (FELs) and is thus of considerable interest for optical applications in this field. However, as in the case of many other optics operated at light source facilities, B 4 C-coated optics are subject to ubiquitous carbon contaminations. Carbon contaminations represent a serious issue for the operation of FEL beamlines due to severe reduction of photon flux, beam coherence, creation of destructive interference, and scattering losses. A variety of B 4 C cleaning technologies were developed at different laboratories with varying success. We present a study regarding the low-pressure RF plasma cleaning of carbon contaminated B 4 C test samples via inductively coupled O 2 /Ar, H 2 /Ar, and pure O 2 RF plasma produced following previous studies using the same ibss GV10x downstream plasma source. Results regarding the chemistry, morphology as well as other aspects of the B 4 C optical coating before and after the plasma cleaning are reported. We conclude that among the above plasma processes only plasma based on pure O 2 feedstock gas exhibits the required chemical selectivity for maintaining the integrity of the B 4 C optical coatings.

  5. Repression of fungal plant pathogens and fungal-related contaminants: Selected ecosystem services by soil fauna communities in agroecosystems

    Science.gov (United States)

    Meyer-Wolfarth, Friederike; Schrader, Stefan; Oldenburg, Elisabeth; Brunotte, Joachim; Weinert, Joachim

    2017-04-01

    In agroecosystems soil-borne fungal plant diseases are major yield-limiting factors which are difficult to control. Fungal plant pathogens, like Fusarium species, survive as a saprophyte in infected tissue like crop residues and endanger the health of the following crop by increasing the infection risk for specific plant diseases. In infected plant organs, these pathogens are able to produce mycotoxins. Mycotoxins like deoxynivalenol (DON) persist during storage, are heat resistant and of major concern for human and animal health after consumption of contaminated food and feed, respectively. Among fungivorous soil organisms, there are representatives of the soil fauna which are obviously antagonistic to a Fusarium infection and the contamination with mycotoxins. Specific members of the soil macro-, meso-, and microfauna provide a wide range of ecosystem services including the stimulation of decomposition processes which may result in the regulation of plant pathogens and the degradation of environmental contaminants. Investigations under laboratory conditions and in field were conducted to assess the functional linkage between soil faunal communities and plant pathogenic fungi (Fusarium culmorum). The aim was to examine if Fusarium biomass and the content of its mycotoxin DON decrease substantially in the presence of soil fauna (earthworms: Lumbricus terrestris, collembolans: Folsomia candida and nematodes: Aphelenchoides saprophilus) in a commercial cropping system managed with conservation tillage located in Northern Germany. The results of our investigations pointed out that the degradation performance of the introduced soil fauna must be considered as an important contribution to the biodegradation of fungal plant diseases and fungal-related contaminants. Different size classes within functional groups and the traits of keystone species appear to be significant for soil function and the provision of ecosystem services as in particular L. terrestris revealed to

  6. Phosphate effect on the content of selected elements in a lettuce variety grown at a contaminated soil

    International Nuclear Information System (INIS)

    Armelin, M.J.A.; Saiki, M.; Maihara, V.A.; Moreira, E.G.; Trevizam, A.R.; Muraoka, T.; Silva, M.L.S.

    2014-01-01

    The purpose of this study was to evaluate the efficiency of superphosphate fertilizer in remediating a contaminated soil with potentially toxic elements. For this, different phosphorus doses were used in a number of lettuce plants. The element concentrations determined in their leaves were compared with those found in control lettuce plants. Instrumental neutron activation analysis was the analytical technique used to determine element concentration in lettuce leave samples. The application of 250 mg kg -1 of P was the most effective treatment to reduce the concentrations of Br, Ca, Cd, Cl, Co, Cr, Fe, K, Mg, Mn, Sb and Zn in lettuce leaves. (author)

  7. AFLP and AMP Fingerprints as Markers to Evaluate Genetic Differences between Medicago truncatula Line Jemalong and 2HA, a New Line Produced by in vitro Culture Selection

    Directory of Open Access Journals (Sweden)

    R.R. Irwanto

    2008-09-01

    Full Text Available A new line, Medicago truncatula cv. Jemalong 2HA (herein known as 2HA has been developed via repetitive regeneration and selection of M. truncatula cv. Jemalong. During somatic embryogenesis, 2HA produces 500 times more embryos than its progenitor, Jemalong. It is interesting to study if those two lines are isogenic or has genetic differences. The main objectives of the study was to evaluate the genotypic differences between Jemalong and 2HA also to evaluate the methylation event in 2HA utilized two DNA fingerprinting techniques, i.e AFLP fingerprints (Amplified Length of Polymorphism and AMP (Amplified Methylation Polymorphism. The results showed that AFLP analysis using eight primers combinations could not detect any differences between Jemalong and 2HA. However, using AMP methylation sensitive primers it could detect 15 polymorphisms out of 840 markers. These results lead to a conclusion that Jemalong and 2HA are isogenic lines. 2HA may have higher regeneration capacities due to methylation process which occurs during the production of 2HA through repetitive regeneration cycles.

  8. SacB-SacR gene cassette as the negative selection marker to suppress Agrobacterium overgrowth in Agrobacterium-mediated plant transformation

    Directory of Open Access Journals (Sweden)

    Yiming Liu

    2016-10-01

    Full Text Available Agrobacterium overgrowth is a common problem in Agrobacterium-mediated plant transfor-mation. To suppress the Agrobacterium overgrowth, various antibiotics have been used during plant tissue culture steps. The antibiotics are expensive and may adversely affect plant cell differentiation and reduce plant transformation efficiency. The SacB-SacR proteins are toxic to most Agrobacterium tumefaciens strains when they are grown on culture medium sup¬plemented with sucrose. Therefore, SacB-SacR genes can be used as negative selection markers to suppress the overgrowth of Agrobacterium tumefaciens in the plant tissue culture process. We generated a mutant Agrobacterium tumefaciens strain GV2260 (recA-SacB/R that has the SacB-SacR cassette inserted into the bacterial genome at the recA gene locus. The mutant Agrobacterium strain is sensitive to sucrose but maintains its ability to transform plant cells in both transient and stable transformation assays. We demonstrated that the mutant strain GV2260 (recA-SacB/R can be inhibited by sucrose that reduces the overgrowth of Agrobacterium and therefore improves the plant transformation efficiency. We employed GV2260 (recA-SacB/R to generate stable transgenic N. benthamiana plants expressing a CRISPR-Cas9 for knocking out a WRKY transcrip¬tion factor.

  9. Antimicrobial Properties of Selected Copper Alloys on Staphylococcus aureus and Escherichia coli in Different Simulations of Environmental Conditions: With vs. without Organic Contamination

    Directory of Open Access Journals (Sweden)

    Anna Różańska

    2017-07-01

    Full Text Available Background: Hospital equipment made from copper alloys can play an important role in complementing traditional methods of disinfection. Aims of the study: The aim of this study was to assess the dynamics of the antimicrobial properties of selected copper alloys in different simulations of environmental conditions (with organic contamination vs. without organic contamination, and to test alternatives to the currently used testing methods. Materials and Methods: A modification of Japanese standard JIS Z 2801 as well as Staphylococcus aureus (SA and Escherichia coli (EC suspended in NaCl vs. tryptic soy broth (TSB were used in tests performed on seven commonly used copper alloys, copper, and stainless steel. Results: A much faster reduction of the bacterial suspension was observed for the inoculum prepared in NaCl than in TSB. A faster reduction for EC than for SA was observed in the inoculum prepared in NaCl. The opposite results were found for the inoculum based on TSB. A significant correlation between the copper concentration in the copper alloys and the time and degree of bacterial suspension reduction was only observed in the case of EC. Conclusions: This study confirmed the antimicrobial properties of copper alloys, and additionally showed that Staphylococcus aureus was more resistant than Escherichia coli in the variant of the experiment without organic contamination. However, even for SA, a total reduction of the bacterial inoculum’s density took no longer than 2 h. Under conditions simulating organic contamination, all of the tested alloys were shown to have bactericidal or bacteriostatic properties, which was contrary to the results from stainless steel.

  10. Antimicrobial Properties of Selected Copper Alloys on Staphylococcus aureus and Escherichia coli in Different Simulations of Environmental Conditions: With vs. without Organic Contamination.

    Science.gov (United States)

    Różańska, Anna; Chmielarczyk, Agnieszka; Romaniszyn, Dorota; Sroka-Oleksiak, Agnieszka; Bulanda, Małgorzata; Walkowicz, Monika; Osuch, Piotr; Knych, Tadeusz

    2017-07-20

    Background: Hospital equipment made from copper alloys can play an important role in complementing traditional methods of disinfection. Aims of the study: The aim of this study was to assess the dynamics of the antimicrobial properties of selected copper alloys in different simulations of environmental conditions (with organic contamination vs. without organic contamination), and to test alternatives to the currently used testing methods. Materials and Methods: A modification of Japanese standard JIS Z 2801 as well as Staphylococcus aureus (SA) and Escherichia coli (EC) suspended in NaCl vs. tryptic soy broth (TSB) were used in tests performed on seven commonly used copper alloys, copper, and stainless steel. Results: A much faster reduction of the bacterial suspension was observed for the inoculum prepared in NaCl than in TSB. A faster reduction for EC than for SA was observed in the inoculum prepared in NaCl. The opposite results were found for the inoculum based on TSB. A significant correlation between the copper concentration in the copper alloys and the time and degree of bacterial suspension reduction was only observed in the case of EC. Conclusions: This study confirmed the antimicrobial properties of copper alloys, and additionally showed that Staphylococcus aureus was more resistant than Escherichia coli in the variant of the experiment without organic contamination. However, even for SA, a total reduction of the bacterial inoculum's density took no longer than 2 h. Under conditions simulating organic contamination, all of the tested alloys were shown to have bactericidal or bacteriostatic properties, which was contrary to the results from stainless steel.

  11. Trace Element Concentration and Speciation in Selected Mining-Contaminated Soils and Water in Willow Creek Floodplain, Colorado

    Directory of Open Access Journals (Sweden)

    R. Burt

    2011-01-01

    Full Text Available Long-term mining activities in the mountains around Creede, Colorado have resulted in significant contamination in soils and water in the Willow Creek floodplain. Total major and trace were determined for soils and water and sequential chemical extraction for soils. Objectives were to determine concentrations and potential reactivity of trace elements and investigate their relationship with other soil and water properties. Water trace elements showed significant variability among sites, ranging from 347 to 12108 μg/L. Relative trend showed (Zn > Sr > Ba > (Mn > W > Cd > (Sn > V ≈ Ni ≈ Cu > Co > (Ag. Soil trace elements showed significant short-range spatial variability, ranging from 2819 to 19274 mg/kg. Relative trend showed (Pb ≈ Zn > Mn > Ba > P > (As > Cu > Sr > V > Cd > Sb ≈ Ag > (Co ≈ Cr > Mo ≈ Sn ≈ Ni > (Be ≈ W > Se ≈ Hg. Predominant fractions were oxide, specifically-sorbed/carbonate bound, and residual. Water soluble and exchangeable fractions showed (Zn ≈ Cd > Pb and Cd > Zn > Pb, respectively. Mobility factors for highly contaminated soils showed Cd ≈ Zn > Pb > Cu > As.

  12. Effects of selected soil properties on phytoremediation applicability for heavy-metal-contaminated soils in the Apulia region, Southern Italy.

    Science.gov (United States)

    Farrag, K; Senesi, N; Rovira, P Soler; Brunetti, G

    2012-11-01

    Phytoremediation is a well-known promising alternative to conventional approaches used for the remediation of diffused and moderated contaminated soils. The evaluation of the accumulation, availability, and interactions of heavy metals in soil is a priority objective for the possible use of phytoremediation techniques such as phytoextraction and phytostabilization. The soils used in this work were collected from a number of sites inside a protected area in the Apulia region (Southern Italy), which were contaminated by various heavy metals originated from the disposal of wastes of different sources of origin. Soils examined contained Cd, Cr, Cu, Ni, Pb, and Zn in amounts exceeding the critical limits imposed by EU and Italian laws. However, the alkaline conditions, high organic matter content, and silty to silty loamy texture of soils examined would suggest a reduced availability of heavy metals to plants. Due to the high total content but the low available fraction of heavy metals analyzed, especially Cr, phytoextraction appears not to be a promising remediation approach in the sites examined, whereas phytostabilization appears to be the best technique for metal decontamination in the studied areas.

  13. Use of a fractal-like gold nanostructure in surface-enhanced raman spectroscopy for detection of selected food contaminants.

    Science.gov (United States)

    He, Lili; Kim, Nam-Jung; Li, Hao; Hu, Zhiqiang; Lin, Mengshi

    2008-11-12

    The safety of imported seafood products because of the contamination of prohibited substances, including crystal violet (CV) and malachite green (MG), raised a great deal of concern in the United States. In this study, a fractal-like gold nanostructure was developed through a self-assembly process and the feasibility of using surface-enhanced Raman spectroscopy (SERS) coupled with this nanostructure for detection of CV, MG, and their mixture (1:1) was explored. SERS was capable of characterizing and differentiating CV, MG, and their mixture on fractal-like gold nanostructures quickly and accurately. The enhancement factor of the gold nanostructures could reach an impressive level of approximately 4 x 10(7), and the lowest detectable concentration for the dye molecules was at approximately 0.2 ppb level. These results indicate that SERS coupled with fractal-like gold nanostructures holds a great potential as a rapid and ultra-sensitive method for detecting trace amounts of prohibited substances in contaminated food samples.

  14. Analysis of arsenic speciation in mine contaminated lacustrine sediment using selective sequential extraction, HR-ICPMS and TEM

    International Nuclear Information System (INIS)

    Haus, Kelly L.; Hooper, Robert L.; Strumness, Laura A.; Mahoney, J. Brian

    2008-01-01

    In order to determine how As speciation in lacustrine sediment changes as a function of local conditions, sediment cores were taken from three lakes with differing hydrologic regimes and subjected to extensive chemical and TEM analysis. The lakes (Killarney, Thompson and Swan Lakes) are located within the Coeur d' Alene River system (northern Idaho, USA), which has been contaminated with trace metals and As, from over 100 a of sulfide mining. Previous analyses of these lakebed sediments have shown an extensive amount of contaminant metals and As associated with sub-μm grains, making them extremely difficult to analyze using standard methods (scanning electron microscopy, X-ray diffraction). Transmission electron microscopy offers great advantages in spatial resolution and can be invaluable in determining As speciation when combined with other techniques. Data indicate that because of differences in local redox conditions, As speciation and stability is dramatically different in these lakes. Killarney and Thompson Lakes experience seasonal water-level fluctuations due to drawdown on a downstream dam, causing changes in O 2 content in sediment exposed during drawdown. Swan Lake has relatively constant water levels as its only inlet is dammed. Consequently, Killarney and Thompson Lakes show an increase in labile As-bearing phases with depth, while Swan Lake data indicate stable As hosts throughout the sediment profile. Based on these observations it can be stated that As in lakebed sediments is much less mobile, and therefore less bioavailable, when water is kept at a constant level

  15. Analysis of arsenic speciation in mine contaminated lacustrine sediment using selective sequential extraction, HR-ICPMS and TEM

    Energy Technology Data Exchange (ETDEWEB)

    Haus, Kelly L. [Department of Geology, Phillips 157, University of Wisconsin - Eau Claire, Eau Claire, WI 54702-4004 (United States)], E-mail: khaus@vt.edu; Hooper, Robert L.; Strumness, Laura A.; Mahoney, J. Brian [Department of Geology, Phillips 157, University of Wisconsin - Eau Claire, Eau Claire, WI 54702-4004 (United States)

    2008-04-15

    In order to determine how As speciation in lacustrine sediment changes as a function of local conditions, sediment cores were taken from three lakes with differing hydrologic regimes and subjected to extensive chemical and TEM analysis. The lakes (Killarney, Thompson and Swan Lakes) are located within the Coeur d' Alene River system (northern Idaho, USA), which has been contaminated with trace metals and As, from over 100 a of sulfide mining. Previous analyses of these lakebed sediments have shown an extensive amount of contaminant metals and As associated with sub-{mu}m grains, making them extremely difficult to analyze using standard methods (scanning electron microscopy, X-ray diffraction). Transmission electron microscopy offers great advantages in spatial resolution and can be invaluable in determining As speciation when combined with other techniques. Data indicate that because of differences in local redox conditions, As speciation and stability is dramatically different in these lakes. Killarney and Thompson Lakes experience seasonal water-level fluctuations due to drawdown on a downstream dam, causing changes in O{sub 2} content in sediment exposed during drawdown. Swan Lake has relatively constant water levels as its only inlet is dammed. Consequently, Killarney and Thompson Lakes show an increase in labile As-bearing phases with depth, while Swan Lake data indicate stable As hosts throughout the sediment profile. Based on these observations it can be stated that As in lakebed sediments is much less mobile, and therefore less bioavailable, when water is kept at a constant level.

  16. EFFECT OF REACTIVE MATERIALS ON THE CONTENT OF SELECTED ELEMENTS IN INDIAN MUSTARD GROWN IN CR(VI-CONTAMINATED SOILS

    Directory of Open Access Journals (Sweden)

    Maja Radziemska

    2016-04-01

    Full Text Available Reactive materials represent a promising agent for environmental co-remediation. The research was aimed to determine the influence of hexavalent chromium in doses of 0, 25, 50, and 150 mg Cr(VI.kg-1 of soil as well as zero valent-iron, and lignite additives on the content of macroelements in the Indian mustard (Brassica juncea L.. The average accumulation of the analysed elements in Indian mustard grown in Cr(VI contaminated soil were found to follow the decreasing order Mg>Na>P>Ca>K. Soil contamination at 150 mg Cr(VI.kg-1 of soil led to the highest increase in magnesium, calcium, sodium, and potassium content in Indian mustard. The application of zero-valent iron had a positive influence on the average Na and K content of the tested plant. The application of lignite had a positive influence on the average magnesium, sodium and calcium content in the above-ground parts of the studied plant. In the non-amended treatments (without reactive materials, the increasing rates of chromium (VI had an explicitly positive effect on the content of phosphorous and sodium in Indian mustard.

  17. Toxocara (Nematoda: Ascaridida and Other Soil-Transmitted Helminth Eggs Contaminating Soils in Selected Urban and Rural Areas in the Philippines

    Directory of Open Access Journals (Sweden)

    Vachel Gay V. Paller

    2014-01-01

    Full Text Available The extent of contamination of soils with soil transmitted helminthes (STH eggs, particularly Toxocara, was determined in selected urban and rural towns of Laguna, Philippines. Soil samples were collected from public schools, house yards, and empty lots. Results revealed that, of the 1480 soil samples collected, 460 (31% were positive for STH eggs. Toxocara sp. was the most prevalent (77%, followed by Ascaris sp. (11%, hookworms/strongyles/free-living nematodes (7%, and Trichuris sp. (5%. Some soil physicochemical parameters were also determined and associated with Toxocara eggs prevalence and density in soil. Results revealed that Toxocara sp. eggs were most prevalent in less acidic, relatively high temperature and high moisture soil conditions. They were also prevalent in sandy, silty, and loamy soil textures but less prevalent in clayey. No significant differences were found between depth 1 (0–5 cm and depth 2 (6–10 cm. This study revealed that Toxocara sp. eggs are ubiquitous and the extent of contamination in soils from the selected towns of Laguna is relatively high. Hence, the data generated in this study can be used in promoting public awareness, particularly for pet owners and local health officials, for effective prevention and control of this parasitosis.

  18. Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-S1 with carcass and meat traits

    Science.gov (United States)

    Genetic markers in casein (CSN1S1) and thyroglobulin (TG) genes have previously been associated with fat distribution in cattle. Determining the nature of these genetic associations (additive, recessive, or dominant) has been difficult because both markers have small minor allele frequencies in mos...

  19. Preparation and application of novel selective and polar materials for sorptive extraction of emerging contaminants from environmental waters

    OpenAIRE

    Gilart Alzuria, Núria

    2014-01-01

    La present Tesi Doctoral té com a objectiu principal el desenvolupament de nous materials per a diferents tècniques d’extracció per sorció, com són l’extracció en fase sòlida i l’extracció mitjançant barres magnètiques agitadores. Ambdues tècniques van ser aplicades a la cromatografia de líquids seguida de l’espectroscòpia de masses en tàndem (LC-MS/MS) per a la determinació de diversos contaminants orgànics considerats com emergents, com són fàrmacs, drogues d’abús i productes d’higiene pers...

  20. Effects of earthworm (Eisenia fetida) and wheat (Triticum aestivum) straw additions on selected properties of petroleum-contaminated soils.

    Science.gov (United States)

    Callaham, Mac A; Stewart, Arthur J; Alarcón, Clara; McMillen, Sara J

    2002-08-01

    Current bioremediation techniques for petroleum-contaminated soils are designed to remove contaminants as quickly and efficiently as possible, but not necessarily with postremediation soil biological quality as a primary objective. To test a simple postbioremediation technique, we added earthworms (Eisenia fetida) or wheat (Triticum aestivum) straw to petroleum land-farm soil and measured biological quality of the soil as responses in plant growth, soil respiration, and oil and grease (O&G) and total petroleum hydrocarbon (TPH) concentrations. Results indicated that plant growth was greater in earthworm-treated land-farm soil. Furthermore, addition of wheat straw resulted in greater total respiration in all soils tested (land-farm soil, noncontaminated reference soil, and a 1:1 mixture of land-farm and reference soils). We observed a 30% increase in soil respiration in straw-amended oily soil, whereas respiration increased by 246% in straw-amended reference soil. Much of the difference between oily and reference soils was attributable to higher basal respiration rates of nonamended oily soil compared to nonamended reference soil. Addition of earthworms resulted in greater total respiration of all soil and straw treatments except two (the land-farm and the 1:1 mixture soil treatments without straw). Straw and earthworm treatments did not affect O&G or TPH concentrations. Nevertheless, our findings that earthworm additions improved plant growth and that straw additions enhanced microbial activity in land-farm soil suggest that these treatments may be compatible with plant-based remediation techniques currently under evaluation in field trials, and could reduce the time required to restore soil ecosystem function.

  1. [The study of the contamination and the levels of Campylobacter spp. during the processing of selected types of foods].

    Science.gov (United States)

    Efimochkina, N R; Bykova, I B; Stetsenko, V V; Minaeva, L P; Pichugina, T V; Markova, Yu M; Korotkevich, Yu V; Kozak, S S; Sheveleva, S A

    2016-01-01

    The purpose of the work was to study the nature of the Campylobacter spp. contamination during the processing of food products of plant and animal origin (raw poultry and beef meat, raw milk, leafy salads, sliced raw vegetables). In the study of 148 samples 50 strains of Campylobacter spp. (33.8%) were found. For the main phenotypic characteristics they were identified as C. jejuni spp. jejuni and C. jejuni spp. doylei (over 75%). The highest level of detection of campylobacteria (over 45%) was set for raw poultry, including the carcasses of chickens broilers, quails, turkeys and their semi-finished products. 19 of the 27 strains from poultry were identified as C. jejuni. Among the strains isolated from the environment, including swabs from equipment surfaces, 91% of the isolates were also presented by C. jejuni. It was found that the investigated foodstuffs were characterized by high levels of contamination with bacteria of the family Enterobacteriaceae, the content of which was comparable with the identified values of total viable bacteria (cfu). Salmonella was detected in 19% of the investigated poultry samples and in 14.3% of raw cow milk. In the study of swabs from surfaces of poultry processing equipment, the frequency of detection of Campylobacter strains was 38.7%, Salmonella - 12.9%. Most commonly Campylobacter and Salmonella were detected in the zones of primary processing of poultry: the frequency of isolation of Salmonella in slaughter corner was 25%, Campylobacter - 43%. When testing the swabs taken in the cooking zone of «fast food» restaurants Campylobacter and Salmonella were not detected. For studying the swabs from equipment surfaces and the environment for the presence of Campylobacter spp. a modified technique of sampling was developed. The method includes a comprehensive analysis in the test area with the use of three types of media for transportation and incubation of Campylobacter spp. (Preston broth with blood, Brucella broth, Cary

  2. Selected Fe and Mn (nano)oxides as perspective amendments for the stabilization of As in contaminated soils.

    Science.gov (United States)

    Michálková, Zuzana; Komárek, Michael; Veselská, Veronika; Číhalová, Sylva

    2016-06-01

    An amorphous Mn oxide (AMO), nanomaghemite, and nanomagnetite were used as potential amendments reducing the mobility of As in three contrasting contaminated soils differing in origin of As contamination. Adsorption experiments and XPS analyses combined with incubation batch experiments and pH-static leaching tests were used. The AMO showed excellent adsorption capacity for As(V) reaching a maximum of 1.79 mmol g(-1) at pH 7 and 8. Interestingly, the adsorption capacity in this case decreases with decreasing pH, probably as a result of AMO dissolution at lower pH values. Chemical sorption of As(V) onto AMO was further confirmed with XPS. Both Fe nano-oxides proved the highest adsorption capacity at pH 4 reaching 11 mg g(-1) of adsorbed As(V). The AMO was also the most efficient amendment for decreasing As concentrations in soil solutions during 8 weeks of incubation. Additionally, pH-static leaching tests were performed at pH 4, 5, 6, 7, and natural pH (not adjusted) and AMO again proved the highest ability to decrease As content in leachate. On the other hand, strong dissolution of this amendment at lower pH values (especially pH 4) was observed. For that reason, AMO appears as a promising stabilizing agent for As, especially in neutral, alkaline, or slightly acidic soils, where As(V) species are expected to be more mobile.

  3. Plasma concentration of selected biochemical markers of endothelial dysfunction in women with various severity of chronic venous insufficiency (CVI-A pilot study.

    Directory of Open Access Journals (Sweden)

    Magdalena Budzyń

    Full Text Available Although the endothelial dysfunction is considered to be implicated in the pathogenesis of chronic venous insufficiency (CVI the endothelial status in patients with venous disorders is still not fully evaluated. Therefore the aim of the study was to measure the concentration of selected markers of endothelial dysfunction: von Willebrand factor (vWf, soluble P-selectin (sP-selectin, soluble thrombomodulin (sTM and soluble VE-cadherin (sVE-cadherin in CVI women who constitute the most numerous group of patients suffering from venous disease.Forty four women with CVI were involved in the study and divided into subgroups based on CEAP classification. Concentration of vWf, sP-selectin, sTM and sVE-cadherin were measured and compared with those obtained in 25 healthy age and sex-matched women.It was found that the concentration of sTM increased and sVEcadherin decreased along with disease severity in CVI women. A significant rise of sTM was observed especially in CVI women, with the highest inflammation status reflected by hsCRP or elastase concentration, and in CVI women with a high oxidative stress manifested by an increased plasma MDA. A significant fall of circulating sVE-cadherin was reported in CVI women with moderate to highest intensity of inflammation and oxidative stress. There was no change in vWF and sP-selectin concentration at any stage of CVI severity.The results of the present study demonstrate the presence of endothelial dysfunction in women suffering from CVI which seems to progress with the disease severity and may be associated with inflammation and enhanced oxidative stress.

  4. Tumors markers

    International Nuclear Information System (INIS)

    Yamaguchi-Mizumoto, N.H.

    1989-01-01

    In order to study blood and cell components alterations (named tumor markers) that may indicate the presence of a tumor, several methods are presented. Aspects as diagnostic, prognostic, therapeutic value and clinical evaluation are discussed. (M.A.C.)

  5. Behavior of nine selected emerging trace organic contaminants in an artificial recharge system supplemented with a reactive barrier.

    Science.gov (United States)

    Valhondo, Cristina; Carrera, Jesús; Ayora, Carlos; Barbieri, Manuela; Nödler, Karsten; Licha, Tobias; Huerta, Maria

    2014-10-01

    Artificial recharge improves several water quality parameters, but has only minor effects on recalcitrant pollutants. To improve the removal of these pollutants, we added a reactive barrier at the bottom of an infiltration basin. This barrier contained aquifer sand, vegetable compost, and clay and was covered with iron oxide dust. The goal of the compost was to sorb neutral compounds and release dissolved organic carbon. The release of dissolved organic carbon should generate a broad range of redox conditions to promote the transformation of emerging trace organic contaminants (EOCs). Iron oxides and clay increase the range of sorption site types. In the present study, we examined the effectiveness of this barrier by analyzing the fate of nine EOCs. Water quality was monitored before and after constructing the reactive barrier. Installation of the reactive barrier led to nitrate-, iron-, and manganese-reducing conditions in the unsaturated zone below the basin and within the first few meters of the saturated zone. Thus, the behavior of most EOCs changed after installing the reactive barrier. The reactive barrier enhanced the removal of some EOCs, either markedly (sulfamethoxazole, caffeine, benzoylecgonine) or slightly (trimethoprim) and decreased the removal rates of compounds that are easily degradable under aerobic conditions (ibuprofen, paracetamol). The barrier had no remarkable effect on 1H-benzotriazole and tolyltriazole.

  6. Selection and Evaluation of Indexes Commonly Used to Determine Contamination with T-2 Toxin in Pacific White Shrimp Litopenaeus vannamei by the Grey Relational Method.

    Science.gov (United States)

    Lu, Pengli; Wang, Yaling; Dai, Zhe; Sun, Lijun; Xu, Defeng; Liu, Ying; Ye, Riying; Gooneratne, Ravi; Bi, Siyuan

    2017-09-01

    The objectives of the present study were to evaluate the effects of different concentrations of the mycotoxin T-2 toxin in feed on muscle performance in the Pacific white shrimp Litopenaeus vannamei, evaluate indexes of physiological variables that indicate T-2 toxin contamination in the shrimp using the grey relational method, and determine the dose-response relationships between T-2 toxin and the indexes. Of the 6 physical, 7 biochemical, and 17 nutritional indexes examined, the values of the grey relational coefficients were highest for the hepatopancreas: body weight ratio (HBR), alanine aminotransferase (ALT) activity, and serine (SER) content (0.83, 0.68, and 0.82, respectively). Therefore, the HBR, ALT activity, and SER content were selected as appropriate indexes for contamination of Pacific white shrimp muscle with T-2 toxin. Based on their dose-response relationship curves, mean effective doses of 1.45, 1.69, and 1.33 mg of T-2 toxin/kg of feed were obtained for the HBR, ALT activity, and SER content, respectively. These results offer technical reference points for the evaluation and control of T-2 toxin in shrimp feed. Received April 28, 2016; accepted April 9, 2017.

  7. Occurrence of and trends in selected sediment-associated contaminants in Caddo Lake, East Texas, 1940-2002

    Science.gov (United States)

    Wilson, Jennifer T.

    2003-01-01

    Bottom-sediment cores were collected from four sites in Caddo Lake in East Texas during May 2002 for analyses of radionuclides (for age dating), organochlorine pesticides, polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and major and trace elements, and to describe the occurrence and trends of these sediment-associated contaminants. The Goose Prairie Creek and Harrison Bayou sites receive drainage from an area that includes parts of the now-closed Longhorn Army Ammunitions Plant. The mid-lake site is relatively close to dense oil and gas operations in the lake. The Carter Lake site receives minimal discharge from developed areas. Sediment age (deposition) dates represented in the cores ranged from 1940 to 2002. The only organochlorine compounds detected in all core samples were the DDT degradation products DDE or DDD, and PCB Aroclors 1242, 1254, and 1260 were detected only at the Goose Prairie Creek site. One or more of the DDE concentrations at all sites exceeded a consensus-based threshold effect concentration (on benthic biota), but none exceeded a consensus-based probable effect concentration. The Goose Prairie Creek site had significant downward trends in concentrations of organochlorine compounds, except for no trend in DDE concentrations. The Ammunitions Plant is a possible historical source of the few organochlorine compounds detected at the Goose Prairie Creek and Harrison Bayou sites. PAH concentrations at all sites were below respective threshold effect concentrations. Highest PAH concentrations at all four sites were of C2- alkylated naphthalenes. Nearly all statistically significant PAH trends in the cores were downward. On the basis of PAH source-indicator ratios, the majority of PAH compounds appear to have originated from uncombusted sources such as leaks or spills from oil and gas operations or vehicles (automobiles, boats, aircraft) in the Caddo Lake area. Concentrations of several of the eight trace elements with

  8. The Swift Turbidity Marker

    Science.gov (United States)

    Omar, Ahmad Fairuz; MatJafri, Mohd Zubir

    2011-01-01

    The Swift Turbidity Marker is an optical instrument developed to measure the level of water turbidity. The components and configuration selected for the system are based on common turbidity meter design concepts but use a simplified methodology to produce rapid turbidity measurements. This work is aimed at high school physics students and is the…

  9. Sustainable nitrate-contaminated water treatment using multi cycle ion-exchange/bioregeneration of nitrate selective resin.

    Science.gov (United States)

    Ebrahimi, Shelir; Roberts, Deborah J

    2013-11-15

    The sustainability of ion-exchange treatment processes using high capacity single use resins to remove nitrate from contaminated drinking water can be achieved by regenerating the exhausted resin and reusing it multiple times. In this study, multi cycle loading and bioregeneration of tributylamine strong base anion (SBA) exchange resin was studied. After each cycle of exhaustion, biological regeneration of the resin was performed using a salt-tolerant, nitrate-perchlorate-reducing culture for 48 h. The resin was enclosed in a membrane to avoid direct contact of the resin with the culture. The results show that the culture was capable of regenerating the resin and allowing the resin to be used in multiple cycles. The concentrations of nitrate in the samples reached a peak in first 0.5-1h after placing the resin in medium because of desorption of nitrate from resin with desorption rate of 0.099 ± 0.003 hr(-1). After this time, since microorganisms began to degrade the nitrate in the aqueous phase, the nitrate concentration was generally non-detectable after 10h. The average of calculated specific degradation rate of nitrate was -0.015 mg NO3(-)/mg VSS h. Applying 6 cycles of resin exhaustion/regeneration shows resin can be used for 4 cycles without a loss of capacity, after 6 cycles only 6% of the capacity was lost. This is the first published research to examine the direct regeneration of a resin enclosed in a membrane, to allow reuse without any disinfection or cleaning procedures. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Population data on D6S2879 and D6S2806 markers located at HLA-DRB1 region in the Iranians: Identifying the signatures of balancing and directional selection

    Directory of Open Access Journals (Sweden)

    Mansoureh Tajadod

    2011-12-01

    Full Text Available In this study, the genetic diversity and neutrality test for the MHC microsatellite loci, D6S2879 and D6S2806, located within the HLA-DRB1 gene region, were investigated. The genotyping data from 73 unrelated individuals were analyzed for Shannon index, the effective allele number of the markers and neutrality test by use of PyPop and Popgene32 programs. The Shannon index for D6S2879 and D6S2806 markers in the studied population was 1.0372 and 0.8601, respectively. The Fnd value computed for D6S2879 and D6S2806 markers were also estimated -0.8449 and 0.9904, respectively. The results obtained from Ewens-Watterson test indicated that D6S2879 and D6S2806 markers were under balancing and directional selection in the Iranian populations, respectively. The data suggested the presence of a selection force on HLA-DRB1 gene region in the Iranian populations.

  11. Atmospheric contamination

    International Nuclear Information System (INIS)

    Gruetter, Juerg

    1997-01-01

    It is about the levels of contamination in center America, the population's perception on the problem, effects of the atmospheric contamination, effects in the environment, causes of the atmospheric contamination, possibilities to reduce the atmospheric contamination and list of Roeco Swisscontac in atmospheric contamination

  12. The pht4;1-3 mutant line contains a loss of function allele in the Fatty Acid Desaturase 7 gene caused by a remnant inactivated selection marker-a cautionary tale.

    Science.gov (United States)

    Nilsson, Anders K; Andersson, Mats X

    2017-01-01

    A striking and unexpected biochemical phenotype was found in an insertion mutant line in the model plant Arabidopsis thaliana . One of two investigated insertion mutant lines in the gene encoding the phosphate transporter PHT4;1 demonstrated a prominent loss of trienoic fatty acids, whereas the other insertion line was indistinguishable from wild type in this aspect. We demonstrate that the loss of trienoic fatty acids was due to a remnant inactive negative selection marker gene in this particular transposon tagged line, pht4;1-3 . This constitutes a cautionary tale that warns of the importance to confirm the loss of this type of selection markers and the importance of verifying the relationship between a phenotype and genotype by more than one independent mutant line or alternatively genetic complementation.

  13. Risk Assessment of Heavy Metals Contamination in Soils and Selected Crops in Zanjan Urban and Industrial Regions

    Directory of Open Access Journals (Sweden)

    A. Afshari

    2016-02-01

    Full Text Available Introduction: Heavy metals are types of elements naturally present in soil or enter into soil as a result of human activities. The most important route of exposure to heavy metals is daily intake of food. Crops grown in contaminated soil (due to mining activities, industrial operations and agriculture may contain high concentrations of heavy metals. Also closeness to cities and industrial centers can have a great influence on the accumulation of heavy metals to agricultural products grown in the region. The study aimed to determine the concentration of heavy metals in soil and agricultural products around urban and industrial areas of Zanjan province (North West of Iran and consumption hazard probability. Materials and Methods: Soil (75 samples of soil from a depth of 0 to 10 cm and plant (101 samples samples, in the summer 2011, were randomly taken from industrial areas as follow: tomatoes (Lycopersicum esculentum M, wheat seed (Triticum vulgare, barley seeds (Hordeum vulgare, alfalfa shoots (Medicago sativa L., potato tubers (Solanumtuberosum L., apple fruit, vegetables and fruits such as Dill (Aniethum graveolens L., leek (Allium porrum L., Gardencress (Barbara verna L. and basil (Ocimum basilicum L.. Plant samples were then washed with distilled water, oven dried for48 hours at a temperature of 70 ´C until constant weight was attained and then they digested using 2 M hydrochloric acid (HCl and nitric acid digestion in 5 M. Concentrations of heavy metals in the soil and crops were determined by atomic absorption spectrometry. DTPA extraction of metals by Lindsay and Norvell (1978 method and sequential extraction method by Tessier et al. (1979 were performed. Statistical analysis was accomplished using the software SPSS 16.0 and the comparison of mean values was done using the Duncan test at the 5% level of significance. Results and Discussion: The magnitude of variations for total copper was from 11.5 to 352.5 (average 52.4, zinc was from 96

  14. Changes in proliferating and apoptotic markers of leiomyoma following treatment with a selective progesterone receptor modulator or gonadotropin-releasing hormone agonist.

    Science.gov (United States)

    Yun, Bo Seong; Seong, Seok Ju; Cha, Dong Hyun; Kim, Ji Yeon; Kim, Mi-La; Shim, Jeong Yun; Park, Ji Eun

    2015-08-01

    To evaluate changes in proliferating and apoptotic markers of myoma tissue from patients treated with a selective progesterone receptor modulator (SPRM) or GnRH agonist by measuring expression of PDGF-A mRNA, IGF-1 mRNA, bcl-2 mRNA, and PCNA and caspase-3 protein. Between December 2013 and July 2014, women with symptomatic leiomyoma were divided into control (no treatment before surgery), SPRM (treatment with ulipristal acetate [SPRM] for 3 months before surgery), and GnRHa (treatment with leuprolide acetate [GnRH agonist] for 3 months before surgery) groups. Tissue specimens were collected from the myoma core and normal myometrium of all patients. The expression of mRNA and protein was assessed by quantitative real-time reverse transcriptase-polymerase chain reaction and Western blot. A total of 38 patients were enrolled (control group, n=14; SPRM group, n=13; GnRHa group, n=11). PDGF-A mRNA expression was lower in both the myoma core and normal myometrium tissues of the SPRM compared with the control group, but there was no difference between the control and GnRHa group. There were also no group differences in bcl-2 mRNA or IGF-1 mRNA expression. Both PCNA and caspase-3 protein expression were higher in the leiomyoma tissue of the SPRM compared with the control group, but there was no difference between the control and GnRHa groups in the expression of either protein. Both proliferation and apoptosis were increased in the leiomyoma of patients after SPRM treatment, but there was no change following GnRH agonist treatment, in vivo. However, PDGF-A mRNA was decreased after SPRM treatment, indicating a dual effect of progesterone on the regulation of growth factors. Furthermore, there was an increase in caspase-3 protein, but not bcl-2 mRNA, expression in the SPRM group suggesting that SPRM may exert its effects in pathways other than the bcl-2 apoptotic pathway. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  15. Oribatid communities and heavy metal bioaccumulation in selected species associated with lichens in a heavily contaminated habitat.

    Science.gov (United States)

    Skubała, Piotr; Rola, Kaja; Osyczka, Piotr

    2016-05-01

    The study examines oribatid communities and heavy metal bioaccumulation in selected species associated with different microhabitats of a post-smelting dump, i.e. three lichen species of Cladonia with various growth forms and the slag substrate. The abundance of oribatids collected from the substrate was significantly lower than observed in lichen thalli. The morphology and chemical properties of lichens, and to some extent varying concentrations of heavy metals in thalli, are probably responsible for significant differences in oribatid communities inhabiting different Cladonia species. Some oribatids demonstrate the ability to accumulate zinc and cadmium with unusual efficiency, whereas lead is the most effectively regulated element by all species. A positive correlation was found between Zn content in all studied oribatids and their microhabitats. Oribatids exploring different food resources, i.e. fungivorous and non-fungivorous grazers, show considerable differences in bioconcentrations of certain elements.

  16. Examination of radioactive contamination in the soil-plant system and their transfer to selected animal tissues

    International Nuclear Information System (INIS)

    Chibowski, S.; Gladysz, A.

    1999-01-01

    This paper investigates gamma emitter radioactivity in a system consisting of soil and plants. Some selected sample of tissues of animals fed with the plants from these sites were also measured. In soil and plant samples artificial ( 137 Cs and 134 Cs) and natural (thorium and uranium series) isotopes were detected. Despite the relatively high content of the natural isotopes in plants and their seeds, their accumulation in animal tissues was not detected.The 40 K isotope was transferred in the chain soil-plant-animal in the highest degree. From the group of the natural isotopes, only 212 Pb was detected in examined animal tissue samples. Other natural isotopes were below detection level. In the samples heavy metal content was also examined. In any sample no element concentration was noticed above trade acceptable limit. (author)

  17. An evaluation of remote sensing technologies for the detection of fugitive contamination at selected Superfund hazardous waste sites in Pennsylvania

    Science.gov (United States)

    Slonecker, E. Terrence; Fisher, Gary B.

    2014-01-01

    This evaluation was conducted to assess the potential for using both traditional remote sensing, such as aerial imagery, and emerging remote sensing technology, such as hyperspectral imaging, as tools for postclosure monitoring of selected hazardous waste sites. Sixteen deleted Superfund (SF) National Priorities List (NPL) sites in Pennsylvania were imaged with a Civil Air Patrol (CAP) Airborne Real-Time Cueing Hyperspectral Enhanced Reconnaissance (ARCHER) sensor between 2009 and 2012. Deleted sites are those sites that have been remediated and removed from the NPL. The imagery was processed to radiance and atmospherically corrected to relative reflectance with standard software routines using the Environment for Visualizing Imagery (ENVI, ITT–VIS, Boulder, Colorado) software. Standard routines for anomaly detection, endmember collection, vegetation stress, and spectral analysis were applied.

  18. Selecting chemical and ecotoxicological test batteries for risk assessment of trace element-contaminated soils (phyto)managed by gentle remediation options (GRO).

    Science.gov (United States)

    Kumpiene, Jurate; Bert, Valérie; Dimitriou, Ioannis; Eriksson, Jan; Friesl-Hanl, Wolfgang; Galazka, Rafal; Herzig, Rolf; Janssen, Jolien; Kidd, Petra; Mench, Michel; Müller, Ingo; Neu, Silke; Oustriere, Nadège; Puschenreiter, Markus; Renella, Giancarlo; Roumier, Pierre-Hervé; Siebielec, Grzegorz; Vangronsveld, Jaco; Manier, Nicolas

    2014-10-15

    During the past decades a number of field trials with gentle remediation options (GRO) have been established on trace element (TE) contaminated sites throughout Europe. Each research group selects different methods to assess the remediation success making it difficult to compare efficacy between various sites and treatments. This study aimed at selecting a minimum risk assessment battery combining chemical and ecotoxicological assays for assessing and comparing the effectiveness of GRO implemented in seven European case studies. Two test batteries were pre-selected; a chemical one for quantifying TE exposure in untreated soils and GRO-managed soils and a biological one for characterizing soil functionality and ecotoxicity. Soil samples from field studies representing one of the main GROs (phytoextraction in Belgium, Sweden, Germany and Switzerland, aided phytoextraction in France, and aided phytostabilization or in situ stabilization/phytoexclusion in Poland, France and Austria) were collected and assessed using the selected test batteries. The best correlations were obtained between NH4NO3-extractable, followed by NaNO3-extractable TE and the ecotoxicological responses. Biometrical parameters and biomarkers of dwarf beans were the most responsive indicators for the soil treatments and changes in soil TE exposures. Plant growth was inhibited at the higher extractable TE concentrations, while plant stress enzyme activities increased with the higher TE extractability. Based on these results, a minimum risk assessment battery to compare/biomonitor the sites phytomanaged by GROs might consist of the NH4NO3 extraction and the bean Plantox test including the stress enzyme activities. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Method for selectively removing fluorine and fluorine-containing contaminants from gaseous UF/sub 6/. [ClF/sub 3/

    Science.gov (United States)

    Jones, R.L.; Otey, M.G.; Perkins, R.W.

    1980-11-24

    This invention is a method for effecting preferential removal and immobilization of certain gaseous contaminants from gaseous UF/sub 6/. The contaminants include fluorine and fluorides which are more reactive with CaCO/sub 3/ than is UF/sub 6/. The method comprises contacting the contaminant-carrying UF/sub 6/ with particulate CaCO/sub 3/ at a temperature effecting reaction of the contaminant and the CaCO/sub 3/.

  20. Determination of contaminants in boric acid used as neutron moderator by means of ion chromatography and selective electrodes

    International Nuclear Information System (INIS)

    Pires, M.A.F.; Abrao, A.

    1988-07-01

    The boric acid used as neutron moderator in reactors must observe restrictions about the concentration of some impurities. According to Westinghouse (1) specification, the highest limits for sodium, sulphate, phosphate, fluoride, and chlorine are: Na + - 0,003%; SO 4 -2 - 0,0006%; PO 4 -3 - 0,003%; F - - 0,00002%; Cl - - 0,00004%. This paper describes the determination of ions above mentioned directly in the boric acid solution. The sample is dissolved in water or in an appropriate eluent and is injected in the ion chromatograph. Na + and F - are determined by means of selective electrodes. The determination limits found for F - (0,0002%) and Cl - (0,0002%) are not sufficiently low to attent the specifications. The determination limits found for SO 4 -2 (0,0005%), PO 4 -3 (0,0003%) and Na + (0,0005%) are good enough for nuclear pure boric acid analysis. In some samples nitrate (detection limit 0,0015%) was found as well. Boric acid from different suppliers were analysed. (author) [pt

  1. (SSR) markers

    African Journals Online (AJOL)

    acer

    2013-06-26

    Jun 26, 2013 ... analysis was in general agreement with PCoA in discrimi- nating the cultivars. Conclusions. Estimation of morphological diversity may provide addi- tional information on the present finding. Nonetheless, the 29 SSR markers provided considerable genetic reso- lution and this genetic diversity analysis ...

  2. (SSR) markers

    African Journals Online (AJOL)

    SAM

    2014-07-30

    Jul 30, 2014 ... India and the country is currently the leading producer, consumer and exporter of ... registration with the competent authority for plant variety protection. Conventionally ... detection of duplicates, parental verification in crosses, gene tagging in .... allelic patterns as revealed by the current set of SSR markers.

  3. Marker lamps

    International Nuclear Information System (INIS)

    Watkins, D.V.

    1980-01-01

    A marker lamp is described which consists of a block of transparent plastics material encapsulated in which is a radioactive light source. These lights comprise a small sealed glass capsule, the hollow inside surface of which is coated with phosphor and which contains tritium or similar radioactive gas. The use of such lamps for identification marking of routes, for example roads, and for identification of underwater oil pipelines is envisaged. (U.K.)

  4. The long-term effect of zinc soil contamination on selected free amino acids playing an important role in plant adaptation to stress and senescence.

    Science.gov (United States)

    Pavlíková, Daniela; Zemanová, Veronika; Procházková, Dagmar; Pavlík, Milan; Száková, Jiřina; Wilhelmová, Naďa

    2014-02-01

    Increased endogenous plant cytokinin (CK) content through transformation with an isopentyl transferase (ipt) gene has been associated with improved plant stress tolerance. The objective of this study is to determine amino acid changes associated with elevated CK production in ipt transgenic tobacco (Nicotiana tabacum L., cv. Wisconsin 38). Nontransformed (WT) and transformed tobacco plants with ipt gene controlled by senescence-activated promoter (SAG) were exposed to zinc soil contamination (tested levels Zn1=250, Zn2=500, Zn3=750 mg kg(-1) soil). The Zn effect on plant stress metabolism resulted in changes in levels of selected free amino acids playing an important role in adaptation to stress and plant senescence (alanine, leucine, proline, methionine and γ-aminobutyrate) and differed for transformed and nontransformed tobacco plants. Analyses of amino acids confirmed that SAG tobacco plants had improved zinc tolerance compared with the WT plants. The enhanced Zn tolerance of SAG plants was associated with the maintenance of accumulation of proline, methionine and γ-aminobutyrate. The concentrations of leucine and alanine did not show significant differences between plant lines. © 2013 Published by Elsevier Inc.

  5. Marker Detection in Aerial Images

    KAUST Repository

    Alharbi, Yazeed

    2017-04-09

    The problem that the thesis is trying to solve is the detection of small markers in high-resolution aerial images. Given a high-resolution image, the goal is to return the pixel coordinates corresponding to the center of the marker in the image. The marker has the shape of two triangles sharing a vertex in the middle, and it occupies no more than 0.01% of the image size. An improvement on the Histogram of Oriented Gradients (HOG) is proposed, eliminating the majority of baseline HOG false positives for marker detection. The improvement is guided by the observation that standard HOG description struggles to separate markers from negatives patches containing an X shape. The proposed method alters intensities with the aim of altering gradients. The intensity-dependent gradient alteration leads to more separation between filled and unfilled shapes. The improvement is used in a two-stage algorithm to achieve high recall and high precision in detection of markers in aerial images. In the first stage, two classifiers are used: one to quickly eliminate most of the uninteresting parts of the image, and one to carefully select the marker among the remaining interesting regions. Interesting regions are selected by scanning the image with a fast classifier trained on the HOG features of markers in all rotations and scales. The next classifier is more precise and uses our method to eliminate the majority of the false positives of standard HOG. In the second stage, detected markers are tracked forward and backward in time. Tracking is needed to detect extremely blurred or distorted markers that are missed by the previous stage. The algorithm achieves 94% recall with minimal user guidance. An average of 30 guesses are given per image; the user verifies for each whether it is a marker or not. The brute force approach would return 100,000 guesses per image.

  6. New approach for isolation of VNTR markers.

    OpenAIRE

    Nakamura, Y; Carlson, M; Krapcho, K; Kanamori, M; White, R

    1988-01-01

    Elsewhere we have reported an efficient method for isolating VNTR (Variable Number of Tandem Repeats) markers. Several of the VNTR markers isolated in those experiments were sequenced, and a DNA sequence of 9 bp (GNNGTGGG) emerged as an apparent consensus sequence for VNTR markers. To confirm this result and to develop more VNTR markers, we synthesized nine different 18-base-long oligonucleotides whose sequences each included GNNGTGGG. When 102 cosmid clones selected by these oligonucleotides...

  7. Genetic variation at selected SNPs in the leptin gene and association of alleles with markers of kidney disease in a Xhosa population of South Africa.

    Directory of Open Access Journals (Sweden)

    Ikechi G Okpechi

    Full Text Available BACKGROUND: Chronic kidney disease (CKD is a significant public health problem that leads to end-stage renal disease (ESRD with as many as 2 million people predicted to need therapy worldwide by 2010. Obesity is a risk factor for CKD and leptin, the obesity hormone, correlates with body fat mass and markers of renal function. A number of clinical and experimental studies have suggested a link between serum leptin and kidney disease. We hypothesised that variants in the leptin gene (LEP may be associated with markers of CKD in indigenous black Africans. METHODOLOGY/PRINCIPAL FINDINGS: Black South Africans of Xhosa (distinct cultural Bantu-speaking population descent were recruited for the study and four common polymorphisms of the LEP (rs7799039, rs791620, rs2167270 and STS-U43653 [ENSSNP5824596] were analysed for genotype and haplotype association with urine albumin-to-creatinine ratio (UACR, estimated glomerular filtration rate (eGFR, Serum creatinine (Scr and serum leptin level. In one of the four single nucleotide polymorphisms (SNPs we examined, an association with the renal phenotypes was observed. Hypertensive subjects with the T allele (CT genotype of the ENSSNP5824596 SNP had a significantly higher eGFR (p = 0.0141, and significantly lower Scr (p = 0.0137. This was confirmed by haplotype analysis. Also, the haplotype GAAC had a modest effect on urine albumin-to-creatinine ratio in normotensive subjects (p = 0.0482. CONCLUSIONS/SIGNIFICANCE: These results suggest that genetic variations of the LEP may be associated with phenotypes that are markers of CKD in black Africans.

  8. Contamination of ground water, surface water, and soil, and evaluation of selected ground-water pumping alternatives in the Canal Creek area of Aberdeen Proving Ground, Maryland

    Science.gov (United States)

    Lorah, Michelle M.; Clark, Jeffrey S.

    1996-01-01

    Chemical manufacturing, munitions filling, and other military-support activities have resulted in the contamination of ground water, surface water, and soil in the Canal Creek area of Aberdeen Proving Ground, Maryland. Chlorinated volatile organic compounds, including 1,1,2,2-tetrachloroethane and trichloroethylene, are widespread ground-water contaminants in two aquifers that are composed of unconsolidated sand and gravel. Distribution and fate of chlorinated organic compounds in the ground water has been affected by the movement and dissolution of solvents in their dense immiscible phase and by microbial degradation under anaerobic conditions. Detection of volatile organic contaminants in adjacent surface water indicates that shallow contaminated ground water discharges to surface water. Semivolatile organic compounds, especially polycyclic aromatic hydrocarbons, are the most prevalent organic contaminants in soils. Various trace elements, such as arsenic, cadmium, lead, and zinc, were found in elevated concentrations in ground water, surface water, and soil. Simulations with a ground-water-flow model and particle tracker postprocessor show that, without remedial pumpage, the contaminants will eventually migrate to Canal Creek and Gunpowder River. Simulations indicate that remedial pumpage of 2.0 million gallons per day from existing wells is needed to capture all particles originating in the contaminant plumes. Simulated pumpage from offsite wells screened in a lower confined aquifer does not affect the flow of contaminated ground water in the Canal Creek area.

  9. Effects of nonpoint and selected point contaminant sources on stream-water quality and relation to land use in Johnson County, northeastern Kansas, October 2002 through June 2004

    Science.gov (United States)

    Lee, Casey J.; Mau, D.P.; Rasmussen, T.J.

    2005-01-01

    Water and sediment samples were collected by the U.S. Geological Survey in 12 watersheds in Johnson County, northeastern Kansas, to determine the effects of nonpoint and selected point contaminant sources on stream-water quality and their relation to varying land use. The streams studied were located in urban areas of the county (Brush, Dykes Branch, Indian, Tomahawk, and Turkey Creeks), developing areas of the county (Blue River and Mill Creek), and in more rural areas of the county (Big Bull, Captain, Cedar, Kill, and Little Bull Creeks). Two base-flow synoptic surveys (73 total samples) were conducted in 11 watersheds, a minimum of three stormflow samples were collected in each of six watersheds, and 15 streambed-sediment sites were sampled in nine watersheds from October 2002 through June 2004. Discharge from seven wastewater treatment facilities (WWTFs) were sampled during base-flow synoptic surveys. Discharge from these facilities comprised greater than 50 percent of streamflow at the farthest downstream sampling site in six of the seven watersheds during base-flow conditions. Nutrients, organic wastewater-indicator compounds, and prescription and nonprescription pharmaceutical compounds generally were found in the largest concentrations during base-flow conditions at sites at, or immediately downstream from, point-source discharges from WWTFs. Downstream from WWTF discharges streamflow conditions were generally stable, whereas nutrient and wastewater-indicator compound concentrations decreased in samples from sites farther downstream. During base-flow conditions, sites upstream from WWTF discharges had significantly larger fecal coliform and Escherichia coli densities than downstream sites. Stormflow samples had the largest suspended-sediment concentrations and indicator bacteria densities. Other than in samples from sites in proximity to WWTF discharges, stormflow samples generally had the largest nutrient concentrations in Johnson County streams. Discharge

  10. Occurrence, distribution, and volume of metals-contaminated sediment of selected streams draining the Tri-State Mining District, Missouri, Oklahoma, and Kansas, 2011–12

    Science.gov (United States)

    Smith, D. Charlie

    2016-12-14

    , Tar Creek, and Spring River in order to characterize the vertical extent of mine waste in select streams in the TSMD. The largest concentrations of lead, zinc, and cadmium in gravel bar-sediment samples generally were detected in Turkey Creek and Tar Creek and the smallest concentrations were detected in Shoal Creek followed by the Spring River. Gravel bar-sediment samples from Turkey Creek exceeded the CPEC for cadmium (minimum of 70 percent of samples), lead (94 percent), and zinc (99 percent) at a slightly higher frequency than similar samples from Tar Creek (69 percent, 88 percent, and 96 percent, respectively). Gravel bar-sediment samples from Turkey Creek also contained the largest concentrations of cadmium (174 milligrams per kilogram [mg/kg]) and lead (7,520 mg/kg) detected; however, the largest zinc concentration (46,600 mg/kg) was detected in a gravel bar-sediment sample from Tar Creek. In contrast, none of the 65 gravel bar-sediment samples from Shoal Creek contained cadmium above the x-ray fluorescence reporting level of 12 mg/kg, and lead and zinc exceeded the CPEC in only 12 percent and 74 percent of samples, respectively. In most cases, concentrations of lead and zinc above the CPEC or TPEC were present at the maximum depth of boring, which indicated that nearly the entire thickness of sediment in the stream has been contaminated by mine wastes. Approximately 284,000 cubic yards of channel sediment from land surface to the maximum depth that exceeded the CPEC and approximately 236,000 cubic yards of channel sediment from land surface to the maximum depth that exceeded the TPEC were estimated along 37.6 of the 55.1 miles of Center Creek, Turkey Creek, Shoal Creek, and Tar Creek examined in this study. Mine-waste contamination reported along additional reaches of these streams is beyond the scope of this study. Flood-plain cores collected in the TSMD generally only had exceedances of the CPEC and TPEC for lead and zinc in the top 1 or 2 feet of soil with

  11. Tumor markers in clinical oncology

    International Nuclear Information System (INIS)

    Novakovic, S.

    2004-01-01

    The subtle differences between normal and tumor cells are exploited in the detection and treatment of cancer. These differences are designated as tumor markers and can be either qualitative or quantitative in their nature. That means that both the structures that are produced by tumor cells as well as the structures that are produced in excessive amounts by host tissues under the influence of tumor cells can function as tumor markers. Speaking in general, the tumor markers are the specific molecules appearing in the blood or tissues and the occurrence of which is associated with cancer. According to their application, tumor markers can be roughly divided as markers in clinical oncology and markers in pathology. In this review, only tumor markers in clinical oncology are going to be discussed. Current tumor markers in clinical oncology include (i) oncofetal antigens, (ii) placental proteins, (iii) hormones, (iv) enzymes, (v) tumor-associated antigens, (vi) special serum proteins, (vii) catecholamine metabolites, and (viii) miscellaneous markers. As to the literature, an ideal tumor marker should fulfil certain criteria - when using it as a test for detection of cancer disease: (1) positive results should occur in the early stages of the disease, (2) positive results should occur only in the patients with a specific type of malignancy, (3) positive results should occur in all patients with the same malignancy, (4) the measured values should correlate with the stage of the disease, (5) the measured values should correlate to the response to treatment, (6) the marker should be easy to measure. Most tumor markers available today meet several, but not all criteria. As a consequence of that, some criteria were chosen for the validation and proper selection of the most appropriate marker in a particular malignancy, and these are: (1) markers' sensitivity, (2) specificity, and (3) predictive values. Sensitivity expresses the mean probability of determining an elevated tumor

  12. Transient dominant host-range selection using Chinese hamster ovary cells to generate marker-free recombinant viral vectors from vaccinia virus.

    Science.gov (United States)

    Liu, Liang; Cooper, Tamara; Eldi, Preethi; Garcia-Valtanen, Pablo; Diener, Kerrilyn R; Howley, Paul M; Hayball, John D

    2017-04-01

    Recombinant vaccinia viruses (rVACVs) are promising antigen-delivery systems for vaccine development that are also useful as research tools. Two common methods for selection during construction of rVACV clones are (i) co-insertion of drug resistance or reporter protein genes, which requires the use of additional selection drugs or detection methods, and (ii) dominant host-range selection. The latter uses VACV variants rendered replication-incompetent in host cell lines by the deletion of host-range genes. Replicative ability is restored by co-insertion of the host-range genes, providing for dominant selection of the recombinant viruses. Here, we describe a new method for the construction of rVACVs using the cowpox CP77 protein and unmodified VACV as the starting material. Our selection system will expand the range of tools available for positive selection of rVACV during vector construction, and it is substantially more high-fidelity than approaches based on selection for drug resistance.

  13. Anthropopression markers in lake bottom sediments

    Science.gov (United States)

    Nadolna, Anna; Nowicka, Barbara

    2014-05-01

    Lakes are vulnerable to various types of anthropogenic disturbances. Responses of lake ecosystems to environmental stressors are varied and depend not only on the type of a factor but also on the lake natural resistance to degradation. Within the EULAKES project an evaluation of anthropogenic stress extent in a flow-through, postglacial, ribbon lake (Lake Charzykowskie) was carried out. It was assumed, that this impact manifests unevenly, depending on a type and degree of the pressure on the shore zones, water quality of tributaries, lake basin shape and dynamics of a water movement. It was stated, that anthropogenic markers are substances accumulated in bottom sediments as a result of allochthonous substances inflow from the catchment and atmosphere. Along the selected transects 105 samples from the top layer of sediments (about 20 cm) was collected representing the contemporary accumulation (about 15 years). The content of selected chemical elements and compounds was examined, including nutrients (TN and TP), heavy metals (arsenic, cadmium, lead, chromium, nickel, copper, zinc, mercury, iron, and manganese) and pesticides (DDT, DDD, DDE, DMDT , γ-HCH). The research was conducted in the deepest points of each lake basin and along the research transects - while choosing the spots, the increased intensity of anthropogenic impact (ports, roads with heavy traffic, wastewater discharge zones, built-up areas) was taken into consideration. The river outlets to the lake, where there are ecotonal zones between limnic and fluvial environment, were also taken into account. Analysis of the markers distribution was carried out against the diversity of chemical characteristics of limnic sediments. Ribbon shape of the lake basin and the dominant wind direction provide an opportunity of easy water mixing to a considerable depth. Intensive waving processes cause removal of the matter from the littoral zone towards lake hollows (separated by the underwater tresholds), where the

  14. Selective dissolution followed by EDDS washing of an e-waste contaminated soil: Extraction efficiency, fate of residual metals, and impact on soil environment.

    Science.gov (United States)

    Beiyuan, Jingzi; Tsang, Daniel C W; Valix, Marjorie; Zhang, Weihua; Yang, Xin; Ok, Yong Sik; Li, Xiang-Dong

    2017-01-01

    To enhance extraction of strongly bound metals from oxide minerals and organic matter, this study examined the sequential use of reductants, oxidants, alkaline solvents and organic acids followed by a biodegradable chelating agent (EDDS, [S,S]-ethylene-diamine-disuccinic-acid) in a two-stage soil washing. The soil was contaminated by Cu, Zn, and Pb at an e-waste recycling site in Qingyuan city, China. In addition to extraction efficiency, this study also examined the fate of residual metals (e.g., leachability, bioaccessibility, and distribution) and the soil quality parameters (i.e., cytotoxicity, enzyme activities, and available nutrients). The reductants (dithionite-citrate-bicarbonate and hydroxylamine hydrochloride) effectively extracted metals by mineral dissolution, but elevated the leachability and bioaccessibility of metals due to the transformation from Fe/Mn oxides to labile fractions. Subsequent EDDS washing was found necessary to mitigate the residual risks. In comparison, prior washing by oxidants (persulphate, hypochlorite, and hydrogen peroxide) was marginally useful because of limited amount of soil organic matter. Prior washing by alkaline solvents (sodium hydroxide and sodium bicarbonate) was also ineffective due to metal precipitation. In contrast, prior washing by low-molecular-weight organic acids (citrate and oxalate) improved the extraction efficiency. Compared to hydroxylamine hydrochloride, citrate and oxalate induced lower cytotoxicity (Microtox) and allowed higher enzyme activities (dehydrogenase, acid phosphatase, and urease) and soil nutrients (available nitrogen and phosphorus), which would facilitate reuse of the treated soil. Therefore, while sequential washing proved to enhance extraction efficacy, the selection of chemical agents besides EDDS should also include the consideration of effects on metal leachability/bioaccessibility and soil quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

    KAUST Repository

    Rodrí guez-Ezpeleta, Naiara; Bradbury, Ian R.; Mendibil, Iñ aki; Á lvarez, Paula; Cotano, Unai; Irigoien, Xabier

    2016-01-01

    : the maximum number of mismatches allowed to merge reads into a locus and the relatedness of the individuals used for genotype calling and SNP selection. Our study resolves the population structure of the Atlantic mackerel, but, most importantly, provides

  16. Evaluation on the effectiveness of 2-deoxyglucose-6-phosphate phosphatase (DOGR1) gene as a selectable marker for oil palm (Elaeis guineensis Jacq.) embryogenic calli transformation mediated by Agrobacterium tumefaciens

    Science.gov (United States)

    Izawati, Abang Masli Dayang; Masani, Mat Yunus Abdul; Ismanizan, Ismail; Parveez, Ghulam Kadir Ahmad

    2015-01-01

    DOGR1, which encodes 2-deoxyglucose-6-phosphate phosphatase, has been used as a selectable marker gene to produce transgenic plants. In this study, a transformation vector, pBIDOG, which contains the DOGR1 gene, was transformed into oil palm embryogenic calli (EC) mediated by Agrobacterium tumefaciens strain LBA4404. Transformed EC were exposed to 400 mg l-1 2-deoxyglucose (2-DOG) as the selection agent. 2-DOG resistant tissues were regenerated into whole plantlets on various regeneration media containing the same concentration of 2-DOG. The plantlets were later transferred into soil and grown in a biosafety screenhouse. PCR and subsequently Southern blot analyses were carried out to confirm the integration of the transgene in the plantlets. A transformation efficiency of about 1.0% was obtained using DOGR1 gene into the genome of oil palm. This result demonstrates the potential of using combination of DOGR1 gene and 2-DOG for regenerating transgenic oil palm. PMID:26442041

  17. Reconnaissance of contaminants in selected wastewater-treatment-plant effluent and stormwater runoff entering the Columbia River, Columbia River Basin, Washington and Oregon, 2008-10

    Science.gov (United States)

    Morace, Jennifer L.

    2012-01-01

    Toxic contamination is a significant concern in the Columbia River Basin in Washington and Oregon. To help water managers and policy makers in decision making about future sampling efforts and toxic-reduction activities, a reconnaissance was done to assess contaminant concentrations directly contributed to the Columbia River through wastewater-treatment-plant (WWTP) effluent and stormwater runoff from adjacent urban environments and to evaluate instantaneous loadings to the Columbia River Basin from these inputs.

  18. Ground-water flow in the surficial aquifer system and potential movement of contaminants from selected waste-disposal sites at Naval Station Mayport, Florida

    Science.gov (United States)

    Halford, K.J.

    1998-01-01

    advective movement of contaminants from selected sites within the solid waste management units to discharge points was simulated using MODPATH. Most of the particles were discharged to the nearest surface-water feature after traveling less than 1,000 feet in the ground-water system. Most areas within 1,000 feet of a surface-water feature or storm sewer had traveltimes of less than 50 years, based on an effective porosity of 40 percent. Contributing areas, traveltimes, and pathlines were identified for 224 wells at Naval Station Mayport under steady-state and transient conditions by back-tracking a particle from the midpoint of the wetted screen of each well. Traveltimes to contributing areas that ranged between 15 and 50 years, estimated by the steady-state model, differed most from the transient traveltime estimates. Estimates of traveltimes and pathlines based on steady-state model results typically were 10 to 20 years more and about twice as long as corresponding estimates from the transient model. The models differed because the steady-state model simulated 1996 conditions when Naval Station Mayport had more impervious surfaces than at any earlier time. The expansion of the impervious surfaces increased the average distance between contributing areas and observation wells.

  19. Selection of candidate radiation bio-markers in the serum of rats exposed to gamma-rays by GC/TOFMS-based metabolomics

    International Nuclear Information System (INIS)

    Liu, H.; Wang, Z.; Zhang, X.; Qiao, Y.; Wu, S.; Dong, F.; Chen, Y.

    2013-01-01

    In the study, gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) techniques coupled with principal components analysis (PCA) were used to investigate metabolite perturbations in the serum of the rats exposed to 0.75, 3 or 8 Gy gamma rays. Male standard deviation rats were gamma-irradiated at doses of 0.75, 3 and 8 Gy (1.9 Gy min -1 ) or sham-irradiated. Serum samples were collected over the first 24 h under the exposure to irradiation in order to analyse the samples by GC/TOFMS. And multivariate data were analysed by PCA. The composition of metabolites in serum yielded distinct metabolomic phenotypes for 0.75, 3 and 8 Gy at 24 h after irradiation. Nine serum metabolites were significantly altered as a result of radiation exposure. Up-regulated metabolites included inositol, serine, lysine, glycine, threonine and glycerol; down regulated metabolites included isocitrate, gluconic acid and stearic acid. The nine metabolites were significantly altered after ionising radiation for they may be the potential bio-markers for the diagnosis of radiation injury. All rights reserved. (authors)

  20. Evaluation of potential prognostic value of Bmi-1 gene product and selected markers of proliferation (Ki-67 and apoptosis (p53 in the neuroblastoma group of tumors

    Directory of Open Access Journals (Sweden)

    Katarzyna Taran

    2016-02-01

    Full Text Available Introduction: Cancer in children is a very important issue in pediatrics. The least satisfactory treatment outcome occurs among patients with clinically advanced neuroblastomas. Despite much research, the biology of this tumor still remains unclear, and new prognostic factors are sought. The Bmi-1 gene product is a currently highly investigated protein which belongs to the Polycomb group (PcG and has been identified as a regulator of primary neural crest cells. It is believed that Bmi‑1 and N-myc act together and are both involved in the pathogenesis of neuroblastoma. The aim of the study was to assess the potential prognostic value of Bmi-1 protein and its relations with mechanisms of proliferation and apoptosis in the neuroblastoma group of tumors.Material/Methods: 29 formalin-fixed and paraffin-embedded neuroblastoma tissue sections were examined using mouse monoclonal antibodies anti-Bmi-1, anti-p53 and anti-Ki-67 according to the manufacturer’s instructions.Results: There were found statistically significant correlations between Bmi-1 expression and tumor histology and age of patients.Conclusions: Bmi-1 seems to be a promising marker in the neuroblastoma group of tumors whose expression correlates with widely accepted prognostic parameters. The pattern of BMI-1 expression may indicate that the examined protein is also involved in maturation processes in tumor tissue.

  1. Immunoliposome-mediated delivery of neomycin phosphotransferase for the lineage-specific selection of differentiated/committed stem cell progenies: potential advantages over transfection with marker genes, fluorescence-activated and magnetic affinity cell-sorting.

    Science.gov (United States)

    Heng, Boon Chin; Cao, Tong

    2005-01-01

    A major challenge in the therapeutic application of stem cells in regenerative medicine is the lineage-specific selection of their committed/differentiated progenies for transplantation. This is necessary to avoid engraftment of undesired lineages at the transplantation site, i.e. fibroblastic scar tissue, as well as to enhance the efficacy of transplantation therapy. Commonly used techniques for lineage-specific selection of committed/differentiated stem cell progenies include marker gene transfection, fluorescence-activated (FACS) and magnetic-affinity (MACS) cell-sorting. Nevertheless, these have their disadvantages for therapeutic applications. Marker gene transfection invariably leads to permanent genetic modification of stem cells, which in turn limits their use in human clinical therapy due to overwhelming ethical and safety concerns. FACS requires expensive instrumentation and highly-skilled personnel, and is unsuited for handling bulk quantities of cells that would almost certainly be required for transplantation therapy. MACS is a cheaper alternative, but the level of purity attained is also reduced. A possible novel approach that has yet to be investigated is immunoliposome-mediated delivery of neomycin phosphotranferase (NPT) for lineage-specific selection of stem cell progenies. This would avoid permanent genetic modification to the cell, unlike recombinant NPT expression linked to activation of specific promoter sequences. Moreover, it could potentially provide a much more practical and cost-effective alternative for handling bulk quantities of cells that would be required for transplantation therapy, as compared to FACS or MACS. As such, this alternative approach needs to be rigorously investigated, in view of its potentially useful applications in stem cell therapeutics.

  2. Disseminated tumor cells as selection marker and monitoring tool for secondary adjuvant treatment in early breast cancer. Descriptive results from an intervention study

    International Nuclear Information System (INIS)

    Synnestvedt, Marit; Schirmer, Cecilie; Nesland, Jahn Martin; Naume, Bjørn; Borgen, Elin; Wist, Erik; Wiedswang, Gro; Weyde, Kjetil; Risberg, Terje; Kersten, Christian; Mjaaland, Ingvil; Vindi, Lise

    2012-01-01

    Presence of disseminated tumor cells (DTCs) in bone marrow (BM) after completion of systemic adjuvant treatment predicts reduced survival in breast cancer. The present study explores the use of DTCs to identify adjuvant insufficiently treated patients to be offered secondary adjuvant treatment intervention, and as a surrogate marker for therapy response. A total of 1121 patients with pN1-3 or pT1c/T2G2-3pN0-status were enrolled. All had completed primary surgery and received 6 cycles of anthracycline-containing chemotherapy. BM-aspiration was performed 8-12 weeks after chemotherapy (BM1), followed by a second BM-aspiration 6 months later (BM2). DTC-status was determined by morphological evaluation of immunocytochemically detected cytokeratin-positive cells. If DTCs were present at BM2, docetaxel (100 mg/m 2 , 3qw, 6 courses) was administered, followed by DTC-analysis 1 month (BM3) and 13 months (BM4) after the last docetaxel infusion. Clinical follow-up (FU) is still ongoing. Here, the descriptive data from the study are presented. Of 1085 patients with a reported DTC result at both BM1 and BM2, 94 patients (8.7%) were BM1 positive and 83 (7.6%) were BM2 positive. The concordance between BM1 and BM2 was 86.5%. Both at BM1 and BM2 DTC-status was significantly associated with lobular carcinomas (p = 0.02 and p = 0.03, respectively; chi-square). In addition, DTC-status at BM2 was also associated with pN-status (p = 0.009) and pT-status (p = 0.03). At BM1 28.8% and 12.8% of the DTC-positive patients had ≥2 DTCs and ≥3 DTCs, respectively. At BM2, the corresponding frequencies were 47.0% and 25.3%. Of 72 docetaxel-treated patients analyzed at BM3 and/or BM4, only 15 (20.8%) had persistent DTCs. Of 17 patients with ≥3 DTCs before docetaxel treatment, 12 patients turned negative after treatment (70.6%). The change to DTC-negativity was associated with the presence of ductal carcinoma (p = 0.009). After docetaxel treatment, the majority of patients experienced

  3. Probing the limits of alpha power lateralisation as a neural marker of selective attention in middle-aged and older listeners.

    Science.gov (United States)

    Tune, Sarah; Wöstmann, Malte; Obleser, Jonas

    2018-02-11

    In recent years, hemispheric lateralisation of alpha power has emerged as a neural mechanism thought to underpin spatial attention across sensory modalities. Yet, how healthy ageing, beginning in middle adulthood, impacts the modulation of lateralised alpha power supporting auditory attention remains poorly understood. In the current electroencephalography study, middle-aged and older adults (N = 29; ~40-70 years) performed a dichotic listening task that simulates a challenging, multitalker scenario. We examined the extent to which the modulation of 8-12 Hz alpha power would serve as neural marker of listening success across age. With respect to the increase in interindividual variability with age, we examined an extensive battery of behavioural, perceptual and neural measures. Similar to findings on younger adults, middle-aged and older listeners' auditory spatial attention induced robust lateralisation of alpha power, which synchronised with the speech rate. Notably, the observed relationship between this alpha lateralisation and task performance did not co-vary with age. Instead, task performance was strongly related to an individual's attentional and working memory capacity. Multivariate analyses revealed a separation of neural and behavioural variables independent of age. Our results suggest that in age-varying samples as the present one, the lateralisation of alpha power is neither a sufficient nor necessary neural strategy for an individual's auditory spatial attention, as higher age might come with increased use of alternative, compensatory mechanisms. Our findings emphasise that explaining interindividual variability will be key to understanding the role of alpha oscillations in auditory attention in the ageing listener. © 2018 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  4. Cross-Sectional Analysis of Selected Genital Tract Immunological Markers and Molecular Vaginal Microbiota in Sub-Saharan African Women, with Relevance to HIV Risk and Prevention.

    Science.gov (United States)

    Kyongo, Jordan K; Crucitti, Tania; Menten, Joris; Hardy, Liselotte; Cools, Piet; Michiels, Johan; Delany-Moretlwe, Sinead; Mwaura, Mary; Ndayisaba, Gilles; Joseph, Sarah; Fichorova, Raina; van de Wijgert, Janneke; Vanham, Guido; Ariën, Kevin K; Jespers, Vicky

    2015-05-01

    Data on immune mediators in the genital tract and the factors that modulate them in sub-Saharan women are limited. Cervicovaginal lavage (CVL) samples from 430 sexually active women from Kenya, South Africa, and Rwanda were analyzed for 12 soluble immune mediators using Bio-Plex and Meso Scale Discovery multiplex platforms, as well as single enzyme-linked immunosorbent assays. Ten bacterial species were quantified in vaginal swab samples. Bacterial vaginosis (BV) was defined by Nugent scoring. CVL samples from HIV-infected women showed a clear-cut proinflammatory profile. Pregnant women, adolescents, and women engaging in traditional vaginal practices differed in specific soluble markers compared to reference groups of adult HIV-negative women. Cervical mucus, cervical ectopy, abnormal vaginal discharge, and having multiple sex partners were each associated with an increase in inflammatory mediators. The levels of interleukin-1α (IL-1α), IL-1β, IL-6, IL-12(p70), and IL-8 were elevated, whereas the IL-1RA/IL-1(α+β) ratio decreased in women with BV. The level of gamma interferon-induced protein 10 was lower in BV-positive than in BV-negative women, suggesting its suppression as a potential immune evasion mechanism by BV-associated bacteria. Lactobacillus crispatus and Lactobacillus vaginalis were associated with decreased proinflammatory cytokines and each BV-associated species with increased proinflammatory cytokines. Remarkably, the in vitro anti-HIV activity of CVL samples from BV-positive women was stronger than that of BV-negative women. In conclusion, we found significant associations of factors, including vaginal microbiota, which can influence immune mediators in the vaginal environment in sexually active women. These factors need to be considered when establishing normative levels or pathogenic cutoffs of biomarkers of inflammation and associated risks in African women. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  5. [Construction of plant expression vectors with PMI gene as selection marker and their utilization in transformation of Salvia miltiorrhiza f. alba].

    Science.gov (United States)

    Tao, Ru; Zhang, You-Can; Fang, Qian; Shi, Ren-Jiu; Li, Yan-Ling; Huang, Lu-Qi; Hao, Gang-Ping

    2014-04-01

    To construct plant expression pCAMBIA1301-PMI by substituting PMI for hygromycin resistance gene in pCAMBIA1301 and obtain transgenic Salvia miltiorrhiza f. alba using PMI-mannose selection system. The 6-phosphomannose isomerase gene (PMI) of Escherichia coli was amplified by PCR. Sequence analysis showed that it shared 100% amino acids identities with the sequences of PMI genes isolates reported in the NCBI. Based on pCAMBIA1305, the plant expression pCAMBIA1305-PMI was constructed successfully by substituting PMI for hygromycin resistance gene in pCAMBIA1305. pCAMBIA1305-PMI was transformed into Agrobacterium tumefaciens LBA4404, and then the leaves of S. miltiorrhiza f. alba were inoculated in LBA4404 with pCAMBIA1305-PMI. Plant expression pCAMBIA1301-PMI was successfully constructed and the leaves of S. miltiorrhiza f. alba inoculated in LBA4404 with pCAMBIA1305-PMI were selected on medium supplemented with a combination of 20 g x L(-1) mannose and 10 g x L(-1) sucrose as a carbon source. The transformation efficiency rate was 23.7%. Genetic transformation was confirmed by PCR, indicating that a new method for obtaining transgenic S. miltiorrhiza f. alba plants was developed using PMI-mannose selection system.

  6. Seleção tradicional e associada a marcadores moleculares na avaliação genética animal Traditional and associated selection with molecular markers in the genetic evaluation of animals

    Directory of Open Access Journals (Sweden)

    Paulo Luiz Souza Carneiro

    2006-04-01

    Full Text Available O objetivo deste trabalho foi comparar a seleção, utilizando valores genéticos preditos pelo BLUP clássico (BLUP, BLUP marcadores (BLUPM e pela seleção individual (SI, usando simulação com o programa Genesys. Para obter a matriz de similaridade genética utilizada no BLUPM, foram simulados cem marcadores moleculares do tipo microssatélite (SSR - Simple Sequence Repeat, por meio de um coeficiente de similaridade correspondente à distância euclideana média para dados quantitativos. A fim de comparar os diferentes métodos, utilizaram-se populações com tamanho efetivo de 66,66 e média de 30 repetições, avaliando-se os valores fenotípicos médios. Os ganhos ao longo das 20 gerações de seleção foram maiores para o BLUP em relação ao BLUPM, e este foi superior à SI. Quanto ao ganho obtido nas cinco primeiras gerações, o BLUPM apresentou ganhos semelhantes ao BLUP e superiores à SI. Diferentes sistemas de acasalamento dos reprodutores selecionados não revelaram diferenças em ganho genético nos métodos baseados no BLUP.The objective of this work was to compare selection based on breeding values predicted by classical best linear unbiased prediction (BLUP, BLUP associated with molecular markers (BLUPM and individual selection (IS using data simulated with the Genesys program. To obtain the genetic similarity matrix to be used in BLUPM, a hundred microsatellite markers (simple sequence repeats were simulated using a similarity coefficient corresponding to the mean Euclidean distance between quantitative data. The different selection methods were compared using populations of an effective size of 66.66 and a mean of 30 repetitions, and mean phenotypic values were determined. Genetic gain obtained over 20 generations of selection was higher for BLUP than BLUPM, which in turn was superior to IS. Similar genetic gains were obtained for BLUPM and BLUP only when the gain for the first five generations was considered, and these

  7. Genomic selection in plant breeding.

    Science.gov (United States)

    Newell, Mark A; Jannink, Jean-Luc

    2014-01-01

    Genomic selection (GS) is a method to predict the genetic value of selection candidates based on the genomic estimated breeding value (GEBV) predicted from high-density markers positioned throughout the genome. Unlike marker-assisted selection, the GEBV is based on all markers including both minor and major marker effects. Thus, the GEBV may capture more of the genetic variation for the particular trait under selection.

  8. Light contamination

    International Nuclear Information System (INIS)

    Cepeda Pena, William Enrique

    1998-01-01

    The article tries on the wrong use of the artificial light, of the main problems of the light contamination, dispersion of the light, noxious effects of the light contamination, ecological effects, effects on the man's biological rhythm, economic effects and effects about the civic and vial security, among other topics

  9. Uso prático de marcadores moleculares para seleção assistida no melhoramento de uvas de mesa apirênicas Practical use of molecular markers for seedlessness assisted selection in grapevine breeding

    Directory of Open Access Journals (Sweden)

    Luís Fernando Revers

    2006-04-01

    Full Text Available A hipótese mais bem aceita atualmente para explicar a genética complexa da estenoespermocarpia, observada na videira, indica que a expressão deste fenótipo é controlada por três genes recessivos, independentemente herdados e controlados por um gene regulador dominante (sdI. Em estudo anterior, Lahogue et al. (1998 identificaram um marcador RAPD (Random Amplified Polymorphic DNA ligado ao gene sdI e utilizaram-no para desenvolver um SCAR (Sequence Characterized Amplified Region co-dominante denominado SCC8, que pode distinguir, em uma progênie, indivíduos com semente como também selecionar indivíduos apirênicos. Neste trabalho, são apresentados resultados da avaliação do potencial de aplicação do marcador molecular SCAR SCC8 para seleção assistida do caráter da apirenia no melhoramento de uvas de mesa sem sementes. A utilização deste marcador na seleção assistida para apirenia em uvas de mesa mostrou-se viável, e as conseqüências da sua utilização no programa de melhoramento da Embrapa Uva e Vinho são discutidas.The inheritance of seedlessness in grapevine is based on a complex genetic system, where the expression of three independently inherited recessive genes is controlled by a dominant regulator gene (sdI. In a previous study, Lahogue et al. (1998 identified a random amplified polymorphic DNA marker, tightly linked to the sdI gene and developed a codominant SCAR (Sequence Characterized Amplified Region marker named SCC8, that allows the distinction of seeded and seedless plants in a segregating progeny. The aim of the present work was to evaluate the usefullness of the SCAR marker SCC8 for assisted selection of the seedlessness character in grape breeding. According to our results, the use of the SCC8 marker is economically viable and the consequences of its use in the grapevine breeding program at Embrapa Uva e Vinho are discussed.

  10. Strategic marker selection to detect quantitative trait loci in chicken Seleção estratégica de marcadores para detecção locos para características quantitativas em aves

    Directory of Open Access Journals (Sweden)

    Deborah Clea Ruy

    2005-04-01

    Full Text Available Selective genotyping for a certain trait in individuals with extreme phenotypes contributes sufficient information to determine linkage between molecular markers and quantitative trait loci (QTL. In this experiment an F2 population, developed by crossing males from a broiler line with females from a layer line, was employed to detect QTL on chromosomes 3 and 5. Twenty-eight performance and carcass traits were measured in F2 offspring, and phenotypic correlations between traits were calculated. Body weight at 42 days (BW42 presented the greatest positive correlations with most other traits, with correlation between body weights at 35 and 41 days, weight gain between birth and 35, 41 and 42 days, as well as weights of carcass and some body parts superior to 0.8. One hundred-and-seventy F2 offspring, representing the top (4.5% and the bottom (4.5% of a normal distribution curve of BW42, were selected with equal proportions of males and females, and within dam family. Samples were genotyped for 19 informative markers on chromosome 3, and 11 markers on chromosome 5. Marker allelic frequencies of phenotypic groups with high and low BW42 were compared with a chi-square test. Four regions on chromosome 3 and three regions on chromosome 5 had markers that were suggestively associated with BW42 (P A genotipagem seletiva de indivíduos com fenótipos extremos para uma determinada característica contribui com informação suficiente para determinar a ligação entre marcadores moleculares e locos para características quantitativas (QTL. Neste estudo uma população F2, formada a partir do cruzamento de uma linha parental de aves para corte com uma linha de postura foi empregada para obtenção de medidas fenotípicas e genotipagem por marcadores microssatélites, posicionados nos cromossomos 3 e 5. Foram medidas 28 características de desempenho e carcaça e determinada a correlação fenotípica entre elas. A característica peso vivo aos 42 dias (BW42

  11. Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

    KAUST Repository

    Rodríguez-Ezpeleta, Naiara

    2016-03-03

    Restriction-site associated DNA sequencing (RAD-seq) and related methods are revolutionizing the field of population genomics in non-model organisms as they allow generating an unprecedented number of single nucleotide polymorphisms (SNPs) even when no genomic information is available. Yet, RAD-seq data analyses rely on assumptions on nature and number of nucleotide variants present in a single locus, the choice of which may lead to an under- or overestimated number of SNPs and/or to incorrectly called genotypes. Using the Atlantic mackerel (Scomber scombrus L.) and a close relative, the Atlantic chub mackerel (Scomber colias), as case study, here we explore the sensitivity of population structure inferences to two crucial aspects in RAD-seq data analysis: the maximum number of mismatches allowed to merge reads into a locus and the relatedness of the individuals used for genotype calling and SNP selection. Our study resolves the population structure of the Atlantic mackerel, but, most importantly, provides insights into the effects of alternative RAD-seq data analysis strategies on population structure inferences that are directly applicable to other species.

  12. Bioaugmentation with Petroleum-Degrading Consortia Has a Selective Growth-Promoting Impact on Crop Plants Germinated in Diesel Oil-Contaminated Soil

    DEFF Research Database (Denmark)

    Graj, Weronika; Lisiecki, Piotr; Szulc, Alicja

    2013-01-01

    or seeds with indigenous rhizospheric populations is a common approach in the rhizoremediation. However, we introduced hydrocarbon-degrading consortia (M10, R3, and K52) that were previously isolated from crude oil-contaminated soil instead of indigenous microbes. Bioaugmentation with these petroleum...... with the rhizospheric microbes. The microorganisms may be stimulated by the secreted root exudates, which results in an increased breakdown of contaminants in the rhizosphere. The main goal of this study was to establish a potential rhizoremediation combination for a diesel-polluted site. Inoculation of plant roots...... degraders was applied to screen four high biomass crop species (Indian mustard, alfalfa, high erucic acid rapeseed, HEAR, and low erucic acid rapeseed, LEAR) for their tolerance towards diesel oil. At no pollution, a promoting effect of M10 bacteria could be observed on germination and root elongation...

  13. [Indoor air studies of mould fungus contamination of homes of selected patients with bronchial asthma (with special regard to evaluation problems)].

    Science.gov (United States)

    Senkpiel, K; Kurowski, V; Ohgke, H

    1996-02-01

    Investigations of indoor air of the homes of seven patients with asthma bronchiale who showed up with positive reactions following intracutaneous application of fungal allergens revealed that their places of residence were contaminated by fungal and bacterial spores. The number of colony forming units of mesophilic fungal spores of the indoor air ranged from 100 to 1000 CFU/m3 and this was much higher than the mould flora of the outdoor air determined simultaneously. The major fungi species found by the indoor investigation were: Penicillium sp. > Aspergillus sp. > Cladosporium sp., Mucor sp., Chrysonilia sp., Verticillium sp. > Geotrichum sp., Trichoderma sp. In two cases Thermoactinomyces species could be detected in the indoor air. The main cause of fungal contamination were moist building materials on room walls, insufficient air ventilation, bad maintenance of the circulating air-machines and insufficient room hygiene (e.g. biological garbage in the kitchen).

  14. Monitoring of selected priority and emerging contaminants in the Guadalquivir River and other related surface waters in the province of Jaén, South East Spain.

    Science.gov (United States)

    Robles-Molina, José; Gilbert-López, Bienvenida; García-Reyes, Juan F; Molina-Díaz, Antonio

    2014-05-01

    The province of Jaén counts with four natural parks, numerous rivers, reservoirs and wetlands; moreover, it is probably the region with higher olive oil production in the world, which makes this zone a proper target to be studied based on the European Water Framework Directive 2000/60/CE. The aim of this survey is to monitor a total number of 373 compounds belonging to different families (pesticides, PAHs, nitrosamines, drugs of abuse, pharmaceuticals and life-style compounds) in surface waters located at different points of the province of Jaén. Among these compounds some priority organic substances (regulated by the EU Directive 2008/105/EC) and pollutants of emerging concern (not regulated yet) can be found. A liquid chromatography electrospray time-of-flight mass spectrometry (LC-TOFMS) method covering 340 compounds was developed and applied, together with a gas chromatography triple-quadrupole mass spectrometry (GC-MS/MS) method which enabled the analysis of 63 organic contaminants (30 of these compounds are analyzed by LC-TOFMS as well). From April 2009 to November 2010 a total of 83 surface water samples were collected (rivers, reservoirs and wetlands). In this period numerous organic contaminants were detected, most of them at the ng L(-1) level. The most frequently priority substances found were chlorpyrifos ethyl, diuron and hexachlorobenzene. Within the other groups, the most frequently detected compounds were: terbuthylazine, oxyfluorfen, desethyl terbuthylazine, diphenylamine (pesticide family); fluorene, phenanthrene, pyrene (PAHs group), codeine, paracetamol (pharmaceuticals compounds) and caffeine, nicotine (life-style compounds). As is could be expected, the total concentration of emerging contaminants is distinctly larger than that of priority pollutants, highlighting the importance of continuing with the study of their presence, fate and effects in aquatic environments. However, concentration levels (at the ng per liter level) are low in

  15. (SSR) markers for drought tolerance in maize

    African Journals Online (AJOL)

    use

    2011-11-21

    Nov 21, 2011 ... and dominance gene effects in inheritance are included in almost all traits related to drought (Shiri et al., 2010a, b). Identifying the complete-linked molecular markers with target gene and mapping its chromosome locus is an important goal in plant breeding for gene cloning and marker-aided selection.

  16. Water Contamination

    Science.gov (United States)

    ... Statistics Training & Education Policy & Recommendations Fast Facts Healthy Water Sites Healthy Water Drinking Water Healthy Swimming Global ... type=”submit” value=”Submit” /> Healthy Water Home Water Contamination Recommend on Facebook Tweet Share Compartir On ...

  17. Índice baseado em RFLPs para seleção de linhagens visando sintéticos de milho RFLP marker index for selection of inbred lines aimed at synthetic maize populations

    Directory of Open Access Journals (Sweden)

    Glauce Cristina Ricardo Rumin

    2001-06-01

    Full Text Available Marcadores moleculares têm sido sugeridos como ferramentas úteis em programas de melhoramento de plantas. Assim, este trabalho teve como objetivo propor um índice de seleção de linhagens visando a geração de populações sintéticas de milho, baseado em marcadores moleculares e dados de campo. Para tanto foram utilizados valores fenotípicos e genotípicos, oriundos de experimentos convencionais de campo e através da genotipagem das plantas-mãe das linhagens por marcadores RFLP, respectivamente. O índice foi examinado quanto à sua capacidade de originar sintéticos com alta freqüência de alelos favoráveis, em comparação com os obtidos baseando-se na seleção convencional. Utilizaram-se inicialmente 157 locos marcadores com distância média de 15,30 cM entre eles. Sessenta e oito linhagens S2, provenientes da geração F2 do cruzamento entre duas linhagens homozigóticas foram cruzadas em topcross e avaliadas em quatro locais de Iowa, EUA, em 1996. Dos 157 locos foram selecionados 18 que explicaram 74,70% da variância genética entre progênies, na média dos locais. O índice proposto leva em conta o comportamento próprio (per se das linhagens e a complementaridade genotípica entre elas, o que não é conseguido utilizando-se apenas dados dos topcrosses. O uso do índice proposto permite obter homólogo de tabela dialélica tendo-se apenas dados de médias de topcrosses. O índice levou à seleção de sintéticos com propriedades superiores às esperadas pela seleção baseada apenas nas médias das progênies topcross. Essa conclusão, no entanto, só é válida para os QTL's abrangidos pelas marcas. A metodologia proposta permite monitoramento muito adequado e útil das propriedades genéticas dos sintéticos a serem obtidos.Molecular markers have been suggested as useful tools in breeding programmes. The purpose of this work was to propose and apply an index for inbred line selection to be used for generating synthetic

  18. Geochemical association of Pu and Am in selected host-phases of contaminated soils from the UK and their susceptibility to chemical and microbiological leaching

    International Nuclear Information System (INIS)

    Kimber, Richard L.; Corkhill, Claire L.; Amos, Sean; Livens, Francis R.; Lloyd, Jonathan R.

    2015-01-01

    Understanding the biogeochemical behaviour and potential mobility of actinides in soils and groundwater is vital for developing remediation and management strategies for radionuclide-contaminated land. Pu is known to have a high Kd in soils and sediments, however remobilization of low concentrations of Pu remains a concern. Here, some of the physicochemical properties of Pu and the co-contaminant, Am, are investigated in contaminated soils from Aldermaston, Berkshire, UK, and the Esk Estuary, Cumbria, UK, to determine their potential mobility. Sequential extraction techniques were used to examine the host-phases of the actinides in these soils and their susceptibility to microbiological leaching was investigated using acidophilic sulphur-oxidising bacteria. Sequential extractions found the majority of 239,240 Pu associated with the highly refractory residual phase in both the Aldermaston (63.8–85.5 %) and Esk Estuary (91.9–94.5%) soils. The 241 Am was distributed across multiple phases including the reducible oxide (26.1–40.0%), organic (45.6–63.6%) and residual fractions (1.9–11.1%). Plutonium proved largely resistant to leaching from microbially-produced sulphuric acid, with a maximum 0.18% leached into solution, although up to 12.5% of the 241 Am was leached under the same conditions. If Pu was present as distinct oxide particles in the soil, then 241 Am, a decay product of Pu, would be expected to be physically retained in the particle. The differences in geochemical association and bioleachability of the two actinides suggest that this is not the case and hence, that significant Pu is not present as distinct particles. These data suggest the majority of Pu in the contaminated soils studied is highly recalcitrant to geochemical changes and is likely to remain immobile over significant time periods, even when challenged with aggressive “bioleaching” bacteria. - Highlights: • Pu in the contaminated soils is associated with the recalcitrant

  19. Evaluation of Diversity Based on Morphological Variabilities and ISSR Molecular Markers in Iranian Cynodon dactylon (L.) Pers. Accessions to Select and Introduce Cold-Tolerant Genotypes.

    Science.gov (United States)

    Akbari, M; Salehi, H; Niazi, A

    2018-04-01

    , Naein, Aligoudarz, and the foreign cultivar. This study may provide useful information for further breeding programs on common bermudagrass. Selected genotypes can be evaluated for other abiotic stresses such as drought and salinity.

  20. Lead and cadmium contamination and exposure risk assessment via consumption of vegetables grown in agricultural soils of five-selected regions of Pakistan

    Science.gov (United States)

    Rehman, Zahir Ur; Khan, Sardar; Brusseau, Mark L; Shah, Mohammad Tahir

    2017-01-01

    Rapid urbanization and industrialization result in serious contamination of soil with toxic metals such as lead (Pb) and cadmium (Cd), which can lead to deleterious health impacts in the exposed population. This study aimed to investigate Pb and Cd contamination in agricultural soils and vegetables in five different agricultural sites in Pakistan. The metal transfer from soil-to-plant, average daily intake of metals, and health risk index (HRI) were also characterized. The Pb concentrations for all soils were below the maximum allowable limits (MAL 350 mg kg−1) set by the State Environmental Protection Administration of China (SEPA), for soils in China. Conversely, Cd concentrations in the soils exceeded the MAL set by SEPA (0.6 mg kg−) and the European Union (1.5 mg kg−1) by 62-74% and 4-34%, respectively. The mean Pb concentration in edible parts of vegetables ranged from 1.8-11 mgkg−1. The Pb concentrations for leafy vegetables were higher than the fruiting and pulpy vegetables. The Pb concentrations exceeded the MAL (0.3 mg kg−1) for leafy vegetables and the MAL for fruity and rooty/tuber vegetables (0.1 mg kg−1) set by FAO/WHO-CODEX.. Likewise, all vegetables except Pisum sativum (0.12 mg kg−1) contained Cd concentrations that exceede