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

PubMed Central

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

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

PubMed

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.

State of the art molecular markers for fecal pollution source tracking in water.

PubMed

Roslev, Peter; Bukh, Annette S

2011-03-01

Most environmental waters are susceptible to fecal contamination from animal and/or human pollution sources. To attenuate or eliminate such contamination, it is often critical that the pollution sources are rapidly and correctly identified. Fecal pollution source tracking (FST) is a promising research area that aims to identify the origin(s) of fecal pollution in water. This mini-review focuses on the potentials and limitations of library independent molecular markers that are exclusively or strongly associated with fecal pollution from humans and different animals. Fecal-source-associated molecular markers include nucleic acid sequences from prokaryotes and viruses associated with specific biological hosts, but also sequences such as mitochondrial DNA retrieved directly from humans and animals. However, some fecal-source-associated markers may not be absolutely specific for a given source type, and apparent specificity and frequency established in early studies are sometimes compromised by new studies suggesting variation in specificity and abundance on a regional, global and/or temporal scale. It is therefore recommended that FST studies are based on carefully selected arrays of markers, and that identification of human and animal contributions are based on a multi-marker toolkit with several markers for each source category. Furthermore, future FST studies should benefit from increased knowledge regarding sampling strategies and temporal and spatial variability of marker ratios. It will also be important to obtain a better understanding of marker persistence and the quantitative relationship between marker abundance and the relative contribution from individual fecal pollution source types. A combination of enhanced pathogen screening methods, and validated quantitative source tracking techniques could then contribute significantly to future management of environmental water quality including improved microbial risk assessment.

Tracking the Sources of Fecal Contaminations: an Interdisciplinary Toolbox

NASA Astrophysics Data System (ADS)

Jeanneau, L.; Jarde, E.; Derrien, M.; Gruau, G.; Solecki, O.; Pourcher, A.; Marti, R.; Wéry, N.; Caprais, M.; Gourmelon, M.; Mieszkin, S.; Jadas-Hécart, A.; Communal, P.

2011-12-01

Fecal contaminations of inland and coastal waters induce risks to human health and economic losses. In order to improve water management, it is necessary to identify the sources of contamination, which implies the development of specific markers. In order to be considered as a valuable host-specific marker, one must (1) be source specific, (2) occur in high concentration in polluting matrices, (3) exhibit extra-intestinal persistence similar to fecal indicator bacteria (FIB) and (4) not grow out of the host. However, up to day no single marker has fulfilled all those criteria. Thus, it has been suggested to use a combination of markers in order to generate more reliable data. This has lead to the development of a Microbial Source Tracking (MST) toolbox including FIB and microbial and chemical specific markers in order to differentiate between human, bovine and porcine fecal contaminations. Those specific markers are, (1) genotypes of F-specific RNA bacteriophages, (2) bacterial markers belonging to the Bacteroidales (human-specific HF183, ruminant-specific Rum-2-Bac and pig-specific Pig-2-Bac markers), to the Bifidobacterium (Bifidobacterium adolescentis) and pig-specific Lactobacillus amylovorus, (3) fecal stanols and (4) caffeine. The development of this MST toolbox was composed of four steps, from the molecular scale to the watershed scale. At the molecular scale, the specificity and the concentration of those markers were studied in cattle and pig manures and in waste water treatment plant (WWTP) effluents and influents. At the microcosm scale, the transfer of bovine and porcine specific markers was investigated by rainfall simulations on agricultural plots amended with cattle or pig manure. Moreover, the relative persistence of FIB and human, porcine and bovine specific markers was investigated in freshwater and seawater microcosms inoculated with a WWTP influent, pig manure and cow manure. Finally, the aforementioned MST toolbox has been validated at the catchment scale by analysing three rivers impacted by fecal contaminations. The development and the application of this MST toolbox have highlighted (1) the specificity of the aforementioned markers, (2) their conservative transfer from soils to rivers and (3) their difference of persistence in seawater and in freshwater. Those results provide useful data in order to identify and manage fecal contaminations of superficial waters. In the case of single source contaminations, the markers provide coherent information: (1) the bovine or porcine markers were not detected in a river impacted by a WWTP effluent; (2) the occurrence of Rum-2-Bac and the distribution of stanols indicated a bovine contamination in a river flowing through cattle pasture. In the case of multiple source contaminations, the combination of markers is necessary to identify the main sources and the statistical treatment of the distribution of stanols could provide an approximation of their proportion.

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

PubMed

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.

Single-Particle Discrimination of Retroviruses from Extracellular Vesicles by Nanoscale Flow Cytometry.

PubMed

Tang, Vera A; Renner, Tyler M; Fritzsche, Anna K; Burger, Dylan; Langlois, Marc-André

2017-12-19

Retroviruses and small EVs overlap in size, buoyant densities, refractive indices and share many cell-derived surface markers making them virtually indistinguishable by standard biochemical methods. This poses a significant challenge when purifying retroviruses for downstream analyses or for phenotypic characterization studies of markers on individual virions given that EVs are a major contaminant of retroviral preparations. Nanoscale flow cytometry (NFC), also called flow virometry, is an adaptation of flow cytometry technology for the analysis of individual nanoparticles such as extracellular vesicles (EVs) and retroviruses. In this study we systematically optimized NFC parameters for the detection of retroviral particles in the range of 115-130 nm, including viral production, sample labeling, laser power and voltage settings. By using the retroviral envelope glycoprotein as a selection marker, and evaluating a number of fluorescent dyes and labeling methods, we demonstrate that it is possible to confidently distinguish retroviruses from small EVs by NFC. Our findings make it now possible to individually phenotype genetically modified retroviral particles that express a fluorescent envelope glycoprotein without removing EV contaminants from the sample.

Microbial cross-contamination by airborne dispersion and contagion during defeathering of poultry.

PubMed

Allen, V M; Hinton, M H; Tinker, D B; Gibson, C; Mead, G C; Wathes, C M

2003-09-01

1. A readily identifiable strain of Escherichia coli K12 was used as a 'marker' organism to determine the sources, routes and patterns of microbial cross-contamination during mechanical defeathering of broiler chicken carcases. 2. Inoculation of scald water with the marker organism led to a relatively even pattern of carcase contamination during subsequent defeathering. Microbial cross-contamination was greater by this route of inoculation than by either surface inoculation of a 'seeder' carcase or oral inoculation of a live bird one day before slaughter. 3. Dispersal of the marker organism was strongly influenced by the mechanical action of the defeathering machines. Forward transmission of the marker occurred by aerosol or large airborne droplets and particulates such as feathers. Moving carcases through the defeathering machines when these were non-operational clearly reduced backward transmission of the marker. 4. Although microbial dispersal was unaffected by increasing the spacing between individual carcases or installing a water curtain at the entry and exit of the defeathering machines, shielding of carcases with aluminium baffles reduced counts of the marker organism from contaminated carcases by > 90%. 5. The results imply that microbial cross-contamination of broiler chicken carcases during defeathering occurs mainly via the airborne route, which could be contained by physical means.

Antioxidative enzymes and expression of rbcL gene as tools to monitor heavy metal-related stress in plants.

PubMed

Jaskulak, Marta; Rorat, Agnieszka; Grobelak, Anna; Kacprzak, Małgorzata

2018-04-14

The aim of the study was to evaluate sensitivity and potential applications of selected biomarkers in phytoremediation under complex heavy metal contamination in Sinapis alba L., Robinia pseudoacacia L. and Lupinus luteus L as a potential tools in effective phytoremediation management. The toxicity assessment was conducted using selected measurement endpoints, both classical and advanced, i.e., germination index, roots length, guaiacol peroxidase activity (GPX), chlorophyll and protein content, the amount of total phenolic compounds (TPC) and level of expression of one of the ribulose-bisphosphate carboxylase genes (rbcL). Moreover, the influence of organic additives: cattle, horse manure, and vermicompost on lowering plant abiotic stress caused by complex heavy metal contamination was studied to assess the possible applications of selected stress markers in large scale phytoremediation planning. The results demonstrated the beneficial effects of selected soil additives on plant development. The 5% difference in the quantity of applied amendment caused statistically significant differences in GPX, TPC, chlorophyll content and expression level of rbcL. Among all endpoints, GPX activity, chlorophyll, and phenolic compounds content, as well as the expression of rbcL, turned out to be the most reliable assays for determination of the type and dosage of selected soil amendments (fertilizers) in the assisted phytoremediation process. Selected markers can be used to achieve the desired level of plant abiotic stress and consequently photosynthesis efficiency and CO 2 sequestration. The results showed, that presented assays can be used in different taxonomical groups such as Fabaceae for planning effective phytoremediation process. Copyright © 2018 Elsevier Ltd. All rights reserved.

Development of Nested PCR-Based Specific Markers for Detection of Peach Rosette Mosaic Virus in Plant Quarantine.

PubMed

Lee, S; Kim, C S; Shin, Y G; Kim, J H; Kim, Y S; Jheong, W H

2016-03-01

The Peach rosette mosaic virus (PRMV) is a plant pathogen of the genus Nepovirus, and has been designated as a controlled quarantine virus in Korea. In this study, a specific reverse transcription (RT)-PCR marker set, nested PCR marker set, and modified-plasmid positive control were developed to promptly and accurately diagnose PRMV at plant-quarantine sites. The final selected PRMV-specific RT-PCR marker was PRMV-N10/C70 (967 bp), and the nested PCR product of 419 bp was finally amplified. The modified-plasmid positive control, in which the SalI restriction-enzyme region (GTCGAC) was inserted, verified PRMV contamination in a comparison with the control, enabling a more accurate diagnosis. It is expected that the developed method will continuously contribute to the plant-quarantine process in Korea.

Partitioning of Antibiotic Resistance Genes and Fecal Indicators Varies Intra and Inter-Storm during Combined Sewer Overflows

PubMed Central

Eramo, Alessia; Delos Reyes, Hannah; Fahrenfeld, Nicole L.

2017-01-01

Combined sewer overflows (CSOs) degrade water quality through the release of microbial contaminants in CSO effluent. Improved understanding of the partitioning of microbial contaminants onto settleable particles can provide insight into their fate in end-of-pipe treatment systems or following release during CSO events. Sampling was performed across the hydrograph for three storm events as well as during baseflow and wet weather in three surface waters impacted by CSO. qPCR was performed for select antibiotic resistance genes (ARG) and a marker gene for human fecal indicator organisms (BacHum) in samples processed the partitioning of microbial contaminants on settleable particles versus suspended in the aqueous phase. Amplicon sequencing was performed on both fractions of storm samples to further define the timing and partitioning of microbial contaminants released during CSO events. Samples collected at the CSO outfall exhibited microbial community signatures of wastewater at select time points early or late in the storm events. CSOs were found to be a source of ARG. In surrounding surface waters, sul1 was higher in samples from select locations during wet weather compared to baseflow. Otherwise, ARG concentrations were variable with no differences between baseflow and wet weather conditions. The majority of ARG at the CSO outfall were observed on the attached fraction of samples: 64–79% of sul1 and 59–88% of tet(G). However, the timing of peak ARG and human fecal indicator marker gene BacHum did not necessarily coincide with observation of the microbial signature of wastewater in CSO effluent. Therefore, unit processes that remove settleable particles (e.g., hydrodynamic separators) operated throughout a CSO event would achieve up to (0.5–0.9)-log removal of ARG and fecal indicators by removing the attached fraction of measured genes. Secondary treatment would be required if greater removal of these targets is needed. PMID:29104562

TRACKING FECAL CONTAMINATION WITH BACTEROIDALES MOLECULAR MARKERS: AN ANALYSIS OF THE DYNAMICS OF FECAL CONTAMINATION IN THE TILLAMOOK BASIN, OREGON

EPA Science Inventory

Although amplification of source-specific molecular markers from Bacteroidales fecal bacteria can identify several different kinds of fecal contamination in water, it remains unclear how this technique relates to fecal indicator measurements in natural waters. The objectives of t...

Engineering Pseudomonas putida KT2440 for simultaneous degradation of organophosphates and pyrethroids and its application in bioremediation of soil.

PubMed

Zuo, Zhenqiang; Gong, Ting; Che, You; Liu, Ruihua; Xu, Ping; Jiang, Hong; Qiao, Chuanling; Song, Cunjiang; Yang, Chao

2015-06-01

Agricultural soils are usually co-contaminated with organophosphate (OP) and pyrethroid pesticides. To develop a stable and marker-free Pseudomonas putida for co-expression of two pesticide-degrading enzymes, we constructed a suicide plasmid with expression cassettes containing a constitutive promoter J23119, an OP-degrading gene (mpd), a pyrethroid-hydrolyzing carboxylesterase gene (pytH) that utilizes the upp gene as a counter-selectable marker for upp-deficient P. putida. By introduction of suicide plasmid and two-step homologous recombination, both mpd and pytH genes were integrated into the chromosome of a robust soil bacterium P. putida KT2440 and no selection marker was left on chromosome. Functional expression of mpd and pytH in P. putida KT2440 was demonstrated by Western blot analysis and enzyme activity assays. Degradation experiments with liquid cultures showed that the mixed pesticides including methyl parathion, fenitrothion, chlorpyrifos, permethrin, fenpropathrin, and cypermethrin (0.2 mM each) were degraded completely within 48 h. The inoculation of engineered strain (10(6) cells/g) to soils treated with the above mixed pesticides resulted in a higher degradation rate than in noninoculated soils. All six pesticides could be degraded completely within 15 days in fumigated and nonfumigated soils with inoculation. Theses results highlight the potential of the engineered strain to be used for in situ bioremediation of soils co-contaminated with OP and pyrethroid pesticides.

The Role of Biomarkers in the Assessment of Aquatic Ecosystem Health

PubMed Central

Hook, Sharon E; Gallagher, Evan P; Batley, Graeme E

2016-01-01

Ensuring the health of aquatic ecosystems and identifying species at risk from the detrimental effects of environmental contaminants can be facilitated by integrating analytical chemical analysis with carefully selected biological endpoints measured in tissues of species of concern. These biological endpoints include molecular, biochemical and physiological markers (i.e. biomarkers) that when integrated, can clarify issues of contaminant bioavailability, bioaccumulation and ecological effects while enabling a better understanding of the effects of non-chemical stressors. In the case of contaminant stressors, an understanding of chemical modes of toxicity can be incorporated with diagnostic markers of aquatic animal physiology to help understand the health status of aquatic organisms in the field. Furthermore, new approaches in functional genomics and bioinformatics can help discriminate individual chemicals, or groups of chemicals among complex mixtures that may contribute to adverse biological effects. While the use of biomarkers is not a new paradigm, such approaches have been underutilized in the context of ecological risk assessment and natural resource damage assessment. From a regulatory standpoint, these approaches can help better assess the complex effects from coastal development activities to assessing ecosystem integrity pre- and post-development or site remediation. PMID:24574147

A novel qPCR protocol for the specific detection and quantification of the fuel-deteriorating fungus Hormoconis resinae.

PubMed

Martin-Sanchez, Pedro M; Gorbushina, Anna A; Kunte, Hans-Jörg; Toepel, Jörg

2016-07-01

A wide variety of fungi and bacteria are known to contaminate fuels and fuel systems. These microbial contaminants have been linked to fuel system fouling and corrosion. The fungus Hormoconis resinae, a common jet fuel contaminant, is used in this study as a model for developing innovative risk assessment methods. A novel qPCR protocol to detect and quantify H. resinae in, and together with, total fungal contamination of fuel systems is reported. Two primer sets, targeting the markers RPB2 and ITS, were selected for their remarkable specificity and sensitivity. These primers were successfully applied on fungal cultures and diesel samples demonstrating the validity and reliability of the established qPCR protocol. This novel tool allows clarification of the current role of H. resinae in fuel contamination cases, as well as providing a technique to detect fungal outbreaks in fuel systems. This tool can be expanded to other well-known fuel-deteriorating microorganisms.

Biomarkers of Contaminant Exposure in Chub (Leuciscus cephalus L.) – Biomonitoring of Major Rivers in the Czech Republic

PubMed Central

Havelkova, Marcela; Blahova, Jana; Kroupova, Hana; Randak, Tomas; Slatinska, Iveta; Leontovycova, Drahomira; Grabic, Roman; Pospisil, Richard; Svobodova, Zdenka

2008-01-01

Biochemical analysis of organisms to assess exposure to environmental contaminants is of great potential use. Biochemical markers, specifically liver enzymes of the first and the second phase of xenobiotic transformation - cytochrome P450 (CYP 450), ethoxyresorufin-O-deethylase (EROD), glutathione-S-transferase (GST) and tripeptide reduced glutathione (GSH) - were used to assess contamination of the aquatic environment at 12 locations near the mouths of major rivers in the Czech Republic. These rivers were the Lužnice, Otava, Sázava, Berounka, Vltava, Labe, Ohře, Svratka, Dyje, Morava and Odra. The indicator species selected was the Chub (Leuciscus cephalus L.). The highest levels of CYP 450 and EROD catalytic activity were found in livers of fish from the Labe (Obříství; (0.32±0.10 nmol mg−1 protein and 1061.38±545.51 pmol min−1 mg−1 protein, respectively). The highest levels of GST catalytic activity and GSH content were found in fish from the Otava (35.39±13.35 nmol min−1 mg−1 protein and 4.29±2.10 nmol GSH mg−1 protein, respectively). They were compared with levels of specific inductors of these biochemical markers in muscle. The results confirmed contamination of some river locations (Labe Obříství, Svratka;. PMID:27879837

Utility of Microbial Source-Tracking Markers for Assessing Fecal Contamination in the Portage River Watershed, Northwestern Ohio, 2008

USGS Publications Warehouse

Kephart, Christopher M.; Bushon, Rebecca N.

2010-01-01

An influx of concentrated animal feeding operations in northwest Ohio has prompted local agencies to examine the effects of these industrial farms on water quality in the upper Portage River watershed. The utility of microbial source-tracking (MST) tools as a means of characterizing sources of fecal contamination in the watershed was evaluated. From 2007 to 2008, scientists with the U.S. Geological Survey, Bowling Green State University, and the Wood County Health Department collected and analyzed 17 environmental samples and 13 fecal source samples for Bacteroides-based host-associated DNA markers. At many of the environmental sites tested, MST marker results corroborated the presumptive fecal contamination sources. Results from this demonstration study support the utility of using MST with host-specific molecular markers to characterize the sources of fecal contamination in the Portage River watershed.

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

PubMed

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.

Faecal contamination of drinking water in a Brazilian shanty town: importance of household storage and new human faecal marker testing.

PubMed

Copeland, Curtis C; Beers, Benjamin B; Thompson, Meghan R; Fitzgerald, Relana P; Barrett, Leah J; Sevilleja, Jesus E; Alencar, Sayonara; Lima, Aldo A M; Guerrant, Richard L

2009-06-01

Worldwide, contaminated drinking water poses a major health threat, particularly to child development. Diarrhoea represents a large part of the water-related disease burden and enteric infections have been linked to nutritional and growth shortfalls as well as long-term physical and cognitive impairment in children. Previous studies detailed the frequency of infection and the consequences for child health in a shanty town in north-east Brazil. To determine the frequency of contaminated water, we measured faecal contamination in primary drinking water samples from 231 randomly selected households. Risk for contamination was compared across source and storage types. Nearly a third of the study households (70/231: 30.3%) had contaminated drinking water; the source with the highest frequency of contamination was well water (23/24: 95.8%). For tap water, the type of storage had a significant effect on the susceptibility to contamination (chi(2) = 12.090; p = 0.007). The observed pattern of contamination demonstrated the relative potential contributions of both source and storage. With evidence that supports the inclusion of source and storage in water quality surveys, this study, like others, suggests that contaminated drinking water in storage vessels may be an important factor for the documented diarrhoea disease burden in the Brazilian shanty town.

Transport of sewage molecular markers through saturated soil column and effect of easily biodegradable primary substrate on their removal.

PubMed

Foolad, Mahsa; Ong, Say Leong; Hu, Jiangyong

2015-11-01

Pharmaceutical and personal care products (PPCPs) and artificial sweeteners (ASs) are emerging organic contaminants (EOCs) in the aquatic environment. The presence of PPCPs and ASs in water bodies has an ecologic potential risk and health concern. Therefore, it is needed to detect the pollution sources by understanding the transport behavior of sewage molecular markers in a subsurface area. The aim of this study was to evaluate transport of nine selected molecular markers through saturated soil column experiments. The selected sewage molecular markers in this study were six PPCPs including acetaminophen (ACT), carbamazepine (CBZ), caffeine (CF), crotamiton (CTMT), diethyltoluamide (DEET), salicylic acid (SA) and three ASs including acesulfame (ACF), cyclamate (CYC), and saccharine (SAC). Results confirmed that ACF, CBZ, CTMT, CYC and SAC were suitable to be used as sewage molecular markers since they were almost stable against sorption and biodegradation process during soil column experiments. In contrast, transport of ACT, CF and DEET were limited by both sorption and biodegradation processes and 100% removal efficiency was achieved in the biotic column. Moreover, in this study the effect of different acetate concentration (0-100mg/L) as an easily biodegradable primary substrate on a removal of PPCPs and ASs was also studied. Results showed a negative correlation (r(2)>0.75) between the removal of some selected sewage chemical markers including ACF, CF, ACT, CYC, SAC and acetate concentration. CTMT also decreased with the addition of acetate, but increasing acetate concentration did not affect on its removal. CBZ and DEET removal were not dependent on the presence of acetate. Copyright © 2015 Elsevier Ltd. All rights reserved.

Human and Animal Fecal Contamination of Community Water Sources, Stored Drinking Water and Hands in Rural India Measured with Validated Microbial Source Tracking Assays

PubMed Central

Schriewer, Alexander; Odagiri, Mitsunori; Wuertz, Stefan; Misra, Pravas R.; Panigrahi, Pinaki; Clasen, Thomas; Jenkins, Marion W.

2015-01-01

We examined pathways of exposure to fecal contamination of human and animal origin in 24 villages in Odisha, India. In a cross-sectional study during the monsoon season, fecal exposure via community water sources (N = 123) and in the home (N = 137) was assessed using human- and nonhuman-associated Bacteroidales microbial source tracking (MST) markers and fecal coliforms (FCs). Detection rates and marker concentrations were examined to pinpoint pathways of human fecal exposure in the public and domestic domains of disease transmission in study communities. Human fecal markers were detected much more frequently in the domestic domain (45% of households) than in public domain sources (8% of ponds; 4% of groundwater drinking sources). Animal fecal markers were widely detected in both domains (74% of ponds, 96% of households, 10% of groundwater drinking sources), indicating ubiquitous risks of exposure to animal feces and zoonotic pathogens. This study confirms an often suggested contamination link from hands to stored water in the home in developing countries separately for mothers' and children's hands and both human and animal fecal contamination. In contrast to MST markers, FCs provided a poor metric to assess risks of exposure to fecal contamination of human origin in this rural setting. PMID:26149868

Ultra Low-Dose Radiation: Stress Responses and Impacts Using Rice as a Grass Model

PubMed Central

Rakwal, Randeep; Agrawal, Ganesh Kumar; Shibato, Junko; Imanaka, Tetsuji; Fukutani, Satoshi; Tamogami, Shigeru; Endo, Satoru; Sahoo, Sarata Kumar; Masuo, Yoshinori; Kimura, Shinzo

2009-01-01

We report molecular changes in leaves of rice plants (Oryza sativa L. - reference crop plant and grass model) exposed to ultra low-dose ionizing radiation, first using contaminated soil from the exclusion zone around Chernobyl reactor site. Results revealed induction of stress-related marker genes (Northern blot) and secondary metabolites (LC-MS/MS) in irradiated leaf segments over appropriate control. Second, employing the same in vitro model system, we replicated results of the first experiment using in-house fabricated sources of ultra low-dose gamma (γ) rays and selected marker genes by RT-PCR. Results suggest the usefulness of the rice model in studying ultra low-dose radiation response/s. PMID:19399245

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.

PubMed

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 potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination. © Crown copyright 2016.

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

PubMed Central

Grabuski, Josey; Sverko, Ed; Edge, Thomas A.

2016-01-01

ABSTRACT 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 log10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log10 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 log10 CFU/100 ml, and 7.65 log10 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. IMPORTANCE Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination. PMID:27542934

The Challenges and Solutions for Cadmium-contaminated Rice in China: A Critical Review.

PubMed

Hu, Yuanan; Cheng, Hefa; Tao, Shu

2016-01-01

The wide occurrence of Cd-contaminated rice in southern China poses significant public health risk and deserves immediate action, which arises primarily from extensive metal (including Cd) contamination of paddies with the fast expansion of nonferrous metal mining and smelting activities. Accumulation of Cd in rice grains can be reduced by removing Cd from the contaminated paddy soils, reducing its bioavailability, and controlling its uptake by rice plants. Although a range of measures can be taken to rehabilitate Cd-contaminated lands, including soil replacement and turnover, chemical washing, and phytoremediation, they are either too expensive and/or too slow. Various amendment materials, including lime, animal manures, and biochar, can be used to immobilize Cd in soils, but such fixation approach can only temporarily reduce Cd availability to rice uptake. Cultivation of alternative crops with low Cd accumulation in edible plant parts is impractical on large scales due to extensive contamination and food security concerns in southern China. Transgenic techniques can help develop rice cultivars with low Cd accumulation in grains, but little public acceptance is expected for such products. As an alternative, selection and development of low-Cd rice varieties and hybrids through plant biotechnology and breeding, particularly, by integration of marker-assisted selection (MAS) with traditional breeding, could be a practical and acceptable option that would allow continued rice production in soils with high bioavailability of Cd. Plant biotechnology and breeding can also help develop Cd-hyperaccumulating rice varieties, which can greatly facilitate phytoremediation of contaminated paddies. To eliminate the long-term risk of Cd entering the food chain, soils contaminated by Cd should be cleaned up when cost-effective remediation measures are available. Copyright © 2016 Elsevier Ltd. All rights reserved.

Human and Animal Fecal Contamination of Community Water Sources, Stored Drinking Water and Hands in Rural India Measured with Validated Microbial Source Tracking Assays.

PubMed

Schriewer, Alexander; Odagiri, Mitsunori; Wuertz, Stefan; Misra, Pravas R; Panigrahi, Pinaki; Clasen, Thomas; Jenkins, Marion W

2015-09-01

We examined pathways of exposure to fecal contamination of human and animal origin in 24 villages in Odisha, India. In a cross-sectional study during the monsoon season, fecal exposure via community water sources (N = 123) and in the home (N = 137) was assessed using human- and nonhuman-associated Bacteroidales microbial source tracking (MST) markers and fecal coliforms (FCs). Detection rates and marker concentrations were examined to pinpoint pathways of human fecal exposure in the public and domestic domains of disease transmission in study communities. Human fecal markers were detected much more frequently in the domestic domain (45% of households) than in public domain sources (8% of ponds; 4% of groundwater drinking sources). Animal fecal markers were widely detected in both domains (74% of ponds, 96% of households, 10% of groundwater drinking sources), indicating ubiquitous risks of exposure to animal feces and zoonotic pathogens. This study confirms an often suggested contamination link from hands to stored water in the home in developing countries separately for mothers' and children's hands and both human and animal fecal contamination. In contrast to MST markers, FCs provided a poor metric to assess risks of exposure to fecal contamination of human origin in this rural setting. © The American Society of Tropical Medicine and Hygiene.

Chemical contaminants (trace metals, persistent organic pollutants) in albacore tuna from western Indian and south-eastern Atlantic Oceans: Trophic influence and potential as tracers of populations.

PubMed

Chouvelon, Tiphaine; Brach-Papa, Christophe; Auger, Dominique; Bodin, Nathalie; Bruzac, Sandrine; Crochet, Sylvette; Degroote, Maxime; Hollanda, Stephanie J; Hubert, Clarisse; Knoery, Joël; Munschy, Catherine; Puech, Alexis; Rozuel, Emmanuelle; Thomas, Bastien; West, Wendy; Bourjea, Jérôme; Nikolic, Natacha

2017-10-15

Albacore tuna (Thunnus alalunga) is a highly commercial fish species harvested in the world's Oceans. Identifying the potential links between populations is one of the key tools that can improve the current management across fisheries areas. In addition to characterising populations' contamination state, chemical compounds can help refine foraging areas, individual flows and populations' structure, especially when combined with other intrinsic biogeochemical (trophic) markers such as carbon and nitrogen stable isotopes. This study investigated the bioaccumulation of seven selected trace metals - chromium, nickel, copper (Cu), zinc (Zn), cadmium (Cd), mercury (Hg) and lead - in the muscle of 443 albacore tunas, collected over two seasons and/or years in the western Indian Ocean (WIO: Reunion Island and Seychelles) and in the south-eastern Atlantic Ocean (SEAO: South Africa). The main factor that explained metal concentration variability was the geographic origin of fish, rather than the size and the sex of individuals, or the season/year of sampling. The elements Cu, Zn, Cd and Hg indicated a segregation of the geographic groups most clearly. For similar sized-individuals, tunas from SEAO had significantly higher concentrations in Cu, Zn and Cd, but lower Hg concentrations than those from WIO. Information inferred from the analysis of trophic markers (δ 13 C, δ 15 N) and selected persistent organic pollutants, as well as information on stomach contents, corroborated the geographical differences obtained by trace metals. It also highlighted the influence of trophic ecology on metal bioaccumulation. Finally, this study evidenced the potential of metals and chemical contaminants in general as tracers, by segregating groups of individuals using different food webs or habitats, to better understand spatial connectivity at the population scale. Limited flows of individuals between the SEAO and the WIO are suggested. Albacore as predatory fish also provided some information on environmental and food web chemical contamination in the different study areas. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparison of enterococci and cow-specific qPAR markers in streams impacted by farms under different management practices

EPA Science Inventory

Nonpoint Sources (NPS) of pollution (e.g., agriculture, wildlife, urban runoff) are major contributors of microbial contaminants to surface waters. However, little is known about the behavior and the effect of environmental determinants on molecular markers of fecal contamination...

Can volatile organic metabolites be used to simultaneously assess microbial and mite contamination level in cereal grains and coffee beans?

PubMed

Salvador, Angelo C; Baptista, Inês; Barros, António S; Gomes, Newton C M; Cunha, Angela; Almeida, Adelaide; Rocha, Silvia M

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC-ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC-ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans.

Can Volatile Organic Metabolites Be Used to Simultaneously Assess Microbial and Mite Contamination Level in Cereal Grains and Coffee Beans?

PubMed Central

Salvador, Ângelo C.; Baptista, Inês; Barros, António S.; Gomes, Newton C. M.; Cunha, Ângela; Almeida, Adelaide; Rocha, Silvia M.

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC×GC–ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC–ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC–ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans. PMID:23613710

Evaluation of the efficacy of a portable LIBS system for detection of CWA on surfaces.

PubMed

L'Hermite, D; Vors, E; Vercouter, T; Moutiers, G

2016-05-01

Laser-induced breakdown spectroscopy (LIBS) is a laser-based optical technique particularly suited for in situ surface analysis. A portable LIBS instrument was tested to detect surface chemical contamination by chemical warfare agents (CWAs). Test of detection of surface contamination was carried out in a toxlab facility with four CWAs, sarin (GB), lewisite (L1), mustard gas (HD), and VX, which were deposited on different substrates, wood, concrete, military green paint, gloves, and ceramic. The CWAs were detected by means of the detection of atomic markers (As, P, F, Cl, and S). The LIBS instrument can give a direct response in terms of detection thanks to an integrated interface for non-expert users or so called end-users. We have evaluated the capability of automatic detection of the selected CWAs. The sensitivity of our portable LIBS instrument was confirmed for the detection of a CWA at surface concentrations above 15 μg/cm(2). The simultaneous detection of two markers may lead to a decrease of the number of false positive.

Multiple-endpoints gene alteration-based (MEGA) assay: A toxicogenomics approach for water quality assessment of wastewater effluents.

PubMed

Fukushima, Toshikazu; Hara-Yamamura, Hiroe; Nakashima, Koji; Tan, Lea Chua; Okabe, Satoshi

2017-12-01

Wastewater effluents contain a significant number of toxic contaminants, which, even at low concentrations, display a wide variety of toxic actions. In this study, we developed a multiple-endpoints gene alteration-based (MEGA) assay, a real-time PCR-based transcriptomic analysis, to assess the water quality of wastewater effluents for human health risk assessment and management. Twenty-one genes from the human hepatoblastoma cell line (HepG2), covering the basic health-relevant stress responses such as response to xenobiotics, genotoxicity, and cytotoxicity, were selected and incorporated into the MEGA assay. The genes related to the p53-mediated DNA damage response and cytochrome P450 were selected as markers for genotoxicity and response to xenobiotics, respectively. Additionally, the genes that were dose-dependently regulated by exposure to the wastewater effluents were chosen as markers for cytotoxicity. The alterations in the expression of an individual gene, induced by exposure to the wastewater effluents, were evaluated by real-time PCR and the results were validated by genotoxicity (e.g., comet assay) and cell-based cytotoxicity tests. In summary, the MEGA assay is a real-time PCR-based assay that targets cellular responses to contaminants present in wastewater effluents at the transcriptional level; it is rapid, cost-effective, and high-throughput and can thus complement any chemical analysis for water quality assessment and management. Copyright © 2017 Elsevier Ltd. All rights reserved.

A novel two-step procedure to expand Sca-1+ cells clonally

PubMed Central

Tang, Yao Liang; Shen, Leping; Qian, Keping; Phillips, M. Ian

2007-01-01

Resident cardiac stem cells (CSCs) are characterized by their capacity to self-renew in culture, and are multi-potent for forming normal cell types in hearts. CSCs were originally isolated directly from enzymatically digested hearts using stem cell markers. However, long exposure to enzymatic digestion can affect the integrity of stem cell markers on the cell surface, and also compromise stem cell function. Alternatively resident CSCs can migrate from tissue explant and form cardiospheres in culture. However, fibroblast contamination can easily occur during CSC culture. To avoid these problems, we developed a two-step procedure by growing the cells before selecting the Sca1+ cells and culturing in cardiac fibroblast conditioned medium, they avoid fibroblast overgrowth. PMID:17577582

Biotechnological advances for combating Aspergillus flavus and aflatoxin contamination in crops.

PubMed

Bhatnagar-Mathur, Pooja; Sunkara, Sowmini; Bhatnagar-Panwar, Madhurima; Waliyar, Farid; Sharma, Kiran Kumar

2015-05-01

Aflatoxins are toxic, carcinogenic, mutagenic, teratogenic and immunosuppressive byproducts of Aspergillus spp. that contaminate a wide range of crops such as maize, peanut, and cotton. Aflatoxin not only affects crop production but renders the produce unfit for consumption and harmful to human and livestock health, with stringent threshold limits of acceptability. In many crops, breeding for resistance is not a reliable option because of the limited availability of genotypes with durable resistance to Aspergillus. Understanding the fungal/crop/environment interactions involved in aflatoxin contamination is therefore essential in designing measures for its prevention and control. For a sustainable solution to aflatoxin contamination, research must be focused on identifying and improving knowledge of host-plant resistance factors to aflatoxin accumulation. Current advances in genetic transformation, proteomics, RNAi technology, and marker-assisted selection offer great potential in minimizing pre-harvest aflatoxin contamination in cultivated crop species. Moreover, developing effective phenotyping strategies for transgenic as well as precision breeding of resistance genes into commercial varieties is critical. While appropriate storage practices can generally minimize post-harvest aflatoxin contamination in crops, the use of biotechnology to interrupt the probability of pre-harvest infection and contamination has the potential to provide sustainable solution. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Breeding aflatoxin-resistant maize lines using recent advances in technologies - a review.

PubMed

Brown, Robert L; Menkir, Abebe; Chen, Zhi-Yuan; Bhatnagar, Deepak; Yu, Jiujiang; Yao, Haibo; Cleveland, Thomas E

2013-01-01

Aflatoxin contamination caused by Aspergillus flavus infection of corn is a significant and chronic threat to corn being used as food or feed. Contamination of crops at levels of 20 ng g(-1) or higher (as regulated by the USFDA) by this toxin and potent carcinogen makes the crop unsalable, resulting in a significant economic burden on the producer. This review focuses on elimination of this contamination in corn which is a major US crop and the basis of many products. Corn is also "nature's example" of a crop containing heritable resistance to aflatoxin contamination, thereby serving as a model for achieving resistance to aflatoxin contamination in other crops as well. This crop is the largest production grain crop worldwide, providing food for billions of people and livestock and critical feedstock for production of biofuels. In 2011, the economic value of the US corn crop was US$76 billion, with US growers producing an estimated 12 billion bushels, more than one-third of the world's supply. Thus, the economics and significance of corn as a food crop and the threat to food safety due to aflatoxin contamination of this major food crop have prompted the many research efforts in many parts of the world to identify resistance in corn to aflatoxin contamination. Plant breeding and varietal selection has been used as a tool to develop varieties resistance to disease. This methodology has been employed in defining a few corn lines that show resistance to A. flavus invasion; however, no commercial lines have been marketed. With the new tools of proteomics and genomics, identification of resistance mechanisms, and rapid resistance marker selection methodologies, there is an increasing possibility of finding significant resistance in corn, and in understanding the mechanism of this resistance.

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence

USGS Publications Warehouse

Stoeckel, D.M.; Stelzer, E.A.; Stogner, R.W.; Mau, D.P.

2011-01-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections-augmented with local observations and land-use patterns-indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. ?? 2011 Elsevier Ltd.

Multicenter evaluation of a new closed system drug-transfer device in reducing surface contamination by antineoplastic hazardous drugs.

PubMed

Bartel, Sylvia B; Tyler, Timothy G; Power, Luci A

2018-02-15

Results of a study to evaluate the effectiveness of a recently introduced closed system drug-transfer device (CSTD) in reducing surface contamination during compounding and simulated administration of antineoplastic hazardous drugs (AHDs) are reported. Wipe samples were collected from 6 predetermined surfaces in compounding and infusion areas of 13 U.S. cancer centers to establish preexisting levels of surface contamination by 2 marker AHDs (cyclophosphamide and fluorouracil). Stainless steel templates were placed over the 6 previously sampled surfaces, and the marker drugs were compounded and infused per a specific protocol using all components of the CSTD. Wipe samples were collected from the templates after completion of tasks and analyzed for both marker AHDs. Aggregated results of wipe sampling to detect preexisting contamination at the 13 study sites showed that overall, 66.7% of samples (104 of 156) had detectable levels of at least 1 marker AHD; subsequent testing after CSTD use per protocol found a sample contamination rate of 5.8% (9 of 156 samples). In the administration areas alone, the rate of preexisting contamination was 78% (61 of 78 samples); with use of the CSTD protocol, the contamination rate was 2.6%. Twenty-six participants rated the CSTD for ease of use, with 100% indicating that they were satisfied or extremely satisfied. A study involving a rigorous protocol and 13 cancer centers across the United States demonstrated that the CSTD reduced surface contamination by cyclophosphamide and fluorouracil during compounding and simulated administration. Participants reported that the CSTD was easy to use. Copyright © 2018 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Microbial Source Tracking in Adjacent Karst Springs.

PubMed

Ohad, Shoshanit; Vaizel-Ohayon, Dalit; Rom, Meir; Guttman, Joseph; Berger, Diego; Kravitz, Valeria; Pilo, Shlomo; Huberman, Zohar; Kashi, Yechezkel; Rorman, Efrat

2015-08-01

Modern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. Microbial source tracking (MST) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. This study was intended to assess karst spring susceptibilities to different fecal sources using MST quantitative PCR (qPCR) assays targeting human, bovine, and swine markers. It involved a dual-time monitoring frame: (i) monthly throughout the calendar year and (ii) daily during a rainfall event. Data integration was taken from both monthly and daily MST profile monitoring and improved identification of spring susceptibility to host fecal contamination; three springs located in close geographic proximity revealed different MST profiles. The Giach spring showed moderate fluctuations of MST marker quantities amid wet and dry samplings, while the Zuf spring had the highest rise of the GenBac3 marker during the wet event, which was mirrored in other markers as well. The revelation of human fecal contamination during the dry season not connected to incidents of raining leachates suggests a continuous and direct exposure to septic systems. Pigpens were identified in the watersheds of Zuf, Shefa, and Giach springs and on the border of the Gaaton spring watershed. Their impact was correlated with partial detection of the Pig-2-Bac marker in Gaaton spring, which was lower than detection levels in all three of the other springs. Ruminant and swine markers were detected intermittently, and their contamination potential during the wet samplings was exposed. These results emphasized the importance of sampling design to utilize the MST approach to delineate subtleties of fecal contamination in the environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Using host-associated genetic markers to investigate sources of fecal contamination in two Vermont streams

USGS Publications Warehouse

Medalie, Laura; Matthews, Leslie J.; Stelzer, Erin A.

2011-01-01

The use of host-associated Bacteroidales-based 16S ribosomal ribonucleic acid genetic markers was investigated as a tool for providing information to managers on sources of bacterial impairment in Vermont streams. The study was conducted during 2009 in two watersheds on the U.S. Environmental Protection Agency's 303(d) List of Impaired Waters, the Huntington and the Mettawee Rivers. Streamwater samples collected during high-flow and base-flow conditions were analyzed for concentrations of Escherichia coli (E. coli) and Bacteroidales genetic markers (General AllBac, Human qHF183 and BacHum, Ruminant BoBac, and Canid BacCan) to identify humans, ruminants, and canids as likely or unlikely major sources of fecal contamination. Fecal reference samples from each of the potential source groups, as well as from common species of wildlife, were collected during the same season and from the same watersheds as water samples. The results were combined with data from other states to assess marker cross reaction and to relate marker results to E. coli, the regulated water-quality parameter, with a higher degree of statistical significance. Results from samples from the Huntington River collected under different flow conditions on three dates indicated that humans were unlikely to be a major source of fecal contamination, except for a single positive result at one station that indicated the potential for human sources. Ruminants (deer, moose, cow, or sheep) were potential sources of fecal contamination at all six stations on the Huntington River during one high-flow event and at all but two stations during the other high-flow event. Canids were potential sources of fecal contamination at some stations during two high-flow events, with genetic-marker concentrations in samples from two of the six stations showing consistent positive results for canids for both storm dates. A base-flow sample showed no evidence of major fecal contamination in the Huntington River from humans, ruminants, or canids. Results from samples from the Mettawee River watershed collected during high-flow conditions (12 storm samples on 2 dates at 6 stations) indicated that there was no evidence of fecal contamination from humans in seven samples and possible evidence in five samples. Results for humans were positive for only one station during both storm events. For two of the five samples with evidence for human fecal contamination, results for two different human genetic markers agreed, but results from three samples were inconsistent. In samples from five of the six Mettawee stations, ruminants were a potential source of fecal contamination on at least one of the three sampled dates, including three positive results for the base-flow sample. Yet samples from all of the stations that showed positive results for ruminants did so for only one or two of the three sampled dates. Samples from only one of the six stations gave consistent results, which were negative for ruminants for all three dates. In the Mettawee River base-flow sample, humans were an unlikely source of major fecal contamination. Factors that may influence results and conclusions include the timing of sample collection relative to the storm event; variability of E. coli and Bacteroidales concentrations in fecal reference samples and in water; sampling and analytical errors; the potential cross reactivity of host-associated genetic markers; and different persistence and survival rates of E. coli bacteria and Bacteroidales genetic markers on land, in water, and by season. These factors interfere with the ability to directly relate Bacteroidales concentrations to E. coli concentrations in river samples. It must be recognized that while use of Bacteroidales genetic markers as a source tracking tool coupled with the interpretive approach described in this report cannot be used quantitatively to pinpoint sources, it can be used to exclude potential sources as major contributors to fecal contamination.

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

USDA-ARS?s Scientific Manuscript database

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. These contaminants can be mobilized into the water column due to resuspension events, thus affecting overall water quality. Along with the contaminants, other markers such as microbia...

EFFECTS OF A HIGHLY-CONTAMINATED URBAN HARBOR ON AN ESTUARINE FISH SPECIES: NEUTRAL MARKERS OF POPULATION GENETIC STRUCTURE

EPA Science Inventory

Fundulus heteroclitus populations indigenous to certain highly contaminated sites demonstrate an inherited tolerance to the toxic effects of local chemical contaminants. Our initial studies examining populations of F. heterclitus indigenous to a PCB-contaminated Superfund site at...

Canine scent detection and microbial source tracking of human waste contamination in storm drains.

PubMed

Van De Werfhorst, Laurie C; Murray, Jill L S; Reynolds, Scott; Reynolds, Karen; Holden, Patricia A

2014-06-01

Human fecal contamination of surface waters and drains is difficult to diagnose. DNA-based and chemical analyses of water samples can be used to specifically quantify human waste contamination, but their expense precludes routine use. We evaluated canine scent tracking, using two dogs trained to respond to the scent of municipal wastewater, as a field approach for surveying human fecal contamination. Fecal indicator bacteria, as well as DNA-based and chemical markers of human waste, were analyzed in waters sampled from canine scent-evaluated sites (urban storm drains and creeks). In the field, the dogs responded positively (70% and 100%) at sites for which sampled waters were then confirmed as contaminated with human waste. When both dogs indicated a negative response, human waste markers were absent. Overall, canine scent tracking appears useful for prioritizing sampling sites for which DNA-based and similarly expensive assays can confirm and quantify human waste contamination.

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii

PubMed Central

Caffaro-Filho, Roberto A.; Wong, Mayee; Harwood, Valerie J.; Moravcik, Philip; Fujioka, Roger S.

2016-01-01

ABSTRACT Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. IMPORTANCE This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and Escherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers. PMID:27613686

Isolation and gene expression analysis of single potential human spermatogonial stem cells.

PubMed

von Kopylow, K; Schulze, W; Salzbrunn, A; Spiess, A-N

2016-04-01

It is possible to isolate pure populations of single potential human spermatogonial stem cells without somatic contamination for down-stream applications, for example cell culture and gene expression analysis. We isolated pure populations of single potential human spermatogonial stem cells (hSSC) without contaminating somatic cells and analyzed gene expression of these cells via single-cell real-time RT-PCR. The isolation of a pure hSSC fraction could enable clinical applications such as fertility preservation for prepubertal boys and in vitro-spermatogenesis. By utilizing largely nonspecific markers for the isolation of spermatogonia (SPG) and hSSC, previously published cell selection methods are not able to deliver pure target cell populations without contamination by testicular somatic cells. However, uniform cell populations free of somatic cells are necessary to guarantee defined growth conditions in cell culture experiments and to prevent unintended stem cell differentiation. Fibroblast growth factor receptor 3 (FGFR3) is a cell surface protein of human undifferentiated A-type SPG and a promising candidate marker for hSSC. It is exclusively expressed in small, non-proliferating subgroups of this spermatogonial cell type together with the pluripotency-associated protein and spermatogonial nuclear marker undifferentiated embryonic cell transcription factor 1 (UTF1). We specifically selected the FGFR3-positive spermatogonial subpopulation from two 30 mg biopsies per patient from a total of 37 patients with full spermatogenesis and three patients with meiotic arrest. We then employed cell selection with magnetic beads in combination with a fluorescence-activated cell sorter antibody directed against human FGFR3 to tag and visually identify human FGFR3-positive spermatogonia. Positively selected and bead-labeled cells were subsequently picked with a micromanipulator. Analysis of the isolated cells was carried out by single-cell real-time RT-PCR, real-time RT-PCR, immunocytochemistry and live/dead staining. Single-cell real-time RT-PCR and real-time RT-PCR of pooled cells indicate that bead-labeled single cells express FGFR3 with high heterogeneity at the mRNA level, while bead-unlabeled cells lack FGFR3 mRNA. Furthermore, isolated cells exhibit strong immunocytochemical staining for the stem cell factor UTF1 and are viable. The cell population isolated in this study has to be tested for their potential stem cell characteristics via xenotransplantation. Due to the small amount of the isolated cells, propagation by cell culture will be essential. Other potential hSSC without FGFR3 surface expression will not be captured with the provided experimental design. The technical approach as developed in this work could encourage the scientific community to test other established or novel hSSC markers on single SPG that present with potential stem cell-like features. The project was funded by the DFG Research Unit FOR1041 Germ cell potential (SCH 587/3-2) and DFG grants to K.v.K. (KO 4769/2-1) and A.-N.S. (SP 721/4-1). The authors declare no competing interests. © The Author 2016. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence.

PubMed

Stoeckel, Donald M; Stelzer, Erin A; Stogner, Robert W; Mau, David P

2011-05-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections--augmented with local observations and land-use patterns--indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. Copyright © 2011 Elsevier Ltd. All rights reserved.

New methods to improve the safety assessment of cryopreserved ovarian tissue for fertility preservation in breast cancer patients.

PubMed

Rodríguez-Iglesias, Beatriz; Novella-Maestre, Edurne; Herraiz, Sonia; Díaz-García, César; Pellicer, Nuria; Pellicer, Antonio

2015-12-01

To develop a novel molecular panel of markers to detect breast cancer (BC) disseminated malignant cells in ovarian tissue, and to improve the safety of ovarian tissue transplantation. Experimental study. University hospital. Ten ovarian biopsies from healthy patients, 13 biopsies with diagnosed BC metastasis, and 4 biopsies from primary BC tumor for designing a diagnostic panel of BC cell contamination; 60 ovarian biopsies from BC patients undergoing fertility preservation for validating the panel. Female nude mice. A novel panel for BC malignant cell detection by reverse-transcription polymerase chain reaction (RT-PCR), inmmunohistochemical analysis, in vitro invasion assay and xenotransplantation assayed in ovarian tissue from BC patients. Expression of GCDFP15, MGB1, SBEM, MUC1, WT-1, and NY-BR-01, selected as markers, assessed by quantitative RT-PCR in samples with confirmed BC metastasis. The most sensitive markers were confirmed by immunohistochemistry, and tested in vitro and in vivo. GCDFP15, MGB1, and SBEM were the most sensitive and specific markers to detect BC metastatic cells when at least one was expressed by quantitative RT-PCR. The panel was validated in 60 patients and confirmed in an in vitro invasion assay, where no invasive cells were observed. Samples negative for BC cells cannot develop disease when xenografted. GCDFP15, MGB1, and SBEM were the most sensitive molecules to create a diagnostic panel for BC malignant cell contamination, which may make ovarian tissue cryopreservation and transplantation a safe technique for fertility preservation in BC patients. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Distribution and decline of human pathogenic bacteria in soil after application in irrigation water and the potential for soil-splash-mediated dispersal onto fresh produce.

PubMed

Monaghan, J M; Hutchison, M L

2012-05-01

To improve our understanding of the survival and splash-mediated transfer of zoonotic agents and faecal indicator bacteria introduced into soils used for crop cultivation via contaminated irrigation waters. Zoonotic agents and an Escherichia coli marker bacterium were inoculated into borehole water, which was applied to two different soil types in early-, mid- and late summer. Decline of the zoonotic agents was influenced by soil type. Marker bacteria applied to columns of two soil types in irrigation water did not concentrate at the surface of the soils. Decline of zoonotic agents at the surface was influenced by soil type and environmental conditions. Typically, declines were rapid and bacteria were not detectable after 5 weeks. Selective agar strips were used to determine that the impact of water drops 24-87 μl could splash marker bacteria from soil surfaces horizontal distances of at least 25 cm and heights of 20 cm. Soil splash created by rain-sized water droplets can transfer enteric bacteria from soil to ready-to-eat crops. Persistence of zoonotic agents was reduced at the hottest part of the growing season when irrigation is most likely. Soil splash can cause crop contamination. We report the penetration depths and seasonally influenced declines of bacteria applied in irrigation water into two soil types. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation.

PubMed

Chikere, Chioma B; Surridge, Karen; Okpokwasili, Gideon C; Cloete, Thomas E

2012-03-01

Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The present study therefore demonstrated that the soil investigated harbours hydrocarbon-degrading bacterial populations which can be biostimulated to achieve effective bioremediation of oil-contaminated soil.

Surface contamination of hazardous drug pharmacy storage bins and pharmacy distributor shipping containers.

PubMed

Redic, Kimberly A; Fang, Kayleen; Christen, Catherine; Chaffee, Bruce W

2018-03-01

Purpose This study was conducted to determine whether there is contamination on exterior drug packaging using shipping totes from the distributor and carousel storage bins as surrogate markers of external packaging contamination. Methods A two-part study was conducted to measure the presence of 5-fluorouracil, ifosfamide, cyclophosphamide, docetaxel and paclitaxel using surrogate markers for external drug packaging. In Part I, 10 drug distributor shipping totes designated for transport of hazardous drugs provided a snapshot view of contamination from regular use and transit in and out of the pharmacy. An additional two totes designated for transport of non-hazardous drugs served as controls. In Part II, old carousel storage bins (i.e. those in use pre-study) were wiped for snapshot view of hazardous drug contamination on storage bins. New carousel storage bins were then put into use for storage of the five tested drugs and used for routine storage and inventory maintenance activities. Carousel bins were wiped at time intervals 0, 8, 16 and 52 weeks to measure surface contamination. Results Two of the 10 hazardous shipping totes were contaminated. Three of the five-old carousel bins were contaminated with cyclophosphamide. One of the old carousel bins was also contaminated with ifosfamide. There were no detectable levels of hazardous drugs on any of the new storage bins at time 0, 8 or 16 weeks. However, at the Week 52, there was a detectable level of 5-FU present in the 5-FU carousel bin. Conclusions Contamination of the surrogate markers suggests that external packaging for hazardous drugs is contaminated, either during the manufacturing process or during routine chain of custody activities. These results demonstrate that occupational exposure may occur due to contamination from shipping totes and storage bins, and that handling practices including use of personal protective equipment is warranted.

Use of Bacteroidales Microbial Source Tracking To Monitor Fecal Contamination in Fresh Produce Production

PubMed Central

Ravaliya, Kruti; Garcia, Santos; Heredia, Norma; Fabiszewski de Aceituno, Anna; Bartz, Faith E.; Leon, Juan S.; Jaykus, Lee-Ann

2014-01-01

In recent decades, fresh and minimally processed produce items have been associated with an increasing proportion of food-borne illnesses. Most pathogens associated with fresh produce are enteric (fecal) in origin, and contamination can occur anywhere along the farm-to-fork chain. Microbial source tracking (MST) is a tool developed in the environmental microbiology field to identify and quantify the dominant source(s) of fecal contamination. This study investigated the utility of an MST method based on Bacteroidales 16S rRNA gene sequences as a means of identifying potential fecal contamination, and its source, in the fresh produce production environment. The method was applied to rinses of fresh produce, source and irrigation waters, and harvester hand rinses collected over the course of 1 year from nine farms (growing tomatoes, jalapeño peppers, and cantaloupe) in Northern Mexico. Of 174 samples, 39% were positive for a universal Bacteroidales marker (AllBac), including 66% of samples from cantaloupe farms (3.6 log10 genome equivalence copies [GEC]/100 ml), 31% of samples from tomato farms (1.7 log10 GEC/100 ml), and 18% of samples from jalapeño farms (1.5 log10 GEC/100 ml). Of 68 AllBac-positive samples, 46% were positive for one of three human-specific markers, and none were positive for a bovine-specific marker. There was no statistically significant correlation between Bacteroidales and generic Escherichia coli across all samples. This study provides evidence that Bacteroidales markers may serve as alternative indicators for fecal contamination in fresh produce production, allowing for determination of both general contamination and that derived from the human host. PMID:24212583

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

PubMed

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

2011-05-01

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

Development of swine-specific DNA markers for biosensor-based halal authentication.

PubMed

Ali, M E; Hashim, U; Kashif, M; Mustafa, S; Che Man, Y B; Abd Hamid, S B

2012-06-29

The pig (Sus scrofa) mitochondrial genome was targeted to design short (15-30 nucleotides) DNA markers that would be suitable for biosensor-based hybridization detection of target DNA. Short DNA markers are reported to survive harsh conditions in which longer ones are degraded into smaller fragments. The whole swine mitochondrial-genome was in silico digested with AluI restriction enzyme. Among 66 AluI fragments, five were selected as potential markers because of their convenient lengths, high degree of interspecies polymorphism and intraspecies conservatism. These were confirmed by NCBI blast analysis and ClustalW alignment analysis with 11 different meat-providing animal and fish species. Finally, we integrated a tetramethyl rhodamine-labeled 18-nucleotide AluI fragment into a 3-nm diameter citrate-tannate coated gold nanoparticle to develop a swine-specific hybrid nanobioprobe for the determination of pork adulteration in 2.5-h autoclaved pork-beef binary mixtures. This hybrid probe detected as low as 1% pork in deliberately contaminated autoclaved pork-beef binary mixtures and no cross-species detection was recorded, demonstrating the feasibility of this type of probe for biosensor-based detection of pork adulteration of halal and kosher foods.

Combining yeast display and competitive FACS to select rare hapten-specific clones from recombinant antibody libraries

DOE PAGES

Sun, Yue; Ban, Bhupal; Bradbury, Andrew; ...

2016-08-29

The development of antibodies to low molecular weight haptens remains challenging due to both the low immunogenicity of many haptens and the cross-reactivity of the protein carriers used to generate the immune response. Recombinant antibodies and novel display technologies have greatly advanced antibody development; however, new techniques are still required to select rare hapten-specific antibodies from large recombinant libraries. In the present study, we used a combination of phage and yeast display to screen an immune antibody library (size, 4.4 × 10 6 ) against hapten markers for petroleum contamination (phenanthrene and methylphenanthrenes). Selection via phage display was used firstmore » to enrich the library between 20- and 100- fold for clones that bound to phenanthrene-protein conjugates. The enriched libraries were subsequently transferred to a yeast display system and a newly developed competitive FACS procedure was employed to select rare hapten-specific clones. Competitive FACS increased the frequency of hapten-specific scFvs in our yeast-displayed scFvs from 0.025 to 0.005% in the original library to between 13 and 35% in selected pools. The presence of hapten-specific scFvs was confirmed by competitive ELISA using periplasmic protein. Three distinct antibody clones that recognize phenanthrene and methylphenanthrenes were selected, and their distinctive binding properties were characterized. To our knowledge, these are first antibodies that can distinguish between methylated (petrogenic) versus unmethylated (pyrogenic) phenanthrenes; such antibodies will be useful in detecting the sources of environmental contamination. Furthermore, this selection method could be generally adopted in the selection of other hapten-specific recombinant antibodies.« less

Combining yeast display and competitive FACS to select rare hapten-specific clones from recombinant antibody libraries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Yue; Ban, Bhupal; Bradbury, Andrew

The development of antibodies to low molecular weight haptens remains challenging due to both the low immunogenicity of many haptens and the cross-reactivity of the protein carriers used to generate the immune response. Recombinant antibodies and novel display technologies have greatly advanced antibody development; however, new techniques are still required to select rare hapten-specific antibodies from large recombinant libraries. In the present study, we used a combination of phage and yeast display to screen an immune antibody library (size, 4.4 × 10 6 ) against hapten markers for petroleum contamination (phenanthrene and methylphenanthrenes). Selection via phage display was used firstmore » to enrich the library between 20- and 100- fold for clones that bound to phenanthrene-protein conjugates. The enriched libraries were subsequently transferred to a yeast display system and a newly developed competitive FACS procedure was employed to select rare hapten-specific clones. Competitive FACS increased the frequency of hapten-specific scFvs in our yeast-displayed scFvs from 0.025 to 0.005% in the original library to between 13 and 35% in selected pools. The presence of hapten-specific scFvs was confirmed by competitive ELISA using periplasmic protein. Three distinct antibody clones that recognize phenanthrene and methylphenanthrenes were selected, and their distinctive binding properties were characterized. To our knowledge, these are first antibodies that can distinguish between methylated (petrogenic) versus unmethylated (pyrogenic) phenanthrenes; such antibodies will be useful in detecting the sources of environmental contamination. Furthermore, this selection method could be generally adopted in the selection of other hapten-specific recombinant antibodies.« less

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii.

PubMed

Kirs, Marek; Caffaro-Filho, Roberto A; Wong, Mayee; Harwood, Valerie J; Moravcik, Philip; Fujioka, Roger S

2016-11-15

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and Escherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

What is in your cup of tea? DNA Verity Test to characterize black and green commercial teas

PubMed Central

Comparone, Maria; Di Maio, Antonietta; Del Guacchio, Emanuele; Menale, Bruno; Troisi, Jacopo; Aliberti, Francesco

2017-01-01

In this study, we used several molecular techniques to develop a fast and reliable protocol (DNA Verity Test, DVT) for the characterization and confirmation of the species or taxa present in herbal infusions. As a model plant for this protocol, Camellia sinensis, a traditional tea plant, was selected due to the following reasons: its historical popularity as a (healthy) beverage, its high selling value, the importation of barely recognizable raw product (i.e., crushed), and the scarcity of studies concerning adulterants or contamination. The DNA Verity Test includes both the sequencing of DNA barcoding markers and genotyping of labeled-PCR DNA barcoding fragments for each sample analyzed. This protocol (DVT) was successively applied to verify the authenticity of 32 commercial teas (simple or admixture), and the main results can be summarized as follows: (1) the DVT protocol is suitable to detect adulteration in tea matrices (contaminations or absence of certified ingredients), and the method can be exported for the study of other similar systems; (2) based on the BLAST analysis of the sequences of rbcL+matK±rps7-trnV(GAC) chloroplast markers, C. sinensis can be taxonomically characterized; (3) rps7-trnV(GAC) can be employed to discriminate C. sinensis from C. pubicosta; (4) ITS2 is not an ideal DNA barcode for tea samples, reflecting potential incomplete lineage sorting and hybridization/introgression phenomena in C. sinensis taxa; (5) the genotyping approach is an easy, inexpensive and rapid pre-screening method to detect anomalies in the tea templates using the trnH(GUG)-psbA barcoding marker; (6) two herbal companies provided no authentic products with a contaminant or without some of the listed ingredients; and (7) the leaf matrices present in some teabags could be constituted using an admixture of different C. sinensis haplotypes and/or allied species (C. pubicosta). PMID:28542606

Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake.

PubMed

Staley, Christopher; Reckhow, Kenneth H; Lukasik, Jerzy; Harwood, Valerie J

2012-11-01

We investigated the potential for a variety of environmental reservoirs to harbor or contribute fecal indicator bacteria (FIB), DNA markers of human fecal contamination, and human pathogens to a freshwater lake. We hypothesized that submerged aquatic vegetation (SAV), sediments, and stormwater act as reservoirs and/or provide inputs of FIB and human pathogens to this inland water. Analysis included microbial source tracking (MST) markers of sewage contamination (Enterococcus faecium esp gene, human-associated Bacteroides HF183, and human polyomaviruses), pathogens (Salmonella, Cryptosporidium, Giardia, and enteric viruses), and FIB (fecal coliforms, Escherichia coli, and enterococci). Bayesian analysis was used to assess relationships among microbial and physicochemical variables. FIB in the water were correlated with concentrations in SAV and sediment. Furthermore, the correlation of antecedent rainfall and major rain events with FIB concentrations and detection of human markers and pathogens points toward multiple reservoirs for microbial contaminants in this system. Although pathogens and human-source markers were detected in 55% and 21% of samples, respectively, markers rarely coincided with pathogen detection. Bayesian analysis revealed that low concentrations (<45 CFU × 100 ml(-1)) of fecal coliforms were associated with 93% probability that pathogens would not be detected; furthermore the Bayes net model showed associations between elevated temperature and rainfall with fecal coliform and enterococci concentrations, but not E. coli. These data indicate that many under-studied matrices (e.g. SAV, sediment, stormwater) are important reservoirs for FIB and potentially human pathogens and demonstrate the usefulness of Bayes net analysis for water quality assessment. Copyright © 2012 Elsevier Ltd. All rights reserved.

Targeted Approach to Identify Genetic Loci Associated with ...

EPA Pesticide Factsheets

Extreme tolerance to highly toxic dioxin-like contaminants (DLCs) has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly contaminated urban/industrialized estuaries of the US Atlantic coast. We hypothesized that comparisons among tolerant populations and in contrast to their sensitive neighboring killifish might reveal genetic loci associated with DLC tolerance. Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, we identified single nucleotide polymorphisms (SNPs) from 43 genes associated with the AHR to serve as targeted markers. Wild fish from the four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Consistent with other killifish population genetic analyses, our results revealed strong genetic differentiation among populations, consistent with isolation by distance models. Pairwise comparisons of nearby tolerant and sensitive populations revealed differentiation among these loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP) 1A and 3A30, and the NADH ubiquinone oxidoreductase MLRQ subunit. By grouping tolerant versus sensitive populations, we also identified cytochrome P450 1A and the AHR2 loci as under selection, lend

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

EPA Science Inventory

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...

Fluorescent marker for the detection of crop and upper gastrointestinal leakage in poultry processing plants.

PubMed

Byrd, J A; Hargis, B M; Corrier, D E; Brewer, R L; Caldwell, D J; Bailey, R H; McReynolds, J L; Herron, K L; Stanker, L H

2002-01-01

Previous published research has identified the crop as a source of Salmonella and Campylobacter contamination for broiler carcasses and reported that broiler crops are 86 times more likely to rupture than ceca during commercial processing. Presently, we evaluated leakage of crop and upper gastrointestinal contents from broilers using a fluorescent marker at commercial processing plants. Broilers were orally gavaged with a fluorescent marker paste (corn meal-fluorescein dye-agar) within 30 min of live hang. Carcasses were collected at several points during processing and were examined for upper gastrointestinal leakage using long-wavelength black light. This survey indicated that 67% of the total broiler carcasses were positive for the marker at the rehang station following head and shank removal. Crops were mechanically removed from 61% of the carcasses prior to the cropper, and visual online examination indicated leakage of crop contents following crop removal by the pack puller. Examination of the carcasses prior to the cropper detected the marker in the following regions: neck (50.5% positive), thoracic inlet (69.7% positive), thoracic cavity (35.4% positive), and abdominal cavity (34.3% positive). Immediately prior to chill immersion, 53.2% of the carcasses contained some degree of visually identifiable marker contamination, as follows: neck (41.5% positive), thoracic inlet (45.2% positive), thoracic cavity (26.2% positive), and abdominal cavity (30.2% positive). These results suggest that this fluorescent marker technique may serve as a useful tool for rapid identification of potential changes, which could reduce the incidence of crop rupture and contamination of carcasses at processing.

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

NASA Astrophysics Data System (ADS)

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.

Quantitative microbial risk assessment of microbial source tracking markers in recreational water contaminated with fresh untreated and secondary treated sewage.

PubMed

Ahmed, Warish; Hamilton, Kerry A; Lobos, Aldo; Hughes, Bridie; Staley, Christopher; Sadowsky, Michael J; Harwood, Valerie J

2018-05-14

Microbial source tracking (MST) methods have provided the means to identify sewage contamination in recreational waters, but the risk associated with elevated levels of MST targets such as sewage-associated Bacteroides HF183 and other markers is uncertain. Quantitative microbial risk assessment (QMRA) modeling allows interpretation of MST data in the context of the risk of gastrointestinal (GI) illness caused by exposure to known reference pathogens. In this study, five sewage-associated, quantitative PCR (qPCR) MST markers [Bacteroides HF183 (HF183), Methanobrevibacter smithii nifH (nifH), human adenovirus (HAdV), human polyomavirus (HPyV) and pepper mild mottle virus (PMMoV)] were evaluated to determine at what concentration these nucleic acid markers reflected a significant health risk from exposure to fresh untreated or secondary treated sewage in beach water. The QMRA models were evaluated for a target probability of illness of 36 GI illnesses/1000 swimming events (i.e., risk benchmark 0.036) for the reference pathogens norovirus (NoV) and human adenovirus 40/41 (HAdV 40/41). Sewage markers at several dilutions exceeded the risk benchmark for reference pathogens NoV and HAdV 40/41. HF183 concentrations 3.22 × 10 3 (for both NoV and HAdV 40/41) gene copies (GC)/100 mL of water contaminated with fresh untreated sewage represented risk >0.036. Similarly, HF183 concentrations 3.66 × 10 3 (for NoV and HAdV 40/41) GC/100 mL of water contaminated with secondary treated sewage represented risk >0.036. HAdV concentration as low as 4.11 × 10 1 GC/100 mL of water represented risk >0.036 when water was contaminated with secondary treated sewage. Results of this study provide a valuable context for water quality managers to evaluate human health risks associated with contamination from fresh sewage. The approach described here may also be useful in the future for evaluating health risks from contamination with aged or treated sewage or feces from other animal sources as more data are made available. Copyright © 2018 Elsevier Ltd. All rights reserved.

Role of chromatography in the development of Standard Reference Materials for organic analysis.

PubMed

Wise, Stephen A; Phinney, Karen W; Sander, Lane C; Schantz, Michele M

2012-10-26

The certification of chemical constituents in natural-matrix Standard Reference Materials (SRMs) at the National Institute of Standards and Technology (NIST) can require the use of two or more independent analytical methods. The independence among the methods is generally achieved by taking advantage of differences in extraction, separation, and detection selectivity. This review describes the development of the independent analytical methods approach at NIST, and its implementation in the measurement of organic constituents such as contaminants in environmental materials, nutrients and marker compounds in food and dietary supplement matrices, and health diagnostic and nutritional assessment markers in human serum. The focus of this review is the important and critical role that separation science techniques play in achieving the necessary independence of the analytical steps in the measurement of trace-level organic constituents in natural matrix SRMs. Published by Elsevier B.V.

Short communication: Quantification of the transmission of microorganisms to milk via dirt attached to the exterior of teats.

PubMed

Vissers, M M M; Driehuis, F; Te Giffel, M C; De Jong, P; Lankveld, J M G

2007-08-01

Pathogens and spoilage microorganisms can be transmitted to milk via dirt (e.g., feces, bedding material, soil, or a combination of these) attached to the exterior of the cows' teats. To determine the relevance of this pathway and to perform quantitative microbial risk analysis of the microbial contamination of farm tank milk (FTM), it is important to know the amount of dirt transmitted to milk via the exterior of teats. In this study at 11 randomly selected Dutch farms the amount of dirt transmitted to milk via the exterior of teats is determined using spores of mesophilic aerobic bacteria as a marker for transmitted dirt. The amount of transmitted dirt to milk varied among farms from approximately 3 to 300 mg/L, with an average of 59 mg/L. The usefulness of the data for microbial risk analyses is briefly illustrated using the contamination of FTM with spores of butyric acid bacteria as a case study. In a similar way the data can be used to identify measures to control the contamination of FTM with other microorganisms or chemical residues.

Development of goose- and duck-specific DNA markers to determine sources of Escherichia coli in waterways.

PubMed

Hamilton, Matthew J; Yan, Tao; Sadowsky, Michael J

2006-06-01

The contamination of waterways with fecal material is a persistent threat to public health. Identification of the sources of fecal contamination is a vital component for abatement strategies and for determination of total maximum daily loads. While phenotypic and genotypic techniques have been used to determine potential sources of fecal bacteria in surface waters, most methods require construction of large known-source libraries, and they often fail to adequately differentiate among environmental isolates originating from different animal sources. In this study, we used pooled genomic tester and driver DNAs in suppression subtractive hybridizations to enrich for host source-specific DNA markers for Escherichia coli originating from locally isolated geese. Seven markers were identified. When used as probes in colony hybridization studies, the combined marker DNAs identified 76% of the goose isolates tested and cross-hybridized, on average, with 5% of the human E. coli strains and with less than 10% of the strains obtained from other animal hosts. In addition, the combined probes identified 73% of the duck isolates examined, suggesting that they may be useful for determining the contribution of waterfowl to fecal contamination. However, the hybridization probes reacted mainly with E. coli isolates obtained from geese in the upper midwestern United States, indicating that there is regional specificity of the markers identified. Coupled with high-throughput, automated macro- and microarray screening, these markers may provide a quantitative, cost-effective, and accurate library-independent method for determining the sources of genetically diverse E. coli strains for use in source-tracking studies. However, future efforts to generate DNA markers specific for E. coli must include isolates obtained from geographically diverse animal hosts.

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

PubMed

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.

Deoxynivalenol Impairs Weight Gain and Affects Markers of Gut Health after Low-Dose, Short-Term Exposure of Growing Pigs

PubMed Central

Alizadeh, Arash; Braber, Saskia; Akbari, Peyman; Garssen, Johan; Fink-Gremmels, Johanna

2015-01-01

Deoxynivalenol (DON) is one of the major mycotoxins produced by Fusarium fungi, and exposure to this mycotoxin requires an assessment of the potential adverse effects, even at low toxin levels. The aim of this study was to investigate the effects of a short-term, low-dose DON exposure on various gut health parameters in pigs. Piglets received a commercial feed or the same feed contaminated with DON (0.9 mg/kg feed) for 10 days, and two hours after a DON bolus (0.28 mg/kg BW), weight gain was determined and samples of different segments of the intestine were collected. Even the selected low dose of DON in the diet negatively affected weight gain and induced histomorphological alterations in the duodenum and jejunum. The mRNA expression of different tight junction (TJ) proteins, especially occludin, of inflammatory markers, like interleukin-1 beta and interleukin-10 and the oxidative stress marker heme-oxigenase1, were affected along the intestine by low levels of DON in the diet. Taken together, our results indicate that even after low-level exposure to DON, which has been generally considered as acceptable in animal feeds, clinically-relevant changes are measurable in markers of gut health and integrity. PMID:26067367

Estimation of Pig Fecal Contamination in a River Catchment by Real-Time PCR Using Two Pig-Specific Bacteroidales 16S rRNA Genetic Markers▿

PubMed Central

Mieszkin, Sophie; Furet, Jean-Pierre; Corthier, Gérard; Gourmelon, Michèle

2009-01-01

The microbiological quality of coastal or river water can be affected by fecal contamination from human or animal sources. To discriminate pig fecal pollution from other pollution, a library-independent microbial source tracking method targeting Bacteroidales host-specific 16S rRNA gene markers by real-time PCR was designed. Two pig-specific Bacteroidales markers (Pig-1-Bac and Pig-2-Bac) were designed using 16S rRNA gene Bacteroidales clone libraries from pig feces and slurry. For these two pig markers, 98 to 100% sensitivity and 100% specificity were obtained when tested by TaqMan real-time PCR. A decrease in the concentrations of Pig-1-Bac and Pig-2-Bac markers was observed throughout the slurry treatment chain. The two newly designed pig-specific Bacteroidales markers, plus the human-specific (HF183) and ruminant-specific (BacR) Bacteroidales markers, were then applied to river water samples (n = 24) representing 14 different sites from the French Daoulas River catchment (Brittany, France). Pig-1-Bac and Pig-2-Bac were quantified in 25% and 62.5%, respectively, of samples collected around pig farms, with concentrations ranging from 3.6 to 4.1 log10 copies per 100 ml of water. They were detected in water samples collected downstream from pig farms but never detected near cattle farms. HF183 was quantified in 90% of water samples collected downstream near Daoulas town, with concentrations ranging between 3.6 and 4.4 log10 copies per 100 ml of water, and BacR in all water samples collected around cattle farms, with concentrations ranging between 4.6 and 6.0 log10 copies per 100 ml of water. The results of this study highlight that pig fecal contamination was not as frequent as human or bovine fecal contamination and that fecal pollution generally came from multiple origins. The two pig-specific Bacteroidales markers can be applied to environmental water samples to detect pig fecal pollution. PMID:19329663

Improvement of mineral oil saturated and aromatic hydrocarbons determination in edible oil by liquid-liquid-gas chromatography with dual detection.

PubMed

Zoccali, Mariosimone; Barp, Laura; Beccaria, Marco; Sciarrone, Danilo; Purcaro, Giorgia; Mondello, Luigi

2016-02-01

Mineral oils, which are mainly composed of saturated hydrocarbons and aromatic hydrocarbons, are widespread food contaminants. Liquid chromatography coupled to gas chromatography with flame ionization detection represents the method of choice to determine these two families. However, despite the high selectivity of this technique, the presence of olefins (particularly squalene and its isomers) in some samples as in olive oils, does not allow the correct quantification of the mineral oil aromatic hydrocarbons fraction, requiring additional off-line tools to eliminate them. In the present research, a novel on-line liquid chromatography coupled to gas chromatography method is described for the determination of hydrocarbon contamination in edible oils. Two different liquid chromatography columns, namely a silica one (to retain the bulk of the matrix) and a silver-ion one (which better retains the olefins), were coupled in series to obtain the mineral oil aromatic hydrocarbons hump free of interfering peaks. Furthermore, the use of a simultaneous dual detection, flame ionization detector and triple quadrupole mass spectrometer allowed us not only to quantify the mineral oil contamination, but also to evaluate the presence of specific markers (i.e. hopanes) to confirm the petrogenic origin of the contamination. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of an anaesthesia workstation barrier device to decrease contamination in a simulated operating room.

PubMed

Hunter, S; Katz, D; Goldberg, A; Lin, H-M; Pasricha, R; Benesh, G; Le Grand, B; DeMaria, S

2017-06-01

Strategies to achieve reductions in perioperative infections have focused on hand hygiene among anaesthestists but have been of limited efficacy. We performed a study in a simulated operating room to determine whether a barrier covering the anaesthesia workstation during induction and intubation might reduce the risk of contamination of the area and possibly, by extension, the patient. Forty-two attending and resident anaesthetists unaware of the study design were enrolled in individual simulation sessions in which they were asked to induce and intubate a human simulator that had been prepared with fluorescent marker in its oropharynx as a marker of potentially pathogenic bacteria. Twenty-one participants were assigned to a control group, whereas the other 21 performed the simulation with a barrier device covering the anaesthesia workstation. After the simulation, an investigator examined 14 target sites with an ultraviolet light to assess spread of the fluorescent marker of contamination to those sites. The difference in rates of contamination between the control group and the barrier group was highly significant, with 44.8% (2.5%) of sites contaminated in the control group vs 19.4% (2.6%) of sites in the barrier group ( P <0.001). Several key clinical sites showed significant differences in addition to this overall decrement. The results of this study suggest that application of a barrier device to the anaesthesia workstation during induction and intubation might reduce contamination of the intraoperative environment. © The Author 2017. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Spiked GBS: A unified, open platform for single marker genotyping and whole-genome profiling

USDA-ARS?s Scientific Manuscript database

In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Typically, marker platforms have addressed only one of t...

Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers

PubMed Central

Letellier, Ann; Fravalo, Philippe; Brassard, Julie; L'Homme, Yvan

2016-01-01

ABSTRACT Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively. IMPORTANCE Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country. PMID:27940545

Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers.

PubMed

Lachapelle, Virginie; Letellier, Ann; Fravalo, Philippe; Brassard, Julie; L'Homme, Yvan

2017-02-15

Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively. Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country. © Crown copyright 2017.

Antimicrobial-Resistance Genetic Markers in Potentially Pathogenic Gram Positive Cocci Isolated from Brazilian Soft Cheese.

PubMed

Resende, Juliana Alves; Fontes, Cláudia Oliveira; Ferreira-Machado, Alessandra Barbosa; Nascimento, Thiago César; Silva, Vânia Lúcia; Diniz, Cláudio Galuppo

2018-02-01

Although most Brazilian dairy products meet high technological standards, there are quality issues regarding milk production, which may reduce the final product quality. Several microbial species may contaminate milk during manufacture and handling. If antimicrobial usage remains uncontrolled in dairy cattle, the horizontal transfer of antimicrobial resistance genes in foodstuffs may be of particular concern for both food producers and dairy industry. This study focused on the evaluation of putative Gram positive cocci in Minas cheese and of antimicrobial and biocide resistance genes among the isolated bacteria. Representative samples of 7 different industrially trademarked Minas cheeses (n = 35) were processed for selective culture and isolation of Gram positive cocci. All isolated bacteria were identified by DNA sequencing of the 16S rRNA gene. Antimicrobial resistance genes were screened by PCR. Overall, 208 strains were isolated and identified as follows: Enterococcus faecalis (47.6%), Macrococcus caseolyticus (18.3%), Enterococcus faecium (11.5%), Enterococcus caseliflavus (7.7%), Staphylococcus haemolyticus (7.2%), Staphylococcus aureus (4.3%), Staphylococcus epidermidis (2.9%), and Enterococcus hirae (0.5%). The genetic markers mecA (78.0%) and smr (71.4%) were the most prevalent, but others were also detected, such as blaZ (65.2%), msrA (60.9%), msrB (46.6%), linA (54.7%), and aacA-aphD (47.6%). The occurrence of opportunist pathogenic bacteria harboring antimicrobial resistance markers in the cheese samples are of special concern, since these bacteria are not considered harmful contaminating agents according to the Brazilian sanitary regulations. However, they are potentially pathogenic bacteria and the cheese may be considered a reservoir for antimicrobial resistance genes available for horizontal transfer through the food chain, manufacturing personnel and consumers. © 2018 Institute of Food Technologists®.

Short-term microbial release during rain events from on-site sewers and cattle in a surface water source.

PubMed

Aström, Johan; Pettersson, Thomas J R; Reischer, Georg H; Hermansson, Malte

2013-09-01

The protection of drinking water from pathogens such as Cryptosporidium and Giardia requires an understanding of the short-term microbial release from faecal contamination sources in the catchment. Flow-weighted samples were collected during two rainfall events in a stream draining an area with on-site sewers and during two rainfall events in surface runoff from a bovine cattle pasture. Samples were analysed for human (BacH) and ruminant (BacR) Bacteroidales genetic markers through quantitative polymerase chain reaction (qPCR) and for sorbitol-fermenting bifidobacteria through culturing as a complement to traditional faecal indicator bacteria, somatic coliphages and the parasitic protozoa Cryptosporidium spp. and Giardia spp. analysed by standard methods. Significant positive correlations were observed between BacH, Escherichia coli, intestinal enterococci, sulphite-reducing Clostridia, turbidity, conductivity and UV254 in the stream contaminated by on-site sewers. For the cattle pasture, no correlation was found between any of the genetic markers and the other parameters. Although parasitic protozoa were not detected, the analysis for genetic markers provided baseline data on the short-term faecal contamination due to these potential sources of parasites. Background levels of BacH and BacR makers in soil emphasise the need to including soil reference samples in qPCR-based analyses for Bacteroidales genetic markers.

Cholinesterase characterization of two autochthonous species of Ria de Aveiro (Diopatra neapolitana and Solen marginatus) and comparison of sensitivities towards a series of common contaminants.

PubMed

Nunes, Bruno; Resende, Sara Teixeira

2017-05-01

Biomonitoring of chemical contamination requires the use of well-established and validated tools, including biochemical markers that can be potentially affected by exposure to important environmental toxicants. Cholinesterases (ChEs) are present in a large number of species and have been successfully used for decades to discriminate the environmental presence of specific groups of pollutants. The success of cholinesterase inhibition has been due to their usefulness as a biomarker to address the presence of organophosphate (OP) and carbamate (CB) pesticides. However, its use in ecotoxicology has not been limited to such chemicals, and several other putative classes of contaminants have been implicated in cholinesterasic impairment. Nevertheless, the use of cholinesterases as a monitoring tool requires its full characterization in species to be used as test organisms. This study analyzed and differentiated the various cholinesterase forms present in two autochthonous organisms from the Ria de Aveiro (Portugal) area, namely the polychaete Diopatra neapolitana and the bivalve Solen marginatus, to be used in subsequent monitoring studies. In addition, this study also validated the putative use of the now characterized cholinesterasic forms by analyzing the in vitro effects of common anthropogenic contaminants, such as detergents, pesticides, and metals. The predominant cholinesterasic form found in tissues of D. neapolitana was acetylcholinesterase, while homogenates of S. marginatus were shown to possess an atypical cholinesterasic form, with a marked preference for propionylthiocholine. Cholinesterases from D. neapolitana were generally non-responsive towards the majority of the selected chemicals. On the contrary, strong inhibitory effects were reported for ChEs of S. marginatus following exposure to the selected pesticides.

Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters.

PubMed

Ahmed, Warish; Zhang, Qian; Lobos, Aldo; Senkbeil, Jacob; Sadowsky, Michael J; Harwood, Valerie J; Saeidi, Nazanin; Marinoni, Oswald; Ishii, Satoshi

2018-07-01

Stormwater contamination can threaten the health of aquatic ecosystems and human exposed to runoff via nutrient and pathogen influxes. In this study, the concentrations of 11 bacterial pathogens and 47 antibiotic resistance genes (ARGs) were determined by using high-throughput microfluidic qPCR (MFQPCR) in several storm drain outfalls (SDOs) during dry and wet weather in Tampa Bay, Florida, USA. Data generated in this study were also compared with the levels of fecal indicator bacteria (FIB) and sewage-associated molecular markers (i.e., Bacteroides HF183 and crAssphage markers) in same SDOs collected in a recent study (Ahmed et al., 2018). Concentration of FIB, sewage-associated markers, bacterial pathogens and many ARGs in water samples were relatively high and SDOs may be potentially hotspots for microbial contamination in Tampa Bay. Mean concentrations of culturable E. coli and Enterococcus spp. were tenfold higher in wet compared to dry weather. The majority of microbiological contaminants followed this trend. E. coli eaeA, encoding the virulence factor intimin, was correlated with levels of 20 ARGs, and was more frequently detected in wet weather than dry weather samples. The bla KPC gene associated with carbapenem resistant Enterobacteriaceae and the beta-lactam resistant gene (bla NPS ) were only detected in wet weather samples. Frequency of integron genes Intl2 and Intl3 detection increased by 42% in wet weather samples. Culturable E. coli and Enterococcus spp. significantly correlated with 19 of 47 (40%) ARG tested. Sewage-associated markers crAssphage and HF183 significantly correlated (p < 0.05) with the following ARGs: intl1, sul1, tet(M), ampC, mexB, and tet(W). The presence of sewage-associated marker genes along with ARGs associated with sewage suggested that aging sewage infrastructure contributed to contaminant loading in the Bay. Further research should focus on collecting spatial and temporal data on the microbiological contaminants especially viruses in SDOs. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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.

Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

USGS Publications Warehouse

Nevers, Meredith; Byappanahalli, Muruleedhara; Phanikumar, Mantha S.; Whitman, Richard L.

2016-01-01

Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches

PubMed Central

Hamilton, K. A.; Gyawali, P.; Toze, S.; Haas, C. N.

2016-01-01

ABSTRACT Avian and possum fecal droppings may negatively impact roof-harvested rainwater (RHRW) water quality due to the presence of zoonotic pathogens. This study was aimed at evaluating the performance characteristics of a possum feces-associated (PSM) marker by screening 210 fecal and wastewater samples from possums (n = 20) and a range of nonpossum hosts (n = 190) in Southeast Queensland, Australia. The host sensitivity and specificity of the PSM marker were 0.90 and 0.95 (maximum value, 1.00), respectively. The mean concentrations of the GFD marker in possum fecal DNA samples (8.8 × 107 gene copies per g of feces) were two orders of magnitude higher than those in the nonpossum fecal DNA samples (5.0 × 105 gene copies per g of feces). The host sensitivity, specificity, and concentrations of the avian feces-associated GFD marker were reported in our recent study (W. Ahmed, V. J. Harwood, K. Nguyen, S. Young, K. Hamilton, and S. Toze, Water Res 88:613–622, 2016, http://dx.doi.org/10.1016/j.watres.2015.10.050). The utility of the GFD and PSM markers was evaluated by testing a large number of tank water samples (n = 134) from the Brisbane and Currumbin areas. GFD and PSM markers were detected in 39 of 134 (29%) and 11 of 134 (8%) tank water samples, respectively. The GFD marker concentrations in PCR-positive samples ranged from 3.7 × 102 to 8.5 × 105 gene copies per liter, whereas the concentrations of the PSM marker ranged from 2.0 × 103 to 6.8 × 103 gene copies per liter of water. The results of this study suggest the presence of fecal contamination in tank water samples from avian and possum hosts. This study has established an association between the degradation of microbial tank water quality and avian and possum feces. Based on the results, we recommend disinfection of tank water, especially for tanks designated for potable use. IMPORTANCE The use of roof-harvested rainwater (RHRW) for domestic purposes is a globally accepted practice. The presence of pathogens in rainwater tanks has been reported by several studies, supporting the necessity for the management of potential health risks. The sources of fecal pollution in rainwater tanks are unknown. However, the application of microbial source tracking (MST) markers has the potential to identify the sources of fecal contamination in a rainwater tank. In this study, we provide evidence of avian and possum fecal contamination in tank water samples using molecular markers. This study established a potential link between the degradation of the microbial quality of tank water and avian and possum feces. PMID:27208100

Genomic selection in plant breeding.

PubMed

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.

PAH body burden and biomarker responses in mussels (Mytilus edulis) exposed to produced water from a North Sea oil field: laboratory and field assessments.

PubMed

Sundt, Rolf C; Pampanin, Daniela M; Grung, Merete; Baršienė, Janina; Ruus, Anders

2011-07-01

In order to study the impact of produced water (PW) from a North Sea oil field on blue mussels (Mytilus edulis), chemical and biological markers were selected. A laboratory exposure (0.125%, 0.25% and 0.5% of PW) and a field study (6 stations 0.2-2 km from a PW discharge point) were conducted. In the laboratory study, PAH bioaccumulation increased in mussel soft tissue even at the lowest exposure dose. Micronuclei frequency demonstrated a dose-response pattern, whereas lysosomal membrane stability showed tendency towards a dose-response pattern. The same markers were assessed in the field study, biomarker analyses were consistent with the contamination level, as evaluated by mussel polycyclic aromatic hydrocarbons body burden. Overall, obtained results confirmed the value of an ecotoxicological approach for a scientifically sound characterisation of biological effects induced by offshore oilfield operational discharges. Copyright © 2011 Elsevier Ltd. All rights reserved.

Hydrophilic anthropogenic markers for quantification of wastewater contamination in ground- and surface waters.

PubMed

Kahle, Maren; Buerge, Ignaz J; Müller, Markus D; Poiger, Thomas

2009-12-01

Hydrophilic, persistent markers are useful to detect, locate, and quantify contamination of natural waters with domestic wastewater. The present study focused on occurrence and fate of seven marker candidates including carbamazepine (CBZ), 10,11-dihydro-10,11-dihydroxycarbamazepine (DiOH-CBZ), primidone (PMD), crotamiton (CTMT), N-acetyl-4-aminoantipyrine (AAA), N-formyl-4-aminoantipyrine (FAA), and benzotriazole (BTri) in wastewater treatment plants (WWTPs), lakes, and groundwater. In WWTPs, concentrations from 0.14 microg/L to several micrograms per liter were observed for all substances, except CTMT, which was detected at lower concentrations. Loads determined in untreated and treated wastewater indicated that removal of the potential markers in WWTPs is negligible; only BTri was partly eliminated (average 33%). In lakes, five compounds, CBZ, DiOH-CBZ, FAA, AAA, and BTri, were consistently detected in concentrations of 2 to 70 ng/L, 3 to 150 ng/L, less than the limit of quantification to 30 ng/L, 2 to 80 ng/L, and 11 to 920 ng/L, respectively. Mean per capita loads in the outflows of the lakes suggested possible dissipation in surface waters, especially of AAA and FAA. Nevertheless, concentrations of CBZ, DiOH-CBZ, and BTri correlated with the actual anthropogenic burden of the lakes by domestic wastewater, indicating that these compounds are suitable for quantification of wastewater contamination in lakes. Marker candidates were also detected in a number of groundwater samples. Carbamazepine concentrations up to 42 ng/L were observed in aquifers with significant infiltration of river water, receiving considerable wastewater discharges from WWTPs. Concentration ratios between compounds indicated some elimination of BTri and DiOH-CBZ during subsurface passage or in groundwater, while CBZ and PMD appeared to be more stable and thus are promising wastewater markers for groundwater. The wastewater burden in groundwater, estimated with the markers CBZ and PMD, reached up to 6%.

Contamination of soils by metals and organic micropollutants: case study of the Parisian conurbation.

PubMed

Gaspéri, Johnny; Ayrault, Sophie; Moreau-Guigon, Elodie; Alliot, Fabrice; Labadie, Pierre; Budzinski, Hélène; Blanchard, Martine; Muresan, Bogdan; Caupos, Emilie; Cladière, Mathieu; Gateuille, David; Tassin, Bruno; Bordier, Louise; Teil, Marie-Jeanne; Bourges, Catherine; Desportes, Annie; Chevreuil, Marc; Moilleron, Régis

2016-11-10

Soils are playing a central role in the transfer and accumulation of anthropogenic pollutants in urbanized regions. Hence, this study aimed at examining the contamination levels of selected soils collected within and around the Paris conurbation (France). This also evaluated factors controlling contamination. Twenty-three trace and major elements as well as 82 organic micropollutants including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalates (PAEs), polybrominated diphenyl ethers (PBDEs), alkylphenols (APs), and perfluoroalkylated substances (PFASs) were analyzed. Results reinforced the concern raised by the occurrence and levels of metals such as Zn, Pb, Cu, and Hg, identified as metallic markers of anthropogenic activities, but also pointed out the ubiquitous contamination of soils by organic micropollutants in the 0.2-55,000-μg/kg dw range. For well-documented compounds like PAHs, PCBs, and to a lesser extent PBDEs, contents were in the range of background levels worldwide. The pollutant stock in tested soil was compared to the annual atmospheric input. For PAHs; Pb; and to a lesser extent Zn, Cu, Cd, Hg, Sb, PAEs, and APs, a significant stock was observed, far more important than the recent annual atmospheric fluxes. This resulted from both (i) the persistence of a fraction of pollutants in surface soils and (ii) the cumulative atmospheric inputs over several decades. Regarding PBDEs and PFASs, stronger atmospheric input contributions were observed, thereby highlighting their recent dispersal into the environment.

Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.)

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) and marker-assisted selection (MAS) rely on marker-trait associations and are both routinely used for breeding purposes. Although similar, these two approaches differ in their applications and how markers are used to estimate breeding values. In this study, GS and MAS were com...

Optimal selection of markers for validation or replication from genome-wide association studies.

PubMed

Greenwood, Celia M T; Rangrej, Jagadish; Sun, Lei

2007-07-01

With reductions in genotyping costs and the fast pace of improvements in genotyping technology, it is not uncommon for the individuals in a single study to undergo genotyping using several different platforms, where each platform may contain different numbers of markers selected via different criteria. For example, a set of cases and controls may be genotyped at markers in a small set of carefully selected candidate genes, and shortly thereafter, the same cases and controls may be used for a genome-wide single nucleotide polymorphism (SNP) association study. After such initial investigations, often, a subset of "interesting" markers is selected for validation or replication. Specifically, by validation, we refer to the investigation of associations between the selected subset of markers and the disease in independent data. However, it is not obvious how to choose the best set of markers for this validation. There may be a prior expectation that some sets of genotyping data are more likely to contain real associations. For example, it may be more likely for markers in plausible candidate genes to show disease associations than markers in a genome-wide scan. Hence, it would be desirable to select proportionally more markers from the candidate gene set. When a fixed number of markers are selected for validation, we propose an approach for identifying an optimal marker-selection configuration by basing the approach on minimizing the stratified false discovery rate. We illustrate this approach using a case-control study of colorectal cancer from Ontario, Canada, and we show that this approach leads to substantial reductions in the estimated false discovery rates in the Ontario dataset for the selected markers, as well as reductions in the expected false discovery rates for the proposed validation dataset. Copyright 2007 Wiley-Liss, Inc.

CHEMICAL MARKERS OF HUMAN WASTE ...

EPA Pesticide Factsheets

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 densities that they can be measured easily. However, most of these microbes, for example E. coli, do not serve as specific markers for any one host species and many can have origins other than feces. As an alternative, chemicals shed in feces and urine might be used to detect human waste contamination of environmental waters. One potential chemical marker of human waste is the compound urobilin. Urobilin is one of the final by-products of hemoglobin breakdown. Urobilin is excreted in both the urine and feces from many mammals, particularly humans. Source waters from 21 sites in New England, Nevada, and Michigan were extracted using hydrophilic-lipophilic balance (HLB) cartridges and then analyzed by high performance liquid chromatography-electrospray-mass spectrometry (HPLC-ES-MS). As a marker of human waste, urobilin was detected in many of the source waters at concentrations ranging from not detectable to 300 ng/L. Besides urobilin, zithromycin, an antibiotic widely prescribed for human-use only in the US, was also detected in many of these waters, with concentrations ranging from not detectable to 77 ng/L. This methodology, using both urobilin and azithromycin (or any other human-use

Altering the selection capabilities of common cloning vectors via restriction enzyme mediated gene disruption

PubMed Central

2013-01-01

Background The cloning of gene sequences forms the basis for many molecular biological studies. One important step in the cloning process is the isolation of bacterial transformants carrying vector DNA. This involves a vector-encoded selectable marker gene, which in most cases, confers resistance to an antibiotic. However, there are a number of circumstances in which a different selectable marker is required or may be preferable. Such situations can include restrictions to host strain choice, two phase cloning experiments and mutagenesis experiments, issues that result in additional unnecessary cloning steps, in which the DNA needs to be subcloned into a vector with a suitable selectable marker. Results We have used restriction enzyme mediated gene disruption to modify the selectable marker gene of a given vector by cloning a different selectable marker gene into the original marker present in that vector. Cloning a new selectable marker into a pre-existing marker was found to change the selection phenotype conferred by that vector, which we were able to demonstrate using multiple commonly used vectors and multiple resistance markers. This methodology was also successfully applied not only to cloning vectors, but also to expression vectors while keeping the expression characteristics of the vector unaltered. Conclusions Changing the selectable marker of a given vector has a number of advantages and applications. This rapid and efficient method could be used for co-expression of recombinant proteins, optimisation of two phase cloning procedures, as well as multiple genetic manipulations within the same host strain without the need to remove a pre-existing selectable marker in a previously genetically modified strain. PMID:23497512

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

USDA-ARS?s Scientific Manuscript database

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...

Water quality and sources of fecal coliform bacteria in the Meduxnekeag River, Houlton, Maine

USGS Publications Warehouse

Culbertson, Charles W.; Huntington, Thomas G.; Stoeckel, Donald M.; Caldwell, James M.; O'Donnell, Cara

2014-01-01

In response to bacterial contamination in the Meduxnekeag River and the desire to manage the watershed to reduce contaminant sources, the Houlton Band of Maliseet Indians (HBMI) and the U.S. Geological Survey began a cooperative effort to establish a baseline of water-quality data that can be used in future studies and to indicate potential sources of nutrient and bacterial contamination. This study was conducted during the summer of 2005 in the Meduxnekeag River Basin near Houlton, Maine. Continuously recorded specific conductance can be a good indicator for water quality. Specific conductance increased downstream from the town of Houlton, between runoff events, and decreased sharply following major runoff events. Collections of discrete samples during the summer of 2005 indicated seasonal positive concentration-discharge relations for total phosphorus and total nitrogen; these results indicate that storm runoff may mobilize and transport these nutrients from the terrestrial environment to the river. Data collected by the HBMI on fecal coliform bacteria indicated that bacterial contamination enters the Meduxnekeag River from multiple paths including tributaries and surface drains (ditches) in developed areas in Houlton, Maine. The Houlton wastewater treatment discharge was not an important source of bacterial contamination. Bacteroidales-based tests for general fecal contamination (Bac32 marker) were predominantly positive in samples that had excessive fecal contamination as indicated by Enterococci density greater than 104 colony-forming units per 100 millilters. Of the 22 samples tested for Bacteroidales-based markers of human-associated fecal contamination (HF134 and HF183), 8 were positive. Of the 22 samples tested for Bacteroidales-based markers of ruminant-associated fecal contamination (CF128 and CF193), 7 were positive. Human fecal contamination was detected consistently at two sites (surface drains in urban areas in the town of Houlton) and occasionally detected at one site (Moose Brook) but was not detected at other sites. Fecal contamination (as indicated by fecal coliform density) apparently is localized under normal flow conditions with the highest levels restricted to drains in urban areas and to a lesser extent B Stream, Pearce Brook, and Big Brook, all tributaries to the main stem of the Meduxnekeag River. Coliphage were enumerated as an alternate indicator of fecal contamination with the intent of typing the virus into host-associated classes (human or ruminant), as was done for Enterococci; however, insufficient coliphage were isolated to provide more than preliminary indications. In spite of low coliphage enumeration, the preliminary results strengthen the conclusion that the Enterococci data correctly indicated the samples that contained human and ruminant fecal contamination. The finding that contamination was in many of the tributaries following storms in mid-July indicates that storm runoff likely carries fecal contaminants to more locations than runoff under lower flow conditions.

Anthropopression markers in lake bottom sediments

NASA Astrophysics Data System (ADS)

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 top layer of sediments consists of organic sediment ("sapropel" type). The littoral zone is dominated by sandy material from the shores denudation. In river mouths sandy deltas are formed. The most contaminated sediments are deposited in the central pool, which is a natural trap for the substances flowing with the river that is draining wastewaters from urban areas. At its mouth the sediment samples were significantly contaminated with chromium, zinc, cadmium, copper, nickel, lead and mercury. A high content of total phosphorus was also detected. A different role is played by a large river flowing through the lake. While flushing the sediments it reduces their pollution. The lowest content of markers was detected in headwater areas and in littoral zones exposed to waving.

Phytoremediation of the organic Xenobiotic simazine by p450-1a2 transgenic Arabidopsis thaliana plants.

PubMed

Azab, Ehab; Hegazy, Ahmad K; El-Sharnouby, Mohamed E; Abd Elsalam, Hassan E

2016-01-01

The potential use of human P450-transgenic plants for phytoremediation of pesticide contaminated soils was tested in laboratory and greenhouse experiments. The transgenic P450 CYP1A2 gene Arabidopsis thaliana plants metabolize number of herbicides, insecticides and industrial chemicals. The P450 isozymes CYP1A2 expressed in A. thaliana were examined regarding the herbicide simazine (SIM). Transgenic A. thaliana plants expressing CYP1A2 gene showed significant resistance to SIM supplemented either in plant growth medium or sprayed on foliar parts. The results showed that SIM produces harmful effect on both rosette diameter and primary root length of the wild type (WT) plants. In transgenic A. thaliana lines, the rosette diameter and primary root length were not affected by SIM concentrations used in this experiment. The results indicate that CYP1A2 can be used as a selectable marker for plant transformation, allowing efficient selection of transgenic lines in growth medium and/or in soil-grown plants. The transgenic A. thaliana plants exhibited a healthy growth using doses of up to 250 μmol SIM treatments, while the non-transgenic A. thaliana plants were severely damaged with doses above 50 μmol SIM treatments. The transgenic A. thaliana plants can be used as phytoremediator of environmental SIM contaminants.

Building associations between markers of environmental stressors and adverse human health impacts using frequent itemset mining

EPA Science Inventory

Building associations between markers of exposure and effect using frequent itemset mining The human-health impact of environmental contaminant exposures is unclear. While some exposure-effect relationships are well studied, health effects are unknown for the vast majority of the...

IDENTIFICATION OF BACTERIAL DNA MARKERS FOR THE DETECTION OF HUMAN FECAL POLLUTION IN WATER

EPA Science Inventory

We used genome fragment enrichment and bioinformatics to identify several microbial DNA sequences with high potential for use as markers in PCR assays for detection of human fecal contamination in water. Following competitive solution-phase hybridization of total DNA from human a...

The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.

EPA Science Inventory

Although molecular source tracking for human fecal contamination is used on a wide range of sample types, little is known about comparative decay of proposed molecular markers under different conditions, or correlation with pathogen decay. Our purpose was to measure correlations ...

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

EPA Science Inventory

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...

Factors affecting the presence of human-associated and fecal indicator real-time quantitative PCR genetic markers in urban-impacted recreational beaches

EPA Science Inventory

Urban runoff can carry a variety of pollutants into recreational beaches, often including bacterial pathogens and indicators of fecal contamination. To develop complete recreational criteria and risk assessments, it is necessary to understand conditions under which human contamin...

Distribution of Gull Specific Molecular Marker in Coastal Areas of Lake Ontario

EPA Science Inventory

Gulls have been implicated as primary sources of fecal contamination in the Great Lakes, a fact that may have health implications due to the potential spread of microbial pathogens by waterfowl. To better understand the spatial variability of gull fecal contamination, a gull-spe...

Peptide biomarkers used for the selective breeding of a complex polygenic trait in honey bees.

PubMed

Guarna, M Marta; Hoover, Shelley E; Huxter, Elizabeth; Higo, Heather; Moon, Kyung-Mee; Domanski, Dominik; Bixby, Miriam E F; Melathopoulos, Andony P; Ibrahim, Abdullah; Peirson, Michael; Desai, Suresh; Micholson, Derek; White, Rick; Borchers, Christoph H; Currie, Robert W; Pernal, Stephen F; Foster, Leonard J

2017-08-21

We present a novel way to select for highly polygenic traits. For millennia, humans have used observable phenotypes to selectively breed stronger or more productive livestock and crops. Selection on genotype, using single-nucleotide polymorphisms (SNPs) and genome profiling, is also now applied broadly in livestock breeding programs; however, selection on protein/peptide or mRNA expression markers has not yet been proven useful. Here we demonstrate the utility of protein markers to select for disease-resistant hygienic behavior in the European honey bee (Apis mellifera L.). Robust, mechanistically-linked protein expression markers, by integrating cis- and trans- effects from many genomic loci, may overcome limitations of genomic markers to allow for selection. After three generations of selection, the resulting marker-selected stock outperformed an unselected benchmark stock in terms of hygienic behavior, and had improved survival when challenged with a bacterial disease or a parasitic mite, similar to bees selected using a phenotype-based assessment for this trait. This is the first demonstration of the efficacy of protein markers for industrial selective breeding in any agricultural species, plant or animal.

Genomic selection in plant breeding

USDA-ARS?s Scientific Manuscript database

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 ...

A Site-Specific Recombinase-Based Method to Produce Antibiotic Selectable Marker Free Transgenic Cattle

PubMed Central

Tong, Qi; Liu, Xu; Su, Feng; Quan, Fusheng; Guo, Zekun; Zhang, Yong

2013-01-01

Antibiotic selectable marker genes have been widely used to generate transgenic animals. Once transgenic animals have been obtained, the selectable marker is no longer necessary but raises public concerns regarding biological safety. The aim of this study was to prepare competent antibiotic selectable marker free transgenic cells for somatic cell nuclear transfer (SCNT). PhiC31 intergrase was used to insert a transgene cassette into a “safe harbor” in the bovine genome. Then, Cre recombinase was employed to excise the selectable marker under the monitoring of a fluorescent double reporter. By visually tracking the phenotypic switch from red to green fluorescence, antibiotic selectable marker free cells were easily detected and sorted by fluorescence-activated cell sorting. For safety, we used phiC31 mRNA and cell-permeant Cre protein in this study. When used as donor nuclei for SCNT, these safe harbor integrated marker-free transgenic cells supported a similar developmental competence of SCNT embryos compared with that of non-transgenic cells. After embryo transfer, antibiotic selectable marker free transgenic cattle were generated and anti-bacterial recombinant human β-defensin-3 in milk was detected during their lactation period. Thus, this approach offers a rapid and safe alternative to produce antibiotic selectable marker free transgenic farm animals, thereby making it a valuable tool to promote the healthy development and welfare of transgenic farm animals. PMID:23658729

Comparison of two alternative dominant selectable markers for wine yeast transformation.

PubMed

Cebollero, Eduardo; Gonzalez, Ramon

2004-12-01

Genetic improvement of industrial yeast strains is restricted by the availability of selectable transformation markers. Antibiotic resistance markers have to be avoided for public health reasons, while auxotrophy markers are generally not useful for wine yeast strain transformation because most industrial Saccharomyces cerevisiae strains are prototrophic. For this work, we performed a comparative study of the usefulness of two alternative dominant selectable markers in both episomic and centromeric plasmids. Even though the selection for sulfite resistance conferred by FZF1-4 resulted in a larger number of transformants for a laboratory strain, the p-fluoro-DL-phenylalanine resistance conferred by ARO4-OFP resulted in a more suitable selection marker for all industrial strains tested. Both episomic and centromeric constructions carrying this marker resulted in transformation frequencies close to or above 10(3) transformants per microg of DNA for the three wine yeast strains tested.

Spread of an enteric 'marker' organism during evisceration of New York dressed poultry in a simulated kitchen environment.

PubMed

Mead, G C; Scott, M J

1997-05-01

1. Five volunteers, with experience of eviscerating poultry or game birds in the home, each eviscerated three New York dressed chicken carcases that had been artificially inoculated in the colon with a readily identifiable "marker' strain of Escherichia coli. 2. In all cases, evisceration resulted in breakage of the intestines at one or more sites, often with leakage of gut contents, or extrusion of faeces from the cloaca because of pressure on the colon during the manipulations involved. 3. The marker organism was detected in the vent region and abdominal cavity of each carcase and sometimes on the breast and back, which appeared to reflect the degree of handling during evisceration, because the hands of each individual became heavily contaminated. 4. With some individuals, the marker also spread beyond the immediate preparation area and was detected on exposure plates. 5. Results support the view that evisceration of poultry in a domestic environment could lead to cross-contamination of other foods with any food-borne human pathogens present.

DYNAMICS OF AQUATIC FECAL CONTAMINATION, FECAL SOURCE IDENTIFICATION, AND CORRELATION OF BACTEROIDALES HOST-SPECIFIC MARKERS DETECTION WITH FECAL PATHOGENS

EPA Science Inventory

Fecal pollution impairs the health and productivity of coastal waters and causes human disease. PCR of host-specific 16S rDNA sequences from anaerobic Bacteroidales bacteria offers a promising method of tracking fecal contamination and identifying its source(s). Before Bacteroida...

Correlation of quantitative PCR for a poultry-specific brevibacterium marker gene with bacterial and chemical indicators of water pollution in a watershed impacted by land application of poultry litter.

PubMed

Weidhaas, Jennifer L; Macbeth, Tamzen W; Olsen, Roger L; Harwood, Valerie J

2011-03-01

The impact of fecal contamination from human and agricultural animal waste on water quality is a major public health concern. Identification of the dominant source(s) of fecal pollution in a watershed is necessary for assessing the safety of recreational water and protecting water resources. A field study was conducted using quantitative PCR (qPCR) for the 16S rRNA gene of Brevibacterium sp. LA35 to track feces-contaminated poultry litter in environmental samples. Based on sensitivity and specificity characteristics of the qPCR method, the Bayesian conditional probability that detection of the LA35 marker gene in a water sample represented a true-positive result was 93%. The marker's covariance with fecal indicator bacteria (FIB) and metals associated with poultry litter was also assessed in litter, runoff, surface water, and groundwater samples. LA35 was detected in water and soil samples collected throughout the watershed, and its concentration covaried with concentrations of Escherichia coli, enterococci, As, Cu, P, and Zn. Significantly greater concentrations of FIB, As, Cu, P, and Zn were observed in edge-of-field runoff samples in which LA35 was detected, compared to samples in which it was not detected. Furthermore, As, Cu, P, and Zn concentrations covaried in environmental samples in which LA35 was detected and typically did not in samples in which the marker gene was not detected. The covariance of the poultry-specific LA35 marker gene with these known contaminants from poultry feces provides further evidence that it is a useful tool for assessing the impact of poultry-derived fecal pollution in environmental waters.

Bridging the gap between marker-assisted and genomic selection of heading time and plant height in hybrid wheat.

PubMed

Zhao, Y; Mette, M F; Gowda, M; Longin, C F H; Reif, J C

2014-06-01

Based on data from field trials with a large collection of 135 elite winter wheat inbred lines and 1604 F1 hybrids derived from them, we compared the accuracy of prediction of marker-assisted selection and current genomic selection approaches for the model traits heading time and plant height in a cross-validation approach. For heading time, the high accuracy seen with marker-assisted selection severely dropped with genomic selection approaches RR-BLUP (ridge regression best linear unbiased prediction) and BayesCπ, whereas for plant height, accuracy was low with marker-assisted selection as well as RR-BLUP and BayesCπ. Differences in the linkage disequilibrium structure of the functional and single-nucleotide polymorphism markers relevant for the two traits were identified in a simulation study as a likely explanation for the different trends in accuracies of prediction. A new genomic selection approach, weighted best linear unbiased prediction (W-BLUP), designed to treat the effects of known functional markers more appropriately, proved to increase the accuracy of prediction for both traits and thus closes the gap between marker-assisted and genomic selection.

Bridging the gap between marker-assisted and genomic selection of heading time and plant height in hybrid wheat

PubMed Central

Zhao, Y; Mette, M F; Gowda, M; Longin, C F H; Reif, J C

2014-01-01

Based on data from field trials with a large collection of 135 elite winter wheat inbred lines and 1604 F1 hybrids derived from them, we compared the accuracy of prediction of marker-assisted selection and current genomic selection approaches for the model traits heading time and plant height in a cross-validation approach. For heading time, the high accuracy seen with marker-assisted selection severely dropped with genomic selection approaches RR-BLUP (ridge regression best linear unbiased prediction) and BayesCπ, whereas for plant height, accuracy was low with marker-assisted selection as well as RR-BLUP and BayesCπ. Differences in the linkage disequilibrium structure of the functional and single-nucleotide polymorphism markers relevant for the two traits were identified in a simulation study as a likely explanation for the different trends in accuracies of prediction. A new genomic selection approach, weighted best linear unbiased prediction (W-BLUP), designed to treat the effects of known functional markers more appropriately, proved to increase the accuracy of prediction for both traits and thus closes the gap between marker-assisted and genomic selection. PMID:24518889

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

PubMed Central

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

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

PubMed

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

2015-10-01

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

Bacterial Contamination of Hospital Bed-Control Handsets in a Surgical Setting: A Potential Marker of Contamination of the Healthcare Environment

PubMed Central

Brady, RRW; Kalima, P; Damani, NN; Wilson, RG; Dunlop, MG

2007-01-01

INTRODUCTION Patients undergoing colorectal surgical resections have a high incidence of surgical site infection (SSI). Many patient-specific risk factors have been recognised in association with SSI in such patients, but environmental contamination is increasingly recognised as a contributor to hospital-acquired infection (HAI). This study set out to describe the bacterial contamination of the patient environment, using hospital bed-control handsets, as they are frequently handled by both staff and patients and represent a marker of environmental contamination. PATIENTS AND METHODS On two unannounced sampling events, 1 week apart, 140 bacteriological assessments were made of 70 hospital bed control handsets within a specialist colorectal surgical unit. RESULTS Of the handsets examined, 67 (95.7%) demonstrated at least one bacterial species (52.9% grew 1, 30% grew 2 and 12.9% grew 3 or more bacterial species). Of these, 29 (41.4%) bed-control handsets grew bacteria known to cause nosocomial infection, including 22 (31.4%) handsets which grew Enterococcus spp., 9 (12.9%) which grew MRSA, 2 (2.9%) which grew MSSA, 2 (2.9%) which grew coliforms, and 1 (1.4%) handset which grew anaerobes. At 1-week follow-up, 31 bed-control handsets showed evidence of contamination by the same bacterial species. CONCLUSIONS This study revealed high levels of bacteria known to cause HAI, contaminating hospital bed-control handsets in a surgical setting. Further study is now required to confirm whether hospital environmental contamination is causally involved in SSI. PMID:17959000

Development and evaluation of a culture-independent method for source determination of fecal wastes in surface and storm waters using reverse transcriptase-PCR detection of FRNA coliphage genogroup gene sequences.

PubMed

Paar, Jack; Doolittle, Mark M; Varma, Manju; Siefring, Shawn; Oshima, Kevin; Haugland, Richard A

2015-05-01

A method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for detecting interferences in RNA recovery and analysis, was developed for the direct, culture-independent detection of genetic markers from FRNA coliphage genogroups I, II & IV in water samples. Results were obtained from an initial evaluation of the performance of this method in analyses of waste water, ambient surface water and stormwater drain and outfall samples from predominantly urban locations. The evaluation also included a comparison of the occurrence of the FRNA genetic markers with genetic markers from general and human-related bacterial fecal indicators determined by current or pending EPA-validated qPCR methods. Strong associations were observed between the occurrence of the putatively human related FRNA genogroup II marker and the densities of the bacterial markers in the stormwater drain and outfall samples. However fewer samples were positive for FRNA coliphage compared to either the general bacterial fecal indicator or the human-related bacterial fecal indicator markers particularly for ambient water samples. Together, these methods show promise as complementary tools for the identification of contaminated storm water drainage systems as well as the determination of human and non-human sources of contamination. Published by Elsevier B.V.

Effect of Toxic Metals on Indigenous Soil β-Subgroup Proteobacterium Ammonia Oxidizer Community Structure and Protection against Toxicity by Inoculated Metal-Resistant Bacteria

PubMed Central

Stephen, John R.; Chang, Yun-Juan; Macnaughton, Sarah J.; Kowalchuk, George A.; Leung, Kam T.; Flemming, Cissy A.; White, David C.

1999-01-01

Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia oxidizers that are members of the beta subgroup of the Proteobacteria (β-subgroup ammonia oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4+ levels in soil samples. The gene encoding the α-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the β-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from cultured Nitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of β-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of β-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment. PMID:9872765

Distribution and abundance of human-specific Bacteroides and relation to traditional indicators in an urban tropical catchment

PubMed Central

Nshimyimana, J P; Ekklesia, E; Shanahan, P; Chua, L H C; Thompson, J R

2014-01-01

Aims The study goals were to determine the relationship between faecal indicator bacteria (FIB), the HF183 marker and land use, and the phylogenetic diversity of HF183 marker sequences in a tropical urban watershed. Methods and Results Total coliforms, Escherichia coli, and HF183 were quantified in 81 samples categorized as undeveloped, residential and horticultural from the Kranji Reservoir and Catchment in Singapore. Quantitative-PCR for HF183 followed by analysis of variance indicated that horticultural areas had significantly higher geometric means for marker levels (4·3 × 104 HF183-GE 100 ml−1) than nonhorticultural areas (3·07 × 103 HF183-GE 100 ml−1). E. coli and HF183 were moderately correlated in horticultural areas (R = 0·59, P = 0·0077), but not elsewhere in the catchment. Initial upstream surveys of candidate sources revealed elevated HF183 in a wastewater treatment effluent but not in aquaculture ponds. The HF183 marker was cloned, sequenced and determined by phylogenetic analysis to match the original marker description. Conclusion We show that quantification of the HF183 marker is a useful tool for mapping the spatial distribution and potential sources of human sewage contamination in tropical environments such as Singapore. Significance and Impact A major challenge for assessment of water quality in tropical environments is the natural occurrence and nonconservative behaviour of FIB. The HF183 marker has been employed in temperate environments as an alternative indicator for human sewage contamination. Our study supports the use of the HF183 marker as an indicator for human sewage in Singapore and motivates further work to determine HF183 marker levels that correspond to public health risk in tropical environments. PMID:24460587

Use of Spatial Sampling and Microbial Source-Tracking Tools for Understanding Fecal Contamination at Two Lake Erie Beaches

USGS Publications Warehouse

Francy, Donna S.; Bertke, Erin E.; Finnegan, Dennis P.; Kephart, Christopher M.; Sheets, Rodney A.; Rhoades, John; Stumpe, Lester

2006-01-01

Source-tracking tools were used to identify potential sources of fecal contamination at two Lake Erie bathing beaches: an urban beach (Edgewater in Cleveland, Ohio) and a beach in a small city (Lakeshore in Ashtabula, Ohio). These tools included identifying spatial patterns of Escherichia coli (E. coli) concentrations in each area, determining weather patterns that caused elevated E. coli, and applying microbial source tracking (MST) techniques to specific sites. Three MST methods were used during this study: multiple antibiotic resistance (MAR) indexing of E. coli isolates and the presence of human-specific genetic markers within two types of bacteria, the genus Bacteroides and the species Enterococcus faecium. At Edgewater, sampling for E. coli was done during 2003-05 at bathing-area sites, at nearshore lake sites, and in shallow ground water in foreshore and backshore areas. Spatial sampling at nearshore lake sites showed that fecal contamination was most likely of local origin; E. coli concentrations near the mouths of rivers and outfalls remote to the beach were elevated (greater than 235 colony-forming units per 100 milliliters (CFU/100 mL)) but decreased along transport pathways to the beach. In addition, E. coli concentrations were generally highest in bathing-area samples collected at 1- and 2-foot water depths, midrange at 3-foot depths, and lowest in nearshore lake samples typically collected 150 feet from the shoreline. Elevated E. coli concentrations at bathing-area sites were generally associated with increased wave heights and rainfall, but not always. E. coli concentrations were often elevated in shallow ground-water samples, especially in samples collected less than 10 feet from the edge of water (near foreshore area). The interaction of shallow ground water and waves may be a mechanism of E. coli storage and accumulation in foreshore sands. Infiltration of bird feces through sand with surface water from rainfall and high waves may be concentrating E. coli in shallow ground water in foreshore and backshore sands. At Lakeshore, sampling for E. coli was done at bathing-area, nearshore lake, and parking-lot sites during 2004-05. Low concentrations of E. coli at nearshore lake sites furthest from the shoreline indicated that fecal contamination was most likely of local origin. High concentrations of E. coli in water and bed sediments at several nearshore lake sites showed that contamination was emanating from several points along the shoreline during wet and dry weather, including the boat ramp, an area near the pond drainage, and parking-lot sediments. Physical evidence confirmed that runoff from the parking lot leads to degradation of water quality at the beach. MST samples were collected to help interpret spatial findings and determine whether sources of fecal contamination were from wastewater or bird feces and if a human-specific marker was present. MAR indices were useful in distinguishing between bird feces and wastewater sources because they were about 10 times higher in the latter. The results from MAR indices agreed with results from the two human-specific markers in some but not all of the samples tested. Bacteroides and enterococci human-specific markers were found on one day at Edgewater and two days at Lakeshore. On three days at Edgewater and two days at Lakeshore, the MAR index indicated a mixed source, but neither marker was found in bathing-water samples; this may be because bacterial indicator concentrations were too low to detect a marker. Multiple tools are needed to help identify sources of fecal contamination at coastal beaches. Spatial sampling identified patterns in E. coli concentrations and yielded information on the physical pathways of contamination. MST methods provided information on whether the source was likely of human or nonhuman origin only; however, MST did not provide information on the pathways of contamination.

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

PubMed

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.

A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: A case study for marker assisted selection in grapevine

USDA-ARS?s Scientific Manuscript database

Marker assisted selection (MAS) has become widely used in perennial crop breeding programs to accelerate and enhance cultivar development via selection during the juvenile phase and parental selection prior to crossing. Next generation sequencing (NGS) has been widely used for whole genome molecular...

A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker assisted selection in grapevine

USDA-ARS?s Scientific Manuscript database

Marker assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next generation sequencing (NGS) and its derivative technologies have been used for genome-wid...

Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities.

PubMed

Coelho, Francisco J R C; Cleary, Daniel F R; Rocha, Rui J M; Calado, Ricardo; Castanheira, José M; Rocha, Sílvia M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Lillebø, Ana I; Almeida, Adelaide; Cunha, Ângela; Lopes, Isabel; Ribeiro, Rui; Moreira-Santos, Matilde; Marques, Catarina R; Costa, Rodrigo; Pereira, Ruth; Gomes, Newton C M

2015-05-01

There is growing concern that modifications to the global environment such as ocean acidification and increased ultraviolet radiation may interact with anthropogenic pollutants to adversely affect the future marine environment. Despite this, little is known about the nature of the potential risks posed by such interactions. Here, we performed a multifactorial microcosm experiment to assess the impact of ocean acidification, ultraviolet B (UV-B) radiation and oil hydrocarbon contamination on sediment chemistry, the microbial community (composition and function) and biochemical marker response of selected indicator species. We found that increased ocean acidification and oil contamination in the absence of UV-B will significantly alter bacterial composition by, among other things, greatly reducing the relative abundance of Desulfobacterales, known to be important oil hydrocarbon degraders. Along with changes in bacterial composition, we identified concomitant shifts in the composition of oil hydrocarbons in the sediment and an increase in oxidative stress effects on our indicator species. Interestingly, our study identifies UV-B as a critical component in the interaction between these factors, as its presence alleviates harmful effects caused by the combination of reduced pH and oil pollution. The model system used here shows that the interactive effect of reduced pH and oil contamination can adversely affect the structure and functioning of sediment benthic communities, with the potential to exacerbate the toxicity of oil hydrocarbons in marine ecosystems. © 2014 John Wiley & Sons Ltd.

Regional Assessment of Human Fecal Contamination in Southern California Coastal Drainages

PubMed Central

Cao, Yiping; Raith, Meredith R.; Smith, Paul D.; Griffith, John F.; Weisberg, Stephen B.; Schriewer, Alexander; Sheldon, Andrew; Crompton, Chris; Gregory, Jason; Guzman, Joe; Othman, Laila; Manasjan, Mayela; Choi, Samuel; Rapoport, Shana; Steele, Syreeta; Nguyen, Tommy; Yu, Xueyuan

2017-01-01

Host-associated genetic markers that allow for fecal source identification have been used extensively as a diagnostic tool to determine fecal sources within watersheds, but have not been used in routine monitoring to prioritize remediation actions among watersheds. Here, we present a regional assessment of human marker prevalence among drainages that discharge to the U.S. southern California coast. Approximately 50 samples were analyzed for the HF183 human marker from each of 22 southern California coastal drainages under summer dry weather conditions, and another 50 samples were targeted from each of 23 drainages during wet weather. The HF183 marker was ubiquitous, detected in all but two sites in dry weather and at all sites during wet weather. However, there was considerable difference in the extent of human fecal contamination among sites. Similar site ranking was produced regardless of whether the assessment was based on frequency of HF183 detection or site average HF183 concentration. However, site ranking differed greatly between dry and wet weather. Site ranking also differed greatly when based on enterococci, which do not distinguish between pollution sources, vs. HF183, which distinguishes higher risk human fecal sources from other sources, indicating the additional value of the human-associated marker as a routine monitoring tool. PMID:28777324

Run-off studies demonstrate parallel transport behaviour for a marker of poultry fecal contamination and Staphylococcus aureus.

PubMed

Weidhaas, J; Garner, E; Basden, T; Harwood, V J

2014-08-01

To determine whether poultry litter marker gene LA35 is correlated with pathogens and fecal indicator bacteria (FIB) in run-off from poultry litter-amended plots. A rainfall simulator with various vegetative filter strip lengths was employed to evaluate the correlation of a microbial source tracking (MST) marker for poultry feces/litter (the 16S rRNA gene of Brevibacterium sp. LA35 [LA35] measured by quantitative PCR) with pathogens and FIB in run-off. LA35 was correlated with Staphylococcus aureus, Escherichia coli, Enterococcus spp. and Bacteroidales levels. Salmonella was present at low concentration in litter, but became undetectable by qPCR in run-off. Escherichia coli, LA35 and Staph. aureus exhibited mass-based first flush behaviour in the run-off. Correlation of LA35 with FIB and pathogens in run-off from poultry litter-amended fields suggest comparable transport mechanisms and that LA35 is a useful tracer for harmful bacteria in the environment released from poultry litter. To protect human health, an effective marker for poultry fecal contamination should exhibit similar fate and transport characteristics compared to pathogens. This study is among the first to demonstrate such a relationship in run-off for a MST marker. © 2014 The Society for Applied Microbiology.

Regional Assessment of Human Fecal Contamination in Southern California Coastal Drainages.

PubMed

Cao, Yiping; Raith, Meredith R; Smith, Paul D; Griffith, John F; Weisberg, Stephen B; Schriewer, Alexander; Sheldon, Andrew; Crompton, Chris; Amenu, Geremew G; Gregory, Jason; Guzman, Joe; Goodwin, Kelly D; Othman, Laila; Manasjan, Mayela; Choi, Samuel; Rapoport, Shana; Steele, Syreeta; Nguyen, Tommy; Yu, Xueyuan

2017-08-04

Host-associated genetic markers that allow for fecal source identification have been used extensively as a diagnostic tool to determine fecal sources within watersheds, but have not been used in routine monitoring to prioritize remediation actions among watersheds. Here, we present a regional assessment of human marker prevalence among drainages that discharge to the U.S. southern California coast. Approximately 50 samples were analyzed for the HF183 human marker from each of 22 southern California coastal drainages under summer dry weather conditions, and another 50 samples were targeted from each of 23 drainages during wet weather. The HF183 marker was ubiquitous, detected in all but two sites in dry weather and at all sites during wet weather. However, there was considerable difference in the extent of human fecal contamination among sites. Similar site ranking was produced regardless of whether the assessment was based on frequency of HF183 detection or site average HF183 concentration. However, site ranking differed greatly between dry and wet weather. Site ranking also differed greatly when based on enterococci, which do not distinguish between pollution sources, vs. HF183, which distinguishes higher risk human fecal sources from other sources, indicating the additional value of the human-associated marker as a routine monitoring tool.

Lipidomics as an important key for the identification of beer-spoilage bacteria.

PubMed

Řezanka, T; Matoulková, D; Benada, O; Sigler, K

2015-06-01

Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was used for characterizing intact plasmalogen phospholipid molecules in beer-spoilage bacteria. Identification of intact plasmalogens was carried out using collision-induced dissociation and the presence of suitable marker molecular species, both qualitative and quantitative, was determined in samples containing the anaerobic bacteria Megasphaera and Pectinatus. Using selected ion monitoring (SIM), this method had a limit of detection at 1 pg for the standard, i.e. 1-(1Z-octadecenyl)-2-oleoyl-sn-glycero-3-phosphoethanolamine and be linear in the range of four orders of magnitude from 2 pg to 20 ng. This technique was applied to intact plasmalogen extracts from the samples of contaminated and uncontaminated beer without derivatization and resulted in the identification of contamination of beer by Megasphaera and Pectinatus bacteria. The limit of detection was about 830 cells of anaerobic bacteria, i.e. bacteria containing natural cyclopropane plasmalogenes (c-p-19:0/15:0), which is the majority plasmalogen located in both Megasphaera and Pectinatus. The SIM ESI-MS method has been shown to be useful for the analysis of low concentration of plasmalogens in all biological samples, which were contaminated with anaerobic bacteria, e.g. juice, not only in beer. Significance and impact of the study: Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) using collision-induced dissociation was used to characterize intact plasmalogen phospholipid molecules in beer-spoilage anaerobic bacteria Megasphaera and Pectinatus. Using selected ion monitoring (SIM), this method has a detection limit of 1 pg for the standard 1-(1Z-octadecenyl)-2-oleoyl-sn-glycero-3-phosphoethanolamine and is linear within four orders of magnitude (2 pg to 20 ng). The limit of detection was about 830 cells of bacteria containing natural cyclopropane plasmalogen (c-p-19:0/15:0). SIM ESI-MS method is useful for analyzing low concentrations of plasmalogens in biological samples contaminated with anaerobic bacteria, e.g. beer or juice. © 2015 The Society for Applied Microbiology.

Paternity and Nested-within-Family Marker Assisted Selection in Space Planted Red Clover Nurseries

USDA-ARS?s Scientific Manuscript database

Presented is a cost effective marker assisted selection methodology that utilizes individual plant phenotypes, seed production based knowledge of maternity, molecular marker determined paternity, and nested within halfsib family linkage relationships. Combining all above listed components, selection...

Quality specifications for articles of botanical origin from the United States Pharmacopeia.

PubMed

Ma, Cuiying; Oketch-Rabah, Hellen; Kim, Nam-Cheol; Monagas, Maria; Bzhelyansky, Anton; Sarma, Nandakumara; Giancaspro, Gabriel

2018-06-01

In order to define appropriate quality of botanical dietary supplements, botanical drugs, and herbal medicines, the United States Pharmacopeia (USP) and the Herbal Medicines Compendium (HMC) contain science-based quality standards that include multiple interrelated tests to provide a full quality characterization for each article in terms of its identity, purity, and content. To provide a comprehensive description of the pharmacopeial tests and requirements for articles of botanical origin in the aforementioned compendia. Selective chromatographic procedures, such as high-performance liquid chromatography (HPLC) and high-performance thin-layer chromatography (HPTLC), are used as Identification tests in pharmacopeial monographs to detect species substitution or other confounders. HPLC quantitative tests are typically used to determine the content of key constituents, i.e., the total or individual amount of plant secondary metabolites that are considered bioactive constituents or analytical marker compounds. Purity specifications are typically set to limit the content of contaminants such as toxic elements, pesticides, and fungal toxins. Additional requirements highlight the importance of naming, definition, use of reference materials, and packaging/storage conditions. Technical requirements for each section of the monographs were illustrated with specific examples. Tests were performed on authentic samples using pharmacopeial reference standards. The chromatographic analytical procedures were validated to provide characteristic profiles for the identity and/or accurate determination of the content of quality markers. The multiple tests included in each monograph complement each other to provide an appropriate pharmacopeial quality characterization for the botanicals used as herbal medicines and dietary supplements. The monographs provide detailed specifications for identity, content of bioactive constituents or quality markers, and limits of contaminants, adulterants, and potentially toxic substances. Additional requirements such as labeling and packaging further contribute to preserve the quality of these products. Compliance with pharmacopeial specifications should be required to ensure the reliability of botanical articles used for health care purposes. Copyright © 2018. Published by Elsevier GmbH.

Genome-wide association analysis of bacterial cold water disease resistance in rainbow trout reveals the potential of a hybrid approach between genomic selection and marker assisted selection

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) simultaneously incorporates dense SNP marker genotypes with phenotypic data from related animals to predict animal-specific genomic breeding value (GEBV), which circumvents the need to measure the disease phenotype in potential breeders. Marker assisted selection (MAS) involv...

A Novel Yeast Genomics Method for Identifying New Breast Cancer Susceptibility

DTIC Science & Technology

2005-05-01

selectable marker and tracing this marker through several passages in nonselective medium. The selectable marker will be the hygromycin phosphotransferase ... hygromycin and sensitivity to (32), thereby providing both positive and negative selectivity. The assay involved measurement of the frequency of gancyclovir

Sewage pollution in urban stormwater runoff as evident from the widespread presence of multiple microbial and chemical source tracking markers.

PubMed

Sidhu, J P S; Ahmed, W; Gernjak, W; Aryal, R; McCarthy, D; Palmer, A; Kolotelo, P; Toze, S

2013-10-01

The concurrence of human sewage contamination in urban stormwater runoff (n=23) from six urban catchments across Australia was assessed by using both microbial source tracking (MST) and chemical source tracking (CST) markers. Out of 23 stormwater samples human adenovirus (HAv), human polyomavirus (HPv) and the sewage-associated markers; Methanobrevibacter smithii nifH and Bacteroides HF183 were detected in 91%, 56%, 43% and 96% of samples, respectively. Similarly, CST markers paracetamol (87%), salicylic acid (78%) acesulfame (96%) and caffeine (91%) were frequently detected. Twenty one samples (91%) were positive for six to eight sewage related MST and CST markers and remaining two samples were positive for five and four markers, respectively. A very good consensus (>91%) observed between the concurrence of the HF183, HAv, acesulfame and caffeine suggests good predictability of the presence of HAv in samples positive for one of the three markers. High prevalence of HAv (91%) also suggests that other enteric viruses may also be present in the stormwater samples which may pose significant health risks. This study underscores the benefits of employing a set of MST and CST markers which could include monitoring for HF183, adenovirus, caffeine and paracetamol to accurately detect human sewage contamination along with credible information on the presence of human enteric viruses, which could be used for more reliable public health risk assessments. Based on the results obtained in this study, it is recommended that some degree of treatment of captured stormwater would be required if it were to be used for non-potable purposes. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

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

PubMed

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.

Mapping QTL for popping expansion volume in popcorn with simple sequence repeat markers.

PubMed

Lu, H-J; Bernardo, R; Ohm, H W

2003-02-01

Popping expansion volume is the most important quality trait in popcorn ( Zea mays L.), but its genetics is not well understood. The objectives of this study were to map quantitative trait loci (QTLs) responsible for popping expansion volume in a popcorn x dent corn cross, and to compare the predicted efficiencies of phenotypic selection, marker-based selection, and marker-assisted selection for popping expansion volume. Of 259 simple sequence repeat (SSR) primer pairs screened, 83 pairs were polymorphic between the H123 (dent corn) and AG19 (popcorn) parental inbreds. Popping test data were obtained for 160 S(1) families developed from the [AG19(H123 x AG19)] BC(1) population. The heritability ( h(2)) for popping expansion volume on an S(1) family mean basis was 0.73. The presence of the gametophyte factor Ga1(s) in popcorn complicates the analysis of popcorn x dent corn crosses. But, from a practical perspective, the linkage between a favorable QTL allele and Ga1(s) in popcorn will lead to selection for the favorable QTL allele. Four QTLs, on chromosomes 1S, 3S, 5S and 5L, jointly explained 45% of the phenotypic variation. Marker-based selection for popping expansion volume would require less time and work than phenotypic selection. But due to the high h(2) of popping expansion volume, marker-based selection was predicted to be only 92% as efficient as phenotypic selection. Marker-assisted selection, which comprises index selection on phenotypic and marker scores, was predicted to be 106% as efficient as phenotypic selection. Overall, our results suggest that phenotypic selection will remain the preferred method for selection in popcorn x dent corn crosses.

Recent patents on biosafety strategies of selectable marker genes in genetically modified crops.

PubMed

Jiang, Yiming; Hu, Xiaoning; Huang, Haiying

2014-01-01

Genetically modified crops (GMCs) have been planted world wide since 1990s, but the potential insecurity of selectable marker genes raises the questions about GMC safety. Therefore, several researches have been conducted on marker gene safety issues and recently several patents have been issued on this subject. There are two main approaches to achieve this goal: seeking the biosafety selectable marker and eliminating these insecure marker genes after transformation. Results show that these two systems are quite effective. Recent patents on the two ways are discussed in this review.

An integrated evaluation of some faecal indicator bacteria (FIB) and chemical markers as potential tools for monitoring sewage contamination in subtropical estuaries.

PubMed

Cabral, Ana Caroline; Stark, Jonathan S; Kolm, Hedda E; Martins, César C

2018-04-01

Sewage input and the relationship between chemical markers (linear alkylbenzenes and coprostanol) and fecal indicator bacteria (FIB, Escherichia coli and enterococci), were evaluated in order to establish thresholds values for chemical markers in suspended particulate matter (SPM) as indicators of sewage contamination in two subtropical estuaries in South Atlantic Brazil. Both chemical markers presented no linear relationship with FIB due to high spatial microbiological variability, however, microbiological water quality was related to coprostanol values when analyzed by logistic regression, indicating that linear models may not be the best representation of the relationship between both classes of indicators. Logistic regression was performed with all data and separately for two sampling seasons, using 800 and 100 MPN 100 mL -1 of E. coli and enterococci, respectively, as the microbiological limits of sewage contamination. Threshold values of coprostanol varied depending on the FIB and season, ranging between 1.00 and 2.23 μg g -1 SPM. The range of threshold values of coprostanol for SPM are relatively higher and more variable than those suggested in literature for sediments (0.10-0.50 μg g -1 ), probably due to higher concentration of coprostanol in SPM than in sediment. Temperature may affect the relationship between microbiological indicators and coprostanol, since the threshold value of coprostanol found here was similar to tropical areas, but lower than those found during winter in temperate areas, reinforcing the idea that threshold values should be calibrated for different climatic conditions. Copyright © 2018 Elsevier Ltd. All rights reserved.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

PubMed

Parks, Donovan H; Imelfort, Michael; Skennerton, Connor T; Hugenholtz, Philip; Tyson, Gene W

2015-07-01

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. © 2015 Parks et al.; Published by Cold Spring Harbor Laboratory Press.

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

PubMed

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.

Potential for gulls to transport bacteria from human waste sites to beaches.

PubMed

Alm, Elizabeth W; Daniels-Witt, Quri R; Learman, Deric R; Ryu, Hodon; Jordan, Dustin W; Gehring, Thomas M; Santo Domingo, Jorge

2018-02-15

Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparison of three different sterilization and disinfection methods on orthodontic markers

PubMed Central

Omidkhoda, Maryam; Rashed, Roozbeh; Bagheri, Zahra; Ghazvini, Kiarash; Shafaee, Hooman

2016-01-01

Background: Marking pencils which are frequently used in orthodontics may cause microbial contamination. The purpose of this study was to evaluate and compare the effectiveness of three disinfection and sterilization methods (autoclave, glutaraldehyde solution, and Deconex spray) on orthodontic markers. Materials and Methods: One hundred and twenty orthodontic markers were divided into four groups each 30 pencils: One control group and three groups for three different disinfection/sterilization methods. To evaluate the effectiveness of these methods, pencils were initially contaminated by common pathogen by immersing the pencils in a suspension containing 1.5 × 108 CFU/ml organisms. Then, the pencils were subjected to corresponding disinfection/sterilization methods, and the number of remaining microorganisms was calculated and compared with control group. Results: In the control group, the mean number of Escherichia coli was significantly higher than the other two microorganisms (P = 0.01, P = 0.031). However, the mean numbers of Staphylococcus aureus and Candida albicans were not significantly different (P = 0.1). After sterilization with autoclave and glutaraldehyde, no microbial growth was observed, whereas after disinfection with Deconx spray some colonies of microorganisms still could be observed. Conclusion: Autoclaving and glutaraldehyde solution are the best methods for disinfecting orthodontic markers. PMID:26998472

Dispersal of micro-organisms in commercial defeathering systems.

PubMed

Allen, V M; Tinker, D B; Hinton, M H; Wathes, C M

2003-03-01

1. The extent of cross contamination between carcases and the dispersal of micro-organisms to the environs during defeathering was measured in a commercial processing plant. 2. Defeathering reduced the numbers of a marker organism, a nalidixic acid-resistant strain of Escherichia coli K12, on inoculated carcases but dispersed the organism on to preceding and following carcases. 3. The pattern of microbial dispersal during defeathering was similar for naturally occurring bacteria on the carcase, for example, total aerobic counts and counts of presumptive coliforms, suggesting that the marker organism mimics the natural situation realistically. 4. The majority of feathers, together with micro-organisms, were removed during the first 10 s of the defeathering process, which was completed in 45 s, indicating that control measures to minimise cross contamination would be most effective if applied in the early stages of the process. 5. The method of defeathering used by the machine influenced the pattern of microbial dispersal and the extent of cross contamination to other carcases on the same processing line.

Understanding the contamination of food with mineral oil: the need for a confirmatory analytical and procedural approach.

PubMed

Spack, Lionel W; Leszczyk, Gabriela; Varela, Jesus; Simian, Hervé; Gude, Thomas; Stadler, Richard H

2017-06-01

The contamination of food by mineral oil hydrocarbons (MOHs) found in packaging is a long-running concern. A main source of MOHs in foods is the migration of mineral oil from recycled board into the packed food products. Consequently, the majority of food manufacturers have taken protective measures, e.g., by using virgin board instead of recycled fibres and, where feasible, introducing functional barriers to mitigate migration. Despite these protective measures, MOHs may still be observed in low amounts in certain food products, albeit due to different entry points across the food supply chain. In this study, we successfully apply gas chromatography coupled to mass spectrometry (GC-MS) to demonstrate, through marker compounds and the profile of the hydrocarbon response, the possible source of contamination using mainly chocolate and cereals as food matrices. The conventional liquid chromatography-one-dimensional GC coupled to a flame ionisation detector (LC-GC-FID) is a useful screening method, but in cases of positive samples it must be complemented by a confirmatory method such as, for example, GC-MS, allowing a verification of mineral oil contamination. The procedural approach proposed in this study entails profile analysis, marker identification, and interpretation and final quantification.

Potential and limits to unravel the genetic architecture and predict the variation of Fusarium head blight resistance in European winter wheat (Triticum aestivum L.).

PubMed

Jiang, Y; Zhao, Y; Rodemann, B; Plieske, J; Kollers, S; Korzun, V; Ebmeyer, E; Argillier, O; Hinze, M; Ling, J; Röder, M S; Ganal, M W; Mette, M F; Reif, J C

2015-03-01

Genome-wide mapping approaches in diverse populations are powerful tools to unravel the genetic architecture of complex traits. The main goals of our study were to investigate the potential and limits to unravel the genetic architecture and to identify the factors determining the accuracy of prediction of the genotypic variation of Fusarium head blight (FHB) resistance in wheat (Triticum aestivum L.) based on data collected with a diverse panel of 372 European varieties. The wheat lines were phenotyped in multi-location field trials for FHB resistance and genotyped with 782 simple sequence repeat (SSR) markers, and 9k and 90k single-nucleotide polymorphism (SNP) arrays. We applied genome-wide association mapping in combination with fivefold cross-validations and observed surprisingly high accuracies of prediction for marker-assisted selection based on the detected quantitative trait loci (QTLs). Using a random sample of markers not selected for marker-trait associations revealed only a slight decrease in prediction accuracy compared with marker-based selection exploiting the QTL information. The same picture was confirmed in a simulation study, suggesting that relatedness is a main driver of the accuracy of prediction in marker-assisted selection of FHB resistance. When the accuracy of prediction of three genomic selection models was contrasted for the three marker data sets, no significant differences in accuracies among marker platforms and genomic selection models were observed. Marker density impacted the accuracy of prediction only marginally. Consequently, genomic selection of FHB resistance can be implemented most cost-efficiently based on low- to medium-density SNP arrays.

Selective purge for hydrogenation reactor recycle loop

DOEpatents

Baker, Richard W.; Lokhandwala, Kaaeid A.

2001-01-01

Processes and apparatus for providing improved contaminant removal and hydrogen recovery in hydrogenation reactors, particularly in refineries and petrochemical plants. The improved contaminant removal is achieved by selective purging, by passing gases in the hydrogenation reactor recycle loop or purge stream across membranes selective in favor of the contaminant over hydrogen.

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

PubMed Central

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 selection algorithm, in combination with a genetic search algorithm, proved to yield best performance accuracy for selecting optimum markers. PACS numbers: 87.55.km, 87.56.Fc PMID:26894358

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

PubMed

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 combination with a genetic search algorithm, proved to yield best performance accuracy for selecting optimum markers.

Imputation of unordered markers and the impact on genomic selection accuracy

USDA-ARS?s Scientific Manuscript database

Genomic selection, a breeding method that promises to accelerate rates of genetic gain, requires dense, genome-wide marker data. Genotyping-by-sequencing can generate a large number of de novo markers. However, without a reference genome, these markers are unordered and typically have a large propo...

Demonstrating Cost-Effective Marker Assisted Selection for Biomass Yield in Red Clover (Trifolium pratense L.) – Part 1: Paternity Testing

USDA-ARS?s Scientific Manuscript database

Many methods have been proposed to incorporate molecular markers into breeding programs. Presented is a cost effective marker assisted selection (MAS) methodology that utilizes individual plant phenotypes, seed production-based knowledge of maternity, and molecular marker-determined paternity. Proge...

A Comparison Between Genotyping-by-sequencing and Array-based Scoring of SNPs for Genomic Prediction Accuracy in Winter Wheat

USDA-ARS?s Scientific Manuscript database

The utilization of DNA molecular markers in plant breeding to maximize selection response via marker assisted selection (MAS) and genomic selection (GS) has the potential to revolutionize plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotypying-...

[A comparison study of hpt and bar as selection marker gene of transgenic rice].

PubMed

Zhang, Chun-Yu; Li, Hong-Yu; Liu, Bin

2012-12-01

The decision of using selection marker is one of the key factors for success of plant genetic transformation and offspring screening. As two commonly used selection markers, hpt and bar genes are widely used in tissue culture-based rice transformation. To experimentally compare their performance, we investigated the efficiency of two transformation systems using Hygromycin and Bialaphos as the selection agents, respectively. The result indicated that the system using hpt gene as the selection marker saved 10 days and had double transformation efficiency and lower transgene copy number in comparison to the system using bar gene. Then, we assessed the feasibility of screening transgenic rice in the field by soaking the wild-type and transgenic seeds in a series of solutions containing step diluted hygromycin for two days. We targeted the suitable concentration for distinguishing the transgenic seeds from WT Kitaake seeds was 167 mg L(-1). However, the cost of screening by hygromycin is still much higher than that of Basta in field test. Therefore, this study experimentally demonstrated the advantages and disadvantages of the hpt and bar gene as the selection markers and thus provided a reference for choose of an appropriate selection marker according to the practical applications.

Development of a U.S. EPA Method for the Analysis of Selected Drinking Water Contaminants by LC/MS/MS

EPA Science Inventory

The U.S. Environmental Protection Agency’s (U.S. EPA) Office of Ground Water and Drinking Water (OGWDW) collects national occurrence data on drinking water contaminants using Unregulated Contaminant Monitoring Regulations (UCMRs). These contaminants may be selected from the Drin...

Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis).

PubMed

Fischer, Martin C; Foll, Matthieu; Heckel, Gerald; Excoffier, Laurent

2014-01-01

Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolutionary periods and even geographic scale, thus leads to low levels of divergence between populations at selected loci. However, little is known about the relative importance of these two selective forces in shaping genomic diversity, partly due to difficulties in recognizing balancing selection in species showing low levels of differentiation. Here we address this problem by studying genomic diversity in the European common vole (Microtus arvalis) presenting high levels of differentiation between populations (average F ST = 0.31). We studied 3,839 Amplified Fragment Length Polymorphism (AFLP) markers genotyped in 444 individuals from 21 populations distributed across the European continent and hence over different environmental conditions. Our statistical approach to detect markers under selection is based on a Bayesian method specifically developed for AFLP markers, which treats AFLPs as a nearly codominant marker system, and therefore has increased power to detect selection. The high number of screened populations allowed us to detect the signature of balancing selection across a large geographic area. We detected 33 markers potentially under balancing selection, hence strong evidence of stabilizing selection in 21 populations across Europe. However, our analyses identified four-times more markers (138) being under positive selection, and geographical patterns suggest that some of these markers are probably associated with alpine regions, which seem to have environmental conditions that favour adaptation. We conclude that despite favourable conditions in this study for the detection of balancing selection, this evolutionary force seems to play a relatively minor role in shaping the genomic diversity of the common vole, which is more influenced by positive selection and neutral processes like drift and demographic history.

Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

PubMed

Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

2015-03-15

Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance

PubMed Central

Hawkins, Leigh K.; Mylroie, J. Erik; Oliveira, Dafne A.; Smith, J. Spencer; Ozkan, Seval; Windham, Gary L.; Williams, W. Paul; Warburton, Marilyn L.

2015-01-01

Maize (Zea mays L.) is a crop of global importance, but prone to contamination by aflatoxins produced by fungi in the genus Aspergillus. The development of resistant germplasm and the identification of genes contributing to resistance would aid in the reduction of the problem with a minimal need for intervention by farmers. Chitinolytic enzymes respond to attack by potential pathogens and have been demonstrated to increase insect and fungal resistance in plants. Here, all chitinase genes in the maize genome were characterized via sequence diversity and expression patterns. Recent evolution within this gene family was noted. Markers from within each gene were developed and used to map the phenotypic effect on resistance of each gene in up to four QTL mapping populations and one association panel. Seven chitinase genes were identified that had alleles associated with increased resistance to aflatoxin accumulation and A. flavus infection in field grown maize. The chitinase in bin 1.05 identified a new and highly significant QTL, while chitinase genes in bins 2.04 and 5.03 fell directly beneath the peaks of previously published QTL. The expression patterns of these genes corroborate possible grain resistance mechanisms. Markers from within the gene sequences or very closely linked to them are presented to aid in the use of marker assisted selection to improve this trait. PMID:26090679

Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance.

PubMed

Hawkins, Leigh K; Mylroie, J Erik; Oliveira, Dafne A; Smith, J Spencer; Ozkan, Seval; Windham, Gary L; Williams, W Paul; Warburton, Marilyn L

2015-01-01

Maize (Zea mays L.) is a crop of global importance, but prone to contamination by aflatoxins produced by fungi in the genus Aspergillus. The development of resistant germplasm and the identification of genes contributing to resistance would aid in the reduction of the problem with a minimal need for intervention by farmers. Chitinolytic enzymes respond to attack by potential pathogens and have been demonstrated to increase insect and fungal resistance in plants. Here, all chitinase genes in the maize genome were characterized via sequence diversity and expression patterns. Recent evolution within this gene family was noted. Markers from within each gene were developed and used to map the phenotypic effect on resistance of each gene in up to four QTL mapping populations and one association panel. Seven chitinase genes were identified that had alleles associated with increased resistance to aflatoxin accumulation and A. flavus infection in field grown maize. The chitinase in bin 1.05 identified a new and highly significant QTL, while chitinase genes in bins 2.04 and 5.03 fell directly beneath the peaks of previously published QTL. The expression patterns of these genes corroborate possible grain resistance mechanisms. Markers from within the gene sequences or very closely linked to them are presented to aid in the use of marker assisted selection to improve this trait.

Optimal marker-assisted selection to increase the effective size of small populations.

PubMed

Wang, J

2001-02-01

An approach to the optimal utilization of marker and pedigree information in minimizing the rates of inbreeding and genetic drift at the average locus of the genome (not just the marked loci) in a small diploid population is proposed, and its efficiency is investigated by stochastic simulations. The approach is based on estimating the expected pedigree of each chromosome by using marker and individual pedigree information and minimizing the average coancestry of selected chromosomes by quadratic integer programming. It is shown that the approach is much more effective and much less computer demanding in implementation than previous ones. For pigs with 10 offspring per mother genotyped for two markers (each with four alleles at equal initial frequency) per chromosome of 100 cM, the approach can increase the average effective size for the whole genome by approximately 40 and 55% if mating ratios (the number of females mated with a male) are 3 and 12, respectively, compared with the corresponding values obtained by optimizing between-family selection using pedigree information only. The efficiency of the marker-assisted selection method increases with increasing amount of marker information (number of markers per chromosome, heterozygosity per marker) and family size, but decreases with increasing genome size. For less prolific species, the approach is still effective if the mating ratio is large so that a high marker-assisted selection pressure on the rarer sex can be maintained.

A hyaluronan hydrogel scaffold-based xeno-free culture system for ex vivo expansion of human corneal epithelial stem cells.

PubMed

Chen, D; Qu, Y; Hua, X; Zhang, L; Liu, Z; Pflugfelder, S C; Li, D-Q

2017-06-01

PurposeTo develop a hyaluronan hydrogel scaffold-based xeno-free culture system for ex vivo cultivation of human corneal epithelial stem cells (CESCs).Patients and MethodsCESCs were cultivated from donor limbal explants on the HyStem-C Hydrogel bio-scaffold in 12-well plates for 3 weeks. Group A used the traditional supplemented hormonal epidermal medium (SHEM) and group B used the defined SHEM (without fetal bovine serum and toxin A, adding 20% serum replacement). The growth and morphology of the cultured cells were assessed by phase contrast microscope. The expressions of specific cell markers were assessed by immunofluorescence staining and quantitative real-time PCR (qRT-PCR).ResultsSuccessful cultures of CESCs were obtained in both groups, resulting in multilayered stratified epithelia. Comparing to group A, the cells in group B was grown slightly slower and formed less cellular layers at the end of culture. The corneal specific cytokeratin (K) 12 and differentiation markers, involucrin, and connexin 43, were mainly expressed in the superficial cellular layers in both groups. Interestingly, certain basal cells were immune-positive to proposed stem cell markers such as K19, ABCG2, and integrin β1 in both groups. There was no significant difference between the two groups with regard to the gene expression levels of all these selected corneal markers (all P>0.05).ConclusionsThe hyaluronan hydrogel scaffold-based xeno-free culture system may support the expansion of regenerative CESCs without the risk of xeno component contamination. The regenerated epithelium maintains similar characteristics of native corneal epithelium.

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

USDA-ARS?s Scientific Manuscript database

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...

Presumptive Sources of Fecal Contamination in Four Tributaries to the New River Gorge National River, West Virginia, 2004

USGS Publications Warehouse

Mathes, Melvin V.; O'Brien, Tara L.; Strickler, Kriston M.; Hardy, Joshua J.; Schill, William B.; Lukasik, Jerzy; Scott, Troy M.; Bailey, David E.; Fenger, Terry L.

2007-01-01

Several methods were used to determine the sources of fecal contamination in water samples collected during September and October 2004 from four tributaries to the New River Gorge National River -- Arbuckle Creek, Dunloup Creek, Keeney Creek, and Wolf Creek. All four tributaries historically have had elevated levels of fecal coliform bacteria. The source-tracking methods used yielded various results, possibly because one or more methods failed. Sourcing methods used in this study included the detection of several human-specific and animal-specific biological or molecular markers, and library-dependent pulsed-field gel electrophoresis analysis that attempted to associate Escherichia coli bacteria obtained from water samples with animal sources by matching DNA-fragment banding patterns. Evaluation of the results of quality-control analysis indicated that pulsed-field gel electrophoresis analysis was unable to identify known-source bacteria isolates. Increasing the size of the known-source library did not improve the results for quality-control samples. A number of emerging methods, using markers in Enterococcus, human urine, Bacteroidetes, and host mitochondrial DNA, demonstrated some potential in associating fecal contamination with human or animal sources in a limited analysis of quality-control samples. All four of the human-specific markers were detected in water samples from Keeney Creek, a watershed with no centralized municipal wastewater-treatment facilities, thus indicating human sources of fecal contamination. The human-specific Bacteroidetes and host mitochondrial DNA markers were detected in water samples from Dunloup Creek, Wolf Creek, and to a lesser degree Arbuckle Creek. Results of analysis for wastewater compounds indicate that the September 27 sample from Arbuckle Creek contained numerous human tracer compounds likely from sewage. Dog, horse, chicken, and pig host mitochondrial DNA were detected in some of the water samples with the exception of the October 5 sample from Dunloup Creek. Cow, white-tailed deer, and Canada goose DNA were not detected in any of the samples collected from the four tributaries, despite the presence of these animals in the watersheds. Future studies with more rigorous quality-control analyses are needed to investigate the potential applicability and use of these emerging methods. Because many of the detections for the various methods could vary over time and with flow conditions, repeated sampling during both base flow and storm events would be necessary to more definitively determine the sources of fecal contamination for each watershed.

Microbial source tracking markers at three inland recreational lakes in Ohio, 2011

USGS Publications Warehouse

Francy, Donna S.; Stelzer, Erin A.

2012-01-01

During the 2011 recreational season, samples were collected for E. coli and microbial source tracking (MST) marker concentrations to begin to understand potential sources of fecal contamination at three inland recreational lakes in Ohio - Buckeye, Atwood, and Tappan Lakes. The results from 32 regular samples, 4 field blanks, and 7 field replicates collected at 5 sites are presented in this report. At the three lakes, the ruminant-associated marker was found most often (57-73 percent of samples) but at estimated quantities, followed by the dog-associated marker (30-43 percent of samples). The human-associated marker was found in 14 and 50 percent of samples from Atwood and Tappan Lakes, respectively, but was not found in any samples from the two Buckeye Lake sites. The gull-associated marker was detected in only two samples, both from Tappan Lake.

Mass balance of emerging contaminants in the water cycle of a highly urbanized and industrialized area of Italy.

PubMed

Castiglioni, Sara; Davoli, Enrico; Riva, Francesco; Palmiotto, Marinella; Camporini, Paolo; Manenti, Angela; Zuccato, Ettore

2017-12-22

The occurrence of several classes of emerging contaminants (ECs) was assessed in the River Lambro basin, one of the most urbanized and industrialized areas of Italy. The study aims were to identify the main sources of ECs, quantify their amounts circulating in the water cycle, and study their fate in the aquatic environment. More than 80 ECs were selected among pharmaceuticals (PHARM), personal care products (PCPs), disinfectants (DIS), illicit drugs (IDs), perfluorinated compounds (PERF), alkylphenols and bisphenol A (Alk-BPA), and anthropogenic markers (AM). Specific analytical methods were developed for quantitative analysis based on solid phase extraction and liquid chromatography tandem mass spectrometry. ECs were measured in rivers upstream and downstream of the main city (Milan), and in untreated and treated wastewater from Milan to assess the contribution to river contamination, and in superficial and deep groundwater in the city area to study the relationship between river and groundwater contamination. Samples were collected in a two-year monitoring campaign. Almost all ECs were ubiquitous in untreated wastewater, at concentrations up to the μg/L range, and the most abundant classes were PHARM and AM. Removals during different wastewater treatment processes were studied and the most stable substances were PHARM, PCPs and PERF. The mass loads increased for all the classes of ECs along the River Lambro basin. A mass balance was done in the river basin and allowed to identify the main sources of contamination, which were domestic, from treated or untreated wastewater, for PHARM, PCPs and IDs, mainly industrial for PERF, and both industrial and domestic for Alk-BPA. The study of AM helped to identify direct discharges of untreated wastewater. A substantial contribution of surface water to groundwater contamination was observed. This study improves the knowledge on occurrence, sources and fate of multiple classes of ECs in a highly urbanized area providing useful information to help the establishment of EU regulations for ECs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relevance of Bacteroidales and F-Specific RNA Bacteriophages for Efficient Fecal Contamination Tracking at the Level of a Catchment in France

PubMed Central

Mauffret, Aourell; Caprais, Marie-Paule

2012-01-01

The relevance of three host-associated Bacteroidales markers (HF183, Rum2Bac, and Pig2Bac) and four F-specific RNA bacteriophage genogroups (FRNAPH I to IV) as microbial source tracking markers was assessed at the level of a catchment (Daoulas, France). They were monitored together with fecal indicators (Escherichia coli and enterococci) and chemophysical parameters (rainfall, temperature, salinity, pH, and turbidity) by monthly sampling over 2 years (n = 240 water samples) and one specific sampling following an accidental pig manure spillage (n = 5 samples). During the 2-year regular monitoring, levels of E. coli, enterococci, total F-specific RNA bacteriophages, and the general Bacteroidales marker AllBac were strongly correlated with one another and with Rum2Bac (r = 0.37 to 0.50, P < 0.0001). Their correlations with HF183 and FRNAPH I and II were lower (r = 0.21 to 0.29, P < 0.001 to P < 0.0001), and HF183 and enterococci were associated rather than correlated (Fisher's exact test, P < 0.01). Rum2Bac and HF183 enabled 73% of water samples that had ≥2.7 log10 most probably number (MPN) of E. coli/100 ml to be classified. FRNAPH I and II enabled 33% of samples at this contamination level to be classified. FRNAPH I and II complemented the water sample classification obtained with the two Bacteroidales markers by an additional 8%. Pig2Bac and FRNAPH III and IV were observed in a small number of samples (n = 0 to 4 of 245). The present study validates Rum2Bac and HF183 as relevant tools to trace fecal contamination originating from ruminant or human waste, respectively, at the level of a whole catchment. PMID:22610433

Using SCC8, SCF27 and VMC7f2 markers in grapevine breeding for seedlessness via marker assisted selection.

PubMed

Akkurt, M; Çakır, A; Shidfar, M; Çelikkol, B P; Söylemezoğlu, G

2012-08-13

We used molecular markers associated with seedlessness in grapes, namely SCC8, SCF27 and VMC7f2, to improve the efficiency of seedless grapevine breeding via marker assisted selection (MAS). DNA from 372 F₁ hybrid progeny from the cross between seeded "Alphonse Lavallée" and seedless "Sultani" was amplified by PCR using three markers. After digestion of SCC8 marker amplification products by restriction enzyme BgIII, 40 individuals showed homozygous SCC8+/SCC8+ alleles at the seed development inhibitor (SdI) locus. DNA from 80 of the progeny amplified with the SCF27 marker produced bands; 174 individuals had 198-bp alleles of the VMC7f2 marker associated with seedlessness. In the second year, based on MAS, 183 F₁ hybrids were designated as seedless grapevine candidates because they were positive for a minimum of one marker. Twenty individuals were selected as genetic resources for future studies on seedless grapevine breeding because they carried alleles for the three markers associated with seedlessness. The VMC7f2 SSR marker was identified as the marker most associated with seedlessness.

Efficient Breeding by Genomic Mating.

PubMed

Akdemir, Deniz; Sánchez, Julio I

2016-01-01

Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

Predictive Validity of Explicit and Implicit Threat Overestimation in Contamination Fear

PubMed Central

Green, Jennifer S.; Teachman, Bethany A.

2012-01-01

We examined the predictive validity of explicit and implicit measures of threat overestimation in relation to contamination-fear outcomes using structural equation modeling. Undergraduate students high in contamination fear (N = 56) completed explicit measures of contamination threat likelihood and severity, as well as looming vulnerability cognitions, in addition to an implicit measure of danger associations with potential contaminants. Participants also completed measures of contamination-fear symptoms, as well as subjective distress and avoidance during a behavioral avoidance task, and state looming vulnerability cognitions during an exposure task. The latent explicit (but not implicit) threat overestimation variable was a significant and unique predictor of contamination fear symptoms and self-reported affective and cognitive facets of contamination fear. On the contrary, the implicit (but not explicit) latent measure predicted behavioral avoidance (at the level of a trend). Results are discussed in terms of differential predictive validity of implicit versus explicit markers of threat processing and multiple fear response systems. PMID:24073390

Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius).

PubMed

Yang, Huaan; Jian, Jianbo; Li, Xuan; Renshaw, Daniel; Clements, Jonathan; Sweetingham, Mark W; Tan, Cong; Li, Chengdao

2015-09-02

Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding. We demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome current limitations in molecular plant breeding, which will enable plant breeders to precisely pyramid favourable genes to develop super crop varieties to meet future food demands.

CONTAMINANTS AND REMEDIAL OPTIONS AT SELECTED METAL-CONTAMINATED SITES

EPA Science Inventory

This document provides information that facilitates characterization of the site and selection of treatment technologies at metals-contaminated sites that would be capable of meeting site-specific cleanup levels. he document does not facilitate the determination of cleanup levels...

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

PubMed

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.

Suitability of non-lethal marker and marker-free systems for development of transgenic crop plants: present status and future prospects.

PubMed

Manimaran, P; Ramkumar, G; Sakthivel, K; Sundaram, R M; Madhav, M S; Balachandran, S M

2011-01-01

Genetically modified crops are one of the prudent options for enhancing the production and productivity of crop plants by safeguarding from the losses due to biotic and abiotic stresses. Agrobacterium-mediated and biolistic transformation methods are used to develop transgenic crop plants in which selectable marker genes (SMG) are generally deployed to identify 'true' transformants. The commonly used SMG obtained from prokaryotic sources when employed in transgenic plants pose risks due to their lethal nature during selection process. In the recent past, some non-lethal SMGs have been identified and used for selection of transformants with increased precision and high selection efficiency. Considering the concerns related to bio-safety of the environment, it is desirable to remove the SMG in order to maximize the commercial success through wide adoption and public acceptance of genetically modified (GM) food crops. In this review, we examine the availability, and the suitability of wide range of non-lethal selection markers and elimination of SMG methods to develop marker-free transgenics for achieving global food security. As the strategies for marker-free plants are still in proof-of-concept stage, adaptation of new genomics tools for identification of novel non-lethal marker systems and its application for developing marker-free transgenics would further strengthen the crop improvement program. Copyright © 2011 Elsevier Inc. All rights reserved.

Generation of selectable marker-free transgenic eggplant resistant to Alternaria solani using the R/RS site-specific recombination system.

PubMed

Darwish, Nader Ahmed; Khan, Raham Sher; Ntui, Valentine Otang; Nakamura, Ikuo; Mii, Masahiro

2014-03-01

Marker-free transgenic eggplants, exhibiting enhanced resistance to Alternaria solani , can be generated on plant growth regulators (PGRs)- and antibiotic-free MS medium employing the multi-auto-transformation (MAT) vector, pMAT21 - wasabi defensin , wherein isopentenyl transferase ( ipt ) gene is used as a positive selection marker. Use of the selection marker genes conferring antibiotic or herbicide resistance in transgenic plants has been considered a serious problem for environment and the public. Multi-auto-transformation (MAT) vector system has been one of the tools to excise the selection marker gene and produce marker-free transgenic plants. Ipt gene was used as a selection marker gene. Wasabi defensin gene, isolated from Wasabia japonica (a Japanese horseradish which has been a potential source of antimicrobial proteins), was used as a gene of interest. Wasabi defensin gene was cloned from the binary vector, pEKH-WD, to an ipt-type MAT vector, pMAT21, by gateway cloning technology and transferred to Agrobacterium tumefaciens strain EHA105. Infected cotyledon explants of eggplant were cultured on PGRs- and antibiotic-free MS medium. Extreme shooty phenotype/ipt shoots were produced by the explants infected with the pMAT21-wasabi defensin (WD). The same PGRs- and antibiotic-free MS medium was used in subcultures of the ipt shoots. Subsequently, morphologically normal shoots emerged from the Ipt shoots. Molecular analyses of genomic DNA from transgenic plants confirmed the integration of the WD gene and excision of the selection marker (ipt gene). Expression of the WD gene was confirmed by RT-PCR and Northern blot analyses. In vitro whole plant and detached leaf assay of the marker-free transgenic plants exhibited enhanced resistance against Alternaria solani.

Single cell gene expression profiling in Alzheimer's disease.

PubMed

Ginsberg, Stephen D; Che, Shaoli; Counts, Scott E; Mufson, Elliott J

2006-07-01

Development and implementation of microarray techniques to quantify expression levels of dozens to hundreds to thousands of transcripts simultaneously within select tissue samples from normal control subjects and neurodegenerative diseased brains has enabled scientists to create molecular fingerprints of vulnerable neuronal populations in Alzheimer's disease (AD) and related disorders. A goal is to sample gene expression from homogeneous cell types within a defined region without potential contamination by expression profiles of adjacent neuronal subpopulations and nonneuronal cells. The precise resolution afforded by single cell and population cell RNA analysis in combination with microarrays and real-time quantitative polymerase chain reaction (qPCR)-based analyses allows for relative gene expression level comparisons across cell types under different experimental conditions and disease progression. The ability to analyze single cells is an important distinction from global and regional assessments of mRNA expression and can be applied to optimally prepared tissues from animal models of neurodegeneration as well as postmortem human brain tissues. Gene expression analysis in postmortem AD brain regions including the hippocampal formation and neocortex reveals selectively vulnerable cell types share putative pathogenetic alterations in common classes of transcripts, for example, markers of glutamatergic neurotransmission, synaptic-related markers, protein phosphatases and kinases, and neurotrophins/neurotrophin receptors. Expression profiles of vulnerable regions and neurons may reveal important clues toward the understanding of the molecular pathogenesis of various neurological diseases and aid in identifying rational targets toward pharmacotherapeutic interventions for progressive, late-onset neurodegenerative disorders such as mild cognitive impairment (MCI) and AD.

Improving the selection efficiency of the counter-selection marker pheS* for the genetic engineering of Bacillus amyloliquefaciens.

PubMed

Kharchenko, Maria S; Teslya, Petr N; Babaeva, Maria N; Zakataeva, Natalia P

2018-05-01

Bacillus subtilis pheS was genetically modified to obtain a counter-selection marker with high selection efficiency in Bacillus amyloliquefaciens. The application of the new replication-thermosensitive integrative vector pNZTM1, containing this marker, pheS BsT255S/A309G , with a two-step replacement recombination procedure provides an effective tool for the genetic engineering of industrially important Bacillus species. Copyright © 2018. Published by Elsevier B.V.

[Factors modifying cord blood IgE levels - a pilot study].

PubMed

Petrovičová, O; Bánovčin, P; Babušíková, E; Jeseňák, M

The complex influence of internal and external environmental factors on the individual and his/her immune system and the lack of suitable markers to assess and reduce the risk of the development of allergies during the lifetime can explain the continuous increase in the number of people affected by some form of allergy. According to the results of some studies, cord blood IgE level could be a useful early marker for assessing the risk of atopic diseases, but the studies showed controversial results. In addition, several authors discuss the origin of these antibodies (synthesis in utero, peripartum contamination from maternal blood or placental transfer). The aim of our pilot study was to investigate the possible influence of modifying factors on cord blood IgE level. Our group of patients consisted of 184 retrospectively selected neonates (98 boys, 53.3% and 86 girls, 46.7%) from whom cord blood was collected and cord blood IgE level was measured 25 years ago (PRIST method). The impact of selected modifying factors (sex, type of delivery or month of birth) on cord blood IgE level was assessed retrospectively. Higher cord blood IgE levels were found in boys than in girls, in neonates born by Caesarean section than in those born by natural delivery, and in those born in the winter months than in other seasons of the year. Our findings are in agreement with those of other authors. Based on our results and those of others, we assume that the selected factors affect the cord blood IgE levels to varying degrees. These facts should be taken into consideration while interpreting the cord blood IgE levels.

ErbB2 and bone sialoprotein as markers for metastatic osteosarcoma cells

PubMed Central

Valabrega, G; Fagioli, F; Corso, S; Madon, E; Brach del Prever, A; Biasin, E; Linari, A; Aglietta, M; Giordano, S

2003-01-01

Osteosarcoma is the most common malignant bone neoplasia occurring in young patients in the first two decades of life, and represents 20% of all primitive malignant bone tumours. At present, treatment of metastatic osteosarcoma is unsatisfactory. High-dose chemotherapy followed by CD34+ leukapheresis rescue may improve these poor results. Neoplastic cells contaminating the apheresis may, however, contribute to relapse. To identify markers suitable for detecting osteosarcoma cells in aphereses we analysed the expression of bone-specific genes (Bone Sialoprotein (BSP) and Osteocalcin) and oncogenes (Met and ErbB2) in 22 patients with metastatic osteosarcoma and six healthy stem cell donors. The expression of these genes in aphereses of patients affected by metastatic osteosarcoma was assessed by RT–PCR and Southern blot analysis. Met and Osteocalcin proved to be not useful markers since they are positive in aphereses of both patients with metastatic osteosarcoma and healthy stem cell donors. On the contrary, BSP was expressed at significant levels in 85% of patients. Moreover, 18% of patients showed a strong and significantly positive (seven to 16 times higher than healthy stem cell donors) ErbB2 expression. In all positive cases, neoplastic tissue also expressed ErbB2. Our data show that ErbB2 can be a useful marker for tumour contamination in aphereses of patients affected by ErbB2-expressing osteosarcomas and that analysis of Bone Sialoprotein expression can be an alternative useful marker. PMID:12569382

Hybrid microarray based on double biomolecular markers of DNA and carbohydrate for simultaneous genotypic and phenotypic detection of cholera toxin-producing Vibrio cholerae.

PubMed

Shin, Hwa Hui; Seo, Jeong Hyun; Kim, Chang Sup; Hwang, Byeong Hee; Cha, Hyung Joon

2016-05-15

Life-threatening diarrheal cholera is usually caused by water or food contaminated with cholera toxin-producing Vibrio cholerae. For the prevention and surveillance of cholera, it is crucial to rapidly and precisely detect and identify the etiological causes, such as V. cholerae and/or its toxin. In the present work, we propose the use of a hybrid double biomolecular marker (DBM) microarray containing 16S rRNA-based DNA capture probe to genotypically identify V. cholerae and GM1 pentasaccharide capture probe to phenotypically detect cholera toxin. We employed a simple sample preparation method to directly obtain genomic DNA and secreted cholera toxin as target materials from bacterial cells. By utilizing the constructed DBM microarray and prepared samples, V. cholerae and cholera toxin were detected successfully, selectively, and simultaneously; the DBM microarray was able to analyze the pathogenicity of the identified V. cholerae regardless of whether the bacteria produces toxin. Therefore, our proposed DBM microarray is a new effective platform for identifying bacteria and analyzing bacterial pathogenicity simultaneously. Copyright © 2015 Elsevier B.V. All rights reserved.

Migration and generation of contaminants from launch through recovery: LDEF case history

NASA Technical Reports Server (NTRS)

Crutcher, E. R.; Nishimura, L. S.; Warner, K. J.; Wascher, W. W.

1992-01-01

It is possible to recreate the contamination history of the Long Duration Exposure Facility (LDEF) through an analysis of its contaminants and selective samples that were collected from surfaces with better documented exposure histories. This data was then used to compare estimates based on monitoring methods that were selected for the purpose of tracking LDEF's exposure to contaminants. The LDEF experienced much more contamination than would have been assumed based on the monitors. Work is still in progress but much of what was learned so far is already being used in the selection of materials and in the design of systems for space. Now experiments are being prepared for flight to resolve questions created by the discoveries on the LDEF. A summary of what was learned about LDEF contaminants over the first year since recovery and deintegration is presented. Over 35 specific conclusions in 5 contamination related categories are listed.

Genomic Selection in Multi-environment Crop Trials.

PubMed

Oakey, Helena; Cullis, Brian; Thompson, Robin; Comadran, Jordi; Halpin, Claire; Waugh, Robbie

2016-05-03

Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers. Copyright © 2016 Oakey et al.

CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization

USDA-ARS?s Scientific Manuscript database

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC III) was subjected to marker assisted selection for multiple years to equalize specific marker frequencies to 1) estimate effect size an...

µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies

USDA-ARS?s Scientific Manuscript database

Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size an...

Responses of chub (Leuciscus cephalus) populations to chemical stress, assessed by genetic markers, DNA damage and cytochrome P4501A induction.

PubMed

Larno, V; Laroche, J; Launey, S; Flammarion, P; Devaux, A

2001-06-01

Indicators of effects at the population level (genetic variation using allozymes) and early indicators of pollution (EROD activity and DNA strand break formation) were analysed in chub (Leuciscus cephalus) living in weakly and heavily contaminated stations of the Rhône River watershed. The genetic erosion was mainly detected in a fish population living in a contaminated small river system, through modifications in allelic and genotypic frequencies for PGM-2 locus and could be linked to a genetic bottleneck and to the reduced gene flow from upstream unable to maintain or restore the genetic diversity. In a contaminated large river system, the genetic diversity for PGM-2 and other loci was maintained and was probably the consequence of a high gene flow from upstream, linked to a sustained drift of larvae and juveniles in the system. A convergent increase of the frequency of the 90 allele at PGM-2 was observed in two contaminated stations compared with the reference station, this trend being confirmed on a more extensive geographic scale over the Rhône River basin. A high level of EROD activity was detected in both contaminated sites but only the fish in the large river system showed a significant DNA damage level compared to the reference population. The low DNA damage level and high hepato-somatic ratio characterized the impacted population of the small river system and could be associated to a chronic high-level exposure of fish to pollutants which selected individuals exhibiting a high level of DNA damage repair. In the two contaminated systems, some genotypes at the PGM-2 and EST-2 loci showed a low level of DNA damage and/or a high EROD activity and may be considered as being tolerant to pollutants. A higher tolerance of the most heterozygous fish was also detected in the contaminated large system and confirmed that a high level of heterozygosity may be necessary for survival in such a system.

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

PubMed

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.

[A comparative analysis of Ungulata species by different molecular genetic markers (proteins, RAPD-PCR)].

PubMed

Glazko, V I; Zelenaia, L B; Iasinetskaia, N A

1997-01-01

The investigation of genetic interrelation between a number of Artiodactyla and Perissodactyla species with the use of different types of molecular-genetic markers (proteins, RAPD-PCR) were carried out. The marker-specific features of interspecific relations and their similarities on the groups of markers of both types were revealed. The distinctions between interspecies genetic relations and ones estimated from the phylogeny on the determined group of different types of markers were observed. It was supposed that these discrepancies may be related with common selection factors and involving this marker group in selection in some species.

Molecular plant breeding: methodology and achievements.

PubMed

Varshney, Rajeev K; Hoisington, Dave A; Nayak, Spurthi N; Graner, Andreas

2009-01-01

The progress made in DNA marker technology has been remarkable and exciting in recent years. DNA markers have proved valuable tools in various analyses in plant breeding, for example, early generation selection, enrichment of complex F(1)s, choice of donor parent in backcrossing, recovery of recurrent parent genotype in backcrossing, linkage block analysis and selection. Other main areas of applications of molecular markers in plant breeding include germplasm characterization/fingerprinting, determining seed purity, systematic sampling of germplasm, and phylogenetic analysis. Molecular markers, thus, have proved powerful tools in replacing the bioassays and there are now many examples available to show the efficacy of such markers. We have illustrated some basic concepts and methodology of applying molecular markers for enhancing the selection efficiency in plant breeding. Some successful examples of product developments of molecular breeding have also been presented.

Logistic regression trees for initial selection of interesting loci in case-control studies

PubMed Central

Nickolov, Radoslav Z; Milanov, Valentin B

2007-01-01

Modern genetic epidemiology faces the challenge of dealing with hundreds of thousands of genetic markers. The selection of a small initial subset of interesting markers for further investigation can greatly facilitate genetic studies. In this contribution we suggest the use of a logistic regression tree algorithm known as logistic tree with unbiased selection. Using the simulated data provided for Genetic Analysis Workshop 15, we show how this algorithm, with incorporation of multifactor dimensionality reduction method, can reduce an initial large pool of markers to a small set that includes the interesting markers with high probability. PMID:18466557

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

USDA-ARS?s Scientific Manuscript database

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...

Selective sweep mapping of genes with large phenotypic effects.

PubMed

Pollinger, John P; Bustamante, Carlos D; Fledel-Alon, Adi; Schmutz, Sheila; Gray, Melissa M; Wayne, Robert K

2005-12-01

Many domestic dog breeds have originated through fixation of discrete mutations by intense artificial selection. As a result of this process, markers in the proximity of genes influencing breed-defining traits will have reduced variation (a selective sweep) and will show divergence in allele frequency. Consequently, low-resolution genomic scans can potentially be used to identify regions containing genes that have a major influence on breed-defining traits. We model the process of breed formation and show that the probability of two or three adjacent marker loci showing a spurious signal of selection within at least one breed (i.e., Type I error or false-positive rate) is low if highly variable and moderately spaced markers are utilized. We also use simulations with selection to demonstrate that even a moderately spaced set of highly polymorphic markers (e.g., one every 0.8 cM) has high power to detect regions targeted by strong artificial selection in dogs. Further, we show that a gene responsible for black coat color in the Large Munsterlander has a 40-Mb region surrounding the gene that is very low in heterozygosity for microsatellite markers. Similarly, we survey 302 microsatellite markers in the Dachshund and find three linked monomorphic microsatellite markers all within a 10-Mb region on chromosome 3. This region contains the FGFR3 gene, which is responsible for achondroplasia in humans, but not in dogs. Consequently, our results suggest that the causative mutation is a gene or regulatory region closely linked to FGFR3.

Algorithms for selecting informative marker panels for population assignment.

PubMed

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.

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

PubMed Central

Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

2016-01-01

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection. PMID:26799713

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding.

PubMed

Fan, Wei; Zong, Jie; Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

2016-01-01

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.

Organic Geochemistry of the Tohoku Tsunami Deposits of 2011 (Japan)

NASA Astrophysics Data System (ADS)

Reicherter, K. R.; Schwarzbauer, J.; Szczucinski, W.; Jaffe, B. E.

2014-12-01

Geochemical investigations on paleotsunami deposits have mainly focused on inorganic proxies. Organic geochemistry has been used to distinguish between terrestrial and marine matter within the sediments, reflecting the mixture and transport of marine and terrestrial matter. The approach using organic substances with indicative properties (anthropogenic and xenobiotic compounds) for recent tsunami deposits is novel, but the approach of using specific bio- and anthropogenic markers indicators to determine (pre)historic and recent processes and impacts already exists. The Tohoku-oki tsunami in March 2011 showed the huge threat that tsunamis pose to society and landscape, including flooding of coastal lowlands and erosion/deposition of sediments. The mainly sandy tsunamites reach more than 4.5 km inland as there were run-up heights of ca. 10 m in the Sendai plain near the Sendai airport. The destruction of infrastructure by wave action and flooding was accompanied by the release of environmental pollutants (e.g. fuels, fats, tarmac, plastics, heavy metals, etc.) contaminating the coastal areas and ocean over large areas. To detect and characterize this process, we analyzed several sedimentary archives from the Bay of Sendai area (by using the same sample material as Szczucinski et al., 2012 from rice paddies of the Sendai Plain, Japan). The layers representing the tsunami deposits have been compared with pre-tsunami samples (supposedly to be unaffected) by means of organic-geochemical analyses based on GC/MS. Natural compounds and their diagenetic transformation products have been tested as marker compounds and proxies. The relative composition of fatty acids, n-alkanes, sesquiterpenes and further substances pointed to significant variations before and after the tsunami event. Additionally, anthropogenic marker compounds (such as soil derived pesticides, source specific PAHs, halogenated aromatics from industrial sources) have been detected and quantified. Concentration profiles of distinct terrestrial pollutants revealed shifts either to increasing but for selected compounds also to decreasing contamination levels. We will extend and test the approach in future on paleotsunami deposits of the 869 AD Jogan event and others. Szczucinski et al. 2012, Sed. Geol., 282:40-56.

Organic-geochemical investigations on soil layers affected by theTohoku-oki tsunami (March 2011)

NASA Astrophysics Data System (ADS)

Reicherter, Klaus; Schwarzbauer, Jan; Jaffe, Bruce; Szczucinski, Witold

2014-05-01

Geochemical investigations on tsunami deposits, in particular palaeotsunamites, have mainly focused on inorganic indicators that have been used to distinguish between terrestrial and marine matter in sedimentary archives. Observable tsunami deposits may also be characterised by organic-geochemical parameters reflecting the mixture and unexpected transport of marine and terrestrial matter. The application of organic substances with indicative properties has so far not been used, although the approach of using specific indicators to determine prehistoric, historic and recent processes and impacts (so-called biomarker and anthropogenic marker approach) already exists. In particular, for recent tsunami deposit the analysis of anthropogenic or even xenobiotic compounds as indicators for assessing the impact of tsunamis has been neglected so far. The Tohoku-oki tsunami in March 2011 showed the huge threat that tsunamis, and subsequent flooding of coastal lowlands, pose to society. The mainly sandy deposits of this mega-tsunami reach more than 4.5 km inland as there were run-up heights of ca. 10 m (wave height). The destruction of infrastructure by wave action and flooding is accompanied by the release of environmental pollutants (e.g. fuels, fats, tarmac, plastics, heavy metals, etc.) contaminating the coastal areas and ocean. To characterize this event in the sedimentary deposits, we analyzed several soil archives from the Bay of Sendai area. Soil layers representing the tsunami deposits have been contrasted with unaffected pre-tsunami samples by means of organic-geochemical analyses based on GC/MS. Natural compounds and their diagenetic transformation products have been tested as marker compounds for monitoring this recent tsunami. The relative composition of fatty acids, n-alkanes, sesquiterpenes and further substances pointed to significant variations before and after the tsunami event. Additionally, anthropogenic marker compounds (such as soil derived pesticides, source specific PAHs, halogenated aromatics from industrial sources) have been detected and quantified. Concentration profiles of distinct terrestrial pollutants revealed shifts either to increasing but for selected compounds also to decreasing contamination levels. Generally, this preliminary study points to the usefulness of organic indicator compounds for characterising the two-dimensional expansion of recent but in particular historic tsunami events as well as its time scales.

Chemical Contaminants as Stratigraphic Markers for the Anthropocene

NASA Astrophysics Data System (ADS)

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 long-term stratigraphic record, establishing markers of the Anthropocene Epoch for millions of years to come.

Biomarker responses to environmental contamination in estuaries: A comparative multi-taxa approach.

PubMed

Duarte, Irina A; Reis-Santos, Patrick; França, Susana; Cabral, Henrique; Fonseca, Vanessa F

2017-08-01

Estuaries are highly productive ecosystems subjected to numerous anthropogenic pressures with consequent environmental quality degradation. In this study, multiple biomarker responses [superoxide dismutase (SOD), catalase (CAT), ethoxyresorufin O-deethylase (EROD) and glutathione S-transferase (GST) activities, as well as lipid peroxidation (LPO) and DNA damage (DNAd)] were determined in two fish (Dicentrarchus labrax and Pomatoschistus microps) and four macroinvertebrate species (Carcinus maenas, Crangon crangon, Hediste diversicolor and Scrobicularia plana) from the Ria de Aveiro and Tejo estuaries over distinct months. Two sites per estuarine system were selected based on anthropogenic pressures and magnitude of environmental contamination. Antioxidant enzyme activities in fish species suggested a ubiquitous response to oxidative stress, while biotransformation and effect biomarkers exhibited higher spatial and temporal variation. In invertebrate species, biotransformation enzyme activity was clearly less variable than in fish evidencing lower xenobiotic transformation capability. Overall, largest biomarker responses were found in the most contaminated sites (Tejo), yet species-specific patterns were evident. These should be factored in multi-taxa approaches, considering that the differential functional traits of species, such as habitat use, life-stage, feeding or physiology can influence exposure routes and biomarker responses. The Integrated Biomarker Response index highlighted patterns in biomarker responses which were not immediately evident when analyzing biomarkers individually. Overall, results provided insights into the complexity of species responses to contamination in naturally varying estuarine environments. Ultimately, multi-taxa and multi-biomarker approaches provide a comprehensive and complementary view of ecosystem health, encompassing diverse forms of biological integration and exposure routes, and allow the validation of results among markers and species. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction.

PubMed

Brøndum, R F; Su, G; Janss, L; Sahana, G; Guldbrandtsen, B; Boichard, D; Lund, M S

2015-06-01

This study investigated the effect on the reliability of genomic prediction when a small number of significant variants from single marker analysis based on whole genome sequence data were added to the regular 54k single nucleotide polymorphism (SNP) array data. The extra markers were selected with the aim of augmenting the custom low-density Illumina BovineLD SNP chip (San Diego, CA) used in the Nordic countries. The single-marker analysis was done breed-wise on all 16 index traits included in the breeding goals for Nordic Holstein, Danish Jersey, and Nordic Red cattle plus the total merit index itself. Depending on the trait's economic weight, 15, 10, or 5 quantitative trait loci (QTL) were selected per trait per breed and 3 to 5 markers were selected to tag each QTL. After removing duplicate markers (same marker selected for more than one trait or breed) and filtering for high pairwise linkage disequilibrium and assaying performance on the array, a total of 1,623 QTL markers were selected for inclusion on the custom chip. Genomic prediction analyses were performed for Nordic and French Holstein and Nordic Red animals using either a genomic BLUP or a Bayesian variable selection model. When using the genomic BLUP model including the QTL markers in the analysis, reliability was increased by up to 4 percentage points for production traits in Nordic Holstein animals, up to 3 percentage points for Nordic Reds, and up to 5 percentage points for French Holstein. Smaller gains of up to 1 percentage point was observed for mastitis, but only a 0.5 percentage point increase was seen for fertility. When using a Bayesian model accuracies were generally higher with only 54k data compared with the genomic BLUP approach, but increases in reliability were relatively smaller when QTL markers were included. Results from this study indicate that the reliability of genomic prediction can be increased by including markers significant in genome-wide association studies on whole genome sequence data alongside the 54k SNP set. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Transmission of Salmonella to broilers by contaminated larval and adult lesser mealworms, Alphitobius diaperinus (Coleoptera: Tenebrionidae).

PubMed

Roche, A J; Cox, N A; Richardson, L J; Buhr, R J; Cason, J A; Fairchild, B D; Hinkle, N C

2009-01-01

The ability of the lesser mealworm, Alphitobius diaperinus (Panzer), commonly known as the darkling beetle, to transmit marker Salmonella Typhimurium to day-of-hatch broiler chicks was evaluated, as well as the spread to nonchallenged pen mates. In trial 1, day-of-hatch chicks were orally gavaged with 4 larval or 4 adult beetles that had been exposed to marker Salmonella-inoculated feed for 72 h. In addition, chicks were gavaged with the marker Salmonella in saline solution. These chicks were then placed into pens to serve as challenged broilers. In trial 2, all pens received 2 challenged chicks that were gavaged with larvae or beetles that had been exposed to marker Salmonella-inoculated feed for 24 h and then removed from the inoculated feed for a period of 7 d. At 3 wk of age, cecal samples from the marker Salmonella-challenged broilers and from 5 pen mates in trial 1, or 10 pen mates in trial 2, were evaluated for the presence of the marker Salmonella in their ceca, and at 6 wk of age, all remaining pen mates were sampled. To monitor the presence of the marker Salmonella within pens, stepped-on drag swab litter samples were taken weekly. For the Salmonella-saline pens, 29 to 33% of the broilers that had been challenged and 10 to 55% of the pen mates were positive at 3 wk of age, and only 2 to 6% had positive ceca at 6 wk. For the pens challenged with adult beetles, 0 to 57% of the challenged broilers and 20 to 40% of the pen mates had positive ceca at 3 wk, and 4 to 7% were positive at 6 wk. The pens challenged with larvae had the greatest percentage of marker Salmonella-positive broilers; 25 to 33% of the challenged broilers and 45 to 58% of pen mates were positive at 3 wk, and 11 to 27% were positive at 6 wk. These results demonstrated that ingestion of larval or adult beetles contaminated with a marker Salmonella could be a significant vector for transmission to broilers.

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

USGS Publications Warehouse

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-specific marker of enterococci, the esp gene, were negative in the seven samples tested, including the composite sample of HSTS water. DNA with the general Bacteroidales marker was detected in samples from four wells, but the tests for both the human- and ruminant-associated markers were negative. The presence of the PCR (polymerase chain reaction) -detectable DNA for the general fecal Bacteroidales marker is indicative of fecal contamination and recently recharged water.

Charles W. Stuber: Maize geneticist and pioneer of marker-assisted selection

USDA-ARS?s Scientific Manuscript database

Charles W. Stuber is considered a pioneer of quantitative genetic mapping and marker-assisted selection in maize. The achievements of his four decade career in research include the development of genetic marker systems used in maize and adapted in many other crops, the first methods and studies to i...

DNA fingerprinting sets for four southern pines

Treesearch

Craig Echt; Sedley Josserand

2018-01-01

DNA markers can provide valuable genetic information for forest tree research, breeding, conservation, and restoration programs. When properly evaluated, selected sets of DNA markers can be used to efficiently get information about genetic diversity in regions, forests, or stands, or in seed lots and orchards. Selected markers also can be used to determine parentage or...

A Technical Guide to Ground-Water Model Selection at Sites Contaminated with Radioactive Substances

EPA Pesticide Factsheets

This report addresses the selection of ground-water flow and contaminant transport models and is intended to be used by hydrogeologists and geoscientists responsible for selecting transport models for use at sites containing radioactive materials.

Selection for avian immune response: a commercial breeding company challenge.

PubMed

Fulton, J E

2004-04-01

Selection for immune function in the commercial breeding environment is a challenging proposition for commercial breeding companies. Immune response is only one of many traits that are under intensive selection, thus selection pressure needs to be carefully balanced across multiple traits. The selection environment (single bird cages, biosecure facilities, controlled environment) is a very different environment than the commercial production facilities (multiple bird cages, potential disease exposure, variable environment) in which birds are to produce. The testing of individual birds is difficult, time consuming, and expensive. It is essential that the results of any tests be relevant to actual disease or environmental challenge in the commercial environment. The use of genetic markers as indicators of immune function is being explored by breeding companies. Use of genetic markers would eliminate many of the limitations in enhancing immune function currently encountered by commercial breeding companies. Information on genetic markers would allow selection to proceed without subjecting breeding stock to disease conditions and could be done before production traits are measured. These markers could be candidate genes with known interaction or involvement with disease pathology or DNA markers that are closely linked to genetic regions that influence the immune response. The current major limitation to this approach is the paucity of mapped chicken immune response genes and the limited number of DNA markers mapped on the chicken genome. These limitations should be eliminated once the chicken genome is sequenced.

Contaminant loading in remote Arctic lakes affects cellular stress-related proteins expression in feral charr.

USGS Publications Warehouse

Wiseman, Steve; Jorgensen, Even H.; Maule, Alec G.; Vijayan, Mathilakath M.

2011-01-01

The remote Arctic lakes on Bjornoya Island, Norway, offer a unique opportunity to study possible affect of lifelong contaminant exposure in wild populations of landlocked Arctic charr (Salvelinus alpinus). This is because Lake Ellasjoen has persistent organic pollutant (POP) levels that are significantly greater than in the nearby Lake Oyangen. We examined whether this differential contaminant loading was reflected in the expression of protein markers of exposure and effect in the native fish. We assessed the expressions of cellular stress markers, including cytochrome P4501A (Cyp1A), heat shock protein 70 (hsp70), and glucocorticoid receptor (GR) in feral charr from the two lakes. The average polychlorinated biphenyl (PCB) load in the charr liver from Ellasjoen was approximately 25-fold higher than in individuals from Oyangen. Liver Cyp1A protein expression was significantly higher in individuals from Ellasjoen compared with Oyangen, confirming differential PCB exposure. There was no significant difference in hsp70 protein expression in charr liver between the two lakes. However, brain hsp70 protein expression was significantly elevated in charr from Ellasjoen compared with Oyangen. Also, liver GR protein expression was significantly higher in the Ellasjoen charr compared with Oyangen charr. Taken together, our results suggest changes to cellular stress-related protein expression as a possible adaptation to chronic-contaminant exposure in feral charr in the Norwegian high-Arctic.

Semi volatile organic compounds in the snow of Russian Arctic islands: Archipelago Novaya Zemlya.

PubMed

Lebedev, A T; Mazur, D M; Polyakova, O V; Kosyakov, D S; Kozhevnikov, A Yu; Latkin, T B; Andreeva Yu, I; Artaev, V B

2018-04-18

Environmental contamination of the Arctic has widely been used as a worldwide pollution marker. Various classes of organic pollutants such as pesticides, personal care products, PAHs, flame retardants, biomass burning markers, and many others emerging contaminants have been regularly detected in Arctic samples. Although numerous papers have been published reporting data from the Canadian, Danish, and Norwegian Arctic regions, the environmental situation in Russian Arctic remains mostly underreported. Snow analysis is known to be used for monitoring air pollution in the regions with cold climate in both short-term and long-term studies. This paper presents the results of a nontargeted study on the semivolatile organic compounds detected and identified in snow samples collected at the Russian Artic Archipelago Novaya Zemlya in June 2016. Gas chromatography coupled to a high-resolution time-of-flight mass spectrometer enabled the simultaneous detection and quantification of a variety of pollutants including those from the US Environmental Protection Agency (EPA) priority pollutants list, emerging contaminants (plasticizers, flame retardants-only detection), as well as the identification of novel Arctic organic pollutants, (e.g., fatty acid amides and polyoxyalkanes). The possible sources of these novel pollutants are also discussed. GC-HRMS enabled the detection and identification of emerging contaminants and novel organic pollutants in the Arctic, e.g., fatty amides and polyoxyalkanes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Superfund Record of Decision Amendment (EPA Region 10): McCormick and Baxter Creosoting Company (Portland Plant), Portland, OR, March 17, 1998

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-09-01

This ROD Amendment changes a component of the selected remedial action for contaminated soil. The original selected remedy documented in the March 1996 Record of Decision (ROD) is a series of remedial actions that address the principal threats at the Site, by removing the most highly contaminated soil, extracting nonaqueous phase liquid (NAPL) from and treating contaminated groundwater, and capping the most highly contaminated sediment. Because significant levels of dioxin are present in soil areas originally identified for excavation and on-site biological treatment (i.e, areas where contamination exceeds the action levels for PCP and PAHs), it now appears unlikely thatmore » this intended treatment will achieve the level of risk reduction contemplated in the 1996 ROD. Accordingly, DEQ and EPA have selected an alternative remedy for contaminated soil at the McCormick and Baxter site.« less

Diversity among strains of Pseudomonas aeruginosa from manure and soil, evaluated by multiple locus variable number tandem repeat analysis and antibiotic resistance profiles.

PubMed

Youenou, Benjamin; Brothier, Elisabeth; Nazaret, Sylvie

2014-01-01

The results of a multiple locus variable number of tandem repeat (VNTR) analysis (MLVA)-based study designed to understand the genetic diversity of soil and manure-borne Pseudomonas aeruginosa isolates, and the relationship between these isolates and a set of clinical and environmental isolates, are hereby reported. Fifteen described VNTR markers were first selected, and 62 isolates recovered from agricultural and industrial soils in France and Burkina Faso, and from cattle and horse manure, along with 26 snake-related isolates and 17 environmental and clinical isolates from international collections, were genotyped. Following a comparison with previously published 9-marker MLVA schemes, an optimal 13-marker MLVA scheme (MLVA13-Lyon) was identified that was found to be the most efficient, as it showed high typability (90%) and high discriminatory power (0.987). A comparison of MLVA with PFGE for typing of the snake-related isolates confirmed the MLVA13-Lyon scheme to be a robust method for quickly discriminating and inferring genetic relatedness among environmental isolates. The 62 isolates displayed wide diversity, since 41 MLVA types (i.e. MTs) were observed, with 26 MTs clustered in 10 MLVA clonal complexes (MCs). Three and eight MCs were found among soil and manure isolates, respectively. Only one MC contained both soil and manure-borne isolates. No common MC was observed between soil and manure-borne isolates and the snake-related or environmental and clinical isolates. Antibiotic resistance profiles were performed to determine a potential link between resistance properties and the selective pressure that might be present in the various habitats. Except for four soil and manure isolates resistant to ticarcillin and ticarcillin/clavulanic acid and one isolate from a hydrocarbon-contaminated soil resistant to imipenem, all environmental isolates showed wild-type antibiotic profiles. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

A bifunctional aminoglycoside acetyltransferase/phosphotransferase conferring tobramycin resistance provides an efficient selectable marker for plastid transformation.

PubMed

Tabatabaei, Iman; Ruf, Stephanie; Bock, Ralph

2017-02-01

A new selectable marker gene for stable transformation of the plastid genome was developed that is similarly efficient as the aadA, and produces no background of spontaneous resistance mutants. More than 25 years after its development for Chlamydomonas and tobacco, the transformation of the chloroplast genome still represents a challenging technology that is available only in a handful of species. The vast majority of chloroplast transformation experiments conducted thus far have relied on a single selectable marker gene, the spectinomycin resistance gene aadA. Although a few alternative markers have been reported, the aadA has remained unrivalled in efficiency and is, therefore, nearly exclusively used. The development of new marker genes for plastid transformation is of crucial importance to all efforts towards extending the species range of the technology as well as to those applications in basic research, biotechnology and synthetic biology that involve the multistep engineering of plastid genomes. Here, we have tested a bifunctional resistance gene for its suitability as a selectable marker for chloroplast transformation. The bacterial enzyme aminoglycoside acetyltransferase(6')-Ie/aminoglycoside phosphotransferase(2″)-Ia possesses an N-terminal acetyltransferase domain and a C-terminal phosphotransferase domain that can act synergistically and detoxify aminoglycoside antibiotics highly efficiently. We report that, in combination with selection for resistance to the aminoglycoside tobramycin, the aac(6')-Ie/aph(2″)-Ia gene represents an efficient marker for plastid transformation in that it produces similar numbers of transplastomic lines as the spectinomycin resistance gene aadA. Importantly, no spontaneous antibiotic resistance mutants appear under tobramycin selection.

Genome-enabled prediction models for yield related traits in chickpea

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped...

Label-Free Biosensing with High Selectivity in Complex Media using Microtoroidal Optical Resonators

NASA Astrophysics Data System (ADS)

Ozgur, Erol; Toren, Pelin; Aktas, Ozan; Huseyinoglu, Ersin; Bayindir, Mehmet

2015-08-01

Although label-free biosensors comprised of optical microcavities inherently possess the capability of resolving molecular interactions at individual level, this extreme sensitivity restricts their convenience for large scale applications by inducing vulnerability towards non-specific interactions that readily occur within complex media. Therefore, the use of optical microresonators for biosensing is mostly limited within strictly defined laboratory conditions, instead of field applications as early detection of cancer markers in blood, or identification of contamination in food. Here, we propose a novel surface modification strategy suitable for but not limited to optical microresonator based biosensors, enabling highly selective biosensing with considerable sensitivity as well. Using a robust, silane-based surface coating which is simultaneously protein resistant and bioconjugable, we demonstrate that it becomes possible to perform biosensing within complex media, without compromising the sensitivity or reliability of the measurement. Functionalized microtoroids are successfully shown to resist nonspecific interactions, while simultaneously being used as sensitive biological sensors. This strategy could pave the way for important applications in terms of extending the use of state-of-the-art biosensors for solving problems similar to the aforementioned.

Analyte separation utilizing temperature programmed desorption of a preconcentrator mesh

DOEpatents

Linker, Kevin L.; Bouchier, Frank A.; Theisen, Lisa; Arakaki, Lester H.

2007-11-27

A method and system for controllably releasing contaminants from a contaminated porous metallic mesh by thermally desorbing and releasing a selected subset of contaminants from a contaminated mesh by rapidly raising the mesh to a pre-determined temperature step or plateau that has been chosen beforehand to preferentially desorb a particular chemical specie of interest, but not others. By providing a sufficiently long delay or dwell period in-between heating pulses, and by selecting the optimum plateau temperatures, then different contaminant species can be controllably released in well-defined batches at different times to a chemical detector in gaseous communication with the mesh. For some detectors, such as an Ion Mobility Spectrometer (IMS), separating different species in time before they enter the IMS allows the detector to have an enhanced selectivity.

Platinum and lead markers as indicators of transportation impact.

DOT National Transportation Integrated Search

2009-08-20

The intent of this study was to provide information necessary to characterize the present concentrations of an emerging transportation related contaminant, the platinum group metals (PGM), and to provide background information necessary to explore th...

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shugart, L.R.; Adams, S.M.; Jimenez, B.D.

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 exposuremore » 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.« less

Microbiological aspects of polyphosphate injection in the processing and chill storage of poultry.

PubMed Central

Mead, G. C.; Adams, B. W.

1979-01-01

During commercial processing of broiler chickens, injection of polyphosphate (Puron 604 or 6040) resulted in microorganisms being added to the deep breast muscle. The level of contamination was related to the microbiological condition of the injection solution. Injection of polyphosphate had no effect on the shelf-life of fresh chilled carcasses held at 1 degree of 10 degrees C but changes were observed in the growth rate of microorganisms in the deep muscle and in the composition of the muscle microflora following storage. Cross-contamination of carcasses and the transfer of organisms from the skin to the deep muscle during injection was demonstrated with a marker strain of Clostridium perfringens. However, both processes were influenced by the number of marker organisms applied initially to the skin. The above findings are discussed in relation to the possible behaviour of any food poisoning bacteria present. PMID:216743

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

PubMed

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 identified that significantly improved average chip quality after cold storage and tuber starch content. In F1 progeny of a single-cross combination, MAS with six markers did not give the expected result. Reasons and implications for MAS in potato are discussed.

A Marker-Based Approach for the Automated Selection of a Single Segmentation from a Hierarchical Set of Image Segmentations

NASA Technical Reports Server (NTRS)

Tarabalka, Y.; Tilton, J. C.; Benediktsson, J. A.; Chanussot, J.

2012-01-01

The Hierarchical SEGmentation (HSEG) algorithm, which combines region object finding with region object clustering, has given good performances for multi- and hyperspectral image analysis. This technique produces at its output a hierarchical set of image segmentations. The automated selection of a single segmentation level is often necessary. We propose and investigate the use of automatically selected markers for this purpose. In this paper, a novel Marker-based HSEG (M-HSEG) method for spectral-spatial classification of hyperspectral images is proposed. Two classification-based approaches for automatic marker selection are adapted and compared for this purpose. Then, a novel constrained marker-based HSEG algorithm is applied, resulting in a spectral-spatial classification map. Three different implementations of the M-HSEG method are proposed and their performances in terms of classification accuracies are compared. The experimental results, presented for three hyperspectral airborne images, demonstrate that the proposed approach yields accurate segmentation and classification maps, and thus is attractive for remote sensing image analysis.

Selecting soybean resistant to the cyst nematode Heterodera glycines using simple sequence repeat (microssatellite) markers.

PubMed

Espindola, S M C G; Hamawaki, O T; Oliveira, A P; Hamawaki, C D L; Hamawaki, R L; Takahashi, L M

2016-03-11

The soybean cyst nematode (SCN) is a major cause of soybean yield reduction. The objective of this study was to evaluate the efficiency of marker-assisted selection to identify genotypes resistant to SCN race 3 infection, using Sat_168 and Sat-141 resistance quantitative trait loci. The experiment was carried out under greenhouse conditions, using soybean populations originated from crosses between susceptible and resistant parent stock: CD-201 (susceptible) and Foster IAC (resistant), Conquista (susceptible) and S83-30 (resistant), La-Suprema (susceptible) and S57-11 (resistant), and Parecis (susceptible) and S65-50 (resistant). Plants were inoculated with SCN and evaluated according to the female index (FI), those with FI < 10% were classified as resistant to nematode infection. Plants were genotyped for SCN resistance using microsatellite markers Sat-141 and Sat_168. Marker selection efficiency was analyzed by a contingency table, taking into account genotypic versus phenotypic evaluations for each line. These markers were shown to be useful tool for selection of SCN race 3.

Aircraft Recirculation Filter for Air-Quality and Incident Assessment

PubMed Central

Eckels, Steven J.; Jones, Byron; Mann, Garrett; Mohan, Krishnan R.; Weisel, Clifford P.

2015-01-01

The current research examines the possibility of using recirculation filters from aircraft to document the nature of air-quality incidents on aircraft. These filters are highly effective at collecting solid and liquid particulates. Identification of engine oil contaminants arriving through the bleed air system on the filter was chosen as the initial focus. A two-step study was undertaken. First, a compressor/bleed air simulator was developed to simulate an engine oil leak, and samples were analyzed with gas chromatograph-mass spectrometry. These samples provided a concrete link between tricresyl phosphates and a homologous series of synthetic pentaerythritol esters from oil and contaminants found on the sample paper. The second step was to test 184 used aircraft filters with the same gas chromatograph-mass spectrometry system; of that total, 107 were standard filters, and 77 were nonstandard. Four of the standard filters had both markers for oil, with the homologous series synthetic pentaerythritol esters being the less common marker. It was also found that 90% of the filters had some detectable level of tricresyl phosphates. Of the 77 nonstandard filters, 30 had both markers for oil, a significantly higher percent than the standard filters. PMID:25641977

Aircraft Recirculation Filter for Air-Quality and Incident Assessment.

PubMed

Eckels, Steven J; Jones, Byron; Mann, Garrett; Mohan, Krishnan R; Weisel, Clifford P

The current research examines the possibility of using recirculation filters from aircraft to document the nature of air-quality incidents on aircraft. These filters are highly effective at collecting solid and liquid particulates. Identification of engine oil contaminants arriving through the bleed air system on the filter was chosen as the initial focus. A two-step study was undertaken. First, a compressor/bleed air simulator was developed to simulate an engine oil leak, and samples were analyzed with gas chromatograph-mass spectrometry. These samples provided a concrete link between tricresyl phosphates and a homologous series of synthetic pentaerythritol esters from oil and contaminants found on the sample paper. The second step was to test 184 used aircraft filters with the same gas chromatograph-mass spectrometry system; of that total, 107 were standard filters, and 77 were nonstandard. Four of the standard filters had both markers for oil, with the homologous series synthetic pentaerythritol esters being the less common marker. It was also found that 90% of the filters had some detectable level of tricresyl phosphates. Of the 77 nonstandard filters, 30 had both markers for oil, a significantly higher percent than the standard filters.

Removing Contamination-Induced Reconstruction Artifacts from Cryo-electron Tomograms

PubMed Central

Fernandez, Jose-Jesus; Laugks, Ulrike; Schaffer, Miroslava; Bäuerlein, Felix J.B.; Khoshouei, Maryam; Baumeister, Wolfgang; Lucic, Vladan

2016-01-01

Imaging of fully hydrated, vitrified biological samples by electron tomography yields structural information about cellular protein complexes in situ. Here we present a computational procedure that removes artifacts of three-dimensional reconstruction caused by contamination present in samples during imaging by electron microscopy. Applying the procedure to phantom data and electron tomograms of cellular samples significantly improved the resolution and the interpretability of tomograms. Artifacts caused by surface contamination associated with thinning by focused ion beam, as well as those arising from gold fiducial markers and from common, lower contrast contamination, could be removed. Our procedure is widely applicable and is especially suited for applications that strive to reach a higher resolution and involve the use of recently developed, state-of-the-art instrumentation. PMID:26743046

Genetic diversity and trait genomic prediction in a pea diversity panel.

PubMed

Burstin, Judith; Salloignon, Pauline; Chabert-Martinello, Marianne; Magnin-Robert, Jean-Bernard; Siol, Mathieu; Jacquin, Françoise; Chauveau, Aurélie; Pont, Caroline; Aubert, Grégoire; Delaitre, Catherine; Truntzer, Caroline; Duc, Gérard

2015-02-21

Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.

Energy and Nutrient Intake Monitoring

NASA Technical Reports Server (NTRS)

Luckey, T. D.; Venugopal, B.; Hutcheson, D. P.

1975-01-01

A passive system to determine the in-flight intake of nutrients is developed. Nonabsorbed markers placed in all foods in proportion to the nutrients selected for study are analyzed by neutron activation analysis. Fecal analysis for each market indicates how much of the nutrients were eaten and apparent digestibility. Results of feasibility tests in rats, mice, and monkeys indicate the diurnal variation of several markers, the transit time for markers in the alimentary tract, the recovery of several markers, and satisfactory use of selected markers to provide indirect measurement of apparent digestibility. Recommendations are provided for human feasibility studies.

76 FR 11713 - Revisions to the Unregulated Contaminant Monitoring Regulation (UCMR 3) for Public Water Systems

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-03

... subject to possible selection for virus monitoring. If selected, these systems would be required to permit... selection of 800 small PWSs serving 10,000 or fewer people monitored for List 1 contaminants. This... health effects and occurrence data EPA used to make these selections are contained in ``Possible...

Olfactory Bulb Deep Short-Axon Cells Mediate Widespread Inhibition of Tufted Cell Apical Dendrites

PubMed Central

LaRocca, Greg

2017-01-01

In the main olfactory bulb (MOB), the first station of sensory processing in the olfactory system, GABAergic interneuron signaling shapes principal neuron activity to regulate olfaction. However, a lack of known selective markers for MOB interneurons has strongly impeded cell-type-selective investigation of interneuron function. Here, we identify the first selective marker of glomerular layer-projecting deep short-axon cells (GL-dSACs) and investigate systematically the structure, abundance, intrinsic physiology, feedforward sensory input, neuromodulation, synaptic output, and functional role of GL-dSACs in the mouse MOB circuit. GL-dSACs are located in the internal plexiform layer, where they integrate centrifugal cholinergic input with highly convergent feedforward sensory input. GL-dSAC axons arborize extensively across the glomerular layer to provide highly divergent yet selective output onto interneurons and principal tufted cells. GL-dSACs are thus capable of shifting the balance of principal tufted versus mitral cell activity across large expanses of the MOB in response to diverse sensory and top-down neuromodulatory input. SIGNIFICANCE STATEMENT The identification of cell-type-selective molecular markers has fostered tremendous insight into how distinct interneurons shape sensory processing and behavior. In the main olfactory bulb (MOB), inhibitory circuits regulate the activity of principal cells precisely to drive olfactory-guided behavior. However, selective markers for MOB interneurons remain largely unknown, limiting mechanistic understanding of olfaction. Here, we identify the first selective marker of a novel population of deep short-axon cell interneurons with superficial axonal projections to the sensory input layer of the MOB. Using this marker, together with immunohistochemistry, acute slice electrophysiology, and optogenetic circuit mapping, we reveal that this novel interneuron population integrates centrifugal cholinergic input with broadly tuned feedforward sensory input to modulate principal cell activity selectively. PMID:28003347

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

PubMed

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.

Marker-Based Hierarchical Segmentation and Classification Approach for Hyperspectral Imagery

NASA Technical Reports Server (NTRS)

Tarabalka, Yuliya; Tilton, James C.; Benediktsson, Jon Atli; Chanussot, Jocelyn

2011-01-01

The Hierarchical SEGmentation (HSEG) algorithm, which is a combination of hierarchical step-wise optimization and spectral clustering, has given good performances for hyperspectral image analysis. This technique produces at its output a hierarchical set of image segmentations. The automated selection of a single segmentation level is often necessary. We propose and investigate the use of automatically selected markers for this purpose. In this paper, a novel Marker-based HSEG (M-HSEG) method for spectral-spatial classification of hyperspectral images is proposed. First, pixelwise classification is performed and the most reliably classified pixels are selected as markers, with the corresponding class labels. Then, a novel constrained marker-based HSEG algorithm is applied, resulting in a spectral-spatial classification map. The experimental results show that the proposed approach yields accurate segmentation and classification maps, and thus is attractive for hyperspectral image analysis.

Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

PubMed Central

Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

2014-01-01

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

A TaqMan real-time PCR method based on alternative oxidase genes for detection of plant species in animal feed samples.

PubMed

Campos, Maria Doroteia; Valadas, Vera; Campos, Catarina; Morello, Laura; Braglia, Luca; Breviario, Diego; Cardoso, Hélia G

2018-01-01

Traceability of processed food and feed products has been gaining importance due to the impact that those products can have on human/animal health and to the associated economic and legal concerns, often related to adulterations and frauds as it can be the case for meat and milk. Despite mandatory traceability requirements for the analysis of feed composition, few reliable and accurate methods are presently available to enforce the legislative frame and allow the authentication of animal feeds. In this study, nine sensitive and species-specific real-time PCR TaqMan MGB assays are described for plant species detection in animal feed samples. The method is based on selective real-time qPCR (RT-qPCR) amplification of target genes belonging to the alternative oxidase (AOX) gene family. The plant species selected for detection in feed samples were wheat, maize, barley, soybean, rice and sunflower as common components of feeds, and cotton, flax and peanut as possible undesirable contaminants. The obtained results were compared with end-point PCR methodology. The applicability of the AOX TaqMan assays was evaluated through the screening of commercial feed samples, and by the analysis of plant mixtures with known composition. The RT-qPCR methodology allowed the detection of the most abundant species in feeds but also the identification of contaminant species present in lower amounts, down to 1% w/w. AOX-based methodology provides a suitable molecular marker approach to ascertain plant species composition of animal feed samples, thus supporting feed control and enforcement of the feed sector and animal production.

Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas.

PubMed

Szekeres, Edina; Chiriac, Cecilia Maria; Baricz, Andreea; Szőke-Nagy, Tiberiu; Lung, Ildiko; Soran, Maria-Loredana; Rudi, Knut; Dragos, Nicolae; Coman, Cristian

2018-05-01

Groundwater is an essential public and drinking water supply and its protection is a goal for global policies. Here, we investigated the presence and prevalence of antibiotic residues, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial contamination in groundwater environments at various distances from urban areas. Antibiotic concentrations ranged from below detection limit to 917 ng/L, being trimethoprim, macrolide, and sulfonamide the most abundant antibiotic classes. A total of eleven ARGs (aminoglycoside, β-lactam, chloramphenicol, Macrolide-Lincosamide-Streptogramin B - MLSB, sulfonamide, and tetracycline), one antiseptic resistance gene, and two MGEs were detected by qPCR with relative abundances ranging from 6.61 × 10 -7 to 2.30 × 10 -1 copies/16S rRNA gene copies. ARGs and MGEs were widespread in the investigated groundwater environments, with increased abundances not only in urban, but also in remote areas. Distinct bacterial community profiles were observed, with a higher prevalence of Betaproteobacteria and Bacteroidetes in the less-impacted areas, and that of Firmicutes in the contaminated groundwater. The combined characteristics of increased species diversity, distinct phylogenetic composition, and the possible presence of fecal and/or pathogenic bacteria could indicate different types of contamination. Significant correlations between ARGs, MGEs and specific taxa within the groundwater bacterial community were identified, revealing the potential hosts of resistance types. Although no universal marker gene could be determined, a co-selection of int1, qacEΔ1 and sulI genes, a proxy group for anthropogenic pollution, with the tetC, tetO, tetW resistance genes was identified. As the tet group was observed to follow the pattern of environmental contamination for the groundwater samples investigated in this study, our results strongly support the proposal of this group of genes as an environmental tracer of human impact. Overall, the present study investigated several emerging contaminants in groundwater habitats that may be included in monitoring programs to enable further regulatory and protection measures. Copyright © 2018 Elsevier Ltd. All rights reserved.

Investigation of the optimum location of external markers for patient setup accuracy enhancement at external beam radiotherapy

PubMed Central

Torshabi, Ahmad Esmaili; Nankali, Saber

2016-01-01

In external beam radiotherapy, one of the most common and reliable methods for patient geometrical setup and/or predicting the tumor location is use of external markers. In this study, the main challenging issue is increasing the accuracy of patient setup by investigating external markers location. Since the location of each external marker may yield different patient setup accuracy, it is important to assess different locations of external markers using appropriate selective algorithms. To do this, two commercially available algorithms entitled a) canonical correlation analysis (CCA) and b) principal component analysis (PCA) were proposed as input selection algorithms. They work on the basis of maximum correlation coefficient and minimum variance between given datasets. The proposed input selection algorithms work in combination with an adaptive neuro‐fuzzy inference system (ANFIS) as a correlation model to give patient positioning information as output. Our proposed algorithms provide input file of ANFIS correlation model accurately. The required dataset for this study was prepared by means of a NURBS‐based 4D XCAT anthropomorphic phantom that can model the shape and structure of complex organs in human body along with motion information of dynamic organs. Moreover, a database of four real patients undergoing radiation therapy for lung cancers was utilized in this study for validation of proposed strategy. Final analyzed results demonstrate that input selection algorithms can reasonably select specific external markers from those areas of the thorax region where root mean square error (RMSE) of ANFIS model has minimum values at that given area. It is also found that the selected marker locations lie closely in those areas where surface point motion has a large amplitude and a high correlation. PACS number(s): 87.55.km, 87.55.N PMID:27929479

Marker-Assisted Introgression in Backcross Breeding Programs

PubMed Central

Visscher, P. M.; Haley, C. S.; Thompson, R.

1996-01-01

The efficiency of marker-assisted introgression in backcross populations derived from inbred lines was investigated by simulation. Background genotypes were simulated assuming that a genetic model of many genes of small effects in coupling phase explains the observed breed difference and variance in backcross populations. Markers were efficient in introgression backcross programs for simultaneously introgressing an allele and selecting for the desired genomic background. Using a marker spacing of 10-20 cM gave an advantage of one to two backcross generations selection relative to random or phenotypic selection. When the position of the gene to be introgressed is uncertain, for example because its position was estimated from a trait gene mapping experiment, a chromosome segment should be introgressed that is likely to include the allele of interest. Even for relatively precisely mapped quantitative trait loci, flanking markers or marker haplotypes should cover ~10-20 cM around the estimated position of the gene, to ensure that the allele frequency does not decline in later backcross generations. PMID:8978075

Recent advances in development of marker-free transgenic plants: regulation and biosafety concern.

PubMed

Tuteja, Narendra; Verma, Shiv; Sahoo, Ranjan Kumar; Raveendar, Sebastian; Reddy, I N Bheema Lingeshwara

2012-03-01

During the efficient genetic transformation of plants with the gene of interest, some selectable marker genes are also used in order to identify the transgenic plant cells or tissues. Usually, antibiotic- or herbicide-selective agents and their corresponding resistance genes are used to introduce economically valuable genes into crop plants. From the biosafety authority and consumer viewpoints, the presence of selectable marker genes in released transgenic crops may be transferred to weeds or pathogenic microorganisms in the gastrointestinal tract or soil, making them resistant to treatment with herbicides or antibiotics, respectively. Sexual crossing also raises the problem of transgene expression because redundancy of transgenes in the genome may trigger homology-dependent gene silencing. The future potential of transgenic technologies for crop improvement depends greatly on our abilities to engineer stable expression of multiple transgenic traits in a predictable fashion and to prevent the transfer of undesirable transgenic material to non-transgenic crops and related species. Therefore, it is now essential to develop an efficient marker-free transgenic system. These considerations underline the development of various approaches designed to facilitate timely elimination of transgenes when their function is no longer needed. Due to the limiting number of available selectable marker genes, in future the stacking of transgenes will be increasingly desirable. The production of marker-free transgenic plants is now a critical requisite for their commercial deployment and also for engineering multiple and complex trait. Here we describe the current technologies to eliminate the selectable marker genes (SMG) in order to develop marker-free transgenic plants and also discuss the regulation and biosafety concern of genetically modified (GM) crops.

A Tightly Regulated Genetic Selection System with Signaling-Active Alleles of Phytochrome B.

PubMed

Hu, Wei; Lagarias, J Clark

2017-01-01

Selectable markers derived from plant genes circumvent the potential risk of antibiotic/herbicide-resistance gene transfer into neighboring plant species, endophytic bacteria, and mycorrhizal fungi. Toward this goal, we have engineered and validated signaling-active alleles of phytochrome B (eYHB) as plant-derived selection marker genes in the model plant Arabidopsis (Arabidopsis thaliana). By probing the relationship of construct size and induction conditions to optimal phenotypic selection, we show that eYHB-based alleles are robust substitutes for antibiotic/herbicide-dependent marker genes as well as surprisingly sensitive reporters of off-target transgene expression. © 2017 American Society of Plant Biologists. All Rights Reserved.

A Tightly Regulated Genetic Selection System with Signaling-Active Alleles of Phytochrome B1[OPEN

PubMed Central

2017-01-01

Selectable markers derived from plant genes circumvent the potential risk of antibiotic/herbicide-resistance gene transfer into neighboring plant species, endophytic bacteria, and mycorrhizal fungi. Toward this goal, we have engineered and validated signaling-active alleles of phytochrome B (eYHB) as plant-derived selection marker genes in the model plant Arabidopsis (Arabidopsis thaliana). By probing the relationship of construct size and induction conditions to optimal phenotypic selection, we show that eYHB-based alleles are robust substitutes for antibiotic/herbicide-dependent marker genes as well as surprisingly sensitive reporters of off-target transgene expression. PMID:27881727

Contamination of food by crude oil affects food selection and growth performance, but not appetite, in an Arctic fish the polar cod (Boreogadus saida)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christiansen, J.S.; George, S.G.

The polar cod (Boreogadus saida) is recognized as a key species in Arctic marine food webs and it may, therefore, be important for the transfer of xenobiotics from lower trophic levels to its main predators, birds and sea mammals. The present work examines the effects of foods contaminated with 200 or 400 ppm crude oil on food selection patterns and appetite-growth relationship in polar cod using X-radiography. It is shown that sexually mature polar cod consumed mixtures of uncontaminated and oil-contaminated foods, and did not show a reduced overall appetite as compared with fish provided with uncontaminated food only. Foodmore » selection was, however, influenced by both sex and individual appetite. Male fish selected uncontaminated food when appetite was low, whereas females ingested contaminated and uncontaminated foods equally, irrespective of appetite level. The ingestion of oil-contaminated food led to a significant depression in growth performance in both male and female fish. Food contaminated with oil at a concentration of 500 ppm was completely rejected by both sexes. 6 refs., 4 figs., 2 tabs.« less

Marker-assisted selection in plant breeding for salinity tolerance.

PubMed

Ashraf, M; Akram, N A; Mehboob-Ur-Rahman; Foolad, M R

2012-01-01

Marker-assisted selection (MAS) is the process of using morphological, biochemical, or DNA markers as indirect selection criteria for selecting agriculturally important traits in crop breeding. This process is used to improve the effectiveness or efficiency of selection for the traits of interest in breeding programs. The significance of MAS as a tool for crop improvement has been extensively investigated in different crop -species and for different traits. The use of MAS for manipulating simple/qualitative traits is straightforward and has been well reported. However, MAS for the improvement of complex/polygenic traits, including plant tolerance/resistance to abiotic stresses, is more complicated, although its usefulness has been recognized. With the recent advances in marker technology, including high-throughput genotyping of plants, together with the development of nested association mapping populations, it is expected that the utility of MAS for breeding for stress tolerance traits will increase. In this chapter, we describe the basic procedure for using MAS in crop breeding for salt tolerance.

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

PubMed

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.

Decontamination and decommissioning of the BORAX-V leach pond. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, D.L.

1985-01-01

This report describes the decontamination and decommissioning (D and D) of the BORAX-V leach pond located at the Idaho National Engineering Laboratory (INEL). The leach pond became radioactively contaminated from the periodic discharge of low-level liquid waste during operation of the Boiling Water Reactor Experiments (BORAX) from 1954 to 1964. This report describes work performed to accomplish the D and D objectives of stabilizing the leach pond and preventing the spread of contamination. D and D of the BORAX-V leach pond consisted to backfilling the pond with clean soil, grading and seeding the area, and erecting a permanent marker tomore » identify very low-level subsurface contamination.« less

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

USDA-ARS?s Scientific Manuscript database

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...

Financial feasibility of marker-aided selection in Douglas-fir.

Treesearch

G.R. Johnson; N.C. Wheeler; S.H. Strauss

2000-01-01

The land area required for a marker-aided selection (MAS) program to break-even (i.e., have equal costs and benefits) was estimated using computer simulation for coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in the Pacific Northwestern United States. We compared the selection efficiency obtained when using an index that included the...

PubMed Central

Ceriale, E.; Messina, G.; Lenzi, D.; Manzi, P.

2017-01-01

Summary Introduction. Contamination of hospital surfaces plays an important role in the transmission of several healthcare-associated microorganisms, therefore methods for evaluating hospital surfaces' cleaning gain particular importance. Among these, there are visual inspection, quantitative microbiology, fluorescent markers and adenosine triphosphate (ATP) bioluminescence. The latter seems to provide interesting features, detecting the presence of ATP on surface (as Relative Light Units, RLU), a proxy of organic matter and microbial contamination. Several studies have investigated the effectiveness of this technology; with this research, we aim to summarize the most significant results. Methods. A systematic review was conducted. The keywords (namely, "ATP", "bioluminescence", "hospital" and "surfaces") were searched in PubMed/MEDLINE and Scopus databases, in order to find relevant data, from January 2000 to October 2014. After the selection, we globally considered 27 articles. Results. Most of the studies were conducted in United Kingdom and in USA. Different threshold RLU benchmark values were identified by analyzed studies. Fourteen of these researches compared the ATP bioluminescence with microbiological methods, 11 identified a significant correlation between the two methods, although poor or not complete for 5. Discussion. ATP bioluminescence is not a standardized methodology: each tool has different benchmark values, not always clearly defined. At the moment, we can say that the technique could be used to assess, in real time, hospital surfaces where cleanliness is required, but not sterility. PMID:28900359

Alkylphenol metabolites in fish bile as biomarkers of exposure to offshore oil industry produced water in feral fish.

PubMed

Beyer, Jonny; Sundt, Rolf C; Sanni, Steinar; Sydnes, Magne O; Jonsson, Grete

2011-01-01

The measurement of low-concentration alkylphenol (AP) exposure in fish is relevant in connection with monitoring and risk assessment of offshore oil industry produced water (PW) discharges. Detection of AP markers in fish bile offers significantly greater sensitivity than detection of AP in tissues such as liver. Recent studies revealed that gas chromatography-mass spectrometry in electron ionization mode (GC-EI-MS) enabled a selective and sensitive analytical detection of PW AP in mixtures with unknown composition. A procedure consisting of enzymatic deconjugation of metabolites in fish bile followed by derivatization with bis(trimethylsilyl)trifluoroacetamide and then separation and quantification of derivatized AP using GC-EI-MS is presented. The use of this procedure as a possible recommended approach for assessment and biomonitoring of AP contamination in fish populations living down-current from offshore oil production fields is presented.

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

PubMed

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.

Superfund record of decision (EPA Region 3): Stanley Kessler Superfund Site, King of Prussia, PA, September 1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1994-09-29

This decision document presents the final selected remedial action for the Stanley Kessler Superfund Site (the Site). The selected remedy for the Site will restore contaminated ground water to its beneficial use by cleaning up the ground water to background levels as established by EPA or the appropriate Maximum Contaminant Levels or non-zero Maximum Contaminant Level Goals established under the Federal Safe Drinking Water Act whichever is more stringent. The selected remedy is the only planned action for the Site.

Optimizing of the basophil activation test: Comparison of different basophil identification markers.

PubMed

Eberlein, Bernadette; Hann, Rebekka; Eyerich, Stefanie; Pennino, Davide; Ring, Johannes; Schmidt-Weber, Carsten B; Buters, Jeroen

2015-01-01

Flowcytometric identification of basophils is a prerequisite for measuring activation of basophils with IgE-dependent or IgE-independent stimuli. Aim of this study was to compare different marker combinations in a simultaneous multicolor flowcytometric measurement. Ten patients with a grass pollen allergy and three controls were included in the study. Basophilic cells were gated by using anti-CCR3, anti-IgE, anti-CRTH2, anti-CD203c, and anti-CD3. Cells were activated by a monoclonal anti-FcεRI antibody, N-formyl-methionyl-leucyl-phenylalanine (fMLP), and the allergen extract Phleum pratense. The activation marker anti-CD63 was used. The highest relative number of basophils was found with anti-CCR3+ cells, anti-IgE+ and anti-IgE+ /anti-CD203c+ cells, the lowest with CRTH2+/CD203c+/CD3- cells. A very good and good concordance of CCR3+ cells was seen with CCR3+/CD3- cells and CRTH2+/CD203c+/CD3- cells in all experiments. The contamination of the CCR3+ population with CD3+ cells and the contamination of the IgE+-population with CCR3- cells and CD203- cells were the lowest compared to all other marker combinations. As the highest relative number of basophils was identified by anti-CCR3 followed by the anti-IgE and anti-IgE/antiCD203c positive population in most cases, these markers can generally be recommended for identification of basophils. If a basophil population with very high purity is needed, anti-IgE should be chosen. © 2014 International Clinical Cytometry Society.

Arcobacter in Lake Erie beach waters: an emerging gastrointestinal pathogen linked with human-associated fecal contamination.

PubMed

Lee, Cheonghoon; Agidi, Senyo; Marion, Jason W; Lee, Jiyoung

2012-08-01

The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. To better characterize the health risk posed by this emerging waterborne pathogen, we investigated the occurrence of Arcobacter spp. in Lake Erie beach waters. During the summer of 2010, water samples were collected 35 times from the Euclid, Villa Angela, and Headlands (East and West) beaches, located along Ohio's Lake Erie coast. After sample concentration, Arcobacter was quantified by real-time PCR targeting the Arcobacter 23S rRNA gene. Other fecal genetic markers (Bacteroides 16S rRNA gene [HuBac], Escherichia coli uidA gene, Enterococcus 23S rRNA gene, and tetracycline resistance genes) were also assessed. Arcobacter was detected frequently at all beaches, and both the occurrence and densities of Arcobacter spp. were higher at the Euclid and Villa Angela beaches (with higher levels of fecal contamination) than at the East and West Headlands beaches. The Arcobacter density in Lake Erie beach water was significantly correlated with the human-specific fecal marker HuBac according to Spearman's correlation analysis (r = 0.592; P < 0.001). Phylogenetic analysis demonstrated that most of the identified Arcobacter sequences were closely related to Arcobacter cryaerophilus, which is known to cause gastrointestinal diseases in humans. Since human-pathogenic Arcobacter spp. are linked to human-associated fecal sources, it is important to identify and manage the human-associated contamination sources for the prevention of Arcobacter-associated public health risks at Lake Erie beaches.

Bioremediation of contaminated groundwater

DOEpatents

Hazen, T.C.; Fliermans, C.B.

1994-01-01

Disclosed is an apparatus and method for in situ remediation of contaminated subsurface soil or groundwater contaminated by chlorinated hydrocarbons. A nutrient fluid (NF) is selected to simulated the growth and reproduction of indigenous subsurface microorganisms capable of degrading the contaminants; an oxygenated fluid (OF) is selected to create an aerobic environment with anaerobic pockets. NF is injected periodically while OF is injected continuously and both are extracted so that both are drawn across the plume. NF stimulates microbial colony growth; withholding it periodically forces the larger, healthy colony of microbes to degrade the contaminants. Treatment is continued until the subsurface concentration of contaminants is acceptable. NF can be methane and OF be air, for stimulating production of methanotrophs to break down chlorohydrocarbons, especially TCE and tetrachloroethylene.

Use of a fluoride channel as a new selection marker for fission yeast plasmids and application to fast genome editing with CRISPR/Cas9

PubMed Central

Fernandez, Ronan; Berro, Julien

2017-01-01

Fission yeast is a powerful model organism that has provided insights into important cellular processes thanks to the ease of its genome editing by homologous recombination. However, creation of strains with a large number of targeted mutations or containing plasmids has been challenging because only a very small number of selection markers is available in Schizosaccharomyces pombe. In this paper, we identify two fission yeast fluoride exporter channels (Fex1p and Fex2p) and describe the development of a new strategy using Fex1p as a selection marker for transformants in rich media supplemented with fluoride. To our knowledge this is the first positive selection marker identified in S. pombe that does not use auxotrophy or drug resistance and that can be used for plasmids transformation or genomic integration in rich media. We illustrate the application of our new marker by significantly accelerating the protocol for genome edition using CRISPR/Cas9 in S. pombe. PMID:27327046

Enteric pathogens in stored drinking water and on caregiver's hands in Tanzanian households with and without reported cases of child diarrhea.

PubMed

Mattioli, Mia Catharine; Boehm, Alexandria B; Davis, Jennifer; Harris, Angela R; Mrisho, Mwifadhi; Pickering, Amy J

2014-01-01

Diarrhea is one of the leading causes of mortality in young children. Diarrheal pathogens are transmitted via the fecal-oral route, and for children the majority of this transmission is thought to occur within the home. However, very few studies have documented enteric pathogens within households of low-income countries. The presence of molecular markers for three enteric viruses (enterovirus, adenovirus, and rotavirus), seven Escherichia coli virulence genes (ECVG), and human-specific Bacteroidales was assessed in hand rinses and household stored drinking water in Bagamoyo, Tanzania. Using a matched case-control study design, we examined the relationship between contamination of hands and water with these markers and child diarrhea. We found that the presence of ECVG in household stored water was associated with a significant decrease in the odds of a child within the home having diarrhea (OR = 0.51; 95% confidence interval 0.27-0.93). We also evaluated water management and hygiene behaviors. Recent hand contact with water or food was positively associated with detection of enteric pathogen markers on hands, as was relatively lower volumes of water reportedly used for daily hand washing. Enteropathogen markers in stored drinking water were more likely found among households in which the markers were also detected on hands, as well as in households with unimproved water supply and sanitation infrastructure. The prevalence of enteric pathogen genes and the human-specific Bacteroidales fecal marker in stored water and on hands suggests extensive environmental contamination within homes both with and without reported child diarrhea. Better stored water quality among households with diarrhea indicates caregivers with sick children may be more likely to ensure safe drinking water in the home. Interventions to increase the quantity of water available for hand washing, and to improve food hygiene, may reduce exposure to enteric pathogens in the domestic environment.

Enteric Pathogens in Stored Drinking Water and on Caregiver’s Hands in Tanzanian Households with and without Reported Cases of Child Diarrhea

PubMed Central

Mattioli, Mia Catharine; Boehm, Alexandria B.; Davis, Jennifer; Harris, Angela R.; Mrisho, Mwifadhi; Pickering, Amy J.

2014-01-01

Background Diarrhea is one of the leading causes of mortality in young children. Diarrheal pathogens are transmitted via the fecal-oral route, and for children the majority of this transmission is thought to occur within the home. However, very few studies have documented enteric pathogens within households of low-income countries. Methods and Findings The presence of molecular markers for three enteric viruses (enterovirus, adenovirus, and rotavirus), seven Escherichia coli virulence genes (ECVG), and human-specific Bacteroidales was assessed in hand rinses and household stored drinking water in Bagamoyo, Tanzania. Using a matched case-control study design, we examined the relationship between contamination of hands and water with these markers and child diarrhea. We found that the presence of ECVG in household stored water was associated with a significant decrease in the odds of a child within the home having diarrhea (OR = 0.51; 95% confidence interval 0.27–0.93). We also evaluated water management and hygiene behaviors. Recent hand contact with water or food was positively associated with detection of enteric pathogen markers on hands, as was relatively lower volumes of water reportedly used for daily hand washing. Enteropathogen markers in stored drinking water were more likely found among households in which the markers were also detected on hands, as well as in households with unimproved water supply and sanitation infrastructure. Conclusions The prevalence of enteric pathogen genes and the human-specific Bacteroidales fecal marker in stored water and on hands suggests extensive environmental contamination within homes both with and without reported child diarrhea. Better stored water quality among households with diarrhea indicates caregivers with sick children may be more likely to ensure safe drinking water in the home. Interventions to increase the quantity of water available for hand washing, and to improve food hygiene, may reduce exposure to enteric pathogens in the domestic environment. PMID:24392161

Molecular Investigations of Bacteroides as Microbial Source Tracking Tools in Southeast Louisiana Watersheds

NASA Astrophysics Data System (ADS)

Schulz, C. J.; Childers, G. W.; Engel, A. S.

2006-12-01

Microbial Source Tracking (MST) is a developing field that is gaining increased attention. MST refers to a host of techniques that discriminates among the origins of fecal material found in natural waters from different sources (e.g. human, livestock, and wildlife) by using microbial indicator species with specificity to only certain host organisms. The development of species-specific molecular markers would allow for better evaluation of public health risks and tracking of nutrient sources impacting a watershed. Although several MST methods have been reported with varying levels of success, few offer general applicability for natural waters due to spatial and temporal constraints associated with these methods. One group of molecular MST markers that show promise for broad environmental applications are molecular 16S rDNA probes for Bacteroides. This method is based on 16S rDNA detection directly from environmental samples without the need for a preliminary cultivation step. In this study we have expanded previous sampling efforts to compile a database of over 1000 partial 16S rRNA Bacteroides genes retrieved from the fecal material of 15 different host species (human, cat, dog, pig, kangaroo). To characterize survival of Bacteroides outside of the host, survival time of the Bacteroides marker was compared to that of E.coli under varying natural environmental conditions (temperature and salinity). Bacteroides displayed a survival curve with shouldering and tailing similar to that of E.coli, but log reduction times differed with treatment. In summary, MST marker stability was identified within host species and the overall Bacteroides community structure correlated to host diet, suggesting that detection of a Bacteroides community could confidently identify fecal contamination point sources. Natural water samples from southeast Louisiana were collected for MST including the Tangipahoa River watershed where the source of fecal contamination has been hotly debated. The Bacteroides tool repeatedly demonstrated the presence of cattle related Bacteroides markers and the absence of human markers.This study is now being expanded to include the entire Lake Pontchartrain Basin.

Isolation and characterization of novel microsatellite markers from the sika deer (Cervus nippon) genome.

PubMed

Li, Y M; Bai, C Y; Niu, W P; Yu, H; Yang, R J; Yan, S Q; Zhang, J Y; Zhang, M J; Zhao, Z H

2015-09-28

Microsatellite markers are widely and evenly distributed, and are highly polymorphic. Rapid and convenient detection through automated analysis means that microsatellite markers are widely used in the construction of plant and animal genetic maps, in quantitative trait loci localization, marker-assisted selection, identification of genetic relationships, and genetic diversity and phylogenetic tree construction. However, few microsatellite markers remain to be isolated. We used streptavidin magnetic beads to affinity-capture and construct a (CA)n microsatellite DNA-enriched library from sika deer. We selected sequences containing more than six repeats to design primers. Clear bands were selected, which were amplified using non-specific primers following PCR amplification to screen polymorphisms in a group of 65 unrelated sika deer. The positive clone rate reached 82.9% by constructing the enriched library, and we then selected positive clones for sequencing. There were 395 sequences with CA repeats, and the CA repeat number was 4-105. We selected sequences containing more than six repeats to design primers, of which 297 pairs were designed. We next selected clear bands and used non-specific primers to amplify following PCR amplification. In total, 245 pairs of primers were screened. We then selected 50 pairs of primers to randomly screen for polymorphisms. We detected 47 polymorphic and 3 monomorphic loci in 65 unrelated sika deer. These newly isolated and characterized microsatellite loci can be used to construct genetic maps and for lineage testing in deer. In addition, they can be used for comparative genomics between Cervidae species.

Selective DNA Pooling for Determination of Linkage between a Molecular Marker and a Quantitative Trait Locus

PubMed Central

Darvasi, A.; Soller, M.

1994-01-01

Selective genotyping is a method to reduce costs in marker-quantitative trait locus (QTL) linkage determination by genotyping only those individuals with extreme, and hence most informative, quantitative trait values. The DNA pooling strategy (termed: ``selective DNA pooling'') takes this one step further by pooling DNA from the selected individuals at each of the two phenotypic extremes, and basing the test for linkage on marker allele frequencies as estimated from the pooled samples only. This can reduce genotyping costs of marker-QTL linkage determination by up to two orders of magnitude. Theoretical analysis of selective DNA pooling shows that for experiments involving backcross, F(2) and half-sib designs, the power of selective DNA pooling for detecting genes with large effect, can be the same as that obtained by individual selective genotyping. Power for detecting genes with small effect, however, was found to decrease strongly with increase in the technical error of estimating allele frequencies in the pooled samples. The effect of technical error, however, can be markedly reduced by replication of technical procedures. It is also shown that a proportion selected of 0.1 at each tail will be appropriate for a wide range of experimental conditions. PMID:7896115

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

NASA Astrophysics Data System (ADS)

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 waters.

A protocol for identifying suitable biomarkers to assess fish health: A systematic review

PubMed Central

2017-01-01

Background Biomarkers have been used extensively to provide the connection between external levels of contaminant exposure, internal levels of tissue contamination, and early adverse effects in organisms. Objectives To present a three-step protocol for identifying suitable biomarkers to assess fish health in coastal and marine ecosystems, using Gladstone Harbour (Australia) as a case study. Methods Prior to applying our protocol, clear working definitions for biomarkers were developed to ensure consistency with the global literature on fish health assessment. First, contaminants of concern were identified based on the presence of point and diffuse sources of pollution and available monitoring data for the ecosystem of interest. Second, suitable fish species were identified using fisheries dependent and independent data, and prioritised based on potential pathways of exposure to the contaminants of concern. Finally, a systematic and critical literature review was conducted on the use of biomarkers to assess the health of fish exposed to the contaminants of concern. Results/Discussion We present clear working definitions for bioaccumulation markers, biomarkers of exposure, biomarkers of effect and biomarkers of susceptibility. Based on emission and concentration information, seven metals were identified as contaminants of concern for Gladstone Harbour. Twenty out of 232 fish species were abundant enough to be potentially suitable for biomarker studies; five of these were prioritised based on potential pathways of exposure and susceptibility to metals. The literature search on biomarkers yielded 5,035 articles, of which 151met the inclusion criteria. Based on our review, the most suitable biomarkers include bioaccumulation markers, biomarkers of exposure (CYP1A, EROD, SOD, LPOX, HSP, MT, DNA strand breaks, micronuclei, apoptosis), and biomarkers of effect (histopathology, TAG:ST). Conclusion Our protocol outlines a clear pathway to identify suitable biomarkers to assess fish health in coastal and marine ecosystems, which can be applied to biomarker studies in aquatic ecosystems around the world. PMID:28403149

Ameliorative effect of a microbial feed additive on infectious bronchitis virus antibody titer and stress index in broiler chicks fed deoxynivalenol.

PubMed

Ghareeb, K; Awad, W A; Böhm, J

2012-04-01

Although acute mycotoxicoses are rare in poultry production, chronic exposure to low levels of mycotoxins is responsible for reduced productivity and increased susceptibility to infectious diseases. Deoxynivalenol (DON) is known to modulate immune function, but only a few studies have investigated the effect of DON on the vaccinal immune response. In addition, the effects of Mycofix select (Biomin GmbH, Herzogenburg, Austria) supplementation to DON-contaminated broiler diets have not yet been demonstrated. Therefore, an experiment with 1-d-old male broilers (Ross 308) was carried out to examine the effects of feeding DON-contaminated low-protein grower diets on performance, serum biochemical parameters, lymphoid organ weight, and antibody titers to infectious bronchitis vaccination in serum and to evaluate the effects of Mycofix select dietary supplementation in either the presence or absence of DON in broilers. In total, thirty-two 1-d-old broiler chicks were randomly assigned to 1 of the 4 dietary treatments for 5 wk. The dietary treatments were 1) control; 2) artificially contaminated diets with 10 mg of DON/kg of diet; 3) DON-contaminated diets supplemented with Mycofix select; and 4) control diet supplemented with Mycofix select. Feeding of contaminated diets decreased (P = 0.000) the feed intake, BW (P = 0.001), BW gain (P = 0.044), and feed efficiency during the grower phase. Deoxynivalenol affected the blood biochemistry, whereas plasma total protein and uric acid concentrations in birds fed contaminated grains were decreased compared with those of the controls. Moreover, in birds fed contaminated feeds, there was a tendency to reduce triglycerides in the plasma (P = 0.090), suggesting that DON in the diets affected protein and lipid metabolism in broiler chickens. The feeding of contaminated diets altered the immune response in broilers by reducing the total lymphocyte count. Similarly, the antibody response against infectious bronchitis vaccination antigens was decreased (P = 0.003) after feeding contaminated diets, compared with the controls. Moreover, contamination of the broiler diet with DON increased the heteropil:lymphocyte ratio (stress index), suggesting that DON elevated the physiological stress responses of broilers. However, feeding of DON-containing diets did not alter the other plasma constituents, including activities of enzymes. Mycofix select addition to the DON-contaminated feed led to normal immunological and physiological functions in broilers that were comparable with those of the control group, indicating that the addition of the additive to the DON-contaminated feed of the broilers effectively alleviated the alterations caused by DON. It was concluded that broiler performance and some blood and immunological parameters were adversely affected by feeding diets contaminated with the Fusarium mycotoxin DON. However, the dietary Mycofix select supplementation as a detoxifying agent was successful in overcoming the mycotoxin-related effects.

Human fecal source identification with real-time quantitative PCR

EPA Science Inventory

Waterborne diseases represent a significant public health risk worldwide, and can originate from contact with water contaminated with human fecal material. We describe a real-time quantitative PCR (qPCR) method that targets a Bacteroides dori human-associated genetic marker for...

Towards establishing a human fecal contamination index in microbial source tracking

EPA Science Inventory

There have been significant advances in development of PCR-based methods to detect source associated DNA sequences (markers), but method evaluation has focused on performance with individual challenge samples. Little attention has been given to integration of multiple samples fro...

Monitoring dredging effectiveness using biological and chemical markers of exposure

EPA Science Inventory

Sediments in portions of the Ashtabula and Ottawa rivers are contaminated with polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs) and both rivers have been designated by the International Joint Commission as a Great Lakes Area of Concern. Approximately 550,000...

ADDRESSING EMERGING ISSUES IN WATER QUALITY THROUGH ENVIRONMENTAL CHEMISTRY

EPA Science Inventory

Public concern over cleanliness and safety of source and recreational waters has prompted researchers to look for indicators of water quality. Giving public water authorities multiple tools to measure and monitor levels of chemical contaminants, as well as chemical markers of c...

Development of Rapid Canine Fecal Source Identification PCR-based Assays

EPA Science Inventory

The extent to which dogs contribute to aquatic fecal contamination is unknown despite the potential for zoonotic transfer of harmful human pathogens. We used Genome Fragment Enrichment (GFE) to identify novel non-ribosomal microbial genetic markers potentially useful for detectin...

Global Inter-Laboratory Fecal Source Identification Methods Comparison Study

EPA Science Inventory

Source tracking is key to identifying sources of fecal contamination for remediation as well as risk assessment. Previous intra- and inter-lab studies have investigated the performance of human and cow-associated source tracking markers, as well as library-dependent fecal source ...

Pesticide alters oviposition site selection in gray treefrogs.

PubMed

Vonesh, James R; Buck, Julia C

2007-11-01

Understanding the impacts of pesticides on non-target organisms is an important issue for conservation biology. Research into the environmental consequences of pesticides has largely focused on pesticide toxicity. We have less understanding of the nonlethal effects of pesticides, and the consequences of nonlethal effects for species and communities. For example, we know very little about whether pesticides alter habitat selection behavior. Understanding whether pesticides alter habitat selection is important because pesticide-induced shifts in habitat selection could either magnify or reduce the toxic effects of contaminants by funneling organisms into or directing them away from contaminated sites. Here we present four field experiments that examine the effect of the commercial pesticide Sevin and its active ingredient, carbaryl, on oviposition site selection by the gray treefrog (Hyla chrysoscelis). Our results show that uncontaminated pools consistently received 2-3 times more eggs than contaminated pools; that treefrogs appeared to respond to Sevin directly, not indirectly via its effects on the aquatic food web, and that this preference persisted across a range of temporal and spatial scales. Both Sevin and carbaryl per se reduced oviposition, while other volatile chemicals (e.g., our solvent control, acetone) had no effect. These findings suggest that in order to understanding the consequences of contaminants in aquatic systems we will need to consider not only toxicity, but also how contaminant effects on habitat selection alter the way organisms distribute themselves in the environment.

Geophysical and flow-weighted natural-contaminant characterization of three water-supply wells in New Hampshire

USGS Publications Warehouse

Mack, Thomas J.; Belaval, Marcel; Degnan, James R.; Roy, Stephen J.; Ayotte, Joseph D.

2011-01-01

The water-supply systems investigated were typical of small community water systems in New Hampshire where a water system may serve 100 connections or less. Each water system consisted of two wells, approximately 300 to 400 feet deep, in generally low-yielding (about 10 gallons per minute or less) crystalline bedrock. The wells were typically operated a few hours per day to fill a storage tank and had tens of feet of drawdown caused by the low well yields. The systems selected had contaminant concentrations slightly above MCL, or a low-level contamination. One of the water systems investigated had low-level (10 to 24 micrograms per liter) arsenic contamination, and two of the water systems had low-level uranium (30 to 40 micrograms per liter) contamination. The contaminant values were blended-water concentrations from the two wells in a system. Each water system had differences in contaminant concentrations between the two wells. In each case, the well with the greater concentration of the two was selected for investigation. In two of the three systems investigated, there was either not enough variation in the borehole contaminant concentration or not enough water-yielding fractures for borehole modifications to be a viable potential remedy to elevated contamination. However, borehole and contaminant conditions in one of the bedrock supply-well systems may be favorable to potential improvement of supplied water by borehole modification where selected fracture zones are sealed off from supplying water to the well.

The Effect of Airborne Contaminants on Fuel Cell Performance and Durability

DOE Office of Scientific and Technical Information (OSTI.GOV)

St-Pierre, Jean; Pasaogullari, Ugur; Cheng, Tommy

The impact of contaminants on fuel cell performance was examined to document air filter specifications (prevention) and devise recovery procedures (maintenance) that are effective at the system level. Eight previously undocumented airborne contaminants were selected for detailed studies and characterization data was used to identify operating conditions that intensifying contamination effects. The use of many and complementary electrochemical, chemical and physical characterization methods and the derivation of several mathematical models supported the formulation of contamination mechanisms and the development of recovery procedures. The complexity of these contamination mechanisms suggests a shift to prevention and generic maintenance measures. Only two ofmore » the selected contaminants led to cell voltage losses after injection was interrupted. Proposed recovery procedures for calcium ions, a component of road de-icers, dessicants, fertilizers and soil conditioners, were either ineffective or partly effective, whereas for bromomethane, a fumigant, the cell voltage was recovered to its initial value before contamination by manipulating and sequencing operating conditions. However, implementation for a fuel cell stack and system remains to be demonstrated. Contamination mechanisms also led to the identification of membrane durability stressors. All 8 selected contaminants promote the formation of hydrogen peroxide, a known agent that can produce radicals that attack the ionomer and membrane molecular structure whereas the dehydrating effect of calcium ions on the ionomer and membrane increases their brittleness and favors the creation of pinholes under mechanical stresses. Data related to acetylene, acetonitrile and calcium ions are emphasized in the report.« less

Identification of critical contaminants in wastewater effluent for managed aquifer recharge.

PubMed

Yuan, Jie; Van Dyke, Michele I; Huck, Peter M

2017-04-01

Managed aquifer recharge (MAR) using highly treated effluent from municipal wastewater treatment plants has been recognized as a promising strategy for indirect potable water reuse. Treated wastewater effluent can contain a number of residual contaminants that could have adverse effects on human health, and some jurisdictions have regulations in place to govern these. For those that do not, but where reuse may be under consideration, it is of crucial importance to develop a strategy for identifying priority contaminants, which can then be used to understand the water treatment technologies that might be required. In this study, a multi-criteria approach to identify critical contaminants in wastewater effluent for MAR was developed and applied using a case study site located in southern Ontario, Canada. An important aspect of this approach was the selection of representative compounds for each group of contaminants, based on potential for occurrence in wastewater and expected health or environmental impacts. Due to a lack of MAR regulations in Canada, the study first proposed potential recharge water quality targets. Predominant contaminants, potential additional contaminants, and potential emerging contaminants, which together comprise critical contaminants for MAR with reclaimed water, were then selected based on the case study wastewater effluent monitoring data and literature data. This paper proposes an approach for critical contaminant selection, which will be helpful to guide future implementation of MAR projects using wastewater treatment plant effluents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Seamless Genome Editing in Rice via Gene Targeting and Precise Marker Elimination.

PubMed

Nishizawa-Yokoi, Ayako; Saika, Hiroaki; Toki, Seiichi

2016-01-01

Positive-negative selection using hygromycin phosphotransferase (hpt) and diphtheria toxin A-fragment (DT-A) as positive and negative selection markers, respectively, allows enrichment of cells harboring target genes modified via gene targeting (GT). We have developed a successful GT system employing positive-negative selection and subsequent precise marker excision via the piggyBac transposon derived from the cabbage looper moth to introduce desired modifications into target genes in the rice genome. This approach could be applied to the precision genome editing of almost all endogenous genes throughout the genome, at least in rice.

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment

PubMed Central

Liang, L.; Goh, S. G.; Vergara, G. G. R. V.; Fang, H. M.; Rezaeinejad, S.; Chang, S. Y.; Bayen, S.; Lee, W. A.; Sobsey, M. D.; Rose, J. B.

2014-01-01

The suitability of traditional microbial indicators (i.e., Escherichia coli and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (Bacteroides thetaiotaomicron, Methanobrevibacter smithii, human polyomaviruses [HPyVs], and F+ and somatic coliphages) and pathogens (Salmonella spp., Pseudomonas aeruginosa, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore. Salmonella and P. aeruginosa had significant positive correlations with most of the microbial indicators, especially E. coli and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e., B. thetaiotaomicron, M. smithii, and HPyVs) with E. coli and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of M. smithii and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions. PMID:25416765

Bacteriophages infecting Bacteroides as a marker for microbial source tracking.

PubMed

Jofre, Joan; Blanch, Anicet R; Lucena, Francisco; Muniesa, Maite

2014-05-15

Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Alternative fecal indicators and their empirical relationships with enteric viruses, Salmonella enterica, and Pseudomonas aeruginosa in surface waters of a tropical urban catchment.

PubMed

Liang, L; Goh, S G; Vergara, G G R V; Fang, H M; Rezaeinejad, S; Chang, S Y; Bayen, S; Lee, W A; Sobsey, M D; Rose, J B; Gin, K Y H

2015-02-01

The suitability of traditional microbial indicators (i.e., Escherichia coli and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (Bacteroides thetaiotaomicron, Methanobrevibacter smithii, human polyomaviruses [HPyVs], and F+ and somatic coliphages) and pathogens (Salmonella spp., Pseudomonas aeruginosa, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore. Salmonella and P. aeruginosa had significant positive correlations with most of the microbial indicators, especially E. coli and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e., B. thetaiotaomicron, M. smithii, and HPyVs) with E. coli and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of M. smithii and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Toxicity assessment of mycotoxins extracted from contaminated commercial dog pelleted feed on canine blood mononuclear cells.

PubMed

Singh, Sanil D; Sheik Abdul, Naeem; Phulukdaree, Alisa; Tiloke, Charlette; Nagiah, Savania; Baijnath, Sooraj; Chuturgoon, Anil A

2018-04-01

Raw ingredients of pet food are often contaminated with mycotoxins. This is a serious health problem to pets and causes emotional and economical stress to the pet owners. The aim of this study was to determine the immunotoxicity of the most common mycotoxins (aflatoxin, fumonisin, ochratoxin A and zearalenone) by examining 20 samples of extruded dry dog food found on the South African market [10 samples from standard grocery store lines (SB), 10 from premium veterinarian lines (PB)]. Pelleted dog food was subjected to extraction protocols optimized for the above mentioned mycotoxins. Dog lymphocytes were treated with the extracts (24 h incubation and final concentration 40 μg/ml) to determine cell viability, mitochondrial function, oxidative stress, and markers of cell death using spectrophotometry, luminometry and flow cytometry. Malondialdehyde, a marker of oxidative stress showed no significant difference between SB and PB, however, GSH was significantly depleted in SB extract treatments. Markers of apoptosis (phosphatidylserine externalization) and necrosis (propidium iodide incorporation) were elevated in both food lines when compared to untreated control cells, interestingly SB extracts were significantly higher than PB. We also observed decreased ATP levels and increased mitochondrial depolarization in cells treated with both lines of feed with SB showing the greatest differences when compared to the control. This study provides evidence that irrespective of price, quality or marketing channels, pet foods present a high risk of mycotoxin contamination. Though in this study PB fared better than SB in regards to cell toxicity, there is a multitude of other factors that need to be studied which may have an influence on other negative outcomes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Assessment of molecular marker compounds as an index of the biodegradation of diesel fuel hydrocarbons in soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voos, G.; Mills, G.; O`Neill, J.

1996-10-01

The weathering of petroleum hydrocarbons in the soil environment is the sum of biological, physical and chemical processes. It is often difficult to clearly discern microbial from abiotic contributions to the overall process. This is especially important in assessing the effectiveness of various in-situ bioremediation technologies. We examined molecular marker compounds, including pristane, phytane, diterpenoid hydrocarbons, farnesane and norpristane, and the ratios n-C17/pristane and n-C18/phytane to evaluate their use as an index of biodegradation of diesel fuel in contaminated soil. The study was conducted using microcosms containing 200 g of contaminated soil. Microcosms were destructively sampled on days 0, 1,more » 2, 4, 8, 14, 33 and 64 of the experiment. The soil was analyzed for straight-chained, branched-chained, and alicyclic petroleum hydrocarbons using high-resolution gas chromatography. Results indicate that by day 33 of the experiment, pristane and phytane were present at significantly greater concentrations than their corresponding n-alkanes and the other marker compounds analyzed. There is a strong correlation between the amount of pristane and phytane present in the soil and the amount of total extractable petroleum hydrocarbons (TEPH) measured during the course of the experiment.« less

Chemical markers for bacteria in extraterrestrial samples.

PubMed

Fox, Alvin

2002-11-01

Interplanetary missions to collect pristine Martian surface samples for analysis of organic molecules, and to search for evidence of life, are in the planning phases. The only extraterrestrial samples currently on Earth are lunar dust and rocks, brought back by the Apollo (U.S.) and Luna (Soviet Union) missions to the moon, and meteorites. Meteorites are contaminated when they pass through the Earth's atmosphere, and during environmental exposure on Earth. Lunar fines have been stored on Earth for over 30 years under conditions designed to avoid chemical but not microbiological contamination. It has been extremely difficult to draw firm conclusions about the origin of chemicals (including amino acids) in extraterrestrial samples. Of particular concern has been the possibility of bacterial contamination. Recent work using state-of-the-art gas chromatography tandem mass spectrometry (GC-MS/MS) has dramatically lowered the chemical background, allowing a clear demonstration that lunar fines are remarkably different from terrestrial dust in that they generally lack certain chemical markers (muramic acid and 3-hydroxy fatty acids) characteristic of Earth's bacteria. Thus, lunar dust might be used as a negative control, in conjunction with GC-MS/MS analyses, in future analytical studies of lunar dust and meteorites. Such analyses may also be important in studies designed to search for the presence of life on Mars. Copyright 2002 Wiley-Liss, Inc.

Olfactory Bulb Deep Short-Axon Cells Mediate Widespread Inhibition of Tufted Cell Apical Dendrites.

PubMed

Burton, Shawn D; LaRocca, Greg; Liu, Annie; Cheetham, Claire E J; Urban, Nathaniel N

2017-02-01

In the main olfactory bulb (MOB), the first station of sensory processing in the olfactory system, GABAergic interneuron signaling shapes principal neuron activity to regulate olfaction. However, a lack of known selective markers for MOB interneurons has strongly impeded cell-type-selective investigation of interneuron function. Here, we identify the first selective marker of glomerular layer-projecting deep short-axon cells (GL-dSACs) and investigate systematically the structure, abundance, intrinsic physiology, feedforward sensory input, neuromodulation, synaptic output, and functional role of GL-dSACs in the mouse MOB circuit. GL-dSACs are located in the internal plexiform layer, where they integrate centrifugal cholinergic input with highly convergent feedforward sensory input. GL-dSAC axons arborize extensively across the glomerular layer to provide highly divergent yet selective output onto interneurons and principal tufted cells. GL-dSACs are thus capable of shifting the balance of principal tufted versus mitral cell activity across large expanses of the MOB in response to diverse sensory and top-down neuromodulatory input. The identification of cell-type-selective molecular markers has fostered tremendous insight into how distinct interneurons shape sensory processing and behavior. In the main olfactory bulb (MOB), inhibitory circuits regulate the activity of principal cells precisely to drive olfactory-guided behavior. However, selective markers for MOB interneurons remain largely unknown, limiting mechanistic understanding of olfaction. Here, we identify the first selective marker of a novel population of deep short-axon cell interneurons with superficial axonal projections to the sensory input layer of the MOB. Using this marker, together with immunohistochemistry, acute slice electrophysiology, and optogenetic circuit mapping, we reveal that this novel interneuron population integrates centrifugal cholinergic input with broadly tuned feedforward sensory input to modulate principal cell activity selectively. Copyright © 2017 the authors 0270-6474/17/371117-22$15.00/0.

Development of Protoporphyrinogen Oxidase as an Efficient Selection Marker for Agrobacterium tumefaciens-Mediated Transformation of Maize

PubMed Central

Li, Xianggan; Volrath, Sandy L.; Nicholl, David B.G.; Chilcott, Charles E.; Johnson, Marie A.; Ward, Eric R.; Law, Marcus D.

2003-01-01

In this article, we report the isolation of plant protoporphyrinogen oxidase (PPO) genes and the isolation of herbicide-tolerant mutants. Subsequently, an Arabidopsis double mutant (Y426M + S305L) was used to develop a selectable marker system for Agrobacterium tumefaciens-mediated transformation of maize (Zea mays) and to obtain multiple events tolerant to the PPO family of herbicides. Maize transformants were produced via butafenacil selection using a flexible light regime to increase selection pressure. Butafenacil selection per se did not change transgene copy number distribution relative to other selectable marker systems, but the most tolerant events identified in the greenhouse were more likely to contain multiple copies of the introduced mutant PPO gene. To date, more than 2,500 independent transgenic maize events have been produced using butafenacil selection. The high frequency of A. tumefaciens-mediated transformation via PPO selection enabled us to obtain single-copy transgenic maize lines tolerant to field levels of butafenacil. PMID:12972658

Metabolite and transcript markers for the prediction of potato drought tolerance.

PubMed

Sprenger, Heike; Erban, Alexander; Seddig, Sylvia; Rudack, Katharina; Thalhammer, Anja; Le, Mai Q; Walther, Dirk; Zuther, Ellen; Köhl, Karin I; Kopka, Joachim; Hincha, Dirk K

2018-04-01

Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars (Panax ginseng).

PubMed

Jo, Ick Hyun; Kim, Young Chang; Kim, Dong Hwi; Kim, Kee Hong; Hyun, Tae Kyung; Ryu, Hojin; Bang, Kyong Hwan

2017-10-01

The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.

Bioremediation of contaminated groundwater

DOEpatents

Hazen, Terry C.; Fliermans, Carl B.

1995-01-01

An apparatus and method for in situ remediation of contaminated subsurface soil or groundwater contaminated by chlorinated hydrocarbons. A nutrient fluid is selected to stimulate the growth and reproduction of indigenous subsurface microorganisms that are capable of degrading the contaminants; an oxygenated fluid is selected to create a generally aerobic environment for these microorganisms to degrade the contaminants, leaving only pockets that are anaerobic. The nutrient fluid is injected periodically while the oxygenated fluid is injected continuously and both are extracted so that both are drawn across the plume. The nutrient fluid stimulates microbial colony growth; withholding it periodicially forces the larger, healthy colony of microbes to degrade the contaminants. Treatment is continued until the subsurface concentration of contaminants is reduced to an acceptable, preselected level. The nutrient fluid can be methane and the oxygenated fluid air for stimulating production of methanotrophs to break down chlorohydrocarbons, especially trichloroethylene (TCE) and tetrachloroethylene.

Bioremediation of contaminated groundwater

DOEpatents

Hazen, T.C.; Fliermans, C.B.

1995-01-24

An apparatus and method are described for in situ remediation of contaminated subsurface soil or groundwater contaminated by chlorinated hydrocarbons. A nutrient fluid is selected to stimulate the growth and reproduction of indigenous subsurface microorganisms that are capable of degrading the contaminants. An oxygenated fluid is selected to create a generally aerobic environment for these microorganisms to degrade the contaminants, leaving only pockets that are anaerobic. The nutrient fluid is injected periodically while the oxygenated fluid is injected continuously and both are extracted so that both are drawn across the plume. The nutrient fluid stimulates microbial colony growth. Withholding it periodically forces the larger, healthy colony of microbes to degrade the contaminants. Treatment is continued until the subsurface concentration of contaminants is reduced to an acceptable, preselected level. The nutrient fluid can be methane and the oxygenated fluid air for stimulating production of methanotrophs to break down chlorohydrocarbons, especially trichloroethylene (TCE) and tetrachloroethylene. 3 figures.

Combining markers with and without the limit of detection

PubMed Central

Dong, Ting; Liu, Catherine Chunling; Petricoin, Emanuel F.; Tang, Liansheng Larry

2014-01-01

In this paper, we consider the combination of markers with and without the limit of detection (LOD). LOD is often encountered when measuring proteomic markers. Because of the limited detecting ability of an equipment or instrument, it is difficult to measure markers at a relatively low level. Suppose that after some monotonic transformation, the marker values approximately follow multivariate normal distributions. We propose to estimate distribution parameters while taking the LOD into account, and then combine markers using the results from the linear discriminant analysis. Our simulation results show that the ROC curve parameter estimates generated from the proposed method are much closer to the truth than simply using the linear discriminant analysis to combine markers without considering the LOD. In addition, we propose a procedure to select and combine a subset of markers when many candidate markers are available. The procedure based on the correlation among markers is different from a common understanding that a subset of the most accurate markers should be selected for the combination. The simulation studies show that the accuracy of a combined marker can be largely impacted by the correlation of marker measurements. Our methods are applied to a protein pathway dataset to combine proteomic biomarkers to distinguish cancer patients from non-cancer patients. PMID:24132938

Surrogate biochemical markers: precise measurement for strategic drug and biologics development.

PubMed

Lee, J W; Hulse, J D; Colburn, W A

1995-05-01

More efficient drug and biologics development is necessary for future success of pharmaceutical and biotechnology companies. One way to achieve this objective is to use rationally selected surrogate markers to improve the early decision-making process. Using typical clinical chemistry methods to measure biochemical markers may not ensure adequate precision and reproducibility. In contrast, using analytical methods that meet good laboratory practices along with rational selection and validation of biochemical markers can give those who use them a competitive advantage over those who do not by providing meaningful data for earlier decision making.

Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads

PubMed Central

2013-01-01

Background Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads. Results A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis. Conclusions We show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species. PMID:23324172

Dominant selectable markers for Penicillium spp. transformation and gene function studies

USDA-ARS?s Scientific Manuscript database

Penicillium spp. has been genetically manipulated and gene function studies have utilized single gene deletion strains for phenotypic analysis. Fungal transformation experiments have relied on hygromycin and hygromycin phosphotransferase (hph) as the main dominant selectable marker (DSM) system in P...

Using Microbial Source Tracking Markers to Predict Occurrence of Waterborne Pathogens in Urban and Agricultural Watershed

EPA Science Inventory

Runoff from agricultural fields and urban landscapes may carry a variety of microbial contaminants that compromises water quality and increases the possibility of human exposure to pathogenic microorganisms. Establishing the relationship between microbial source tracking (MST) ma...

Real-time, in-situ detection of volatile profiles for the prevention of aflatoxin fungal contamination in pistachios

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bond, Tiziana C.; Chang, Allan; Zhou, Jenny

The objective in this project is to provide a proof of concept will demonstrate the feasibility of a Raman, in-situ warning system for detecting and removing developing fungal hot spots from pistachio stockpiles and transit containers, thus decreasing human health risks and product loss as a result of contamination. The proposed project has the following goals: to calibrate the Raman fingerprinting of biomarkers, standalone and in premixed samples, to build a database with the vibrational profiles distinctive to the signatures of the bouquet emitted by the contaminated pistachios; to test the improvement in the detection of the detectable markers withmore » enhanced Raman on a small probe.« less

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

PubMed Central

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

Development of sustainable Palladium-based catalysts for removal of persistent contaminants from drinking water

NASA Astrophysics Data System (ADS)

Shuai, Danmeng

Pd-based catalytic reduction has emerged as an advanced treatment technology for drinking water decontamination, and a suite of persistent contaminants including oxyanions, N-nitrosoamines, and halogenated compounds are amenable to catalytic reduction. The primary goal of this study is to develop novel Pd-based catalysts with enhanced performance (i.e., activity, selectivity, and sustainability) to remove contaminants from drinking water. The effects of water quality (i.e., co-contaminants in water matrix), catalyst support, and catalyst metal were explored, and they provide insights for preparing catalysts with faster kinetics, higher selectivity, and extended lifetime. Azo dyes are wide-spread contaminants, and they are potentially co-exisiting with target contaminants amenable for catalytic removal. The probe azo dye methyl orange (MO) enhanced catalytic reduction kinetics of a suite of oxyanions (i.e., nitrate, nitrite, bromate, chlorate, and perchlorate) and diatrizoate significantly but not N-nitrosodimethylamine (NDMA) with a variety of Pd-based catalysts. Nitrate was selected as a probe contaminant, and several different azo dyes (i.e., (methyl orange, methyl red, fast yellow AB, metanil yellow, acid orange 7, congo red, eriochrome black T, acid red 27, acid yellow 11, and acid yellow 17) were evaluated for their ability to enhance reduction. A hydrogen atom shuttling mechanism was proposed and a kinetic model was proposed based on Bronsted-Evans-Polanyi (BEP) theory, and they suggest sorbed azo dyes and reduced hydrazo dyes shuttle hydrogen atoms to oxyanions or diatrizoate to enhance their reduction kinetics. Next, vapor-grown carbon nanofiber (CNF) supports were used to explore the effects of Pd nanoparticle size and interior versus exterior loading on nitrite reduction activity and selectivity (i.e., dinitrogen over ammonia production). In order to evaluate the amount of interior versus exterior loading of Pd nanoparticles, a fast and accurate geometric model was developed based on two-dimensional transmission electron microscopy (2D TEM). Results from my method agree adequately with 3D scanning transmission electron microscopy (3D TEM), which is recognized as a convincing method to evaluate interior versus exterior loading. By using Pd CNF catalysts for nitrite reduction, results show that both activity and selectivity are not significantly impacted by Pd interior versus exterior loading. Turnover frequencies (TOFs) among all CNF catalysts are consistent, suggesting faster kinetics are achieved on catalysts with smaller Pd nanoparticles, and suggesting nitrite reduction is neither sensitive to Pd location on CNFs nor Pd structure. However selectivity to dinitrogen is more favorable on larger Pd nanoparticles. Therefore, an optimum Pd nanoparticle size on CNFs balances high reduction kinetics and selectivity to dinitrogen. CNF Pd catalysts perform better than conventional activated or alumina supported Pd catalysts in term of kinetics and selectivity for nitrite reduction, and they maintain consistent activity during multiple reduction cycles. Lastly, the structure-sensitivity of catalytic activity and selectivity for contaminant nitrite, NDMA, and diatrizoate removal were investigated on shape- and size-controlled Pd nanoparticles. Results show that TOFs for nitrite, NDMA, and diatrizoate are dependent on coordination numbers of surface Pd sites at low contaminant concentration, but TOFs for nitrite at high concentration are consistent. Selectivity to ammonia for nitrite reduction decreases with increasing surface Pd sites, i.e., decreasing Pd nanoparticle size irrespective of nitrite concentration, but NDMA reduction is neither shape- nor size-specific, and it exclusively proceeds to ammonia and dimethylamine. Diatrizoate reduction selectivity is also likely to be nonspecific to shape and size, and a series of deiodinated intermediates, 3,5-diacetamidobenzoic acid, and iodide are the produced. Hence, this study suggests that contaminant reduction kinetics and selectivity are Pd shape and size dependent, and the dependence varies by contaminant type and concentration. In summary, Pd-based catalysts can be tailored for enhanced activity, selectivity, and longevity, and catalytic treatment holds the promise for advanced drinking water treatment.

Development of selectable marker free, insect resistant, transgenic mustard (Brassica juncea) plants using Cre/lox mediated recombination

PubMed Central

2013-01-01

Background Antibiotic/ herbicide resistant marker genes have been proven to be very useful in plant transformation for the initial selection of desired transgenic events. However, presence of these genes in the genetically modified crops may render the crop less acceptable to the consumers. Among several different approaches, the effectiveness of Cre/lox mediated recombination strategy for selectable marker gene (SMG) elimination has previously been demonstrated by different groups in several plants including Brassica. In the present study exploiting Cre/lox mediated recombination strategy, attempt has been made for selectable marker gene elimination from Allium sativum leaf agglutinin (ASAL) expressing Brassica plants with hemipteran insect resistant phenotype. Results Allium sativum leaf agglutinin (ASAL) linked with lox flanked hygromycin resistant (hpt) gene was introduced in mustard. Cre recombinase gene cassette was also integrated in separate event. A Cre/lox mediated recombination using crossing strategy was adopted to remove the hpt gene from the subsequent generation of selected hybrid events. Reciprocal crosses were made between T1ASAL-lox-hpt-lox and cre-bar plants. Marker gene elimination was confirmed in the resulting F1 hybrid progenies by PCR analysis, using hpt, cre and ASAL specific primers followed by Southern hybridization. In marker free plants, expression of ASAL was also confirmed by western blotting and ELISA analysis. Retention of functionality of expressed ASAL was investigated by agglutination assay using rabbit erythrocytes. Expressed ASAL was also found to be thermo-sensitive. In planta insect bioassay on F1 hybrid progenies exhibited detrimental effect on the performance of devastating target pest, Lipaphis erysimi. The F1 hybrid hpt negative, ASAL positive plants were allowed to self- fertilize to obtain F2 progeny plants. In some of these plants cre gene was found to be segregated out of the ASAL gene by genetic segregation yielding completely marker free plants. Conclusions The present study establishes the efficient expression of the newly introduced insect resistant ASAL gene even after Cre/lox mediated recombination resulting in elimination of selectable marker gene. PMID:24144281

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

PubMed Central

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

Internal amplification control of PCR for the Glu1-Dx5 allele in wheat.

PubMed

Heim, H N; Vieira, E S N; Polo, L R T; Lima, N K; Silva, G J; Linde, G A; Colauto, N B; Schuster, I

2017-08-17

One of the limiting factors in using dominant markers is the unique amplification of the target fragment. Therefore, failures in polymerase chain reaction (PCR) or non-amplifications can be interpreted as an absence of the allele. The possibility of false negatives implies in reduced efficiency in the selection process in genetic breeding programs besides the loss of valuable genetic material. Thus, this study aimed to evaluate the viability of a microsatellite marker as an internal amplification control with a dominant marker for the wheat Glu1-Dx5 gene. A population of 77 wheat cultivars/breeding lines was analyzed. Fourteen microsatellite markers were analyzed in silico regarding the formation of dimers and clamps. The biplex reaction conditions were optimized, and the Xbarc117 marker was selected as the internal amplification control with a Glu1-Dx5 marker in wheat. It was concluded that the Xbarc117 microsatellite marker was effective in the simultaneous amplification with a dominant Glu1-Dx5 marker, making biplex PCR viable in wheat for the studied markers.

Single-tube tetradecaplex panel of highly polymorphic microsatellite markers < 1 Mb from F8 for simplified preimplantation genetic diagnosis of hemophilia A.

PubMed

Zhao, M; Chen, M; Tan, A S C; Cheah, F S H; Mathew, J; Wong, P C; Chong, S S

2017-07-01

Essentials Preimplantation genetic diagnosis (PGD) of severe hemophilia A relies on linkage analysis. Simultaneous multi-marker screening can simplify selection of informative markers in a couple. We developed a single-tube tetradecaplex panel of polymorphic markers for hemophilia A PGD use. Informative markers can be used for linkage analysis alone or combined with mutation detection. Background It is currently not possible to perform single-cell preimplantation genetic diagnosis (PGD) to directly detect the common inversion mutations of the factor VIII (F8) gene responsible for severe hemophilia A (HEMA). As such, PGD for such inversion carriers relies on indirect analysis of linked polymorphic markers. Objectives To simplify linkage-based PGD of HEMA, we aimed to develop a panel of highly polymorphic microsatellite markers located near the F8 gene that could be simultaneously genotyped in a multiplex-PCR reaction. Methods We assessed the polymorphism of various microsatellite markers located ≤ 1 Mb from F8 in 177 female subjects. Highly polymorphic markers were selected for co-amplification with the AMELX/Y indel dimorphism in a single-tube reaction. Results Thirteen microsatellite markers located within 0.6 Mb of F8 were successfully co-amplified with AMELX/Y in a single-tube reaction. Observed heterozygosities of component markers ranged from 0.43 to 0.84, and ∼70-80% of individuals were heterozygous for ≥ 5 markers. The tetradecaplex panel successfully identified fully informative markers in a couple interested in PGD for HEMA because of an intragenic F8 point mutation, with haplotype phasing established through a carrier daughter. In-vitro fertilization (IVF)-PGD involved single-tube co-amplification of fully informative markers with AMELX/Y and the mutation-containing F8 amplicon, followed by microsatellite analysis and amplicon mutation-site minisequencing analysis. Conclusions The single-tube multiplex-PCR format of this highly polymorphic microsatellite marker panel simplifies identification and selection of informative markers for linkage-based PGD of HEMA. Informative markers can also be easily co-amplified with mutation-containing F8 amplicons for combined mutation detection and linkage analysis. © 2017 International Society on Thrombosis and Haemostasis.

Avian Disease and Oncology Laboratory (ADOL) research update

USDA-ARS?s Scientific Manuscript database

GENOMICS To meet the growing demands of consumers, the poultry industry will need to continue to improve methods of selection in breeding programs for production and associated traits. One possible solution is genome-wide marker-assisted selection (GWMAS). In brief, evenly-spaced genetic markers s...

Evaluation of three herbicide resistance genes for use in genetic transformations and for potential crop protection in algae production.

PubMed

Brueggeman, Andrew J; Kuehler, Daniel; Weeks, Donald P

2014-09-01

Genes conferring resistance to the herbicides glyphosate, oxyfluorfen and norflurazon were developed and tested for use as dominant selectable markers in genetic transformation of Chlamydomonas reinhardtii and as potential tools for the protection of commercial-scale algal production facilities against contamination by organisms sensitive to these broad-spectrum herbicides. A synthetic glyphosate acetyltransferase (GAT) gene, when fitted with a strong Chlamydomonas promoter, conferred a 2.7×-fold increase in tolerance to the EPSPS inhibitor, glyphosate, in transgenic cells compared with progenitor WT cells. A mutant Chlamydomonas protoporphyrinogen oxidase (protox, PPO) gene previously shown to produce an enzyme insensitive to PPO-inhibiting herbicides, when genetically engineered, generated transgenic cells able to tolerate up to 136× higher levels of the PPO inhibitor, oxyfluorfen, than nontransformed cells. Genetic modification of the Chlamydomonas phytoene desaturase (PDS) gene-based gene sequences found in various norflurazon-resistant organisms allowed production of transgenic cells tolerant to 40× higher levels of norflurazon than nontransgenic cells. The high efficiency of all three herbicide resistance genes in producing transgenic cells demonstrated their suitability as dominant selectable markers for genetic transformation of Chlamydomonas and, potentially, other eukaryotic algae. However, the requirement for high concentrations of glyphosate and its associated negative effects on cell growth rates preclude its consideration for use in large-scale production facilities. In contrast, only low doses of norflurazon and oxyfluorfen (~1.5 μm and ~0.1 μm, respectively) are required for inhibition of cell growth, suggesting that these two herbicides may prove effective in large-scale algal production facilities in suppressing growth of organisms sensitive to these herbicides. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Molecular breeding for the development of multiple disease resistance in Basmati rice.

PubMed

Singh, Atul; Singh, Vikas K; Singh, S P; Pandian, R T P; Ellur, Ranjith K; Singh, Devinder; Bhowmick, Prolay K; Gopala Krishnan, S; Nagarajan, M; Vinod, K K; Singh, U D; Prabhu, K V; Sharma, T R; Mohapatra, T; Singh, A K

2012-01-01

Basmati rice grown in the Indian subcontinent is highly valued for its unique culinary qualities. Production is, however, often constrained by diseases such as bacterial blight (BB), blast and sheath blight (ShB). The present study developed Basmati rice with inbuilt resistance to BB, blast and ShB using molecular marker-assisted selection. The rice cultivar 'Improved Pusa Basmati 1' (carrying the BB resistance genes xa13 and Xa21) was used as the recurrent parent and cultivar 'Tetep' (carrying the blast resistance gene Pi54 and ShB resistance quality trait loci (QTL), qSBR11-1) was the donor. Marker-assisted foreground selection was employed to identify plants possessing resistance alleles in the segregating generations along with stringent phenotypic selection for faster recovery of the recurrent parent genome (RPG) and phenome (RPP). Background analysis with molecular markers was used to estimate the recovery of RPG in improved lines. Foreground selection coupled with stringent phenotypic selection identified plants homozygous for xa13, Xa21 and Pi54, which were advanced to BC(2)F(5) through pedigree selection. Marker-assisted selection for qSBR11-1 in BC(2)F(5) using flanking markers identified seven homozygous families. Background analysis revealed that RPG recovery was up to 89.5%. Screening with highly virulent isolates of BB, blast and ShB showed that the improved lines were resistant to all three diseases and were on a par with 'Improved Pusa Basmati 1' for yield, duration and Basmati grain quality. This is the first report of marker-assisted transfer of genes conferring resistance to three different diseases in rice wherein genes xa13 and Xa21 for BB resistance, Pi54 for blast resistance, and a major QTL qSBR11-1 have been combined through marker-assisted backcross breeding. In addition to offering the potential for release as cultivars, the pyramided lines will serve as useful donors of gene(s) for BB, blast and ShB in future Basmati rice breeding programmes.

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

PubMed

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.

Development of disease-resistant marker-free tomato by R/RS site-specific recombination.

PubMed

Khan, Raham Sher; Nakamura, Ikuo; Mii, Masahiro

2011-06-01

The selection marker genes, imparting antibiotic or herbicide resistance, in the final transgenics have been criticized by the public and considered a hindrance in their commercialization. Multi-auto-transformation (MAT) vector system has been one of the strategies to produce marker-free transgenic plants without using selective chemicals and plant growth regulators (PGRs). In the study reported here, isopentenyltransferase (ipt) gene was used as a selection marker and wasabi defensin (WD) gene, isolated from Wasabia japonica as a target gene. WD was cloned from the binary vector, pEKH-WD to an ipt-type MAT vector, pMAT21 by gateway cloning and transferred to Agrobacterium tumefaciens strain EHA105. Infected cotyledons of tomato cv. Reiyo were cultured on PGR- and antibiotic-free MS medium. Adventitious shoots were developed by the explants infected with the pMAT21/wasabi defensin. The same PGR- and antibiotic-free MS medium was used in subcultures of the adventitious shoot lines (ASLs) to produce ipt and normal shoots. Approximately, 6 months after infection morphologically normal shoots were produced. Molecular analyses of the developed shoots confirmed the integration of gene of interest (WD) and excision of the selection marker (ipt). Expression of WD was confirmed by Northern blot and Western blot analyses. The marker-free transgenic plants exhibited enhanced resistance against Botrytis cinerea (gray mold), Alternaria solani (early blight), Fusarium oxysporum (Fusarium wilt) and Erysiphe lycopersici (powdery mildew).

Methods for removing contaminant matter from a porous material

DOEpatents

Fox, Robert V [Idaho Falls, ID; Avci, Recep [Bozeman, MT; Groenewold, Gary S [Idaho Falls, ID

2010-11-16

Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.

Bacterial inosine 5'-monophosphate dehydrogenase ("IMPDH") DNA as a dominant selectable marker in mammals and other eukaryotes

DOEpatents

Huberman, Eliezer [Chicago, IL; Baccam, Mekhine J [Woodridge, IL

2007-02-27

The present invention relates to a nucleic acid sequence and its corresponding protein sequence useful as a dominant selectable marker in eukaryotes. More specifically the invention relates to a nucleic acid encoding a bacterial IMPDH gene that has been engineered into a eukaryotic expression vectors, thereby permitting bacterial IMPDH expression in mammalian cells. Bacterial IMPDH expression confers resistance to MPA which can be used as dominant selectable marker in eukaryotes including mammals. The invention also relates to expression vectors and cells that express the bacterial IMPDH gene as well as gene therapies and protein synthesis.

DEVELOPMENT OF MARKERS OF EXPOSURE TO COPPER, NONYLPHENOL AND ATRAZINE USING SUTRACTIVE HYBRIDIZATION

EPA Science Inventory

Daphnia have been among the most commonly used test organisms for aquatic toxicity studies due to their sensitivity to contaminants. This sensitivity makes them excellent candidates for development as sentinels to monitor the occurrence of chemicals in the environment. The sequen...

Occurrence of host-associated fecal markers on child hands, household soil, and drinking water in rural Bangladeshi households

EPA Science Inventory

Improper feces disposal can lead to environmental contamination and enteric disease transmission. Using the platform of a randomized controlled trial, we evaluated whether provision of improved sanitation hardware (toilets and child feces management tools) and associated behavior...

Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

PubMed Central

Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

2017-01-01

Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding.

PubMed

Yang, Huaan; Tao, Ye; Zheng, Zequn; Shao, Di; Li, Zhenzhong; Sweetingham, Mark W; Buirchell, Bevan J; Li, Chengdao

2013-02-01

Selection for phomopsis stem blight disease (PSB) resistance is one of the key objectives in lupin (Lupinus angustifolius L.) breeding programs. A cross was made between cultivar Tanjil (resistant to PSB) and Unicrop (susceptible). The progeny was advanced into F(8) recombinant inbred lines (RILs). The RIL population was phenotyped for PSB disease resistance. Twenty plants from the RIL population representing disease resistance and susceptibility was subjected to next-generation sequencing (NGS)-based restriction site-associated DNA sequencing on the NGS platform Solexa HiSeq2000, which generated 7,241 single nucleotide polymorphisms (SNPs). Thirty-three SNP markers showed the correlation between the marker genotypes and the PSB disease phenotype on the 20 representative plants, which were considered as candidate markers linked to a putative R gene for PSB resistance. Seven candidate markers were converted into sequence-specific PCR markers, which were designated as PhtjM1, PhtjM2, PhtjM3, PhtjM4, PhtjM5, PhtjM6 and PhtjM7. Linkage analysis of the disease phenotyping data and marker genotyping data on a F(8) population containing 187 RILs confirmed that all the seven converted markers were associated with the putative R gene within the genetic distance of 2.1 CentiMorgan (cM). One of the PCR markers, PhtjM3, co-segregated with the R gene. The seven established PCR markers were tested in the 26 historical and current commercial cultivars released in Australia. The numbers of "false positives" (showing the resistance marker allele band but lack of the putative R gene) for each of the seven PCR markers ranged from nil to eight. Markers PhtjM4 and PhtjM7 are recommended in marker-assisted selection for PSB resistance in the Australian national lupin breeding program due to its wide applicability on breeding germplasm and close linkage to the putative R gene. The results demonstrated that application of NGS technology is a rapid and cost-effective approach in development of markers for molecular plant breeding.

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

PubMed

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 reserved.

The Power to Detect Linkage Disequilibrium with Quantitative Traits in Selected Samples

PubMed Central

Abecasis, Gonçalo R.; Cookson, William O. C.; Cardon, Lon R.

2001-01-01

Results from power studies for linkage detection have led to many ongoing and planned collections of phenotypically extreme nuclear families. Given the great expense of collecting these families and the imminent availability of a dense diallelic marker map, the families are likely to be used in allelic-association as well as linkage studies. However, optimal selection strategies for linkage may not be equally powerful for association. We examine the power to detect linkage disequilibrium for quantitative traits after phenotypic selection. The results encompass six selection strategies that are in widespread use, including single selection (two designs), affected sib pairs, concordant and discordant pairs, and the extreme-concordant and -discordant design. Selection of sibships on the basis of one extreme proband with high or low trait scores provides as much power as discordant sib pairs but requires the screening and phenotyping of substantially fewer initial families from which to select. Analysis of the role of allele frequencies within each selection design indicates that common trait alleles generally offer the most power, but similarities between the marker- and trait-allele frequencies are much more important than the trait-locus frequency alone. Some of the most widespread selection designs, such as single selection, yield power gains only when both the marker and quantitative trait loci (QTL) are relatively rare in the population. In contrast, discordant pairs and the extreme-proband design provide power for the broadest range of QTL–marker-allele frequency differences. Overall, proband selection from either tail provides the best balance of power, robustness, and simplicity of ascertainment for family-based association analysis. PMID:11349228

Ochratoxin A and citrinin loads in stored wheat grains: impact of grain dust and possible prediction using ergosterol measurement.

PubMed

Tangni, E K; Pussemier, L

2006-02-01

Crop storage should be carried out under hygienic conditions to ensure safe products, but sometimes grain dust which has settled from previous storage may be left over and incorporated to the following stored grains. This paper describes the results obtained using a lab model developed in order to assess the impact of grain dust incorporation for its direct contribution as a contaminant but also as an inoculum in stored wheat. Settled grain dust (4 samples) released from Belgian grain storages were collected and analysed by HPLC for ergosterol, ochratoxin A (OTA) and citrinin (CIT) content. For OTA and for ergosterol, there was a high degree of variability in concentrations found in the dust samples (from 17.3-318 ng g(-1) and from 39-823 microg g(-1), respectively) whilst for CIT, the range was less significant (from 137-344 ng g(-1)). Incorporation of grain dust into wheat storage contributed to an increase in the concentrations of mycotoxins in the stored grain. Dust acts as a contaminant and as an inoculum. According to these two ways, patterns of mycotoxin generation vary with the nature of the mycotoxin, the mycotoxigenic potential of dust and the water activity of the wheat. OTA and CIT showed a very versatile image when considering the amounts of toxins produced under the selected experimental conditions. The development of a robust tool to forecast the mycotoxigenicity of dust was based on the determination of ergosterol content as a general marker of fungal biomass. Present results suggest that this predictive tool would only be valid for predicting the contamination level of CIT and OTA at reasonable moisture content (14-20%). The potential risk of having highly contaminated batches from stock to stock may thus occur and this paper discusses possible pathways leading to OTA and CIT contamination either under wet or dry storage conditions. We therefore, recommend taking precautionary measures not only by controlling and maintaining moisture at a reasonable level during storage of the raw materials but also by paying more attention to the cleaning of the stores before loading in the new harvests.

Selectively active markers for solving of the partial occlusion problem in matchmoving and chromakeying workflow

NASA Astrophysics Data System (ADS)

Mazurek, Przemysław

2013-09-01

Matchmoving (Match Moving) is the process used for the estimation of camera movements for further integration of acquired video image with computer graphics. The estimation of movements is possible using pattern recognition, 2D and 3D tracking algorithms. The main problem for the workflow is the partial occlusion of markers by the actor, because manual rotoscoping is necessary for fixing of the chroma-keyed footage. In the paper, the partial occlusion problem is solved using the invented, selectively active electronic markers. The sensor network with multiple infrared links detects occlusion state (no-occlusion, partial, full) and switch LED's based markers.

Validation of consensus quantitative trait loci associated with resistance to multiple foliar pathogens of maize.

PubMed

Asea, Godfrey; Vivek, Bindiganavile S; Bigirwa, George; Lipps, Patrick E; Pratt, Richard C

2009-05-01

Maize production in sub-Saharan Africa incurs serious losses to epiphytotics of foliar diseases. Quantitative trait loci conditioning partial resistance (rQTL) to infection by causal agents of gray leaf spot (GLS), northern corn leaf blight (NCLB), and maize streak have been reported. Our objectives were to identify simple-sequence repeat (SSR) molecular markers linked to consensus rQTL and one recently identified rQTL associated with GLS, and to determine their suitability as tools for selection of improved host resistance. We conducted evaluations of disease severity phenotypes in separate field nurseries, each containing 410 F2:3 families derived from a cross between maize inbred CML202 (NCLB and maize streak resistant) and VP31 (a GLS-resistant breeding line) that possess complimentary rQTL. F2:3 families were selected for resistance based on genotypic (SSR marker), phenotypic, or combined data and the selected F3:4 families were reevaluated. Phenotypic values associated with SSR markers for consensus rQTL in bins 4.08 for GLS, 5.04 for NCLB, and 1.04 for maize streak significantly reduced disease severity in both generations based on single-factor analysis of variance and marker-interval analysis. These results were consistent with the presence of homozygous resistant parent alleles, except in bin 8.06, where markers were contributed by the NCLB-susceptible parent. Only one marker associated with resistance could be confirmed in bins 2.09 (GLS) and 3.06 (NCLB), illustrating the need for more robust rQTL discovery, fine-mapping, and validation prior to undertaking marker-based selection.

Molecular markers of neuropsychological functioning and Alzheimer's disease.

PubMed

Edwards, Melissa; Balldin, Valerie Hobson; Hall, James; O'Bryant, Sid

2015-03-01

The current project sought to examine molecular markers of neuropsychological functioning among elders with and without Alzheimer's disease (AD) and determine the predictive ability of combined molecular markers and select neuropsychological tests in detecting disease presence. Data were analyzed from 300 participants (n = 150, AD and n = 150, controls) enrolled in the Texas Alzheimer's Research and Care Consortium. Linear regression models were created to examine the link between the top five molecular markers from our AD blood profile and neuropsychological test scores. Logistical regressions were used to predict AD presence using serum biomarkers in combination with select neuropsychological measures. Using the neuropsychological test with the least amount of variance overlap with the molecular markers, the combined neuropsychological test and molecular markers was highly accurate in detecting AD presence. This work provides the foundation for the generation of a point-of-care device that can be used to screen for AD.

Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers.

PubMed

Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J; Iqbal, Nayyer

2015-01-01

Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program.

Targeted Proteomics Approach for Precision Plant Breeding.

PubMed

Chawade, Aakash; Alexandersson, Erik; Bengtsson, Therese; Andreasson, Erik; Levander, Fredrik

2016-02-05

Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that enables precise quantitation of hundreds of peptides in a single run. This technique provides new opportunities for multiplexed protein biomarker measurements. For precision plant breeding, DNA-based markers have been used extensively, but the potential of protein biomarkers has not been exploited. In this work, we developed an SRM marker panel with assays for 104 potato (Solanum tuberosum) peptides selected using univariate and multivariate statistics. Thereafter, using random forest classification, the prediction markers were identified for Phytopthora infestans resistance in leaves, P. infestans resistance in tubers, and plant yield in potato leaf secretome samples. The results suggest that the marker panel has the predictive potential for three traits, two of which have no commercial DNA markers so far. Furthermore, the marker panel was also tested and found to be applicable to potato clones not used during the marker development. The proposed workflow is thus a proof-of-concept for targeted proteomics as an efficient readout in accelerated breeding for complex and agronomically important traits.

Paternity testing a non-linkage based marker assisted selection scheme for outbred forage species

USDA-ARS?s Scientific Manuscript database

In many major perennial forage species, genomic tools and infrastructure development has advanced enough that their utilization in marker assisted selection (MAS) can be cheaply explored. This paper presents a paternity testing MAS in diploid red clover (Trifolium pratense L.). Utilizing individual ...

Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat

PubMed Central

Bernardo, Amy; Wang, Shan; St. Amand, Paul; Bai, Guihua

2015-01-01

With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat ( Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat. PMID:26625271

Development of a Traceability System Based on a SNP Array for Large-Scale Production of High-Value White Spruce (Picea glauca)

PubMed Central

Godbout, Julie; Tremblay, Laurence; Levasseur, Caroline; Lavigne, Patricia; Rainville, André; Mackay, John; Bousquet, Jean; Isabel, Nathalie

2017-01-01

Biological material is at the forefront of research programs, as well as application fields such as breeding, aquaculture, and reforestation. While sophisticated techniques are used to produce this material, all too often, there is no strict monitoring during the “production” process to ensure that the specific varieties are the expected ones. Confidence rather than evidence is often applied when the time comes to start a new experiment or to deploy selected varieties in the field. During the last decade, genomics research has led to the development of important resources, which have created opportunities for easily developing tools to assess the conformity of the material along the production chains. In this study, we present a simple methodology that enables the development of a traceability system which, is in fact a by-product of previous genomic projects. The plant production system in white spruce (Picea glauca) is used to illustrate our purpose. In Quebec, one of the favored strategies to produce elite varieties is to use somatic embryogenesis (SE). In order to detect human errors both upstream and downstream of the white spruce production process, this project had two main objectives: (i) to develop methods that make it possible to trace the origin of plants produced, and (ii) to generate a unique genetic fingerprint that could be used to differentiate each embryogenic cell line and ensure its genetic monitoring. Such a system had to rely on a minimum number of low-cost DNA markers and be easy to use by non-specialists. An efficient marker selection process was operationalized by testing different classification methods on simulated datasets. These datasets were generated using in-house bioinformatics tools that simulated crosses involved in the breeding program for which genotypes from hundreds of SNP markers were already available. The rate of misidentification was estimated and various sources of mishandling or contamination were identified. The method can easily be applied to other production systems for which genomic resources are already available. PMID:28791035

ALTERED GENE EXPRESSION AND DEVELOPMENT OF POTENTIAL BIOMARKERS IN MEDAKA (ORYZIAS LATIPES) BRAIN, LIVER AND TESTIS FOLLOWING EXPOSURE TO FIBRATE PHARMACEUTICALS

EPA Science Inventory

To help address the consequences of increasing levels of environmental contaminants and to identify potentially novel markers of toxicity, we examined gene expression profiles from medaka (Oryzias latipes) exposed to a prototypical fibrate pharmaceutical. Changes in gene express...

Use of molecular markers to compare Escherichia coli transport to traditional groundwater tracers in epikarst

USDA-ARS?s Scientific Manuscript database

Bacterial contamination of karst aquifers is a concern as water quality across the globe deteriorates in the face of decreasing water security. Traditional groundwater tracers (dye and microspheres) do not exhibit surface properties similar to bacteria and pathogens and therefore are not good proxie...

Correlative Assessment of Fecal Indicators Using Human Mitochondrial DNA as a Direct Marker

EPA Science Inventory

Identifying the source of surface water fecal contamination is paramount to mitigating pollution and risk to human health. Fecal bacteria such as E. coli have been staple indicator organisms for over a century, however there remains uncertainty with E. coli-based metrics since t...

Monitoring dredging effectiveness using biological and chemical markers of exposure in brown bullheads and benthic macroinvertebrates

EPA Science Inventory

Sediments in portions of the Ashtabula River in Northeastern, Ohio are heavily contaminated with polychlorinated biphenyls (PCBs), and the river has been designated by the International Joint Commission as a Great Lakes Area of Concern (www.epa.gov/glnpo/aoc). Approximately 550,0...

Presence of Pharmaceuticals in Groundwater Down Gradient from Wastewater Lagoons Receiving Partially Treated Wastewater

EPA Science Inventory

Wastewater can contain traces of the pharmaceutical compounds that are used within a given household or community. These chemicals can act as markers of the wastewater, and their presence can help determine potential sources of contamination of water resources. For this study, gr...

A structural abnormality associated with graded levels of thyroid hormone insufficiency: Dose dependent increases in heterotopia volume

EPA Science Inventory

A large number of environmental contaminants reduce circulating levels of thyroid hormone (TH), but clear markers of neurological insult associated with modest TH insufficiency are lacking. We have previously identified the presence of an abnormal cluster of misplaced neurons in ...

DEVELOPMENT OF HOST-SPECIFIC METAGENOMIC MARKERS FOR MICROBIAL SOURCE TRACKING USING A NOVEL METAGENOMIC APPROACH

EPA Science Inventory

Fecal contamination of source waters is an important issue to the drinking water industry. Improper disposal of animal waste, leaky septic tanks, storm runoff, and wildlife can all be responsible for spreading enteric pathogens into source waters. As a result, methods that can pi...

Identification of Maize Breeding Markers through Investigations of Proteins Associated with Aflatoxin-Resistance

USDA-ARS?s Scientific Manuscript database

The goal of a collaborative research project between International Institute of Tropical Agriculture (IITA) in Nigeria and ARS-Southern Regional Research Center (SRRC) in New Orleans is to develop maize inbred lines with resistance against aflatoxin contamination by Aspergillus flavus. A second goal...

Advancing our understanding of plant adaptation to metal polluted environments - new insights from Biscutella laevigata

NASA Astrophysics Data System (ADS)

Babst-Kostecka, Alicja; Waldmann, Patrik; Frérot, Hélène; Vollenweider, Pierre

2016-04-01

The legacy of industrial pollution alters ecosystems, particularly at post-mining sites where metal trace elements have created toxic conditions that trigger rapid plant adaptation. Apart from the purely scientific merits, in-depth knowledge of the mechanisms underlying plant adaptation to metal contamination is beneficial for the economic and societal sectors because of its application in bioengineering (e.g. phytoremediation or biofortification). An important process is the evolution and/or enhancement of metal tolerance, a trait that has predominantly been studied by applying acute metal stress on species that allocate large quantities of certain metals to their foliage (so-called hyperaccumulators). As the vast majority of vascular plants does not hyperaccumulate metals, more efforts are needed to investigate non-hyperaccumulating species and thereby broaden understanding of biological mechanisms underlying metal tolerance. The pseudometallophyte Biscutella laevigata has shown potential in this respect, but its characteristics are insufficiently understood. We determined the zinc tolerance level and various plant responses to environmentally relevant zinc concentrations in ten metallicolous and non-metallicolous B. laevigata populations. In a two-phase hydroponic experiment, we scored multiple morphological and physiological traits (e.g. biomass, visible stress symptoms, element content in foliage) and assessed phenotypic variability within plant families. The structure of these quantitative traits was compared to that of neutral molecular markers to test, whether natural selection caused population differentiation in zinc tolerance. While all genotypes were tolerant compared to a zinc sensitive reference species, we found congruent trends toward higher tolerance in metallicolous compared to non-metallicolous plants. We identified the most indicative parameters for these differences and find that enhanced zinc tolerance in metallicolous populations is driven by divergent selection in response to metal contamination. These findings promote B. laevigata as constitutively zinc tolerant but non-hyperaccumulating organism to study plant adaptation to contaminated environments. Remarkably, tolerance differences between edaphic types emerged already at an environmentally relevant zinc concentration. This opens an unusual perspective on plant adaptation that should be tested in other non-hyperaccumulating species.

A Population Genetics Model of Marker-Assisted Selection

PubMed Central

Luo, Z. W.; Thompson, R.; Woolliams, J. A.

1997-01-01

A deterministic two-loci model was developed to predict genetic response to marker-assisted selection (MAS) in one generation and in multiple generations. Formulas were derived to relate linkage disequilibrium in a population to the proportion of additive genetic variance used by MAS, and in turn to an extra improvement in genetic response over phenotypic selection. Predictions of the response were compared to those predicted by using an infinite-loci model and the factors affecting efficiency of MAS were examined. Theoretical analyses of the present study revealed the nonlinearity between the selection intensity and genetic response in MAS. In addition to the heritability of the trait and the proportion of the marker-associated genetic variance, the frequencies of the selectively favorable alleles at the two loci, one marker and one quantitative trait locus, were found to play an important role in determining both the short- and long-term efficiencies of MAS. The evolution of linkage disequilibrium and thus the genetic response over several generations were predicted theoretically and examined by simulation. MAS dissipated the disequilibrium more quickly than drift alone. In some cases studied, the rate of dissipation was as large as that to be expected in the circumstance where the true recombination fraction was increased by three times and selection was absent. PMID:9215918

Evaluation of the effect and profitability of gene-assisted selection in pig breeding system*

PubMed Central

Li, Ya-lan; Zhang, Qin; Chen, Yao-sheng

2007-01-01

Objective: To evaluate the effect and profitability of using the quantitative trait loci (QTL)-linked direct marker (DR marker) in gene-assisted selection (GAS). Methods: Three populations (100, 200, or 300 sows plus 10 boars within each group) with segregating QTL were simulated stochastically. Five economic traits were investigated, including number of born alive (NBA), average daily gain to 100 kg body weight (ADG), feed conversion ratio (FCR), back fat at 100 kg body weight (BF) and intramuscular fat (IMF). Selection was based on the estimated breeding value (EBV) of each trait. The starting frequencies of the QTL’s favorable allele were 0.1, 0.3 and 0.5, respectively. The economic return was calculated by gene flow method. Results: The selection efficiency was higher than 100% when DR markers were used in GAS for 5 traits. The selection efficiency for NBA was the highest, and the lowest was for ADG whose QTL had the lowest variance. The mixed model applied DR markers and obtained higher extra genetic gain and extra economic returns. We also found that the lower the frequency of the favorable allele of the QTL, the higher the extra return obtained. Conclusion: GAS is an effective selection scheme to increase the genetic gain and the economic returns in pig breeding. PMID:17973344

Evaluation of the effect and profitability of gene-assisted selection in pig breeding system.

PubMed

Li, Ya-Lan; Zhang, Qin; Chen, Yao-Sheng

2007-11-01

To evaluate the effect and profitability of using the quantitative trait loci (QTL)-linked direct marker (DR marker) in gene-assisted selection (GAS). Three populations (100, 200, or 300 sows plus 10 boars within each group) with segregating QTL were simulated stochastically. Five economic traits were investigated, including number of born alive (NBA), average daily gain to 100 kg body weight (ADG), feed conversion ratio (FCR), back fat at 100 kg body weight (BF) and intramuscular fat (IMF). Selection was based on the estimated breeding value (EBV) of each trait. The starting frequencies of the QTL's favorable allele were 0.1, 0.3 and 0.5, respectively. The economic return was calculated by gene flow method. The selection efficiency was higher than 100% when DR markers were used in GAS for 5 traits. The selection efficiency for NBA was the highest, and the lowest was for ADG whose QTL had the lowest variance. The mixed model applied DR markers and obtained higher extra genetic gain and extra economic returns. We also found that the lower the frequency of the favorable allele of the QTL, the higher the extra return obtained. GAS is an effective selection scheme to increase the genetic gain and the economic returns in pig breeding.

Does microbial contamination influence the success of the hematopoietic cell transplantation outcomes?

PubMed

Dal, Mehmet Sinan; Tekgündüz, Emre; Çakar, Merih Kızıl; Kaya, Ali Hakan; Namdaroğu, Sinem; Batgi, Hikmetullah; Bekdemir, Filiz; Uncu Ulu, Bahar; Yiğenoğlu, Tuğçe Nur; Kılınç, Ali; İskender, Dicle; Uğur, Bilge; Koçubaba, Şerife; İskender, Gülşen; Altuntaş, Fevzi

2016-08-01

Microbial contamination can be a marker for faulty process and is assumed to play an important role in the collection of hematopoietic progenitor cell (HPC) and infusion procedure. We aimed to determine the microbial contamination rates and evaluate the success of hematopoietic cell transplantation (HCT) in patients who received contaminated products. We analyzed microbial contamination records of HPC grafts between 2012 and 2015, retrospectively. Contamination rates of autologous donors were evaluated for at three steps: at the end of mobilization, following processing with dimethyl sulfoxide, and just before stem cell infusion. Grafts of allogeneic donors were assessed only before HCT. A total of 445 mobilization procedures were carried out on 333 (167 autologous and 166 allogeneic) donors. The microbiological contamination of peripheral blood (323/333 donations) and bone marrow (10/333 donations) products were analyzed. Bacterial contamination was detected in 18 of 1552 (1.15 %) culture bottles of 333 donors. During the study period 248 patients underwent HCT and among these patients microbial contamination rate on sample basis was 1.3 % (16/1212). Microbial contamination detected in nine patients (7 autologous; 2 allogeneic). In 8 of 9 patients, a febrile neutropenic attack was observed. The median day for the neutropenic fever was 4 days (0-9). None of the patients died within the post-transplant 30 days who received contaminated products. The use of contaminated products with antibiotic prophylaxis may be safe in terms of the first day of fever, duration of fever, neutrophil, platelet engraftment and duration of hospitalization. Copyright © 2016 Elsevier Ltd. All rights reserved.

Self-excising Cre/mutant lox marker recycling system for multiple gene integrations and consecutive gene deletions in Aspergillus oryzae.

PubMed

Zhang, Silai; Ban, Akihiko; Ebara, Naoki; Mizutani, Osamu; Tanaka, Mizuki; Shintani, Takahiro; Gomi, Katsuya

2017-04-01

In this study, we developed a self-excising Cre/loxP-mediated marker recycling system with mutated lox sequences to introduce a number of biosynthetic genes into Aspergillus oryzae. To construct the self-excising marker cassette, both the selectable marker, the Aspergillus nidulans adeA gene, and the Cre recombinase gene (cre), conditionally expressed by the xylanase-encoding gene promoter, were designed to be located between the mutant lox sequences, lox66 and lox71. However, construction of the plasmid failed, possibly owing to a slight expression of cre downstream of the fungal gene promoter in Escherichia coli. Hence, to avoid the excision of the cassette in E. coli, a 71-bp intron of the A. oryzae xynG2 gene was inserted into the cre gene. The A. oryzae adeA deletion mutant was transformed with the resulting plasmid in the presence of glucose, and the transformants were cultured in medium containing xylose as the sole carbon source. PCR analysis of genomic DNA from resultant colonies revealed the excision of both the marker and Cre expression construct, indicating that the self-excising marker cassette was efficient at removing the selectable marker. Using the marker recycling system, hyperproduction of kojic acid could be achieved in A. oryzae by the introduction of two genes that encode oxidoreductase and transporter. Furthermore, we also constructed an alternative marker recycling cassette bearing the A. nidulans pyrithiamine resistant gene (ptrA) as a dominant selectable marker. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

REVIEW OF SEPARATION TECHNOLOGIES FOR TREATING PESTICIDE-CONTAMINATED SOIL

EPA Science Inventory

Pesticide contamination results from manufacturing, improper storage, handling, or disposal of pesticides, and from agricultural processes. Since most pesticides are mixtures of different compounds, selecting a remedy for pesticide-contaminated soils can be a complicated process....

Superfund Record of Decision (EPA Region 7): Bee Cee Manufacturing Co., Malden, MO, September 30, 1997

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

This decision document presents the remedial action selected to cleanup groundwater contaminant at the Bee Cee Manufacturing site in Malden, Missouri. The remedy selected to remediate contaminated groundwater at the Bee Cee Manufacturing site is natural attenuation, groundwater monitoring and institutional controls.

Gene expression profiling and environmental contaminant assessment of migrating Pacific salmon in the Fraser River watershed of British Columbia.

PubMed

Veldhoen, Nik; Ikonomou, Michael G; Dubetz, Cory; Macpherson, Nancy; Sampson, Tracy; Kelly, Barry C; Helbing, Caren C

2010-05-05

The health and physiological condition of anadromous salmon is of concern as their upriver migration requires navigation of human-impacted waterways and metabolism of stored energy reserves containing anthropogenic contaminants. Such factors may affect reproductive success of fish stocks. This study investigates chemical contaminant burdens and select gene expression profiles in Pacific Sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon which traverse the Fraser River watershed during their spawning migration. Chemical analyses of muscle tissue and eggs of salmon collected from the lower Fraser River (pre-migration) and from upstream spawning grounds (post-migration) during the 2007 migration revealed the presence of numerous chemical contaminants, including PCBs, dioxins/furans, pesticides, and heavy metals. However, muscle tissue residue concentrations were well below human health consumption guidelines and 2,3,7,8 TCDD toxic equivalents (SigmaTEQs) in salmon eggs, calculated using WHO toxic equivalency factors (WHO-TEFs) for fish health, did not exceed the 0.3pgg(-1) wet weight toxicological threshold level previously associated with 30% egg mortality in salmon populations. Quantitative real-time PCR probes were generated and used to assess differences in abundance of key mRNA transcripts encoding nine gene products associated with reproduction, stress, metal toxicity, and exposure to environmental contaminants. Gene expression profiles were characterized in liver and muscle tissue of pre- and post-migration Sockeye and Chinook salmon. The results of stock-matched animals indicate that dynamic changes in mRNA levels occur for a number of genes in both species during migration and suggest that Sockeye salmon exhibit a greater level of biological stress compared to the Chinook salmon population. Using a male-specific genotypic marker, we found that out of the 154 animals examined, one Sockeye was genotypically male but phenotypically female. This individual's gene expression profile in liver and muscle was reminiscent of, but not identical to, the female expression profile. These studies provide the first glimpse of the dynamic yet common nature of changes in the transcriptome that are shared between species during in-migration and highlight differences that may relate to population success. Continued longitudinal assessment will further define the association between contaminant burden, physiological stress, and modulation of gene expression in migrating Pacific salmon.

Superfund record of decision (EPA Region 10): McCormick and Baxter Creosoting Company, Portland Plant, Portland, OR, March 29, 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-08-01

The decision document presents the selected final remedial actions for the McCormick and Baxter Creosoting Company, Portland Plant site (McCormick and Baxter or site) located in Portland, Oregon. The selected remedy is a series of remedial actions that address the principal threats at the site by treating the most highly contaminated soil, extracting nonaqueous phase liquid (NAPL) and treating contaminated groundwater, and capping the most highly contaminated sediment.

An Assessment of the Spatial and Temporal Variability of Biological Responses to Municipal Wastewater Effluent in Rainbow Darter (Etheostoma caeruleum) Collected along an Urban Gradient

PubMed Central

Bragg, Leslie M.; Tetreault, Gerald R.; Bahamonde, Paulina A.; Tanna, Rajiv N.; Bennett, Charles J.; McMaster, Mark E.; Servos, Mark R.

2016-01-01

Municipal wastewater effluent (MWWE) and its constituents, such as chemicals of emerging concern, pose a potential threat to the sustainability of fish populations by disrupting key endocrine functions in aquatic organisms. While studies have demonstrated changes in biological markers of exposure of aquatic organisms to groups of chemicals of emerging concern, the variability of these markers over time has not been sufficiently described in wild fish species. The aim of this study was to assess the spatial and temporal variability of biological markers in response to MWWE exposure and to test the consistency of these responses between seasons and among years. Rainbow darter (Etheostoma caeruleum) were collected in spring and fall seasons over a 5-year period in the Grand River, Ontario, Canada. In addition to surface water chemistry (nutrients and selected pharmaceuticals), measures were taken across levels of biological organization in rainbow darter. The measurements of hormone production, gonad development, and intersex severity were temporally consistent and suggested impaired reproduction in male fish collected downstream of MWWE outfalls. In contrast, ovarian development and hormone production in females appeared to be influenced more by urbanization than MWWE. Measures of gene expression and somatic indices were highly variable between sites and years, respectively, and were inconclusive in terms of the impacts of MWWE overall. Robust biomonitoring programs must consider these factors in both the design and interpretation of results, especially when spatial and temporal sampling of biological endpoints is limited. Assessing the effects of contaminants and other stressors on fish in watersheds would be greatly enhanced by an approach that considers natural variability in the endpoints being measured. PMID:27776151

Tracing Asian Seabass Individuals to Single Fish Farms Using Microsatellites

PubMed Central

Yue, Gen Hua; Xia, Jun Hong; Liu, Peng; Liu, Feng; Sun, Fei; Lin, Grace

2012-01-01

Traceability through physical labels is well established, but it is not highly reliable as physical labels can be easily changed or lost. Application of DNA markers to the traceability of food plays an increasingly important role for consumer protection and confidence building. In this study, we tested the efficiency of 16 polymorphic microsatellites and their combinations for tracing 368 fish to four populations where they originated. Using the maximum likelihood and Bayesian methods, three most efficient microsatellites were required to assign over 95% of fish to the correct populations. Selection of markers based on the assignment score estimated with the software WHICHLOCI was most effective in choosing markers for individual assignment, followed by the selection based on the allele number of individual markers. By combining rapid DNA extraction, and high-throughput genotyping of selected microsatellites, it is possible to conduct routine genetic traceability with high accuracy in Asian seabass. PMID:23285169

Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

PubMed Central

Zaki, Noorhariza Mohd; Singh, Rajinder; Rosli, Rozana; Ismail, Ismanizan

2012-01-01

Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (Ho) (0.164) and highly positive fixation indices (Fis) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family. PMID:22605966

Testing human hair for drugs of abuse. IV. Environmental cocaine contamination and washing effects.

PubMed

Wang, W L; Cone, E J

1995-01-05

Active cocaine use results in sequestration of parent drug in hair. In addition, hair has unique physicochemical properties that permit absorption of cocaine from the environment. When hair is tested for evidence of cocaine, it is important to consider whether the positive test resulted from active drug use or environmental contamination. In a series of laboratory experiments, it was found that exposure of 'cut' hair to cocaine vapor ('crack' smoke) and to aqueous solutions of cocaine hydrochloride resulted in significant contamination of hair samples. Similar results were obtained with two subjects who were exposed to cocaine vapor in an unventilated room. The amount of contamination adsorbed by hair depended upon both time and extent of exposure. Washing the hair samples with methanol removed > 70% of the cocaine contaminant after cocaine vapor exposure, but was less effective (< 50%) following contamination with aqueous cocaine. Shampoo treatment cycles (overnight soaking) progressively removed increasing amounts of cocaine from the contaminated hair, but residual cocaine remained after 10 cycles. Studies were also performed to determine the usefulness of benzoylecgonine as a marker of active cocaine administration. Small amounts of benzoylecgonine (ca. 1 ng/mg) were formed in hair as a result of environmental contamination with cocaine. Also, it was found that benzoylecgonine could be adsorbed from illicit cocaine contaminated with benzoylecgonine. It was concluded that positive hair test results should be interpreted cautiously due to the possibility of environmental contamination from cocaine and related constituents.

Fungal bioremediation of the creosote-contaminated soil: influence of Pleurotus ostreatus and Irpex lacteus on polycyclic aromatic hydrocarbons removal and soil microbial community composition in the laboratory-scale study.

PubMed

Byss, Marius; Elhottová, Dana; Tříska, Jan; Baldrian, Petr

2008-11-01

The aim of this study was to determine the efficacy of selected basidiomycetes in the removing of polycyclic aromatic hydrocarbons (PAH) from the creosote-contaminated soil. Fungi Pleurotus ostreatus and Irpex lacteus were supplemented with creosote-contaminated (50-200 mg kg(-1) PAH) soil originating from a wood-preserving plant and incubated at 15 °C for 120 d. Either fungus degraded PAH with 4-6 aromatic rings more efficiently than the microbial community present initially in the soil. PAH removal was higher in P. ostreatus treatments (55-67%) than in I. lacteus treatments (27-36%) in general. P. ostreatus (respectively, I. lacteus) removed 86-96% (47-59%) of 2-rings PAH, 63-72% (33-45%) of 3-rings PAH, 32-49% (9-14%) of 4-rings PAH and 31-38% (11-13%) of 5-6-rings PAH. MIS (Microbial Identification System) Sherlock analysis of the bacterial community determined the presence of dominant Gram-negative bacteria (G-) Pseudomonas in the inoculated soil before the application of fungi. Complex soil microbial community was characterized by phospholipid fatty acids analysis followed by GC-MS/MS. Either fungus induced the decrease of bacterial biomass (G- bacteria in particular), but the soil microbial community was influenced by P. ostreatus in a different way than by I. lacteus. The bacterial community was stressed more by the presence of I. lacteus than P. ostreatus (as proved by the ratio of the fungal/bacterial markers and by the ratio of trans/cis mono-unsaturated fatty acids). Moreover, P. ostreatus stimulated the growth of Gram-positive bacteria (G+), especially actinobacteria and these results indicate the potential of the positive synergistic interaction of this fungus and actinobacteria in creosote biodegradation.

Flow cytometry of sputum: assessing inflammation and immune response elements in the bronchial airways

PubMed Central

Lay, John C.; Peden, David B.; Alexis, Neil E.

2012-01-01

Background The evaluation of sputum leukocytes by flow cytometry is an opportunity to assess characteristics of cells residing in the central airways, yet it is hampered by certain inherent properties of sputum including mucus and large amounts of contaminating cells and debris. Objective To develop a gating strategy based on specific antibody panels in combination with light scatter properties for flow cytometric evaluation of sputum cells. Methods Healthy and mild asthmatic volunteers underwent sputum induction. Manually selected mucus “plug” material was treated with dithiothrietol, filtered and total leukocytes acquired. Multicolor flow cytometry was performed using specific gating strategies based on light scatter properties, differential expression of CD45 and cell lineage markers to discriminate leukocytes from squamous epithelial cells and debris. Results The combination of forward scatter and CD45 expression reliably segregated sputum leukocytes from contaminating squamous epithelial cells and debris. Overlap of major leukocyte populations (neutrophils, macrophages/monocytes) required the use of specific antibodies (e.g. CD16, CD64, CD14, HLA-DR) that differentiated granulocytes from monocytes and macrophages. These gating strategies allowed identification of small populations of eosinophils, CD11c+ myeloid dendritic cells, B cells and NK cells. Conclusions Multicolor flow cytometry can be successfully applied to sputum samples to identify and characterize leukocyte populations residing on the surfaces of the central airways. PMID:21639708

CHEMICAL MARKERS OF HUMAN WASTE ...

EPA Pesticide Factsheets

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 public water authorities a rapid (24- hrs) and definitive method for measuring human waste contamination The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-soluble pharmaceuticals in source waters at levels that could be environmentally significant (at concentrations less than parts per billion, ppb). IAG with USGS ends in FY05. APM 20 due in FY05.Subtask 2: Coordination of interagency research and public outreach activities for PPCPs. Participate on NSTC Health and Environment subco

CHEMICAL MARKERS OF HUMAN WASTE ...

EPA Pesticide Factsheets

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 public water authorities a rapid (24- hrs) and definitive method for measuring human waste contamination. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-soluble pharmaceuticals in source waters at levels that could be environmentally significant (at concentrations less than parts per billion, ppb). IAG with USGS ends in FY05. APM 20 due in FY05.Subtask 2: Coordination of interagency research and public outreach activities for PPCPs. Participate on NSTC Health and Environment subc

ADDRESSING EMERGING ISSUES IN WATER QUALITY ...

EPA Pesticide Factsheets

Public concern over cleanliness and safety of source and recreational waters has prompted researchers to look for indicators of water quality. Giving public water authorities multiple tools to measure and monitor levels of chemical contaminants, as well as chemical markers of contamination, simply and rapidly would enhance public protection. The goals of water quality are outlined in the Water Quality Multi-year Plan [http://intranet.epa.gov/ospintra/Planning/wq.pdf] and the research in this task falls under GPRA Goal 2, 2.3.2, Long Term Goals 1, 2, and 4. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-soluble pharmaceuticals in source waters at levels that could be environmentally significant (at concentrations less than parts per billion, ppb). IAG

Verification of STS markers for leaf rust resistance genes of wheat by seven European laboratories.

PubMed

Błaszczyk, Lidia; Chełkowski, Jerzy; Korzun, Victor; Kraic, Jan; Ordon, Frank; Ovesná, Jaroslava; Purnhauser, Laszlo; Tar, Melinda; Vida, Gyula

2004-01-01

A set of Thatcher near-isogenic lines and two breeding lines were used to examine sequence tagged site (STS) markers linked to leaf rust resistance genes Lr9, Lr10, Lr19, Lr24, Lr28, Lr29, Lr35, and a simple sequenced repeat (SSR) marker for Lr39. The selected STS markers for resistance genes Lr9, Lr10, Lr19, Lr24 and Lr28 were identified in seven accessions by seven European laboratories. Near-isogenic lines of the spring wheat Thatcher were used as positive controls. Markers for resistance genes Lr9, Lr10, Lr19, Lr24 were identified in all seven laboratories as amplification products of 1100 bp, 310 bp, 130 bp and 310 bp, respectively. The STS markers linked to resistance genes Lr9, Lr10, Lr19, Lr24, Lr29, Lr35 and the SSR marker for Lr39 were robust and highly specific for these genes and will be useful in marker-assisted selection in wheat. However, the amplification product of 378 bp that corresponded with resistance gene Lr28 was detected in all accessions including genotypes lacking this gene in all seven laboratories. This marker needs to be improved.

Polyphosphazine-based polymer materials

DOEpatents

Fox, Robert V.; Avci, Recep; Groenewold, Gary S.

2010-05-25

Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.

Genome wide selection in Citrus breeding.

PubMed

Gois, I B; Borém, A; Cristofani-Yaly, M; de Resende, M D V; Azevedo, C F; Bastianel, M; Novelli, V M; Machado, M A

2016-10-17

Genome wide selection (GWS) is essential for the genetic improvement of perennial species such as Citrus because of its ability to increase gain per unit time and to enable the efficient selection of characteristics with low heritability. This study assessed GWS efficiency in a population of Citrus and compared it with selection based on phenotypic data. A total of 180 individual trees from a cross between Pera sweet orange (Citrus sinensis Osbeck) and Murcott tangor (Citrus sinensis Osbeck x Citrus reticulata Blanco) were evaluated for 10 characteristics related to fruit quality. The hybrids were genotyped using 5287 DArT_seq TM (diversity arrays technology) molecular markers and their effects on phenotypes were predicted using the random regression - best linear unbiased predictor (rr-BLUP) method. The predictive ability, prediction bias, and accuracy of GWS were estimated to verify its effectiveness for phenotype prediction. The proportion of genetic variance explained by the markers was also computed. The heritability of the traits, as determined by markers, was 16-28%. The predictive ability of these markers ranged from 0.53 to 0.64, and the regression coefficients between predicted and observed phenotypes were close to unity. Over 35% of the genetic variance was accounted for by the markers. Accuracy estimates with GWS were lower than those obtained by phenotypic analysis; however, GWS was superior in terms of genetic gain per unit time. Thus, GWS may be useful for Citrus breeding as it can predict phenotypes early and accurately, and reduce the length of the selection cycle. This study demonstrates the feasibility of genomic selection in Citrus.

Integrative Analysis of High-throughput Cancer Studies with Contrasted Penalization

PubMed Central

Shi, Xingjie; Liu, Jin; Huang, Jian; Zhou, Yong; Shia, BenChang; Ma, Shuangge

2015-01-01

In cancer studies with high-throughput genetic and genomic measurements, integrative analysis provides a way to effectively pool and analyze heterogeneous raw data from multiple independent studies and outperforms “classic” meta-analysis and single-dataset analysis. When marker selection is of interest, the genetic basis of multiple datasets can be described using the homogeneity model or the heterogeneity model. In this study, we consider marker selection under the heterogeneity model, which includes the homogeneity model as a special case and can be more flexible. Penalization methods have been developed in the literature for marker selection. This study advances from the published ones by introducing the contrast penalties, which can accommodate the within- and across-dataset structures of covariates/regression coefficients and, by doing so, further improve marker selection performance. Specifically, we develop a penalization method that accommodates the across-dataset structures by smoothing over regression coefficients. An effective iterative algorithm, which calls an inner coordinate descent iteration, is developed. Simulation shows that the proposed method outperforms the benchmark with more accurate marker identification. The analysis of breast cancer and lung cancer prognosis studies with gene expression measurements shows that the proposed method identifies genes different from those using the benchmark and has better prediction performance. PMID:24395534

Efficient transformation and regeneration of transgenic cassava using the neomycin phosphotransferase gene as aminoglycoside resistance marker gene.

PubMed

Niklaus, Michael; Gruissem, Wilhelm; Vanderschuren, Hervé

2011-01-01

Cassava is one of the most important crops in the tropics. Its industrial use for starch and biofuel production is also increasing its importance for agricultural production in tropical countries. In the last decade cassava biotechnology has emerged as a valuable alternative to the breeding constraints of this highly heterozygous crop for improved trait development of cassava germplasm. Cassava transformation remains difficult and time-consuming because of limitations in selecting transgenic tissues and regeneration of transgenic plantlets. We have recently reported an efficient and robust cassava transformation protocol using the hygromycin phosphotransferase II (hptII) gene as selection marker and the aminoglycoside hygromycin at optimal concentrations to maximize the regeneration of transgenic plantlets. In the present work, we expanded the transformation protocol to the use of the neomycin phosphotransferase II (nptII) gene as selection marker. Several aminoglycosides compatible with the use of nptII were tested and optimal concentrations for cassava transformation were determined. Given its efficiency equivalent to hptII as selection marker with the described protocol, the use of nptII opens new possibilities to engineer transgenic cassava lines with multiple T-DNA insertions and to produce transgenic cassava with a resistance marker gene that is already deregulated in several commercial transgenic crops.

Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis

PubMed Central

Cao, Li-Jun; Li, Ze-Min; Wang, Ze-Hua; Zhu, Liang; Gong, Ya-Jun; Chen, Min; Wei, Shu-Jun

2016-01-01

Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy–Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies. PMID:27197749

Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis.

PubMed

Cao, Li-Jun; Li, Ze-Min; Wang, Ze-Hua; Zhu, Liang; Gong, Ya-Jun; Chen, Min; Wei, Shu-Jun

2016-05-20

Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy-Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies.

Pion contamination in the MICE muon beam

NASA Astrophysics Data System (ADS)

Adams, D.; Alekou, A.; Apollonio, M.; Asfandiyarov, R.; Barber, G.; Barclay, P.; de Bari, A.; Bayes, R.; Bayliss, V.; Bertoni, R.; Blackmore, V. J.; Blondel, A.; Blot, S.; Bogomilov, M.; Bonesini, M.; Booth, C. N.; Bowring, D.; Boyd, S.; Brashaw, T. W.; Bravar, U.; Bross, A. D.; Capponi, M.; Carlisle, T.; Cecchet, G.; Charnley, C.; Chignoli, F.; Cline, D.; Cobb, J. H.; Colling, G.; Collomb, N.; Coney, L.; Cooke, P.; Courthold, M.; Cremaldi, L. M.; DeMello, A.; Dick, A.; Dobbs, A.; Dornan, P.; Drews, M.; Drielsma, F.; Filthaut, F.; Fitzpatrick, T.; Franchini, P.; Francis, V.; Fry, L.; Gallagher, A.; Gamet, R.; Gardener, R.; Gourlay, S.; Grant, A.; Greis, J. R.; Griffiths, S.; Hanlet, P.; Hansen, O. M.; Hanson, G. G.; Hart, T. L.; Hartnett, T.; Hayler, T.; Heidt, C.; Hills, M.; Hodgson, P.; Hunt, C.; Iaciofano, A.; Ishimoto, S.; Kafka, G.; Kaplan, D. M.; Karadzhov, Y.; Kim, Y. K.; Kuno, Y.; Kyberd, P.; Lagrange, J.-B.; Langlands, J.; Lau, W.; Leonova, M.; Li, D.; Lintern, A.; Littlefield, M.; Long, K.; Luo, T.; Macwaters, C.; Martlew, B.; Martyniak, J.; Mazza, R.; Middleton, S.; Moretti, A.; Moss, A.; Muir, A.; Mullacrane, I.; Nebrensky, J. J.; Neuffer, D.; Nichols, A.; Nicholson, R.; Nugent, J. C.; Oates, A.; Onel, Y.; Orestano, D.; Overton, E.; Owens, P.; Palladino, V.; Pasternak, J.; Pastore, F.; Pidcott, C.; Popovic, M.; Preece, R.; Prestemon, S.; Rajaram, D.; Ramberger, S.; Rayner, M. A.; Ricciardi, S.; Roberts, T. J.; Robinson, M.; Rogers, C.; Ronald, K.; Rubinov, P.; Rucinski, P.; Sakamato, H.; Sanders, D. A.; Santos, E.; Savidge, T.; Smith, P. J.; Snopok, P.; Soler, F. J. P.; Speirs, D.; Stanley, T.; Stokes, G.; Summers, D. J.; Tarrant, J.; Taylor, I.; Tortora, L.; Torun, Y.; Tsenov, R.; Tunnell, C. D.; Uchida, M. A.; Vankova-Kirilova, G.; Virostek, S.; Vretenar, M.; Warburton, P.; Watson, S.; White, C.; Whyte, C. G.; Wilson, A.; Winter, M.; Yang, X.; Young, A.; Zisman, M.

2016-03-01

The international Muon Ionization Cooling Experiment (MICE) will perform a systematic investigation of ionization cooling with muon beams of momentum between 140 and 240 MeV/c at the Rutherford Appleton Laboratory ISIS facility. The measurement of ionization cooling in MICE relies on the selection of a pure sample of muons that traverse the experiment. To make this selection, the MICE Muon Beam is designed to deliver a beam of muons with less than ~1% contamination. To make the final muon selection, MICE employs a particle-identification (PID) system upstream and downstream of the cooling cell. The PID system includes time-of-flight hodoscopes, threshold-Cherenkov counters and calorimetry. The upper limit for the pion contamination measured in this paper is fπ < 1.4% at 90% C.L., including systematic uncertainties. Therefore, the MICE Muon Beam is able to meet the stringent pion-contamination requirements of the study of ionization cooling.

Pion contamination in the MICE muon beam

DOE PAGES

Adams, D.; Alekou, A.; Apollonio, M.; ...

2016-03-01

Here, the international Muon Ionization Cooling Experiment (MICE) will perform a systematic investigation of ionization cooling with muon beams of momentum between 140 and 240\\,MeV/c at the Rutherford Appleton Laboratory ISIS facility. The measurement of ionization cooling in MICE relies on the selection of a pure sample of muons that traverse the experiment. To make this selection, the MICE Muon Beam is designed to deliver a beam of muons with less thanmore » $$\\sim$$1% contamination. To make the final muon selection, MICE employs a particle-identification (PID) system upstream and downstream of the cooling cell. The PID system includes time-of-flight hodoscopes, threshold-Cherenkov counters and calorimetry. The upper limit for the pion contamination measured in this paper is $$f_\\pi < 1.4\\%$$ at 90% C.L., including systematic uncertainties. Therefore, the MICE Muon Beam is able to meet the stringent pion-contamination requirements of the study of ionization cooling.« less

Association Mapping of Disease Resistance Traits in Rainbow Trout Using Restriction Site Associated DNA Sequencing

PubMed Central

Campbell, Nathan R.; LaPatra, Scott E.; Overturf, Ken; Towner, Richard; Narum, Shawn R.

2014-01-01

Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site−associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs. PMID:25354781

Incorporating expert judgments in utility evaluation of bacteroidales qPCR assays for microbial source tracking in a drinking water source.

PubMed

Åström, Johan; Pettersson, Thomas J R; Reischer, Georg H; Norberg, Tommy; Hermansson, Malte

2015-02-03

Several assays for the detection of host-specific genetic markers of the order Bacteroidales have been developed and used for microbial source tracking (MST) in environmental waters. It is recognized that the source-sensitivity and source-specificity are unknown and variable when introducing these assays in new geographic regions, which reduces their reliability and use. A Bayesian approach was developed to incorporate expert judgments with regional assay sensitivity and specificity assessments in a utility evaluation of a human and a ruminant-specific qPCR assay for MST in a drinking water source. Water samples from Lake Rådasjön were analyzed for E. coli, intestinal enterococci and somatic coliphages through cultivation and for human (BacH) and ruminant-specific (BacR) markers through qPCR assays. Expert judgments were collected regarding the probability of human and ruminant fecal contamination based on fecal indicator organism data and subjective information. Using Bayes formula, the conditional probability of a true human or ruminant fecal contamination given the presence of BacH or BacR was determined stochastically from expert judgments and regional qPCR assay performance, using Beta distributions to represent uncertainties. A web-based computational tool was developed for the procedure, which provides a measure of confidence to findings of host-specific markers and demonstrates the information value from these assays.

Incorporating Expert Judgments in Utility Evaluation of Bacteroidales qPCR Assays for Microbial Source Tracking in a Drinking Water Source

PubMed Central

Åström, Johan; Pettersson, Thomas J. R.; Reischer, Georg H.; Norberg, Tommy; Hermansson, Malte

2017-01-01

Several assays for the detection of host-specific genetic markers of the order Bacteroidales have been developed and used for microbial source tracking (MST) in environmental waters. It is recognized that the source-sensitivity and source-specificity are unknown and variable when introducing these assays in new geographic regions, which reduces their reliability and use. A Bayesian approach was developed to incorporate expert judgments with regional assay sensitivity and specificity assessments in a utility evaluation of a human and a ruminant-specific qPCR assay for MST in a drinking water source. Water samples from Lake Rådasjön were analyzed for E. coli, intestinal enterococci and somatic coliphages through cultivation and for human (BacH) and ruminant-specific (BacR) markers through qPCR assays. Expert judgments were collected regarding the probability of human and ruminant fecal contamination based on fecal indicator organism data and subjective information. Using Bayes formula, the conditional probability of a true human or ruminant fecal contamination given the presence of BacH or BacR was determined stochastically from expert judgments and regional qPCR assay performance, using Beta distributions to represent uncertainties. A web-based computational tool was developed for the procedure, which provides a measure of confidence to findings of host-specific markers and demonstrates the information value from these assays. PMID:25545113

Fine Mapping for Identification of Citrus Alternaria Brown Spot Candidate Resistance Genes and Development of New SNP Markers for Marker-Assisted Selection

PubMed Central

Cuenca, Jose; Aleza, Pablo; Garcia-Lor, Andres; Ollitrault, Patrick; Navarro, Luis

2016-01-01

Alternaria brown spot (ABS) is a serious disease affecting susceptible citrus genotypes, which is a strong concern regarding citrus breeding programs. Resistance is conferred by a recessive locus (ABSr) previously located by our group within a 3.3 Mb genome region near the centromere in chromosome III. This work addresses fine-linkage mapping of this region for identifying candidate resistance genes and develops new molecular markers for ABS-resistance effective marker-assisted selection (MAS). Markers closely linked to ABSr locus were used for fine mapping using a 268-segregating diploid progeny derived from a heterozygous susceptible × resistant cross. Fine mapping limited the genomic region containing the ABSr resistance gene to 366 kb, flanked by markers at 0.4 and 0.7 cM. This region contains nine genes related to pathogen resistance. Among them, eight are resistance (R) gene homologs, with two of them harboring a serine/threonine protein kinase domain. These two genes along with a gene encoding a S-adenosyl-L-methionine-dependent-methyltransferase protein, should be considered as strong candidates for ABS-resistance. Moreover, the closest SNP was genotyped in 40 citrus varieties, revealing very high association with the resistant/susceptible phenotype. This new marker is currently used in our citrus breeding program for ABS-resistant parent and cultivar selection, at diploid, triploid and tetraploid level. PMID:28066498

Associations among Human-Associated Fecal Contamination, Microcystis aeruginosa, and Microcystin at Lake Erie Beaches.

PubMed

Lee, Cheonghoon; Marion, Jason W; Cheung, Melissa; Lee, Chang Soo; Lee, Jiyoung

2015-09-11

Lake Erie beaches exhibit impaired water quality due to fecal contamination and cyanobacterial blooms, though few studies address potential relationships between these two public health hazards. Using quantitative polymerase chain reaction (qPCR), Microcystis aeruginosa was monitored in conjunction with a human-associated fecal marker (Bacteroides fragilis group; g-Bfra), microcystin, and water quality parameters at two beaches to evaluate their potential associations. During the summer of 2010, water samples were collected 32 times from both Euclid and Villa Angela beaches. The phycocyanin intergenic spacer (PC-IGS) and the microcystin-producing (mcyA) gene in M. aeruginosa were quantified with qPCR. PC-IGS and mcyA were detected in 50.0% and 39.1% of samples, respectively, and showed increased occurrences after mid-August. Correlation and regression analyses showed that water temperature was negatively correlated with M. aeruginosa markers and microcystin. The densities of mcyA and the g-Bfra were predicted by nitrate, implicating fecal contamination as contributing to the growth of M. aeruginosa by nitrate loading. Microcystin was correlated with mcyA (r = 0.413, p < 0.01), suggesting toxin-producing M. aeruginosa populations may significantly contribute to microcystin production. Additionally, microcystin was correlated with total phosphorus (r = 0.628, p < 0.001), which was higher at Euclid (p < 0.05), possibly contributing to higher microcystin concentrations at Euclid.

Associations among Human-Associated Fecal Contamination, Microcystis aeruginosa, and Microcystin at Lake Erie Beaches

PubMed Central

Lee, Cheonghoon; Marion, Jason W.; Cheung, Melissa; Lee, Chang Soo; Lee, Jiyoung

2015-01-01

Lake Erie beaches exhibit impaired water quality due to fecal contamination and cyanobacterial blooms, though few studies address potential relationships between these two public health hazards. Using quantitative polymerase chain reaction (qPCR), Microcystis aeruginosa was monitored in conjunction with a human-associated fecal marker (Bacteroides fragilis group; g-Bfra), microcystin, and water quality parameters at two beaches to evaluate their potential associations. During the summer of 2010, water samples were collected 32 times from both Euclid and Villa Angela beaches. The phycocyanin intergenic spacer (PC-IGS) and the microcystin-producing (mcyA) gene in M. aeruginosa were quantified with qPCR. PC-IGS and mcyA were detected in 50.0% and 39.1% of samples, respectively, and showed increased occurrences after mid-August. Correlation and regression analyses showed that water temperature was negatively correlated with M. aeruginosa markers and microcystin. The densities of mcyA and the g-Bfra were predicted by nitrate, implicating fecal contamination as contributing to the growth of M. aeruginosa by nitrate loading. Microcystin was correlated with mcyA (r = 0.413, p < 0.01), suggesting toxin-producing M. aeruginosa populations may significantly contribute to microcystin production. Additionally, microcystin was correlated with total phosphorus (r = 0.628, p < 0.001), which was higher at Euclid (p < 0.05), possibly contributing to higher microcystin concentrations at Euclid. PMID:26378564

Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

PubMed Central

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

2012-01-01

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod. PMID:22428056

Comparison of Models and Whole-Genome Profiling Approaches for Genomic-Enabled Prediction of Septoria Tritici Blotch, Stagonospora Nodorum Blotch, and Tan Spot Resistance in Wheat.

PubMed

Juliana, Philomin; Singh, Ravi P; Singh, Pawan K; Crossa, Jose; Rutkoski, Jessica E; Poland, Jesse A; Bergstrom, Gary C; Sorrells, Mark E

2017-07-01

The leaf spotting diseases in wheat that include Septoria tritici blotch (STB) caused by , Stagonospora nodorum blotch (SNB) caused by , and tan spot (TS) caused by pose challenges to breeding programs in selecting for resistance. A promising approach that could enable selection prior to phenotyping is genomic selection that uses genome-wide markers to estimate breeding values (BVs) for quantitative traits. To evaluate this approach for seedling and/or adult plant resistance (APR) to STB, SNB, and TS, we compared the predictive ability of least-squares (LS) approach with genomic-enabled prediction models including genomic best linear unbiased predictor (GBLUP), Bayesian ridge regression (BRR), Bayes A (BA), Bayes B (BB), Bayes Cπ (BC), Bayesian least absolute shrinkage and selection operator (BL), and reproducing kernel Hilbert spaces markers (RKHS-M), a pedigree-based model (RKHS-P) and RKHS markers and pedigree (RKHS-MP). We observed that LS gave the lowest prediction accuracies and RKHS-MP, the highest. The genomic-enabled prediction models and RKHS-P gave similar accuracies. The increase in accuracy using genomic prediction models over LS was 48%. The mean genomic prediction accuracies were 0.45 for STB (APR), 0.55 for SNB (seedling), 0.66 for TS (seedling) and 0.48 for TS (APR). We also compared markers from two whole-genome profiling approaches: genotyping by sequencing (GBS) and diversity arrays technology sequencing (DArTseq) for prediction. While, GBS markers performed slightly better than DArTseq, combining markers from the two approaches did not improve accuracies. We conclude that implementing GS in breeding for these diseases would help to achieve higher accuracies and rapid gains from selection. Copyright © 2017 Crop Science Society of America.

Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers.

PubMed

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

2012-01-01

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.

RNA-Seq identifies SNP markers for growth traits in rainbow trout.

PubMed

Salem, Mohamed; Vallejo, Roger L; Leeds, Timothy D; Palti, Yniv; Liu, Sixin; Sabbagh, Annas; Rexroad, Caird E; Yao, Jianbo

2012-01-01

Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n = 54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker development in non-model species lacking complete and well-annotated genome reference sequences.

Reconstructing Contaminant Deposition in a San Francisco Bay Marina, California

PubMed Central

Love, Adam H.; Esser, Bradley K.; Hunt, James R.

2010-01-01

Two sediment cores were collected from a marina in the San Francisco Bay to characterize historical sediment contamination resulting from the direct discharge of industrial wastewater from Naval Air Station Alameda. Depth profiles of trace metals, petroleum hydrocarbons, and radionuclides were determined with a 12-cm spacing down to a depth of 120 cm. The chronology of sediment accumulation is established by depth profiles of sedimentary time markers in conjunction with information on site history. The traditional approach of determining sediment accumulation rates by measuring atmospheric 210Pb deposition was obscured by a larger source of 210Pb in the sediments from the decay of anthropogenic 226Ra, likely from luminescent paints used at this facility and released to the marina. The sedimentation rates inferred from the data indicate that the greatest amount of contamination by trace metals and petroleum hydrocarbons took place between 1940 and 1960. In addition, anthropogenic 226Ra activities are positively correlated with some of the contaminants in the sediments, allowing the wastewater discharged from the facility to be distinguished from baywide contamination. In locations such as this, where there is a complex history of contaminant deposition, a source-specific tracer may be the only feasible method of attributing historical contamination to a point source. PMID:20333267

Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus var. lanatus)

USDA-ARS?s Scientific Manuscript database

The inheritance of foreground stripe pattern in rind of watermelon fruits [Citrullus lanatus (Thunb.) Matsum. & Nakai] was evaluated and the molecular markers for selecting the JT stripe pattern were developed based on bulked segregant analysis (BSA). Divergence in rind pattern among F2 progeny deri...

Advances and Challenges in Genomic Selection for Disease Resistance.

PubMed

Poland, Jesse; Rutkoski, Jessica

2016-08-04

Breeding for disease resistance is a central focus of plant breeding programs, as any successful variety must have the complete package of high yield, disease resistance, agronomic performance, and end-use quality. With the need to accelerate the development of improved varieties, genomics-assisted breeding is becoming an important tool in breeding programs. With marker-assisted selection, there has been success in breeding for disease resistance; however, much of this work and research has focused on identifying, mapping, and selecting for major resistance genes that tend to be highly effective but vulnerable to breakdown with rapid changes in pathogen races. In contrast, breeding for minor-gene quantitative resistance tends to produce more durable varieties but is a more challenging breeding objective. As the genetic architecture of resistance shifts from single major R genes to a diffused architecture of many minor genes, the best approach for molecular breeding will shift from marker-assisted selection to genomic selection. Genomics-assisted breeding for quantitative resistance will therefore necessitate whole-genome prediction models and selection methodology as implemented for classical complex traits such as yield. Here, we examine multiple case studies testing whole-genome prediction models and genomic selection for disease resistance. In general, whole-genome models for disease resistance can produce prediction accuracy suitable for application in breeding. These models also largely outperform multiple linear regression as would be applied in marker-assisted selection. With the implementation of genomic selection for yield and other agronomic traits, whole-genome marker profiles will be available for the entire set of breeding lines, enabling genomic selection for disease at no additional direct cost. In this context, the scope of implementing genomics selection for disease resistance, and specifically for quantitative resistance and quarantined pathogens, becomes a tractable and powerful approach in breeding programs.

Endogenous enzyme activities and polyamine levels in diverse rice cultivars depend on the genetic background and are not affected by the presence of the hygromycin phosphotransferase selectable marker.

PubMed

Lepri, O.; Bassie, L.; Thu-Hang, P.; Christou, P.; Capell, T.

2002-09-01

We used the polyamine biosynthetic pathway and rice as a relevant model to understand the genetic basis of variation in endogenous levels of metabolites and key enzymes involved in the pathway. Wild-type tissues and also tissues containing a commonly used selectable marker gene were employed. We detected a wide variation in levels of arginine decarboxylase activity and in the three polyamines, putrescine, spermidine and spermine, in different tissues and varieties, but this was not dependent on the presence of the selectable marker. A more-extensive profile of enzyme activities (ADC, ODC, SAMDC, DAO and PAO) and polyamine levels in different tissues was generated in two different varieties. Our results indicate that genetic background is important in terms of the basal levels of metabolites and enzyme activity, particularly in situations in which we aim to engineer metabolic pathways that are also encoded by homologous endogenous genes. We did not find any evidence that the presence of a selectable marker in any way influences enzyme activity or metabolite levels.

Association of RGA-SSCP markers with resistance to downy mildew and anthracnose in grapevines.

PubMed

Tantasawat, P A; Poolsawat, O; Prajongjai, T; Chaowiset, W; Tharapreuksapong, A

2012-07-02

Downy mildew (Plasmopara viticola) and anthracnose (Sphaceloma ampelinum) are two major diseases that severely affect most grapevine (Vitis vinifera) cultivars grown commercially in Thailand. Progress of conventional breeding programs of grapevine for improved resistance to these diseases can be speeded up by selection of molecular markers associated with resistance traits. We evaluated the association between 13 resistance gene analog (RGA)-single-strand conformation polymorphism (SSCP) markers with resistance to downy mildew and anthracnose in 71 segregating progenies of seven cross combinations between susceptible cultivars and resistant lines. F(1) hybrids from each cross were assessed for resistance to downy mildew and anthracnose (isolates Nk4-1 and Rc2-1) under laboratory conditions. Association of resistance traits with RGA-SSCP markers was evaluated using simple linear regression analysis. Three RGA-SSCP markers were found to be significantly correlated with anthracnose resistance, whereas significant correlation with downy mildew resistance was observed for only one RGA-SSCP marker. These results demonstrate the usefulness of RGA-SSCP markers. Four candidate markers with significant associations to resistance to these two major diseases of grapevine were identified. However, these putative associations between markers and resistance need to be verified with larger segregating populations before they can be used for marker-assisted selection.

A family of LRR sequences in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris and its potential use in marker-assisted selection.

PubMed

Geffroy, V; Creusot, F; Falquet, J; Sévignac, M; Adam-Blondon, A F; Bannerot, H; Gepts, P; Dron, M

1998-03-01

Molecular markers offer new opportunities for breeding for disease resistance. Resistance gene pyramiding in a single cultivar, as a strategy for durable resistance, can be facilitated by marker-assisted selection (MAS). A RAPD marker, ROH20(450), linked to the Mesoamerican Co-2 anthracnose resistance gene, was previously transformed into a SCAR marker, SCH20. In the present paper we have further characterized the relevance of the SCH20 SCAR marker in different genetic backgrounds. Since this SCAR marker was found to be useful mainly in the Andean gene pool, we identified a new PCR-based marker (SCAreoli) for indirect scoring of the presence of the Co-2 gene. The SCAreoli SCAR marker is polymorphic in the Mesoamerican as well as in the Andean gene pool and should be useful in MAS. We also report that PvH20, the cloned sequence corresponding to the 450-bp RAPD marker ROH20(450), contains six imperfect leucine-rich repeats, and reveals a family of related sequences in the vicinity of the Co-2 locus. These results are discussed in the context of the recent cloning of some plant resistance genes.

Comparison of Spacecraft Contamination Models with Well-Defined Flight Experiment

NASA Technical Reports Server (NTRS)

Pippin, G. H.

1998-01-01

The report presents analyzed surface areas on particular experiment trays from the Long Duration Exposure Facility (LDEF) for silicone-based molecular contamination. The trays for examination were part of the Ultra-Heavy Cosmic Ray Experiment (UHCRE). These particular trays were chosen because each tray was identical to the others in construction, and the materials on each tray were well known, documented, and characterized. In particular, a known specific source of silicone contamination was present on each tray. Only the exposure conditions varied from tray to tray. The results of post-flight analyses of surfaces of three trays were compared with the predictions of the three different spacecraft molecular contamination models. Phase one tasks included: 1) documenting the detailed geometry of the hardware; 2) determining essential properties of the anodized aluminum, Velcro(Tm), silverized Teflon(Tm), silicone gaskets, and DC6-1104(Tm) silicone adhesive materials used to make the trays, tray covers, and thermal control blankets; 3) selecting and removing areas from each tray; and 4) beginning surface analysis of the selected tray walls. Phase two tasks included: 1) completion of surface analysis measurements of the selected tray surface, 2) obtaining auger depth profiles at selected locations, and 3) running versions of the ISEM, MOFLUX, and PLIMP (Plume Impingement) contamination prediction models and making comparisons with experimental results.

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents.

PubMed

Mayer, René E; Reischer, Georg H; Ixenmaier, Simone K; Derx, Julia; Blaschke, Alfred Paul; Ebdon, James E; Linke, Rita; Egle, Lukas; Ahmed, Warish; Blanch, Anicet R; Byamukama, Denis; Savill, Marion; Mushi, Douglas; Cristóbal, Héctor A; Edge, Thomas A; Schade, Margit A; Aslan, Asli; Brooks, Yolanda M; Sommer, Regina; Masago, Yoshifumi; Sato, Maria I; Taylor, Huw D; Rose, Joan B; Wuertz, Stefan; Shanks, Orin C; Piringer, Harald; Mach, Robert L; Savio, Domenico; Zessner, Matthias; Farnleitner, Andreas H

2018-05-01

Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750-4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log 10 7.2-8.0 marker equivalents (ME) 100 mL -1 ) and biologically treated wastewater samples (median log 10 4.6-6.0 ME 100 mL -1 ) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.

Genomic selection & association mapping in rice: effect of trait genetic architecture, training population composition, marker number & statistical model on accuracy of rice genomic selection in elite, tropical rice breeding

USDA-ARS?s Scientific Manuscript database

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 ef...

µ-Calpain (CAPN1), calpastatin (CAST), and growth hormone receptor (GHR) genetic effects on Angus beef heifer performance traits and reproduction

USDA-ARS?s Scientific Manuscript database

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to equalize CAPN1 haplotypes, CAST, and GHR genetic marker frequencies. The objective was t...

21 CFR 500.86 - Marker residue and target tissue.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Marker residue and target tissue. 500.86 Section...-Producing Animals § 500.86 Marker residue and target tissue. (a) For each edible tissue, the sponsor shall...) From these data, FDA will select a target tissue and a marker residue and designate the concentration...

21 CFR 500.86 - Marker residue and target tissue.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Marker residue and target tissue. 500.86 Section...-Producing Animals § 500.86 Marker residue and target tissue. (a) For each edible tissue, the sponsor shall...) From these data, FDA will select a target tissue and a marker residue and designate the concentration...

A framework linkage map of perennial ryegrass based on SSR markers

Treesearch

G.P. Gill; P.L. Wilcox; D.J. Whittaker; R.A. Winz; P. Bickerstaff; Craig E. Echt; J. Kent; M.O. Humphreys; K.M. Elborough; R.C. Gardner

2006-01-01

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third ( 124) of the SSR markers were developed from GeneThresher libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci...

[DNA marker-assisted selection of medicinal plants (Ⅰ) .Breeding research of disease-resistant cultivars of Panax notoginseng].

PubMed

Dong, Lin-Lin; Chen, Zhong-Jian; Wang, Yong; Wei, Fu-Gang; Zhang, Lian-Juan; Xu, Jiang; Wei, Guang-Fei; Wang, Rui; Yang, Juan; Liu, Wei-Lin; Li, Xi-Wen; Yu, Yu-Qi; Chen, Shi-Lin

2017-01-01

DNA marker-assisted selection of medicinal plants is based on the DNA polymorphism, selects the DNA sequences related to the phenotypes such as high yields, superior quality, stress-resistance and so on according to the technologies of molecular hybridization, polymerase chain reaction and high-throughput sequencing, and assists the breeding of new cultivars. This study bred the first disease-resistant cultivar of notoginseng "Miaoxiang Kangqi 1" using the technology of DNA marker-assisted selection of medicinal plants and systematic breeding. The disease-resistant cultivar of notoginseng contained 12 special SNPs based on the analysis of Restriction-site Associated DNA Sequencing (RAD-Seq). Among the SNP (record_519688) was related to the root rot-resistant characteristics, which indicated this SNP could serve as genetic markers of disease-resistant cultivars and assist the systematic breeding. Compared to the conventional cultivated cultivars, the incidence rate of root-rot and rust-rot in notoginseng seedlings decreased by 83.6% and 71.8%, respectively. The incidence rate of root-rot respectively declined by 43.6% and 62.9% in notoginseng cultivation for 2 and 3 years compared with those of the conventional cultivated cultivars. Additionally, the potential disease-resistant groups were screened based on the relative SNP, and this model enlarged the target groups and advanced the breeding efficiency. DNA marker-assisted selection of medicinal plants accelerated the breeding and promotion of new cultivars, and guaranteed the healthy development of Chinese medicinal materials industry. Copyright© by the Chinese Pharmaceutical Association.

Comparison of two freshwater turtle species as monitors of radionuclide and chemical contamination: DNA damage and residue analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyers-Schoene, L.; Shugart, L.R.; Beauchamp, J.J.

1993-08-01

Two species of turtles that occupy different ecological niches were compared for their usefulness as monitors of freshwater ecosystems where both low-level radioactive and nonradioactive contaminants are present. The pond slider (Trachemys scripta) and common snapping turtle (Chelydra serpentina) were analyzed for the presence of [sup 90]Sr, [sup 137]Cs, [sup 60]Co, and Hg, radionuclides and chemicals known to be present at the contaminated site, and single-strand breaks in liver DNA. The integrity of the DNA was examined by the alkaline unwinding assay, a technique that detects strand breaks as a biological marker of possible exposure to genotoxic agents. This measuremore » of DNA damage was significantly increased in both species of turtles at the contaminated site compared with turtles of the same species at a reference site, and shows that contaminant-exposed populations were under more severe genotoxic stress than those at the reference site. The level of strand breaks observed at the contaminated site was high and in the range reported for other aquatic species exposed to deleterious concentrations of genotoxic agents such as chemicals and ionizing radiation. Statistically significantly higher concentrations of radionuclides and Hg were detected in the turtles from the contaminated area. Mercury concentrations were significantly higher in the more carnivorous snapping turtle compared with the slider; however, both species were effective monitors of the contaminants.« less

INNOVATIVE PROCESSES FOR RECLAMATION OF CONTAMINATED SUBSURFACE ENVIRONMENTS

EPA Science Inventory

Research to better assess the capabilities and limitations of fixed-film bioreactors for removing selected organic contaminants from ground water or from contaminated vapor streams produced by air stripping of polluted ground water and by soil venting operations is described. ...

Screening and identification of a microsatellite marker associated with sex in Wami tilapia, Oreochromis urolepis hornorum.

PubMed

Zhu, Huaping; Liu, Zhigang; Lu, Maixin; Gao, Fengying; Ke, Xiaoli; Ma, Dongmei; Huang, Zhanghan; Cao, Jianmeng; Wang, Miao

2016-06-01

In this study, primer pairs of 15 microsatellite markers associated with sex determination of tilapia were selected and amplified in Wami tilapia, Oreochromis urolepis hornorum. While one marker, UNH168, on linkage group 3 (LG3) was associated (P <0.001) with the phenotypic sex in the experimental population, nine genotypes were detected in both sexes. Only 99-bp allele was detected in the female samples, while 141, 149 and 157-bp alleles were present in both male and female samples. UNH168 was localized by fluorescence in situ hybridization (FISH) on the long arm of the largest tilapia chromosome pair (chromosome 1, equivalent to LG3). This sex-linked microsatellite marker could potentially be used for marker-assisted selection in tilapia breeding programmes to produce monosex male tilapia.

Internal contamination in the space station

NASA Technical Reports Server (NTRS)

Poythress, C.

1985-01-01

Atmosphere trace contaminant control systems used in the past (Lunar Module and Skylab) and present (nuclear submarines and Shuttle) are discussed. Recommendations are made for the future Space Station contaminant control system. The prevention and control methods used are judicious material selection, detection, and specific removal equipment. Sources and effects of contamination relating to crew and equipment are also discussed.

CombiROC: an interactive web tool for selecting accurate marker combinations of omics data.

PubMed

Mazzara, Saveria; Rossi, Riccardo L; Grifantini, Renata; Donizetti, Simone; Abrignani, Sergio; Bombaci, Mauro

2017-03-30

Diagnostic accuracy can be improved considerably by combining multiple markers, whose performance in identifying diseased subjects is usually assessed via receiver operating characteristic (ROC) curves. The selection of multimarker signatures is a complicated process that requires integration of data signatures with sophisticated statistical methods. We developed a user-friendly tool, called CombiROC, to help researchers accurately determine optimal markers combinations from diverse omics methods. With CombiROC data from different domains, such as proteomics and transcriptomics, can be analyzed using sensitivity/specificity filters: the number of candidate marker panels rising from combinatorial analysis is easily optimized bypassing limitations imposed by the nature of different experimental approaches. Leaving to the user full control on initial selection stringency, CombiROC computes sensitivity and specificity for all markers combinations, performances of best combinations and ROC curves for automatic comparisons, all visualized in a graphic interface. CombiROC was designed without hard-coded thresholds, allowing a custom fit to each specific data: this dramatically reduces the computational burden and lowers the false negative rates given by fixed thresholds. The application was validated with published data, confirming the marker combination already originally described or even finding new ones. CombiROC is a novel tool for the scientific community freely available at http://CombiROC.eu.

Development of EST Intron-Targeting SNP Markers for Panax ginseng and Their Application to Cultivar Authentication.

PubMed

Wang, Hongtao; Li, Guisheng; Kwon, Woo-Saeng; Yang, Deok-Chun

2016-06-04

Panax ginseng is one of the most valuable medicinal plants in the Orient. The low level of genetic variation has limited the application of molecular markers for cultivar authentication and marker-assisted selection in cultivated ginseng. To exploit DNA polymorphism within ginseng cultivars, ginseng expressed sequence tags (ESTs) were searched against the potential intron polymorphism (PIP) database to predict the positions of introns. Intron-flanking primers were then designed in conserved exon regions and used to amplify across the more variable introns. Sequencing results showed that single nucleotide polymorphisms (SNPs), as well as indels, were detected in four EST-derived introns, and SNP markers specific to "Gopoong" and "K-1" were first reported in this study. Based on cultivar-specific SNP sites, allele-specific polymerase chain reaction (PCR) was conducted and proved to be effective for the authentication of ginseng cultivars. Additionally, the combination of a simple NaOH-Tris DNA isolation method and real-time allele-specific PCR assay enabled the high throughput selection of cultivars from ginseng fields. The established real-time allele-specific PCR assay should be applied to molecular authentication and marker assisted selection of P. ginseng cultivars, and the EST intron-targeting strategy will provide a potential approach for marker development in species without whole genomic DNA sequence information.

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

PubMed

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.

Molecular mapping and marker development for the Triticum dicoccoides-derived stripe rust resistance gene YrSM139-1B in bread wheat cv. Shaanmai 139.

PubMed

Zhang, Hong; Zhang, Lu; Wang, Changyou; Wang, Yajuan; Zhou, Xinli; Lv, Shikai; Liu, Xinlun; Kang, Zhensheng; Ji, Wanquan

2016-02-01

YrSM139-1B maybe a new gene for effective resistance to stripe rust and useful flanking markers for marker-assisted selection were developed. Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important foliar disease of wheat. Two dominant stripe rust resistant genes YrSM139-1B and YrSM139-2D were pyramided in bread wheat cultivar Shaanmai 139; one from wild emmer and the other from Thinopyrum intermedium. Three near-isogenic F7:8 line pairs (contrasting RILs), N122-1013R/S, N122-185R/S, and N122-1812R/S, independently derived from different F2 plants and differing at the YrSM139-1B locus were generated from the cross Shaanmai 139 × Hu 901-19 through marker-assisted selection. A large F2:3 population from cross N122-1013R × N122-1013S tested for stripe rust response and subjected to analysis with markers in the 1BS10-0.5 bin region using SSR expressed sequence tags (EST) and site-specific sequence markers developed from the 90 K Illumina iSelect SNP array. Five EST-STS markers and four allele-specific PCR markers were mapped to the YrSM139-1B region. The 30.5 cM genetic map for YrSM139-1B consisted of nine markers, two of which were closer to YrSM139-1B than Xgwm273, which was used in producing the contrasting RIL pairs. Race response data and allelism tests showed that YrSM139-1B is different from Yr10, Yr15, and Yr24/26/CH42.

Determination of microbial colonisation in water-damaged buildings using chemical marker analysis by gas chromatography-mass spectrometry.

PubMed

Szponar, B; Larsson, L

2000-03-01

Gas chromatography-mass spectrometry was used to determine the microbial contents of building materials subjected to water damage in a laboratory experiment and of materials collected from houses affected by water during the flood in Klodzko in south-western Poland, July 1997. The samples were examined for 3-hydroxy fatty acids, markers of bacterial endotoxin, and ergosterol, marker of fungal biomass. The amounts of both 3-hydroxy fatty acids and ergosterol were higher in materials that had been exposed to water than in unexposed ones. All markers were stable in the building materials for at least 6 weeks at room temperature and could thus be used to reveal microbial contamination even when cultivation results for bacteria and fungi were negative. Direct measurement of 3-hydroxy fatty acids and ergosterol in human environments could be a useful method, e.g. in monitoring indoor air as regards presence of potentially harmful microorganisms and microbial constituents.

Pathogenic bacteria and microbial-source tracking markers in Brandywine Creek Basin, Pennsylvania and Delaware, 2009-10

USGS Publications Warehouse

Duris, Joseph W.; Reif, Andrew G.; Olson, Leif E.; Johnson, Heather E.

2011-01-01

The City of Wilmington, Delaware, is in the downstream part of the Brandywine Creek Basin, on the main stem of Brandywine Creek. Wilmington uses this stream, which drains a mixed-land-use area upstream, for its main drinking-water supply. Because the stream is used for drinking water, Wilmington is in need of information about the occurrence and distribution of specific fecally derived pathogenic bacteria (disease-causing bacteria) and their relations to commonly measured fecal-indicator bacteria (FIB), as well as information regarding the potential sources of the fecal pollution and pathogens in the basin. This study focused on five routinely sampled sites within the basin, one each on the West Branch and the East Branch of Brandywine Creek and at three on the main stem below the confluence of the West and East Branches. These sites were sampled monthly for 1 year. Targeted event samples were collected on two occasions during high flow and two occasions during normal flow. On the basis of this study, high flows in the Brandywine Creek Basin were related to increases in FIB densities, and in the frequency of selected pathogen and source markers, in the West Branch and main stem of Brandywine Creek, but not in the East Branch. Water exceeding the moderate fullbody-contact single-sample recreational water-quality criteria (RWQC) for Escherichia coli (E. coli) was more likely to contain selected markers for pathogenic E. coli (eaeA,stx1, and rfbO157 gene markers) and bovine fecal sources (E. hirae and LTIIa gene markers), whereas samples exceeding the enterococci RWQC were more likely to contain the same pathogenic markers but also were more likely to carry a marker indicative of human source (esp gene marker). On four sample dates, during high flow between October and March, the West Branch was the only observed potential contributor of selected pathogen and bovine source markers to the main stem of Brandywine Creek. Indeed, the stx2 marker, which indicates a highly virulent type of pathogenic E. coli, was found only in the West Branch and main stem at high flow but was not found in the East Branch under similar conditions. However, it must be noted that throughout the entire year of sampling there were occasions, during both high and normal flows, when both the East and West Branches were potential contributors of pathogen and microbial-source tracking markers to the main stem. Therefore, this study indicates that under selected conditions (high flow, October through March), West Branch Brandywine Creek Basin was the most likely source of elevated FIB densities in the main stem. These elevated densities are associated with more frequent detection of selected pathogenic E. coli markers (rfbO157 stx1) and are associated with MST markers of bovine source. However, during other times of the year, both the West Branch and East Branch Basins are acting as potential sources of FIB and fecally derived pathogens.

A 48 SNP set for grapevine cultivar identification

PubMed Central

2011-01-01

Background Rapid and consistent genotyping is an important requirement for cultivar identification in many crop species. Among them grapevine cultivars have been the subject of multiple studies given the large number of synonyms and homonyms generated during many centuries of vegetative multiplication and exchange. Simple sequence repeat (SSR) markers have been preferred until now because of their high level of polymorphism, their codominant nature and their high profile repeatability. However, the rapid application of partial or complete genome sequencing approaches is identifying thousands of single nucleotide polymorphisms (SNP) that can be very useful for such purposes. Although SNP markers are bi-allelic, and therefore not as polymorphic as microsatellites, the high number of loci that can be multiplexed and the possibilities of automation as well as their highly repeatable results under any analytical procedure make them the future markers of choice for any type of genetic identification. Results We analyzed over 300 SNP in the genome of grapevine using a re-sequencing strategy in a selection of 11 genotypes. Among the identified polymorphisms, we selected 48 SNP spread across all grapevine chromosomes with allele frequencies balanced enough as to provide sufficient information content for genetic identification in grapevine allowing for good genotyping success rate. Marker stability was tested in repeated analyses of a selected group of cultivars obtained worldwide to demonstrate their usefulness in genetic identification. Conclusions We have selected a set of 48 stable SNP markers with a high discrimination power and a uniform genome distribution (2-3 markers/chromosome), which is proposed as a standard set for grapevine (Vitis vinifera L.) genotyping. Any previous problems derived from microsatellite allele confusion between labs or the need to run reference cultivars to identify allele sizes disappear using this type of marker. Furthermore, because SNP markers are bi-allelic, allele identification and genotype naming are extremely simple and genotypes obtained with different equipments and by different laboratories are always fully comparable. PMID:22060012

Systems and strippable coatings for decontaminating structures that include porous material

DOEpatents

Fox, Robert V [Idaho Falls, ID; Avci, Recep [Bozeman, MT; Groenewold, Gary S [Idaho Falls, ID

2011-12-06

Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.

Human-associated fecal qPCR measurements and predicted risk of gastrointestinal illness in recreational waters contaminated with raw sewage

EPA Science Inventory

We used quantitative microbial risk assessment (QMRA) to estimate the risk of gastrointestinal (GI) illness associated with swimming in recreational waters containing different concentrations of human-associated fecal qPCR markers from raw sewage– HF183 and HumM2. The volume/volu...

Microbial Source Tracking Markers for Detection of Fecal Contamination in Environmental Waters: Relationships Between Pathogens and Human Health Outcomes

EPA Science Inventory

Microbial source tracking (MST) describes a suite of methods and an investigative strategy designed to identify the dominant sources of fecal pollution in environmental waters. The methods rely on the close association of certain fecal microorganisms with a particular host speci...

DEVELOPMENT OF HOST-SPECIFIC METAGENOMIC MARKERS FOR MICROBIAL SOURCE TRACKING USING A NOVEL METAGENOMIC APPROACH

EPA Science Inventory

Fecal contamination of source water has always been an important issue to the drinking water industry. Improper disposal of animal waste, leaky septic tanks, storm runoff, and the abundance of wildlife in natural water systems can all be responsible for the spread of enteric path...

Efficacy of chemical sprays to eliminate inoculated Salmonella from defeathered broiler breast skin

USDA-ARS?s Scientific Manuscript database

Contamination of poultry with Salmonella is a food safety concern. Because Salmonella-free broilers cannot always be produced on the farm, antimicrobials are used in the processing plant. The objective of this study was to look at the efficacy of several chemicals to eliminate 104 cells of a marker...

New approach to the determination of contaminants of emerging concern in natural water: study of alprazolam employing adsorptive cathodic stripping voltammetry.

PubMed

Nunes, Chalder Nogueira; Pauluk, Lucas Ely; Dos Anjos, Vanessa Egéa; Lopes, Mauro Chierici; Quináia, Sueli Pércio

2015-08-01

Contaminants of emerging concern (CECs) are chemicals, including pharmaceutical and personal care products, not commonly monitored in the aquatic environment. Pharmaceuticals are nowadays considered as an important environmental contaminant. Chromatography methods which require expensive equipment and complicated sample pretreatment are used for detection of CECs in natural water. Thus, in this study we proposed a simple, fast, and low-cost voltammetric method as a screening tool for the determination of CECs in natural water prior to chromatography. A case study was conducted with alprazolam (benzodiazepine). The method was optimized and validated in-house. The limit of quantification was 0.4 μg L(-1) for a 120 s preconcentration time. The recoveries ranged from 93 to 120 % for accuracy tests. A further proposal aim was to determine for the first time the occurrence of alprazolam in Brazilian river water and to evaluate its potential use as a marker of contamination by wastewater.

Anaerobic microbial dehalogenation and its key players in the contaminated Bitterfeld-Wolfen megasite.

PubMed

Nijenhuis, Ivonne; Stollberg, Reiner; Lechner, Ute

2018-04-01

The megasite Bitterfeld-Wolfen is highly contaminated as a result of accidents and because of dumping of wastes from local chemical industries in the last century. A variety of contaminants including chlorinated ethenes and benzenes, hexachlorohexanes and chlorinated dioxins can still be found in the groundwater and (river) sediments. Investigations of the in situ microbial transformation of organohalides have been performed only over the last two decades at this megasite. In this review, we summarise the research on the activity of anaerobic dehalogenating bacteria at the field site in Bitterfeld-Wolfen, focusing on chlorinated ethenes, monochlorobenzene and chlorinated dioxins. Various methods and concepts were applied including ex situ cultivation and isolation, and in situ analysis of hydrochemical parameters, compound-specific stable isotope analysis of contaminants, 13C-tracer studies and molecular markers. Overall, biotransformation of organohalides is ongoing at the field site and Dehalococcoides mccartyi species play an important role in the detoxification process in the Bitterfeld-Wolfen region.

Influence of fly ash aided phytostabilisation of Pb, Cd and Zn highly contaminated soils on Lolium perenne and Trifolium repens metal transfer and physiological stress.

PubMed

Lopareva-Pohu, Alena; Verdin, Anthony; Garçon, Guillaume; Lounès-Hadj Sahraoui, Anissa; Pourrut, Bertrand; Debiane, Djouher; Waterlot, Christophe; Laruelle, Frédéric; Bidar, Géraldine; Douay, Francis; Shirali, Pirouz

2011-06-01

Due to anthropogenic activities, large extends of soils are highly contaminated by Metal Trace Element (MTE). Aided phytostabilisation aims to establish a vegetation cover in order to promote in situ immobilisation of trace elements by combining the use of metal-tolerant plants and inexpensive mineral or organic soil amendments. Eight years after Coal Fly Ash (CFA) soil amendment, MTE bioavailability and uptake by two plants, Lolium perenne and Trifolium repens, were evaluated, as some biological markers reflecting physiological stress. Results showed that the two plant species under study were suitable to reduce the mobility and the availability of these elements. Moreover, the plant growth was better on CFA amended MTE-contaminated soils, and the plant sensitivity to MTE-induced physiological stress, as studied through photosynthetic pigment contents and oxidative damage was lower or similar. In conclusion, these results supported the usefulness of aided phytostabilisation of MTE-highly contaminated soils. Copyright © 2011 Elsevier Ltd. All rights reserved.

In vitro pyrogen test for toxic or immunomodulatory drugs.

PubMed

Daneshian, Mardas; Guenther, Armin; Wendel, Albrecht; Hartung, Thomas; von Aulock, Sonja

2006-06-30

Pyrogenic contaminations of some classes of injectable drugs, e.g. toxic or immunomodulatory as well as false-positive drugs, represent a major risk which cannot yet be excluded due to the limitations of current tests. Here we describe a modification of the In vitro Pyrogen Test termed AWIPT (Adsorb, Wash, In vitro Pyrogen Test), which addresses this problem by introducing a pre-incubation step in which pyrogenic contaminations in the test sample are adsorbed to albumin-coated beads. After rinsing, the beads are incubated with human whole blood and the release of the endogenous pyrogen interleukin-1beta is measured as a marker of pyrogenic activity. Intentional contaminations with lipopolysaccharide were retrieved from the chemotherapeutic agents paclitaxel, cisplatin and liposomal daunorubicin, the antibiotic gentamicin, the antifungal agent liposomal amphotericin B, and the corticosteroid prednisolone at lower dilutions than in the standard in vitro pyrogen test. This represents a promising new approach for the detection of pyrogenic contamination in drugs or in drugs containing interfering additives and should lead to improved safety levels.

Hydrocarbons in sediments along a tropical estuary-shelf transition area: Sources and spatial distribution.

PubMed

Maciel, Daniele Claudino; de Souza, José Roberto Botelho; Taniguchi, Satie; Bícego, Márcia Caruso; Schettini, Carlos Augusto França; Zanardi-Lamardo, Eliete

2016-12-15

Estuaries generally act as sediment traps and may retain a range of contaminants associated to this matrix. Aliphatic hydrocarbons (AHs) were investigated in Capibaribe Estuarine System and adjacent shelf, Northeast of Brazil, to evaluate the contamination and to better understand its functionality related to the coast. Fourteen sediment samples were analyzed, using gas chromatography with flame ionization detection. Total AHs concentrations ranged from 7.5 to 190.3μgg -1 and n-alkanes ranged from below detection limit (

FINE-SCALE GENETIC DIFFERENTIATION BETWEEN CONTAMINANT-TOLERANT AND CONTAMINANT SENSITIVE FISH POPULATIONS

EPA Science Inventory

Studies have suggested that environmental contaminants can act as selective forces on exposed populations of wildlife species. Chronically exposed populations have shown reduced genetic diversity and/or demonstrated other genetic changes. We evaluated the genetic structure of pop...

Construction, Characterization, and Preliminary BAC-End Sequence Analysis of a Bacterial Artificial Chromosome Library of the Tea Plant (Camellia sinensis)

PubMed Central

Lin, Jinke; Kudrna, Dave; Wing, Rod A.

2011-01-01

We describe the construction and characterization of a publicly available BAC library for the tea plant, Camellia sinensis. Using modified methods, the library was constructed with the aim of developing public molecular resources to advance tea plant genomics research. The library consists of a total of 401,280 clones with an average insert size of 135 kb, providing an approximate coverage of 13.5 haploid genome equivalents. No empty vector clones were observed in a random sampling of 576 BAC clones. Further analysis of 182 BAC-end sequences from randomly selected clones revealed a GC content of 40.35% and low chloroplast and mitochondrial contamination. Repetitive sequence analyses indicated that LTR retrotransposons were the most predominant sequence class (86.93%–87.24%), followed by DNA retrotransposons (11.16%–11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers. PMID:21234344

Microsatellite diversity of isolates of the parasitic nematode Haemonchus contortus.

PubMed

Otsen, M; Plas, M E; Lenstra, J A; Roos, M H; Hoekstra, R

2000-09-01

The alarming development of anthelmintic resistance in important gastrointestinal nematode parasites of man and live-stock is caused by selection for specific genotypes. In order to provide genetic tools to study the nematode populations and the consequences of anthelmintic treatment, we isolated and sequenced 59 microsatellites of the sheep and goat parasite Haemonchus contortus. These microsatellites consist typically of 2-10 tandems CA/GT repeats that are interrupted by sequences of 1-10 bp. A predominant cause of the imperfect structure of the microsatellites appeared mutations of G/C bp in the tandem repeat. About 44% of the microsatellites were associated with the HcREP1 direct repeat, and it was demonstrated that a generic HcREP1 primer could be used to amplify HcREP1-associated microsatellites. Thirty microsatellites could be typed by polymerase chain reaction (PCR) of which 27 were polymorphic. A number of these markers were used to detect genetic contamination of an experimental inbred population. The microsatellites may also contribute to the genetic mapping of drug resistance genes.

Small serine recombination systems ParA-MRS and CinH-RS2 perform precise excision of plastid DNA

USDA-ARS?s Scientific Manuscript database

Selectable marker genes (SMGs) are necessary for selection of transgenic plants. However, once stable transformants have been identified, the marker gene is no longer needed. In this study, we demonstrate the use of the small serine recombination systems, ParA-MRS and CinH-RS2, to precisely excise ...

Development of next-generation mapping populations: Multi-parent Advanced Generation Inter-Cross (MAGIC) and Marker-Assisted Recurrent Selection (MARS) populations in peanut

USDA-ARS?s Scientific Manuscript database

Generation Inter-Cross (MAGIC) and Marker-Assisted Recurrent Selection (MARS) have been proposed and used in many crops to dissect complex traits or QTL. MAGIC allows for dissecting genomic structure, and for improving breeding populations by integrating multiple alleles from different parents. MAR...

Accuracy and training population design for genomic selection in elite north american oats

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) is a method to estimate the breeding values of individuals by using markers throughout the genome. We evaluated the accuracies of GS using data from five traits on 446 oat lines genotyped with 1005 Diversity Array Technology (DArT) markers and two GS methods (RR-BLUP and Bayes...

Adverse effects of salivary contamination for adhesives in restorative dentistry. A literature review.

PubMed

Nair, Pooja; Hickel, Reinhard; Ilie, Nicoleta

2017-06-01

To review and critically analyze the literature concerning the influence of salivary contamination on the bond quality of adhesives used in restorative materials by comparing and contrasting the different adhesive materials. A detailed search on PUBMED, Cochrane Library, Google Scholar and Web of Science was carried out to identify publications on salivary contamination and dental adhesive materials, from 1990-2017 (March) which resulted in a total of 6,202 web-identified publications. After screening titles/abstracts and de-duplicating, 54 publications were selected that matched the requirements for this review. The condition for selection was English literature concerning the effect of salivary contamination on the adhesives used in restorative dentistry. The obtained articles were systematically evaluated. Salivary contamination of adhesives during restorative procedures statistically (64.6%) showed an adverse effect on adhesives, occurring either at one or many stages of restoration. Methodological dissimilarities impeded the direct comparison of the selected studies. Nevertheless, the 2-step etch and rinse adhesives were relatively less vulnerable to salivary contamination than the others. 65% of the evaluated studies for decontamination achieved improved bonding when the contaminated surface was subjected to some kind of decontamination procedure. However, the duration and other specificities were not standard in all the evaluations and need further research to assess the course of action. It is necessary to do long term studies to evaluate the effectiveness of contaminated adhesive over time. Salivary contamination is a potential cause for poor bond quality of adhesive systems during restorative procedures and to provide a successful treatment, proper care must be taken to ensure the operating area is free from contamination. Understanding the properties of the materials and its constituents as well as considering measures to manage the potential vulnerabilities due to salivary contamination in the area of bonding might help a clinician to produce better results.

Single nucleotide polymorphisms from Theobroma cacao expressed sequence tags associated with witches' broom disease in cacao.

PubMed

Lima, L S; Gramacho, K P; Carels, N; Novais, R; Gaiotto, F A; Lopes, U V; Gesteira, A S; Zaidan, H A; Cascardo, J C M; Pires, J L; Micheli, F

2009-07-14

In order to increase the efficiency of cacao tree resistance to witches' broom disease, which is caused by Moniliophthora perniciosa (Tricholomataceae), we looked for molecular markers that could help in the selection of resistant cacao genotypes. Among the different markers useful for developing marker-assisted selection, single nucleotide polymorphisms (SNPs) constitute the most common type of sequence difference between alleles and can be easily detected by in silico analysis from expressed sequence tag libraries. We report the first detection and analysis of SNPs from cacao-M. perniciosa interaction expressed sequence tags, using bioinformatics. Selection based on analysis of these SNPs should be useful for developing cacao varieties resistant to this devastating disease.

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

PubMed Central

Bartkiewicz, Annette M.; Chilla, Friederike; Terefe-Ayana, Diro; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Linde, Marcus; Debener, Thomas

2018-01-01

Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP) array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL) for four phenotypic traits. PMID:29868076

Fish health and environmental health.

PubMed Central

Murchelano, R A

1990-01-01

Surveys conducted to evaluate the health of marine-bottom fishes have been conducted in the eastern and western North Atlantic for the past 15 years, usually in conjunction with fish stock assessment cruises. The health of the fish sampled was evaluated using certain integumental and skeletal lesions and anomalies as markers to signify compromised health status. The results of these surveys indicate that fish health is poorer in coastal waters that have been anthropogenically degraded. Monitoring programs to determine the status and trends in levels of inorganic and organic contaminants in fish tissue and sediments have disclosed high levels of chemical contaminants in several coastal areas of the northeastern United States. Histopathological examinations of liver tissues of winter flounder, Pseudopleuronectes americanus, from Boston Harbor, one of the more chemically contaminated sites, has revealed a high prevalence of hepatocarcinoma. PMID:2401261

[Production of marker-free plants expressing the gene of the hepatitis B virus surface antigen].

PubMed

Rukavtsova, E B; Gaiazova, A R; Chebotareva, E N; Bur'ianova, Ia I

2009-08-01

The pBM plasmid, carrying the gene of hepatitis B virus surface antigen (HBsAg) and free of any selection markers of antibiotic or herbicide resistance, was constructed for genetic transformation of plants. A method for screening transformed plant seedlings on nonselective media was developed. Enzyme immunoassay was used for selecting transgenic plants with HBsAg gene among the produced regenerants; this method provides for a high sensitivity detection of HBsAg in plant extracts. Tobacco and tomato transgenic lines synthesizing this antigen at a level of 0.01-0.05% of the total soluble protein were obtained. The achieved level of HBsAg synthesis is sufficient for preclinical trials of the produced plants as a new generation safe edible vaccine. The developed method for selecting transformants can be used for producing safe plants free of selection markers.

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

USGS Publications Warehouse

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.

Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs.

PubMed

Morin, Alexander M; Gatev, Evan; McEwen, Lisa M; MacIsaac, Julia L; Lin, David T S; Koen, Nastassja; Czamara, Darina; Räikkönen, Katri; Zar, Heather J; Koenen, Karestan; Stein, Dan J; Kobor, Michael S; Jones, Meaghan J

2017-01-01

Cord blood is a commonly used tissue in environmental, genetic, and epigenetic population studies due to its ready availability and potential to inform on a sensitive period of human development. However, the introduction of maternal blood during labor or cross-contamination during sample collection may complicate downstream analyses. After discovering maternal contamination of cord blood in a cohort study of 150 neonates using Illumina 450K DNA methylation (DNAm) data, we used a combination of linear regression and random forest machine learning to create a DNAm-based screening method. We identified a panel of DNAm sites that could discriminate between contaminated and non-contaminated samples, then designed pyrosequencing assays to pre-screen DNA prior to being assayed on an array. Maternal contamination of cord blood was initially identified by unusual X chromosome DNA methylation patterns in 17 males. We utilized our DNAm panel to detect contaminated male samples and a proportional amount of female samples in the same cohort. We validated our DNAm screening method on an additional 189 sample cohort using both pyrosequencing and DNAm arrays, as well as 9 publically available cord blood 450K data sets. The rate of contamination varied from 0 to 10% within these studies, likely related to collection specific methods. Maternal blood can contaminate cord blood during sample collection at appreciable levels across multiple studies. We have identified a panel of markers that can be used to identify this contamination, either post hoc after DNAm arrays have been completed, or in advance using a targeted technique like pyrosequencing.

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

PubMed Central

Li, Y. H.; Chu, H. P.; Jiang, Y. N.; Lin, C. Y.; Li, S. H.; Li, K. T.; Weng, G. J.; Cheng, C. C.; Lu, D. J.; Ju, Y. T.

2014-01-01

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 is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations. PMID:25049996

Development of novel low-copy nuclear markers for Hieraciinae (Asteraceae) and their perspective for other tribes.

PubMed

Krak, Karol; Alvarez, Inés; Caklová, Petra; Costa, Andrea; Chrtek, Jindrich; Fehrer, Judith

2012-02-01

The development of three low-copy nuclear markers for low taxonomic level phylogenies in Asteraceae with emphasis on the subtribe Hieraciinae is reported. Marker candidates were selected by comparing a Lactuca complementary DNA (cDNA) library with public DNA sequence databases. Interspecific variation and phylogenetic signal of the selected genes were investigated for diploid taxa from the subtribe Hieraciinae and compared to a reference phylogeny. Their ability to cross-amplify was assessed for other Asteraceae tribes. All three markers had higher variation (2.1-4.5 times) than the internal transcribed spacer (ITS) in Hieraciinae. Cross-amplification was successful in at least seven other tribes of the Asteraceae. Only three cases indicating the presence of paralogs or pseudogenes were detected. The results demonstrate the potential of these markers for phylogeny reconstruction in the Hieraciinae as well as in other Asteraceae tribes, especially for very closely related species.

Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.).

PubMed

Robarts, Daniel W H; Wolfe, Andrea D

2014-07-01

In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.

Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

PubMed Central

Robarts, Daniel W. H.; Wolfe, Andrea D.

2014-01-01

In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

Detection of aflatoxin and surface mould contaminated figs by using Fourier transform near-infrared reflectance spectroscopy.

PubMed

Durmuş, Efkan; Güneş, Ali; Kalkan, Habil

2017-01-01

Aflatoxins are toxic metabolites that are mainly produced by members of the Aspergillus section Flavi on many agricultural products. Certain agricultural products such as figs are known to be high risk products for aflatoxin contamination. Aflatoxin contaminated figs may show a bright greenish yellow fluorescence (BGYF) under ultraviolet (UV) light at a wavelength of 365 nm. Traditionally, BGYF positive figs are manually selected by workers. However, manual selection depends on the expertise level of the workers and it may cause them skin-related health problems due to UV radiation. In this study, we propose a non-invasive approach to detect aflatoxin and surface mould contaminated figs by using Fourier transform near-infrared (FT-NIR) reflectance spectroscopy. A classification accuracy of 100% is achieved for classifying the figs into aflatoxin contaminated/uncontaminated and surface mould contaminated/uncontaminated categories. In addition, a strong correlation has been found between aflatoxin and surface mould. Combined with pattern classification methods, the NIR spectroscopy can be used to detect aflatoxin contaminated figs non-invasively. Furthermore, a positive correlation between surface mould and aflatoxin contamination leads to a promising alternative indicator for the detection of aflatoxin-contaminated figs. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California.

PubMed

Steele, Joshua A; Blackwood, A Denene; Griffith, John F; Noble, Rachel T; Schiff, Kenneth C

2018-06-01

Along southern California beaches, the concentrations of fecal indicator bacteria (FIB) used to quantify the potential presence of fecal contamination in coastal recreational waters have been previously documented to be higher during wet weather conditions (typically winter or spring) than those observed during summer dry weather conditions. FIB are used for management of recreational waters because measurement of the bacterial and viral pathogens that are the potential causes of illness in beachgoers exposed to stormwater can be expensive, time-consuming, and technically difficult. Here, we use droplet digital Polymerase Chain Reaction (digital PCR) and digital reverse transcriptase PCR (digital RT-PCR) assays for direct quantification of pathogenic viruses, pathogenic bacteria, and source-specific markers of fecal contamination in the stormwater discharges. We applied these assays across multiple storm events from two different watersheds that discharge to popular surfing beaches in San Diego, CA. Stormwater discharges had higher FIB concentrations as compared to proximal beaches, often by ten-fold or more during wet weather. Multiple lines of evidence indicated that the stormwater discharges contained human fecal contamination, despite the presence of separate storm sewer and sanitary sewer systems in both watersheds. Human fecal source markers (up to 100% of samples, 20-12440 HF183 copies per 100 ml) and human norovirus (up to 96% of samples, 25-495 NoV copies per 100 ml) were routinely detected in stormwater discharge samples. Potential bacterial pathogens were also detected and quantified: Campylobacter spp. (up to 100% of samples, 16-504 gene copies per 100 ml) and Salmonella (up to 25% of samples, 6-86 gene copies per 100 ml). Other viral human pathogens were also measured, but occurred at generally lower concentrations: adenovirus (detected in up to 22% of samples, 14-41 AdV copies per 100 ml); no enterovirus was detected in any stormwater discharge sample. Higher concentrations of avian source markers were noted in the stormwater discharge located immediately downstream of a large bird sanctuary along with increased Campylobacter concentrations and notably different Campylobacter species composition than the watershed that had no bird sanctuary. This study is one of the few to directly measure an array of important bacterial and viral pathogens in stormwater discharges to recreational beaches, and provides context for stormwater-based management of beaches during high risk wet-weather periods. Furthermore, the combination of culture-based and digital PCR-derived data is demonstrated to be valuable for assessing hydrographic relationships, considering delivery mechanisms, and providing foundational exposure information for risk assessment. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed

Clevenger, Josh; Chu, Ye; Chavarro, Carolina; Botton, Stephanie; Culbreath, Albert; Isleib, Thomas G; Holbrook, C C; Ozias-Akins, Peggy

2018-01-01

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.

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

PubMed Central

Clevenger, Josh; Chu, Ye; Chavarro, Carolina; Botton, Stephanie; Culbreath, Albert; Isleib, Thomas G.; Holbrook, C. C.; Ozias-Akins, Peggy

2018-01-01

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. PMID:29459876

On prediction of genetic values in marker-assisted selection.

PubMed Central

Lange, C; Whittaker, J C

2001-01-01

We suggest a new approximation for the prediction of genetic values in marker-assisted selection. The new approximation is compared to the standard approach. It is shown that the new approach will often provide substantially better prediction of genetic values; furthermore the new approximation avoids some of the known statistical problems of the standard approach. The advantages of the new approach are illustrated by a simulation study in which the new approximation outperforms both the standard approach and phenotypic selection. PMID:11729177

Selection of recombinant MVA by rescue of the essential D4R gene.

PubMed

Ricci, Patricia S; Schäfer, Birgit; Kreil, Thomas R; Falkner, Falko G; Holzer, Georg W

2011-12-12

Modified vaccinia virus Ankara (MVA) has become a promising vaccine vector due to its immunogenicity and its proven safety in humans. As a general approach for stringent and rapid selection of recombinant MVA, we assessed marker rescue of the essential viral D4R gene in an engineered deletion mutant that is fully replication defective in wild-type cells. Recombinant, replicating virus was obtained by re-introduction of the deleted viral gene as a dominant selection marker into the deletion mutant.

Contamination of grazing incidence EUV mirrors - An assessment

NASA Technical Reports Server (NTRS)

Osantowski, John F.; Fleetwood, C. F.

1988-01-01

Contamination assessment for space optical systems requires an understanding of the sensitivity of component performance, e.g. mirror reflectance, to materials deposited on the mirror surface. In a previous study, the sensitivity of typical normal incidence mirror coatings to surface deposits of generic hydrocarbons was reported. Recent activity in the development of grazing incidence telescopes for extreme ultraviolet space astronomy has stimulated the need for a similar assessment in the spectral region extending from approximately 100 A to 1000 A. The model used for analysis treats the contamination layer as a continuous thin film deposited on the mirror surface. The mirror surfaces selected for this study are opaque vacuum deposited gold and the uncoated and polished Zerodur. Scatter caused by film irregularities or particulates are not included in this assessment. Parametric evaluations at 100, 500, and 1000 A determine the sensitivity of mirror reflectance to a range of optical constants selected for the generic contaminants. This sensitivity analysis combined with the limited amount of optical data in the EUV for hydrocarbons, is used to select representative optical constants for the three wavelength regions. Reflectance versus contamination layer thickness curves are then calculated and used to determine critical thickness limits based on allowable reflectance change. Initial observations indicate that thickness limits will be highly dependent on the real part of the complex index of refraction of the contaminant film being less than 1.0. Preliminary laboratory measurements of samples contaminated with some commonly encountered hydrocarbons confirm trends indicated in the analytical studies.

Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean

PubMed Central

Galeano, Carlos H.; Fernandez, Andrea C.; Franco-Herrera, Natalia; Cichy, Karen A.; McClean, Phillip E.; Vanderleyden, Jos; Blair, Matthew W.

2011-01-01

Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364×G19833 (DG) and BAT93×JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning. PMID:22174773

An overview of the on-orbit contamination of the Long Duration Exposure Facility (LDEF)

NASA Technical Reports Server (NTRS)

Stuckey, W. K.

1993-01-01

Contamination that leads to degradation of critical surfaces becomes a vital design issue for many spacecraft programs. One of the processes that must be considered is the on-orbit accumulation of contaminants. The Long Duration Exposure Facility (LDEF) has presented an opportunity to examine the deposits on surfaces returned from orbit in order to help in understanding the deposition processes and the current models used to predict spacecraft contamination levels. The results from various investigators on the contamination of LDEF have implications for material selection, contamination models, and contamination control plans for the design of future spacecraft.

RAPD-SCAR Markers for Genetically Improved NEW GIFT Nile Tilapia (Oreochromis niloticus niloticus L.) and Their Application in Strain Identification.

PubMed

Li, Si-Fa; Tang, Shou-Jie; Cai, Wan-Qi

2010-04-01

The NEW GIFT Nile tilapia (Oreochromis niloticus niloticus L.) is a nationally certificated new strain selected over 14 years and 9 generations from the base strain of GIFT Nile tilapia, introduced in 1994. This new variety has been extended in most of areas of China. The management of genetically improved strains, including the genetic markers for identification is needed urgently. RAPD analysis was conducted and their conversion to SCAR markers was developed. From NEW GIFT Nile tilapia, two strain-specific RAPD bands, S(304 )(624 bp ) and S(36 )(568 bp ) were identified. The strain-specific RAPD bands were gel-purified, cloned, and sequenced. Locus-specific primers were then designed to amplify the strain-specific bands. PCR amplification was conducted to test the variations in allele frequencies of two converted SCAR markers among the NEW GIFT Nile tilapia and its base strains, as well as 7 additional farmed strains worldwide. The frequency of SCAR marker I (553 bp) was 85.7% in NEW GIFT Nile tilapia, but 16.7% in the base strain. The frequency of SCAR marker II (558 bp) was 91.4% in NEW GIFT Nile tilapia, but 0% - 70% in the 7 other strains. In order to confirm the utility of these two markers, an examination was conducted for a wild population from Egypt, resulted the frequency of SCAR I and II was 10% and 70%, respectively, much lower than that of New GIFT strain. The increase in allele frequency of these two SCAR markers suggests that these markers might be genetically linked to the quantitative trait loci (QTL) underlining the performance traits by long term selection, and indicate the bright potential of SCAR marker technology for tracking generations during selection progress and for distinguishing among genetically improved strain and other strains.

Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat.

PubMed

Mourad, Amira M I; Sallam, Ahmed; Belamkar, Vikas; Wegulo, Stephen; Bowden, Robert; Jin, Yue; Mahdy, Ezzat; Bakheit, Bahy; El-Wafaa, Atif A; Poland, Jesse; Baenziger, Peter S

2018-01-01

Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat ( Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r 2 ) was found between the significant SNPs and the specific SSR marker for the Sr6 gene ( Xcfd43 ). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene. Novel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.

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.

PubMed

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.

SURFACTANT SELECTION FOR ENHANCING EX SITU SOIL WASHING. (R825511C064)

EPA Science Inventory

Ex situ soil washing is commonly used for treating contaminated soils by separating the most contaminated fraction of the soil for disposal. Surfactant-enhanced soil washing is being considered with increasing frequency to actually achieve soil-contaminant separation. I...

Technology Performance Review: Selecting And Using Solidification/Stabilization Treatment For Site Remediation

EPA Science Inventory

Solidification/Stabilization (S/S) is a widely used treatment technology to prevent migration and exposure of contaminants from a contaminated media (i.e., soil, sludge and sediment). Solidification refers to a process that binds a contaminated media with a reagent changing its ...

Remediation of petroleum hydrocarbon-contaminated sites by DNA diagnosis-based bioslurping technology.

PubMed

Kim, Seungjin; Krajmalnik-Brown, Rosa; Kim, Jong-Oh; Chung, Jinwook

2014-11-01

The application of effective remediation technologies can benefit from adequate preliminary testing, such as in lab-scale and Pilot-scale systems. Bioremediation technologies have demonstrated tremendous potential with regards to cost, but they cannot be used for all contaminated sites due to limitations in biological activity. The purpose of this study was to develop a DNA diagnostic method that reduces the time to select contaminated sites that are good candidates for bioremediation. We applied an oligonucleotide microarray method to detect and monitor genes that lead to aliphatic and aromatic degradation. Further, the bioremediation of a contaminated site, selected based on the results of the genetic diagnostic method, was achieved successfully by applying bioslurping in field tests. This gene-based diagnostic technique is a powerful tool to evaluate the potential for bioremediation in petroleum hydrocarbon contaminated soil. Copyright © 2014 Elsevier B.V. All rights reserved.

[Disinfectants and main sanitary and preventive measures for protection of ventilation and air-conditioning systems from Legionella contamination].

PubMed

Gerasimov, V N; Golov, E A; Khramov, M V; Diatlov, I A

2008-01-01

The study was devoted to selection and assessment of disinfecting preparations for prevention of contamination by Legionella. Using system of criteria for quality assessment of disinfectants, seven newdomestic ones belonging to quaternary ammonium compounds class or to oxygen-containing preparations and designed for disinfecting of air-conditioning and ventilation systems were selected. Antibacterial and disinfecting activities of working solutions of disinfectants were tested in laboratory on the test-surfaces and test-objects of premises' air-conditioning and ventilation systems contaminated with Legionella. High antimicrobial and disinfecting activity of new preparations "Dezactiv-M", "ExtraDez", "Emital-Garant", "Aquasept Plus", "Samarovka", "Freesept", and "Ecobreeze Oxy" during their exposure on objects and materials contaminated with Legionella was shown. Main sanitary and preventive measures for defending of air-conditioning and ventilation systems from contamination by Legionella species were presented.

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

PubMed

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.

Method for selectively removing fluorine and fluorine-containing contaminants from gaseous UF.sub.6

DOEpatents

Jones, Robert L.; Otey, Milton G.; Perkins, Roy W.

1982-01-01

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.

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

USDA-ARS?s Scientific Manuscript database

Expressed sequence tag (EST) simple sequence repeats (SSRs) in Prunus were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability. A total of 12,618 contigs were assembled from 84,727 ESTs, along with 34...

Microbial contamination in intraoral phosphor storage plates: the dilemma.

PubMed

de Souza, Tricia Murielly Pereira Andrade; de Castro, Ricardo Dias; de Vasconcelos, Laís César; Pontual, Andréa Dos Anjos; de Moraes Ramos Perez, Flávia Maria; Pontual, Maria Luiza Dos Anjos

2017-01-01

The aims of this study were to evaluate microbial contamination in phosphor storage plates in dental radiology services and discuss the possible origin of this contamination. The sample comprised 50 phosphor plates: 14 plates from service A, 30 from service B, and 6 in the control group, consisting of plates never used. Damp sterile swabs were rubbed on the phosphor plates, and then transferred to tests tubes containing sterile saline solution. Serial dilutions were made, and then inoculated in triplicate on Mueller Hinton agar plates and incubated at 37 °C/48 h, before counting the colony-forming units (CFU). The samples were also seeded in brain-heart infusion medium to confirm contamination by turbidity of the culture medium. All solutions, turbid and clean, were seeded in selective and non-selective media. At service A and B, 50 and 73.3 % of the phosphor plates were contaminated, respectively. This contamination was mainly due to bacteria of the genus Staphylococcus. CFU counts ranged from 26.4 to 80.0 CFU/plate. Most of the phosphor plates evaluated shown to be contaminated, mainly by Staphylococcus ssp. Quantitatively, this contamination occurred at low levels, possibly arising from handling of the plates. The use of a second plastic barrier may have diminished contamination by microorganisms from the oral cavity. There is a risk of cross-contamination by phosphor storage plates used in dental radiology services.

Comparison of genetic diversity and population structure of Pacific Coast whitebark pine across multiple markers

Treesearch

Andrew D. Bower; Bryce A. Richardson; Valerie Hipkins; Regina Rochefort; Carol Aubry

2011-01-01

Analysis of "neutral" molecular markers and "adaptive" quantitative traits are common methods of assessing genetic diversity and population structure. Molecular markers typically reflect the effects of demographic and stochastic processes but are generally assumed to not reflect natural selection. Conversely, quantitative (or "adaptive")...

Evaluating Chemical Tracers as Indicators of Nitrate-Nitrogen Sources in Groundwater

NASA Astrophysics Data System (ADS)

Nitka, A.; DeVita, W.; McGinley, P.

2014-12-01

Groundwater nitrate-N concentrations greater than 3 mg/L usually indicate contamination from either agriculture or wastewater disposal. The objective of this study was to use chemical indicators to reliably determine sources of nitrate contamination in private wells. We developed an analytical method for a suite of human waste indicators. The selection of chemical tracers was based on their likely occurrence and mobility in groundwater. The suite included artificial sweeteners, pharmaceuticals and personal care products. Pesticide metabolites were used to identify contamination due to agricultural practices. A densely populated suburban area with adjacent agricultural land was selected. Eighteen private water supply wells and six monitoring wells were analyzed for nitrate-N and contaminant indicators. All of the wells with nitrate concentrations greater than 3 mg/L had at least one chemical indicator. Of these, 90% had two or more human waste contaminants, 40% had pesticide metabolites, and 30% had both. Of the wells with nitrate greater than 10 mg/L, 80% had two or more human waste indicators, 70% had pesticide metabolites, and 50% had both. The results of this research will help direct land management decisions and selection of appropriate water treatment options.

Analysis of Environmental Contamination resulting from ...

EPA Pesticide Factsheets

Catastrophic incidents can generate a large number of samples with 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 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 safe 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 illu

Extraction of contaminants from a gas

DOEpatents

Babko-Malyi, Sergei

2000-01-01

A method of treating industrial gases to remove contaminants is disclosed. Ions are generated in stream of injectable gas. These ions are propelled through the contaminated gas as it flows through a collection unit. An electric field is applied to the contaminated gas. The field causes the ions to move through the contaminated gases, producing electrical charges on the contaminants. The electrically charged contaminants are then collected at one side of the electric field. The injectable gas is selected to produce ions which will produce reactions with particular contaminants. The process is thus capable of removing particular contaminants. The process does not depend on diffusion as a transport mechanism and is therefore suitable for removing contaminants which exist in very low concentrations.

Apparatus for extraction of contaminants from a gas

DOEpatents

Babko-Malyi, Sergei

2001-01-01

A method of treating industrial gases to remove contaminants is disclosed. Ions are generated in stream of injectable gas. These ions are propelled through the contaminated gas as it flows through a collection unit. An electric field is applied to the contaminated gas. The field causes the ions to move through the contaminated gases, producing electrical charges on the contaminants. The electrically charged contaminants are then collected at one side of the electric field. The injectable gas is selected to produce ions which will produce reactions with particular contaminants. The process is thus capable of removing particular contaminants. The process does not depend on diffusion as a transport mechanism and is therefore suitable for removing contaminants which exist in very low concentrations.

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents

PubMed Central

2018-01-01

Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750–4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log10 7.2–8.0 marker equivalents (ME) 100 mL–1) and biologically treated wastewater samples (median log10 4.6–6.0 ME 100 mL–1) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe. PMID:29570973

Muddying the Waters: A New Area of Concern for Drinking Water Contamination in Cameroon

PubMed Central

Healy Profitós, Jessica M.; Mouhaman, Arabi; Lee, Seungjun; Garabed, Rebecca; Moritz, Mark; Piperata, Barbara; Tien, Joe; Bisesi, Michael; Lee, Jiyoung

2014-01-01

In urban Maroua, Cameroon, improved drinking water sources are available to a large majority of the population, yet this water is frequently distributed through informal distribution systems and stored in home containers (canaries), leaving it vulnerable to contamination. We assessed where contamination occurs within the distribution system, determined potential sources of environmental contamination, and investigated potential pathogens. Gastrointestinal health status (785 individuals) was collected via health surveys. Drinking water samples were collected from drinking water sources and canaries. Escherichia coli and total coliform levels were evaluated and molecular detection was performed to measure human-associated faecal marker, HF183; tetracycline-resistance gene, tetQ; Campylobacter spp.; and Staphylococcus aureus. Statistical analyses were performed to evaluate the relationship between microbial contamination and gastrointestinal illness. Canari samples had higher levels of contamination than source samples. HF183 and tetQ were detected in home and source samples. An inverse relationship was found between tetQ and E. coli. Presence of tetQ with lower E. coli levels increased the odds of reported diarrhoeal illness than E. coli levels alone. Further work is warranted to better assess the relationship between antimicrobial-resistant bacteria and other pathogens in micro-ecosystems within canaries and this relationship’s impact on drinking water quality. PMID:25464137

Detection of chicken contamination in beef meatball using duplex-PCR Cyt b gene

NASA Astrophysics Data System (ADS)

Sari, E. P.; Kartikasari, L. R.; Cahyadi, M.

2017-04-01

Beef is one of expensive animal protein sources compared to other meats, on the other hand, chicken is cheap animal protein source. Mixing of chicken into beef meatball is possibly performed to decrease production cost. The aim of this study was to detect chicken contamination in beef meatball using Cytochrome b (Cyt b) gene by duplex-PCR. Sample was designed and prepared as follows, 100% of chicken meatball, 100% of beef meatball and serial level of chicken contaminations in beef meatball (1, 5, 10 and 25%, respectively). Isolation of DNA genome from meatball was according to the guideline of gSYNCTM DNA Extraction Kit for animal tissue. The PCR reaction was carried out using KAPA2G Fast Multiplex Mix. This study found that the DNA genome was succesfully extracted. Moreover, chicken contamination in beef meatball was indicated by the presence of 227 bp DNA band on 2% of agarose gels. Current study revealed that duplex-PCR using Cyt b gene as a genetic marker was able to detect chicken contamination in beef meatball until 1% of chicken meat in the sample. It can be effectively used to identify contamination and also authenticate species origin in animal products to protect consumer from undesirable contents in the food.

Muddying the waters: a new area of concern for drinking water contamination in Cameroon.

PubMed

Profitós, Jessica M Healy; Mouhaman, Arabi; Lee, Seungjun; Garabed, Rebecca; Moritz, Mark; Piperata, Barbara; Tien, Joe; Bisesi, Michael; Lee, Jiyoung

2014-11-28

In urban Maroua, Cameroon, improved drinking water sources are available to a large majority of the population, yet this water is frequently distributed through informal distribution systems and stored in home containers (canaries), leaving it vulnerable to contamination. We assessed where contamination occurs within the distribution system, determined potential sources of environmental contamination, and investigated potential pathogens. Gastrointestinal health status (785 individuals) was collected via health surveys. Drinking water samples were collected from drinking water sources and canaries. Escherichia coli and total coliform levels were evaluated and molecular detection was performed to measure human-associated faecal marker, HF183; tetracycline-resistance gene, tetQ; Campylobacter spp.; and Staphylococcus aureus. Statistical analyses were performed to evaluate the relationship between microbial contamination and gastrointestinal illness. Canari samples had higher levels of contamination than source samples. HF183 and tetQ were detected in home and source samples. An inverse relationship was found between tetQ and E. coli. Presence of tetQ with lower E. coli levels increased the odds of reported diarrhoeal illness than E. coli levels alone. Further work is warranted to better assess the relationship between antimicrobial-resistant bacteria and other pathogens in micro-ecosystems within canaries and this relationship's impact on drinking water quality.

Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

PubMed

Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

2014-01-01

Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

Development of EST Intron-Targeting SNP Markers for Panax ginseng and Their Application to Cultivar Authentication

PubMed Central

Wang, Hongtao; Li, Guisheng; Kwon, Woo-Saeng; Yang, Deok-Chun

2016-01-01

Panax ginseng is one of the most valuable medicinal plants in the Orient. The low level of genetic variation has limited the application of molecular markers for cultivar authentication and marker-assisted selection in cultivated ginseng. To exploit DNA polymorphism within ginseng cultivars, ginseng expressed sequence tags (ESTs) were searched against the potential intron polymorphism (PIP) database to predict the positions of introns. Intron-flanking primers were then designed in conserved exon regions and used to amplify across the more variable introns. Sequencing results showed that single nucleotide polymorphisms (SNPs), as well as indels, were detected in four EST-derived introns, and SNP markers specific to “Gopoong” and “K-1” were first reported in this study. Based on cultivar-specific SNP sites, allele-specific polymerase chain reaction (PCR) was conducted and proved to be effective for the authentication of ginseng cultivars. Additionally, the combination of a simple NaOH-Tris DNA isolation method and real-time allele-specific PCR assay enabled the high throughput selection of cultivars from ginseng fields. The established real-time allele-specific PCR assay should be applied to molecular authentication and marker assisted selection of P. ginseng cultivars, and the EST intron-targeting strategy will provide a potential approach for marker development in species without whole genomic DNA sequence information. PMID:27271615

Potential impacts of leakage from deep CO2 geosequestration on overlying freshwater aquifers.

PubMed

Little, Mark G; Jackson, Robert B

2010-12-01

Carbon Capture and Storage may use deep saline aquifers for CO(2) sequestration, but small CO(2) leakage could pose a risk to overlying fresh groundwater. We performed laboratory incubations of CO(2) infiltration under oxidizing conditions for >300 days on samples from four freshwater aquifers to 1) understand how CO(2) leakage affects freshwater quality; 2) develop selection criteria for deep sequestration sites based on inorganic metal contamination caused by CO(2) leaks to shallow aquifers; and 3) identify geochemical signatures for early detection criteria. After exposure to CO(2), water pH declines of 1-2 units were apparent in all aquifer samples. CO(2) caused concentrations of the alkali and alkaline earths and manganese, cobalt, nickel, and iron to increase by more than 2 orders of magnitude. Potentially dangerous uranium and barium increased throughout the entire experiment in some samples. Solid-phase metal mobility, carbonate buffering capacity, and redox state in the shallow overlying aquifers influence the impact of CO(2) leakage and should be considered when selecting deep geosequestration sites. Manganese, iron, calcium, and pH could be used as geochemical markers of a CO(2) leak, as their concentrations increase within 2 weeks of exposure to CO(2).

Searching for Life on Mars: Selection of Molecular Targets for ESA's Aurora ExoMars Mission

NASA Astrophysics Data System (ADS)

Parnell, John; Cullen, David; Sims, Mark R.; Bowden, Stephen; Cockell, Charles S.; Court, Richard; Ehrenfreund, Pascale; Gaubert, Francois; Grant, William; Parro, Victor; Rohmer, Michel; Sephton, Mark; Stan-Lotter, Helga; Steele, Andrew; Toporski, Jan; Vago, Jorge

2007-08-01

The European Space Agency's ExoMars mission will seek evidence of organic compounds of biological and non-biological origin at the martian surface. One of the instruments in the Pasteur payload may be a Life Marker Chip that utilizes an immunoassay approach to detect specific organic molecules or classes of molecules. Therefore, it is necessary to define and prioritize specific molecular targets for antibody development. Target compounds have been selected to represent meteoritic input, fossil organic matter, extant (living, recently dead) organic matter, and contamination. Once organic molecules are detected on Mars, further information is likely to derive from the detailed distribution of compounds rather than from single molecular identification. This will include concentration gradients beneath the surface and gradients from generic to specific compounds. The choice of biomarkers is informed by terrestrial biology but is wide ranging, and nonterrestrial biology may be evident from unexpected molecular distributions. One of the most important requirements is to sample where irradiation and oxidation are minimized, either by drilling or by using naturally excavated exposures. Analyzing regolith samples will allow for the search of both extant and fossil biomarkers, but sequential extraction would be required to optimize the analysis of each of these in turn.

Searching for life on Mars: selection of molecular targets for ESA's aurora ExoMars mission.

PubMed

Parnell, John; Cullen, David; Sims, Mark R; Bowden, Stephen; Cockell, Charles S; Court, Richard; Ehrenfreund, Pascale; Gaubert, Francois; Grant, William; Parro, Victor; Rohmer, Michel; Sephton, Mark; Stan-Lotter, Helga; Steele, Andrew; Toporski, Jan; Vago, Jorge

2007-08-01

The European Space Agency's ExoMars mission will seek evidence of organic compounds of biological and non-biological origin at the martian surface. One of the instruments in the Pasteur payload may be a Life Marker Chip that utilizes an immunoassay approach to detect specific organic molecules or classes of molecules. Therefore, it is necessary to define and prioritize specific molecular targets for antibody development. Target compounds have been selected to represent meteoritic input, fossil organic matter, extant (living, recently dead) organic matter, and contamination. Once organic molecules are detected on Mars, further information is likely to derive from the detailed distribution of compounds rather than from single molecular identification. This will include concentration gradients beneath the surface and gradients from generic to specific compounds. The choice of biomarkers is informed by terrestrial biology but is wide ranging, and nonterrestrial biology may be evident from unexpected molecular distributions. One of the most important requirements is to sample where irradiation and oxidation are minimized, either by drilling or by using naturally excavated exposures. Analyzing regolith samples will allow for the search of both extant and fossil biomarkers, but sequential extraction would be required to optimize the analysis of each of these in turn.

Coating cells with colloidal silica for high yield isolation of plasma membrane sheets and identification of transmembrane proteins.

PubMed

Chaney, L K; Jacobson, B S

1983-08-25

Plasma membrane (PM) can be isolated by binding to a positively charged solid support. Using this concept, we have developed a novel method of PM isolation using cationic colloidal silica. The method is designed for the comparative study of various physiological states of PM and for transbilayer protein mapping. The procedure consists of coating intact cells with a dense pellicle of silica particles and polyanion. Since cells remain intact during pellicle formation, the external face of the PM is selectively coated. The pellicle greatly enhances PM density and stabilizes it against vesiculation or lateral reorientation. Upon cell lysis, large open sheets of PM are rapidly isolated by centrifugation. PM from Dictyostelium discoideum was prepared by this method. Marker enzymes, cell surface labeling and microscopy demonstrate that the PM was isolated in high yield (70-80%) with a 10-17-fold purification and only low levels of cytoplasmic contamination. The pellicle remains intact during cell lysis and membrane isolation, shielding the external surface of the membranes up to 92% from chemical or enzymatic attack. The PM can thus be labeled selectively from inside and/or outside. Transmembrane proteins were identified in Dictyostelium PM by means of lactoperoxidase iodination and autoradiography.

High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.).

PubMed

Ma, G J; Song, Q J; Markell, S G; Qi, L L

2018-07-01

A novel rust resistance gene, R 15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R 15 were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F 2 individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R 15 ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R 15 was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.

Treatment Of Arsenic-Contaminated Materials Using Selected Stabilization And Solidification Technologies

EPA Science Inventory

Arsenic contamination of soil, sediment and groundwater is a widespread problem in certain areas and has caused great public concern due to increased awareness of the health risks. Often the contamination is naturally occurring, but it can also be a result of waste generated fro...

Development of LC/MS/MS Methods for Implementation in US EPA’s Drinking Water Unregulated Contaminant Monitoring Regulations

EPA Science Inventory

Well-characterized and standardized methods are the foundation upon which monitoring of regulated and unregulated contaminants in drinking water are based. To obtain reliable, high quality data for trace analysis of contaminants, these methods must be rugged, selective and sensit...

A method for estimation of historic contaminant loads using dated sediment cores

EPA Science Inventory

Dated sediment cores were used to assess the history of contaminant loads. The contaminant selected must be one that is not significantly remobilized by post depositional processes such as diagenesis. In addition, the core must be from an area with a high deposition rate and litt...

Human-Associated Fecal Quantitative Polymerase Chain ReactionMeasurements and Simulated Risk of Gastrointestinal Illness in Recreational Waters Contaminated with Raw Sewage

EPA Science Inventory

We used quantitative microbial risk assessment (QMRA) to estimate the risk of gastrointestinal (GI) illness associated with swimming in recreational waters containing different concentrations of human-associated fecal qPCR markers from raw sewage– HF183 and HumM2. The volume/volu...

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

EPA Science Inventory

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial ...

NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--HUMAN BIOLOGICAL MARKERS:BLOOD AND URINE SAMPLE COLLECTION AND ANALYSES (EOHSI-AP-209-040)

EPA Science Inventory

This procedure describes the process for collecting and analyzing blood and urine samples. The presence of chemical contaminants in biological specimens such as blood, urine, and hair represent a measure of the internal dose or body burden for a given individual derived from the ...

A BASIN-WIDE ANALYSIS OF THE DYNAMICS OF FECAL CONTAMINATION AND FECAL SOURCE IDENTIFICATION IN TILLAMOOK BAY, OREGON

EPA Science Inventory

The objectives of this study were to determine if spatial and temporal dynamics exist in source-specific Bacteroidales 16S rRNA genetic marker data across a watershed, to study these in relation to fecal indicator counts, general measurements of water quality, and climat...

Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters

EPA Science Inventory

Before new, rapid quantitative PCR (qPCR) methods for recreational water quality assessment and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant soure has been...

Study of the genetic diversity of the aflatoxin biosynthesis cluster in Aspergillus section Flavi using insertion/deletion markers in peanut seeds from Georgia, USA

USDA-ARS?s Scientific Manuscript database

Aflatoxins are among the most powerful carcinogens in nature. The major aflatoxin-producing fungi are Aspergillus flavus and A. parasiticus. Numerous crops, including peanut, are susceptible to aflatoxin contamination by these fungi. There has been an increased use of RNA interference (RNAi) technol...

Contaminated Larval and Adult Lesser Mealworms, Alphitobius diaperinus (Coleoptera: Tenebrionidae)can Transmit Salmonella Typhimurium in a Broiler Flock

USDA-ARS?s Scientific Manuscript database

The ability of the lesser mealworm, Alphitobius diaperinus (Panzer), commonly known as the darkling beetle, to transmit a marker strain Salmonella Typhimurium to day-of-hatch broiler chicks was evaluated, as well as the spread to non-challenged pen mates. Day-of-hatch chicks were orally gavaged wit...

Selection of plants for phytoremediation of soils contaminated with radionuclides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Entry J.A.; Vance, N.C.; Watrud, L.S.

1996-12-31

Remediation of soil contaminated with radionuclides typically requires that soil be removed from the site and treated with various dispersing and chelating chemicals. Numerous studies have shown that radionuclides are generally not leached from the top 0.4 meters of soil, where plant roots actively accumulate elements. Restoration of large areas of land contaminated with low levels of radionuclides may be feasible using phytoremediation. Criteria for the selection of plants for phytoremediation, molecular approaches to increase radio nuclide uptake, effects of cultural practices on uptake and assessment of environmental effects of phytoremediation will be discussed.

Cryptosporidium and Giardia in tropical recreational marine waters contaminated with domestic sewage: estimation of bathing-associated disease risks.

PubMed

Betancourt, Walter Q; Duarte, Diana C; Vásquez, Rosa C; Gurian, Patrick L

2014-08-15

Sewage is a major contributor to pollution problems involving human pathogens in tropical coastal areas. This study investigated the occurrence of intestinal protozoan parasites (Giardia and Cryptosporidium) in tropical recreational marine waters contaminated with sewage. The potential risks of Cryptosporidium and Giardia infection from recreational water exposure were estimated from the levels of viable (oo) cysts (DIC+, DAPI+, PI-) found in near-shore swimming areas using an exponential dose response model. A Monte Carlo uncertainty analysis was performed in order to determine the probability distribution of risks. Microbial indicators of recreational water quality (enterococci, Clostridium perfringens) and genetic markers of sewage pollution (human-specific Bacteroidales marker [HF183] and Clostridium coccoides) were simultaneously evaluated in order to estimate the extent of water quality deterioration associated with human wastes. The study revealed the potential risk of parasite infections via primary contact with tropical marine waters contaminated with sewage; higher risk estimates for Giardia than for Cryptosporidium were found. Mean risks estimated by Monte Carlo were below the U.S. EPA upper bound on recreational risk of 0.036 for cryptosporidiosis and giardiasis for both children and adults. However, 95th percentile estimates for giardiasis for children exceeded the 0.036 level. Environmental surveillance of microbial pathogens is crucial in order to control and eradicate the effects that increasing anthropogenic impacts have on marine ecosystems and human health. Copyright © 2014 Elsevier Ltd. All rights reserved.

Characterization of a chromosomally integrated luxCDABE marker for investigation of shiga toxin-producing Escherichia coli O91:H21 shedding in cattle

NASA Astrophysics Data System (ADS)

Hong, Yingying; Mathew, Alan G.

2011-06-01

Shiga toxin-producing Escherichia coli (STEC) O91:H21 has been recognized as a potential life-threatening foodborne pathogen and is commonly involved in human infections in European countries. Fecal shedding of the organism by cattle is considered to be the ultimate source for contaminations. Studies examining STEC shedding patterns often include inoculation of strains carrying antibiotic resistance makers for identifiable recovery. However, indigenous intestinal microflora exhibiting similar antibiotic resistance patterns can confound such studies. Such was the case in a study by our group when attempting to characterize shedding patterns of O91:H21 in calves. A chromosomally integrated bioluminescence marker using a luxCDABE cassette from Photorhabdus luminescens was developed in O91:H21 to overcome such shortcomings of antibiotic resistance markers during animal challenge experiment. The marker was validated in various aspects and was shown to have no impact on metabolic reactions, isotype virulence gene patterns, cost to growth, and additionally demonstrated high in vitro stability. Together, the results indicated that a chromosomally integrated luxCDABE based marker may be a superior system for the study of STEC colonization and shedding in cattle.

Global occurrence of Torque teno virus in water systems.

PubMed

Charest, A J; Plummer, J D; Long, S C; Carducci, A; Verani, M; Sidhu, J P S

2015-09-01

Bacterial indicator organisms are used globally to assess the microbiological safety of waters. However, waterborne viral outbreaks have occurred in drinking water systems despite negative bacterial results. Using viral markers may therefore provide more accurate health risk assessment data. In this study, fecal, wastewater, stormwater, surface water (fresh and salt), groundwater, and drinking water samples were analyzed for the presence or concentration of traditional indicators, innovative indicators and viral markers. Samples were obtained in the United States, Italy, and Australia and results compared to those reported for studies conducted in Asia and South America as well. Indicators included total coliforms, Escherichia coli, enterococci, male-specific coliphages, somatic coliphages and microviradae. Viral markers included adenovirus, polyomavirus, and a potential new surrogate, Torque teno virus (TTV). TTV was more frequently found in wastewaters (38-100%) and waters influenced by waste discharges (25%) than in surface waters used as drinking water sources (5%). TTV was also specific to human rather than animal feces. While TTV numbers were strongly correlated to other viral markers in wastewaters, suggesting its utility as a fecal contamination marker, data limitations and TTV presence in treated drinking waters demonstrates that additional research is needed on this potential viral indicator.

Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

PubMed

Ren, Jing; Chen, Liang; Jin, Xiaoli; Zhang, Miaomiao; You, Frank M; Wang, Jirui; Frenkel, Vladimir; Yin, Xuegui; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2017-01-01

Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ F ST ≤ 0.15) or high genetic differentiation ( F ST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different F ST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.

Balancing Selection and Its Effects on Sequences in Nearby Genome Regions

PubMed Central

Charlesworth, Deborah

2006-01-01

Our understanding of balancing selection is currently becoming greatly clarified by new sequence data being gathered from genes in which polymorphisms are known to be maintained by selection. The data can be interpreted in conjunction with results from population genetics models that include recombination between selected sites and nearby neutral marker variants. This understanding is making possible tests for balancing selection using molecular evolutionary approaches. Such tests do not necessarily require knowledge of the functional types of the different alleles at a locus, but such information, as well as information about the geographic distribution of alleles and markers near the genes, can potentially help towards understanding what form of balancing selection is acting, and how long alleles have been maintained. PMID:16683038

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.).

PubMed

Elkot, Ahmed Fawzy Abdelnaby; Chhuneja, Parveen; Kaur, Satinder; Saluja, Manny; Keller, Beat; Singh, Kuldeep

2015-01-01

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA)-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS), the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection) and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in several BC2F1 plants. Thus, in addition to PM resistance, these progeny might also carry resistance to stem rust race Ug99.

The GCP molecular marker toolkit, an instrument for use in breeding food security crops.

PubMed

Van Damme, Veerle; Gómez-Paniagua, Humberto; de Vicente, M Carmen

2011-12-01

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access, particularly those in developing countries. This situation separates them from developed countries, which have better endowed programs for developing varieties. To close this growing knowledge gap, we conducted an intensive literature review and consulted with more than 150 crop experts on the use of molecular markers in the breeding program of 19 food security crops. The result was a list of effectively used and highly reproducible sequence tagged site (STS), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and sequence characterized amplified region (SCAR) markers. However, only 12 food crops had molecular markers suitable for improvement. That is, marker-assisted selection is not yet used for Musa spp., coconut, lentils, millets, pigeonpea, sweet potato, and yam. For the other 12 crops, 214 molecular markers were found to be effectively used in association with 74 different traits. Results were compiled as the GCP Molecular Marker Toolkit, a free online tool that aims to promote the adoption of molecular approaches in breeding activities.

[Prognostic and predictive molecular markers for urologic cancers].

PubMed

Hartmann, A; Schlomm, T; Bertz, S; Heinzelmann, J; Hölters, S; Simon, R; Stoehr, R; Junker, K

2014-04-01

Molecular prognostic factors and genetic alterations as predictive markers for cancer-specific targeted therapies are used today in the clinic for many malignancies. In recent years, many molecular markers for urogenital cancers have also been identified. However, these markers are not clinically used yet. In prostate cancer, novel next-generation sequencing methods revealed a detailed picture of the molecular changes. There is growing evidence that a combination of classical histopathological and validated molecular markers could lead to a more precise estimation of prognosis, thus, resulting in an increasing number of patients with active surveillance as a possible treatment option. In patients with urothelial carcinoma, histopathological factors but also the proliferation of the tumor, mutations in oncogenes leading to an increasing proliferation rate and changes in genes responsible for invasion and metastasis are important. In addition, gene expression profiles which could distinguish aggressive tumors with high risk of metastasis from nonmetastasizing tumors have been recently identified. In the future, this could potentially allow better selection of patients needing systemic perioperative treatment. In renal cell carcinoma, many molecular markers that are associated with metastasis and survival have been identified. Some of these markers were also validated as independent prognostic markers. Selection of patients with primarily organ-confined tumors and increased risk of metastasis for adjuvant systemic therapy could be clinically relevant in the future.

Method for selectively removing fluorine and fluorine-containing contaminants from gaseous UF/sub 6/. [ClF/sub 3/

DOEpatents

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/.

CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.

PubMed

Bhawna; Chaduvula, Pavan K; Bonthala, Venkata S; Manjusha, Verma; Siddiq, Ebrahimali A; Polumetla, Ananda K; Prasad, Gajula M N V

2015-01-01

Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

Comparison of Marker-Based Genomic Estimated Breeding Values and Phenotypic Evaluation for Selection of Bacterial Spot Resistance in Tomato.

PubMed

Liabeuf, Debora; Sim, Sung-Chur; Francis, David M

2018-03-01

Bacterial spot affects tomato crops (Solanum lycopersicum) grown under humid conditions. Major genes and quantitative trait loci (QTL) for resistance have been described, and multiple loci from diverse sources need to be combined to improve disease control. We investigated genomic selection (GS) prediction models for resistance to Xanthomonas euvesicatoria and experimentally evaluated the accuracy of these models. The training population consisted of 109 families combining resistance from four sources and directionally selected from a population of 1,100 individuals. The families were evaluated on a plot basis in replicated inoculated trials and genotyped with single nucleotide polymorphisms (SNP). We compared the prediction ability of models developed with 14 to 387 SNP. Genomic estimated breeding values (GEBV) were derived using Bayesian least absolute shrinkage and selection operator regression (BL) and ridge regression (RR). Evaluations were based on leave-one-out cross validation and on empirical observations in replicated field trials using the next generation of inbred progeny and a hybrid population resulting from selections in the training population. Prediction ability was evaluated based on correlations between GEBV and phenotypes (r g ), percentage of coselection between genomic and phenotypic selection, and relative efficiency of selection (r g /r p ). Results were similar with BL and RR models. Models using only markers previously identified as significantly associated with resistance but weighted based on GEBV and mixed models with markers associated with resistance treated as fixed effects and markers distributed in the genome treated as random effects offered greater accuracy and a high percentage of coselection. The accuracy of these models to predict the performance of progeny and hybrids exceeded the accuracy of phenotypic selection.

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

PubMed

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.

Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite ... cattle

USDA-ARS?s Scientific Manuscript database

Selection of the composite MARC III population for markers allowed better estimates of effects and inheritance of markers for targeted carcass quality traits (n=254) and nontargeted traits and an evaluation of SNP specific residual variance models for tenderness. Genotypic effects of CAPN1 haplotyp...

Trichothecene resistance in wheat: Development of molecular markers for PDR-type ABC transporter genes.

PubMed

Mitterbauer, R; Heinrich, M; Rauscher, R; Lemmens, M; Bürstmayr, H; Adam, G

2003-03-01

Infection withFusarium graminearum andF. culmorum not only causes severe yield and quality losses, the most relevant concern is the contamination of cereal foods and feeds with trichothecenes (e.g. deoxynivalenol, DON). The ability to synthesize trichothecenes has been shown to be a virulence factor ofF. graminearum on wheat and, on the other hand, toxin resistance is most likely an important component of field resistance. Our hypothesis is that pleiotropic drug resistance mediated by PDR-type ABC transporter proteins (acting as membrane located drug efflux pumps) is a relevant mechanism of DON resistance not only in yeast but also in wheat. Goal of this project is the development of molecular markers for this gene family for use in marker-assisted plant breeding programs. The technical difficulties caused by the large size of the PDR-family are discussed.

Multi-year microbial source tracking study characterizing fecal contamination in an urban watershed

USGS Publications Warehouse

Bushon, Rebecca N.; Brady, Amie M. G.; Christensen, Eric D.; Stelzer, Erin A.

2017-01-01

Microbiological and hydrological data were used to rank tributary stream contributions of bacteria to the Little Blue River in Independence, Missouri. Concentrations, loadings and yields of E. coli and microbial source tracking (MST) markers, were characterized during base flow and storm events in five subbasins within Independence, as well as sources entering and leaving the city through the river. The E. coli water quality threshold was exceeded in 29% of base-flow and 89% of storm-event samples. The total contribution of E. coli and MST markers from tributaries within Independence to the Little Blue River, regardless of streamflow, did not significantly increase the median concentrations leaving the city. Daily loads and yields of E. coli and MST markers were used to rank the subbasins according to their contribution of each constituent to the river. The ranking methodology used in this study may prove useful in prioritizing remediation in the different subbasins.

Identification of body fluid-specific DNA methylation markers for use in forensic science.

PubMed

Park, Jong-Lyul; Kwon, Oh-Hyung; Kim, Jong Hwan; Yoo, Hyang-Sook; Lee, Han-Chul; Woo, Kwang-Man; Kim, Seon-Young; Lee, Seung-Hwan; Kim, Yong Sung

2014-11-01

DNA methylation, which occurs at the 5'-position of the cytosine in CpG dinucleotides, has great potential for forensic identification of body fluids, because tissue-specific patterns of DNA methylation have been demonstrated, and DNA is less prone to degradation than proteins or RNA. Previous studies have reported several body fluid-specific DNA methylation markers, but DNA methylation differences are sometimes low in saliva and vaginal secretions. Moreover, specific DNA methylation markers in four types of body fluids (blood, saliva, semen, and vaginal secretions) have not been investigated with genome-wide profiling. Here, we investigated novel DNA methylation markers for identification of body fluids for use in forensic science using the Illumina HumanMethylation 450K bead array, which contains over 450,000 CpG sites. Using methylome data from 16 samples of blood, saliva, semen, and vaginal secretions, we first selected 2986 hypermethylated or hypomethylated regions that were specific for each type of body fluid. We then selected eight CpG sites as novel, forensically relevant DNA methylation markers: cg06379435 and cg08792630 for blood, cg26107890 and cg20691722 for saliva, cg23521140 and cg17610929 for semen, and cg01774894 and cg14991487 for vaginal secretions. These eight selected markers were evaluated in 80 body fluid samples using pyrosequencing, and all showed high sensitivity and specificity for identification of the target body fluid. We suggest that these eight DNA methylation markers may be good candidates for developing an effective molecular assay for identification of body fluids in forensic science. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

PubMed Central

2012-01-01

Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species. PMID:22805587

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

PubMed

Yang, Huaan; Tao, Ye; Zheng, Zequn; Li, Chengdao; Sweetingham, Mark W; Howieson, John G

2012-07-17

In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species.

Evaluating Contaminants of Emerging Concern as tracers of wastewater from septic systems.

PubMed

James, C Andrew; Miller-Schulze, Justin P; Ultican, Shawn; Gipe, Alex D; Baker, Joel E

2016-09-15

Bacterial and nutrient contamination from anthropogenic sources impacts fresh and marine waters, reducing water quality and restricting recreational and commercial activities. In many cases the source of this contamination is ambiguous, and a tracer or set of tracers linking contamination to source would be valuable. In this work, the effectiveness of utilizing a suite of Contaminants of Emerging Concern (CECs) as tracers of bacteria from human septic system effluent is investigated. Field sampling was performed at more than 20 locations over approximately 18 months and analyzed for a suite of CECs and fecal coliform bacteria. The sampling locations included seeps and small freshwater discharges to the shoreline. Sites were selected and grouped according to level of impact by septic systems as determined by previous field sampling programs. A subset of selected locations had been positively identified as being impacted by effluent from failing septic systems through dye testing. The CECs were selected based on their predominant use, their frequency of use, and putative fate and transport properties. In addition, two rounds of focused sampling were performed at selected sites to characterize short-term variations in CEC and fecal coliform concentrations, and to evaluate environmental persistence following source correction activities. The results indicate that a suite of common use compounds are suitable as generalized tracers of bacterial contamination from septic systems and that fate and transport properties are important in tracer selection. Highly recalcitrant or highly labile compounds likely follow different loss profiles in the subsurface compared to fecal bacteria and are not suitable tracers. The use of more than one tracer compound is recommended due to source variability of septic systems and to account for variations in the subsurface condition. In addition, concentrations of some CECs were measured in receiving waters at levels which suggested the potential for environmental harm, indicating that the possible risk presented from these sources warrants further investigation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Marker development for rice blast resistance gene Pi66(t) and application in USDA rice mini-core collection

USDA-ARS?s Scientific Manuscript database

Molecular markers are useful for the identification of critical genes controlling agricultural traits of interest in crop germplasm and for the utilization of these genes in crop improvement using marker assisted selection (MAS). The improvement of blast disease resistance of rice varieties is one o...

Microsatellite markers reveal the below ground distribution of genets in two species of Rhizopogon forming tuberculate ectomycorrhizas on Douglas-fir.

Treesearch

Annette M. Kretzer; Susie Dunham; Randy Molina; Joseph W. Spatafora

2003-01-01

We have developed microsatellite markers for two sister species of Rhizopogon, R. vesiculosus and R. vinicolor (Boletales, Basidiomycota), and used selected markers to investigate genet size and distribution from ectomycorrhizal samples. Both species form ectomycorrhizas with tuberculate morphology on Douglas-fir (...

Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit.

PubMed

Pantalião, Gabriel Feresin; Narciso, Marcelo; Guimarães, Cléber; Castro, Adriano; Colombari, José Manoel; Breseghello, Flavio; Rodrigues, Luana; Vianello, Rosana Pereira; Borba, Tereza Oliveira; Brondani, Claudio

2016-12-01

The identification of rice drought tolerant materials is crucial for the development of best performing cultivars for the upland cultivation system. This study aimed to identify markers and candidate genes associated with drought tolerance by Genome Wide Association Study analysis, in order to develop tools for use in rice breeding programs. This analysis was made with 175 upland rice accessions (Oryza sativa), evaluated in experiments with and without water restriction, and 150,325 SNPs. Thirteen SNP markers associated with yield under drought conditions were identified. Through stepwise regression analysis, eight SNP markers were selected and validated in silico, and when tested by PCR, two out of the eight SNP markers were able to identify a group of rice genotypes with higher productivity under drought. These results are encouraging for deriving markers for the routine analysis of marker assisted selection. From the drought experiment, including the genes inherited in linkage blocks, 50 genes were identified, from which 30 were annotated, and 10 were previously related to drought and/or abiotic stress tolerance, such as the transcription factors WRKY and Apetala2, and protein kinases.

Luciferase-Specific Coelenterazine Analogues for Optical Contamination-Free Bioassays.

PubMed

Nishihara, Ryo; Abe, Masahiro; Nishiyama, Shigeru; Citterio, Daniel; Suzuki, Koji; Kim, Sung Bae

2017-04-19

Spectral overlaps among the multiple optical readouts commonly cause optical contamination in fluorescence and bioluminescence. To tackle this issue, we created five-different lineages of coelenterazine (CTZ) analogues designed to selectively illuminate a specific luciferase with unique luciferase selectivity. In the attempt, we found that CTZ analogues with ethynyl or styryl groups display dramatically biased bioluminescence to specific luciferases and pHs by modifying the functional groups at the C-2 and C-6 positions of the imidazopyradinone backbone of CTZ. The optical contamination-free feature was exemplified with the luciferase-specific CTZ analogues, which illuminated anti-estrogenic and rapamycin activities in a mixture of optical probes. This unique bioluminescence platform has great potential for specific and high throughput imaging of multiple optical readouts in bioassays without optical contamination.

Estimation by simulation of the efficiency of the French marker-assisted selection program in dairy cattle (Open Access publication)

PubMed Central

Guillaume, François; Fritz, Sébastien; Boichard, Didier; Druet, Tom

2008-01-01

The efficiency of the French marker-assisted selection (MAS) was estimated by a simulation study. The data files of two different time periods were used: April 2004 and 2006. The simulation method used the structure of the existing French MAS: same pedigree, same marker genotypes and same animals with records. The program simulated breeding values and new records based on this existing structure and knowledge on the QTL used in MAS (variance and frequency). Reliabilities of genetic values of young animals (less than one year old) obtained with and without marker information were compared to assess the efficiency of MAS for evaluation of milk, fat and protein yields and fat and protein contents. Mean gains of reliability ranged from 0.015 to 0.094 and from 0.038 to 0.114 in 2004 and 2006, respectively. The larger number of animals genotyped and the use of a new set of genetic markers can explain the improvement of MAS reliability from 2004 to 2006. This improvement was also observed by analysis of information content for young candidates. The gain of MAS reliability with respect to classical selection was larger for sons of sires with genotyped progeny daughters with records. Finally, it was shown that when superiority of MAS over classical selection was estimated with daughter yield deviations obtained after progeny test instead of true breeding values, the gain was underestimated. PMID:18096117

Associations between urinary phenol and paraben concentrations and markers of oxidative stress and inflammation among pregnant women in Puerto Rico.

PubMed

Watkins, Deborah J; Ferguson, Kelly K; Anzalota Del Toro, Liza V; Alshawabkeh, Akram N; Cordero, José F; Meeker, John D

2015-03-01

Phenols and parabens are used in a multitude of consumer products resulting in ubiquitous human exposure. Animal and in vitro studies suggest that exposure to these compounds may be related to a number of adverse health outcomes, as well as potential mediators such as oxidative stress and inflammation. We examined urinary phenol (bisphenol A (BPA), triclosan (TCS), benzophenone-3 (BP-3), 2,4-dichlorophenol (24-DCP), 2,5-dichlorophenol (25-DCP)) and paraben (butyl paraben (B-PB), methyl paraben (M-PB), propyl paraben (P-PB)) concentrations measured three times during pregnancy in relation to markers of oxidative stress and inflammation among participants in the Puerto Rico Testsite for Exploring Contamination Threats (PROTECT) project. Serum markers of inflammation (c-reactive protein (CRP), IL-1β, IL-6, IL-10, and tumor necrosis factor-α (TNF-α)) were measured twice during pregnancy (n=105 subjects, 187 measurements) and urinary markers of oxidative stress (8-hydroxydeoxyguanosine (OHdG) and isoprostane) were measured three times during pregnancy (n=54 subjects, 146 measurements). We used linear mixed models to assess relationships between natural log-transformed exposure and outcome biomarkers while accounting for within individual correlation across study visits. After adjustment for urinary specific gravity, study visit, maternal pre-pregnancy BMI, and maternal education, an interquartile range (IQR) increase in urinary BPA was associated with 21% higher OHdG (p=0.001) and 29% higher isoprostane (p=0.0002), indicating increased oxidative stress. The adjusted increase in isoprostane per IQR increase in marker of exposure was 17% for BP-3, 27% for B-PB, and 20% for P-PB (all p<0.05). An IQR increase in triclosan (TCS) was associated with 31% higher serum concentrations of IL-6 (p=0.007), a pro-inflammatory cytokine. In contrast, IQR increases in BP-3 and B-PB were significantly associated with 16% and 18% lower CRP, a measure of systemic inflammation. Our findings suggest that exposure to BPA, select parabens, and TCS during pregnancy may be related to oxidative stress and inflammation, potential mechanisms by which exposure to these compounds may influence birth outcomes and other adverse health effects, but additional research is needed. Copyright © 2014 Elsevier GmbH. All rights reserved.

Associations between urinary phenol and paraben concentrations and markers of oxidative stress and inflammation among pregnant women in Puerto Rico

PubMed Central

Watkins, Deborah J.; Ferguson, Kelly K.; Toro, Liza V. Anzalota Del; Alshawabkeh, Akram N.; Cordero, José F.; Meeker, John D.

2014-01-01

Phenols and parabens are used in a multitude of consumer products resulting in ubiquitous human exposure. Animal and in vitro studies suggest that exposure to these compounds may be related to a number of adverse health outcomes, as well as potential mediators such as oxidative stress and inflammation. We examined urinary phenol (bisphenol A (BPA), triclosan (TCS), benzophenone-3 (BP-3), 2,4-dichlorophenol (24-DCP), 2,5-dichlorophenol (25-DCP)) and paraben (butyl paraben (B-PB), methyl paraben (M-PB), propyl paraben (P-PB)) concentrations measured three times during pregnancy in relation to markers of oxidative stress and inflammation among participants in the Puerto Rico Testsite for Exploring Contamination Threats (PROTECT) project. Serum markers of inflammation (c-reactive protein (CRP), IL-1β, IL-6, IL-10, and tumor necrosis factor-α (TNF-α)) were measured twice during pregnancy (n=105 subjects, 187 measurements) and urinary markers of oxidative stress (8-hydroxydeoxyguanosine (OHdG) and isoprostane) were measured three times during pregnancy (n=54 subjects, 146 measurements). We used linear mixed models to assess relationships between natural log-transformed exposure and outcome biomarkers while accounting for within individual correlation across study visits. After adjustment for urinary specific gravity, study visit, maternal pre-pregnancy BMI, and maternal education, an interquartile range (IQR) increase in urinary BPA was associated with 21% higher OHdG (p=0.001) and 29% higher isoprostane (p=0.0002), indicating increased oxidative stress. The adjusted increase in isoprostane per IQR increase in marker of exposure was 17% for BP-3, 27% for B-PB, and 20% for P-PB (all p<0.05). An IQR increase in triclosan (TCS) was associated with 31% higher serum concentrations of IL-6 (p=0.007), a pro-inflammatory cytokine. In contrast, IQR increases in BP-3 and B-PB were significantly associated with 16% and 18% lower CRP, a measure of systemic inflammation. Our findings suggest that exposure to BPA, select parabens, and TCS during pregnancy may be related to oxidative stress and inflammation, potential mechanisms by which exposure to these compounds may influence birth outcomes and other adverse health effects, but additional research is needed. PMID:25435060

Supplemental Groundwater Remediation Technologies to Protect the Columbia River at Hanford, WA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, K. M.; Petersen, Scott W.; Fruchter, Jonathan S.

2007-12-15

Nine projects have been recently selected by the US Department of Energy (EM-22) to address groundwater contaminant migration at the Hanford Site. This paper summarizes the background and objectives of these projects. Five of the selected projects are targeted at hexavalent chromium contamination in Hanford 100 Area groundwater. These projects represent an integrated approach towards identifying the source of hexavalent chromium contamination in the Hanford 100-D Area and treating the groundwater contamination. Currently, there is no effective method to stop strontium-90 associated with the riparian zone sediments from leaching into the river. Phytoremediation may be a possible way to treatmore » this contamination. Its use at the 100-N Area will be investigated. Another technology currently being tested for strontium-90 contamination at the 100-N Area involves injection (through wells) of a calcium-citrate-phosphate solution, which will precipitate apatite, a natural calcium-phosphate mineral. Apatite will adsorb the strontium-90, and then incorporate it as part of the apatite structure, isolating the strontium-90 contamination from entering the river. This EM-22 funded apatite project will develop a strategy for infiltrating the apatite solution from ground surface or a shallow trench to provide treatment over the upper portion of the contaminated zone, which is unsaturated during low river stage.« less

Accumulation and transfer of contaminants in killer whales (Orcinus orca) from Norway: indications for contaminant metabolism.

PubMed

Wolkers, Hans; Corkeron, Peter J; Van Parijs, Sofie M; Similä, Tiu; Van Bavel, Bert

2007-08-01

Blubber tissue of one subadult and eight male adult killer whales was sampled in Northern Norway in order to assess the degree and type of contaminant exposure and transfer in the herring-killer whale link of the marine food web. A comprehensive selection of contaminants was targeted, with special attention to toxaphenes and polybrominated diphenyl ethers (PBDEs). In addition to assessing exposure and food chain transfer, selective accumulation and metabolism issues also were addressed. Average total polychlorinated biphenyl (PCB) and pesticide levels were similar, approximately 25 microg/g lipid, and PBDEs were approximately 0.5 microg/g. This makes killer whales one of the most polluted arctic animals, with levels exceeding those in polar bears. Comparing the contamination of the killer whale's diet with the diet of high-arctic species such as white whales reveals six to more than 20 times higher levels in the killer whale diet. The difference in contaminant pattern between killer whales and their prey and the metabolic index calculated suggested that these cetaceans have a relatively high capacity to metabolize contaminants. Polychlorinated biphenyls, chlordanes, and dichlorodiphenyldichloro-ethylene (DDE) accumulate to some degree in killer whales, although toxaphenes and PBDEs might be partly broken down.

Molecular-level removal of proteinaceous contamination from model surfaces and biomedical device materials by air plasma treatment.

PubMed

Banerjee, K K; Kumar, S; Bremmell, K E; Griesser, H J

2010-11-01

Established methods for cleaning and sterilising biomedical devices may achieve removal of bioburden only at the macroscopic level while leaving behind molecular levels of contamination (mainly proteinaceous). This is of particular concern if the residue might contain prions. We investigated at the molecular level the removal of model and real-life proteinaceous contamination from model and practical surfaces by air plasma (ionised air) treatment. The surface-sensitive technique of X-ray photoelectron spectroscopy (XPS) was used to assess the removal of proteinaceous contamination, with the nitrogen (N1s) photoelectron signal as its marker. Model proteinaceous contamination (bovine serum albumin) adsorbed on to a model surface (silicon wafer) and the residual proteinaceous contamination resulting from incubating surgical stainless steel (a practical biomaterial) in whole human blood exhibited strong N1s signals [16.8 and 18.5 atomic percent (at.%), respectively] after thorough washing. After 5min air plasma treatment, XPS detected no nitrogen on the sample surfaces, indicating complete removal of proteinaceous contamination, down to the estimated XPS detection limit 10ng/cm(2). Applying the same plasma treatment, the 7.7at.% nitrogen observed on a clinically cleaned dental bur was reduced to a level reflective of new, as-received burs. Contact angle measurements and atomic force microscopy also indicated complete molecular-level removal of the proteinaceous contamination upon air plasma treatment. This study demonstrates the effectiveness of air plasma treatment for removing proteinaceous contamination from both model and practical surfaces and offers a method for ensuring that no molecular residual contamination such as prions is transferred upon re-use of surgical and dental instruments. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

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

PubMed

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.

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks.

PubMed

Billiard, Sylvain; Ferrière, Régis; Méléard, Sylvie; Tran, Viet Chi

2015-11-01

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.