Comparison of the Abbott RealTime High Risk HPV test and the Roche cobas 4800 HPV test using urine samples.

PubMed

Lim, Myong Cheol; Lee, Do-Hoon; Hwang, Sang-Hyun; Hwang, Na Rae; Lee, Bomyee; Shin, Hye Young; Jun, Jae Kwan; Yoo, Chong Woo; Lee, Dong Ock; Seo, Sang-Soo; Park, Sang-Yoon; Joo, Jungnam

2017-05-01

Human papillomavirus (HPV) testing based on cervical samples is important for use in cervical cancer screening. However, cervical sampling is invasive. Therefore, non-invasive methods for detecting HPV, such as urine samples, are needed. For HPV detection in urine samples, two real-time PCR (RQ-PCR) tests, Roche cobas 4800 test (Roche_HPV; Roche Molecular Diagnostics) and Abbott RealTime High Risk HPV test (Abbott_HPV; Abbott Laboratories) were compared to standard cervical samples. The performance of Roche_HPV and Abbott_HPV for HPV detection was evaluated at the National Cancer Center using 100 paired cervical and urine samples. The tests were also compared using urine samples stored at various temperatures and for a range of durations. The overall agreement between the Roche_HPV and Abbott_HPV tests using urine samples for any hrHPV type was substantial (86.0% with a kappa value of 0.7173), and that for HPV 16/18 was nearly perfect (99.0% with a kappa value of 0.9668). The relative sensitivities (based on cervical samples) for HPV 16/18 detection using Roche_HPV and Abbott_HPV with urine samples were 79.2% (95% CI; 57.9-92.9%) and 81.8% (95% CI; 59.7-94.8%), respectively. When the cut-off C T value for Abbott_HPV was extended to 40 for urine samples, the relative sensitivity of Abbott_HPV increased to 91.7% from 81.8% for HPV16/18 detection and to 87.0% from 68.5% for other hrHPV detection. The specificity was not affected by the change in the C T threshold. Roche_HPV and Abbott_HPV showed high concordance. However, HPV DNA detection using urine samples was inferior to HPV DNA detection using cervical samples. Interestingly, when the cut-off C T value was set to 40, Abbott_HPV using urine samples showed high sensitivity and specificity, comparable to those obtained using cervical samples. Fully automated DNA extraction and detection systems, such as Roche_HPV and Abbott_HPV, could reduce the variability in HPV detection and accelerate the standardization of HPV detection in urine. Thus, urine samples may be an effective alternative for HPV detection in women who hesitate to participate in cervical cancer screening programs. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection of Legionella species in environmental water by the quantitative PCR method in combination with ethidium monoazide treatment.

PubMed

Inoue, Hiroaki; Takama, Tomoko; Yoshizaki, Miwa; Agata, Kunio

2015-01-01

We detected Legionella species in 111 bath water samples and 95 cooling tower water samples by using a combination of conventional plate culture, quantitative polymerase chain reaction (qPCR) and qPCR combined with ethidium monoazide treatment (EMA-qPCR) methods. In the case of bath water samples, Legionella spp. were detected in 30 samples by plate culture, in 85 samples by qPCR, and in 49 samples by EMA-qPCR. Of 81 samples determined to be Legionella-negative by plate culture, 56 and 23 samples were positive by qPCR and EMA-qPCR, respectively. Therefore, EMA treatment decreased the number of Legionella-positive bath water samples detected by qPCR. In contrast, EMA treatment had no effect on cooling tower water samples. We therefore expect that EMA-qPCR is a useful method for the rapid detection of viable Legionella spp. from bath water samples.

Fishing in the Water: Effect of Sampled Water Volume on Environmental DNA-Based Detection of Macroinvertebrates.

PubMed

Mächler, Elvira; Deiner, Kristy; Spahn, Fabienne; Altermatt, Florian

2016-01-05

Accurate detection of organisms is crucial for the effective management of threatened and invasive species because false detections directly affect the implementation of management actions. The use of environmental DNA (eDNA) as a species detection tool is in a rapid development stage; however, concerns about accurate detections using eDNA have been raised. We evaluated the effect of sampled water volume (0.25 to 2 L) on the detection rate for three macroinvertebrate species. Additionally, we tested (depending on the sampled water volume) what amount of total extracted DNA should be screened to reduce uncertainty in detections. We found that all three species were detected in all volumes of water. Surprisingly, however, only one species had a positive relationship between an increased sample volume and an increase in the detection rate. We conclude that the optimal sample volume might depend on the species-habitat combination and should be tested for the system where management actions are warranted. Nevertheless, we minimally recommend sampling water volumes of 1 L and screening at least 14 μL of extracted eDNA for each sample to reduce uncertainty in detections when studying macroinvertebrates in rivers and using our molecular workflow.

Discreet passive explosive detection through 2-sided waveguided fluorescence

DOEpatents

Harper, Ross James [Stillwater, OK; la Grone, Marcus [Cushing, OK; Fisher, Mark [Stillwater, OK

2011-10-18

The current invention provides a passive sampling device suitable for collecting and detecting the presence of target analytes. In particular, the passive sampling device is suitable for detecting nitro-aromatic compounds. The current invention further provides a passive sampling device reader suitable for determining the collection of target analytes. Additionally, the current invention provides methods for detecting target analytes using the passive sampling device and the passive sampling device reader.

Method for chromium analysis and speciation

DOEpatents

Aiken, Abigail M.; Peyton, Brent M.; Apel, William A.; Petersen, James N.

2004-11-02

A method of detecting a metal in a sample comprising a plurality of metal is disclosed. The method comprises providing the sample comprising a metal to be detected. The sample is added to a reagent solution comprising an enzyme and a substrate, where the enzyme is inhibited by the metal to be detected. An array of chelating agents is used to eliminate the inhibitory effects of additional metals in the sample. An enzymatic activity in the sample is determined and compared to an enzymatic activity in a control solution to detect the metal to be detected. A method of determining a concentration of the metal in the sample is also disclosed. A method of detecting a valence state of a metal is also disclosed.

Ex vivo spontaneous generation of 19-norandrostenedione and nandrolone detected in equine plasma and urine.

PubMed

Guan, Fuyu; Uboh, Cornelius E; Soma, Lawrence R; You, Youwen; Li, Xiaoqing; McDonnell, Sue

2012-01-01

19-Norandrostenedione (NAED) and nandrolone are anabolic-androgenic steroids (AASs). Nandrolone was regarded solely as a synthetic AAS until the 1980s when trace concentrations of apparently endogenous nandrolone were detected in urine samples obtained from intact male horses (stallions). Since then, its endogenous origin has been reported in boars and bulls; endogenous NAED and nandrolone have been identified in plasma and urine samples collected from stallions. More recently, however, it was suggested that NAED and nandrolone detected in urine samples from stallions are primarily artifacts due to the analytical procedure. The present study was undertaken to determine whether NAED and nandrolone detected in plasma and urine samples collected from stallions are truly endogenous or artifacts from sample processing. To answer this question, fresh plasma and urine samples from ≥8 stallions were analyzed for the two AASs, soon after collection, by liquid chromatography hyphenated to tandem mass spectrometry (LC-MS/MS). NAED and nandrolone were not detected in fresh plasma samples but detected in the same samples post storage. Concentrations of both AASs increased with storage time, and the increases were greater at a higher storage temperature (37°C versus 4°C, and ambient temperature versus 4°C). Although NAED was detected in some fresh stallion urine samples, its concentration (<407 pg/mL) was far lower (<0.4%) than that in the same samples post storage (at ambient temperature for 15 days). Nandrolone was not detected in most of fresh urine samples but detected in the same samples post storage. Based on these results, it is concluded that all NAED and nandrolone detected in stored plasma samples of stallions and most of them in the stored urine samples are not from endogenous origins but spontaneously generated during sample storage, most likely from spontaneous decarboxylation of androstenedione-19-oic acid and testosterone-19-oic acid. To our knowledge, it is the first time that all NAED and nandrolone detected in plasma of stallions and most of them detected in the urine have been shown to be spontaneously generated in vitro during sample storage. This finding would have significant implications with regard to the regulation of the two steroids in horse racing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Determination of the influence of dispersion pattern of pesticide-resistant individuals on the reliability of resistance estimates using different sampling plans.

PubMed

Shah, R; Worner, S P; Chapman, R B

2012-10-01

Pesticide resistance monitoring includes resistance detection and subsequent documentation/ measurement. Resistance detection would require at least one (≥1) resistant individual(s) to be present in a sample to initiate management strategies. Resistance documentation, on the other hand, would attempt to get an estimate of the entire population (≥90%) of the resistant individuals. A computer simulation model was used to compare the efficiency of simple random and systematic sampling plans to detect resistant individuals and to document their frequencies when the resistant individuals were randomly or patchily distributed. A patchy dispersion pattern of resistant individuals influenced the sampling efficiency of systematic sampling plans while the efficiency of random sampling was independent of such patchiness. When resistant individuals were randomly distributed, sample sizes required to detect at least one resistant individual (resistance detection) with a probability of 0.95 were 300 (1%) and 50 (10% and 20%); whereas, when resistant individuals were patchily distributed, using systematic sampling, sample sizes required for such detection were 6000 (1%), 600 (10%) and 300 (20%). Sample sizes of 900 and 400 would be required to detect ≥90% of resistant individuals (resistance documentation) with a probability of 0.95 when resistant individuals were randomly dispersed and present at a frequency of 10% and 20%, respectively; whereas, when resistant individuals were patchily distributed, using systematic sampling, a sample size of 3000 and 1500, respectively, was necessary. Small sample sizes either underestimated or overestimated the resistance frequency. A simple random sampling plan is, therefore, recommended for insecticide resistance detection and subsequent documentation.

Performance of Traditional and Molecular Methods for Detecting Biological Agents in Drinking Water

USGS Publications Warehouse

Francy, Donna S.; Bushon, Rebecca N.; Brady, Amie M.G.; Bertke, Erin E.; Kephart, Christopher M.; Likirdopulos, Christina A.; Mailot, Brian E.; Schaefer, Frank W.; Lindquist, H.D. Alan

2009-01-01

To reduce the impact from a possible bioterrorist attack on drinking-water supplies, analytical methods are needed to rapidly detect the presence of biological agents in water. To this end, 13 drinking-water samples were collected at 9 water-treatment plants in Ohio to assess the performance of a molecular method in comparison to traditional analytical methods that take longer to perform. Two 100-liter samples were collected at each site during each sampling event; one was seeded in the laboratory with six biological agents - Bacillus anthracis (B. anthracis), Burkholderia cepacia (as a surrogate for Bu. pseudomallei), Francisella tularensis (F. tularensis), Salmonella Typhi (S. Typhi), Vibrio cholerae (V. cholerae), and Cryptospordium parvum (C. parvum). The seeded and unseeded samples were processed by ultrafiltration and analyzed by use of quantiative polymerase chain reaction (qPCR), a molecular method, and culture methods for bacterial agents or the immunomagnetic separation/fluorescent antibody (IMS/FA) method for C. parvum as traditional methods. Six replicate seeded samples were also processed and analyzed. For traditional methods, recoveries were highly variable between samples and even between some replicate samples, ranging from below detection to greater than 100 percent. Recoveries were significantly related to water pH, specific conductance, and dissolved organic carbon (DOC) for all bacteria combined by culture methods, but none of the water-quality characteristics tested were related to recoveries of C. parvum by IMS/FA. Recoveries were not determined by qPCR because of problems in quantifying organisms by qPCR in the composite seed. Instead, qPCR results were reported as detected, not detected (no qPCR signal), or +/- detected (Cycle Threshold or 'Ct' values were greater than 40). Several sample results by qPCR were omitted from the dataset because of possible problems with qPCR reagents, primers, and probes. For the remaining 14 qPCR results (including some replicate samples), F. tularensis and V. cholerae were detected in all samples after ultrafiltration, B. anthracis was detected in 13 and +/- detected in 1 sample, and C. parvum was detected in 9 and +/- detected in 4 samples. Bu. cepacia was detected in nine samples, +/- detected in two samples, and not detected in three samples (for two out of three samples not detected, a different strain was used). The qPCR assay for V. cholerae provided two false positive - but late - signals in one unseeded sample. Numbers found by qPCR after ultrafiltration were significantly or nearly significantly related to those found by traditional methods for B. anthracis, F. tularensis, and V. cholerae but not for Bu. cepacia and C. parvum. A qPCR assay for S. Typhi was not available. The qPCR method can be used to rapidly detect B. anthracis, F. tularensis, and V. cholerae with some certainty in drinking-water samples, but additional work would be needed to optimize and test qPCR for Bu. cepacia and C. parvum and establish relations to traditional methods. The specificity for the V. cholerae assay needs to be further investigated. Evidence is provided that ultrafiltration and qPCR are promising methods to rapidly detect biological agents in the Nation's drinking-water supplies and thus reduce the impact and consequences from intentional bioterrorist events. To our knowledge, this is the first study to compare the use of traditional and qPCR methods to detect biological agents in large-volume drinking-water samples.

Discreet passive explosive detection through 2-sided wave guided fluorescence

DOEpatents

Harper, Ross James; la Grone, Marcus; Fisher, Mark

2012-10-16

The current invention provides a passive sampling device suitable for collecting and detecting the presence of target analytes. In particular, the passive sampling device is suitable for detecting nitro-aromatic compounds. The current invention further provides a passive sampling device reader suitable for determining the collection of target analytes. Additionally, the current invention provides methods for detecting target analytes using the passive sampling device and the passive sampling device reader.

Monoclonal antibodies to cyclodiene insecticides and method for detecting the same

DOEpatents

Stanker, Larry H.; Vanderlaan, Martin; Watkins, Bruce E.

1994-01-01

Methods are described for making specific monoclonal antibodies useful for detection of cyclodienes in foods and environmental samples. Monoclonal antibodies specifically reactive with cyclodienes can detect accumulated pesticides in food, tissue or environmental samples. Extraction and preparation of organic samples for immunoassay in a polar-nonpolar reaction medium permits detection of halogenated organic ring structures at concentrations in samples.

I Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader.

PubMed

Smart, Adam S; Tingley, Reid; Weeks, Andrew R; van Rooyen, Anthony R; McCarthy, Michael A

2015-10-01

Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental variables (water depth, rainfall, ambient temperature) were not clearly correlated with detection probabilities estimated via trapping, whereas eDNA detection probabilities were negatively correlated with water depth, possibly reflecting higher eDNA concentrations at lower water levels. Our findings demonstrate that eDNA sampling can be an order of magnitude more sensitive than traditional methods, and illustrate that traditional- and eDNA-based surveys can provide independent information on species distributions when occupancy surveys are conducted over short timescales.

Pharmaceutical compounds in shallow groundwater in non-agricultural areas of Minnesota: study design, methods, and data, 2013

USGS Publications Warehouse

Elliott, Sarah M.; Erickson, Melinda L.

2014-01-01

The U.S. Geological Survey, in cooperation with the Minnesota Pollution Control Agency, completed a study on the occurrence of pharmaceutical compounds and other contaminants of emerging concern in shallow groundwater in non-agricultural areas of Minnesota during 2013. This report describes the study design and methods for the study on the occurrence of pharmaceuticals and other contaminants of emerging concern, and presents the data collected on pharmaceutical compounds. Samples were analyzed by the U.S. Geological Survey National Water Quality Laboratory for 110 pharmaceutical compounds using research method 9017. Samples from 21 of 45 wells had detectable concentrations of at least one of the 110 compounds analyzed. One sample contained detectable concentrations of nine compounds, which was the most detected in a single sample. Fewer than five compounds were detected in most samples. Among all samples, 27 of the 110 compounds were detected in groundwater from at least one well. Desmethyldiltiazem and nicotine were the most frequently detected compounds, each detected in 5 of 46 environmental samples (one well was sampled twice so a total of 46 environmental samples were collected from 45 wells). Caffeine had the highest detectable concentration of all the compounds at 2,060 nanograms per liter.

Water- and air-quality and surficial bed-sediment monitoring of the Sweetwater Reservoir watershed, San Diego County, California, 2003-09

USGS Publications Warehouse

Mendez, Gregory O.; Majewski, Michael S.; Foreman, William T.; Morita, Andrew Y.

2015-01-01

Sampling results show concentrations of the gasoline oxygenate methyl tert-butyl ether in water and air samples declined after it was phased out by the State of California in January 2004. The largest concentrations of gasoline hydrocarbons benzene and toluene in water were detected at or near the surface of the SWR. Isophorone and phenol were the two most frequently detected BNA compounds in water. Diuron, prometon, and simazine were the most frequently detected pesticide compounds in water. Concentrations of benzene and toluene in air samples were highest during the cooler months and had a consistent seasonal pattern over time. Ten PAH compounds were detected frequently in air samples. Twelve pesticide compounds were also detected in air samples. Surficial bed-sediment samples were analyzed for 53 PAHs; 22 of the compounds had one or more detections. Surficial bed-sediment samples were analyzed for 22 organic compounds; only 6 compounds had one or more detections. Surficial bed-sediment samples were analyzed for 37 metals.

Dissolved pesticide concentrations entering the Sacramento-San Joaquin Delta from the Sacramento and San Joaquin Rivers, California, 2012-13

USGS Publications Warehouse

Orlando, James L.; McWayne, Megan; Sanders, Corey; Hladik, Michelle

2014-01-01

Surface-water samples were collected from the Sacramento and San Joaquin Rivers where they enter the Sacramento–San Joaquin Delta, and analyzed by the U.S. Geological Survey for a suite of 99 current-use pesticides and pesticide degradates. Samples were collected twice per month from May 2012 through July 2013 and from May 2012 through April 2013 at the Sacramento River at Freeport, and the San Joaquin River near Vernalis, respectively. Samples were analyzed by two separate laboratory methods by using gas chromatography with mass spectrometry or liquid chromatography with tandem mass spectrometry. Method detection limits ranged from 0.9 to 10.5 nanograms per liter (ng/L). A total of 37 pesticides and degradates were detected in water samples collected during the study (18 herbicides, 11 fungicides, 7 insecticides, and 1 synergist). The most frequently detected pesticides overall were the herbicide hexazinone (detected in 100 percent of the samples); 3,4-dichloroaniline (97 percent), which is a degradate of the herbicides diuron and propanil; the fungicide azoxystrobin (83 percent); and the herbicides diuron (72 percent), simazine (66 percent), and metolachlor (64 percent). Insecticides were rarely detected during the study. Pesticide concentrations varied from below the method detection limits to 984 ng/L (hexazinone). Twenty seven pesticides and (or) degradates were detected in Sacramento River samples, and the average number of pesticides per sample was six. The most frequently detected compounds in these samples were hexazinone (detected in 100 percent of samples), 3,4-dichloroaniline (97 percent), azoxystrobin (88 percent), diuron (56 percent), and simazine (50 percent). Pesticides with the highest detected maximum concentrations in Sacramento River samples included the herbicide clomazone (670 ng/L), azoxystrobin (368 ng/L), 3,4-dichloroaniline (364 ng/L), hexazinone (130 ng/L), and propanil (110 ng/L), and all but hexazinone are primarily associated with rice agriculture. In addition to the twice monthly sampling, surface-water samples were collected from the Sacramento River on 5 consecutive days following a rainfall event in the Sacramento urban area. Samples collected following this event contained an average of 11 pesticides. The insecticides carbaryl, fipronil, and imidacloprid; the herbicide DCPA; and the fungicide imazalil were only detected in the Sacramento River during this storm-runoff event, and two detections of fipronil during this period exceeded the U.S. Environmental Protection Agency Aquatic Life Benchmark (11 ng/L) for chronic toxicity to invertebrates in freshwater. In San Joaquin River samples, 26 pesticides and (or) degradates were detected, and the average number detected per sample was 9. The most frequently detected compounds in these samples were hexazinone and metolachlor (detected in 100 percent of samples); diuron (96 percent); the fungicide boscalid (96 percent); the degradates 3,4-dicloroaniline (92 percent) and NN-(3,4-Dichlorophenyl)-N’-methylurea (DCPMU; 83 percent); simazine (83 percent); and azoxystrobin (75 percent). The pesticides with the highest detected maximum concentrations were hexazinone (984 ng/L), diuron (695 ng/L), simazine (524 ng/L), the herbicide prometryn (155 ng/L), metolachlor (127 ng/L), boscalid (112 ng/L), DCPMU (111 ng/L), and the herbicide pendimethalin (108 ng/L).

Salmonella detection in poultry samples. Comparison of two commercial real-time PCR systems with culture methods for the detection of Salmonella spp. in environmental and fecal samples of poultry.

PubMed

Sommer, D; Enderlein, D; Antakli, A; Schönenbrücher, H; Slaghuis, J; Redmann, T; Lierz, M

2012-01-01

The efficiency of two commercial PCR methods based on real-time technology, the foodproof® Salmonella detection system and the BAX® PCR Assay Salmonella system was compared to standardized culture methods (EN ISO 6579:2002 - Annex D) for the detection of Salmonella spp. in poultry samples. Four sample matrices (feed, dust, boot swabs, feces) obtained directly from poultry flocks, as well as artificially spiked samples of the same matrices, were used. All samples were tested for Salmonella spp. using culture methods first as the gold standard. In addition samples spiked with Salmonella Enteridis were tested to evaluate the sensitivity of both PCR methods. Furthermore all methods were evaluated in an annual ring-trial of the National Salmonella Reference Laboratory of Germany. Salmonella detection in the matrices feed, dust and boot swabs were comparable in both PCR systems whereas the results from feces differed markedly. The quality, especially the freshness, of the fecal samples had an influence on the sensitivity of the real-time PCR and the results of the culture methods. In fresh fecal samples an initial spiking level of 100cfu/25g Salmonella Enteritidis was detected. Two-days-dried fecal samples allowed the detection of 14cfu/25g. Both real- time PCR protocols appear to be suitable for the detection of Salmonella spp. in all four matrices. The foodproof® system detected eight samples more to be positive compared to the BAX® system, but had a potential false positive result in one case. In 7-days-dried samples none of the methods was able to detect Salmonella likely through letal cell damage. In general the advantage of PCR analyses over the culture method is the reduction of working time from 4-5 days to only 2 days. However, especially for the analysis of fecal samples official validation should be conducted according to the requirement of EN ISO6579:2002 - Annex D.

Occurrence of pesticides in surface water and sediments from three central California coastal watersheds, 2008-2009

USGS Publications Warehouse

Smalling, Kelly L.; Orlando, James L.

2011-01-01

Water and sediment (bed and suspended) were collected from January 2008 through October 2009 from 12 sites in 3 of the largest watersheds along California's Central Coast (Pajaro, Salinas, and Santa Maria Rivers) and analyzed for a suite of pesticides by the U.S. Geological Survey. Water samples were collected in each watershed from the estuaries and major tributaries during 4 storm events and 11 dry season sampling events in 2008 and 2009. Bed sediments were collected from depositional zones at the tributary sampling sites three times over the course of the study. Suspended sediment samples were collected from the major tributaries during the four storm events and in the tributaries and estuaries during three dry season sampling events in 2009. Water samples were analyzed for 68 pesticides using gas chromatography/mass spectrometry. A total of 38 pesticides were detected in 144 water samples, and 13 pesticides were detected in more than half the samples collected over the course of the study. Dissolved pesticide concentrations ranged from below their method detection limits to 36,000 nanograms per liter (boscalid). The most frequently detected pesticides in water from all the watersheds were azoxystrobin, boscalid, chlorpyrifos, DCPA, diazinon, oxyfluorfen, prometryn, and propyzamide, which were found in more than 80 percent of the samples. On average, detection frequencies and concentrations were higher in samples collected during winter storm events compared to the summer dry season. With the exception of the fungicide, myclobutanil, the Santa Maria estuary watershed exhibited higher pesticide detection frequencies than the Pajaro and Salinas watersheds. Bed and suspended sediment samples were analyzed for 55 pesticides using accelerated solvent extraction, gel permeation chromatography for sulfur removal, and carbon/alumina stacked solid-phase extraction cartridges to remove interfering sediment matrices. In bed sediment samples, 17 pesticides were detected including pyrethroid and organophosphate (OP) insecticides, p,p'-DDT and its degradates, as well as several herbicides. The only pesticides detected more than half the time were p,p'-DDD, p,p'-DDE, and p,p'-DDT. Maximum pesticide concentrations ranged from less than their respective method detection limits to 234 micrograms per kilogram (p,p'-DDE). Four pyrethroids (bifenthrin, &# 955;-cyhalothrin, permethrin, and &# 964;-fluvalinate) were detected in bed sediment samples, though concentrations were relatively low (less than 10 microgram per kilogram). The greatest number of pesticides were detected in samples collected from Lower Orcutt Creek, the major tributary to the Santa Maria estuary. In suspended sediment samples, 19 pesticides were detected, and maximum concentrations ranged from less than the method detection limits to 549 micrograms per kilogram (chlorpyrifos). The most frequently detected pesticides were p,p'-DDE (49 percent), p,p'-DDT (38 percent), and chlorpyrifos (32 percent). During storm events, 19 pesticides were detected in suspended sediment samples compared to 10 detected during the dry season. Pesticide concentrations commonly were higher in suspended sediments during storm events than during the dry season, as well.

Comparison of Immunohistochemistry and Direct Sanger Sequencing for Detection of the BRAFV600E Mutation in Thyroid Neoplasm

PubMed Central

Oh, Hye-Seon; Kwon, Hyemi; Park, Suyeon; Kim, Mijin; Jeon, Min Ji; Kim, Tae Yong; Shong, Young Kee; Kim, Won Bae; Choi, Jene

2018-01-01

Background The BRAFV600E mutation is the most common genetic alteration identified in papillary thyroid carcinoma (PTC). Because of its costs effectiveness and sensitivity, direct Sanger sequencing has several limitations. The aim of this study was to evaluate the efficiency of immunohistochemistry (IHC) as an alternative method to detect the BRAFV600E mutation in preoperative and postoperative tissue samples. Methods We evaluated 71 patients who underwent thyroid surgery with the result of direct sequencing of the BRAFV600E mutation. IHC staining of the BRAFV600E mutation was performed in 49 preoperative and 23 postoperative thyroid specimens. Results Sixty-two patients (87.3%) had PTC, and of these, BRAFV600E was confirmed by direct sequencing in 57 patients (91.9%). In 23 postoperative tissue samples, the BRAFV600E mutation was detected in 16 samples (70%) by direct sequencing and 18 samples (78%) by IHC. In 24 fine needle aspiration (FNA) samples, BRAFV600E was detected in 18 samples (75%) by direct sequencing and 16 samples (67%) by IHC. In 25 core needle biopsy (CNB) samples, the BRAFV600E mutation was detected in 15 samples (60%) by direct sequencing and 16 samples (64%) by IHC. The sensitivity and specificity of IHC for detecting the BRAFV600E mutation were 77.8% and 66.7% in FNA samples and 99.3% and 80.0% in CNB samples. Conclusion IHC could be an alternative method to direct Sanger sequencing for BRAFV600E mutation detection both in postoperative and preoperative samples. However, application of IHC to detect the BRAFV600E mutation in FNA samples is of limited value compared with direct sequencing. PMID:29388401

Monoclonal antibodies to cyclodiene insecticides and method for detecting the same

DOEpatents

Stanker, L.H.; Vanderlaan, M.; Watkins, B.E.

1994-08-02

Methods are described for making specific monoclonal antibodies useful for detection of cyclodienes in foods and environmental samples. Monoclonal antibodies specifically reactive with cyclodienes can detect accumulated pesticides in food, tissue or environmental samples. Extraction and preparation of organic samples for immunoassay in a polar-nonpolar reaction medium permits detection of halogenated organic ring structures at concentrations in samples. 13 figs.

Screening Test for Shed Skin Cells by Measuring the Ratio of Human DNA to Staphylococcus epidermidis DNA.

PubMed

Nakanishi, Hiroaki; Ohmori, Takeshi; Hara, Masaaki; Takahashi, Shirushi; Kurosu, Akira; Takada, Aya; Saito, Kazuyuki

2016-05-01

A novel screening method for shed skin cells by detecting Staphylococcus epidermidis (S. epidermidis), which is a resident bacterium on skin, was developed. Staphylococcus epidermidis was detected using real-time PCR. Staphylococcus epidermidis was detected in all 20 human skin surface samples. Although not present in blood and urine samples, S. epidermidis was detected in 6 of 20 saliva samples, and 5 of 18 semen samples. The ratio of human DNA to S. epidermidisDNA was significantly smaller in human skin surface samples than in saliva and semen samples in which S. epidermidis was detected. Therefore, although skin cells could not be identified by detecting only S. epidermidis, they could be distinguished by measuring the S. epidermidis to human DNA ratio. This method could be applied to casework touch samples, which suggests that it is useful for screening whether skin cells and human DNA are present on potential evidentiary touch samples. © 2016 American Academy of Forensic Sciences.

Occurrence of fungicides and other pesticides in surface water, groundwater, and sediment from three targeted-use areas in the United States, 2009

USGS Publications Warehouse

Orlando, James L.; Smalling, Kelly L.; Reilly, Timothy J.; Boehlke, Adam; Meyer, Michael T.; Kuivila, Kathryn

2013-01-01

Surface-water, groundwater, and suspended- and bedsediment samples were collected in three targeted-use areas in the United States where potatoes were grown during 2009 and analyzed for an extensive suite of fungicides and other pesticides by gas chromatograph/mass spectrometry and liquid chromatography with tandem mass spectrometry. Fungicides were detected in all environmental matrices sampled during the study. The most frequently detected fungicides were azoxystrobin, boscalid, chlorothalonil, and pyraclostrobin. Other pesticides that were detected frequently included amino phosphonic acid (AMPA), atrazine, metolaclor, and the organochlorine insecticide p,p’-DDT and its degradates p,p’-DDD and p,p’-DDE. A greater number of pesticides were detected in surface water relative to the other environmental matrices sampled, and at least one pesticide was detected in 62 of the 63 surfacewater samples. The greatest numbers of pesticides and the maximum observed concentrations for most pesticides were measured in surface-water samples from Idaho. In eight surface- water samples (six from Idaho and two from Wisconsin), concentrations of bifenthrin, metolachlor, or malathion exceeded U.S. Environmental Protection Agency freshwater aquatic-life benchmarks for chronic toxicity to invertebrates. Thirteen pesticides, including seven fungicides, were detected in groundwater samples. Shallow groundwater samples collected beneath recently harvested potato fields contained more pesticides and had higher concentrations of pesticides than samples collected from other groundwater sources sampled during the study. Generally, pesticide concentrations were lower in groundwater samples than in surfacewater or sediment samples, with the exception of the fungicide boscalid, which was found to have its highest concentration in a shallow groundwater sample collected in Wisconsin. Thirteen pesticides, including four fungicides, were detected in suspended-sediment samples. The most frequently detected compounds were the fungicides boscalid, pyraclostrobin, and zoxamide, and the degradates p,p’-DDD and p,p’-DDE. Twenty pesticides, including six fungicides, were detected in bed-sediment samples. The most frequently detected compounds were pyraclostrobin, p,p’-DDT, p,p’-DDD, and p,p’-DDE.

Year-round presence of neonicotinoid insecticides in tributaries to the Great Lakes, USA

USGS Publications Warehouse

Hladik, Michelle; Corsi, Steven; Kolpin, Dana W.; Baldwin, Austin K.; Blackwell, Brett R.; Cavallin, Jenna E.

2018-01-01

To better characterize the transport of neonicotinoid insecticides to the world's largest freshwater ecosystem, monthly samples (October 2015–September 2016) were collected from 10 major tributaries to the Great Lakes, USA. For the monthly tributary samples, neonicotinoids were detected in every month sampled and five of the six target neonicotinoids were detected. At least one neonicotinoid was detected in 74% of the monthly samples with up to three neonicotinoids detected in an individual sample (10% of all samples). The most frequently detected neonicotinoid was imidacloprid (53%), followed by clothianidin (44%), thiamethoxam (22%), acetamiprid (2%), and dinotefuran (1%). Thiacloprid was not detected in any samples. The maximum concentration for an individual neonicotinoid was 230 ng L−1 and the maximum total neonicotinoids in an individual sample was 400 ng L−1. The median detected individual neonicotinoid concentrations ranged from non-detect to 10 ng L−1. The detections of clothianidin and thiamethoxam significantly increased as the percent of cultivated crops in the basins increased (ρ = 0.73, P = .01; ρ = 0.66, P = .04, respectively). In contrast, imidacloprid detections significantly increased as the percent of the urbanization in the basins increased (ρ = 0.66, P = .03). Neonicotinoid concentrations generally increased in spring through summer coinciding with the planting of neonicotinoid-treated seeds and broadcast applications of neonicotinoids. More spatially intensive samples were collected in an agriculturally dominated basin (8 sites along the Maumee River, Ohio) twice during the spring, 2016 planting season to provide further information on neonicotinoid inputs to the Great Lakes. Three neonicotinoids were ubiquitously detected (clothianidin, imidacloprid, thiamethoxam) in all water samples collected within this basin. Maximum individual neonicotinoid concentrations was 330 ng L−1 and maximum total neonicotinoid concentration was 670 ng L−1; median detected individual neonicotinoid concentrations were 7.0 to 39 ng L−1.

Ultrasensitive Detection of Shigella Species in Blood and Stool.

PubMed

Luo, Jieling; Wang, Jiapeng; Mathew, Anup S; Yau, Siu-Tung

2016-02-16

A modified immunosensing system with voltage-controlled signal amplification was used to detect Shigella in stool and blood matrixes at the single-digit CFU level. Inactivated Shigella was spiked in these matrixes and detected directly. The detection was completed in 78 min. Detection limits of 21 CFU/mL and 18 CFU/mL were achieved in stool and blood, respectively, corresponding to 2-7 CFUs immobilized on the detecting electrode. The outcome of the detection of extremely low bacterium concentration, i.e., below 100 CFU/mL, blood samples show a random nature. An analysis of the detection probabilities indicates the correlation between the sample volume and the success of detection and suggests that sample volume is critical for ultrasensitive detection of bacteria. The calculated detection limit is qualitatively in agreement with the empirically determined detection limit. The demonstrated ultrasensitive detection of Shigella on the single-digit CFU level suggests the feasibility of the direct detection of the bacterium in the samples without performing a culture.

Ground-water quality in the Chemung River Basin, New York, 2003

USGS Publications Warehouse

Hetcher-Aguila, Kari K.

2005-01-01

Water samples were collected from 24 public-supply wells and 13 private residential wells during the summer of 2003 and analyzed to describe the chemical quality of ground water throughout the Chemung River basin, upgradient from Waverly, N.Y, on the Pennsylvania border. Wells were selected to represent areas of heaviest ground-water use and greatest vulnerability to contamination, and to obtain a geographical distribution across the 1,130 square-mile basin. Samples were analyzed for physical properties, inorganic constituents, nutrients, metals and radionuclides, pesticides, volatile organic compounds, and bacteria.The cations that were detected in the highest concentrations were calcium and sodium; the anions that were detected in the greatest concentrations were bicarbonate, chloride, and sulfate. The predominant nutrient was nitrate. Nitrate concentrations in samples from wells finished in sand and gravel were greater than in those from wells finished in bedrock, except for one bedrock well, which had the highest nitrate concentration of any sample in this study. The most commonly detected metals were aluminum, barium, iron, manganese, and strontium. The range of tritium concentrations (0.6 to 12.5 tritium units) indicates that the water ages ranged from less than 10 years old to more than 50 years old. All but one of the 15 pesticides detected were herbicides; those detected most frequently were atrazine, deethylatrazine, and two degradation products of metolachlor (metachlor ESA and metachlor OA), which were the pesticides detected at the highest concentrations. Not every sample collected was analyzed for pesticides, and pesticides were detected only in wells finished in sand and gravel. Volatile organic compounds were detected in 15 samples, and the concentrations were at or near the analytical detection limits. Total coliform were detected in 12 samples; fecal coliform were detected in 7 samples; and Escherichia coli was detected in 6 samples. These bacteria were detected in water from bedrock as well as sand-and-gravel aquifers.Federal and State water-quality standards were exceeded in several samples. Two samples exceeded the chloride U.S. Environmental Protection Agency Secondary Maximum Contaminant Level of 250 milligrams per liter. The U.S. Environmental Protection Agency Drinking Water Advisory for sodium (30 to 60 milligrams per liter) was exceeded in 11 samples. The upper limit of the Secondary Maximum Contaminant Level range for aluminum (200 micrograms per liter) was exceeded in one sample. The Maximum Contaminant Level for barium (2,000 micrograms per liter) was exceeded in one sample. The Secondary Maximum Contaminant Level for iron (300 micrograms per liter) was exceeded in 11 samples. The Secondary Maximum Contaminant Level for manganese (50 micrograms per liter) was exceeded in 20 samples. The proposed Maximum Contaminant Level for radon (300 picocuries per liter) was exceeded in 34 samples.

Pesticides in Water and Suspended Sediment of the Alamo and New Rivers, Imperial Valley/Salton Sea Basin, California, 2006-2007

USGS Publications Warehouse

Orlando, James L.; Smalling, Kelly L.; Kuivila, Kathryn

2008-01-01

Water and suspended-sediment samples were collected at eight sites on the Alamo and New Rivers in the Imperial Valley/Salton Sea Basin of California and analyzed for both current-use and organochlorine pesticides by the U.S. Geological Survey. Samples were collected in the fall of 2006 and spring of 2007, corresponding to the seasons of greatest pesticide use in the basin. Large-volume water samples (up to 650 liters) were collected at each site and processed using a flow-through centrifuge to isolate suspended sediments. One-liter water samples were collected from the effluent of the centrifuge for the analysis of dissolved pesticides. Additional samples were collected for analysis of dissolved organic carbon and for suspended-sediment concentrations. Water samples were analyzed for a suite of 61 current-use and organochlorine pesticides using gas chromatography/mass spectrometry. A total of 25 pesticides were detected in the water samples, with seven pesticides detected in more than half of the samples. Dissolved concentrations of pesticides observed in this study ranged from below their respective method detection limits to 8,940 nanograms per liter (EPTC). The most frequently detected compounds in the water samples were chlorpyrifos, DCPA, EPTC, and trifluralin, which were observed in more than 75 percent of the samples. The maximum concentrations of most pesticides were detected in samples from the Alamo River. Maximum dissolved concentrations of carbofuran, chlorpyrifos, diazinon, and malathion exceeded aquatic life benchmarks established by the U.S. Environmental Protection Agency for these pesticides. Suspended sediments were analyzed for 87 current-use and organochlorine pesticides using microwave-assisted extraction, gel permeation chromatography for sulfur removal, and either carbon/alumina stacked solid-phase extraction cartridges or deactivated Florisil for removal of matrix interferences. Twenty current-use pesticides were detected in the suspended-sediment samples, including pyrethroid insecticides and fungicides. Fourteen legacy organochlorine pesticides also were detected in the suspended-sediment samples. Greater numbers of current-use and organochlorine pesticides were observed in the Alamo River samples in comparison with the New River samples. Maximum concentrations of current-use pesticides in suspended-sediment samples ranged from below their method detection limits to 174 micrograms per kilogram (pendimethalin). Most organochlorine pesticides were detected at or below their method detection limits, with the exception of p,p'-DDE, which had a maximum concentration of 54.2 micrograms per kilogram. The most frequently detected current-use pesticides in the suspended-sediment samples were chlorpyrifos, permethrin, tetraconazole, and trifluralin, which were observed in more than 83 percent of the samples. The organochlorine degradates p,p'-DDD and p,p'-DDE were detected in all suspended-sediment samples.

46 CFR 161.002-15 - Sample extraction smoke detection systems.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 6 2010-10-01 2010-10-01 false Sample extraction smoke detection systems. 161.002-15..., CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL ELECTRICAL EQUIPMENT Fire-Protective Systems § 161.002-15 Sample extraction smoke detection systems. The smoke detecting system must consist of a means for...

Ground-Water Quality in the Upper Susquehanna River Basin, New York, 2004-05

USGS Publications Warehouse

Hetcher-Aguila, Kari K.; Eckhardt, David A.V.

2006-01-01

Water samples were collected from 20 production wells and 13 private residential wells throughout the upper Susquehanna River Basin (upstream from the Pennsylvania border) during the fall of 2004 and the spring of 2005 and analyzed to describe the chemical quality of ground water in the upper basin. Wells were selected to represent areas of greatest ground-water use and highest vulnerability to contamination, and to provide a representative sampling from the entire (4,516 square-mile) upper basin. Samples were analyzed for physical properties, nutrients, inorganic constituents, metals, radionuclides, pesticides, volatile organic compounds, and bacteria. The cations that were detected in the highest concentrations were calcium, magnesium, and sodium; the anions that were detected in the greatest concentrations were bicarbonate, chloride, and sulfate. The predominant nutrient was nitrate, the concentrations of which were greater in samples from sand and gravel aquifers than in samples from bedrock. The metals barium, boron, cobalt, copper, and nickel were detected in every sample; the metals with the highest concentrations were barium, boron, iron, manganese, strontium, and lithium. The pesticide compounds detected most frequently were atrazine, deethylatrazine, alachlor ESA, and two degradation products of metolachlor (metolachlor ESA and metolachlor OA); the compounds detected in highest concentration were metolachlor ESA and OA. Volatile organic compounds were detected in 11 samples, and concentrations of 3 of these compounds exceeded 1 microgram per liter (?g/L). Methyl tert-butyl ether (MTBE), a gasollline additive, was not detected in any sample. Several analytes were found in concentrations that exceeded Federal and New York State water-quality standards, which are typically identical. Chloride concentrations exceeded the U.S. Environmental Protection Agency (USEPA) Secondary Maximum Contaminant Level (SMCL) of 250 milligrams per liter (mg/L) in two samples, and sulfate concentrations exceeded the SMCL of 250 mg/L in one sample. Sodium concentrations exceeded the USEPA Drinking Water Advisory of 60 mg/L in six samples. Nitrate concentrations exceeded the USEPA Maximum Contaminant Level (MCL) of 10 mg/L in one sample and approached this limit (at 9.84 mg/L) in another sample. Barium concentrations exceeded the MCL of 2,000 ?g/L in one sample. Iron concentrations exceeded the SMCL of 300 ?g/L in five samples, and manganese concentrations exceeded the SMCL of 50 ?g/L in 14 samples. Arsenic was detected in seven samples, and the MCL for arsenic (10 ?g/L) was exceeded in two samples. Radon-222 exceeded the proposed MCL of 300 picocuries per liter in 24 samples. Any detection of total coliform or fecal coliform bacteria is considered a violation of New York State health regulations; in this study, total coliform was detected in six samples and fecal coliform was detected in one sample, but Escherichia coli (E. coli) was not detected in any sample.

Scanning electron microscopy coupled with energy-dispersive X-ray spectrometry for quick detection of sulfur-oxidizing bacteria in environmental water samples

NASA Astrophysics Data System (ADS)

Sun, Chengjun; Jiang, Fenghua; Gao, Wei; Li, Xiaoyun; Yu, Yanzhen; Yin, Xiaofei; Wang, Yong; Ding, Haibing

2017-01-01

Detection of sulfur-oxidizing bacteria has largely been dependent on targeted gene sequencing technology or traditional cell cultivation, which usually takes from days to months to carry out. This clearly does not meet the requirements of analysis for time-sensitive samples and/or complicated environmental samples. Since energy-dispersive X-ray spectrometry (EDS) can be used to simultaneously detect multiple elements in a sample, including sulfur, with minimal sample treatment, this technology was applied to detect sulfur-oxidizing bacteria using their high sulfur content within the cell. This article describes the application of scanning electron microscopy imaging coupled with EDS mapping for quick detection of sulfur oxidizers in contaminated environmental water samples, with minimal sample handling. Scanning electron microscopy imaging revealed the existence of dense granules within the bacterial cells, while EDS identified large amounts of sulfur within them. EDS mapping localized the sulfur to these granules. Subsequent 16S rRNA gene sequencing showed that the bacteria detected in our samples belonged to the genus Chromatium, which are sulfur oxidizers. Thus, EDS mapping made it possible to identify sulfur oxidizers in environmental samples based on localized sulfur within their cells, within a short time (within 24 h of sampling). This technique has wide ranging applications for detection of sulfur bacteria in environmental water samples.

Self-sampling for human papillomavirus DNA detection: a preliminary study of compliance and feasibility in BOLIVIA.

PubMed

Surriabre, Pedro; Allende, Gustavo; Prado, Marcela; Cáceres, Leyddy; Bellot, Diego; Torrico, Andrea; Ustariz, Karina; Rojas, Shirley; Barriga, Jaime; Calle, Pamela; Villarroel, Ligia; Yañez, Rosse Mary; Baay, Marc; Rodriguez, Patricia; Fontaine, Véronique

2017-12-22

Cervical cancer incidence and mortality rates in Bolivia are among the highest in Latin America. This investigation aims to evaluate the possibility of using simple devices, e.g. a cotton swab and a glass slide, for self-sampling in order to detect human papillomavirus (HPV) DNA by PCR in cervico-vaginal cells. In the first phase of our study we evaluated the use of a glass slide as a transport medium for cervical cells. A physician took paired-cervical samples from 235 women. One sample was transported in Easyfix® solution and the other sample was smeared over a glass slide. Both were further analyzed and compared for human DNA recovery and HPV detection. A kappa value was determined to evaluate the agreement between the HPV DNA detection rates. In the second phase of the study, 222 women from the urban, peri-urban and rural regions of Cochabamba were requested to perform self-sampling using the following devices: a cotton swab combined with a glass slide, and a vaginal tampon. Women gave their opinion about the self-sampling technique. Finally, the agreement for high risk-HPV detection between self- and physician-collected samples was performed in 201 samples in order to evaluate the self-sampling technique. Firstly, the comparison between Easyfix® solution and the glass slide to transport clinical samples gave a good agreement for HPV DNA detection (κ = 0.71, 95% CI 0.60-0.81). Secondly, self-sampling, especially with cotton swab combined with glass slide, would generally be preferred over clinician sampling for a screening program based on HPV detection. Finally, we showed a good agreement between self- and physician collected samples for high risk-HPV detection (κ = 0.71, 95% CI 0.55-0.88). Simple devices such as a cotton swab and a glass slide can be used to perform self-sampling and HPV DNA detection. Furthermore, most Bolivian women preferred self-sampling over clinician-sampling for cervical cancer screening.

Metals, pesticides, and semivolatile organic compounds in sediment in Valley Forge National Historical Park, Montgomery County, Pennsylvania

USGS Publications Warehouse

Reif, Andrew G.; Sloto, Ronald A.

1997-01-01

The Schuylkill River flows through Valley Forge National Historical Park in Lower Providence and West Norriton Townships in Montgomery County, Pa. The concentration of selected metals, pesticides, semivolatile organic compounds, and total carbon in stream-bottom sediments from Valley Forge National Historical Park were determined for samples collected once at 12 sites in and around the Schuylkill River.Relatively low concentrations of arsenic, chromium, copper, and lead were detected in all samples. The concentrations of these metals are similar to concentrations in other stream-bottom sediment samples collected in the region. The concentrations of iron, manganese, and zinc were elevated in samples from four sites in the Schuylkill River, and the concentration of mercury was elevated in a sample from an impoundment along the river.The organophosphorus insecticide diazinon was detected in relatively low concentrations in half of the 12 samples analyzed. The organo-chlorine insecticide DDE was detected in all 12 samples analyzed; dieldrin was detected in 10 samples, chlordane, DDD, and DDT were detected in 9 samples, and heptachlor epoxide was detected in one sample. The concentrations of organo-chlorine and organophosphorus insecticides were relatively low and similar to concentrations in samples collected in the region.Detectable concentrations of 17 semivolatile organic compounds were measured in the 12 samples analyzed. The most commonly detected compounds were fluoranthene, phenanthrene, and pyrene. The maximum concentration detected was 4,800 micrograms per kilogram of phenanthrene. The highest concentrations of compounds were detected in Lamb Run, a small tributary to the Schuylkill River with headwaters in an industrial corporate center. The concentration of compounds in the Schuylkill River below Lamb Run is higher than the Schuylkill River above Lamb Run, indicating that sediment from Lamb Run is increasing the concentration of semivolatile organic compounds in sediment from the Schuylkill River. Concentrations of semivolatile organic compounds are lower in sediment from the Schuylkill River below Myer's Run than above Myer's Run because of the addition of relatively clean sediment from Myer's Run. Samples collected from the floodplain, impounding basin, and wetland along the Schuylkill River contained the lowest concen-trations of semivolatile organic compounds.Detectable concentrations of polychlorinated biphenyls (PCB's) were measured in 11 of the 12 samples analyzed. The maximum PCB concentration was 37 micrograms per kilogram. Sediment samples from Lamb Run contained the highest concentrations of semivolatile organic compounds and PCB's.

[Detection of Cryptospordium spp. in environmental water samples by FTA-PCR].

PubMed

Zhang, Xiao-Ping; Zhu, Qian; He, Yan-Yan; Jiang, Li; Jiang, Shou-Fu

2011-02-01

To establish a FTA-polymeras chain reaction (FTA-PCR) method in detection of Cryptospordium spp. in different sources of water. The semi automated immunomagnetic separation (IMS) of Cryptospordium oocysts in environmental water samples was performed firstly, and then genomic DNA of Cryptospordium oocysts was extracted by FTA filters disk. Oligonucleotide primers were designed based on the DNA fragment of the 18 S rRNA gene from C. parvum. Plate DNA was amplified with primers in PCR. The control DNA samples from Toxoplasma gondii,Sarcocystis suihominis, Echinococcus granulosus, and Clonorchis sinensis were amplified simultaneously. All PCR products were detected by agar electrophoresis dyed with ethidium bromide. The 446 bp fragment of DNA was detected in all samples of C. parvum, C. andersoni, and C. baileyi, while it was not detected in control groups in laboratory. No positive samples were found from 10 samples collected from tape water in 5 districts of Shanghai City by FTA-PCR. Nine positive samples were detected totally from 70 different environmental water samples, there were 0 out of 15 samples from the source of tape water, 2 out of 25 from the Huangpu River, 5 out of 15 from rivers around the animal farmers, 1 out of 9 from output water of contaminating water treatment factory, 1 out of 6 from the out gate of living contaminating water. The 446 bp fragment was detected from all the amplified positive water samples. FTA-PCR is an efficient method for gene detection of Cryptospordium oocysts, which could be used in detection of environmental water samples. The contamination degree of Cryptospordium oocysts in the river water around animal farms is high.

Laboratory evaluation of sample collection methods (organs vs swabs) for Tasmanian salmon reovirus detection in farmed Atlantic salmon, Salmo salar L.

PubMed

Zainathan, S C; Carson, J; Crane, M St J; Nowak, B F

2013-04-01

The use of swabs relative to organs as a sample collection method for the detection of Tasmanian salmon reovirus (TSRV) in farmed Tasmanian Atlantic salmon, Salmo salar L., was evaluated by RT-qPCR. Evaluation of individual and pooled sample collection (organs vs swabs) was carried out to determine the sensitivity of the collection methods and the effect of pooling of samples for the detection of TSRV. Detection of TSRV in individual samples was as sensitive when organs were sampled compared to swabs, and in pooled samples, organs demonstrated a sensitivity of one 10-fold dilution higher than sampling of pooled swabs. Storage of swabs at 4 °C for t = 24 h demonstrated results similar to those at t = 0. Advantages of using swabs as a preferred sample collection method for the detection of TSRV compared to organ samples are evident from these experimental trials. © 2012 Blackwell Publishing Ltd.

A Field-Based Cleaning Protocol for Sampling Devices Used in Life-Detection Studies

NASA Astrophysics Data System (ADS)

Eigenbrode, Jennifer; Benning, Liane G.; Maule, Jake; Wainwright, Norm; Steele, Andrew; Amundsen, Hans E. F.

2009-06-01

Analytical approaches to extant and extinct life detection involve molecular detection often at trace levels. Thus, removal of biological materials and other organic molecules from the surfaces of devices used for sampling is essential for ascertaining meaningful results. Organic decontamination to levels consistent with null values on life-detection instruments is particularly challenging at remote field locations where Mars analog field investigations are carried out. Here, we present a seven-step, multi-reagent decontamination method that can be applied to sampling devices while in the field. In situ lipopolysaccharide detection via low-level endotoxin assays and molecular detection via gas chromatography-mass spectrometry were used to test the effectiveness of the decontamination protocol for sampling of glacial ice with a coring device and for sampling of sediments with a rover scoop during deployment at Arctic Mars-analog sites in Svalbard, Norway. Our results indicate that the protocols and detection technique sufficiently remove and detect low levels of molecular constituents necessary for life-detection tests.

A field-based cleaning protocol for sampling devices used in life-detection studies.

PubMed

Eigenbrode, Jennifer; Benning, Liane G; Maule, Jake; Wainwright, Norm; Steele, Andrew; Amundsen, Hans E F

2009-06-01

Analytical approaches to extant and extinct life detection involve molecular detection often at trace levels. Thus, removal of biological materials and other organic molecules from the surfaces of devices used for sampling is essential for ascertaining meaningful results. Organic decontamination to levels consistent with null values on life-detection instruments is particularly challenging at remote field locations where Mars analog field investigations are carried out. Here, we present a seven-step, multi-reagent decontamination method that can be applied to sampling devices while in the field. In situ lipopolysaccharide detection via low-level endotoxin assays and molecular detection via gas chromatography-mass spectrometry were used to test the effectiveness of the decontamination protocol for sampling of glacial ice with a coring device and for sampling of sediments with a rover scoop during deployment at Arctic Mars-analog sites in Svalbard, Norway. Our results indicate that the protocols and detection technique sufficiently remove and detect low levels of molecular constituents necessary for life-detection tests.

Detection of hepatitis B virus infection markers in dried plasma spots among patients in Congo-Brazzaville.

PubMed

Alidjinou, Enagnon Kazali; Moukassa, Donatien; Sané, Famara; Twagirimana Nyenyeli, Séraphin; Akoko, Estina Chandrelle; Mountou, Michèle Valy; Bocket, Laurence; Ibara, Jean-Rosaire; Hober, Didier

2014-03-01

The detection of hepatitis B virus (HBV) infection markers by using dried plasma spots from 32 patients living in Congo has been assessed. Considering frozen plasma samples as gold standard, the sensitivity and specificity of HBV serologic markers detection in dried plasma eluted from filter paper were 100%. The sensitivity and the specificity of HBV DNA detection reached 96% and 100%, respectively, with plasma samples dried on filter paper compared to standard samples. Dried plasma samples can represent an alternative to conventional sampling for HBV detection and management of the infection in developing countries. Copyright © 2014 Elsevier Inc. All rights reserved.

Occurrence of pesticides in water and sediment collected from amphibian habitats located throughout the United States, 2009-10

USGS Publications Warehouse

Smalling, Kelly L.; Orlando, James L.; Calhoun, Daniel; Battaglin, William A.; Kuivila, Kathryn

2012-01-01

Water and bed-sediment samples were collected by the U.S. Geological Survey (USGS) in 2009 and 2010 from 11 sites within California and 18 sites total in Colorado, Georgia, Idaho, Louisiana, Maine, and Oregon, and were analyzed for a suite of pesticides by the USGS. Water samples and bed-sediment samples were collected from perennial or seasonal ponds located in amphibian habitats in conjunction with research conducted by the USGS Amphibian Research and Monitoring Initiative and the USGS Toxic Substances Hydrology Program. Sites selected for this study in three of the states (California, Colorado, and Orgeon) have no direct pesticide application and are considered undeveloped and remote. Sites selected in Georgia, Idaho, Louisiana, and Maine were in close proximity to either agricultural or suburban areas. Water and sediment samples were collected once in 2009 during amphibian breeding seasons. In 2010, water samples were collected twice. The first sampling event coincided with the beginning of the frog breeding season for the species of interest, and the second event occurred 10-12 weeks later when pesticides were being applied to the surrounding areas. Additionally, water was collected during each sampling event to measure dissolved organic carbon, nutrients, and the fungus, Batrachochytrium dendrobatidis, which has been linked to amphibian declines worldwide. Bed-sediment samples were collected once during the beginning of the frog breeding season, when the amphibians are thought to be most at risk to pesticides. Results of this study are reported for the following two geographic scales: (1) for a national scale, by using data from the 29 sites that were sampled from seven states, and (2) for California, by using data from the 11 sampled sites in that state. Water samples were analyzed for 96 pesticides by using gas chromatography/mass spectrometry. A total of 24 pesticides were detected in one or more of the 54 water samples, including 7 fungicides, 10 herbicides, 4 insecticides, 1 synergist, and 2 pesticide degradates. On a national scale, aminomethylphosphonic acid (AMPA), the primary degradate of the herbicide glyphosate, which is the active ingredient in Roundup®, was the most frequently detected pesticide in water (16 of 54 samples) followed by glyphosate (8 of 54 samples). The maximum number of pesticides observed at a single site was nine compounds in a water sample from a site in Louisiana. The maximum concentration of a pesticide or degradate observed in water was 2,880 nanograms per liter of clomazone (a herbicide) at a site in Louisiana. In California, a total of eight pesticides were detected among all of the low and high elevation sites; AMPA was the most frequently detected pesticide, but glyphosate was detected at the highest concentrations (1.1 micrograms per liter). Bed-sediment samples were analyzed for 94 pesticides by using accelerated solvent extraction, gel permeation chromatography for sulfur removal, and carbon/alumina stacked solid-phase extraction cartridges to remove interfering sediment matrices. In bed sediment, 22 pesticides were detected in one or more of the samples, including 9 fungicides, 3 pyrethroid insecticides, p,p'-dichlorodiphenyltrichloroethane (p,p'-DDT) and its major degradates, as well as several herbicides. Pyraclostrobin, a strobilurin fungicide, and bifenthrin, a pyrethroid insecticide, were detected most frequently. Maximum pesticide concentrations ranged from less than their respective method detection limits to 1,380 micrograms per kilogram (tebuconazole in California). The number of pesticides detected in samples from each site ranged from zero to six compounds. The sites with the greatest number of pesticides were in Maine and Oregon with six pesticides detected in one sample from each state, followed by Georgia with four pesticides in one sample. For California, a total of 10 pesticides were detected among all sites, and 4 pesticides were detected at both low and high elevation sites; tebuconazole and pyraclostrobin were the two most frequently detected pesticides in California. For the other six selected states, the most frequently detected pesticides in bed sediment were pyraclostrobin (detected in 17 of 42 samples), bifenthrin (detected in 14 of 42 samples), and tebuconazole (detected in 10 of 42 samples). The fungus, Batrachochytrium dendrobatidis (Bd), was detected in water samples in sites from four of the seven states during 2009 and 2010, and the number of zoospore equivalents per liter of water in samples where Bd was detected ranged from 1.6 to 343. Bd was not detected in water samples from sites in Georgia, Louisiana, and Oregon.

Real time viability detection of bacterial spores

DOEpatents

Vanderberg, Laura A.; Herdendorf, Timothy J.; Obiso, Richard J.

2003-07-29

This invention relates to a process for detecting the presence of viable bacterial spores in a sample and to a spore detection system, the process including placing a sample in a germination medium for a period of time sufficient for commitment of any present viable bacterial spores to occur, mixing the sample with a solution of a lanthanide capable of forming a fluorescent complex with dipicolinic acid, and, measuring the sample for the presence of dipicolinic acid, and the system including a germination chamber having inlets from a sample chamber, a germinant chamber and a bleach chamber, the germination chamber further including an outlet through a filtering means, the outlet connected to a detection chamber, the detection chamber having an inlet from a fluorescence promoting metal chamber and the detection chamber including a spectral excitation source and a means of measuring emission spectra from a sample, the detection chamber further connected to a waste chamber. A germination reaction mixture useful for promoting commitment of any viable bacterial spores in a sample including a combination of L-alanine, L-asparagine and D-glucose is also described.

Water quality and possible sources of nitrate in the Cimarron Terrace Aquifer, Oklahoma, 2003

USGS Publications Warehouse

Masoner, Jason R.; Mashburn, Shana L.

2004-01-01

Water from the Cimarron terrace aquifer in northwest Oklahoma commonly has nitrate concentrations that exceed the maximum contaminant level of 10 milligrams per liter of nitrite plus nitrate as nitrogen (referred to as nitrate) set by the U.S. Environmental Protection Agency for public drinking water supplies. Starting in July 2003, the U.S. Geological Survey, in cooperation with the Oklahoma Department of Environmental Quality, conducted a study in the Cimarron terrace aquifer to assess the water quality and possible sources of nitrate. A qualitative and quantitative approach based on multiple lines of evidence from chemical analysis of nitrate, nitrogen isotopes in nitrate, pesticides (indicative of cropland fertilizer application), and wastewater compounds (indicative of animal or human wastewater) were used to indicate possible sources of nitrate in the Cimarron terrace aquifer. Nitrate was detected in 44 of 45 ground-water samples and had the greatest median concentration (8.03 milligrams per liter) of any nutrient analyzed. Nitrate concentrations ranged from <0.06 to 31.8 milligrams per liter. Seventeen samples had nitrate concentrations exceeding the maximum contaminant level of 10 milligrams per liter. Nitrate concentrations in agricultural areas were significantly greater than nitrate concentrations in grassland areas. Pesticides were detected in 15 of 45 ground-water samples. Atrazine and deethylatrazine, a metabolite of atrazine, were detected most frequently. Deethylatrazine was detected in water samples from 9 wells and atrazine was detected in samples from 8 wells. Tebuthiuron was detected in water samples from 5 wells; metolachlor was detected in samples from 4 wells; prometon was detected in samples from 4 wells; and alachlor was detected in 1 well. None of the detected pesticide concentrations exceeded the maximum contaminant level or health advisory level set by the U.S. Environmental Protection Agency. Wastewater compounds were detected in 28 of 45 groundwater samples. Of the 20 wastewater compounds detected, 11 compounds were from household chemicals, 3 compounds were hydrocarbons, 2 compounds were industrial chemicals, 2 compounds were pesticides, 1 compound was of animal source, and 1 compound was a detergent compound. The most frequently detected wastewater compound was phenol, which was detected in 23 wells. N,N-diethyl-meta-toluamide (DEET) was detected in water samples from 5 wells. Benzophenone, ethanol- 2-butoxy-phosphate, and tributylphosphate were detected in water samples from 3 wells. Fertilizer was determined to be the possible source of nitrate in samples from 13 of 45 wells sampled, with a15N values ranging from 0.43 to 3.46 permil. The possible source of nitrate for samples from the greatest number of wells (22 wells) was from mixed sources of nitrate from fertilizer, septic or manure, or natural sources. Mixed nitrate sources had a 15N values ranging from 0.25 to 9.83 permil. Septic or manure was determined as the possible source of nitrate in samples from 2 wells. Natural sources were determined to be the possible source of nitrate in samples from 7 wells, with a 15N values ranging from 0.83 to 9.44 permil.

Nationwide reconnaissance of contaminants of emerging concern in source and treated drinking waters of the United States: Pharmaceuticals.

PubMed

Furlong, Edward T; Batt, Angela L; Glassmeyer, Susan T; Noriega, Mary C; Kolpin, Dana W; Mash, Heath; Schenck, Kathleen M

2017-02-01

Mobile and persistent chemicals that are present in urban wastewater, such as pharmaceuticals, may survive on-site or municipal wastewater treatment and post-discharge environmental processes. These pharmaceuticals have the potential to reach surface and groundwaters, essential drinking-water sources. A joint, two-phase U.S. Geological Survey-U.S. Environmental Protection Agency study examined source and treated waters from 25 drinking-water treatment plants from across the United States. Treatment plants that had probable wastewater inputs to their source waters were selected to assess the prevalence of pharmaceuticals in such source waters, and to identify which pharmaceuticals persist through drinking-water treatment. All samples were analyzed for 24 pharmaceuticals in Phase I and for 118 in Phase II. In Phase I, 11 pharmaceuticals were detected in all source-water samples, with a maximum of nine pharmaceuticals detected in any one sample. The median number of pharmaceuticals for all 25 samples was five. Quantifiable pharmaceutical detections were fewer, with a maximum of five pharmaceuticals in any one sample and a median for all samples of two. In Phase II, 47 different pharmaceuticals were detected in all source-water samples, with a maximum of 41 pharmaceuticals detected in any one sample. The median number of pharmaceuticals for all 25 samples was eight. For 37 quantifiable pharmaceuticals in Phase II, median concentrations in source water were below 113ng/L. For both Phase I and Phase II campaigns, substantially fewer pharmaceuticals were detected in treated water samples than in corresponding source-water samples. Seven different pharmaceuticals were detected in all Phase I treated water samples, with a maximum of four detections in any one sample and a median of two pharmaceuticals for all samples. In Phase II a total of 26 different pharmaceuticals were detected in all treated water samples, with a maximum of 20 pharmaceuticals detected in any one sample and a median of 2 pharmaceuticals detected for all 25 samples. Source-water type influences the presence of pharmaceuticals in source and treated water. Treatment processes appear effective in reducing concentrations of most pharmaceuticals. Pharmaceuticals more consistently persisting through treatment include carbamazepine, bupropion, cotinine, metoprolol, and lithium. Pharmaceutical concentrations and compositions from this study provide an important base data set for further sublethal, long-term exposure assessments, and for understanding potential effects of these and other contaminants of emerging concern upon human and ecosystem health. Copyright © 2016. Published by Elsevier B.V.

Presence of selected chemicals of emerging concern in water and bottom sediment from the St. Louis River, St. Louis Bay, and Superior Bay, Minnesota and Wisconsin, 2010

USGS Publications Warehouse

Christensen, Victoria G.; Lee, Kathy E.; Kieta, Kristen A.; Elliott, Sarah M.

2012-01-01

The St. Louis Bay of Lake Superior receives substantial urban runoff, wastewater treatment plant effluent, and industrial effluent. In 1987, the International Joint Commission designated the St. Louis Bay portion of the lower St. Louis River as one of the Great Lakes Areas of Concern. Concerns exist about the potential effects of chemicals of emerging concern on aquatic biota because many of these chemicals, including endocrine active chemicals, have been shown to affect the endocrine systems of fish. To determine the occurrence of chemicals of emerging concern in the St. Louis River, the St. Louis Bay, and Superior Bay, the U.S. Geological Survey in cooperation with the Minnesota Pollution Control Agency and the Wisconsin Department of Natural Resources collected water and bottom-sediment samples from 40 sites from August through October 2010. The objectives of this study were to (1) identify the extent to which chemicals of emerging concern, including pharmaceuticals, hormones, and other organic chemicals, occur in the St. Louis River, St. Louis Bay, and Superior Bay, and (2) identify the extent to which the chemicals may have accumulated in bottom sediment of the study area. Samples were analyzed for selected wastewater indicators, hormones, sterols, bisphenol A, and human-health pharmaceuticals. During this study, 33 of 89 chemicals of emerging concern were detected among all water samples collected and 56 of 104 chemicals of emerging concern were detected in bottom-sediment samples. The chemical N,N-diethyl-meta-toluamide (DEET) was the most commonly detected chemical in water samples and 2,6-dimethylnaphthalene was the most commonly detected chemical in bottom-sediment samples. In general, chemicals of emerging concern were detected at a higher frequency in bottom-sediment samples than in water samples. Estrone (a steroid hormone) and hexahydrohexamethyl cyclopentabensopyran (a synthetic fragrance) were the most commonly detected endocrine active chemicals in water samples; beta-sitosterol (a plant sterol), estrone, and 4-tert-octylphenol (an alkylphenol) were the most commonly detected endocrine active chemicals in bottom-sediment samples. The greater detection frequency of chemicals in bottom-sediment samples compared to the detection frequency in water samples indicates that bottom sediment is an important sink for chemicals of emerging concern. At least one polycyclic aromatic hydrocarbon was detected in every sample; and in most samples, all nine polycyclic aromatic hydrocarbons included in analyses were detected. Bottom sediment collected from Superior Bay had the most polycyclic aromatic hydrocarbon detections of the sediment sampling locations.

Occurrence and distribution of selected contaminants in public drinking-water supplies in the surficial aquifer in Delaware

USGS Publications Warehouse

Ferrari, Matthew J.

2001-01-01

Water samples were collected from August through November 2000 from 30 randomly selected public drinking-water supply wells screened in the unconfined aquifer in Delaware, and analyzed to assess the occurrence and distribution of selected pesticide compounds, volatile organic compounds, major inorganic ions, and nutrients. Water from a subset of 10 wells was sampled and analyzed for radium and radon. The average age of ground water entering the well screens in all the wells was determined to be generally less than 20 years. Low concentrations of pesticide compounds and volatile organic compounds were detected throughout the State of Delaware, with several compounds often detected in each water sample. Pesticide and metabolite (pesticide degradation products) concentrations were generally less than 1 microgram per liter, and were detected in sam-ples from 27 of 30 wells. Of the 45 pesticides and 13 metabolites analyzed, 19 compounds (13 pesticides and 6 metabolites) were detected in at least 1 of the 30 samples. Desethylatrazine, alachlor ethane sulfonic acid, metolachlor ethane sulfonic acid, metolachlor, and atrazine were the most frequently detected pesticide compounds, and were present in at least half the samples. None of the pesticide detections was above the U.S. Environmental Protection Agency's Primary Maximum Contaminant Levels or Health Advisories. Volatile organic compounds also were present at low concentrations (generally less than 1 microgram per liter) in samples from all 30 wells. Of the 85 volatile organic com-pounds analyzed, 34 compounds were detected in at least 1 of the 30 samples. Chloroform, tetrachloroethene, and methyl tert-butyl ether were the most frequently detected volatile organic compounds, and were found in at least half the samples. None of the volatile organic compound detections was above U.S. Environmental Protection Agency's Primary Maximum Contaminant Levels or Health Advisories. A few samples contained compounds with concentrations above the U.S. Environmental Protection Agency's Primary Maximum Contaminant Levels or Secondary Maximum Contaminant Levels for inorganic compounds and radionuclides. One sample out of 30 contained a concentration of nitrite plus nitrate above the U.S. Environmental Protection Agency's Primary Maximum Contaminant Level of 10 milligrams per liter as nitrogen. Iron and manganese concentrations above the U.S. Environmental Protection Agency's Secondary Maximum Contaminant Levels were found in 7 of 30 ground-water samples, most of them from Sussex County. In the 10 wells sampled for radionuclides, only one sample had detectable levels of radium-224 and -226, and another sample contained detectable levels of radium-228; both of these samples also had detectable gross-alpha and gross-beta activities. None of these activities were above the U.S. Environ-mental Protection Agency's Primary Maximum Contaminant Levels or Secondary Maximum Contaminant Levels. Radon was detected in all 10 samples, but was above the current U.S. Environmental Protection Agency's proposed Primary Maximum Contaminant Level of 300 picocuries per liter in only one sample.

[Identification of hepatitis B virus YMDD point mutation using peptide nucleic acid clamping PCR].

PubMed

Zhang, Yingying; He, Haitang; Yang, Jie; Hou, Jinlin

2013-06-01

To establish a peptide nucleic acid clamping PCR assay for detecting hepatitis B virus (HBV) drug resistance mutation. RtM204I (ATT) mutant, rtM204V (GTG) mutant and rtM204 (ATG) wild-type plasmids mixed at different ratios were detected for mutations by PNA clamping PCR assay and direct sequencing, and the sensitivity and specificity of the two methods were compared. Serum samples from 85 patients with chronic HBV infection were detected for drug resistance using the two methods. The sensitivity of PNA-PCR assay was 0.001% in a 10(5)-fold excess of wild-type HBV DNA with a detection limit of 10(1) copies. The sensitivity of direct sequencing was 10% with a detection limit of 10(4) copies. Mutants were detected in 73 of the 85 serum samples (85.9%), including YIDD in 40 samples, YVDD in 23 samples, and YIDD+YVDD in 10 samples. The agreement of PNA-PCR assay with direct sequencing was only 40% (34/85, YIDD in 21 samples, YVDD in 11 samples, and YIDD+YVDD in 2 samples). Neither of the two methods yielded positive results for the negative control samples, suggesting their good specificity. PNA-PCR assay appears to be a more sensitive and rapid assay for detection of HBV genotypic resistance.

46 CFR 161.002-15 - Sample extraction smoke detection systems.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 6 2014-10-01 2014-10-01 false Sample extraction smoke detection systems. 161.002-15...-15 Sample extraction smoke detection systems. The smoke detecting system must consist of a means for... smoke, together with visual and audible alarms for indicating the presence of smoke. [CGD 94-108, 61 FR...

46 CFR 161.002-15 - Sample extraction smoke detection systems.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 6 2011-10-01 2011-10-01 false Sample extraction smoke detection systems. 161.002-15...-15 Sample extraction smoke detection systems. The smoke detecting system must consist of a means for... smoke, together with visual and audible alarms for indicating the presence of smoke. [CGD 94-108, 61 FR...

46 CFR 161.002-15 - Sample extraction smoke detection systems.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 6 2012-10-01 2012-10-01 false Sample extraction smoke detection systems. 161.002-15...-15 Sample extraction smoke detection systems. The smoke detecting system must consist of a means for... smoke, together with visual and audible alarms for indicating the presence of smoke. [CGD 94-108, 61 FR...

46 CFR 161.002-15 - Sample extraction smoke detection systems.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 6 2013-10-01 2013-10-01 false Sample extraction smoke detection systems. 161.002-15...-15 Sample extraction smoke detection systems. The smoke detecting system must consist of a means for... smoke, together with visual and audible alarms for indicating the presence of smoke. [CGD 94-108, 61 FR...

Anthropogenic Organic Compounds in Source and Finished Water from Community Water System Wells in Western and Central Connecticut, 2002-2004

USGS Publications Warehouse

Trombley, Thoams J.; Brown, Craig J.; Delzer, Gregory C.

2007-01-01

A water-quality assessment by the U.S. Geological Survey (USGS) determined the occurrence of anthropogenic (manmade) organic compounds (AOCs) in water from 15 community water system (CWS) wells and associated finished drinking water. The study, which focused on water from the unconfined glacial stratified aquifer in western and central Connecticut, was conducted as part of the USGS National Water-Quality Assessment Program (NAWQA) Source Water-Quality Assessment (SWQA) project and included analysis of water samples for 88 volatile organic compounds (VOCs), 120 pesticides, and 50 other anthropogenic organic compounds (OAOCs). During Phase I of the study, 25 AOCs were detected (12 VOCs, 10 pesticides, and 3 OAOCs) in source-water samples collected from 15 CWS wells sampled once from October 2002 to May 2003. Although concentrations generally were low (less than 1 microgram per liter), four compounds were detected at higher concentrations in ground water from four wells. The most frequently occurring AOCs were detected in more than half of the samples and included chloroform (87 percent), methyl tert-butyl ether (MTBE, 80 percent), 1,1,1-trichloroethane (67 percent), atrazine (60 percent), deethylatrazine (60 percent), perchloroethene (PCE, 53 percent), and simazine (53 percent). Trichloroethene (TCE) was detected in 47 percent of samples. Samples generally contained a mixture of compounds ranging from 2 to 19 detected compounds, with an average of 8 detected compounds per sample. During Phase II of the study, 42 AOCs were detected in source-water samples collected from 10 resampled CWS wells or their associated finished water. Trihalomethanes accounted for most of the VOCs detections with all concentrations less than 1 microgram per liter. Chloroform, the most frequently detected VOC, was found in all source-water and all finished-water samples. As with the Phase I samples, other frequently detected VOCs included MTBE, and the solvents 1,1,1-trichloroethane, PCE, and TCE. Triazine herbicides and their degradation products accounted for most of the detected pesticides.

Comparing efficiency of American Fisheries Society standard snorkeling techniques to environmental DNA sampling techniques

USGS Publications Warehouse

Ulibarri, Roy M.; Bonar, Scott A.; Rees, Christopher B.; Amberg, Jon J.; Ladell, Bridget; Jackson, Craig

2017-01-01

Analysis of environmental DNA (eDNA) is an emerging technique used to detect aquatic species through water sampling and the extraction of biological material for amplification. Our study compared the efficacy of eDNA methodology to American Fisheries Society (AFS) standard snorkeling surveys with regard to detecting the presence of rare fish species. Knowing which method is more efficient at detecting target species will help managers to determine the best way to sample when both traditional sampling methods and eDNA sampling are available. Our study site included three Navajo Nation streams that contained Navajo Nation Genetic Subunit Bluehead Suckers Catostomus discobolus and Zuni Bluehead Suckers C. discobolus yarrowi. We first divided the entire wetted area of streams into consecutive 100-m reaches and then systematically selected 10 reaches/stream for snorkel and eDNA surveys. Surface water samples were taken in 10-m sections within each 100-m reach, while fish presence was noted via snorkeling in each 10-m section. Quantitative PCR was run on each individual water sample in quadruplicate to test for the presence or absence of the target species. With eDNA sampling techniques, we were able to positively detect both species in two out of the three streams. Snorkeling resulted in positive detection of both species in all three streams. In streams where the target species were detected with eDNA sampling, snorkeling detected fish at 11–29 sites/stream, whereas eDNA detected fish at 3–12 sites/stream. Our results suggest that AFS standard snorkeling is more effective than eDNA for detecting target fish species. To improve our eDNA procedures, the amount of water collected and tested should be increased. Additionally, filtering water on-site may improve eDNA techniques for detecting fish. Future research should focus on standardization of eDNA sampling to provide a widely operational sampling tool.

Detection of Classical swine fever virus infection by individual oral fluid of pigs following experimental inoculation.

PubMed

Petrini, Stefano; Pierini, Ilaria; Giammarioli, Monica; Feliziani, Francesco; De Mia, Gian Mario

2017-03-01

We evaluated the use of oral fluid as an alternative to serum samples for Classical swine fever virus (CSFV) detection. Individual oral fluid and serum samples were collected at different times post-infection from pigs that were experimentally inoculated with CSFV Alfort 187 strain. We found no evidence of CSFV neutralizing antibodies in swine oral fluid samples under our experimental conditions. In contrast, real-time reverse transcription-polymerase chain reaction could detect CSFV nucleic acid from the oral fluid as early as 8 d postinfection, which also coincided with the time of initial detection in blood samples. The probability of CSFV detection in oral fluid was identical or even higher than in the corresponding blood sample. Our results support the feasibility of using this sampling method for CSFV genome detection, which may represent an additional cost-effective tool for CSF control.

Detection of Circulating Paracoccidioides brasiliensis Antigen in Urine of Paracoccidioidomycosis Patients before and during Treatment

PubMed Central

Salina, Margarete Aparecida; Shikanai-Yasuda, Maria Aparecida; Mendes, Rinaldo Poncio; Barraviera, Benedito; Mendes Giannini, Maria José Soares

1998-01-01

For the diagnosis and follow-up of paracoccidioidomycosis patients undergoing therapy, we evaluated two methods (immunoblotting and competition enzyme immunoassay) for the detection of circulating antigen in urine samples. A complex pattern of reactivity was observed in the immunoblot test. Bands of 70 and 43 kDa were detected more often in urine samples from patients before treatment. The immunoblot method detected gp43 and gp70 separately or concurrently in 11 (91.7%) of 12 patients, whereas the competition enzyme immunoassay detected antigenuria in 9 (75%) of 12 patients. Both tests appeared to be highly specific (100%), considering that neither fraction detectable by immunoblotting was present in urine samples from the control group. gp43 remained present in the urine samples collected during the treatment period, with a significant decrease in reactivity in samples collected during clinical recovery and increased reactivity in samples collected during relapses. Reactivity of some bands was also detected in urine specimens from patients with “apparent cure.” The detection of Paracoccidioides brasiliensis antigens in urine appears to be a promising method for diagnosing infection, for evaluating the efficacy of treatment, and for detecting relapse. PMID:9620407

Comparison of two sampling and culture systems for detection of Salmonella enterica in the environment of a large animal hospital.

PubMed

Ruple-Czerniak, A; Bolte, D S; Burgess, B A; Morley, P S

2014-07-01

Nosocomial salmonellosis is an important problem in veterinary hospitals that treat horses and other large animals. Detection and mitigation of outbreaks and prevention of healthcare-associated infections often require detection of Salmonella enterica in the hospital environment. To compare 2 previously published methods for detecting environmental contamination with S. enterica in a large animal veterinary teaching hospital. Hospital-based comparison of environmental sampling techniques. A total of 100 pairs of environmental samples were collected from stalls used to house large animal cases (horses, cows or New World camelids) that were confirmed to be shedding S. enterica by faecal culture. Stalls were cleaned and disinfected prior to sampling, and the same areas within each stall were sampled for the paired samples. One method of detection used sterile, premoistened sponges that were cultured using thioglycolate enrichment before plating on XLT-4 agar. The other method used electrostatic wipes that were cultured using buffered peptone water, tetrathionate and Rappaport-Vassiliadis R10 broths before plating on XLT-4 agar. Salmonella enterica was recovered from 14% of samples processed using the electrostatic wipe sampling and culture procedure, whereas S. enterica was recovered from only 4% of samples processed using the sponge sampling and culture procedure. There was test agreement for 85 pairs of culture-negative samples and 3 pairs of culture-positive samples. However, the remaining 12 pairs of samples with discordant results created significant disagreement between the 2 detection methods (P<0.01). Persistence of Salmonella in the environment of veterinary hospitals can occur even with rigorous cleaning and disinfection. Use of sensitive methods for detection of environmental contamination is critical when detecting and mitigating this problem in veterinary hospitals. These results suggest that the electrostatic wipe sampling and culture method was more sensitive than the sponge sampling and culture method. © 2013 EVJ Ltd.

Molecular detection of airborne Coccidioides in Tucson, Arizona

USGS Publications Warehouse

Chow, Nancy A.; Griffin, Dale W.; Barker, Bridget M.; Loparev, Vladimir N.; Litvintseva, Anastasia P.

2016-01-01

Environmental surveillance of the soil-dwelling fungus Coccidioides is essential for the prevention of Valley fever, a disease primarily caused by inhalation of the arthroconidia. Methods for collecting and detectingCoccidioides in soil samples are currently in use by several laboratories; however, a method utilizing current air sampling technologies has not been formally demonstrated for the capture of airborne arthroconidia. In this study, we collected air/dust samples at two sites (Site A and Site B) in the endemic region of Tucson, Arizona, and tested a variety of air samplers and membrane matrices. We then employed a single-tube nested qPCR assay for molecular detection. At both sites, numerous soil samples (n = 10 at Site A and n = 24 at Site B) were collected and Coccidioides was detected in two samples (20%) at Site A and in eight samples (33%) at Site B. Of the 25 air/dust samples collected at both sites using five different air sampling methods, we detected Coccidioides in three samples from site B. All three samples were collected using a high-volume sampler with glass-fiber filters. In this report, we describe these methods and propose the use of these air sampling and molecular detection strategies for environmental surveillance of Coccidioides.

Giardia and Cryptosporidium spp. dissemination during wastewater treatment and comparative detection via immunofluorescence assay (IFA), nested polymerase chain reaction (nested PCR) and loop mediated isothermal amplification (LAMP).

PubMed

Gallas-Lindemann, Carmen; Sotiriadou, Isaia; Plutzer, Judit; Noack, Michael J; Mahmoudi, Mohammad Reza; Karanis, Panagiotis

2016-06-01

Environmental water samples from the Lower Rhine area in Germany were investigated via immunofluorescence assays (IFAs), nested polymerase chain reaction (nested PCR) and loop-mediated isothermal amplification (LAMP) to detect the presence of Giardia spp. (n=185) and Cryptosporidium spp. (n=227). The samples were concentrated through filtration or flocculation, and oocysts were purified via centrifugation through a sucrose density gradient. For all samples, IFA was performed first, followed by DNA extraction for the nested PCR and LAMP assays. Giardia cysts were detected in 105 samples (56.8%) by IFA, 62 samples (33.5%) by nested PCR and 79 samples (42.7%) by LAMP. Cryptosporidium spp. were detected in 69 samples (30.4%) by IFA, 95 samples (41.9%) by nested PCR and 99 samples (43.6%) by LAMP. According to these results, the three detection methods are complementary for monitoring Giardia and Cryptosporidium in environmental waters. Copyright © 2016 Elsevier B.V. All rights reserved.

Anomalies in the detection of change: When changes in sample size are mistaken for changes in proportions.

PubMed

Fiedler, Klaus; Kareev, Yaakov; Avrahami, Judith; Beier, Susanne; Kutzner, Florian; Hütter, Mandy

2016-01-01

Detecting changes, in performance, sales, markets, risks, social relations, or public opinions, constitutes an important adaptive function. In a sequential paradigm devised to investigate detection of change, every trial provides a sample of binary outcomes (e.g., correct vs. incorrect student responses). Participants have to decide whether the proportion of a focal feature (e.g., correct responses) in the population from which the sample is drawn has decreased, remained constant, or increased. Strong and persistent anomalies in change detection arise when changes in proportional quantities vary orthogonally to changes in absolute sample size. Proportional increases are readily detected and nonchanges are erroneously perceived as increases when absolute sample size increases. Conversely, decreasing sample size facilitates the correct detection of proportional decreases and the erroneous perception of nonchanges as decreases. These anomalies are however confined to experienced samples of elementary raw events from which proportions have to be inferred inductively. They disappear when sample proportions are described as percentages in a normalized probability format. To explain these challenging findings, it is essential to understand the inductive-learning constraints imposed on decisions from experience.

[Detection of astrovirus RNA from sewage works, seawater and native oysters samples in Chiba City, Japan using reverse transcription-polymerase chain reaction].

PubMed

Yokoi, H; Kitahashi, T; Tanaka, T; Utagawa, E

2001-04-01

Through a year from April, 1999 to March, 2000, 20 samples, which consisted of raw sewage (2), chlorine-treated sewage (2), seawater (10) and naturally grown oysters (6), were collected monthly both from the sewage works at Mihama-ku, Chiba City and at a yacht harbor in Chiba City Bay, Japan. Astrovirus RNA were detected by reverse transcription-polymerase chain reaction (RT-PCR) and was typed by direct sequencing. Astrovirus positive products were detected from 9 samples (raw sewage; 1/2, chlorine-treated sewage; 2/2, seawater; 5/10 and oysters; 1/6) collected in April, 1999. In May, positive products were detected from 4 samples (raw sewage; 2/2 and seawater; 2/10). In June, only 1 positive product was detected from raw sewage. The number of positive samples showed a tendency to decrease and no positive products were detected from samples collected in July, 1999 to January, 2000. After that period, positive products were again detected from 3 samples (raw sewage; 1/2, chlorine-treated sewage; 2/2) collected in February, 2000. In March, the number of positive samples showed the peak and positive products were detected from 12 samples (raw sewage; 2/2, chlorine-treated sewage; 2/2, seawater; 7/10 and oysters: 1/6). Astrovirus positive products detected in April, May, June, July, 1999 and February, 2000 were classified into type 1 or 2 by sequencing, whereas in March, 2000 were type 1, 2, 3, 6 and 7.

Effects of sampling strategy, detection probability, and independence of counts on the use of point counts

USGS Publications Warehouse

Pendleton, G.W.; Ralph, C. John; Sauer, John R.; Droege, Sam

1995-01-01

Many factors affect the use of point counts for monitoring bird populations, including sampling strategies, variation in detection rates, and independence of sample points. The most commonly used sampling plans are stratified sampling, cluster sampling, and systematic sampling. Each of these might be most useful for different objectives or field situations. Variation in detection probabilities and lack of independence among sample points can bias estimates and measures of precision. All of these factors should be con-sidered when using point count methods.

Concentrations and distribution of manmade organic compounds in the Lake Tahoe Basin, Nevada and California, 1997-99

USGS Publications Warehouse

Lico, Michael S.; Pennington, Nyle

1999-01-01

The U.S. Geological Survey, in cooperation with the Tahoe Regional Planning Agency and the Lahontan Regional Water-Quality Control Board, sampled Lake Tahoe, major tributary streams to Lake Tahoe, and several other lakes in the Lake Tahoe Basin for manmade organic compounds during 1997-99. Gasoline components were found in all samples collected from Lake Tahoe during the summer boating season. Methyl tert-butyl ether (MTBE), benzene, toluene, ethylbenzene, and xylenes (BTEX) were the commonly detected compounds in these samples. Most samples from tributary streams and lakes with no motorized boating had no detectable concentrations of gasoline components. Motorized boating activity appears to be directly linked in space and time to the occurrence of these gasoline components. Other sources of gasoline components to Lake Tahoe, such as the atmosphere, surface runoff, and subsurface flow, are minor compared to the input by motorized boating. Water sampled from Lake Tahoe during mid-winter, when motorized boating activity is low, had no MTBE and only one sample had any detectable BTEX compounds. Soluble pesticides rarely were detected in water samples from the Lake Tahoe Basin. The only detectable concentrations of these compounds were in samples from Blackwood and Taylor Creeks collected during spring runoff. Concentrations found in these samples were low, in the 1 to 4 nanograms per liter range. Organochlorine compounds were detected in samples collected from semipermeable membrane devices (SPMD's) collected from Lake Tahoe, tributary streams, and Upper Angora Lake. In Lake Tahoe, SPMD samples collected offshore from urbanized areas contained the largest number and highest concentrations of organochlorine compounds. The most commonly detected organochlorine compounds were cis- and trans-chlordane, p, p'-DDE, and hexachlorobenzene. In tributary streams, SPMD samples collected during spring runoff generally had higher combined concentrations of organochlorine compounds than those collected during baseflow conditions. Upper Angora Lake had the fewest number of organochlorine compounds detected of all lake samples. Dioxins and furans were not detected in SPMD samples from two sites in Lake Tahoe or from two tributary streams. The number of polycyclic aromatic hydrocarbon (PAH) compounds and their combined concentrations generally were higher in samples from Lake Tahoe than those from tributary streams. Areas of high-motorized boating activity at Lake Tahoe had the largest number and highest concentrations of PAH's. PAH compounds were detected in samples from SPMD's in four of six tributary streams during spring runoff, all tributary streams during baseflow conditions, and at all lake sites. The most commonly detected PAH's in tributary streams during spring runoff were phenanthrene, fluoranthene, pyrene, and chrysene, and during baseflow conditions were phenanthrene, 1-methylphenanthrene, diethylnaphthalene, and pyrene. Upper Truckee River, which has an urban area in its drainage basin, had the largest number and highest combined concentration of PAH's of all stream samples. Bottom-sediment from Lake Tahoe had detectable concentrations of p-cresol, a phenol, in all but one sample. A sample collected near Chambers Lodge contained phenol at an estimated concentration of 4 micrograms per kilogram (?g/kg). Bottom-sediment samples from tributary streams had no detectable concentrations of organochlorine or PAH compounds. Several compounds were detected in bottom sediment from Upper Angora Lake at high concentrations. These compounds and their concentrations were p, p'-DDD (10 ?g/kg), p, p'-DDE (7.4 ?g/kg), 2,6-dimethylnaphthalene (estimated at 190 ?g/kg), pentachlorophenol (3,000 ?g/kg), and p-cresol (4,400 ?g/kg).

Longitudinal study of Escherichia coli O157 shedding and super shedding in dairy heifers.

PubMed

Williams, K J; Ward, M P; Dhungyel, O P

2015-04-01

A longitudinal study was conducted to assess the methods available for detection of Escherichia coli O157 and to investigate the prevalence and occurrence of long-term shedding and super shedding in a cohort of Australian dairy heifers. Samples were obtained at approximately weekly intervals from heifers at pasture under normal management systems. Selective sampling techniques were used with the aim of identifying heifers with a higher probability of shedding or super shedding. Rectoanal mucosal swabs (RAMS) and fecal samples were obtained from each heifer. Direct culture of feces was used for detection and enumeration. Feces and RAMS were tested by enrichment culture. Selected samples were further tested retrospectively by immunomagnetic separation of enriched samples. Of 784 samples obtained, 154 (19.6%) were detected as positive using culture methods. Adjusting for selective sampling, the prevalence was 71 (15.6%) of 454. In total, 66 samples were detected as positive at >10(2) CFU/g of which 8 were >10(4) CFU/g and classed as super shedding. A significant difference was observed in detection by enriched culture of RAMS and feces. Dairy heifers within this cohort exhibited variable E. coli O157 shedding, consistent with previous estimates of shedding. Super shedding was detected at a low frequency and inconsistently from individual heifers. All detection methods identified some samples as positive that were not detected by any other method, indicating that the testing methods used will influence survey results.

A method for detecting fungal contaminants in wall cavities.

PubMed

Spurgeon, Joe C

2003-01-01

This article describes a practical method for detecting the presence of both fungal spores and culturable fungi in wall cavities. Culturable fungi were collected in 25 mm cassettes containing 0.8 microm mixed cellulose ester filters using aggressive sampling conditions. Both culturable fungi and fungal spores were collected in modified slotted-disk cassettes. The sample volume was 4 L. The filters were examined microscopically and dilution plated onto multiple culture media. Collecting airborne samples in filter cassettes was an effective method for assessing wall cavities for fungal contaminants, especially because this method allowed the sample to be analyzed by both microscopy and culture media. Assessment criteria were developed that allowed the sample results to be used to classify wall cavities as either uncontaminated or contaminated. As a criterion, wall cavities with concentrations of culturable fungi below the limit of detection (LOD) were classified as uncontaminated, whereas those cavities with detectable concentrations of culturable fungi were classified as contaminated. A total of 150 wall cavities was sampled as part of a field project. The concentrations of culturable fungi were below the LOD in 34% of the samples, whereas Aspergillus and/or Penicillium were the only fungal genera detected in 69% of the samples in which culturable fungi were detected. Spore counting resulted in the detection of Stachybotrys-like spores in 25% of the samples that were analyzed, whereas Stachybotrys chartarum colonies were only detected on 2% of malt extract agar plates and on 6% of corn meal agar plates.

Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients.

PubMed

Taly, Valerie; Pekin, Deniz; Benhaim, Leonor; Kotsopoulos, Steve K; Le Corre, Delphine; Li, Xinyu; Atochin, Ivan; Link, Darren R; Griffiths, Andrew D; Pallier, Karine; Blons, Hélène; Bouché, Olivier; Landi, Bruno; Hutchison, J Brian; Laurent-Puig, Pierre

2013-12-01

Multiplex digital PCR (dPCR) enables noninvasive and sensitive detection of circulating tumor DNA with performance unachievable by current molecular-detection approaches. Furthermore, picodroplet dPCR facilitates simultaneous screening for multiple mutations from the same sample. We investigated the utility of multiplex dPCR to screen for the 7 most common mutations in codons 12 and 13 of the KRAS (Kirsten rat sarcoma viral oncogene homolog) oncogene from plasma samples of patients with metastatic colorectal cancer. Fifty plasma samples were tested from patients for whom the primary tumor biopsy tissue DNA had been characterized by quantitative PCR. Tumor characterization revealed that 19 patient tumors had KRAS mutations. Multiplex dPCR analysis of the plasma DNA prepared from these samples identified 14 samples that matched the mutation identified in the tumor, 1 sample contained a different KRAS mutation, and 4 samples had no detectable mutation. Among the tumor samples that were wild type for KRAS, 2 KRAS mutations were identified in the corresponding plasma samples. Duplex dPCR (i.e., wild-type and single-mutation assay) was also used to analyze plasma samples from patients with KRAS-mutated tumors and 5 samples expected to contain the BRAF (v-raf murine sarcoma viral oncogene homolog B) V600E mutation. The results for the duplex analysis matched those for the multiplex analysis for KRAS-mutated samples and, owing to its higher sensitivity, enabled detection of 2 additional samples with low levels of KRAS-mutated DNA. All 5 samples with BRAF mutations were detected. This work demonstrates the clinical utility of multiplex dPCR to screen for multiple mutations simultaneously with a sensitivity sufficient to detect mutations in circulating DNA obtained by noninvasive blood collection.

Ground-water quality in the Central High Plains Aquifer, Colorado, Kansas, New Mexico, Oklahoma, and Texas, 1999

USGS Publications Warehouse

Becker, Mark F.; Bruce, Breton W.; Pope, Larry M.; Andrews, William J.

2002-01-01

A network of 74 randomly distributed domestic water-supply wells completed in the central High Plains aquifer was sampled and analyzed from April to August 1999 as part of the High Plains Regional Ground-Water Study conducted by the U. S. Geological Survey National Water-Quality Assessment Program to provide a broad-scale assessment of the ground-water-quality in this part of the High Plains aquifer. Water properties were relatively consistent across the aquifer, with water being alkaline and well oxidized. Water was mostly of the calcium and magnesium-bicarbonate type and very hard. Sulfate concentrations in water from three wells and chloride concentration in water from one well exceeded Secondary Maximum Contaminant Levels. Fluoride concentration was equal to the Maximum Contaminant Level in one sample. Nitrate concentrations was relatively small in most samples, with the median concentration of 2.3 milligrams per liter. Dissolved organic carbon concentration was relatively low, with a median concentration of 0.5 milligram per liter. The Maximum Contaminant Level set by the U.S. Environmental Protection Agency for nitrate as nitrogen of 10 milligrams per liter was exceeded by water samples from three wells. Most samples contained detectable concentrations of the trace elements aluminum, arsenic, barium, chromium, molybdenum, selenium, zinc, and uranium. Only a few samples had trace element concentrations exceeding Maximum Contaminant Levels. Fifty-five of the samples had radon concentrations exceeding the proposed Maximum Contaminant Level of 300 picocuries per liter. The greatest radon concentrations were detected where the Ogallala Formation overlies sandstones, shales and limestones of Triassic, Jurassic, or Cretaceous age. Volatile organic compounds were detected in 9 of 74 samples. Toluene was detected in eight of those nine samples. All volatile organic compound concentrations were substantially less than Maximum Contaminant Levels. Detections of toluene may have been artifacts of the sampling and analytical processes. Pesticides were detected in 18 of the 74 water samples. None of the pesticide concentrations exceeded Maximum Contaminant Levels. The most frequently detected pesticides were atrazine and its metabolite deethylatrazine, which were detected in water from 15 and 17 wells, respectively. Most of the samples with a detectable pesticide had at least two detectable pesticides. Six of the samples had more than two detectable pesticides. Tritium concentrations was greater than 0.5 tritium unit in 10 of 51 samples, indicating recent recharge to the aquifer. Twenty-one of the samples that had nitrate concentrations greater than 4.0 milligrams per liter were assumed to have components of recent recharge. Detection of volatile organic compounds was not associated with those indicators of recent recharge, with most of volatile organic compounds being detected in water from wells with small tritium and nitrate concentrations. Detection of pesticides was associated with greater tritium or nitrate concentrations, with 16 of the 18 wells producing water with pesticides also having tritium or nitrate concentrations indicating recent recharge.

Comparative Assessment of a Self-sampling Device and Gynecologist Sampling for Cytology and HPV DNA Detection in a Rural and Low Resource Setting: Malaysian Experience.

PubMed

Latiff, Latiffah A; Ibrahim, Zaidah; Pei, Chong Pei; Rahman, Sabariah Abdul; Akhtari-Zavare, Mehrnoosh

2015-01-01

This study was conducted to assess the agreement and differences between cervical self-sampling with a Kato device (KSSD) and gynecologist sampling for Pap cytology and human papillomavirus DNA (HPV DNA) detection. Women underwent self-sampling followed by gynecologist sampling during screening at two primary health clinics. Pap cytology of cervical specimens was evaluated for specimen adequacy, presence of endocervical cells or transformation zone cells and cytological interpretation for cells abnormalities. Cervical specimens were also extracted and tested for HPV DNA detection. Positive HPV smears underwent gene sequencing and HPV genotyping by referring to the online NCBI gene bank. Results were compared between samplings by Kappa agreement and McNemar test. For Pap specimen adequacy, KSSD showed 100% agreement with gynecologist sampling but had only 32.3% agreement for presence of endocervical cells. Both sampling showed 100% agreement with only 1 case detected HSIL favouring CIN2 for cytology result. HPV DNA detection showed 86.2%agreement (K=0.64, 95% CI 0.524-0.756, p=0.001) between samplings. KSSD and gynaecologist sampling identified high risk HPV in 17.3% and 23.9% respectively (p= 0.014). The self-sampling using Kato device can serve as a tool in Pap cytology and HPV DNA detection in low resource settings in Malaysia. Self-sampling devices such as KSSD can be used as an alternative technique to gynaecologist sampling for cervical cancer screening among rural populations in Malaysia.

Comparison of the detection of periodontal pathogens in bacteraemia after tooth brushing by culture and molecular techniques.

PubMed

Marín, M-J; Figuero, E; González, I; O'Connor, A; Diz, P; Álvarez, M; Herrera, D; Sanz, M

2016-05-01

The prevalence and amounts of periodontal pathogens detected in bacteraemia samples after tooth brushing-induced by means of four diagnostic technique, three based on culture and one in a molecular-based technique, have been compared in this study. Blood samples were collected from thirty-six subjects with different periodontal status (17 were healthy, 10 with gingivitis and 9 with periodontitis) at baseline and 2 minutes after tooth brushing. Each sample was analyzed by three culture-based methods [direct anaerobic culturing (DAC), hemo-culture (BACTEC), and lysis-centrifugation (LC)] and one molecular-based technique [quantitative polymerase chain reaction (qPCR)]. With culture any bacterial isolate was detected and quantified, while with qPCR only Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans were detected and quantified. Descriptive analyses, ANOVA and Chi-squared tests, were performed. Neither BACTEC nor qPCR detected any type of bacteria in the blood samples. Only LC (2.7%) and DAC (8.3%) detected bacteraemia, although not in the same patients. Fusobacterium nucleatum was the most frequently detected bacterial species. The disparity in the results when the same samples were analyzed with four different microbiological detection methods highlights the need for a proper validation of the methodology to detect periodontal pathogens in bacteraemia samples, mainly when the presence of periodontal pathogens in blood samples after tooth brushing was very seldom.

Limitation in the detection of Listeria monocytogenes in food in the presence of competing Listeria innocua.

PubMed

Oravcová, K; Trncíková, T; Kuchta, T; Kaclíková, E

2008-02-01

Detectability of Listeria monocytogenes at 10(0) CFU per food sample in the presence of Listeria innocua using standard microbiological detection was evaluated and compared with the real-time PCR-based method. Enrichment in half-Fraser broth followed by subculture in Fraser broth according to EN ISO 11290-1 was used. False-negative detection of 10(0) CFU L. monocytogenes was obtained in the presence of 10(1) CFU L. innocua per sample using the standard detection method in contrast to more than 10(5) CFU L. innocua per sample using real-time PCR. Identification of L. monocytogenes on the chromogenic medium by the standard procedure was impossible if L. innocua was able to overgrow L. monocytogenes by more than three orders of magnitude after the enrichment in model samples. These results were confirmed using naturally contaminated food samples. Standard microbiological method was insufficient for the reliable detection of 10(0) CFU L. monocytogenes in the presence of more than 10(0) CFU of L. innocua per sample. On the other hand, if the growth of L. monocytogenes was sufficient to reach the concentration equal to the detection limit of PCR, the amount of the other microflora present in the food sample including L. innocua was not relevant for success of the PCR detection of L. monocytogenes. After the enrichment, the PCR detection is more convenient than the standard one as PCR detection is not compromised by other present microflora.

Detection and molecular characterization of Vibrio parahaemolyticus isolated from seafood harvested along the southwest coast of India.

PubMed

Raghunath, Pendru; Acharya, Sadananda; Bhanumathi, Amarbahadur; Karunasagar, Iddya; Karunasagar, Indrani

2008-09-01

The levels of total and tdh(+)Vibrio parahaemolyticus were estimated in 83 seafood samples from southwest coast of India by colony hybridization. Conventional enrichment and isolation technique was also used to study the prevalence. Polymerase chain reaction (PCR) was performed on bacterial cell lyates for detection of total and pathogenic V. parahaemolyticus by amplification of specific genes. Of 83 samples tested, V. parahaemolyticus could be detected in 74 (89.2%) samples and tdh(+)V. parahaemolyticus in 5 (6.0%) samples by colony hybridization. V. parahaemolyticus was detected in 68 (81.9%) of 83 samples after 18 h of enrichment by PCR, and isolated from 63 (75.9%) of 83 samples by conventional isolation. The virulence genes tdh and trh could be detected in 8.4% and 25.3%, respectively, in the sample enrichment broths by PCR. Use of colony hybridization following enrichment to achieve sensitive detection of tdh(+)V. parahaemolyticus in seafood was evaluated using another set of 58 seafood samples. Thirty pathogenic V. parahaemolyticus strains isolated during the study were screened by PCR for genetic markers to be specific for the detection of the pandemic clone. Results of this study suggest that the GS-PCR may serve as a reliable genetic marker for the pandemic clone of V. parahaemolyticus.

Sensitivity of bhk-21 cells supplemented with diethylaminoethyl-dextran for detection of street rabies virus in saliva samples.

PubMed Central

Larghi, O P; Nebel, A E; Lazaro, L; Savy, V L

1975-01-01

A tissue culture system for detecting rabies virus from saliva samples of suspected animals was developed and compared to suckling mouse inoculation. Swab samples were obtained from the mouth of the animal heads received for rabies diagnosis; these swabs were submerged in maintenance medium. The maintenance medium was inoculated intracerebrally into suckling mice and onto BHK-21 cells with diethylaminoethyl (DEAE)-dextran (BHK/DEAE) and without (BHK). Rabies immunofluorescence was performed on the brain of the mice dying during the observation period and also on both tissue culture systems every day after infection. The BHK-DEAE system detected 28 positive samples obtained from 48 rabid animals and the BHK system detected 18. By suckling mouse inoculation only 11 of the same positive samples were detected. A total of 90 samples was studied by the three methods. Rabies virus was detected by the tissue culture methods earlier than by suckling mouse inoculation. The BHK-DEAE method was an economic and fast method for rabies virus detection in saliva samples, which could be used for ecological and pathogenesis studies, as well for rabies diagnosis before the death of the suspected animal. PMID:1100655

A direct immersion solid-phase microextraction gas chromatography/mass spectrometry method for the simultaneous detection of levamisole and minor cocaine congeners in hair samples from chronic abusers.

PubMed

Fucci, Nadia; Gambelunghe, Cristiana; Aroni, Kyriaki; Rossi, Riccardo

2014-12-01

Because levamisole has been increasingly found as a component of illicit drugs, a robust method to detect its presence in hair samples is needed. However, no systematic research on the detection of levamisole in hair samples has been published. The method presented here uses direct immersion solid-phase microextraction coupled with gas chromatography and mass spectrometry (DI-SPME-GC/MS) to detect levamisole and minor cocaine congeners in hair samples using a single-extraction method. Fifty hair samples taken in the last 4 years were obtained from cocaine abusers, along with controls taken from drug-free volunteers. Sampling was performed using direct immersion with a 30-μm polydimethylsiloxane fused silica/stainless steel fiber. Calibration curves were prepared by adding known amounts of analytes and deuterated internal standards to the hair samples taken from drug-free volunteers. This study focused on the adulterant levamisole and some minor cocaine congeners (tropococaine, norcocaine, and cocaethylene). Levamisole was detected in 38% of the hair samples analyzed; its concentration ranged from 0.2 to 0.8 ng/mg. The limit of quantification and limit of detection for levamisole, tropococaine, norcocaine, and cocaine were 0.2 and 0.1 ng/mg, respectively. DI-SPME-GC/MS is a sensitive and specific method to detect the presence of levamisole and cocaine congeners in hair samples.

Detection of rotavirus species A, B and C in domestic mammalian animals with diarrhoea and genotyping of bovine species A rotavirus strains.

PubMed

Otto, Peter H; Rosenhain, Stefanie; Elschner, Mandy C; Hotzel, Helmut; Machnowska, Patrycja; Trojnar, Eva; Hoffmann, Kathrin; Johne, Reimar

2015-09-30

Rotaviruses (RVs) are a major cause of neonatal diarrhoea in humans and animals worldwide. In this study, 425 faecal samples were collected between 1999 and 2013 from diarrhoeic livestock and companion animals at different locations in Germany and tested for RVs. A previously published real-time RT-PCR assay was optimized for detection of a larger variety of RV species A (RVA) strains, and real-time RT-PCR assays for detection of RV species B (RVB) and C (RVC) were newly developed. The detection limits of the assays were 1.54×10(2), 3.95×10(2) and 3.60×10(3) genome copies for RVA, RVB and RVC, respectively. RVA was identified in 85.2% of bovine samples, 51.2% of porcine samples, 50.0% of feline samples, 43.2% of equine samples and 39.7% of canine samples. RVB was found in 3.0% of bovine samples, 2.7% of equine samples and 1.6% of porcine samples. RVC was detected in 31.0% of porcine samples, 21.7% of feline samples, 9.0% of canine samples and 6.0% of bovine samples. For genotyping, 101 RVA-positive bovine samples were further analysed by semi-nested RT-PCR. Genotype combination G6P[5] was most frequently detected (67.3% of samples), followed by G6P[11] (13.9%), G10P[5] (4.0%), G8P[11] (3.0%), G6P[1] (1.0%), and G10P[11] (1.0%). Mixed RVA infections were detected in 5.9% of samples; no or incomplete typing was possible in 4.0% of the samples. This first overview on RV species and RVA genotypes in diarrhoeic livestock and companion animals from Germany indicates a broad circulation of a large variety of RVs. Copyright © 2015 Elsevier B.V. All rights reserved.

Cell block samples from malignant pleural effusion might be valid alternative samples for anaplastic lymphoma kinase detection in patients with advanced non-small-cell lung cancer.

PubMed

Zhou, Jianya; Yao, Hongtian; Zhao, Jing; Zhang, Shumeng; You, Qihan; Sun, Ke; Zou, Yinying; Zhou, Caicun; Zhou, Jianying

2015-06-01

To evaluate the clinical value of cell block samples from malignant pleural effusion (MPE) as alternative samples to tumour tissue for anaplastic lymphoma kinase (ALK) detection in patients with advanced non-small-cell lung cancer (NSCLC). Fifty-two matched samples were eligible for analysis. ALK status was detected by Ventana immunohistochemistry (IHC) (with the D5F3 clone), reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in-situ hybridization (FISH) in MPE cell block samples, and by FISH in tumour tissue block samples. In total, ALK FISH results were obtained for 52 tumour tissue samples and 41 MPE cell block samples. Eight cases (15.4%) were ALK-positive in tumour tissue samples by FISH, and among matched MPE cell block samples, five were ALK-positive by FISH, seven were ALK-positive by RT-PCR, and eight were ALK-positive by Ventana IHC. The ALK status concordance rates between tumour tissue and MPE cell block samples were 78.9% by FISH, 98.1% by RT-PCR, and 100% by Ventana IHC. In MPE cell block samples, the sensitivity and specificity of Ventana IHC (100% and 100%) and RT-PCR (87.5% and 100%) were higher than those of FISH (62.5% and 100%). Malignant pleural effusion cell block samples had a diagnostic performance for ALK detection in advanced NSCLC that was comparable to that of tumour tissue samples. MPE cell block samples might be valid alternative samples for ALK detection when tissue is not available. Ventana IHC could be the most suitable method for ALK detection in MPE cell block samples. © 2014 John Wiley & Sons Ltd.

Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation

USGS Publications Warehouse

Walker, Donald M.; Leys, Jacob E.; Dunham, Kelly E.; Oliver, Joshua C.; Schiller, Emily E.; Stephenson, Kelsey S.; Kimrey, John T.; Wooten, Jessica; Rogers, Mark W.

2017-01-01

Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations.

Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation.

PubMed

Walker, Donald M; Leys, Jacob E; Dunham, Kelly E; Oliver, Joshua C; Schiller, Emily E; Stephenson, Kelsey S; Kimrey, John T; Wooten, Jessica; Rogers, Mark W

2017-11-01

Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations. © 2017 John Wiley & Sons Ltd.

Cryptosporidium spp. and Giardia duodenalis as pathogenic contaminants of water in Galicia, Spain: the need for safe drinking water.

PubMed

Castro-Hermida, José Antonio; González-Warleta, Marta; Mezo, Mercedes

2015-01-01

The objectives of this cross-sectional study were to detect the presence of Cryptosporidium spp. and Giardia duodenalis in drinking water treatments plants (DWTPs) in Galicia (NW Spain) and to identify which species and genotype of these pathogenic protozoans are present in the water. Samples of untreated water (surface or ground water sources) and of treated drinking water (in total, 254 samples) were collected from 127 DWTPs and analysed by an immunofluorescence antibody test (IFAT) and by PCR. Considering the untreated water samples, Cryptosporidium spp. were detected in 69 samples (54.3%) by IFAT, and DNA of this parasite was detected in 57 samples (44.8%) by PCR, whereas G. duodenalis was detected in 76 samples (59.8%) by IFAT and in 56 samples (44.0%) by PCR. Considering the treated drinking water samples, Cryptosporidium spp. was detected in 52 samples (40.9%) by IFAT, and the parasite DNA was detected in 51 samples (40.1%) by PCR, whereas G. duodenalis was detected in 58 samples (45.6%) by IFAT and in 43 samples (33.8%) by PCR. The percentage viability of the (oo)cysts ranged between 90.0% and 95.0% in all samples analysed. Cryptosporidium andersoni, C. hominis, C. parvum and assemblages A-I, A-II, E of G. duodenalis were identified. The results indicate that Cryptosporidium spp. and G. duodenalis are widespread in the environment and that DWTPs are largely ineffective in reducing/inactivating these pathogens in drinking water destined for human and animal consumption in Galicia. In conclusion, the findings suggest the need for better monitoring of water quality and identification of sources of contamination. Copyright © 2014 Elsevier GmbH. All rights reserved.

Introduction to Mars Sampling Handling Workshop Series. Workshop on Life Detection: Issues and Topics

NASA Technical Reports Server (NTRS)

Rummel, John D.

2001-01-01

Before martian soil and rock samples can be distributed to the research community, the returned materials will initially be quarantined and examined in a proposed BSL-4 containment facility to assure that no putative martian microorganisms or attendant potential biohazards exist. During the initial quarantine, state-of-the-art life detection and biohazard testing of the returned martian samples will be conducted. Life detection, as defined here in regard to Mars sample return missions, is the detection of living organisms and/or materials that have been derived from living organisms that may be present in the sample.

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

PubMed Central

Friis-Nielsen, Jens; Vinner, Lasse; Hansen, Thomas Arn; Richter, Stine Raith; Fridholm, Helena; Herrera, Jose Alejandro Romero; Lund, Ole; Brunak, Søren; Izarzugaza, Jose M. G.; Mourier, Tobias; Nielsen, Lars Peter

2016-01-01

Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition. PMID:26818667

Fountain Flow cytometry, a new technique for the rapid detection and enumeration of microorganisms in aqueous samples.

PubMed

Johnson, Paul E; Deromedi, Anthony J; Lebaron, Philippe; Catala, Philippe; Cash, Jennifer

2006-12-01

Pathogenic microorganisms are known to cause widespread waterborne disease worldwide. There is an urgent need to develop a technique for the real-time detection of pathogens in environmental samples at low concentrations, <10 microorganisms/ml, in large sample volumes, > or =100 ml. A novel method, Fountain Flowtrade mark cytometry, for the rapid and sensitive detection of individual microorganisms in aqueous samples is presented. Each sample is first incubated with a fluorescent label and then passed as a stream in front of a laser, which excites the label. The fluorescence is detected with a CCD imager as the sample flows toward the imager along its optical axis. The feasibility of Fountain Flow cytometry (FFC) is demonstrated by the detection of Escherichia coli labeled with ChemChrome CV6 and SYBR Gold in buffer and natural river water. Detections of labeled E. coli were made in aqueous suspensions with an efficiency of 96% +/- 14% down to a concentration approximately 200 bacteria/ml. The feasibility of FFC is demonstrated by the detection of E. coli in buffer and natural river water. FFC should apply to the detection of a wide range of pathogenic microorganisms including amoebae.

The prevalence of Escherichia coli O157 and O157:H7 in ground beef and raw meatball by immunomagnetic separation and the detection of virulence genes using multiplex PCR.

PubMed

Cadirci, Ozgür; Siriken, Belgin; Inat, Gökhan; Kevenk, Tahsin Onur

2010-03-01

The present study was conducted to investigate the presence of Escherichia coli O157 and O157:H7 strains and to detect the presence of the stx1, stx2, and eaeA genes in isolates derived from 200 samples (100 samples from fresh ground beef and 100 samples from raw meatball). The samples were purchased from the Samsun Province in Turkey, over a period of 1 year. Enrichment-based immunomagnetic separation and multiplex polymerase chain reaction were applied for these analyses. E. coli O157 was detected in five of the 200 (2.5%) samples tested (one isolated from ground beef and four from meatball samples), whereas E. coli O157: H7 was not detected in any sample. During the analysis, eight strains of E. coli O157 were obtained. The genes stx1, stx2, and eaeA were detected in two E. coli O157 isolates obtained from two meatball samples, whereas only the eaeA and the stx2 genes were detected in four E. coli O157 strains that were isolated from one meatball sample. None of the stx1, stx2, and eaeA was detected in the E. coli O157 isolates obtained from the ground beef and the one meatball samples. Copyright 2009 Elsevier Ltd. All rights reserved.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

USGS Publications Warehouse

Keiter, David A.; Cunningham, Fred L.; Rhodes, Olin E.; Irwin, Brian J.; Beasley, James

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

Chemical contaminants in water and sediment near fish nesting sites in the Potomac River basin: determining potential exposures to smallmouth bass (Micropterus dolomieu)

USGS Publications Warehouse

Kolpin, Dana W.; Blazer, Vicki; Gray, James L.; Focazio, Michael J.; Young, John A.; Alvarez, David A.; Iwanowicz, Luke R.; Foreman, William T.; Furlong, Edward T.; Speiran, Gary K.; Zaugg, Steven D.; Hubbard, Laura E.; Meyer, Michael T.; Sandstrom, Mark W.; Barber, Larry B.

2013-01-01

The Potomac River basin is an area where a high prevalence of abnormalities such as testicular oocytes (TO), skin lesions, and mortality has been observed in smallmouth bass (SMB, Micropterus dolomieu). Previous research documented a variety of chemicals in regional streams, implicating chemical exposure as one plausible explanation for these biological effects. Six stream sites in the Potomac basin (and one out-of-basin reference site) were sampled to provide an assessment of chemicals in these streams. Potential early life-stage exposure to chemicals detected was assessed by collecting samples in and around SMB nesting areas. Target chemicals included those known to be associated with important agricultural and municipal wastewater sources in the Potomac basin. The prevalence and severity of TO in SMB were also measured to determine potential relations between chemistry and biological effects. A total of 39 chemicals were detected at least once in the discrete-water samples, with atrazine, caffeine, deethylatrazine, simazine, and iso-chlorotetracycline being most frequently detected. Of the most frequently detected chemicals, only caffeine was detected in water from the reference site. No biogenic hormones/sterols were detected in the discrete-water samples. In contrast, 100 chemicals (including six biogenic hormones/sterols) were found in a least one passive-water sample, with 25 being detected at all such samples. In addition, 46 chemicals (including seven biogenic hormones/sterols) were found in the bed-sediment samples, with caffeine, cholesterol, indole, para-cresol, and sitosterol detected in all such samples. The number of herbicides detected in discrete-water samples per site had a significant positive relation to TOrank (a nonparametric indicator of TO), with significant positive relations between TOrank and atrazine concentrations in discrete-water samples and to total hormone/sterol concentration in bed-sediment samples. Such significant correlations do not necessarily imply causation, as these chemical compositions and concentrations likely do not adequately reflect total SMB exposure history, particularly during critical life stages.

An iterative and targeted sampling design informed by habitat suitability models for detecting focal plant species over extensive areas.

PubMed

Wang, Ophelia; Zachmann, Luke J; Sesnie, Steven E; Olsson, Aaryn D; Dickson, Brett G

2014-01-01

Prioritizing areas for management of non-native invasive plants is critical, as invasive plants can negatively impact plant community structure. Extensive and multi-jurisdictional inventories are essential to prioritize actions aimed at mitigating the impact of invasions and changes in disturbance regimes. However, previous work devoted little effort to devising sampling methods sufficient to assess the scope of multi-jurisdictional invasion over extensive areas. Here we describe a large-scale sampling design that used species occurrence data, habitat suitability models, and iterative and targeted sampling efforts to sample five species and satisfy two key management objectives: 1) detecting non-native invasive plants across previously unsampled gradients, and 2) characterizing the distribution of non-native invasive plants at landscape to regional scales. Habitat suitability models of five species were based on occurrence records and predictor variables derived from topography, precipitation, and remotely sensed data. We stratified and established field sampling locations according to predicted habitat suitability and phenological, substrate, and logistical constraints. Across previously unvisited areas, we detected at least one of our focal species on 77% of plots. In turn, we used detections from 2011 to improve habitat suitability models and sampling efforts in 2012, as well as additional spatial constraints to increase detections. These modifications resulted in a 96% detection rate at plots. The range of habitat suitability values that identified highly and less suitable habitats and their environmental conditions corresponded to field detections with mixed levels of agreement. Our study demonstrated that an iterative and targeted sampling framework can address sampling bias, reduce time costs, and increase detections. Other studies can extend the sampling framework to develop methods in other ecosystems to provide detection data. The sampling methods implemented here provide a meaningful tool when understanding the potential distribution and habitat of species over multi-jurisdictional and extensive areas is needed for achieving management objectives.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

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

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

An Iterative and Targeted Sampling Design Informed by Habitat Suitability Models for Detecting Focal Plant Species over Extensive Areas

PubMed Central

Wang, Ophelia; Zachmann, Luke J.; Sesnie, Steven E.; Olsson, Aaryn D.; Dickson, Brett G.

2014-01-01

Prioritizing areas for management of non-native invasive plants is critical, as invasive plants can negatively impact plant community structure. Extensive and multi-jurisdictional inventories are essential to prioritize actions aimed at mitigating the impact of invasions and changes in disturbance regimes. However, previous work devoted little effort to devising sampling methods sufficient to assess the scope of multi-jurisdictional invasion over extensive areas. Here we describe a large-scale sampling design that used species occurrence data, habitat suitability models, and iterative and targeted sampling efforts to sample five species and satisfy two key management objectives: 1) detecting non-native invasive plants across previously unsampled gradients, and 2) characterizing the distribution of non-native invasive plants at landscape to regional scales. Habitat suitability models of five species were based on occurrence records and predictor variables derived from topography, precipitation, and remotely sensed data. We stratified and established field sampling locations according to predicted habitat suitability and phenological, substrate, and logistical constraints. Across previously unvisited areas, we detected at least one of our focal species on 77% of plots. In turn, we used detections from 2011 to improve habitat suitability models and sampling efforts in 2012, as well as additional spatial constraints to increase detections. These modifications resulted in a 96% detection rate at plots. The range of habitat suitability values that identified highly and less suitable habitats and their environmental conditions corresponded to field detections with mixed levels of agreement. Our study demonstrated that an iterative and targeted sampling framework can address sampling bias, reduce time costs, and increase detections. Other studies can extend the sampling framework to develop methods in other ecosystems to provide detection data. The sampling methods implemented here provide a meaningful tool when understanding the potential distribution and habitat of species over multi-jurisdictional and extensive areas is needed for achieving management objectives. PMID:25019621

Optimization of Scat Detection Methods for a Social Ungulate, the Wild Pig, and Experimental Evaluation of Factors Affecting Detection of Scat.

PubMed

Keiter, David A; Cunningham, Fred L; Rhodes, Olin E; Irwin, Brian J; Beasley, James C

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

DOE PAGES

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.; ...

2016-05-25

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Comparison of four sampling methods for the detection of Salmonella in broiler litter.

PubMed

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

2007-01-01

Experiments were conducted to compare litter sampling methods for the detection of Salmonella. In experiment 1, chicks were challenged orally with a suspension of naladixic acid-resistant Salmonella and wing banded, and additional nonchallenged chicks were placed into each of 2 challenge pens. Nonchallenged chicks were placed into each nonchallenge pen located adjacent to the challenge pens. At 7, 8, 10, and 11 wk of age the litter was sampled using 4 methods: fecal droppings, litter grab, drag swab, and sock. For the challenge pens, Salmonella-positive samples were detected in 3 of 16 fecal samples, 6 of 16 litter grab samples, 7 of 16 drag swabs samples, and 7 of 16 sock samples. Samples from the nonchallenge pens were Salmonella positive in 2 of 16 litter grab samples, 9 of 16 drag swab samples, and 9 of 16 sock samples. In experiment 2, chicks were challenged with Salmonella, and the litter in the challenge and adjacent nonchallenge pens were sampled at 4, 6, and 8 wk of age with broilers remaining in all pens. For the challenge pens, Salmonella was detected in 10 of 36 fecal samples, 20 of 36 litter grab samples, 14 of 36 drag swab samples, and 26 of 36 sock samples. Samples from the adjacent nonchallenge pens were positive for Salmonella in 6 of 36 fecal droppings samples, 4 of 36 litter grab samples, 7 of 36 drag swab samples, and 19 of 36 sock samples. Sock samples had the highest rates of Salmonella detection. In experiment 3, the litter from a Salmonella-challenged flock was sampled at 7, 8, and 9 wk by socks and drag swabs. In addition, comparisons with drag swabs that were stepped on during sampling were made. Both socks (24 of 36, 67%) and drag swabs that were stepped on (25 of 36, 69%) showed significantly more Salmonella-positive samples than the traditional drag swab method (16 of 36, 44%). Drag swabs that were stepped on had comparable Salmonella detection level to that for socks. Litter sampling methods that incorporate stepping on the sample material while in contact with the litter appear to detect Salmonella in greater incidence than traditional sampling methods of dragging swabs over the litter surface.

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

USGS Publications Warehouse

Wilcox, Taylor M; Mckelvey, Kevin S.; Young, Michael K.; Sepulveda, Adam; Shepard, Bradley B.; Jane, Stephen F; Whiteley, Andrew R.; Lowe, Winsor H.; Schwartz, Michael K.

2016-01-01

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout (Salvelinus fontinalis) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection > 0.99 at densities of ≥ 3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.

Laser-induced fluorescence fiber optic probe measurement of oil dilution by fuel

DOEpatents

Parks, II, James E [Knoxville, TN; Partridge, Jr., William P [Oak Ridge, TN

2010-11-23

Apparatus for detecting fuel in oil includes an excitation light source in optical communication with an oil sample for exposing the oil sample to excitation light in order to excite the oil sample from a non-excited state to an excited state and a spectrally selective device in optical communication with the oil sample for detecting light emitted from the oil sample as the oil sample returns from the excited state to a non-excited state to produce spectral indicia that can be analyzed to determine the presence of fuel in the oil sample. A method of detecting fuel in oil includes the steps of exposing a oil sample to excitation light in order to excite the oil sample from a non-excited state to an excited state, as the oil sample returns from the excited state to a non-excited state, detecting light emitted from the oil sample to produce spectral indicia; and analyzing the spectral indicia to determine the presence of fuel in the oil sample.

Dissolved pesticides, dissolved organic carbon, and water-quality characteristics in selected Idaho streams, April--December 2010

USGS Publications Warehouse

Reilly, Timothy J.; Smalling, Kelly L.; Wilson, Emma R.; Battaglin, William A.

2012-01-01

Water-quality samples were collected from April through December 2010 from four streams in Idaho and analyzed for a suite of pesticides, including fungicides, by the U.S. Geological Survey. Water samples were collected from two agricultural and two nonagricultural (control) streams approximately biweekly from the beginning of the growing season (April) through the end of the calendar year (December). Samples were analyzed for 90 pesticides using gas chromatography/mass spectrometry. Twenty-three pesticides, including 8 fungicides, 10 herbicides, 3 insecticides, and 2 pesticide degradates, were detected in 45 water samples. The most frequently detected compounds in the two agricultural streams and their detection frequencies were metolachlor, 96 percent; azoxystrobin, 79 percent; boscalid, 79 percent; atrazine, 46 percent; pendimethalin, 33 percent; and trifluralin, 33 percent. Dissolved-pesticide concentrations ranged from below instrumental limits of detection (0.5-1.0 nanograms per liter) to 771 nanograms per liter (hexazinone). The total number of pesticides detected in any given water sample ranged from 0 to 11. Only three pesticides (atrazine, fipronil, and simazine) were detected in samples from the control streams during the sampling period.

The Microbial Detection Array Combined with Random Phi29-Amplification Used as a Diagnostic Tool for Virus Detection in Clinical Samples

PubMed Central

Erlandsson, Lena; Rosenstierne, Maiken W.; McLoughlin, Kevin; Jaing, Crystal; Fomsgaard, Anders

2011-01-01

A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR that can identify one or several viruses in one assay. However, a diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for diagnostic analysis of viruses in clinical samples. PMID:21853040

Mycobacterium avium subspecies paratuberculosis in bioaerosols after depopulation and cleaning of two cattle barns.

PubMed

Eisenberg, S; Nielen, M; Hoeboer, J; Bouman, M; Heederik, D; Koets, A

2011-06-04

Settled dust samples were collected on a commercial dairy farm in the Netherlands with a high prevalence of Mycobacterium avium subspecies paratuberculosis (MAP) (barn A) and on a Dutch experimental cattle farm (barn B) stocked with cattle confirmed to be MAP shedders. Barns were sampled while animals were present, after both barns were destocked and cleaned by cold high-pressure cleaning, and after being kept empty for two weeks (barn A) or after additional disinfection (barn B). MAP DNA was detected by IS900 real-time PCR and viable MAP were detected by liquid culture. MAP DNA was detected in 78 per cent of samples from barn A and 86 per cent of samples from barn B collected while animals were still present. Viable MAP was detected in six of nine samples from barn A and in three of seven samples from barn B. After cold high-pressure cleaning, viable MAP could be detected in only two samples from each barn. After leaving barn A empty for two weeks, and following additional disinfection of barn B, no viable MAP could be detected in any settled dust sample.

Occurrence of anthropogenic organic compounds in ground water and finished water of community water systems in Eagle and Spanish Springs Valleys, Nevada, 2002-2004

USGS Publications Warehouse

Rosen, Michael R.; Shaefer, Donald H.; Toccalino, Patricia A.; Delzer, Gregory C.

2006-01-01

As a part of the U.S. Geological Survey's National Water-Quality Assessment Program, an effort to characterize the quality of major rivers and aquifers used as a source of supply to some of the largest community water systems (CWSs) in the United States has been initiated. These studies, termed Source Water-Quality Assessments (SWQAs), consist of two sampling phases. Phase 1 was designed to determine the frequency of detection and concentrations of about 260 volatile organic compounds (VOCs), pesticides and pesticide degradates, and other anthropogenic organic compounds in source water of 15 CWS wells in each study. Phase 2 monitors concentrations in the source water and also the associated finished water of CWSs for compounds most frequently detected during phase 1. One SWQA was completed in the Nevada Basin and Range area in Nevada. Ten CWS wells in Eagle Valley and five CWS wells in Spanish Springs Valley were sampled. For phase 2, two wells were resampled in Eagle Valley. Samples were collected during 2002-2004 for both phases. Water use in Eagle Valley is primarily for domestic purposes and is supplied through CWSs. Ground-water sources provide about 55 percent of the public-water supply, and surface-water sources supply about 45 percent. Lesser amounts of water are provided by domestic wells. Very little water is used for agriculture or manufacturing. Spanish Springs Valley has water-use characteristics similar to those in Eagle Valley, although there is more agricultural water use in Spanish Springs Valley than in Eagle Valley. Maximum contaminant concentrations were compared to two human-health benchmarks, if available, to describe the water-quality data in a human-health context for these findings. Measured concentrations of regulated contaminants were compared to U.S. Environmental Protection Agency and Nevada Maximum Contaminant Level (MCL) values. Measured concentrations of unregulated contaminants were compared to Health-Based Screening Levels, which are not regulatory standards and are not legally enforceable values. All of the contaminants detected in this study were found at concentrations less than available human-health benchmarks. In the source waters sampled in phase 1, 10 contaminants of the approximately 260 measured were detected in samples collected from Eagle Valley, and 4 contaminants were detected in samples from Spanish Springs Valley. The most frequently detected compounds in the Eagle Valley source water were chloroform (a disinfection by-product), which was detected in samples from four wells, and deethylatrazine (a degradation product of the herbicide atrazine), which was detected in samples from three wells. Each of the four contaminants detected in the Spanish Springs Valley source waters was detected in samples from one well. The detection frequencies of VOCs and pesticides in samples from the SWQA wells were similar to those in samples from both shallow and deep monitoring wells in Carson City, Reno, and Spanish Springs. This indicates that the SWQA sampling is representative of the organic chemical compounds likely to be detected in the aquifers sampled. However, more organic compounds were detected at low frequencies and concentrations in samples from the monitoring wells than in samples from SWQA wells. Three contaminants were detected in one finished-water sample collected from Eagle Valley. Comparison of SWQA results in the Nevada Basin and Range Study Unit to results of an SWQA in the larger urban area of Salt Lake City showed that fewer anthropogenic compounds were detected in Eagle and Spanish Springs Valleys and generally at lower concentrations than in the Salt Lake City study.

Characterization of the nasal and oral microbiota of detection dogs.

PubMed

Isaiah, Anitha; Hoffmann, Aline Rodrigues; Kelley, Russ; Mundell, Paul; Steiner, Jörg M; Suchodolski, Jan S

2017-01-01

Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations-Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (P<0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, P = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, Cardiobacterium and Riemerella were higher in VWD-E dogs, and Sphingobacterium was higher in the P-NDD group. In the oral samples Enterococcus and Capnocytophaga were higher in the P-NDD group. Gemella and Aggregatibacter were higher in S-PE, and Pigmentiphaga, Chryseobacterium, Parabacteroides amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines.

Characterization of the nasal and oral microbiota of detection dogs

PubMed Central

Hoffmann, Aline Rodrigues; Kelley, Russ; Mundell, Paul; Steiner, Jörg M.

2017-01-01

Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations—Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (P<0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, P = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, Cardiobacterium and Riemerella were higher in VWD-E dogs, and Sphingobacterium was higher in the P-NDD group. In the oral samples Enterococcus and Capnocytophaga were higher in the P-NDD group. Gemella and Aggregatibacter were higher in S-PE, and Pigmentiphaga, Chryseobacterium, Parabacteroides amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines. PMID:28934260

System and method for detecting cells or components thereof

DOEpatents

Porter, Marc D [Ames, IA; Lipert, Robert J [Ames, IA; Doyle, Robert T [Ames, IA; Grubisha, Desiree S [Corona, CA; Rahman, Salma [Ames, IA

2009-01-06

A system and method for detecting a detectably labeled cell or component thereof in a sample comprising one or more cells or components thereof, at least one cell or component thereof of which is detectably labeled with at least two detectable labels. In one embodiment, the method comprises: (i) introducing the sample into one or more flow cells of a flow cytometer, (ii) irradiating the sample with one or more light sources that are absorbed by the at least two detectable labels, the absorption of which is to be detected, and (iii) detecting simultaneously the absorption of light by the at least two detectable labels on the detectably labeled cell or component thereof with an array of photomultiplier tubes, which are operably linked to two or more filters that selectively transmit detectable emissions from the at least two detectable labels.

Automated Microorganism Detector

NASA Astrophysics Data System (ADS)

Keahey, Pelham; Hardy, Will; Cradit, Mason; Solis, Steven; Holland, Andrea; Wade, Gerry

2010-10-01

The detection and identification of bacteria in blood samples is crucial for treating patients suspected of having a blood infection. Current hospital methods for pathogen detection are time-consuming processes with multiple steps. This project's goal was to develop an efficient biomedical device to detect bacterial growth in blood samples, based on Gerald J. Wade's 1979 invention (US patents 4250266 and 4267276). Detection was accomplished using a system of electronics to examine the change in the electrochemical properties of a sample in response to bacterial growth, by measuring the sample's electrical charging and charge dispersion characteristics. After initial trials, it was found that a sample yielded consistent voltage measurements of approximately 200 millivolts prior to any detectable microbial growth. The first species tested, Escherichia coli (E. coli), was detected 11.7 hours after its inoculation in a culture bottle at a concentration of approximately 5-10 organisms per milliliter. In future tests, it is expected that detection times will vary in proportion to the growth rate of each species.

Potential of environmental DNA to evaluate Northern pike (Esox lucius) eradication efforts: An experimental test and case study

USGS Publications Warehouse

Dunker, Kristine J.; Sepulveda, Adam; Massengill, Robert L.; Olsen, Jeffrey B.; Russ, Ora L.; Wenburg, John K.; Antonovich, Anton

2016-01-01

Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling is delayed long enough to allow full degradation of DNA in the water.

Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study.

PubMed

Dunker, Kristine J; Sepulveda, Adam J; Massengill, Robert L; Olsen, Jeffrey B; Russ, Ora L; Wenburg, John K; Antonovich, Anton

2016-01-01

Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling is delayed long enough to allow full degradation of DNA in the water.

Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study

PubMed Central

Dunker, Kristine J.; Sepulveda, Adam J.; Massengill, Robert L.; Olsen, Jeffrey B.; Russ, Ora L.; Wenburg, John K.; Antonovich, Anton

2016-01-01

Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling is delayed long enough to allow full degradation of DNA in the water. PMID:27626271

Sample size requirements for indirect association studies of gene-environment interactions (G x E).

PubMed

Hein, Rebecca; Beckmann, Lars; Chang-Claude, Jenny

2008-04-01

Association studies accounting for gene-environment interactions (G x E) may be useful for detecting genetic effects. Although current technology enables very dense marker spacing in genetic association studies, the true disease variants may not be genotyped. Thus, causal genes are searched for by indirect association using genetic markers in linkage disequilibrium (LD) with the true disease variants. Sample sizes needed to detect G x E effects in indirect case-control association studies depend on the true genetic main effects, disease allele frequencies, whether marker and disease allele frequencies match, LD between loci, main effects and prevalence of environmental exposures, and the magnitude of interactions. We explored variables influencing sample sizes needed to detect G x E, compared these sample sizes with those required to detect genetic marginal effects, and provide an algorithm for power and sample size estimations. Required sample sizes may be heavily inflated if LD between marker and disease loci decreases. More than 10,000 case-control pairs may be required to detect G x E. However, given weak true genetic main effects, moderate prevalence of environmental exposures, as well as strong interactions, G x E effects may be detected with smaller sample sizes than those needed for the detection of genetic marginal effects. Moreover, in this scenario, rare disease variants may only be detectable when G x E is included in the analyses. Thus, the analysis of G x E appears to be an attractive option for the detection of weak genetic main effects of rare variants that may not be detectable in the analysis of genetic marginal effects only.

Method and apparatus for data sampling

DOEpatents

Odell, Daniel M. C.

1994-01-01

A method and apparatus for sampling radiation detector outputs and determining event data from the collected samples. The method uses high speed sampling of the detector output, the conversion of the samples to digital values, and the discrimination of the digital values so that digital values representing detected events are determined. The high speed sampling and digital conversion is performed by an A/D sampler that samples the detector output at a rate high enough to produce numerous digital samples for each detected event. The digital discrimination identifies those digital samples that are not representative of detected events. The sampling and discrimination also provides for temporary or permanent storage, either serially or in parallel, to a digital storage medium.

Occurrence of Pesticides in Ground Water of Wyoming, 1995-2006

USGS Publications Warehouse

Bartos, Timothy T.; Eddy-Miller, Cheryl A.; Hallberg, Laura L.

2009-01-01

Little existing information was available describing pesticide occurrence in ground water of Wyoming, so the U.S. Geological Survey, in cooperation with the Wyoming Department of Agriculture and the Wyoming Department of Environmental Quality on behalf of the Wyoming Ground-water and Pesticides Strategy Committee, collected ground-water samples twice (during late summer/early fall and spring) from 296 wells during 1995-2006 to characterize pesticide occurrence. Sampling focused on the State's ground water that was mapped as the most vulnerable to pesticide contamination because of either inherent hydrogeologic sensitivity (for example, shallow water table or highly permeable aquifer materials) or a combination of sensitivity and associated land use. Because of variations in reporting limits among different compounds and for the same compound during this study, pesticide detections were recensored to two different assessment levels to facilitate qualitative and quantitative examination of pesticide detection frequencies - a common assessment level (CAL) of 0.07 microgram per liter and an assessment level that differed by compound, referred to herein as a compound-specific assessment level (CSAL). Because of severe data censoring (fewer than 50 percent of the data are greater than laboratory reporting limits), categorical statistical methods were used exclusively for quantitative comparisons of pesticide detection frequencies between seasons and among various natural and anthropogenic (human-related) characteristics. One or more pesticides were detected at concentrations greater than the CAL in water from about 23 percent of wells sampled in the fall and from about 22 percent of wells sampled in the spring. Mixtures of two or more pesticides occurred at concentrations greater than the CAL in about 9 percent of wells sampled in the fall and in about 10 percent of wells sampled in the spring. At least 74 percent of pesticides detected were classified as herbicides. Considering only detections using the CAL, triazine pesticides were detected much more frequently than all other pesticide classes, and the number of different pesticides classified as triazines was the largest of all classes. More pesticides were detected at concentrations greater than the CSALs in water from wells sampled in the fall (28 different pesticides) than in the spring (21 different pesticides). Many pesticides were detected infrequently as nearly one-half of pesticides detected in the fall and spring at concentrations greater than the CSALs were detected only in one well. Using the CSALs for pesticides analyzed for in 11 or more wells, only five pesticides (atrazine, prometon, tebuthiuron, picloram, and 3,4-dichloroaniline, listed in order of decreasing detection frequency) were each detected in water from more than 5 percent of sampled wells. Atrazine was the pesticide detected most frequently at concentrations greater than the CSAL. Concentrations of detected pesticides generally were small (less than 1 microgram per liter), although many infrequent detections at larger concentrations were noted. All detected pesticide concentrations were smaller than U.S. Environmental Protection Agency (USEPA) drinking-water standards or applicable health advisories. Most concentrations were at least an order of magnitude smaller; however, many pesticides did not have standards or advisories. The largest percentage of pesticide detections and the largest number of different pesticides detected were in samples from wells located in the Bighorn Basin and High Plains/ Casper Arch geographic areas of north-central and southeastern Wyoming. Prometon was the only pesticide detected in all eight geographic areas of the State. Pesticides were detected much more frequently in samples from wells located in predominantly urban areas than in samples from wells located in predominantly agricultural or mixed areas. Pesticides were detected distinctly less often in sa

Human papillomavirus detection and typing using a nested-PCR-RFLP assay.

PubMed

Coser, Janaina; Boeira, Thaís da Rocha; Fonseca, André Salvador Kazantzi; Ikuta, Nilo; Lunge, Vagner Ricardo

2011-01-01

It is clinically important to detect and type human papillomavirus (HPV) in a sensitive and specific manner. Development of a nested-polymerase chain reaction-restriction fragment length polymorphism (nested-PCR-RFLP) assay to detect and type HPV based on the analysis of L1 gene. Analysis of published DNA sequence of mucosal HPV types to select sequences of new primers. Design of an original nested-PCR assay using the new primers pair selected and classical MY09/11 primers. HPV detection and typing in cervical samples using the nested-PCR-RFLP assay. The nested-PCR-RFLP assay detected and typed HPV in cervical samples. Of the total of 128 clinical samples submitted to simple PCR and nested-PCR for detection of HPV, 37 (28.9%) were positive for the virus by both methods and 25 samples were positive only by nested-PCR (67.5% increase in detection rate compared with single PCR). All HPV positive samples were effectively typed by RFLP assay. The method of nested-PCR proved to be an effective diagnostic tool for HPV detection and typing.

Method- and species-specific detection probabilities of fish occupancy in Arctic lakes: Implications for design and management

USGS Publications Warehouse

Haynes, Trevor B.; Rosenberger, Amanda E.; Lindberg, Mark S.; Whitman, Matthew; Schmutz, Joel A.

2013-01-01

Studies examining species occurrence often fail to account for false absences in field sampling. We investigate detection probabilities of five gear types for six fish species in a sample of lakes on the North Slope, Alaska. We used an occupancy modeling approach to provide estimates of detection probabilities for each method. Variation in gear- and species-specific detection probability was considerable. For example, detection probabilities for the fyke net ranged from 0.82 (SE = 0.05) for least cisco (Coregonus sardinella) to 0.04 (SE = 0.01) for slimy sculpin (Cottus cognatus). Detection probabilities were also affected by site-specific variables such as depth of the lake, year, day of sampling, and lake connection to a stream. With the exception of the dip net and shore minnow traps, each gear type provided the highest detection probability of at least one species. Results suggest that a multimethod approach may be most effective when attempting to sample the entire fish community of Arctic lakes. Detection probability estimates will be useful for designing optimal fish sampling and monitoring protocols in Arctic lakes.

Explosive vapor detection payload for small robots

NASA Astrophysics Data System (ADS)

Stimac, Phil J.; Pettit, Michael; Wetzel, John P.; Haas, John W.

2013-05-01

Detection of explosive hazards is a critical component of enabling and improving operational mobility and protection of US Forces. The Autonomous Mine Detection System (AMDS) developed by the US Army RDECOM CERDEC Night Vision and Electronic Sensors Directorate (NVESD) is addressing this challenge for dismounted soldiers. Under the AMDS program, ARA has developed a vapor sampling system that enhances the detection of explosive residues using commercial-off-the-shelf (COTS) sensors. The Explosives Hazard Trace Detection (EHTD) payload is designed for plug-and-play installation and operation on small robotic platforms, addressing critical Army needs for more safely detecting concealed or exposed explosives in areas such as culverts, walls and vehicles. In this paper, we describe the development, robotic integration and performance of the explosive vapor sampling system, which consists of a sampling "head," a vapor transport tube and an extendable "boom." The sampling head and transport tube are integrated with the boom, allowing samples to be collected from targeted surfaces up to 7-ft away from the robotic platform. During sample collection, an IR lamp in the sampling head is used to heat a suspected object/surface and the vapors are drawn through the heated vapor transport tube to an ion mobility spectrometer (IMS) for detection. The EHTD payload is capable of quickly (less than 30 seconds) detecting explosives such as TNT, PETN, and RDX at nanogram levels on common surfaces (brick, concrete, wood, glass, etc.).

Optimization of the elution buffer and concentration method for detecting hepatitis E virus in swine liver using a nested reverse transcription-polymerase chain reaction and real-time reverse transcription-polymerase chain reaction.

PubMed

Son, Na Ry; Seo, Dong Joo; Lee, Min Hwa; Seo, Sheungwoo; Wang, Xiaoyu; Lee, Bog-Hieu; Lee, Jeong-Su; Joo, In-Sun; Hwang, In-Gyun; Choi, Changsun

2014-09-01

The aim of this study was to develop an optimal technique for detecting hepatitis E virus (HEV) in swine livers. Here, three elution buffers and two concentration methods were compared with respect to enhancing recovery of HEV from swine liver samples. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and nested RT-PCR were performed to detect HEV RNA. When phosphate-buffered saline (PBS, pH 7.4) was used to concentrate HEV in swine liver samples using ultrafiltration, real-time RT-PCR detected HEV in 6 of the 26 samples. When threonine buffer was used to concentrate HEV using polyethylene glycol (PEG) precipitation and ultrafiltration, real-time RT-PCR detected HEV in 1 and 3 of the 26 samples, respectively. When glycine buffer was used to concentrate HEV using ultrafiltration and PEG precipitation, real-time RT-PCR detected HEV in 1 and 3 samples of the 26 samples, respectively. When nested RT-PCR was used to detect HEV, all samples tested negative regardless of the type of elution buffer or concentration method used. Therefore, the combination of real-time RT-PCR and ultrafiltration with PBS buffer was the most sensitive and reliable method for detecting HEV in swine livers. Copyright © 2014 Elsevier B.V. All rights reserved.

Ground-water quality in the western part of the Cambrian-Ordovician aquifer in the Western Lake Michigan Drainages, Wisconsin and Michigan

USGS Publications Warehouse

Saad, D.A.

1996-01-01

Seven pesticides or metabolites were detected in ground-water samples, and at least one pesticide was detected in samples from 24 percent (7 of 29) of wells. Most of the pesticides were detected at low concentrations and were from wells in the regionally unconfined, agricultural, southwest part of the study area. Atrazine was the most commonly detected pesticide and was typically detected in samples from wells that produced modern water.

Occurrence of active and inactive herbicide ingredients at selected sites in Iowa

USGS Publications Warehouse

Wang, W.; Liszewski, M.; Buchmiller, R.; Cherryholmes, K.

1995-01-01

Herbicides were detected in 50% of water samples, ranging from 78% of water samples from the Ames site to 25% from the Walnut Creek site. Among herbicides detected, listed in decreasing order of frequency, were atrazine > alachlor > cyanazine > metolachlor > metribuzin. Volatile organic compounds were detected in 11% of water samples. Among the compounds detected, listed in decreasing order of frequency, were xylene > toluene > acetone. One sample contained a detectable amount of aliphatic compound(s), with the empirical formula of C8H18. Results from the Deer Creek site showed that herbicides were detected primarily in the top layer (1.2 m), whereas xylene and other alkylbenzenes were detected at 2.1 m or deeper. Apparently, physico-chemical and other factors are separating herbicides and volatile organic compounds in the shallow unsaturated zone.

Near real time vapor detection and enhancement using aerosol adsorption

DOEpatents

Novick, Vincent J.; Johnson, Stanley A.

1999-01-01

A vapor sample detection method where the vapor sample contains vapor and ambient air and surrounding natural background particles. The vapor sample detection method includes the steps of generating a supply of aerosol that have a particular effective median particle size, mixing the aerosol with the vapor sample forming aerosol and adsorbed vapor suspended in an air stream, impacting the suspended aerosol and adsorbed vapor upon a reflecting element, alternatively directing infrared light to the impacted aerosol and adsorbed vapor, detecting and analyzing the alternatively directed infrared light in essentially real time using a spectrometer and a microcomputer and identifying the vapor sample.

Near real time vapor detection and enhancement using aerosol adsorption

DOEpatents

Novick, V.J.; Johnson, S.A.

1999-08-03

A vapor sample detection method is described where the vapor sample contains vapor and ambient air and surrounding natural background particles. The vapor sample detection method includes the steps of generating a supply of aerosol that have a particular effective median particle size, mixing the aerosol with the vapor sample forming aerosol and adsorbed vapor suspended in an air stream, impacting the suspended aerosol and adsorbed vapor upon a reflecting element, alternatively directing infrared light to the impacted aerosol and adsorbed vapor, detecting and analyzing the alternatively directed infrared light in essentially real time using a spectrometer and a microcomputer and identifying the vapor sample. 13 figs.

Survey of carbamate and organophosphorous pesticide export from a south Florida (U.S.A.) agricultural watershed: implications of sampling frequency on ecological risk estimation.

PubMed

Wilsont, P Chris; Foos, Jane Ferguson

2006-11-01

The objectives of the present study were to characterize the presence of selected carbamate and organophosphorous pesticides in Ten Mile Creek (Fort Pierce, FL, U.S.A.) and to evaluate the implications of sampling frequency on ecological risk estimates. Ten Mile Creek originates in a predominately agricultural watershed that is drained by an extensive network of cross-linked canals. Water samples were collected daily or every other day and were analyzed for azinphos-methyl, chlorpyrifos, diazinon, dimethoate, ethion, fenamiphos, malathion, methidathion, carbaryl, carbofuran, 3-hydroxycarbofuran, methiocarb, methomyl, oxamyl, and propoxur. A total of 457 samples were analyzed for the carbamate suite, and a total of 332 samples were analyzed for the organophosphorous suite. Carbaryl was detected in eight samples; half of these detections occurred on four consecutive days (October 26-29, 2001) at concentrations ranging from 0.33 to 0.95 microg/L. Methomyl was detected in samples collected on five consecutive days (March 30-April 3, 2002) at concentrations ranging from 1.0 to 2.2 microg/L. Oxamyl was detected in four samples, three of which occurred on three consecutive days (February 17-19, 2002) at concentrations ranging from 6.2 to 6.8 microg/L. The carbamates propoxur, 3-hydroxycarbofuran, carbofuran, and methiocarb were not detected. Diazinon and ethion were the only organophosphorous pesticides detected. Diazinon was detected at 0.9 and 0.7 microg/L on January 5, 2002, and on January 6, 2002, respectively. Ethion was detected in 18 consecutive samples (August 3-20, 2001). The mean, maximum, minimum, and median detected concentrations were 0.38, 0.61, 0.30, and 0.33 microg/L, respectively. Results indicate that frequent sampling is necessary to characterize the presence of these pesticides in this intensively drained watershed. This conclusion also may apply to similar canalized watersheds.

Physiologically Relevant Changes in Serotonin Resolved by Fast Microdialysis

PubMed Central

2013-01-01

Online microdialysis is a sampling and detection method that enables continuous interrogation of extracellular molecules in freely moving subjects under behaviorally relevant conditions. A majority of recent publications using brain microdialysis in rodents report sample collection times of 20–30 min. These long sampling times are due, in part, to limitations in the detection sensitivity of high performance liquid chromatography (HPLC). By optimizing separation and detection conditions, we decreased the retention time of serotonin to 2.5 min and the detection threshold to 0.8 fmol. Sampling times were consequently reduced from 20 to 3 min per sample for online detection of serotonin (and dopamine) in brain dialysates using a commercial HPLC system. We developed a strategy to collect and to analyze dialysate samples continuously from two animals in tandem using the same instrument. Improvements in temporal resolution enabled elucidation of rapid changes in extracellular serotonin levels associated with mild stress and circadian rhythms. These dynamics would be difficult or impossible to differentiate using conventional microdialysis sampling rates. PMID:23614776

Reverse line blot hybridisation screening of Pseudallescheria/Scedosporium species in patients with cystic fibrosis.

PubMed

Lu, Q; van den Ende, A H G Gerrits; de Hoog, G S; Li, R; Accoceberry, I; Durand-Joly, I; Bouchara, J-P; Hernandez, F; Delhaes, L

2011-10-01

The PCR-RLB (reverse line blot hybridisation) was applied as a molecular technique for the detection of members of Pseudallescheria and Scedosporium from sputum of patients with cystic fibrosis (CF). Fifty-nine sputum samples were collected from 52 CF patients, which were analysed by culture and PCR-RLB. Conventional and semi-selective culture yielded five positive samples, but the PCR-RLB hybridisation assay permitted the detection of members of Pseudallescheria/Scedosporium in 32 out of 52 patients (61.5%). In total, PCR-RLB yielded 47 positives. Pseudallescheria apiosperma was detected in 20 samples, while Pseudallescheria boydii and Pseudallescheria aurantiacum were detected in 17 and eight samples, respectively. Six samples gave a positive reaction with two distinct species-specific probes and one sample with three probes. In conclusion, the PCR-RLB assay described in this study allows the detection of Scedosporium spp. in CF sputum samples and the identification of Pseudallescheria apiosperma, P. boydii, S. aurantiacum, Scedosporium prolificans and Pseudallescheria minutispora. © 2011 Blackwell Verlag GmbH.

[Contamination of health care institutions environmental objects by Legionella pneumophila].

PubMed

Shkarin, V V; Blagonravova, A S; Chubukova, O A; Korotaeva, S V

2011-01-01

AIM. The extent of environmental objects contamination by Legionella pneumophila in Nizhny Novgorod and Nizhny Novgorod region hospitals evaluation, and detection of potentially hazardous objects. 433 swabs of environmental objects, and 43 hot water supply and pool water samples from various departments of 4 multi-disciplinary hospitals were studies. DNA from environmental samples was detected by using real time PCR. L. pneumophila DNA was detected in 41 (9,47%) samples from environmental objects and in 2 (4,65%) samples from hot water supply. These bacteria were more frequently detected in environmental samples from physiotherapy departments. Repeated detection of legionellae from the same objects was registered. Circulation of legionellae in multidisciplinary hospitals was determined. Circulation high risk departments and risk objects--reservoirs of L. pneumophila in health care institutions were determined.

Sourcing faecal pollution: a combination of library-dependent and library-independent methods to identify human faecal pollution in non-sewered catchments.

PubMed

Ahmed, W; Stewart, J; Gardner, T; Powell, D; Brooks, P; Sullivan, D; Tindale, N

2007-08-01

Library-dependent (LD) (biochemical fingerprinting of Escherichia coli and enterococci) and library-independent (LI) (PCR detection of human-specific biomarkers) methods were used to detect human faecal pollution in three non-sewered catchments. In all, 550 E. coli isolates and 700 enterococci isolates were biochemically fingerprinted from 18 water samples and compared with metabolic fingerprint libraries of 4508 E. coli and 4833 enterococci isolates. E. coli fingerprints identified human unique biochemical phenotypes (BPTs) in nine out of 18 water samples; similarly, enterococci fingerprints identified human faecal pollution in 10 water samples. Seven samples were tested by PCR for the detection of biomarkers. Human-specific HF134 Bacteroides and enterococci surface protein (esp) biomarkers were detected in five samples. Four samples were also positive for HF183 Bacteroides biomarker. The combination of biomarkers detected human faecal pollution in six out of seven water samples. Of the seven samples analysed for both the indicators/markers, at least one indicator/marker was detected in every sample. Four of the seven PCR-positive samples were also positive for one of the human-specific E. coli or enterococci BPTs. The results indicated human faecal pollution in the studied sub-catchments after storm events. LD and LI methods used in this study complimented each other and provided additional information regarding the polluting sources when one method failed to detect human faecal pollution. Therefore, it is recommended that a combination of methods should be used to identify the source(s) of faecal pollution where possible.

Water-quality monitoring for a pilot piling removal field evaluation, Coal Creek Slough, Washington, 2008-09

USGS Publications Warehouse

Nilsen, Elena B.; Alvarez, David A.

2011-01-01

Significant Findings Water and sediment quality monitoring was conducted before and after the removal of a piling field located in Coal Creek Slough near Longview, Washington. Passive chemical samplers and continuous water-quality monitoring instruments were deployed at the piling removal site, Coal Creek Slough Site 1 (CCS1), and at a comparison site, Coal Creek Slough Site 2 (CCS2), before (2008) and after (2009) piling removal. Surface and subsurface (core) sediment samples were collected before and after piling removal and were analyzed for grain size, organic carbon content, and chemicals of concern. Significant findings from this study include: * Phenanthrene was the only compound detected in wood piling samples analyzed for a large suite of semivolatile organic compounds and polycyclic aromatic hydrocarbons (PAHs). Metals potentially associated with wood treatment were detected in the wood piling samples at low concentrations. * Organic carbon was slightly lower in core samples from CCS1 in pre-removal (2008) and post-removal (2009) samples than in surface samples from both sites in both years. * Grain-size class distributions were relatively uniform between sites and years. * Thirty-four out of 110 chemicals of concern were detected in sediments. Eight of those detected were anthropogenic waste indicator (AWI) compounds, 18 were PAHs, 4 were sterols, and 4 were metals potentially associated with wood treatment. * Nearly all reported concentrations of chemicals of concern in sediments are qualified as estimates, primarily due to interferences in extracts resulting from complex sample matrices. Indole, perylene, and fluoranthene are reported without qualification for some of the samples, and the metals are reported without qualification for all samples. * The highest frequency of detection of chemicals of concern was seen in the pre-removal surface samples at both sites. * AWI compounds were detected less frequently and at lower concentrations during the post-removal sampling compared to the pre-removal sampling. * Several PAHs were detected at relatively high concentrations in core samples, likely indicating historical sources. * Most commonly detected PAHs in sediments were 2,6-dimethylnaphthalene, fluoranthene, perylene, and pyrene. * Most commonly detected AWIs in sediments were 3-methyl-1h-indole (skatol), acetophenone, indole, phenol, and paracresol. * Sedimentary concentrations of perylene exceeded available sediment quality guidelines. Perylene is widespread in the environment and has large potential natural sources in addition to its anthropogenic sources. * Concentrations of metals did not exceed sediment quality guidelines. * Multiple organochlorine pesticides, both banned and currently used, were detected at each site using passive samplers. * Commonly detected pesticides included hexachlorobenzene, pentachloroanisole (a degradation product of pentachlorophenol), diazinon, cis-chlordane, endosulfan, DDD, and endosulfan sulfate. * PBDE concentrations detected in passive sampler extracts were less than the method detection limit at all sites with the exception of PBDE-99, detected at a concentration less than the reporting limit. * The fragrance galaxolide was detected at a concentration greater than the method detection limit. * Common PAHs, such as phenanthrene, fluoranthene, and pyrene, were detected in every passive sampler. * Dissolved oxygen concentration was slightly higher at site CCS1 compared to site CCS2 in both years. * Overall, there was no systematic increase in chemicals of concern at the restoration site during post-removal monitoring compared to conditions during pre-removal monitoring. Any immediate, short-duration effects of piling removal on water quality could not be determined because monitoring was not conducted during the removal.

Interlaboratory study of DNA extraction from multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for individual kernel detection system of genetically modified maize.

PubMed

Akiyama, Hiroshi; Sakata, Kozue; Makiyma, Daiki; Nakamura, Kosuke; Teshima, Reiko; Nakashima, Akie; Ogawa, Asako; Yamagishi, Toru; Futo, Satoshi; Oguchi, Taichi; Mano, Junichi; Kitta, Kazumi

2011-01-01

In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.

From the field: Efficacy of detecting Chronic Wasting Disease via sampling hunter-killed white-tailed deer

USGS Publications Warehouse

Diefenbach, D.R.; Rosenberry, C.S.; Boyd, Robert C.

2004-01-01

Surveillance programs for Chronic Wasting Disease (CWD) in free-ranging cervids often use a standard of being able to detect 1% prevalence when determining minimum sample sizes. However, 1% prevalence may represent >10,000 infected animals in a population of 1 million, and most wildlife managers would prefer to detect the presence of CWD when far fewer infected animals exist. We wanted to detect the presence of CWD in white-tailed deer (Odocoileus virginianus) in Pennsylvania when the disease was present in only 1 of 21 wildlife management units (WMUs) statewide. We used computer simulation to estimate the probability of detecting CWD based on a sampling design to detect the presence of CWD at 0.1% and 1.0% prevalence (23-76 and 225-762 infected deer, respectively) using tissue samples collected from hunter-killed deer. The probability of detection at 0.1% prevalence was <30% with sample sizes of ???6,000 deer, and the probability of detection at 1.0% prevalence was 46-72% with statewide sample sizes of 2,000-6,000 deer. We believe that testing of hunter-killed deer is an essential part of any surveillance program for CWD, but our results demonstrated the importance of a multifaceted surveillance approach for CWD detection rather than sole reliance on testing hunter-killed deer.

A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

USGS Publications Warehouse

Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

2017-01-01

A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

Detection of E. coli O157:H7 in complex matrices under varying flow parameters with a robotic fluorometric assay system

NASA Astrophysics Data System (ADS)

Leskinen, Stephaney D.; Schlemmer, Sarah M.; Kearns, Elizabeth A.; Lim, Daniel V.

2009-02-01

The development of rapid assays for detection of microbial pathogens in complex matrices is needed to protect public health due to continued outbreaks of disease from contaminated foods and water. An Escherichia coli O157:H7 detection assay was designed using a robotic, fluorometric assay system. The system integrates optics, fluidics, robotics and software for the detection of foodborne pathogens or toxins in as many as four samples simultaneously. It utilizes disposable fiber optic waveguides coated with biotinylated antibodies for capture of target analytes from complex sample matrices. Computer-controlled rotation of sample cups allows complete contact between the sample and the waveguide. Detection occurs via binding of a fluorophore-labeled antibody to the captured target, which leads to an increase in the fluorescence signal. Assays are completed within twenty-five minutes. Sample matrices included buffer, retentate (material recovered from the filter of the Automated Concentration System (ACS) following hollow fiber ultrafiltration), spinach wash and ground beef. The matrices were spiked with E. coli O157:H7 (103-105 cells/ml) and the limits of detection were determined. The effect of sample rotation on assay sensitivity was also examined. Rotation parameters for each sample matrix included 10 ml with rotation, 5 ml with rotation and 0.1 ml without rotation. Detection occurred at 104 cells/ml in buffer and spinach wash and at 105 cells/ml in retentate and ground beef. Detection was greater for rotated samples in each matrix except ground beef. Enhanced detection of E. coli from large, rotated volumes of complex matrices was confirmed.

Anthropogenic Organic Compounds in Ground Water and Finished Water of Community Water Systems near Dayton, Ohio, 2002-04

USGS Publications Warehouse

Thomas, Mary Ann

2007-01-01

Source water for 15 community-water-system (CWS) wells in the vicinity of Dayton, Ohio, was sampled to evaluate the occurrence of 258 anthropogenic compounds (AOCs). At least one AOC was detected in 12 of the 15 samples. Most samples contained a mixture of compounds (average of four compounds per sample). The compounds that were detected in more than 30 percent of the samples included three volatile organic compounds (VOCs) (trichloroethene, chloroform, and 1,1,1-trichloroethane) and four pesticides or pesticide breakdown products (prometon, simazine, atrazine, and deethylatrazine). In general, VOCs were detected at higher concentrations than pesticides were; among the VOCs, the maximum detected concentration was 4.8 ?g/L (for trichloroethene), whereas among the pesticides, the maximum detected concentration was 0.041 ?g/L (for atrazine). During a later phase of the study, samples of source water from five CWS wells were compared to samples of finished water associated with each well. In general, VOC detections were higher in finished water than in source water, primarily due to the occurrence of trihalomethanes, which are compounds that can form during the treatment process. In contrast, pesticide detections were relatively similar between source- and finished-water samples. To assess the human-health relevance of the data, concentrations of AOCs were compared to their respective human-health benchmarks. For pesticides, the maximum detected concentrations were at least 2 orders of magnitude less than the benchmark values. However, three VOCs - trichloroethene, carbon tetrachloride, and tetrachloromethane - were detected at concentrations that approach human-health benchmarks and therefore may warrant inclusion in a low-concentration, trends monitoring program.

Comparison of droplet digital PCR and conventional quantitative PCR for measuring EGFR gene mutation

PubMed Central

ZHANG, BO; XU, CHUN-WEI; SHAO, YUN; WANG, HUAI-TAO; WU, YONG-FANG; SONG, YE-YING; LI, XIAO-BING; ZHANG, ZHE; WANG, WEN-JING; LI, LI-QIONG; CAI, CONG-LI

2015-01-01

Early detection of epidermal growth factor receptor (EGFR) mutation, particularly EGFR T790M mutation, is of clinical significance. The aim of the present study was to compare the performances of amplification refractory mutation system-based quantitative polymerase chain reaction (ARMS-qPCR) and droplet digital polymerase chain reaction (ddPCR) approaches in the detection of EGFR mutation and explore the feasibility of using ddPCR in the detection of samples with low mutation rates. EGFR gene mutations in plasmid samples with different T790M mutation rates (0.1–5%) and 10 clinical samples were detected using the ARMS-qPCR and ddPCR approaches. The results demonstrated that the ARMS-qPCR method stably detected the plasmid samples (6,000 copies) with 5 and 1% mutation rates, while the ddPCR approach reliably detected those with 5% (398 copies), 1% (57 copies), 0.5% (24 copies) and 0.1% (average 6 copies) mutation rates. For the 10 clinical samples, the results for nine samples by the ARMS-qPCR and ddPCR methods were consistent; however, the sample N006, indicated to be EGFR wild-type by ARMS-qPCR, was revealed to have a clear EGFR T790M mutation with seven copies of mutant alleles in a background of 6,000 wild-type copies using ddPCR technology. This study demonstrates the feasibility of applying the ddPCR system to detect EGFR mutation and identified the advantage of ddPCR in the detection of samples with a low EGFR mutation abundance, particularly the secondary EGFR T790M resistance mutation, which enables early diagnosis before acquired resistance to tyrosine kinase inhibitors becomes clinically detectable. PMID:25780439

Water-quality assessment of the Rio Grande Valley, Colorado, New Mexico, and Texas; occurrence and distribution of selected pesticides and nutrients at selected surface-water sites in the Mesilla Valley, 1994-95

USGS Publications Warehouse

Healy, D.F.

1996-01-01

The Rio Grande Valley study unit of the U.S. Geological Survey National Water-Quality Assessment Program conducted a two-phase synoptic study of the occurrence and distribution of pesticides and nutrients in the surface water of the Mesilla Valley, New Mexico and Texas. Phase one, conducted in April-May 1994 during the high-flow irrigation season, consisted of a 6-week time- series sampling event during which 17 water-column samples were collected at 3 main-stem sites on the Rio Grande and a synoptic irrigation-run sampling event during which 19 water-column samples were collected at 7 main-stem sites, 10 drain sites, and 2 sites at the discharges of wastewater-treatment plants. Three samples are included in both the time-series and irrigation-run events. Phase two, conducted in January 1995 during the low-flow non-irrigation season, consisted of a non-irrigation synoptic sampling event during which 18 water-column samples were collected at seven main-stem sites, nine drain sites, and two sites at the discharges of wastewater-treatment plants and a bed- material sampling event during which 6 bed-material samples were collected at six sites near the mouths of drains that discharge to the Rio Grande. The 51 water-column samples were analyzed for 78 pesticides and metabolites and 8 nutrients along with other constituents. The six bed-material samples were analyzed for 21 pesticides and metabolites, gross polychlorinated biphenyls, and gross polychlorinated naphthalenes. The presence of dissolved pesticides in the surface water of the Mesilla Valley is erratic. A total of 100 detections of 17 different pesticides were detected in 44 of the water-column samples. As many as 38 percent of these detections may be attributed to pesticide use upstream from the valley or to nonagricultural pesticide use within the valley. There were 29 detections of 10 different pesticides in 17 samples during the irrigation run and 41 detections of 13 pesticides in 16 samples during the non-irrigation run. Nine pesticides were detected during both phases of the study. The most commonly detected pesticides in the water-column samples were DCPA, which was detected in 29 samples, and metolachlor, which was detected in 17 of the samples. DCPA was detected throughout the Mesilla Valley, whereas metolachlor was detected mainly in the northern and central parts of the valley. The maximum pesticide concentration found during the study was 0.75 microgram per liter of carbofuran, which was detected at the East Side Drain site during the irrigation run. No water-column pesticide concentration exceeded U.S. Environmental Protection Agency's drinking-water standards or any applicable Federal or State criteria or guidelines. A total of 21 occurrences of six pesticides and metabolites were found in the bed-material samples. Chlordane, diazinon, and methyl parathion were detected once each, whereas DDD, DDE, and DDT were detected at all six bed-material sites. Water-column samples for the analysis of nutrient concentrations were collected at all sampling sites during both phases of the study. The concentrations of each nutrient ranged from at or below the individual minimum reporting level to as much as two or three orders of magnitude larger than the minimum reporting level. The concentration of each nutrient was left skewed with most of the values toward the lower end of the range. The larger concentrations of each nutrient, except dissolved nitrite plus nitrate, were associated with wastewater-treatment- plant sites 4 and 16. The larger concentrations of dissolved nitrite plus nitrate were generally associated with the non- irrigation run; however, the largest concentration was at site 4 during the irrigation run. During this study, the Mesilla Valley as a unit was a source of nutrients to the Rio Grande. Wi

METAL RESISTIVITY MEASURING DEVICE

DOEpatents

Renken, J. Jr.; Myers, R.G.

1960-12-20

An eddy current device is offered for detecting discontinuities in metal samples. Alternate short and long duration pulses are inductively applied to a metal sample via the outer coil of a probe. The long pulses give a resultant signal from the metal sample responsive to probe-tosample spacing and discontinuities within the sample and the shont pulses give a resultant signal responsive only to probe -to-sample spacing. The inner coil of the probe detects the two resultant signals and transmits them to a separation network where the two signals are separated. The two separated signals are then transmitted to a compensation network where the detected signals due to the short pulses are used to compensate for variations due to probe-to-sample spacing contained in the detected signals from the long pulses. Thus, a resultant signal is obtained responsive to discontinuities within the sample and independent of probe-to- sample spacing.

Metal Resistivity Measuring Device

DOEpatents

Renken, Jr, C. J.; Myers, R. G.

1960-12-20

An eddy current device is designed for detecting discontinuities in metal samples. Alternate short and long duration pulses are inductively applied to a metal sample via the outer coil of a probe. The lorg pulses give a resultant signal from the metal sample responsive to probe-tosample spacing and discontinuities with the sample, and the short pulses give a resultant signal responsive only to probe-to-sample spacing. The inner coil of the probe detects the two resultant signals and transmits them to a separation network where the two signals are separated. The two separated signals are then transmitted to a compensation network where the detected signals due to the short pulses are used to compensate for variations due to probeto-sample spacing contained in the detected signals from the long pulses. Thus a resultant signal is obtained responsive to discontinuities within the sample and independent of probe-to- sample spacing.

Nutrients, organic compounds, and mercury in the Meduxnekeag River watershed, Maine, 2003

USGS Publications Warehouse

Schalk, Charles W.; Tornes, Lan

2005-01-01

In 2003, the U.S. Geological Survey, in cooperation with the Houlton Band of Maliseet Indians, sampled streambed sediments and surface water of the Meduxnekeag River watershed in northeastern Maine under various hydrologic conditions for nutrients, hydrophobic organic compounds, and mercury. Nutrients were sampled to address concerns related to summer algal blooms, and organic compounds and mercury were sampled to address concerns about regional depositional patterns and overall watershed quality. In most surface-water samples, phosphorus was not detected or was detected at concentrations below the minimum reporting limit. Nitrate and organic nitrogen were detected in every surface-water sample for which they were analyzed; the highest concentration of total nitrogen was 0.75 milligrams per liter during low flow. Instantaneous nitrogen loads and yields were calculated at four stations for two sampling events. These data indicate that the part of the watershed that includes Houlton, its wastewater-treatment plant, and four small urban brooks may have contributed high concentrations of nitrate to Meduxnekeag River during the high flows on April 23-24 and high concentrations of both organic and nitrate nitrogen on June 2-3. Mercury was detected in all three bed-sediment samples for which it was analyzed; concentrations were similar to those reported from regional studies. Notable organic compounds detected in bed sediments included p,p'-DDE and p,p'-DDT (pesticides of the DDT family) and several polycyclic aromatic hydrocarbons. Polychlorinated biphenyls (PCBs) and phthalates were not detected in any sample, whereas p-cresol was the only phenolic compound detected. Phosphorus was detected at concentrations below 700 milligrams per kilogram in each bed-sediment sample for which it was analyzed. Data were insufficient to establish whether the lack of large algal blooms in 2003 was related to low concentrations of phosphorus.

Occurrence of Selected Organic Compounds in Groundwater Used for Public Supply in the Plio-Pleistocene Deposits in East-Central Nebraska and the Dawson and Denver Aquifers near Denver, Colorado, 2002-2004

USGS Publications Warehouse

Bails, Jeffrey B.; Dietsch, Benjamin J.; Landon, Matthew K.; Paschke, Suzanne S.

2009-01-01

The National Water-Quality Assessment Program of the U.S. Geological Survey has an ongoing Source Water-Quality Assessment program designed to characterize the quality of water in aquifers used as a source of drinking-water supply for some of the largest metropolitan areas in the Nation. In addition to the sampling of the source waters, sampling of finished or treated waters was done in the second year of local studies to evaluate if the organic compounds detected in the source waters also were present in the water supplied to the public. An evaluation of source-water quality used in selected groundwater-supplied public water systems in east-central Nebraska and in the south Denver metropolitan area of Colorado was completed during 2002 through 2004. Fifteen wells in the Plio-Pleistocene alluvial and glacial deposits in east-central Nebraska (the High Plains study) and 12 wells in the Dawson and Denver aquifers, south of Denver (the South Platte study), were sampled during the first year to obtain information on the occurrence and distribution of selected organic chemicals in the source waters. During the second year of the study, two wells in east-central Nebraska were resampled, along with the associated finished water derived from these wells, to determine if organic compounds detected in the source water also were present in the finished water. Selection of the second-phase sampling sites was based on detections of the most-frequently occurring organic compounds from the first-year Source Water-Quality Assessment study results. The second-year sampling also required that finished waters had undergone water-quality treatment processes before being distributed to the public. Sample results from the first year of sampling groundwater wells in east-central Nebraska show that the most-frequently detected organic compounds were the pesticide atrazine and its degradate, deethylatrazine (DEA, otherwise known as 2-chloro-4-isopropylamino-6-amino-s-triazine or CIAT), which were detected in 9 of the 15 wells (60 percent of the samples). The second most frequently detected organic compound was tetrachloroethylene, detected in 4 of the 15 wells (27 percent of the samples), followed by chloroform, trichloroethylene, and 2-hydroxyatrazine (2-hydroxy-4-isopropylamino-6-ethylamino-s-triazine, or OIET), present in 3 of the 15 wells (20 percent of the samples). The pesticide compounds deisopropylatrazine (2-chloro-6-ethylamino-4-amino-s-triazine, or CEAT), metolachlor, and simazine and the volatile organic compound cis-1,2-dichloroethylene were detected in 2 of the 15 wells, and the compounds diuron and 1,2-dichloroethane were detected in only 1 of the 15 wells during the first-year sampling. Most detections of these compounds were at or near the minimum reporting levels, and none were greater than their regulatory maximum contaminant level. There were few detections of organic compounds during the first year of sampling groundwater wells in the South Platte study area. The compounds atrazine, deethylatrazine, picloram, tetrachloroethylene, methyl-tert-butyl-ether (MTBE), tris(2-butoxyethyl)phosphate, and bromoform were detected only once in all the samples from the 12 wells. Most detections of these compounds were at or near the minimum reporting levels, and none were greater than their regulatory maximum contaminant level. Second-year sampling, which included the addition of paired source- and finished-water samples, was completed at two sites in the High Plains study area. Source-water samples from the second-year sampling had detections of atrazine and deethylatrazine; at one site deisopropylatrazine and chloroform also were detected. The finished-water samples, which represent the source water after blending with water from other wells and treatment, indicated a decrease in the concentrations of the pesticides at one site, whereas concentrations remained nearly constant at a second site. The trihalomethanes (THMs or disinfec

Evaluation of volatile organic compounds in two Mojave Desert basins-Mojave River and Antelope Valley-in San Bernardino, Los Angeles, and Kern Counties, California, June-October 2002

USGS Publications Warehouse

Densmore, Jill N.; Belitz, Kenneth; Wright, Michael T.; Dawson, Barbara J.; Johnson, Tyler D.

2005-01-01

The California Aquifer Susceptibility Assessment of the Ground-Water Ambient Monitoring and Assessment Program was developed to assess water quality and susceptibility of ground-water resources to contamination from surficial sources. This study focuses on the Mojave River and the Antelope Valley ground-water basins in southern California. Volatile organic compound (VOC) data were evaluated in conjunction with tritium data to determine a potential correlation with aquifer type, depth to top of perforations, and land use to VOC distribution and occurrence in the Mojave River and the Antelope Valley Basins. Detection frequencies for VOCs were compiled and compared to assess the distribution in each area. Explanatory variables were evaluated by comparing detection frequencies for VOCs and tritium and the number of compounds detected. Thirty-three wells were sampled in the Mojave River Basin (9 in the floodplain aquifer, 15 in the regional aquifer, and 9 in the sewered subset of the regional aquifer). Thirty-two wells were sampled in the Antelope Valley Basin. Quality-control samples also were collected to identify, quantify, and document bias and variability in the data. Results show that VOCs generally were detected slightly more often in the Antelope Valley Basin samples than in the Mojave River Basin samples. VOCs were detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Tritium was detected more frequently in the Mojave River Basin samples than in the Antelope Valley Basin samples, and it was detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Most of the samples collected in both basins for this study contained old water (water recharged prior to 1952). In general, in these desert basins, tritium need not be present for VOCs to be present. When VOCs were detected, young water (water recharge after 1952) was slightly more likely to be contaminated than old water. Trihalomethanes (THMs) were detected less frequently in the Mojave River Basin samples than in the Antelope Valley Basin samples. The THMs that were detected in the Mojave River Basin were detected more frequently in the floodplain aquifer than in the regional aquifer and sewered subset. Solvents were detected more frequently in the Mojave River samples than in the Antelope Valley samples. In the Mojave River Basin samples, solvents were detected less frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Benzene, toluene, ethylbenzene and xylene (BTEX) were not detected in either study area. Methyl tert-butyl ether (MTBE) was detected in one sample from both the Mojave River and Antelope Valley Basins. The most frequently detected compound (detected in more than 10 percent of the wells) in the Mojave River Basin was chloroform. The two most frequently detected compounds in the Antelope Valley Basin were chloroform and tetrachloroethylene (PCE). In the Mojave River Basin, aquifer type and land use within 1,640 ft (500 m) of the well head were not statistically correlated with the number of VOCs detected, although VOCs were detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Depth to the top of the perforations was an explanatory factor for the number of VOCs detected in the Mojave River Basin; the detection frequency was greater for shallow wells than for deep wells. In the Antelope Valley Basin, neither aquifer type, depth to the top of the perforations, nor land use within 1,640 ft of the well head were explanatory factors for the number of VOCs detected. Although aquifer type and depth to top of the perforations did explain the presence of tritium in the Mojave River Basin, land use within 1,640 ft of the well head was not a statistically significant explanatory factor for the presence of tritium in this basin. Aquifer type, depth to the top of the perfora

Method and apparatus for data sampling

DOEpatents

Odell, D.M.C.

1994-04-19

A method and apparatus for sampling radiation detector outputs and determining event data from the collected samples is described. The method uses high speed sampling of the detector output, the conversion of the samples to digital values, and the discrimination of the digital values so that digital values representing detected events are determined. The high speed sampling and digital conversion is performed by an A/D sampler that samples the detector output at a rate high enough to produce numerous digital samples for each detected event. The digital discrimination identifies those digital samples that are not representative of detected events. The sampling and discrimination also provides for temporary or permanent storage, either serially or in parallel, to a digital storage medium. 6 figures.

Summary of pesticide data from streams and wells in the Potomac River Basin, 1993-96

USGS Publications Warehouse

Donnelly, Colleen A.; Ferrari, Matthew J.

1998-01-01

Eighty-five water-soluble pesticides and pesticide degradation products were analyzed in 384 surface-water and ground-water samples collected from the Potomac River Basin during March 1993 through September 1996. Thirty-nine of these compounds were detected in surface-water samples and 16 were detected in ground-water samples. At least one pesticide was detected in 86 percent of the streams sampled and 45 percent of the wells sampled. Pesticides were detected more frequently and at higher concentrations in surface water than in ground water. The following four herbicides and one degradation product were the most frequently detected pesticides in both surface water and ground water: atrazine and metolachlor, which are used primarily on corn and soybean crops; prometon, which is used primarily in nonagricultural (urban and suburban) areas; simazine, which is used in both agricultural and nonagricultural areas, and desethylatrazine, which is one of the degradation products of atrazine. Insecticides were detected more frequently in surface water than in ground water. Diazinon, chlorpyrifos, and gamma-HCH (Undone) were found in more than 10 percent of surface-water samples, but in none of the ground-water samples.

Rope-based oral fluid sampling for early detection of classical swine fever in domestic pigs at group level.

PubMed

Dietze, Klaas; Tucakov, Anna; Engel, Tatjana; Wirtz, Sabine; Depner, Klaus; Globig, Anja; Kammerer, Robert; Mouchantat, Susan

2017-01-05

Non-invasive sampling techniques based on the analysis of oral fluid specimen have gained substantial importance in the field of swine herd management. Methodological advances have a focus on endemic viral diseases in commercial pig production. More recently, these approaches have been adapted to non-invasive sampling of wild boar for transboundary animal disease detection for which these effective population level sampling methods have not been available. In this study, a rope-in-a-bait based oral fluid sampling technique was tested to detect classical swine fever virus nucleic acid shedding from experimentally infected domestic pigs. Separated in two groups treated identically, the course of the infection was slightly differing in terms of onset of the clinical signs and levels of viral ribonucleic acid detection in the blood and oral fluid. The technique was capable of detecting classical swine fever virus nucleic acid as of day 7 post infection coinciding with the first detection in conventional oropharyngeal swab samples from some individual animals. Except for day 7 post infection in the "slower onset group", the chances of classical swine fever virus nucleic acid detection in ropes were identical or higher as compared to the individual sampling. With the provided evidence, non-invasive oral fluid sampling at group level can be considered as additional cost-effective detection tool in classical swine fever prevention and control strategies. The proposed methodology is of particular use in production systems with reduced access to veterinary services such as backyard or scavenging pig production where it can be integrated in feeding or baiting practices.

Low-Level detections of halogenated volatile organic compounds in groundwater: Use in vulnerability assessments

USGS Publications Warehouse

Plummer, Niel; Busenberg, E.; Eberts, S.M.; Bexfield, L.M.; Brown, C.J.; Fahlquist, L.S.; Katz, B.G.; Landon, M.K.

2008-01-01

Concentrations of halogenated volatile organic compounds (VOCs) were determined by gas chromatography (GC) with an electron-capture detector (GC-ECD) and by gas chromatography with mass spectrometry (GC-MS) in 109 groundwater samples from five study areas in the United States. In each case, the untreated water sample was used for drinking-water purposes or was from a monitoring well in an area near a drinking-water source. The minimum detection levels (MDLs) for 25 VOCs that were identified in GC-ECD chromatograms, typically, were two to more than four orders of magnitude below the GC-MS MDLs. At least six halogenated VOCs were detected in all of the water samples analyzed by GC-ECD, although one or more VOCs were detected in only 43% of the water samples analyzed by GC-MS. In nearly all of the samples, VOC concentrations were very low and presented no known health risk. Most of the low-level VOC detections indicated post-1940s recharge, or mixtures of recharge that contained a fraction of post-1940s water. Concentrations of selected halogenated VOCs in groundwater from natural and anthropogenic atmospheric sources were estimated and used to recognize water samples that are being impacted by nonatmospheric sources. A classification is presented to perform vulnerability assessments at the scale of individual wells using the number of halogenated VOC detections and total dissolved VOC concentrations in samples of untreated drinking water. The low-level VOC detections are useful in vulnerability assessments, particularly for samples in which no VOCs are detected by GC-MS analysis.

Multisite tumor sampling enhances the detection of intratumor heterogeneity at all different temporal stages of tumor evolution.

PubMed

Erramuzpe, Asier; Cortés, Jesús M; López, José I

2018-02-01

Intratumor heterogeneity (ITH) is an inherent process of tumor development that has received much attention in previous years, as it has become a major obstacle for the success of targeted therapies. ITH is also temporally unpredictable across tumor evolution, which makes its precise characterization even more problematic since detection success depends on the precise temporal snapshot at which ITH is analyzed. New and more efficient strategies for tumor sampling are needed to overcome these difficulties which currently rely entirely on the pathologist's interpretation. Recently, we showed that a new strategy, the multisite tumor sampling, works better than the routine sampling protocol for the ITH detection when the tumor time evolution was not taken into consideration. Here, we extend this work and compare the ITH detections of multisite tumor sampling and routine sampling protocols across tumor time evolution, and in particular, we provide in silico analyses of both strategies at early and late temporal stages for four different models of tumor evolution (linear, branched, neutral, and punctuated). Our results indicate that multisite tumor sampling outperforms routine protocols in detecting ITH at all different temporal stages of tumor evolution. We conclude that multisite tumor sampling is more advantageous than routine protocols in detecting intratumor heterogeneity.

Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy.

PubMed

Egan, Scott P; Grey, Erin; Olds, Brett; Feder, Jeffery L; Ruggiero, Steven T; Tanner, Carol E; Lodge, David M

2015-04-07

Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.

Red-shouldered hawk occupancy surveys in central Minnesota, USA

USGS Publications Warehouse

Henneman, C.; McLeod, M.A.; Andersen, D.E.

2007-01-01

Forest-dwelling raptors are often difficult to detect because many species occur at low density or are secretive. Broadcasting conspecific vocalizations can increase the probability of detecting forest-dwelling raptors and has been shown to be an effective method for locating raptors and assessing their relative abundance. Recent advances in statistical techniques based on presence-absence data use probabilistic arguments to derive probability of detection when it is <1 and to provide a model and likelihood-based method for estimating proportion of sites occupied. We used these maximum-likelihood models with data from red-shouldered hawk (Buteo lineatus) call-broadcast surveys conducted in central Minnesota, USA, in 1994-1995 and 2004-2005. Our objectives were to obtain estimates of occupancy and detection probability 1) over multiple sampling seasons (yr), 2) incorporating within-season time-specific detection probabilities, 3) with call type and breeding stage included as covariates in models of probability of detection, and 4) with different sampling strategies. We visited individual survey locations 2-9 times per year, and estimates of both probability of detection (range = 0.28-0.54) and site occupancy (range = 0.81-0.97) varied among years. Detection probability was affected by inclusion of a within-season time-specific covariate, call type, and breeding stage. In 2004 and 2005 we used survey results to assess the effect that number of sample locations, double sampling, and discontinued sampling had on parameter estimates. We found that estimates of probability of detection and proportion of sites occupied were similar across different sampling strategies, and we suggest ways to reduce sampling effort in a monitoring program.

Detection of Nitrobenzodiazepines and Their 7-Amino Metabolites in Oral Fluid.

PubMed

Vindenes, Vigdis; Strand, Dag Helge; Koksæter, Paul; Gjerde, Hallvard

2016-05-01

Clonazepam, nitrazepam and flunitrazepam are frequently used benzodiazepines, both as prescribed medication and as drugs of abuse. Little is, however, known about how these drugs are excreted in oral fluid. It has been claimed that the parent drugs are more likely to be detected in oral fluid than the 7-amino metabolites. The aim of this study was to investigate whether the parent drugs or the 7-amino metabolites of the nitrobenzodiazepines were most frequently detected in authentic oral fluid samples. Oral fluid samples were collected from patients undergoing opioid maintenance treatment. Cases where clonazepam, nitrazepam, flunitrazepam and/or their metabolites were detected were included. The samples were collected using the Intercept Oral Specimen Collection Device. A cutoff concentration of 1 nM (∼0.3 ng/mL) in oral fluid-buffer mixture was applied for all the substances. A total of 1,001 oral fluid samples were positive for clonazepam and/or 7-aminoclonazepam; both substances were detected in 707 samples, only the parent drug in 64 cases and only the metabolite in 230 cases. For nitrazepam, both substances were detected in 139 samples; only the parent drug in 16 cases and only the metabolite in 56 cases. Flunitrazepam only was not detected in any sample; both substances were detected in one of these cases, and only the metabolite in three cases. This study revealed that 7-amino metabolites were more likely to be detected in oral fluid than the parent drugs. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Ground-Water Quality in the Genesee River Basin, New York, 2005-2006

USGS Publications Warehouse

Eckhardt, David A.V.; Reddy, J.E.; Tamulonis, Kathryn L.

2007-01-01

Water samples were collected from 7 community water system wells and 15 private domestic wells throughout the Genesee River Basin in New York State (downstream from the Pennsylvania border) from October 2005 through March 2006 and analyzed to characterize the chemical quality of ground water in the basin. The wells were selected to represent areas of greatest ground-water use and to provide a representative sampling from the 2,439 square-mile basin area in New York. Samples were analyzed for five physical properties and 226 constituents that included nutrients, major inorganic ions, trace elements, radionuclides, pesticides, volatile organic compounds, and bacteria. The results show that ground water used for drinking water is generally of good quality in the Genesee River Basin, although concentrations of seven constituents exceeded drinking water standards. The cations that were detected in the highest concentrations were calcium, magnesium, and sodium; the anions that were detected in the greatest concentrations were bicarbonate, chloride, and sulfate. The predominant nutrient was nitrate, and nitrate concentrations were greater in samples from sand and gravel aquifers than in samples from bedrock aquifers. The trace elements barium, boron, cobalt, copper, and nickel were detected in every sample; the highest concentrations were barium, boron, chromium, iron, manganese, strontium, and lithium. Fourteen pesticides including seven pesticide degradates were detected in water from 12 of the 22 wells, but none of the concentrations exceeded Maximum Contaminant Levels (MCLs). Eight volatile organic compounds (VOCs) were detected in six samples, but none of the concentrations exceeded MCLs. Seven chemical analytes and three types of bacteria were present in concentrations that exceeded Federal and New York State water-quality standards, which are typically identical. Sulfate concentrations exceeded the U.S. Environmental Protection Agency (USEPA) Secondary Maximum Contaminant Level (SMCL) of 250 milligrams per liter (mg/L) in three samples; the chloride SMCL (250 mg/L) was exceeded in one sample. Sodium concentrations exceeded the USEPA Drinking Water Health Advisory of 60 mg/L in five samples. The SMCL for iron (300 ug/L) was exceeded in 11 filtered samples; the USEPA SMCL for manganese (50 ug/L) was exceeded in 10 filtered samples, and the New York State MCL (300 ug/L) was exceeded in 1 filtered sample. The MCL for aluminum (200 ug/L) was exceeded in 1 sample, and the MCL for arsenic (10 ug/L) was exceeded in 1 sample. Radon-222 exceeded the proposed USEPA MCL of 300 picocuries per liter in 16 samples. Any detection of total coliform or fecal coliform bacteria is considered a violation of New York State health regulations; in this study, total coliform was detected in eight samples; fecal coliform was detected in two samples, and Escherichia coli was detected in one sample.

Sampling trace organic compounds in water: a comparison of a continuous active sampler to continuous passive and discrete sampling methods

USGS Publications Warehouse

Coes, Alissa L.; Paretti, Nicholas V.; Foreman, William T.; Iverson, Jana L.; Alvarez, David A.

2014-01-01

A continuous active sampling method was compared to continuous passive and discrete sampling methods for the sampling of trace organic compounds (TOCs) in water. Results from each method are compared and contrasted in order to provide information for future investigators to use while selecting appropriate sampling methods for their research. The continuous low-level aquatic monitoring (CLAM) sampler (C.I.Agent® Storm-Water Solutions) is a submersible, low flow-rate sampler, that continuously draws water through solid-phase extraction media. CLAM samplers were deployed at two wastewater-dominated stream field sites in conjunction with the deployment of polar organic chemical integrative samplers (POCIS) and the collection of discrete (grab) water samples. All samples were analyzed for a suite of 69 TOCs. The CLAM and POCIS samples represent time-integrated samples that accumulate the TOCs present in the water over the deployment period (19–23 h for CLAM and 29 days for POCIS); the discrete samples represent only the TOCs present in the water at the time and place of sampling. Non-metric multi-dimensional scaling and cluster analysis were used to examine patterns in both TOC detections and relative concentrations between the three sampling methods. A greater number of TOCs were detected in the CLAM samples than in corresponding discrete and POCIS samples, but TOC concentrations in the CLAM samples were significantly lower than in the discrete and (or) POCIS samples. Thirteen TOCs of varying polarity were detected by all of the three methods. TOC detections and concentrations obtained by the three sampling methods, however, are dependent on multiple factors. This study found that stream discharge, constituent loading, and compound type all affected TOC concentrations detected by each method. In addition, TOC detections and concentrations were affected by the reporting limits, bias, recovery, and performance of each method.

Sampling trace organic compounds in water: a comparison of a continuous active sampler to continuous passive and discrete sampling methods.

PubMed

Coes, Alissa L; Paretti, Nicholas V; Foreman, William T; Iverson, Jana L; Alvarez, David A

2014-03-01

A continuous active sampling method was compared to continuous passive and discrete sampling methods for the sampling of trace organic compounds (TOCs) in water. Results from each method are compared and contrasted in order to provide information for future investigators to use while selecting appropriate sampling methods for their research. The continuous low-level aquatic monitoring (CLAM) sampler (C.I.Agent® Storm-Water Solutions) is a submersible, low flow-rate sampler, that continuously draws water through solid-phase extraction media. CLAM samplers were deployed at two wastewater-dominated stream field sites in conjunction with the deployment of polar organic chemical integrative samplers (POCIS) and the collection of discrete (grab) water samples. All samples were analyzed for a suite of 69 TOCs. The CLAM and POCIS samples represent time-integrated samples that accumulate the TOCs present in the water over the deployment period (19-23 h for CLAM and 29 days for POCIS); the discrete samples represent only the TOCs present in the water at the time and place of sampling. Non-metric multi-dimensional scaling and cluster analysis were used to examine patterns in both TOC detections and relative concentrations between the three sampling methods. A greater number of TOCs were detected in the CLAM samples than in corresponding discrete and POCIS samples, but TOC concentrations in the CLAM samples were significantly lower than in the discrete and (or) POCIS samples. Thirteen TOCs of varying polarity were detected by all of the three methods. TOC detections and concentrations obtained by the three sampling methods, however, are dependent on multiple factors. This study found that stream discharge, constituent loading, and compound type all affected TOC concentrations detected by each method. In addition, TOC detections and concentrations were affected by the reporting limits, bias, recovery, and performance of each method. Published by Elsevier B.V.

Feature Sampling in Detection: Implications for the Measurement of Perceptual Independence

ERIC Educational Resources Information Center

Macho, Siegfried

2007-01-01

The article presents the feature sampling signal detection (FS-SDT) model, an extension of the multivariate signal detection (SDT) model. The FS-SDT model assumes that, because of attentional shifts, different subsets of features are sampled for different presentations of the same multidimensional stimulus. Contrary to the SDT model, the FS-SDT…

Research on Abnormal Detection Based on Improved Combination of K - means and SVDD

NASA Astrophysics Data System (ADS)

Hao, Xiaohong; Zhang, Xiaofeng

2018-01-01

In order to improve the efficiency of network intrusion detection and reduce the false alarm rate, this paper proposes an anomaly detection algorithm based on improved K-means and SVDD. The algorithm first uses the improved K-means algorithm to cluster the training samples of each class, so that each class is independent and compact in class; Then, according to the training samples, the SVDD algorithm is used to construct the minimum superspheres. The subordinate relationship of the samples is determined by calculating the distance of the minimum superspheres constructed by SVDD. If the test sample is less than the center of the hypersphere, the test sample belongs to this class, otherwise it does not belong to this class, after several comparisons, the final test of the effective detection of the test sample.In this paper, we use KDD CUP99 data set to simulate the proposed anomaly detection algorithm. The results show that the algorithm has high detection rate and low false alarm rate, which is an effective network security protection method.

Chemical contaminants in water and sediment near fish nesting sites in the Potomac River basin: determining potential exposures to smallmouth bass (Micropterus dolomieu).

PubMed

Kolpin, Dana W; Blazer, Vicki S; Gray, James L; Focazio, Michael J; Young, John A; Alvarez, David A; Iwanowicz, Luke R; Foreman, William T; Furlong, Edward T; Speiran, Gary K; Zaugg, Steven D; Hubbard, Laura E; Meyer, Michael T; Sandstrom, Mark W; Barber, Larry B

2013-01-15

The Potomac River basin is an area where a high prevalence of abnormalities such as testicular oocytes (TO), skin lesions, and mortality has been observed in smallmouth bass (SMB, Micropterus dolomieu). Previous research documented a variety of chemicals in regional streams, implicating chemical exposure as one plausible explanation for these biological effects. Six stream sites in the Potomac basin (and one out-of-basin reference site) were sampled to provide an assessment of chemicals in these streams. Potential early life-stage exposure to chemicals detected was assessed by collecting samples in and around SMB nesting areas. Target chemicals included those known to be associated with important agricultural and municipal wastewater sources in the Potomac basin. The prevalence and severity of TO in SMB were also measured to determine potential relations between chemistry and biological effects. A total of 39 chemicals were detected at least once in the discrete-water samples, with atrazine, caffeine, deethylatrazine, simazine, and iso-chlorotetracycline being most frequently detected. Of the most frequently detected chemicals, only caffeine was detected in water from the reference site. No biogenic hormones/sterols were detected in the discrete-water samples. In contrast, 100 chemicals (including six biogenic hormones/sterols) were found in a least one passive-water sample, with 25 being detected at all such samples. In addition, 46 chemicals (including seven biogenic hormones/sterols) were found in the bed-sediment samples, with caffeine, cholesterol, indole, para-cresol, and sitosterol detected in all such samples. The number of herbicides detected in discrete-water samples per site had a significant positive relation to TO(rank) (a nonparametric indicator of TO), with significant positive relations between TO(rank) and atrazine concentrations in discrete-water samples and to total hormone/sterol concentration in bed-sediment samples. Such significant correlations do not necessarily imply causation, as these chemical compositions and concentrations likely do not adequately reflect total SMB exposure history, particularly during critical life stages. Published by Elsevier B.V.

Characterization of the quality of water, bed sediment, and fish in Mittry Lake, Arizona, 2014–15

USGS Publications Warehouse

Hermosillo, Edyth; Coes, Alissa L.

2017-03-01

Water, bed-sediment, and fish sampling was conducted in Mittry Lake, Arizona, in 2014–15 to establish current water-quality conditions of the lake. The parameters of temperature, dissolved-oxygen concentration, specific conductance, and alkalinity were measured in the field. Water samples were collected and analyzed for dissolved major ions, dissolved trace elements, dissolved nutrients, dissolved organic carbon, dissolved pesticides, bacteria, and suspended-sediment concentrations. Bed-sediment and fish samples were analyzed for trace elements, halogenated compounds, total mercury, and methylmercury.U.S. Environmental Protection Agency secondary maximum contaminant levels in drinking water were exceeded for sulfate, chloride, and manganese in the water samples. Trace-element concentrations were relatively similar between the inlet, middle, and outlet locations. Concentrations for nutrients in all water samples were below the Arizona Department of Environmental Quality’s water-quality standards for aquatic and wildlife uses, and all bacteria levels were below the Arizona Department of Environmental Quality’s recommended recreational water-quality criteria. Three out of 81 pesticides were detected in the water samples.Trace-element concentrations in bed sediment were relatively consistent between the inlet, middle, and outlet locations. Lead, manganese, nickel, and zinc concentrations, however, decreased from the inlet to outlet locations. Concentrations for lead, nickel, and zinc in some bed-sediment samples exceeded consensus-based sediment-quality guidelines probable effect concentrations. Eleven out of 61 halogenated compounds were detected in bed sediment at the inlet location, whereas three were detected at the middle location, and five were detected at the outlet location. No methylmercury was detected in bed sediment. Total mercury was detected in bed sediment at concentrations below the consensus-based sediment-quality guidelines probable effect concentration.Sixteen trace elements were detected in at least one of the fish-tissue samples, and trace-element concentrations were relatively consistent between the three fish-tissue samples. Seven halogenated compounds were detected in at least one of the whole-body fish samples; four to five compounds were detected in each fish. One fish-tissue sample exceeded the U.S. Environmental Protection Agency human health consumption criteria for methylmercury.

Watershed trend analysis and water-quality assessment using bottom-sediment cores from Cheney Reservoir, south-central Kansas

USGS Publications Warehouse

Pope, Larry M.

1998-01-01

An examination of Cheney Reservoir bottom sediment was conducted in August 1997 to describe long-term trends and document the occurrence of selected constituents at concentrations that may be detrimental to aquatic organisms. Average concentrations of total phosphorus in bottom-sediment cores ranged from 94 to 674 milligrams per kilogram and were statistically related to silt- and (or) clay-size particles. Results from selected sampling sites in Cheney Reservoir indicate an increasing trend in total phosphorus concentrations. This trend is probably of nonpoint-source origin and may be related to an increase in fertilizer sales in the area, which more than doubled between 1965 and 1996, and to livestock production. Few organochlorine compounds were detected in bottom-sediment samples from Cheney Reservoir. DDT, its degradation products DDD and DDE, and dieldrin had detectable concentrations in the seven samples that were analyzed. DDT and DDD were each detected in one sample at concentrations of 1.0 and 0.65 microgram per kilogram, respectively. By far, the most frequently detected organochlorine insecticide was DDE, which was detected in all seven samples, ranging in concentration from 0.31 to 1.3 micrograms per kilogram. A decreasing trend in DDE concentrations was evident in sediment-core data from one sampling site. Dieldrin was detected in one sample from each of two sampling sites at concentrations of 0.21 and 0.22 micrograms per kilogram. Polychlorinated biphenyls were not detected in any bottom-sediment sample analyzed. Selected organophosphate, chlorophenoxy-acid, triazine, and acetanilide pesticides were analyzed in 18 bottom-sediment samples. Of the 23 pesticides analyzed, only the acetanilide herbicide metolachlor was detected (in 22 percent of the samples). Seven bottom-sediment samples were analyzed for major metals and trace elements. The median and maximum concentrations of arsenic and chromium, the maximum concentration of copper, and all concentrations of nickel in the seven samples were in the range where adverse effects to aquatic organisms occasionally occur. No time trends in trace elements were discernable in the August 1997 data.

Water-quality effects and characterization of indicators of onsite wastewater disposal systems in the east-central Black Hills area, South Dakota, 2006-08

USGS Publications Warehouse

Putnam, Larry D.; Hoogestraat, Galen K.; Sawyer, J. Foster

2008-01-01

Onsite wastewater disposal systems (OWDS) are used extensively in the Black Hills of South Dakota where many of the watersheds and aquifers are characterized by fractured or solution-enhanced bedrock with thin soil cover. A study was conducted during 2006-08 to characterize water-quality effects and indicators of OWDS. Water samples were collected and analyzed for potential indicators of OWDS, including chloride, bromide, boron, nitrite plus nitrate (NO2+NO3), ammonia, major ions, nutrients, selected trace elements, isotopes of nitrate, microbiological indicators, and organic wastewater compounds (OWCs). The microbiological indicators were fecal coliforms, Escherichia coli (E. coli), enterococci, Clostridium perfringens (C. perfringens), and coliphages. Sixty ground-water sampling sites were located either downgradient from areas of dense OWDS or in background areas and included 25 monitoring wells, 34 private wells, and 1 spring. Nine surface-water sampling sites were located on selected streams and tributaries either downstream or upstream from residential development within the Precambrian setting. Sampling results were grouped by their hydrogeologic setting: alluvial, Spearfish, Minnekahta, and Precambrian. Mean downgradient dissolved NO2+NO3 concentrations in ground water for the alluvial, Spearfish, Minnekahta, and Precambrian settings were 0.734, 7.90, 8.62, and 2.25 milligrams per liter (mg/L), respectively. Mean downgradient dissolved chloride concentrations in ground water for these settings were 324, 89.6, 498, and 33.2 mg/L, respectively. Mean downgradient dissolved boron concentrations in ground water for these settings were 736, 53, 64, and 43 micrograms per liter (ug/L), respectively. Mean dissolved surface-water concentrations for NO2+NO3, chloride, and boron for downstream sites were 0.222 mg/L, 32.1 mg/L, and 28 ug/L, respectively. Mean values of delta-15N and delta-18O (isotope ratios of 14N to 15N and 18O to 16O relative to standard ratios) for nitrate in ground-water samples were 10.4 and -2.0 per mil (0/100), respectively, indicating a relatively small contribution from synthetic fertilizer and probably a substantial contribution from OWDS. The surface-water sample with the highest dissolved NO2+NO3 concentration of 1.6 mg/L had a delta-15N value of 12.36 0/100, which indicates warm-blooded animals (including humans) as the nitrate source. Fecal coliforms were detected in downgradient ground water most frequently in the Spearfish (19 percent) and Minnekahta (9.7 percent) settings. E. coli was detected most frequently in the Minnekahta (29 percent) and Spearfish (13 percent) settings. Enterococci were detected more frequently than other microbiological indicators in all four settings. Fecal coliforms and E. coli were detected in 73 percent and 95 percent of all surface-water samples, respectively. Enterococci, coliphages (somatic), and C. perfringens were detected in 50, 70, and 50 percent of surface-water samples, respectively. Of the 62 OWC analytes, 12 were detected only in environmental samples, 10 were detected in at least one environmental and one blank sample (not necessarily companion pairs), 2 were detected only in blank samples, and 38 were not detected in any blank, environmental, or replicate sample from either ground or surface water. Eleven different organic compounds were detected in ground-water samples at eight different sites. The most frequently occurring compound was DEET, which was found in 32 percent of the environmental samples, followed by tetrachloroethene, which was detected in 20 percent of the samples. For surface-water samples, 16 organic compounds were detected in 9 of the 10 total samples. The compound with the highest occurrence in surface-water samples was camphor, which was detected in 50 percent of samples. The alluvial setting was characterized by relatively low dissolved NO2+NO3 concentrations, detection of ammonia nitrogen, and relatively high concentr

Validation of the 3M molecular detection system for the detection of listeria in meat, seafood, dairy, and retail environments.

PubMed

Fortes, Esther D; David, John; Koeritzer, Bob; Wiedmann, Martin

2013-05-01

There is a continued need to develop improved rapid methods for detection of foodborne pathogens. The aim of this project was to evaluate the 3M Molecular Detection System (3M MDS), which uses isothermal DNA amplification, and the 3M Molecular Detection Assay Listeria using environmental samples obtained from retail delicatessens and meat, seafood, and dairy processing plants. Environmental sponge samples were tested for Listeria with the 3M MDS after 22 and 48 h of enrichment in 3M Modified Listeria Recovery Broth (3M mLRB); enrichments were also used for cultural detection of Listeria spp. Among 391 samples tested for Listeria, 74 were positive by both the 3M MDS and the cultural method, 310 were negative by both methods, 2 were positive by the 3M MDS and negative by the cultural method, and one sample was negative by the 3M MDS and positive by the cultural method. Four samples were removed from the sample set, prior to statistical analyses, due to potential cross-contamination during testing. Listeria isolates from positive samples represented L. monocytogenes, L. innocua, L. welshimeri, and L. seeligeri. Overall, the 3M MDS and culture-based detection after enrichment in 3M mLRB did not differ significantly (P < 0.05) with regard to the number of positive samples, when chi-square analyses were performed for (i) number of positive samples after 22 h, (ii) number of positive samples after 48 h, and (iii) number of positive samples after 22 and/or 48 h of enrichment in 3M mLRB. Among 288 sampling sites that were tested with duplicate sponges, 67 each tested positive with the 3M MDS and the traditional U.S. Food and Drug Administration Bacteriological Analytical Manual method, further supporting that the 3M MDS performs equivalently to traditional methods when used with environmental sponge samples.

Detection and Molecular Characterization of Gemycircularvirus from Environmental Samples in Brazil.

PubMed

da Silva Assis, Matheus Ribeiro; Vieira, Carmen Baur; Fioretti, Julia Monassa; Rocha, Mônica Simões; de Almeida, Pedro Ivo Neves; Miagostovich, Marize Pereira; Fumian, Tulio Machado

2016-12-01

Gemycircularvirus (GemyCV) is a group of viruses which has been recently proposed as a new viral genus detected in fecal and environmental samples around the world. GemyCVs have been detected in human blood, brain tissue, cerebrospinal fluid, and stool sample. In the present study, we demonstrate for the first time, through molecular detection and characterization, the presence of GemyCVs in environmental samples from Brazil. Our results show a percentage of positivity ranging from 69 (25/36) to 97 % (35/36) in river water samples collected in Manaus, Amazon region, and wastewater from a wastewater treatment plant located in Rio de Janeiro, respectively, revealing GemyCVs as an important environmental contaminant.

Duplex detection of the Mycobacterium tuberculosis complex and medically important non-tuberculosis mycobacteria by real-time PCR based on the rnpB gene.

PubMed

Abdeldaim, Guma; Svensson, Erik; Blomberg, Jonas; Herrmann, Björn

2016-11-01

A duplex real-time PCR based on the rnpB gene was developed for Mycobacterium spp. The assay was specific for the Mycobacterium tuberculosis complex (MTB) and also detected all 19 tested species of non-tuberculous mycobacteria (NTM). The assay was evaluated on 404 clinical samples: 290 respiratory samples and 114 from tissue and other non-respiratory body sites. M. tuberculosis was detected by culture in 40 samples and in 30 samples by the assay. The MTB assay showed a sensitivity similar to Roche Cobas Amplicor MTB-PCR (Roche Molecular Systems, Pleasanton, CA, USA). There were only nine samples with non-tuberculous mycobacteria detected by culture. Six of them were detected by the PCR assay. © 2016 APMIS. Published by John Wiley & Sons Ltd.

Effects of Sampling Strategy, Detection Probability, and Independence of Counts on the Use of Point Counts

Treesearch

Grey W. Pendleton

1995-01-01

Many factors affect the use of point counts for monitoring bird populations, including sampling strategies, variation in detection rates, and independence of sample points. The most commonly used sampling plans are stratified sampling, cluster sampling, and systematic sampling. Each of these might be most useful for different objectives or field situations. Variation...

Early Detection of Foot-And-Mouth Disease Virus from Infected Cattle Using A Dry Filter Air Sampling System.

PubMed

Pacheco, J M; Brito, B; Hartwig, E; Smoliga, G R; Perez, A; Arzt, J; Rodriguez, L L

2017-04-01

Foot-and-mouth disease (FMD) is a highly contagious livestock disease of high economic impact. Early detection of FMD virus (FMDV) is fundamental for rapid outbreak control. Air sampling collection has been demonstrated as a useful technique for detection of FMDV RNA in infected animals, related to the aerogenous nature of the virus. In the current study, air from rooms housing individual (n = 17) or two groups (n = 4) of cattle experimentally infected with FDMV A24 Cruzeiro of different virulence levels was sampled to assess the feasibility of applying air sampling as a non-invasive, screening tool to identify sources of FMDV infection. Detection of FMDV RNA in air was compared with first detection of clinical signs and FMDV RNA levels in serum and oral fluid. FMDV RNA was detected in room air samples 1-3 days prior (seven animals) or on the same day (four animals) as the appearance of clinical signs in 11 of 12 individually housed cattle. Only in one case clinical signs preceded detection in air samples by one day. Overall, viral RNA in oral fluid or serum preceded detection in air samples by 1-2 days. Six individually housed animals inoculated with attenuated strains did not show clinical signs, but virus was detected in air in one of these cases 3 days prior to first detection in oral fluid. In groups of four cattle housed together, air detection always preceded appearance of clinical signs by 1-2 days and coincided more often with viral shedding in oral fluid than virus in blood. These data confirm that air sampling is an effective non-invasive screening method for detecting FMDV infection in confined to enclosed spaces (e.g. auction barns, milking parlours). This technology could be a useful tool as part of a surveillance strategy during FMD prevention, control or eradication efforts. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Water-quality assessment of the Ozark Plateaus study unit, Arkansas, Kansas, Missouri, and Oklahoma; organic compounds in surface water, bed sediment, and biological tissue, 1992-95

USGS Publications Warehouse

Bell, Richard W.; Davis, Jerri V.; Femmer, Suzanne R.; Joseph, Robert L.

1997-01-01

Organic-compound samples, including pesticides and semi-volatiles, were collected from 1992-95 at 43 surface-water and 27 bed-sediment and biological-tissue sampling sites within the Ozark Plateaus National Water-Quality Assessment Program study unit. Most surface-water, bed-sediment, and biological-tissue sites have drainage basins predominantly in the Springfield and Salem Plateaus. At most surface-water sampling sites, one to three pesticide samples were collected in the spring and early summer of 1994 and 1995; two sites had additional samples collected either weekly, biweekly, or monthly from February 1994 through December 1994. At most bed-sediment and biological-tissue sampling sites, a single organic-compounds sample was collected. Agricultural pesticide use was approximately 4.9 million pounds of active ingredients per year from 1987-91 in the study unit and was generally greatest in the Springfield and Salem Plateaus pasturelands and in the Osage Plains and Mississippi Alluvial Plain cropland areas. The most frequently applied pesticide in the study unit was 2,4-D. Atrazine was the second most frequently applied pesticide. Corn, pasture, rice, sorghum, and soybeans received approximately 85 percent of the pesticides applied within the study unit. The highest pesticide application rate occurred on these crops in the Mississippi Alluvial and Osage Plains. Pastureland was the crop type that received the greatest amount of pesticides in 53 of the 96 counties in the study unit. The most commonly detected herbicide (63 samples) in surface water was atrazine. Five other pesticides--desethylatrazine, tebuthiuron, prometon, metolachlor, and simazine--were detected in 15 or more samples. The most commonly detected insecticide (13 samples) was p,p'-DDE. Two other insecticides, diazinon and cis-permethrin, were detected in seven or more samples. Pesticides were detected at 39 surface-water sites; samples collected at Yocum Creek near Oak Grove, Ark. had the most pesticide detections (13). Seventeen other sites had samples with six or more pesticide detections. Analysis of pesticide data collected at surface-water sites indicates that the largest variety of different pesticides detected (18) was in small, agricultural drainage basins; the largest percentage of detections of a single pesticide (about 80) was in medium, agricultural basins. Pesticide concentrations were small, and in most cases, at or near the detection limit. Maximum concentrations ranged from 0.001 to 0.007 micrograms per liter (mg/L) at small, forest sites; 0.001 to 0.029 mg/L at medium, forest sites; 0.001 to 0.079 mg/L at small, agricultural sites; and 0.003 to 0.29 mg/L at medium, agricultural sites. Pesticides were detected significantly more often in medium, agricultural basins in the Springfield Plateau. The most commonly detected (13 samples) organic compound in bed sediment, in concentrations noticeably above background levels, was 2,6-dimethylnaphthalene; the maximum concentration of 2,6-dimethylnaphthalene was 130 micrograms per kilogram. Seventeen or more compounds were detected in bed-sediment samples collected at three sites. Four compounds were detected in biological-tissue samples: p,p'-DDT in Corbicula fluminea (Asiatic clam) tissue collected at the Osage River near St. Thomas, Mo. and cis-chlordane, trans-chlordane, and trans-nonachlor in C. fluminea tissue collected at the James River near Boaz, Mo. Organic compounds collected at surface-water, bed-sediment, or biological-tissue sampling sites were not detected in concentrations that exceeded any health criteria or standards. Based on this information, organic compounds do not pose any widespread or persistent problems in the study unit.

An evaluation of the efficacy of using environmental DNA (eDNA) to detect giant gartersnakes (Thamnophis gigas)

USGS Publications Warehouse

Halstead, Brian J.; Wood, Dustin A.; Bowen, Lizabeth; Waters, Shannon C.; Vandergast, Amy G.; Ersan, Julia S.; Skalos, Shannon M.; Casazza, Michael L.

2017-09-28

Detecting populations of rare or cryptic species is essential for their conservation. For species like giant gartersnakes (Thamnophis gigas), conventional survey methods can be expensive and inefficient. These sampling difficulties might be overcome by modern techniques that detect deoxyribonucleic acid (DNA) shed by organisms into the environment (eDNA). We evaluated the efficacy of detecting giant gartersnake eDNA in water samples from the laboratory and at locations with known giant gartersnake populations in the Sacramento Valley of California, and failed to detect giant gartersnake DNA in most laboratory and all field samples. Aspects of giant gartersnake biology—such as highly keratinized skin and spending extensive time in the terrestrial environment, as well as hot, sunny, and turbid conditions in wetlands and canals of the Sacramento Valley—likely contributed to low detection probabilities. Although detection of eDNA shows promise under many conditions, further development is needed before sampling for eDNA is a viable option for detecting giant gartersnake populations.

Ground-water quality in the Lake Champlain basin, New York, 2004

USGS Publications Warehouse

Nystrom, Elizabeth A.

2006-01-01

Water samples were collected from 11 public-supply wells and 11 private domestic wells in the Lake Champlain basin in New York during the fall of 2004 to characterize the chemical quality of ground water. Wells were selected for sampling based on location and focused on areas of greatest ground-water use. Samples were analyzed for 219 physical properties and constituents, including inorganic compounds, nutrients, metals, radionuclides, pesticides and pesticide degradates, volatile organic compounds, and bacteria. Sixty-eight constituents were detected at concentrations above laboratory reporting levels. The cation and anion with the highest median concentration were calcium (34.8 mg/L) bicarbonate (134 mg/L), respectively. The predominant nutrient was nitrate, which was detected in 14 (64 percent) of the 22 samples. The two metals with the highest median concentrations were iron (175 ?g/L) and strontium (124 ?g/L); concentrations of iron, manganese, aluminum, and zinc exceeded U.S. Environmental Protection Agency secondary drinking-water standards in one or more samples. Radon concentrations were less than 1,000 picocuries per liter (pCi/L) in most samples, but concentrations as high as 6,900 pCi/L were detected and, in eight samples, exceeded the U.S. Environmental Protection Agency proposed maximum contaminant level (300 pCi/L) for radon. The most frequently detected pesticides were degradates of the broadleaf herbicides metolachlor, alachlor, and atrazine. Volatile organic compounds were detected in only three samples; those that were detected typically were fuel oxygenates, such as methyl tert-butyl ether. Coliform bacteria were detected in four samples, two of which also tested positive for E. coli.

Detection of Mycobacterium avium subspecies paratuberculosis in tie-stall dairy herds using a standardized environmental sampling technique and targeted pooled samples.

PubMed

Arango-Sabogal, Juan C; Côté, Geneviève; Paré, Julie; Labrecque, Olivia; Roy, Jean-Philippe; Buczinski, Sébastien; Doré, Elizabeth; Fairbrother, Julie H; Bissonnette, Nathalie; Wellemans, Vincent; Fecteau, Gilles

2016-07-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the etiologic agent of Johne's disease, a chronic contagious enteritis of ruminants that causes major economic losses. Several studies, most involving large free-stall herds, have found environmental sampling to be a suitable method for detecting MAP-infected herds. In eastern Canada, where small tie-stall herds are predominant, certain conditions and management practices may influence the survival and transmission of MAP and recovery (isolation). Our objective was to estimate the performance of a standardized environmental and targeted pooled sampling technique for the detection of MAP-infected tie-stall dairy herds. Twenty-four farms (19 MAP-infected and 5 non-infected) were enrolled, but only 20 were visited twice in the same year, to collect 7 environmental samples and 2 pooled samples (sick cows and cows with poor body condition). Concurrent individual sampling of all adult cows in the herds was also carried out. Isolation of MAP was achieved using the MGIT Para TB culture media and the BACTEC 960 detection system. Overall, MAP was isolated in 7% of the environmental cultures. The sensitivity of the environmental culture was 44% [95% confidence interval (CI): 20% to 70%] when combining results from 2 different herd visits and 32% (95% CI: 13% to 57%) when results from only 1 random herd visit were used. The best sampling strategy was to combine samples from the manure pit, gutter, sick cows, and cows with poor body condition. The standardized environmental sampling technique and the targeted pooled samples presented in this study is an alternative sampling strategy to costly individual cultures for detecting MAP-infected tie-stall dairies. Repeated samplings may improve the detection of MAP-infected herds.

Evaluation of Elecsys Syphilis Assay for Routine and Blood Screening and Detection of Early Infection

PubMed Central

Kremastinou, J.; Polymerou, V.; Lavranos, D.; Aranda Arrufat, A.; Harwood, J.; Martínez Lorenzo, M. J.; Ng, K. P.; Queiros, L.; Vereb, I.

2016-01-01

Treponema pallidum infections can have severe complications if not diagnosed and treated at an early stage. Screening and diagnosis of syphilis require assays with high specificity and sensitivity. The Elecsys Syphilis assay is an automated treponemal immunoassay for the detection of antibodies against T. pallidum. The performance of this assay was investigated previously in a multicenter study. The current study expands on that evaluation in a variety of diagnostic settings and patient populations, at seven independent laboratories. The samples included routine diagnostic samples, blood donation samples, samples from patients with confirmed HIV infections, samples from living organ or bone marrow donors, and banked samples, including samples previously confirmed as syphilis positive. This study also investigated the seroconversion sensitivity of the assay. With a total of 1,965 syphilis-negative routine diagnostic samples and 5,792 syphilis-negative samples collected from blood donations, the Elecsys Syphilis assay had specificity values of 99.85% and 99.86%, respectively. With 333 samples previously identified as syphilis positive, the sensitivity was 100% regardless of disease stage. The assay also showed 100% sensitivity and specificity with samples from 69 patients coinfected with HIV. The Elecsys Syphilis assay detected infection in the same bleed or earlier, compared with comparator assays, in a set of sequential samples from a patient with primary syphilis. In archived serial blood samples collected from 14 patients with direct diagnoses of primary syphilis, the Elecsys Syphilis assay detected T. pallidum antibodies for 3 patients for whom antibodies were not detected with the Architect Syphilis TP assay, indicating a trend for earlier detection of infection, which may have the potential to shorten the time between infection and reactive screening test results. PMID:27358468

Determination of dissolved-phase pesticides in surface water from the Yakima River basin, Washington, using the Goulden large-sample extractor and gas chromatography/mass spectrometer

USGS Publications Warehouse

Foster, Gregory D.; Gates, Paul M.; Foreman, William T.; McKenzie, Stuart W.; Rinella, Frank A.

1993-01-01

Concentrations of pesticides in the dissolved phase of surface water samples from the Yakima River basin, WA, were determined using preconcentration in the Goulden large-sample extractor (GLSE) and gas chromatography/mass spectrometry (GC/MS) analysis. Sample volumes ranging from 10 to 120 L were processed with the GLSE, and the results from the large-sample analyses were compared to those derived from 1-L continuous liquid-liquid extractions Few of the 40 target pesticides were detected in 1-L samples, whereas large-sample preconcentration in the GLSE provided detectable levels for many of the target pesticides. The number of pesticides detected in GLSE processed samples was usually directly proportional to sample volume, although the measured concentrations of the pesticides were generally lower at the larger sample volumes for the same water source. The GLSE can be used to provide lower detection levels relative to conventional liquid-liquid extraction in GC/MS analysis of pesticides in samples of surface water.

Contaminants of emerging concern in ambient groundwater in urbanized areas of Minnesota, 2009-12

USGS Publications Warehouse

Erickson, Melinda L.; Langer, Susan K.; Roth, Jason L.; Kroening, Sharon E.

2014-01-01

The antibiotic sulfamethoxazole was the most frequently detected CEC, detected in a total of 14 of 123 samples (11.4 percent) by one or both analytical methods that include sulfamethoxazole as an analyte. Most (11 of 14, or 79 percent) of the detections of sulfamethoxazole were in samples from domestic wells or monitoring wells located in areas where septic systems or potentially leaking centralized sewers are prevalent. The chemical N,N-Diethyl-meta-toluamide (DEET) was detected at the highest concentration of any CEC, at 7.9 micrograms per liter. Bisphenol A was detected second most frequently of all chemicals. DEET and Bisphenol A were detected most frequently in wells in proximity to closed landfills. Samples from bedrock wells, most of which are drinking water wells that are deeper than glacial wells, had a higher percentage of wells with CEC detections compared to samples from wells completed in glacial aquifers. The higher dissolved oxygen concentrations and lower specific conductance for the bedrock wells sampled indicate shorter duration flow paths from the land surface to these wells than for wells completed in glacial aquifers.

Detection of Helicobacter pylori and fecal indicator bacteria in five North American rivers.

USGS Publications Warehouse

Voytek, M.A.; Ashen, J.B.; Fogarty, L.R.; Kirshtein, J.D.; Landa, E.R.

2005-01-01

This study examines the use of fecal indicator bacteria (FIB) as a predictor of the presence of Helicobacter spp. A combination of standard culture and molecular techniques were used to detect and quantify FIB, Helicobacter spp. and H. pylori from five North American rivers of different size and with different land use characteristics. Primers designed to amplify genes specific to Helicobacter spp. and H. pylori were evaluated for their efficacy in detection and quantification in environmental samples. Helicobacter spp. were detected in 18/33 (55%) of river samples. H. pylori was detected in 11/33 (33%) of river samples. FIB were found in 32/33 (96%) of river samples. When FIB abundance exceeded USEPA water quality standards for single samples, Helicobacter or H. pylori were detected in 7/15 (47%) cases. No numerical correlation was found between the presence of FIB and either Helicobacter spp. or H. pylori. This suggests that the presence of FIB will be of limited use for detection of Helicobacter spp. or H. pylori by public health agencies.

[Analysis of false-positive reaction for bacterial detection of blood samples with the automated microbial detection system BacT/ALERT 3D].

PubMed

Zhu, Li-Wei; Yang, Xue-Mei; Xu, Xiao-Qin; Xu, Jian; Lu, Huang-Jun; Yan, Li-Xing

2008-10-01

This study was aimed to analyze the results of false positive reaction in bacterial detection of blood samples with BacT/ALERT 3D system, to evaluate the specificity of this system, and to decrease the false positive reaction. Each reaction flasks in past five years were processed for bacteria isolation and identification. When the initial cultures were positive, the remaining samples and the corresponding units were recultured if still available. 11395 blood samples were detected. It is worthy of note that the incubator temperature should be stabilized, avoiding fluctuation; when the cultures were alarmed, the reaction flasks showed be kept some hours for further incubation so as to trace a sharply increasing signal to support the judgement of true bacterial growth. The results indicated that 122 samples (1.07%) wee positive at initial culture, out of them 107 samples (88.7%) were found bacterial, and 15 samples (12.3%) were found nothing. The detection curves of positive samples resulted from bacterial growth showed ascent. In conclusion, maintenance of temperature stability and avoidance of temperature fluctuation in incubator could decrease the occurrence of false-positive reaction in detection process. The reaction flasks with positive results at initial culture should be recultured, and whether existence of a sharply ascending logarilhimic growth phase in bacterial growth curve should be further detected, which are helpful to distinguish false-positive reactions from true positive, and thus increase the specificity of the BacT/ALERT system.

Testing the Accuracy of Aerial Surveys for Large Mammals: An Experiment with African Savanna Elephants (Loxodonta africana).

PubMed

Schlossberg, Scott; Chase, Michael J; Griffin, Curtice R

2016-01-01

Accurate counts of animals are critical for prioritizing conservation efforts. Past research, however, suggests that observers on aerial surveys may fail to detect all individuals of the target species present in the survey area. Such errors could bias population estimates low and confound trend estimation. We used two approaches to assess the accuracy of aerial surveys for African savanna elephants (Loxodonta africana) in northern Botswana. First, we used double-observer sampling, in which two observers make observations on the same herds, to estimate detectability of elephants and determine what variables affect it. Second, we compared total counts, a complete survey of the entire study area, against sample counts, in which only a portion of the study area is sampled. Total counts are often considered a complete census, so comparing total counts against sample counts can help to determine if sample counts are underestimating elephant numbers. We estimated that observers detected only 76% ± SE of 2% of elephant herds and 87 ± 1% of individual elephants present in survey strips. Detectability increased strongly with elephant herd size. Out of the four observers used in total, one observer had a lower detection probability than the other three, and detectability was higher in the rear row of seats than the front. The habitat immediately adjacent to animals also affected detectability, with detection more likely in more open habitats. Total counts were not statistically distinguishable from sample counts. Because, however, the double-observer samples revealed that observers missed 13% of elephants, we conclude that total counts may be undercounting elephants as well. These results suggest that elephant population estimates from both sample and total counts are biased low. Because factors such as observer and habitat affected detectability of elephants, comparisons of elephant populations across time or space may be confounded. We encourage survey teams to incorporate detectability analysis in all aerial surveys for mammals.

Testing the Accuracy of Aerial Surveys for Large Mammals: An Experiment with African Savanna Elephants (Loxodonta africana)

PubMed Central

Schlossberg, Scott; Chase, Michael J.; Griffin, Curtice R.

2016-01-01

Accurate counts of animals are critical for prioritizing conservation efforts. Past research, however, suggests that observers on aerial surveys may fail to detect all individuals of the target species present in the survey area. Such errors could bias population estimates low and confound trend estimation. We used two approaches to assess the accuracy of aerial surveys for African savanna elephants (Loxodonta africana) in northern Botswana. First, we used double-observer sampling, in which two observers make observations on the same herds, to estimate detectability of elephants and determine what variables affect it. Second, we compared total counts, a complete survey of the entire study area, against sample counts, in which only a portion of the study area is sampled. Total counts are often considered a complete census, so comparing total counts against sample counts can help to determine if sample counts are underestimating elephant numbers. We estimated that observers detected only 76% ± SE of 2% of elephant herds and 87 ± 1% of individual elephants present in survey strips. Detectability increased strongly with elephant herd size. Out of the four observers used in total, one observer had a lower detection probability than the other three, and detectability was higher in the rear row of seats than the front. The habitat immediately adjacent to animals also affected detectability, with detection more likely in more open habitats. Total counts were not statistically distinguishable from sample counts. Because, however, the double-observer samples revealed that observers missed 13% of elephants, we conclude that total counts may be undercounting elephants as well. These results suggest that elephant population estimates from both sample and total counts are biased low. Because factors such as observer and habitat affected detectability of elephants, comparisons of elephant populations across time or space may be confounded. We encourage survey teams to incorporate detectability analysis in all aerial surveys for mammals. PMID:27755570

Accuracy of dry vaginal self-sampling for detecting high-risk human papillomavirus infection in cervical cancer screening: a cross-sectional study.

PubMed

Haguenoer, K; Giraudeau, B; Gaudy-Graffin, C; de Pinieux, I; Dubois, F; Trignol-Viguier, N; Viguier, J; Marret, H; Goudeau, A

2014-08-01

Cervical cancer screening coverage remains insufficient in most countries. Testing self-collected samples for high-risk human papillomavirus (HR-HPV) could be an alternative to the Pap smear, but costs, sampling methods and transport issues hamper its wide use. Our objective was to compare diagnostic accuracy of 2 vaginal self-collection methods, a dry swab (vsc-DRY) or swab in liquid medium (vsc-LIQ), for detecting HR-HPV cervical infection assessed by a cervical clinician-collected sample in liquid medium (ccc-LIQ). Women 20 to 65 years attending a Pap smear were recruited between September, 2009 and March, 2011. Each sample (3 per woman) underwent HPV DNA testing. Samples were classified as HR-HPV+ with detection of at least one HR-HPV or probable HR-HPV type. Of 734 women included, 722 had complete HPV data. HR-HPV was detected in 20.9% of ccc-LIQ samples. Estimated sensitivity and specificity to detect HR-HPV in vsc-DRY samples were 88.7% and 92.5%, respectively, and in vsc-LIQ samples, 87.4% and 90.9%. Cytology findings were abnormal for 79 women (10.9%): among 27 samples of low-grade squamous intraepithelial lesions, 25 were HR-HPV+ in vsc-DRY, vsc-LIQ and ccc-LIQ samples. Among 6 samples of high-grade squamous intraepithelial lesions, all were HR-HPV+ in vsc-DRY samples, 1 was HR-HPV- in vsc-LIQ samples and 1 was HR-HPV- in ccc-LIQ samples. Vaginal self-sampling with a dry swab is accurate to detect HR-HPV infection as compared with cervical clinician-collection and accurate as compared with cytology results. This cheap and easy-to-ship sampling method could be widely used in a cervical cancer screening program. Copyright © 2014 Elsevier Inc. All rights reserved.

Detection of neutrinos, antineutrinos, and neutrino-like particles

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

Fischbach, Ephraim

An apparatus for detecting the presence of a nuclear reactor by the detection of antineutrinos from the reactor can include a radioactive sample having a measurable nuclear activity level and a decay rate capable of changing in response to the presence of antineutrinos, and a detector associated with the radioactive sample. The detector is responsive to at least one of a particle or radiation formed by decay of the radioactive sample. A processor associated with the detector can correlate rate of decay of the radioactive sample to a flux of the antineutrinos to detect the reactor.

Paper SERS chromatography for detection of trace analytes in complex samples

NASA Astrophysics Data System (ADS)

Yu, Wei W.; White, Ian M.

2013-05-01

We report the application of paper SERS substrates for the detection of trace quantities of multiple analytes in a complex sample in the form of paper chromatography. Paper chromatography facilitates the separation of different analytes from a complex sample into distinct sections in the chromatogram, which can then be uniquely identified using SERS. As an example, the separation and quantitative detection of heroin in a highly fluorescent mixture is demonstrated. Paper SERS chromatography has obvious applications, including law enforcement, food safety, and border protection, and facilitates the rapid detection of chemical and biological threats at the point of sample.

Analysis of volatile organic compounds from illicit cocaine samples

NASA Astrophysics Data System (ADS)

Robins, W. H.; Wright, Bob W.

1994-10-01

Detection of illicit cocaine hydrochloride shipments can be improved if there is a greater understanding of the identity and quantity of volatile compounds present. This study provides preliminary data concerning the volatile organic compounds detected in a limited set of cocaine hydrochloride samples. In all cases, cocaine was one of the major volatile compounds detected. Other tropeines were detected in almost all samples. Low concentrations of compounds which may be residues of processing solvents were observed in some samples. The equilibrium emissivity of cocaine from cocaine hydrochloride was investigated and a value of 83 parts-per-trillion was determined.

Performance of the fourth-generation Bio-Rad GS HIV Combo Ag/Ab enzyme immunoassay for diagnosis of HIV infection in Southern Africa

PubMed Central

Piwowar-Manning, Estelle; Fogel, Jessica M.; Richardson, Paul; Wolf, Shauna; Clarke, William; Marzinke, Mark A.; Fiamma, Agnès; Donnell, Deborah; Kulich, Michal; Mbwambo, Jessie K.K.; Richter, Linda; Gray, Glenda; Sweat, Michael; Coates, Thomas J.; Eshleman, Susan H.

2015-01-01

Background Fourth-generation HIV assays detect both antigen and antibody, facilitating detection of acute/early HIV infection. The Bio-Rad GS HIV Combo Ag/Ab assay (Bio-Rad Combo) is an enzyme immunoassay that simultaneously detects HIV p24 antigen and antibodies to HIV-1 and HIV-2 in serum or plasma. Objective To evaluate the performance of the Bio-Rad Combo assay for detection of HIV infection in adults from Southern Africa. Study design Samples were obtained from adults in Soweto and Vulindlela, South Africa and Dar es Salaam, Tanzania (300 HIV-positive samples; 300 HIV-negative samples; 12 samples from individuals previously classified as having acute/early HIV infection). The samples were tested with the Bio-Rad Combo assay. Additional testing was performed to characterize the 12 acute/early samples. Results All 300 HIV-positive samples were reactive using the Bio-Rad Combo assay; false positive test results were obtained for 10 (3.3%) of the HIV-negative samples (sensitivity: 100%, 95% confidence interval [CI]: 98.8–100%); specificity: 96.7%, 95% CI: 94.0–98.4%). The assay detected 10 of the 12 infections classified as acute/early. The two infections that were not detected had viral loads < 400 copies/mL; one of those samples contained antiretroviral drugs consistent with antiretroviral therapy. Conclusions The Bio-Rad Combo assay correctly classified the majority of study specimens. The specificity reported here may be higher than that seen in other settings, since HIV-negative samples were pre-screened using a different fourth-generation test. The assay also had high sensitivity for detection of acute/early infection. False-negative test results may be obtained in individuals who are virally suppressed. PMID:25542477

Qualitative analysis of seized cocaine samples using desorption electrospray ionization- mass spectrometry (DESI-MS).

PubMed

Stojanovska, Natasha; Tahtouh, Mark; Kelly, Tamsin; Beavis, Alison; Fu, Shanlin

2015-05-01

Desorption electrospray ionization - mass spectrometry (DESI-MS) is a useful technique for the qualitative analysis of compounds found in seized drug material. In this study, DESI-MS was utilized in the screening analysis of illicit cocaine samples. The technique was also applied to the geographical origin determination of these samples. The limit of detection was determined to be 24.3 µg (or 3.47 µg/mm(2) ) and the analysis time was less than 1 minute per sample. The intra-day and inter-day precision for the detection of cocaine was 11 % and 42 %, respectively; therefore the quantitative data provided by DESI-MS was limited in its use for accurate determination of cocaine concentration in a sample. Using the quadrupole time-of-flight (QTOF) mass spectrometer, the presence of cocaine and impurities detected were confirmed by accurate tandem MS data. The qualitative chemical profiles obtained using DESI-MS were compared to two popular analysis techniques, GC-MS and LC-MS. The effects of a range of adulterants including caffeine, procaine, levamisole, lignocaine, paracetamol, and atropine on the detectability of cocaine were also investigated. It was found that the addition of these adulterants in a cocaine sample did not prevent the detection of the analyte itself (there was slight enhancement in some samples), which was useful in drug detection. The detection of truxillines in the seized samples by DESI-MS aided in the preliminary determination of geographical origin, i.e., Bolivian, Peruvian or Colombian leaf origin. The application of DESI-MS to the qualitative analysis and screening of seized cocaine samples demonstrates the potential and applicability of the technique to the fast chemical profiling of illicit samples. Copyright © 2014 John Wiley & Sons, Ltd.

Pesticide concentrations in water and sediment and associated invertebrate toxicity in Del Puerto and Orestimba Creeks, California, 2007-2008.

PubMed

Ensminger, Michael; Bergin, Rick; Spurlock, Frank; Goh, Kean S

2011-04-01

The California's San Joaquin River and its tributaries including Orestimba (ORC) and Del Puerto (DPC) Creeks are listed on the 2006 US EPA Clean Water Act §303(d) list for pesticide impairment. From December 2007 through June 2008, water and sediment samples were collected from both creeks in Stanislaus County to determine concentrations of organophosphorus (OP) and pyrethroid insecticides and to identify toxicity to Ceriodaphnia dubia and Hyalella azteca. OPs were detected in almost half (10 of 21) of the water samples, at concentrations from 0.005 to 0.912 μg L(-1). Diazinon was the most frequently detected OP, followed by chlorpyrifos and dimethoate. Two water samples were toxic to C. dubia; based on median lethal concentrations (LC50), chlorpyrifos was likely the cause of this toxicity. Pyrethroids were detected more frequently in sediment samples (18 detections) than in water samples (three detections). Pyrethroid concentrations in water samples ranged from 0.005 to 0.021 μg L(-1). These concentrations were well below reported C. dubia LC50s, and toxicity was not observed in laboratory bioassays. Cyfluthrin, bifenthrin, esfenvalerate, and λ-cyhalothrin were detected in sediment samples at concentrations ranging from 1.0 to 74.4 ng g(-1), dry weight. At DPC, all but one sediment sample caused 100% toxicity to H. azteca. Based on estimated toxicity units (TUs), bifenthrin was likely responsible for this toxicity and λ-cyhalothrin also contributed. At ORC, survival of H. azteca was significantly reduced in four of the 11 sediment samples. However, pyrethroids were detected in only two of these samples. Based on TUs, bifenthrin and λ-cyhalothrin likely contributed to the toxicity.

Determination of phenylurea herbicides in water samples using online sorptive preconcentration and high-performance liquid chromatography with UV or electrospray mass spectrometric detection.

PubMed

Baltussen, E; Snijders, H; Janssen, H G; Sandra, P; Cramers, C A

1998-04-10

A recently developed method for the extraction of organic micropollutants from aqueous samples based on sorptive enrichment in columns packed with 100% polydimethylsiloxane (PDMS) particles was coupled on-line with HPLC analysis. The sorptive enrichment procedure originally developed for relatively nonpolar analytes was used to preconcentrate polar phenylurea herbicides from aqueous samples. PDMS extraction columns of 5, 10 and 25 cm were used to extract the herbicides from distilled, tap and river water samples. A model that allows prediction of retention and breakthrough volumes is presented. Despite the essentially apolar nature of the PDMS material, it is possible to concentrate sample volumes up to 10 ml on PDMS cartridges without losses of the most polar analyte under investigation, fenuron. For less polar analytes significantly larger sample volumes can be applied. Since standard UV detection does not provide adequate selectivity for river water samples, an electrospray (ES)-MS instrument was used to determine phenylurea herbicides in a water sample from the river Dommel. Methoxuron was present at a level of 80 ng/l. The detection limit of the current set-up, using 10 ml water samples and ES-MS detection is 10 ng/l in river water samples. Strategies for further improvement of the detection limits are identified.

Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

PubMed Central

Gulliksen, Anja; Keegan, Helen; Martin, Cara; O'Leary, John; Solli, Lars A.; Falang, Inger Marie; Grønn, Petter; Karlgård, Aina; Mielnik, Michal M.; Johansen, Ib-Rune; Tofteberg, Terje R.; Baier, Tobias; Gransee, Rainer; Drese, Klaus; Hansen-Hagge, Thomas; Riegger, Lutz; Koltay, Peter; Zengerle, Roland; Karlsen, Frank; Ausen, Dag; Furuberg, Liv

2012-01-01

The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV) E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n = 28) from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection. PMID:22235204

Pesticides detected in urban streams in King County, Washington, 1998-2003

USGS Publications Warehouse

Frans, Lonna M.

2004-01-01

The U.S. Geological Survey and the King County Department of Natural Resources collected water samples from 14 sites on urban streams in King County during storms and during base flow between 1998 and 2003. The samples were analyzed for the presence of 155 pesticides and pesticide transformation products. Thirty-nine of the compounds were detected at least once during the study: 20 herbicides, 9 insecticides, 2 fungicides, 6 pesticide transformation products, and 2 other types of compounds. The most widespread compound was 4-nitrophenol, which was detected at all 14 sampling sites. The most frequently detected compound was pentachlorophenol, a fungicide, which occurred in more than 80 percent of the samples. The most frequently detected herbicides were prometon, trichlopyr, 2,4-D, and MCPP, and the most frequently detected insecticides were diazinon and carbaryl. All of the most frequently detected herbicides and insecticides were sold for homeowner use over the timeframe of this study. More compounds were detected during storms than during base flow, and were detected more frequently and typically at high concentrations during storms. Seven compounds were detected only during storms. Most of the compounds that were detected during storms occurred more frequently during spring storms than during autumn storms.

Culture-free, highly sensitive, quantitative detection of bacteria from minimally processed samples using fluorescence imaging by smartphone.

PubMed

Shrivastava, Sajal; Lee, Won-Il; Lee, Nae-Eung

2018-06-30

A critical unmet need in the diagnosis of bacterial infections, which remain a major cause of human morbidity and mortality, is the detection of scarce bacterial pathogens in a variety of samples in a rapid and quantitative manner. Herein, we demonstrate smartphone-based detection of Staphylococcus aureus in a culture-free, rapid, quantitative manner from minimally processed liquid samples using aptamer-functionalized fluorescent magnetic nanoparticles. The tagged S. aureus cells were magnetically captured in a detection cassette, and then fluorescence was imaged using a smartphone camera with a light-emitting diode as the excitation source. Our results showed quantitative detection capability with a minimum detectable concentration as low as 10 cfu/ml by counting individual bacteria cells, efficiently capturing S. aureus cells directly from a peanut milk sample within 10 min. When the selectivity of detection was investigated using samples spiked with other pathogenic bacteria, no significant non-specific detection occurred. Furthermore, strains of S. aureus from various origins showed comparable results, ensuring that the approach can be widely adopted. Therefore, the quantitative fluorescence imaging platform on a smartphone could allow on-site detection of bacteria, providing great potential assistance during major infectious disease outbreaks in remote and resource-limited settings. Copyright © 2018 Elsevier B.V. All rights reserved.

Explosive detection using high-volume vapor sampling and analysis by trained canines and ultra-trace detection equipment

NASA Astrophysics Data System (ADS)

Fisher, Mark; Sikes, John; Prather, Mark

2004-09-01

The dog's nose is an effective, highly-mobile sampling system, while the canine olfactory organs are an extremely sensitive detector. Having been trained to detect a wide variety of substances with exceptional results, canines are widely regarded as the 'gold standard' in chemical vapor detection. Historically, attempts to mimic the ability of dogs to detect vapors of explosives using electronic 'dogs noses' has proven difficult. However, recent advances in technology have resulted in development of detection (i.e., sampling and sensor) systems with performance that is rapidly approaching that of trained canines. The Nomadics Fido was the first sensor to demonstrate under field conditions the detection of landmines with performance approaching that of canines. More recently, comparative testing of Fido against canines has revealed that electronic vapor detection, when coupled with effective sampling methods, can produce results comparable to that of highly-trained canines. The results of these comparative tests will be presented, as will recent test results in which explosives hidden in cargo were detected using Fido with a high-volume sampling technique. Finally, the use of canines along with electronic sensors will be discussed as a means of improving the performance and expanding the capabilities of both methods.

Volatile organic compounds in ground water from rural private wells, 1986 to 1999

USGS Publications Warehouse

Moran, M.J.; Lapham, W.W.; Rowe, B.L.; Zogorski, J.S.

2004-01-01

The U.S. Geological Survey (USGS) collected or compiled data on volatile organic compounds (VOCs) in samples of untreated ground water from 1,926 rural private wells during 1986 to 1999. At least one VOC was detected in 12 percent of samples from rural private wells. Individual VOCs were not commonly detected with the seven most frequently detected compounds found in only 1 to 5 percent of samples at or above a concentration of 0.2 microgram per liter (??g/l). An assessment level of 0.2 ??g/l was selected so that comparisons of detection frequencies between VOCs could be made. The seven most frequently detected VOCs were: trichloromethane, methyl tert-butyl ether, tetrachloroethene, dichlorodifluoromethane, methylbenzene, 1,1,1-trichloroethane, and 1,2-dibromo-3-chloropropane. Solvents and trihalomethanes were the most frequently detected VOC groups in private wells. The distributions of detections of gasoline oxygenates and fumigants seemed to be related to the use patterns of compounds in these groups. Mixtures were a common mode of occurrence of VOCs with one-quarter of all samples with detections including two or more VOCs. The concentrations of most detected VOCs were relatively small and only 1.4 percent of samples had one or more VOC concentrations that exceeded a federally established drinking water standard or health criterion.

Detectability of the emerald ash borer (Coleoptera: Buprestidae) in asymptomatic urban trees by using branch samples.

PubMed

Ryall, Krista L; Fidgen, Jeffrey G; Turgeon, Jean J

2011-06-01

The emerald ash borer, Agrilus planipennis Fairmaire, is an exotic invasive insect causing extensive mortality to ash trees, Fraxinus spp., in Canada and the United States. Detection of incipient populations of this pest is difficult because of its cryptic life stages and a multiyear time lag between initial attack and the appearance of signs or symptoms of infestation. We sampled branches from open-grown urban ash trees to develop a sample unit suitable for detecting low density A. planipennis infestation before any signs or symptoms are evident. The sample unit that maximized detection rates consisted of one 50-cm-long piece from the base of a branch ≥6 cm diameter in the midcrown. The optimal sample size was two such branches per tree. This sampling method detected ≈75% of asymptomatic trees known to be infested by using more intensive sampling and ≈3 times more trees than sampling one-fourth of the circumference of the trunk at breast height. The method is less conspicuous and esthetically damaging to a tree than the removal of bark from the main stem or the use of trap trees, and could be incorporated into routine sanitation or maintenance of city-owned trees to identify and delineate infested areas. This research indicates that branch sampling greatly reduces false negatives associated with visual surveys and window sampling at breast height. Detection of A. planipennis-infested asymptomatic trees through branch sampling in urban centers would provide landowners and urban foresters with more time to develop and implement management tactics.

Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health

USGS Publications Warehouse

King, Dawn N.; Donohue, Maura J.; Vesper, Stephen J.; Villegas, Eric N.; Ware, Michael W.; Vogel, Megan E.; Furlong, Edward; Kolpin, Dana W.; Glassmeyer, Susan T.; Pfaller, Stacy

2016-01-01

An occurrence survey was conducted on selected pathogens in source and treated drinking water collected from 25 drinking water treatment plants (DWTPs) in the United States. Water samples were analyzed for the protozoa Giardia and Cryptosporidium (EPA Method 1623); the fungi Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus (quantitative PCR [qPCR]); and the bacteria Legionella pneumophila (qPCR), Mycobacterium avium, M. avium subspecies paratuberculosis, and Mycobacterium intracellulare (qPCR and culture). Cryptosporidium and Giardia were detected in 25% and in 46% of the source water samples, respectively (treated waters were not tested). Aspergillus fumigatus was the most commonly detected fungus in source waters (48%) but none of the three fungi were detected in treated water. Legionella pneumophila was detected in 25% of the source water samples but in only 4% of treated water samples. M. avium and M. intracellulare were both detected in 25% of source water, while all three mycobacteria were detected in 36% of treated water samples. Five species of mycobacteria, Mycobacterium mucogenicum, Mycobacterium phocaicum, Mycobacterium triplex, Mycobacterium fortuitum, and Mycobacterium lentiflavum were cultured from treated water samples. Although these DWTPs represent a fraction of those in the U.S., the results suggest that many of these pathogens are widespread in source waters but that treatment is generally effective in reducing them to below detection limits. The one exception is the mycobacteria, which were commonly detected in treated water, even when not detected in source waters.

Evidence of Mycobacterium tuberculosis complex bacteraemia in intradermal skin test positive cattle detected using phage-RPA.

PubMed

Swift, Benjamin M C; Convery, Thomas W; Rees, Catherine E D

2016-10-02

Bovine tuberculosis is a zoonotic infectious disease caused by Mycobacterium bovis that affects cattle and can cause tuberculosis in a range of wildlife animals. A bacteriophage-based method combined with PCR (phage-PCR) has been recently used to detect and identify viable pathogenic mycobacteria in the peripheral blood mononuclear cells (PBMCs) of animals suffering from paratuberculosis. To adapt this method for the detection of M. bovis in blood, a new isothermal DNA amplification protocol using Recombinase Polymerase Amplification (RPA) was developed and was found to be able to detect M. bovis BCG within 48 h, with a limit of detection of approximately 10 cells per ml of blood for artificially inoculated blood samples. When blood samples (2 ml) from a Single Comparative Cervical Intradermal Tuberculin (SCCIT)- negative beef herd were tested, Mycobacterium tuberculosis complex (MTC) cells were not detected from any (45) of the blood samples. However when blood samples from SCCIT-positive animals were tested, viable MTC bacteria were detected in 66 % (27/41) of samples. Of these 41 animals sampled, 32 % (13) had visible lesions. In the visible lesion (VL) group, 85 % (11/13) had detectable levels of MTC whereas only 57 % (16/28) of animals which had no visible lesions (NVL) were found to have detectable mycobacteraemia. These results indicated that this simple, rapid method can be applied for the study of M. bovis infections. The frequency with which viable mycobacteria were detected in the peripheral blood of SCCIT-positive animals changes the paradigm of this disease.

Designing efficient surveys: spatial arrangement of sample points for detection of invasive species

Treesearch

Ludek Berec; John M. Kean; Rebecca Epanchin-Niell; Andrew M. Liebhold; Robert G. Haight

2015-01-01

Effective surveillance is critical to managing biological invasions via early detection and eradication. The efficiency of surveillance systems may be affected by the spatial arrangement of sample locations. We investigate how the spatial arrangement of sample points, ranging from random to fixed grid arrangements, affects the probability of detecting a target...

Detection and monitoring of invasive exotic plants: a comparison of four sampling methods

Treesearch

Cynthia D. Huebner

2007-01-01

The ability to detect and monitor exotic invasive plants is likely to vary depending on the sampling method employed. Methods with strong qualitative thoroughness for species detection often lack the intensity necessary to monitor vegetation change. Four sampling methods (systematic plot, stratified-random plot, modified Whittaker, and timed meander) in hemlock and red...

Monoclonal antibodies to synthetic pyrethroids and method for detecting the same

DOEpatents

Stanker, Larry H.; Vanderlaan, Martin; Watkins, Bruce E.; Van Emon, Jeanette M.; Bigbee, Carolyn L.

1992-01-01

Methods are described for making specific monoclonal antibodies which may be used in a sensitive immunoassay for detection of synthetic pyrethroids in foods and environmental samples. Appropriate sample preparation and enzyme amplification of the immunoassay for this widely-used class of pesticides permits detection at low levels in laboratory and field tested samples.

Monoclonal antibodies to synthetic pyrethroids and method for detecting the same

DOEpatents

Stanker, L.H.; Vanderlaan, M.; Watkins, B.E.; Van Emon, J.M.; Bigbee, C.L.

1992-04-28

Methods are described for making specific monoclonal antibodies which may be used in a sensitive immunoassay for detection of synthetic pyrethroids in foods and environmental samples. Appropriate sample preparation and enzyme amplification of the immunoassay for this widely-used class of pesticides permits detection at low levels in laboratory and field tested samples. 6 figs.

Improved explosive collection and detection with rationally assembled surface sampling materials

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

Chouyyok, Wilaiwan; Bays, J. Timothy; Gerasimenko, Aleksandr A.

Sampling and detection of trace explosives is a key analytical process in modern transportation safety. In this work we have explored some of the fundamental analytical processes for collection and detection of trace level explosive on surfaces with the most widely utilized system, thermal desorption IMS. The performance of the standard muslin swipe material was compared with chemically modified fiberglass cloth. The fiberglass surface was modified to include phenyl functional groups. When compared to standard muslin, the phenyl functionalized fiberglass sampling material showed better analyte release from the sampling material as well as improved response and repeatability from multiple usesmore » of the same swipe. The improved sample release of the functionalized fiberglass swipes resulted in a significant increase in sensitivity. Various physical and chemical properties were systematically explored to determine optimal performance. The results herein have relevance to improving the detection of other explosive compounds and potentially to a wide range of other chemical sampling and field detection challenges.« less

Nuclear resonance tomography with a toroid cavity detector

DOEpatents

Woelk, K.; Rathke, J.W.; Klingler, R.J.

1996-11-12

A toroid cavity detection system is described for determining the spectral properties and distance from a fixed point for a sample using Nuclear Magnetic Resonance. The detection system consists of a toroid with a central conductor oriented along the main axis of the toroidal cylinder and perpendicular to a static uniform magnetic field oriented along the main axis of the toroid. An rf signal is input to the central conductor to produce a magnetic field perpendicular to the central axis of the toroid and whose field strength varies as the inverse of the radius of the toroid. The toroid cavity detection system can be used to encapsulate a sample, or the detection system can be perforated to allow a sample to flow into the detection device or to place the samples in specified sample tubes. The central conductor can also be coated to determine the spectral property of the coating and the coating thickness. The sample is then subjected to the respective magnetic fields and the responses measured to determine the desired properties. 4 figs.

Nuclear resonance tomography with a toroid cavity detector

DOEpatents

Woelk, Klaus; Rathke, Jerome W.; Klingler, Robert J.

1996-01-01

A toroid cavity detection system for determining the spectral properties and distance from a fixed point for a sample using Nuclear Magnetic Resonance. The detection system consists of a toroid with a central conductor oriented along the main axis of the toroidal cylinder and perpendicular to a static uniform magnetic field oriented along the main axis of the toroid. An rf signal is inputted to the central conductor to produce a magnetic field perpendicular to the central axis of the toroid and whose field strength varies as the inverse of the radius of the toroid. The toroid cavity detection system can be used to encapsulate a sample, or the detection system can be perforated to allow a sample to flow into the detection device or to place the samples in specified sample tubes. The central conductor can also be coated to determine the spectral property of the coating and the coating thickness. The sample is then subjected to the respective magnetic fields and the responses measured to determine the desired properties.

Chemical amplification based on fluid partitioning

DOEpatents

Anderson, Brian L [Lodi, CA; Colston, Jr., Billy W.; Elkin, Chris [San Ramon, CA

2006-05-09

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

Sample collection system for gel electrophoresis

DOEpatents

Olivares, Jose A.; Stark, Peter C.; Dunbar, John M.; Hill, Karen K.; Kuske, Cheryl R.; Roybal, Gustavo

2004-09-21

An automatic sample collection system for use with an electrophoretic slab gel system is presented. The collection system can be used with a slab gel have one or more lanes. A detector is used to detect particle bands on the slab gel within a detection zone. Such detectors may use a laser to excite fluorescently labeled particles. The fluorescent light emitted from the excited particles is transmitted to low-level light detection electronics. Upon the detection of a particle of interest within the detection zone, a syringe pump is activated, sending a stream of buffer solution across the lane of the slab gel. The buffer solution collects the sample of interest and carries it through a collection port into a sample collection vial.

Application of Coamplification at Lower Denaturation Temperature-PCR Sequencing for Early Detection of Antiviral Drug Resistance Mutations of Hepatitis B Virus

PubMed Central

Wong, Danny Ka-Ho; Tsoi, Ottilia; Huang, Fung-Yu; Seto, Wai-Kay; Fung, James; Lai, Ching-Lung

2014-01-01

Nucleoside/nucleotide analogue for the treatment of chronic hepatitis B virus (HBV) infection is hampered by the emergence of drug resistance mutations. Conventional PCR sequencing cannot detect minor variants of <20%. We developed a modified co-amplification at lower denaturation temperature-PCR (COLD-PCR) method for the detection of HBV minority drug resistance mutations. The critical denaturation temperature for COLD-PCR was determined to be 78°C. Sensitivity of COLD-PCR sequencing was determined using serially diluted plasmids containing mixed proportions of HBV reverse transcriptase (rt) wild-type and mutant sequences. Conventional PCR sequencing detected mutations only if they existed in ≥25%, whereas COLD-PCR sequencing detected mutations when they existed in 5 to 10% of the viral population. The performance of COLD-PCR was compared to conventional PCR sequencing and a line probe assay (LiPA) using 215 samples obtained from 136 lamivudine- or telbivudine-treated patients with virological breakthrough. Among these 215 samples, drug resistance mutations were detected in 155 (72%), 148 (69%), and 113 samples (53%) by LiPA, COLD-PCR, and conventional PCR sequencing, respectively. Nineteen (9%) samples had mutations detectable by COLD-PCR but not LiPA, while 26 (12%) samples had mutations detectable by LiPA but not COLD-PCR, indicating both methods were comparable (P = 0.371). COLD-PCR was more sensitive than conventional PCR sequencing. Thirty-five (16%) samples had mutations detectable by COLD-PCR but not conventional PCR sequencing, while none had mutations detected by conventional PCR sequencing but not COLD-PCR (P < 0.0001). COLD-PCR sequencing is a simple method which is comparable to LiPA and superior to conventional PCR sequencing in detecting minor lamivudine/telbivudine resistance mutations. PMID:24951803

Pesticides in the Lower Clackamas River Basin, Oregon, 2000-01

USGS Publications Warehouse

Carpenter, Kurt D.

2004-01-01

In 2000-01, the U. S. Geological Survey sampled the Clackamas River and its major lower-basin tributaries during storm runoff conditions for 86 dissolved pesticides and selected breakdown products. Twenty-seven compounds, including 18 herbicides, 7 insecticides, and 2 pesticide breakdown products, were detected in 18 stream samples. The most commonly detected pesticides, in decreasing frequency, included atrazine, simazine, diazinon, metolachlor, and diuron, which variously occurred in 46-92% of samples collected from the tributaries. Of these, atrazine, simazine, and metolachlor, plus six other compounds, also were detected in the main-stem Clackamas River. Pesticides were detected more frequently and at higher concentrations in the four lowermost tributaries (Deep, Richardson, Rock, and Sieben Creeks). In these streams, 12 to 18 pesticides were detected per stream in samples collected during spring and fall. Pesticides always occurred with at least one other pesticide, and about half of the samples, including one sample from the Clackamas River in October 2000, contained six or more pesticides. Nine pesticides, including the insecticide diazinon and the herbicides 2,4-D, atrazine, dichlobenil, diuron, imazaquin, metolachlor, simazine, and trifluralin, were detected in five water samples of Clackamas River water. No pesticides were detected in three samples of treated Clackamas River water used for drinking-water supply. Concentrations of six compounds--carbaryl, chlorpyrifos, diazinon, dieldrin, malathion, and the breakdown product of DDT (p,p'-DDE)--exceeded established or recommended criteria for the protection of aquatic life in some of the tributaries, sometimes for multiple pesticides in one sample. Identifying the sources of pesticides detected in the Clackamas River Basin is difficult because of the diverse land use in the basin and the multiple-use nature of many of the pesticides detected. Of the 25 parent compounds detected, 22 have agricultural uses, 23 have urban uses, 16 are applied to golf courses, 11 are applied along roads and other right-of-ways, and 5 have or had forestry applications. Because only a small fraction of the thousands of pesticide products registered for use in Oregon were tested for in this study, future monitoring could benefit from knowledge of what pesticides are applied so that potential problems can be identified and managed.

Relation of pesticide concentrations to season, streamflow, and land use in seven New Jersey streams

USGS Publications Warehouse

Reiser, Robert G.

1999-01-01

The presence and variability of pesticides in seven New Jersey streams was documented by analyzing 146 samples collected from the streams from April 1996 through June 1998. The samples were analyzed for 85 pesticides, including 50 herbicides, 28 insecticides, and 7 degradation products, at method detection limits that ranged from 0.001 to 0.018 μg/L (micrograms per liter). Pesticides were frequently detected; however, concentrations were generally low. The pesticides most frequently detected were atrazine, in 97 percent of the samples; prometon, 96 percent; metolachlor, 95 percent; desethyl-atrazine, 91 percent; simazine, 88 percent; diazinon, 58 percent; alachlor, 56 percent; and carbaryl, 54 percent. Detection frequencies were highest during the growing season (April-September). At least one pesticide was detected in all but one of these samples, and 49 percent of the samples contained 9 or more pesticides. The numbers of pesticides detected at a given site ranged from 13 to 29. Ten pesticides were detected at concentrations that exceeded established water-quality criteria. Thirty-one of these detections were in samples collected during the growing season and one during the nongrowing season. The pesticides that exceeded the U.S. Environmental Protection Agency (USEPA) maximum contaminant level for drinking water were atrazine, which exceeded 3 μg/L in four samples, and alachlor, 2 μg/L in two samples. Cyanazine exceeded the USEPA liftime health advisory level (HAL) of 1 μg/L in two samples. These eight detections occurred during runoff shortly after spring pesticide applications and represent a potential threat to municipal water supplies in the Raritan River basin. Concentrations of chlorpyrifos, chlorthalonil, diazinon, ethyl-parathion, and methyl-azinphos exceeded the chronic life criteria for the protection of aquatic life (ACQR) in 20 samples at four sites during the growing season. Dieldrin was detected in four samples and DDE in two samples at concentrations that exceeded New Jersey Department of Environmental Protection (NJDEP) human health criteria. Individual and total-pesticide concentrations and total numbers of pesticides detected in the samples varied with season and flow conditions. Median and maximum concentrations of most of the pesticides were highest during runoff in the growing season. Pesticide concentrations were typically lower and less variable in the nongrowing season than in the growing season, regardless of changes in hydrologic conditions; however, median concentrations of most pesticides were slightly lower during runoff than during base flow. The median total-pesticide concentration and median total number of pesticides detected were highest and most variable in runoff samples in the growing season. In the nongrowing season, the median total-pesticide concentration was lowest in runoff samples and least variable during base-flow conditions. Median total numbers of pesticides were lowest and least varibale in the nongrowing season during base-flow conditions at most sites. The highest total-pesticide concentrations were detected in samples from the two small agricultural basins (greater than 25 percent of land use is agricultural) during runoff in late spring and early summer. In general, insecticides were detected more frequently and in greater concentrations at urban sites. Concentrations of agricultural herbicides generally decreased with increasing flow at the four sites with less than 10 percent agriculture land use and increased with increasing flow at the three sites with more than 25 percent agricultural land use. Most of the pesticides that correlated positively with streamflow were detected at sites where land use in the basin would indicate the use of those particular pesticides. Most of the pesticides that correlated negatively with streamflow were present at the site in the Coastal Plain or at sites in which the land use in the basin would not indicate heavy u

Comparison of a novel passive sampler to standard water-column sampling for organic contaminants associated with wastewater effluents entering a New Jersey stream

USGS Publications Warehouse

Alvarez, D.A.; Stackelberg, P.E.; Petty, J.D.; Huckins, J.N.; Furlong, E.T.; Zaugg, S.D.; Meyer, M.T.

2005-01-01

Four water samples collected using standard depth and width water-column sampling methodology were compared to an innovative passive, in situ, sampler (the polar organic chemical integrative sampler or POCIS) for the detection of 96 organic wastewater-related contaminants (OWCs) in a stream that receives agricultural, municipal, and industrial wastewaters. Thirty-two OWCs were identified in POCIS extracts whereas 9-24 were identified in individual water-column samples demonstrating the utility of POCIS for identifying contaminants whose occurrence are transient or whose concentrations are below routine analytical detection limits. Overall, 10 OWCs were identified exclusively in the POCIS extracts and only six solely identified in the water-column samples, however, repetitive water samples taken using the standard method during the POCIS deployment period required multiple trips to the sampling site and an increased number of samples to store, process, and analyze. Due to the greater number of OWCs detected in the POCIS extracts as compared to individual water-column samples, the ease of performing a single deployment as compared to collecting and processing multiple water samples, the greater mass of chemical residues sequestered, and the ability to detect chemicals which dissipate quickly, the passive sampling technique offers an efficient and effective alternative for detecting OWCs in our waterways for wastewater contaminants.

T2 Magnetic Resonance Assay-Based Direct Detection of Three Lyme Disease-Related Borrelia Species in Whole-Blood Samples.

PubMed

Snyder, Jessica L; Giese, Heidi; Bandoski-Gralinski, Cheryl; Townsend, Jessica; Jacobson, Beck E; Shivers, Robert; Schotthoefer, Anna M; Fritsche, Thomas R; Green, Clayton; Callister, Steven M; Branda, John A; Lowery, Thomas J

2017-08-01

In early Lyme disease (LD), serologic testing is insensitive and seroreactivity may reflect active or past infection. In this study, we evaluated a novel assay for the direct detection of three species of Borrelia spirochetes in whole blood. The T2 magnetic resonance (T2MR) assay platform was used to amplify Borrelia DNA released from intact spirochetes and to detect amplicon. Analytical sensitivity was determined from blood spiked with known concentrations of spirochetes, and the assay's limit of detection was found to be in the single-cell-per-milliliter range: 5 cells/ml for B. afzelii and 8 cells/ml for Borrelia burgdorferi and Borrelia garinii Clinical samples ( n = 66) from confirmed or suspected early LD patients were also analyzed. B. burgdorferi was detected using T2MR in 2/2 (100%) of blood samples from patients with confirmed early LD, based on the presence of erythema migrans and documentation of seroconversion or a positive real-time blood PCR. T2MR detected B. burgdorferi in blood samples from 17/54 (31%) of patients with probable LD, based on the presence of erythema migrans without documented seroconversion or of documented seroconversion in patients with a compatible clinical syndrome but without erythema migrans. Out of 21 clinical samples tested by real-time PCR, only 1 was positive and 13 were negative with agreement with T2MR. An additional 7 samples that were negative by real-time PCR were positive with T2MR. Therefore, T2MR enables a low limit of detection (LoD) for Borrelia spp. in whole blood samples and is able to detect B. burgdorferi in clinical samples. Copyright © 2017 American Society for Microbiology.

T2 Magnetic Resonance Assay-Based Direct Detection of Three Lyme Disease-Related Borrelia Species in Whole-Blood Samples

PubMed Central

Giese, Heidi; Bandoski-Gralinski, Cheryl; Townsend, Jessica; Jacobson, Beck E.; Shivers, Robert; Schotthoefer, Anna M.; Fritsche, Thomas R.; Green, Clayton; Callister, Steven M.; Branda, John A.

2017-01-01

ABSTRACT In early Lyme disease (LD), serologic testing is insensitive and seroreactivity may reflect active or past infection. In this study, we evaluated a novel assay for the direct detection of three species of Borrelia spirochetes in whole blood. The T2 magnetic resonance (T2MR) assay platform was used to amplify Borrelia DNA released from intact spirochetes and to detect amplicon. Analytical sensitivity was determined from blood spiked with known concentrations of spirochetes, and the assay's limit of detection was found to be in the single-cell-per-milliliter range: 5 cells/ml for B. afzelii and 8 cells/ml for Borrelia burgdorferi and Borrelia garinii. Clinical samples (n = 66) from confirmed or suspected early LD patients were also analyzed. B. burgdorferi was detected using T2MR in 2/2 (100%) of blood samples from patients with confirmed early LD, based on the presence of erythema migrans and documentation of seroconversion or a positive real-time blood PCR. T2MR detected B. burgdorferi in blood samples from 17/54 (31%) of patients with probable LD, based on the presence of erythema migrans without documented seroconversion or of documented seroconversion in patients with a compatible clinical syndrome but without erythema migrans. Out of 21 clinical samples tested by real-time PCR, only 1 was positive and 13 were negative with agreement with T2MR. An additional 7 samples that were negative by real-time PCR were positive with T2MR. Therefore, T2MR enables a low limit of detection (LoD) for Borrelia spp. in whole blood samples and is able to detect B. burgdorferi in clinical samples. PMID:28566314

Accounting for Incomplete Species Detection in Fish Community Monitoring

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

McManamay, Ryan A; Orth, Dr. Donald J; Jager, Yetta

2013-01-01

Riverine fish assemblages are heterogeneous and very difficult to characterize with a one-size-fits-all approach to sampling. Furthermore, detecting changes in fish assemblages over time requires accounting for variation in sampling designs. We present a modeling approach that permits heterogeneous sampling by accounting for site and sampling covariates (including method) in a model-based framework for estimation (versus a sampling-based framework). We snorkeled during three surveys and electrofished during a single survey in suite of delineated habitats stratified by reach types. We developed single-species occupancy models to determine covariates influencing patch occupancy and species detection probabilities whereas community occupancy models estimated speciesmore » richness in light of incomplete detections. For most species, information-theoretic criteria showed higher support for models that included patch size and reach as covariates of occupancy. In addition, models including patch size and sampling method as covariates of detection probabilities also had higher support. Detection probability estimates for snorkeling surveys were higher for larger non-benthic species whereas electrofishing was more effective at detecting smaller benthic species. The number of sites and sampling occasions required to accurately estimate occupancy varied among fish species. For rare benthic species, our results suggested that higher number of occasions, and especially the addition of electrofishing, may be required to improve detection probabilities and obtain accurate occupancy estimates. Community models suggested that richness was 41% higher than the number of species actually observed and the addition of an electrofishing survey increased estimated richness by 13%. These results can be useful to future fish assemblage monitoring efforts by informing sampling designs, such as site selection (e.g. stratifying based on patch size) and determining effort required (e.g. number of sites versus occasions).« less

Evaluation of a Real-Time PCR Test for the Detection and Discrimination of Theileria Species in the African Buffalo (Syncerus caffer)

PubMed Central

Chaisi, Mamohale E.; Janssens, Michiel E.; Vermeiren, Lieve; Oosthuizen, Marinda C.; Collins, Nicola E.; Geysen, Dirk

2013-01-01

A quantitative real-time PCR (qPCR) assay based on the cox III gene was evaluated for the simultaneous detection and discrimination of Theileria species in buffalo and cattle blood samples from South Africa and Mozambique using melting curve analysis. The results obtained were compared to those of the reverse line blot (RLB) hybridization assay for the simultaneous detection and differentiation of Theileria spp. in mixed infections, and to the 18S rRNA qPCR assay results for the specific detection of Theileria parva. Theileria parva, Theileria sp. (buffalo), Theileria taurotragi, Theileria buffeli and Theileria mutans were detected by the cox III assay. Theileria velifera was not detected from any of the samples analysed. Seventeen percent of the samples had non-species specific melting peaks and 4.5% of the samples were negative or below the detection limit of the assay. The cox III assay identified more T. parva and Theileria sp. (buffalo) positive samples than the RLB assay, and also detected more T. parva infections than the 18S assay. However, only a small number of samples were positive for the benign Theileria spp. To our knowledge T. taurotragi has never been identified from the African buffalo, its identification in some samples by the qPCR assay was unexpected. Because of these discrepancies in the results, cox III qPCR products were cloned and sequenced. Sequence analysis indicated extensive inter- and intra-species variations in the probe target regions of the cox III gene sequences of the benign Theileria spp. and therefore explains their low detection. The cox III assay is specific for the detection of T. parva infections in cattle and buffalo. Sequence data generated from this study can be used for the development of a more inclusive assay for detection and differentiation of all variants of the mildly pathogenic and benign Theileria spp. of buffalo and cattle. PMID:24146782

Evaluation of a real-time PCR test for the detection and discrimination of theileria species in the African buffalo (Syncerus caffer).

PubMed

Chaisi, Mamohale E; Janssens, Michiel E; Vermeiren, Lieve; Oosthuizen, Marinda C; Collins, Nicola E; Geysen, Dirk

2013-01-01

A quantitative real-time PCR (qPCR) assay based on the cox III gene was evaluated for the simultaneous detection and discrimination of Theileria species in buffalo and cattle blood samples from South Africa and Mozambique using melting curve analysis. The results obtained were compared to those of the reverse line blot (RLB) hybridization assay for the simultaneous detection and differentiation of Theileria spp. in mixed infections, and to the 18S rRNA qPCR assay results for the specific detection of Theileria parva. Theileria parva, Theileria sp. (buffalo), Theileria taurotragi, Theileria buffeli and Theileria mutans were detected by the cox III assay. Theileria velifera was not detected from any of the samples analysed. Seventeen percent of the samples had non-species specific melting peaks and 4.5% of the samples were negative or below the detection limit of the assay. The cox III assay identified more T. parva and Theileria sp. (buffalo) positive samples than the RLB assay, and also detected more T. parva infections than the 18S assay. However, only a small number of samples were positive for the benign Theileria spp. To our knowledge T. taurotragi has never been identified from the African buffalo, its identification in some samples by the qPCR assay was unexpected. Because of these discrepancies in the results, cox III qPCR products were cloned and sequenced. Sequence analysis indicated extensive inter- and intra-species variations in the probe target regions of the cox III gene sequences of the benign Theileria spp. and therefore explains their low detection. The cox III assay is specific for the detection of T. parva infections in cattle and buffalo. Sequence data generated from this study can be used for the development of a more inclusive assay for detection and differentiation of all variants of the mildly pathogenic and benign Theileria spp. of buffalo and cattle.

The importance of accounting for larval detectability in mosquito habitat-association studies.

PubMed

Low, Matthew; Tsegaye, Admasu Tassew; Ignell, Rickard; Hill, Sharon; Elleby, Rasmus; Feltelius, Vilhelm; Hopkins, Richard

2016-05-04

Mosquito habitat-association studies are an important basis for disease control programmes and/or vector distribution models. However, studies do not explicitly account for incomplete detection during larval presence and abundance surveys, with potential for significant biases because of environmental influences on larval behaviour and sampling efficiency. Data were used from a dip-sampling study for Anopheles larvae in Ethiopia to evaluate the effect of six factors previously associated with larval sampling (riparian vegetation, direct sunshine, algae, water depth, pH and temperature) on larval presence and detectability. Comparisons were made between: (i) a presence-absence logistic regression where samples were pooled at the site level and detectability ignored, (ii) a success versus trials binomial model, and (iii) a presence-detection mixture model that separately estimated presence and detection, and fitted different explanatory variables to these estimations. Riparian vegetation was consistently highlighted as important, strongly suggesting it explains larval presence (-). However, depending on how larval detectability was estimated, the other factors showed large variations in their statistical importance. The presence-detection mixture model provided strong evidence that larval detectability was influenced by sunshine and water temperature (+), with weaker evidence for algae (+) and water depth (-). For larval presence, there was also some evidence that water depth (-) and pH (+) influenced site occupation. The number of dip-samples needed to determine if larvae were likely present at a site was condition dependent: with sunshine and warm water requiring only two dips, while cooler water and cloud cover required 11. Environmental factors influence true larval presence and larval detectability differentially when sampling in field conditions. Researchers need to be more aware of the limitations and possible biases in different analytical approaches used to associate larval presence or abundance with local environmental conditions. These effects can be disentangled using data that are routinely collected (i.e., multiple dip samples at each site) by employing a modelling approach that separates presence from detectability.

Assessment of two different types of sample for the early detection and isolation of thermophilic Campylobacter in broiler farms.

PubMed

Urdaneta, Saulo; Dolz, Roser; Cerdà-Cuéllar, Marta

2015-01-01

In order to assess the optimal method for the early detection and isolation of thermophilic Campylobacter in broilers at farm level, two types of samples were compared: caecal contents obtained by necropsy and cloacal swabs transported in charcoal Amies medium. The study was conducted in five batches of broilers from five different farms, where weekly samples (caecal contents and cloacal swabs) from 30 birds were obtained. Samples were plated onto selective agar (modified charcoal cefoperazone desoxycholate agar, mCCDA) for Campylobacter isolation. Four out of five batches were positive for Campylobacter. No marked differences in sensitivity of both sample types were observed. However, a higher percentage of positive birds were detected when cloacal swabs were used. The results show that cloacal swab samples are adequate, and in some cases even better than caecal samples for the early detection of Campylobacter in broiler flocks at farm level. Also, this sample avoids sacrificing birds to test Campylobacter, which not only allows saving time in sample collection, transportation and processing at the laboratory, but also improves bird welfare and cost of sampling.

Analysis of phosphorus trends and evaluation of sampling designs in the Quinebaug River Basin, Connecticut

USGS Publications Warehouse

Todd Trench, Elaine C.

2004-01-01

A time-series analysis approach developed by the U.S. Geological Survey was used to analyze trends in total phosphorus and evaluate optimal sampling designs for future trend detection, using long-term data for two water-quality monitoring stations on the Quinebaug River in eastern Connecticut. Trend-analysis results for selected periods of record during 1971?2001 indicate that concentrations of total phosphorus in the Quinebaug River have varied over time, but have decreased significantly since the 1970s and 1980s. Total phosphorus concentrations at both stations increased in the late 1990s and early 2000s, but were still substantially lower than historical levels. Drainage areas for both stations are primarily forested, but water quality at both stations is affected by point discharges from municipal wastewater-treatment facilities. Various designs with sampling frequencies ranging from 4 to 11 samples per year were compared to the trend-detection power of the monthly (12-sample) design to determine the most efficient configuration of months to sample for a given annual sampling frequency. Results from this evaluation indicate that the current (2004) 8-sample schedule for the two Quinebaug stations, with monthly sampling from May to September and bimonthly sampling for the remainder of the year, is not the most efficient 8-sample design for future detection of trends in total phosphorus. Optimal sampling schedules for the two stations differ, but in both cases, trend-detection power generally is greater among 8-sample designs that include monthly sampling in fall and winter. Sampling designs with fewer than 8 samples per year generally provide a low level of probability for detection of trends in total phosphorus. Managers may determine an acceptable level of probability for trend detection within the context of the multiple objectives of the state?s water-quality management program and the scientific understanding of the watersheds in question. Managers may identify a threshold of probability for trend detection that is high enough to justify the agency?s investment in the water-quality sampling program. Results from an analysis of optimal sampling designs can provide an important component of information for the decision-making process in which sampling schedules are periodically reviewed and revised. Results from the study described in this report and previous studies indicate that optimal sampling schedules for trend detection may differ substantially for different stations and constituents. A more comprehensive statewide evaluation of sampling schedules for key stations and constituents could provide useful information for any redesign of the schedule for water-quality monitoring in the Quinebaug River Basin and elsewhere in the state.

Reconnaissance investigation of water quality, bottom sediment, and biota associated with irrigation drainage in the Lower Rio Grande Valley and Laguna Atascosa National Wildlife Refuge, Texas, 1986-87

USGS Publications Warehouse

Wells, Frank C.; Jackson, Gerry A.; Rogers, William J.

1988-01-01

Toxaphene was detected in 11 fish samples; detectable concentrations ranged from 0.98 to 5.1 micrograms per gram, wet weight. DOT also was detected in 11 fish samples with concentrations ranging from 0.021 to 0.066 micrograms per gram, wet weight. ODD was detected in 21 fish samples; concentrations ranged from 0.015 to 0.16 micrograms per gram, wet weight. DDE was detected in all 22 fish samples, and concentrations ranged from 0.36 to 9.9 micrograms per gram, wet weight. The maximum concentrations of DOT and ODD exceeded the 1980-81 baseline concentrations. The median and maximum concentrations of toxaphene and DDE exceeded the 1980-81 baseline concentrations. The largest concentrations of toxaphene, ODD, and DDE in fish were all measured in samples collected at the Main Floodway near Progreso.

LAMP assay for rapid diagnosis of cow DNA in goat milk and meat samples.

PubMed

Deb, R; Sengar, G S; Singh, U; Kumar, S; Raja, T V; Alex, R; Alyethodi, R R; Prakash, B

2017-01-01

Animal species detection is one of the crucial steps for consumer's food analysis. In the present study we developed an in-house built loop-mediated isothermal amplification (LAMP) assay for rapid detection of adulterated cow DNA in goat milk/meat samples. The cow milk/tissue DNA in goat milk/meat samples were identified in the developed LAMP assay by either naked eye visualizing with SYBR Green I dyes or by detecting the typical ladder pattern on gel electrophoresis. This test can detect up to minimum 5% level of cow components admixed in goat milk/meat samples and can be completed within 1 h 40 min starting from DNA extraction from milk/meat samples and can be performed in a water bath. Developed LAMP methodology is simple; rapid and sensitive techniques that can detect adulterant like cow components in goat milk/meat are more accurate than other existing DNA based technologies.

LAMP assay for rapid diagnosis of cow DNA in goat milk and meat samples

PubMed Central

Deb, R.; Sengar, G. S.; Singh, U.; Kumar, S.; Raja, T. V.; Alex, R.; Alyethodi, R. R.; Prakash, B.

2017-01-01

Animal species detection is one of the crucial steps for consumer’s food analysis. In the present study we developed an in-house built loop-mediated isothermal amplification (LAMP) assay for rapid detection of adulterated cow DNA in goat milk/meat samples. The cow milk/tissue DNA in goat milk/meat samples were identified in the developed LAMP assay by either naked eye visualizing with SYBR Green I dyes or by detecting the typical ladder pattern on gel electrophoresis. This test can detect up to minimum 5% level of cow components admixed in goat milk/meat samples and can be completed within 1 h 40 min starting from DNA extraction from milk/meat samples and can be performed in a water bath. Developed LAMP methodology is simple; rapid and sensitive techniques that can detect adulterant like cow components in goat milk/meat are more accurate than other existing DNA based technologies. PMID:28775755

Advancing Explosives Detection Capabilities: Vapor Detection

ScienceCinema

Atkinson, David

2018-05-11

A new, PNNL-developed method provides direct, real-time detection of trace amounts of explosives such as RDX, PETN and C-4. The method selectively ionizes a sample before passing the sample through a mass spectrometer to detect explosive vapors. The method could be used at airports to improve aviation security.

Advancing Explosives Detection Capabilities: Vapor Detection

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

Atkinson, David

2012-10-15

A new, PNNL-developed method provides direct, real-time detection of trace amounts of explosives such as RDX, PETN and C-4. The method selectively ionizes a sample before passing the sample through a mass spectrometer to detect explosive vapors. The method could be used at airports to improve aviation security.

Evaluation of Rectoanal Mucosal Swab Sampling for Molecular Detection of Enterohemorrhagic Escherichia coli in Beef Cattle.

PubMed

Agga, Getahun E; Arthur, Terrance M; Hinkley, Susanne; Bosilevac, Joseph M

2017-04-01

Cattle are a primary reservoir of enterohemorrhagic Escherichia coli (EHEC), and contaminated beef products are a source of human infections. The U.S. Department of Agriculture Food Safety and Inspection Service declared seven EHEC serogroups (O26, O45, O103, O111, O121, O145, and O157) as adulterants in raw ground beef. Sampling a large number of animals for EHEC surveillance or evaluations of EHEC-focused preharvest interventions requires a convenient and robust sampling method. We evaluated the diagnostic performance of rectoanal mucosal swab (RAMS) for the detection of the top seven EHEC serogroups. Paired fecal grab (FG) and RAMS samples were collected from 176 beef cattle and tested using the NeoSEEK Shiga toxin-producing E. coli (STEC) confirmation method. The prevalence of virulence-associated genes (stx 1 , stx 2 , stx 2c , eae, and nleB) was higher in RAMS than in FG samples. The results of the two methods had poor agreement, as indicated by kappa statistics, for the detection of the seven serogroups. When FG and RAMS results were combined for comparison, RAMS was more sensitive than FG for the detection of serogroups O103 (82% versus 39%), O157 (75% versus 67%), and O45 (79% versus 73%) with similar sensitivity for the detection of serogroup O145 (67%). Serogroups O111 and O121 were detected from one and two samples, respectively, by FG and were not detected by RAMS. Serogroup O26 was not detected with either method. RAMS appears to be equivalent or superior to FG sampling for detection of the top seven EHEC serogroups in the feces of beef cattle with the NeoSEEK STEC confirmation test.

Sampling little fish in big rivers: Larval fish detection probabilities in two Lake Erie tributaries and implications for sampling effort and abundance indices

USGS Publications Warehouse

Pritt, Jeremy J.; DuFour, Mark R.; Mayer, Christine M.; Roseman, Edward F.; DeBruyne, Robin L.

2014-01-01

Larval fish are frequently sampled in coastal tributaries to determine factors affecting recruitment, evaluate spawning success, and estimate production from spawning habitats. Imperfect detection of larvae is common, because larval fish are small and unevenly distributed in space and time, and coastal tributaries are often large and heterogeneous. We estimated detection probabilities of larval fish from several taxa in the Maumee and Detroit rivers, the two largest tributaries of Lake Erie. We then demonstrated how accounting for imperfect detection influenced (1) the probability of observing taxa as present relative to sampling effort and (2) abundance indices for larval fish of two Detroit River species. We found that detection probabilities ranged from 0.09 to 0.91 but were always less than 1.0, indicating that imperfect detection is common among taxa and between systems. In general, taxa with high fecundities, small larval length at hatching, and no nesting behaviors had the highest detection probabilities. Also, detection probabilities were higher in the Maumee River than in the Detroit River. Accounting for imperfect detection produced up to fourfold increases in abundance indices for Lake Whitefish Coregonus clupeaformis and Gizzard Shad Dorosoma cepedianum. The effect of accounting for imperfect detection in abundance indices was greatest during periods of low abundance for both species. Detection information can be used to determine the appropriate level of sampling effort for larval fishes and may improve management and conservation decisions based on larval fish data.

Relation between urbanization and water quality of streams in the Austin area, Texas

USGS Publications Warehouse

Veenhuis, J.E.; Slade, R.M.

1990-01-01

The ratio of the number of samples with detectable concentrations to the total number of samples analyzed for 18 inorganic trace elements and the concentrations of many of these minor constituents increased with increasing development classifications. Twenty-two of the 42 synthetic organic compounds for which samples were analyzed were detected in one or more samples. The compounds were detected more frequently and in larger concentrations at the sites with more urban classifications.

Inspection tester for explosives

DOEpatents

Haas, Jeffrey S.; Simpson, Randall L.; Satcher, Joe H.

2007-11-13

An inspection tester that can be used anywhere as a primary screening tool by non-technical personnel to determine whether a surface contains explosives. It includes a body with a sample pad. First and second explosives detecting reagent holders and dispensers are operatively connected to the body and the sample pad. The first and second explosives detecting reagent holders and dispensers are positioned to deliver the explosives detecting reagents to the sample pad. A is heater operatively connected to the sample pad.

Inspection tester for explosives

DOEpatents

Haas, Jeffrey S.; Simpson, Randall L.; Satcher, Joe H.

2010-10-05

An inspection tester that can be used anywhere as a primary screening tool by non-technical personnel to determine whether a surface contains explosives. It includes a body with a sample pad. First and second explosives detecting reagent holders and dispensers are operatively connected to the body and the sample pad. The first and second explosives detecting reagent holders and dispensers are positioned to deliver the explosives detecting reagents to the sample pad. A is heater operatively connected to the sample pad.

An integrated microfluidic analysis microsystems with bacterial capture enrichment and in-situ impedance detection

NASA Astrophysics Data System (ADS)

Liu, Hai-Tao; Wen, Zhi-Yu; Xu, Yi; Shang, Zheng-Guo; Peng, Jin-Lan; Tian, Peng

2017-09-01

In this paper, an integrated microfluidic analysis microsystems with bacterial capture enrichment and in-situ impedance detection was purposed based on microfluidic chips dielectrophoresis technique and electrochemical impedance detection principle. The microsystems include microfluidic chip, main control module, and drive and control module, and signal detection and processing modulet and result display unit. The main control module produce the work sequence of impedance detection system parts and achieve data communication functions, the drive and control circuit generate AC signal which amplitude and frequency adjustable, and it was applied on the foodborne pathogens impedance analysis microsystems to realize the capture enrichment and impedance detection. The signal detection and processing circuit translate the current signal into impendence of bacteria, and transfer to computer, the last detection result is displayed on the computer. The experiment sample was prepared by adding Escherichia coli standard sample into chicken sample solution, and the samples were tested on the dielectrophoresis chip capture enrichment and in-situ impedance detection microsystems with micro-array electrode microfluidic chips. The experiments show that the Escherichia coli detection limit of microsystems is 5 × 104 CFU/mL and the detection time is within 6 min in the optimization of voltage detection 10 V and detection frequency 500 KHz operating conditions. The integrated microfluidic analysis microsystems laid the solid foundation for rapid real-time in-situ detection of bacteria.

Probability of detecting nematode infestations for quarantine sampling with imperfect extraction efficacy

PubMed Central

Chen, Peichen; Liu, Shih-Chia; Liu, Hung-I; Chen, Tse-Wei

2011-01-01

For quarantine sampling, it is of fundamental importance to determine the probability of finding an infestation when a specified number of units are inspected. In general, current sampling procedures assume 100% probability (perfect) of detecting a pest if it is present within a unit. Ideally, a nematode extraction method should remove all stages of all species with 100% efficiency regardless of season, temperature, or other environmental conditions; in practice however, no method approaches these criteria. In this study we determined the probability of detecting nematode infestations for quarantine sampling with imperfect extraction efficacy. Also, the required sample and the risk involved in detecting nematode infestations with imperfect extraction efficacy are presented. Moreover, we developed a computer program to calculate confidence levels for different scenarios with varying proportions of infestation and efficacy of detection. In addition, a case study, presenting the extraction efficacy of the modified Baermann's Funnel method on Aphelenchoides besseyi, is used to exemplify the use of our program to calculate the probability of detecting nematode infestations in quarantine sampling with imperfect extraction efficacy. The result has important implications for quarantine programs and highlights the need for a very large number of samples if perfect extraction efficacy is not achieved in such programs. We believe that the results of the study will be useful for the determination of realistic goals in the implementation of quarantine sampling. PMID:22791911

A Rapid, Presumptive Procedure for the Detection of Salmonella in Foods and Food Ingredients

PubMed Central

Hoben, D. A.; Ashton, D. H.; Peterson, A. C.

1973-01-01

A rapid detection procedure was developed in which a lysine-iron-cystine-neutral red (LICNR) broth medium, originally described by Hargrove et al. in 1971, was modified and used to detect the presence of viable Salmonella organisms in a variety of foods, food ingredients, and feed materials by using a two-step enrichment technique. Tetrathionate broth was used to enrich samples with incubation at 41 C for 20 hr, followed by transfer to LICNR broth and incubation at 37 C for 24 hr for further enrichment and for the detection of Salmonella organisms by color change. One hundred ten samples representing 18 different sample types were evaluated for the presence of viable Salmonella. Ninety-four percent of the samples found to be presumptive positive by this method were confirmed as positive by a culture method. Fluorescent-antibody results also compared closely. A second study was conducted under quality-control laboratory conditions by using procedures currently employed for Salmonella detection. One hundred forty-three samples representing 19 different sample types were evaluated for the presence of viable Salmonella. No false negatives were observed with the rapid-detection method. The usefulness of the LICNR broth procedure as a screening technique to eliminate negative samples rapidly and to identify presumptive positive samples for the presence of viable Salmonella organisms was established in this laboratory. PMID:4568884

Quantitative detection of pathogens in centrifugal microfluidic disks

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

Koh, Chung-Yan; Schaff, Ulrich Y.; Sommer, Gregory Jon

A system and methods for detection of a nucleic acid including forming a plurality of nucleic acid detection complexes are described, each of the complexes including a nucleic acid analyte, a detection agent and a functionalized probe. The method further including binding the nucleic acid detection complexes to a plurality of functionalized particles in a fluid sample and separating the functionalized particles having the nucleic acid detection complexes bound thereto from the fluid sample using a density media. The nucleic acid analyte is detected by detecting the detection agent.

Comparison of Cultivation and PCR-Hybridization for Detection of Salmonella in Porcine Fecal and Water Samples†

PubMed Central

Feder, Ingrid; Nietfeld, Jerome C.; Galland, John; Yeary, Teresa; Sargeant, Jan M.; Oberst, Richard; Tamplin, Mark L.; Luchansky, John B.

2001-01-01

A total of 150 fecal and water samples from four swine farms were tested for the presence of Salmonella enterica using different enrichment techniques as follows: (i) 92 fecal samples from nursery and farrowing barns at three swine farms were preenriched overnight in tryptic soy broth (TSB) at 37°C followed by overnight enrichment in Rappaport-Vassiliadis 10 broth (RV10) at 42°C; (ii) 24 water samples from the third farm were preenriched overnight in 3MC broth at 37°C followed by overnight enrichment in RV10 at 42°C; and (iii) 34 fecal samples from a fourth farm, a finishing farm, were enriched overnight in RV10 at 42°C with no additional enrichment. Following each of the enrichment techniques, samples were subcultured onto modified semisolid Rappaport-Vassiliadis (MSRV) agar prior to transfer to Hektoen Enteric agar plates for the recovery of viable Salmonella bacteria. Presumptive Salmonella isolates were biochemically and serologically confirmed. For the PCR detection of Salmonella, a 1-ml portion was removed from each sample after the first overnight enrichment and the DNA was extracted using a Sepharose CL-6B spin column. Amplicons (457 bp) derived from primers to the invA and invE genes were confirmed as Salmonella specific on ethidium bromide-stained agarose gels by Southern hybridization with a 20-mer oligonucleotide probe specific for the Salmonella invA gene. Neither the standard microbiological method nor the molecular method detected all of the 65 samples that tested positive by both methods or either method alone. Salmonella bacteria were detected by both cultivation and PCR-hybridization in 68% (17 of 25) of the positive samples that were preenriched in TSB, in 73% (11 of 15) of the positive samples preenriched in 3MC broth, and in 24% (6 of 25) of the positive samples enriched in RV10. Agreement between Salmonella detection using cultivation with preenrichment and detection by PCR was 76% using the kappa statistic. However, agreement between Salmonella detection using cultivation without preenrichment and detection by PCR was about 6%; the PCR assay detected 80% (20 of 25) of the 25 positive samples, while Salmonella bacteria were recovered from only 44% (11 of 25) by cultivation. Our results indicate that the PCR-hybridization approach is equivalent to or better than cultivation for detecting Salmonella in swine feces or water samples from swine farms when using the medium combinations evaluated in this study. PMID:11427557

Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

USGS Publications Warehouse

Conroy, M.J.; Runge, J.P.; Barker, R.J.; Schofield, M.R.; Fonnesbeck, C.J.

2008-01-01

Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of abundance of rare and patchily distributed species and is particularly appropriate when sampling in all patches is impossible, but a global estimate of abundance is required.

Water-quality assessment of part of the upper Mississippi River basin, Minnesota and Wisconsin - Volatile organic compounds in surface and ground water, 1978-94

USGS Publications Warehouse

Andrews, W.J.; Fallon, J.D.; Kroening, S.E.

1995-01-01

Examination of water-quality data from widely distributed sampling networks of river sites and wells in the study area led to the following conclusions: 1) trace amounts of chlorinated VOC's were detected sporadically in waters of the Mississippi, Minnesota, St. Croix, and Vermillion Rivers; 2) benzene, ethylbenzene, toluene, and meta+paraxylene were detected sporadically in waters sampled from the chain of lakes used as the municipal supply for St. Paul, Minnesota; 3) the target VOC's were detected in less than five percent of ground-water samples at relatively low concentrations, generally near detection limits which ranged from 1 to 5 micrograms per liter; 4) VOC's were generally detected at similar frequencies, but at higher concentrations, in water samples from wells completed in sand and gravel aquifers than in water samples from wells completed in bedrock aquifers; 5) VOC's were most commonly detected in ground water in the vicinity of identifiable emission sites of VOC's, such as landfills, dumps, or major industries; 6) trichloroethene, a commonly used degreasing agent in dry cleaning, metal cleaning and cleaning septic lines, was the most frequently detected target VOC in ground water sampled from wells completed in both sand and gravel and bedrock aquifers; 7) wells producing water with detectable concentrations of the target VOC's tended to be shallower than wells producing water with no detectable concentrations of those compounds, but the differences in well depths were not statistically significant at a 95 percent confidence level; and 8) chlorination of water substantially increased the frequency of detection of trihalomethane compounds. The low frequencies of detection of the target VOC's and THM's in surface and ground water sampled from widely distributed sampling networks in the study area indicate that, although there are thousands of sites which can potentially emit these compounds to water, soil, and the atmosphere, these compounds have not had a widespread measurable effect on the quality of surface and ground water in the study area.

A rapid, highly sensitive and culture-free detection of pathogens from blood by positive enrichment.

PubMed

Vutukuru, Manjula Ramya; Sharma, Divya Khandige; Ragavendar, M S; Schmolke, Susanne; Huang, Yiwei; Gumbrecht, Walter; Mitra, Nivedita

2016-12-01

Molecular diagnostics is a promising alternative to culture based methods for the detection of bloodstream infections, notably due to its overall lower turnaround time when starting directly from patient samples. Whole blood is usually the starting diagnostic sample in suspected bloodstream infections. The detection of low concentrations of pathogens in blood using a molecular assay necessitates a fairly high starting volume of blood sample in the range of 5-10mL. This large volume of blood sample has a substantial accompanying human genomic content that interferes with pathogen detection. In this study, we have established a workflow using magnetic beads coated with Apolipoprotein H that makes it possible to concentrate pathogens from a 5.0mL whole blood sample, thereby enriching pathogens from whole blood background and also reducing the sample volume to ~200μL or less. We have also demonstrated that this method of enrichment allows detection of 1CFU/mL of Escherichia coli, Enterococcus gallinarum and Candida tropicalis from 5mL blood using quantitative PCR; a detection limit that is not possible in unenriched samples. The enrichment method demonstrated here took 30min to complete and can be easily integrated with various downstream molecular and microbiological techniques. Copyright © 2016 Elsevier B.V. All rights reserved.

Development and validation of a FISH-based method for the detection and quantification of E. coli and coliform bacteria in water samples.

PubMed

Hügler, Michael; Böckle, Karin; Eberhagen, Ingrid; Thelen, Karin; Beimfohr, Claudia; Hambsch, Beate

2011-01-01

Monitoring of microbiological contaminants in water supplies requires fast and sensitive methods for the specific detection of indicator organisms or pathogens. We developed a protocol for the simultaneous detection of E. coli and coliform bacteria based on the Fluorescence in situ Hybridization (FISH) technology. This protocol consists of two approaches. The first allows the direct detection of single E. coli and coliform bacterial cells on the filter membranes. The second approach includes incubation of the filter membranes on a nutrient agar plate and subsequent detection of the grown micro-colonies. Both approaches were validated using drinking water samples spiked with pure cultures and naturally contaminated water samples. The effects of heat, chlorine and UV disinfection were also investigated. The micro-colony approach yielded very good results for all samples and conditions tested, and thus can be thoroughly recommended for usage as an alternative method to detect E. coli and coliform bacteria in water samples. However, during this study, some limitations became visible for the single cell approach. The method cannot be applied for water samples which have been disinfected by UV irradiation. In addition, our results indicated that green fluorescent dyes are not suitable to be used with chlorine disinfected samples.

Determination of aflatoxin B1 levels in organic spices and herbs.

PubMed

Tosun, Halil; Arslan, Recep

2013-01-01

Organically produced spices and herbs were analyzed for determination of aflatoxin B1 (AFB1) by ELISA using immunoaffinity column. For this purpose 93 organic spices and 37 organic herbs were randomly selected from organic markets and organic shops in Turkey. AFB1 was detected in 58 organic spice and 32 organic herb samples. Among organic spice samples, the maximum value was detected in cinnamon sample (53 μg/kg). AFB1 was not detected in thyme samples. AFB1 levels of 41 organic spice samples were above the EU regulatory limit (5 μg/kg). Among organic herb samples the highest concentration of AFB1 (52.5 μg/kg) was detected in a rosehip sample. AFB1 levels of 21 organic herb samples were above the regulatory limits of the European Union. These results showed that more stringent measures must be taken for the prevention of mold contamination in the production of organic spices and herbs.

Determination of Aflatoxin B1 Levels in Organic Spices and Herbs

PubMed Central

Tosun, Halil; Arslan, Recep

2013-01-01

Organically produced spices and herbs were analyzed for determination of aflatoxin B1 (AFB1) by ELISA using immunoaffinity column. For this purpose 93 organic spices and 37 organic herbs were randomly selected from organic markets and organic shops in Turkey. AFB1 was detected in 58 organic spice and 32 organic herb samples. Among organic spice samples, the maximum value was detected in cinnamon sample (53 μg/kg). AFB1 was not detected in thyme samples. AFB1 levels of 41 organic spice samples were above the EU regulatory limit (5 μg/kg). Among organic herb samples the highest concentration of AFB1 (52.5 μg/kg) was detected in a rosehip sample. AFB1 levels of 21 organic herb samples were above the regulatory limits of the European Union. These results showed that more stringent measures must be taken for the prevention of mold contamination in the production of organic spices and herbs. PMID:23766719

Detection and Quantification of Nitrogen Compounds in the First Drilled Martian Solid Samples by the Sample Analysis at Mars (SAM) Instrument Suite on the Mars Science Laboratory (MSL)

NASA Technical Reports Server (NTRS)

Stern, Jennifer C.; Navarro-Gonzalez, Rafael; Freissinet, Caroline; McKay, Christopher P.; Archer, P. Douglas, Jr.; Buch, Arnaud; Coll, Patrice; Eigenbrode, Jennifer L.; Franz, Heather B.; Glavin, Daniel P.;

Rapid filtration separation-based sample preparation method for Bacillus spores in powdery and environmental matrices.

PubMed

Isabel, Sandra; Boissinot, Maurice; Charlebois, Isabelle; Fauvel, Chantal M; Shi, Lu-E; Lévesque, Julie-Christine; Paquin, Amélie T; Bastien, Martine; Stewart, Gale; Leblanc, Eric; Sato, Sachiko; Bergeron, Michel G

2012-03-01

Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of <10 min. This sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation.

Rapid Filtration Separation-Based Sample Preparation Method for Bacillus Spores in Powdery and Environmental Matrices

PubMed Central

Isabel, Sandra; Boissinot, Maurice; Charlebois, Isabelle; Fauvel, Chantal M.; Shi, Lu-E; Lévesque, Julie-Christine; Paquin, Amélie T.; Bastien, Martine; Stewart, Gale; Leblanc, Éric; Sato, Sachiko

2012-01-01

Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of <10 min. This sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation. PMID:22210204

The Power of Low Back Pain Trials: A Systematic Review of Power, Sample Size, and Reporting of Sample Size Calculations Over Time, in Trials Published Between 1980 and 2012.

PubMed

Froud, Robert; Rajendran, Dévan; Patel, Shilpa; Bright, Philip; Bjørkli, Tom; Eldridge, Sandra; Buchbinder, Rachelle; Underwood, Martin

2017-06-01

A systematic review of nonspecific low back pain trials published between 1980 and 2012. To explore what proportion of trials have been powered to detect different bands of effect size; whether there is evidence that sample size in low back pain trials has been increasing; what proportion of trial reports include a sample size calculation; and whether likelihood of reporting sample size calculations has increased. Clinical trials should have a sample size sufficient to detect a minimally important difference for a given power and type I error rate. An underpowered trial is one within which probability of type II error is too high. Meta-analyses do not mitigate underpowered trials. Reviewers independently abstracted data on sample size at point of analysis, whether a sample size calculation was reported, and year of publication. Descriptive analyses were used to explore ability to detect effect sizes, and regression analyses to explore the relationship between sample size, or reporting sample size calculations, and time. We included 383 trials. One-third were powered to detect a standardized mean difference of less than 0.5, and 5% were powered to detect less than 0.3. The average sample size was 153 people, which increased only slightly (∼4 people/yr) from 1980 to 2000, and declined slightly (∼4.5 people/yr) from 2005 to 2011 (P < 0.00005). Sample size calculations were reported in 41% of trials. The odds of reporting a sample size calculation (compared to not reporting one) increased until 2005 and then declined (Equation is included in full-text article.). Sample sizes in back pain trials and the reporting of sample size calculations may need to be increased. It may be justifiable to power a trial to detect only large effects in the case of novel interventions. 3.

Capillary electrophoresis-electrochemical detection microchip device and supporting circuits

DOEpatents

Jackson, Douglas J [New Albany, IN; Roussel, Jr., Thomas J.; Crain, Mark M [Georgetown, IN; Baldwin, Richard P [Louisville, KY; Keynton, Robert S [Louisville, KY; Naber, John F [Prospect, KY; Walsh, Kevin M [Louisville, KY; Edelen, John G [Versailles, KY

2008-03-18

The present invention is a capillary electrophoresis device, comprising a substrate; a first channel in the substrate, and having a buffer arm and a detection arm; a second channel in the substrate intersecting the first channel, and having a sample arm and a waste arm; a buffer reservoir in fluid communication with the buffer arm; a waste reservoir in fluid communication with the waste arm; a sample reservoir in fluid communication with the sample arm; and a detection reservoir in fluid communication with the detection arm. The detection arm and the buffer arm are of substantially equal length.

Re-evaluation of groundwater monitoring data for glyphosate and bentazone by taking detection limits into account.

PubMed

Hansen, Claus Toni; Ritz, Christian; Gerhard, Daniel; Jensen, Jens Erik; Streibig, Jens Carl

2015-12-01

Current regulatory assessment of pesticide contamination of Danish groundwater is exclusively based on samples with pesticide concentrations above detection limit. Here we demonstrate that a realistic quantification of pesticide contamination requires the inclusion of "non-detect" samples i.e. samples with concentrations below the detection limit, as left-censored observations. The median calculated pesticide concentrations are shown to be reduced 10(4) to 10(5) fold for two representative herbicides (glyphosate and bentazone) relative to the median concentrations based upon observations above detection limits alone. Copyright © 2015 Elsevier B.V. All rights reserved.

Semi-Quantitative Method for Streptococci Magnetic Detection in Raw Milk.

PubMed

Duarte, Carla; Costa, Tiago; Carneiro, Carla; Soares, Rita; Jitariu, Andrei; Cardoso, Susana; Piedade, Moisés; Bexiga, Ricardo; Freitas, Paulo

2016-04-27

Bovine mastitis is the most costly disease for dairy farmers and the most frequent reason for the use of antibiotics in dairy cattle; thus, control measures to detect and prevent mastitis are crucial for dairy farm sustainability. The aim of this study was to develop and validate a sensitive method to magnetically detect Streptococcus agalactiae (a Group B streptococci) and Streptococcus uberis in raw milk samples. Mastitic milk samples were collected aseptically from 44 cows with subclinical mastitis, from 11 Portuguese dairy farms. Forty-six quarter milk samples were selected based on bacterial identification by conventional microbiology. All samples were submitted to PCR analysis. In parallel, these milk samples were mixed with a solution combining specific antibodies and magnetic nanoparticles, to be analyzed using a lab-on-a-chip magnetoresistive cytometer, with microfluidic sample handling. This paper describes a point of care methodology used for detection of bacteria, including analysis of false positive/negative results. This immunological recognition was able to detect bacterial presence in samples spiked above 100 cfu/mL, independently of antibody and targeted bacteria used in this work. Using PCR as a reference, this method correctly identified 73% of positive samples for streptococci species with an anti-S. agalactiae antibody, and 41% of positive samples for an anti-GB streptococci antibody.

Semi-Quantitative Method for Streptococci Magnetic Detection in Raw Milk

PubMed Central

Duarte, Carla; Costa, Tiago; Carneiro, Carla; Soares, Rita; Jitariu, Andrei; Cardoso, Susana; Piedade, Moisés; Bexiga, Ricardo; Freitas, Paulo

2016-01-01

Bovine mastitis is the most costly disease for dairy farmers and the most frequent reason for the use of antibiotics in dairy cattle; thus, control measures to detect and prevent mastitis are crucial for dairy farm sustainability. The aim of this study was to develop and validate a sensitive method to magnetically detect Streptococcus agalactiae (a Group B streptococci) and Streptococcus uberis in raw milk samples. Mastitic milk samples were collected aseptically from 44 cows with subclinical mastitis, from 11 Portuguese dairy farms. Forty-six quarter milk samples were selected based on bacterial identification by conventional microbiology. All samples were submitted to PCR analysis. In parallel, these milk samples were mixed with a solution combining specific antibodies and magnetic nanoparticles, to be analyzed using a lab-on-a-chip magnetoresistive cytometer, with microfluidic sample handling. This paper describes a point of care methodology used for detection of bacteria, including analysis of false positive/negative results. This immunological recognition was able to detect bacterial presence in samples spiked above 100 cfu/mL, independently of antibody and targeted bacteria used in this work. Using PCR as a reference, this method correctly identified 73% of positive samples for streptococci species with an anti-S. agalactiae antibody, and 41% of positive samples for an anti-GB streptococci antibody. PMID:27128950

Automated methods for multiplexed pathogen detection.

PubMed

Straub, Timothy M; Dockendorff, Brian P; Quiñonez-Díaz, Maria D; Valdez, Catherine O; Shutthanandan, Janani I; Tarasevich, Barbara J; Grate, Jay W; Bruckner-Lea, Cynthia J

2005-09-01

Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cycler where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides "live vs. dead" capabilities. However, sensitivity of the method will need to be improved for RNA analysis to replace PCR.

Assessing environmental DNA detection in controlled lentic systems.

PubMed

Moyer, Gregory R; Díaz-Ferguson, Edgardo; Hill, Jeffrey E; Shea, Colin

2014-01-01

Little consideration has been given to environmental DNA (eDNA) sampling strategies for rare species. The certainty of species detection relies on understanding false positive and false negative error rates. We used artificial ponds together with logistic regression models to assess the detection of African jewelfish eDNA at varying fish densities (0, 0.32, 1.75, and 5.25 fish/m3). Our objectives were to determine the most effective water stratum for eDNA detection, estimate true and false positive eDNA detection rates, and assess the number of water samples necessary to minimize the risk of false negatives. There were 28 eDNA detections in 324, 1-L, water samples collected from four experimental ponds. The best-approximating model indicated that the per-L-sample probability of eDNA detection was 4.86 times more likely for every 2.53 fish/m3 (1 SD) increase in fish density and 1.67 times less likely for every 1.02 C (1 SD) increase in water temperature. The best section of the water column to detect eDNA was the surface and to a lesser extent the bottom. Although no false positives were detected, the estimated likely number of false positives in samples from ponds that contained fish averaged 3.62. At high densities of African jewelfish, 3-5 L of water provided a >95% probability for the presence/absence of its eDNA. Conversely, at moderate and low densities, the number of water samples necessary to achieve a >95% probability of eDNA detection approximated 42-73 and >100 L, respectively. Potential biases associated with incomplete detection of eDNA could be alleviated via formal estimation of eDNA detection probabilities under an occupancy modeling framework; alternatively, the filtration of hundreds of liters of water may be required to achieve a high (e.g., 95%) level of certainty that African jewelfish eDNA will be detected at low densities (i.e., <0.32 fish/m3 or 1.75 g/m3).

Automated Methods for Multiplexed Pathogen Detection

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

Straub, Tim M.; Dockendorff, Brian P.; Quinonez-Diaz, Maria D.

2005-09-01

Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cyclermore » where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides ''live vs. dead'' capabilities. However, sensitivity of the method will need to be improved for RNA analysis to replace PCR.« less

A New Remote-Sensing Method for Mine Detection using HPM Irradiation and IR Detection.

DTIC Science & Technology

1999-12-01

absorption of microwave energy by the mine. This signature appears at the soil surface after a brief time-delay from the start of HPM illumination. At...detection de cible, l’operation de teledetection, la capacite de detecter des cibles sous un ciel couvert avec peu de dependance du cycle solaire et la...the temperature of the sample depends on the microwave energy absorbed by the sample and varies inversely with the sample thermal heat capacity. The

Ground-Water Quality in Western New York, 2006

USGS Publications Warehouse

Eckhardt, David A.V.; Reddy, James E.; Tamulonis, Kathryn L.

2008-01-01

Water samples were collected from 7 production wells and 26 private residential wells in western New York from August through December 2006 and analyzed to characterize the chemical quality of ground water. Wells at 15 of the sites were screened in sand and gravel aquifers, and 18 were finished in bedrock aquifers. The wells were selected to represent areas of greatest ground-water use and to provide a geographical sampling from the 5,340-square-mile study area. Samples were analyzed for 5 physical properties and 219 constituents that included nutrients, major inorganic ions, trace elements, radionuclides, pesticides, volatile organic compounds (VOC), phenolic compounds, organic carbon, and bacteria. Results indicate that ground water used for drinking supply is generally of acceptable quality, although concentrations of some constituents or bacteria exceeded at least one drinking-water standard at 27 of the 33 wells. The cations that were detected in the highest concentrations were calcium, magnesium, and sodium; anions that were detected in the highest concentrations were bicarbonate, chloride, and sulfate. The predominant nutrients were nitrate and ammonia; nitrate concentrations were higher in samples from sand and gravel aquifers than in samples from bedrock. The trace elements barium, boron, copper, lithium, nickel, and strontium were detected in every sample; the trace elements with the highest concentrations were barium, boron, iron, lithium, manganese, and strontium. Eighteen pesticides, including 9 pesticide degradates, were detected in water from 14 of the 33 wells, but none of the concentrations exceeded State or Federal Maximum Contaminant Levels (MCLs). Fourteen volatile organic compounds were detected in water from 12 of the 33 wells, but none of the concentrations exceeded MCLs. Eight chemical analytes and three types of bacteria were detected in concentrations that exceeded Federal and State drinking-water standards, which are typically identical. Sulfate concentrations exceeded the U.S. Environmental Protection Agency (USEPA) Secondary Maximum Contaminant Level (SMCL) of 250 milligrams per liter (mg/L) in three samples, and chloride concentrations exceeded the SMCL of 250 mg/L in two samples. Sodium concentrations exceeded the USEPA Drinking Water Health Advisory of 60 mg/L in nine samples. Iron concentrations exceeded the SMCL of 300 ug/L (micrograms per liter) in 14 filtered samples, and manganese exceeded the USEPA SMCL of 50 ug/L in 15 filtered samples, as well as the New York State MCL of 300 ug/L in 1 filtered sample. Arsenic exceeded the USEPA MCL of 10 ug/L in two samples, aluminum exceeded the SMCL for aluminum of 50 ug/L in one sample, and lead exceeded the MCL of 15 ug/L in one sample. Radon-222 exceeded the proposed USEPA MCL of 300 picocuries per liter in 24 samples. Any detection of coliform bacteria indicates a violation of New York State health regulations; total coliform was detected in 12 samples, and Escherichia coli was detected in 2 samples. The plate counts for heterotrophic bacteria exceeded the MCL (500 colony-forming units per milliliter) in four samples.

Investigation of Legionella Contamination in Bath Water Samples by Culture, Amoebic Co-Culture, and Real-Time Quantitative PCR Methods.

PubMed

Edagawa, Akiko; Kimura, Akio; Kawabuchi-Kurata, Takako; Adachi, Shinichi; Furuhata, Katsunori; Miyamoto, Hiroshi

2015-10-19

We investigated Legionella contamination in bath water samples, collected from 68 bathing facilities in Japan, by culture, culture with amoebic co-culture, real-time quantitative PCR (qPCR), and real-time qPCR with amoebic co-culture. Using the conventional culture method, Legionella pneumophila was detected in 11 samples (11/68, 16.2%). Contrary to our expectation, the culture method with the amoebic co-culture technique did not increase the detection rate of Legionella (4/68, 5.9%). In contrast, a combination of the amoebic co-culture technique followed by qPCR successfully increased the detection rate (57/68, 83.8%) compared with real-time qPCR alone (46/68, 67.6%). Using real-time qPCR after culture with amoebic co-culture, more than 10-fold higher bacterial numbers were observed in 30 samples (30/68, 44.1%) compared with the same samples without co-culture. On the other hand, higher bacterial numbers were not observed after propagation by amoebae in 32 samples (32/68, 47.1%). Legionella was not detected in the remaining six samples (6/68, 8.8%), irrespective of the method. These results suggest that application of the amoebic co-culture technique prior to real-time qPCR may be useful for the sensitive detection of Legionella from bath water samples. Furthermore, a combination of amoebic co-culture and real-time qPCR might be useful to detect viable and virulent Legionella because their ability to invade and multiply within free-living amoebae is considered to correlate with their pathogenicity for humans. This is the first report evaluating the efficacy of the amoebic co-culture technique for detecting Legionella in bath water samples.

Comparison between Urine and Cervical Samples for HPV DNA Detection and Typing in Young Women in Colombia.

PubMed

Cómbita, Alba Lucía; Gheit, Tarik; González, Paula; Puerto, Devi; Murillo, Raúl Hernando; Montoya, Luisa; Vorsters, Alex; Van Keer, Severien; Van Damme, Pierre; Tommasino, Massimo; Hernández-Suárez, Gustavo; Sánchez, Laura; Herrero, Rolando; Wiesner, Carolina

2016-09-01

Urine sampling for HPV DNA detection has been proposed as an effective method for monitoring the impact of HPV vaccination programs; however, conflicting results have been reported. The goal of this study was to evaluate the performance of optimized urine HPV DNA testing in women aged 19 to 25 years. Optimization process included the use of first void urine, immediate mixing of urine with DNA preservative, and the concentration of all HPV DNA, including cell-free DNA fragments. Urine and cervical samples were collected from 535 young women attending cervical screening at health centers from two Colombian cities. HPV DNA detection and genotyping was performed using an HPV type-specific multiplex genotyping assay, which combines multiplex polymerase chain reaction with bead-based Luminex technology. Concordance between HPV DNA detection in urine and cervical samples was determined using kappa statistics and McNemar tests. The accuracy of HPV DNA testing in urine samples was evaluated measuring sensitivity and specificity using as reference the results obtained from cervical samples. Statistical analysis was performed using STATA11.2 software. The findings revealed an overall HPV prevalence of 60.00% in cervical samples and 64.72% in urine samples, HPV-16 being the most frequent HPV type detected in both specimens. Moreover, our results indicate that detection of HPV DNA in first void urine provides similar results to those obtained with cervical samples and can be used to monitor HPV vaccination trials and programs as evidenced by the substantial concordance found for the detection of the four vaccine types. Cancer Prev Res; 9(9); 766-71. ©2016 AACR. ©2016 American Association for Cancer Research.

Application of PCR to a clinical and environmental investigation of a case of equine botulism.

PubMed

Szabo, E A; Pemberton, J M; Gibson, A M; Thomas, R J; Pascoe, R R; Desmarchelier, P M

1994-08-01

PCR for the detection of botulinum neurotoxin gene types A to E was used in the investigation of a case of equine botulism. Samples from a foal diagnosed with toxicoinfectious botulism in 1985 were reanalyzed by PCR and the mouse bioassay in conjunction with an environmental survey. Neurotoxin B was detected by mouse bioassay in culture enrichments of serum, spleen, feces, and intestinal contents. PCR results compared well with mouse bioassay results, detecting type B neurotoxin genes in these samples and also in a liver sample. Other neurotoxin types were not detected by either test. Clostridium botulinum type B was shown to be prevalent in soils collected from the area in which the foal was raised. Four methods were used to test for the presence of botulinum neurotoxin-producing organisms in 66 soil samples taken within a 5-km radius: PCR and agarose gel electrophoresis (types A to E), PCR and an enzyme-linked assay (type B), hybridization of crude alkaline cell lysates with a type B-specific probe, and the mouse bioassay (all types). Fewer soil samples were positive for C. botulinum type B by the mouse bioassay (15%) than by any of the DNA-based detection systems. Hybridization of a type B-specific probe to DNA dot blots (26% of the samples were positive) and PCR-enzyme-linked assay (77% of the samples were positive) were used for the rapid analysis of large numbers of samples, with sensitivity limits of 3 x 10(6) and 3,000 cells, respectively. Conventional detection of PCR products by gel electrophoresis was the most sensitive method (300-cell limit), and in the present environmental survey, neurotoxin B genes only were detected in 94% of the samples.

Application of PCR to a clinical and environmental investigation of a case of equine botulism.

PubMed Central

Szabo, E A; Pemberton, J M; Gibson, A M; Thomas, R J; Pascoe, R R; Desmarchelier, P M

1994-01-01

PCR for the detection of botulinum neurotoxin gene types A to E was used in the investigation of a case of equine botulism. Samples from a foal diagnosed with toxicoinfectious botulism in 1985 were reanalyzed by PCR and the mouse bioassay in conjunction with an environmental survey. Neurotoxin B was detected by mouse bioassay in culture enrichments of serum, spleen, feces, and intestinal contents. PCR results compared well with mouse bioassay results, detecting type B neurotoxin genes in these samples and also in a liver sample. Other neurotoxin types were not detected by either test. Clostridium botulinum type B was shown to be prevalent in soils collected from the area in which the foal was raised. Four methods were used to test for the presence of botulinum neurotoxin-producing organisms in 66 soil samples taken within a 5-km radius: PCR and agarose gel electrophoresis (types A to E), PCR and an enzyme-linked assay (type B), hybridization of crude alkaline cell lysates with a type B-specific probe, and the mouse bioassay (all types). Fewer soil samples were positive for C. botulinum type B by the mouse bioassay (15%) than by any of the DNA-based detection systems. Hybridization of a type B-specific probe to DNA dot blots (26% of the samples were positive) and PCR-enzyme-linked assay (77% of the samples were positive) were used for the rapid analysis of large numbers of samples, with sensitivity limits of 3 x 10(6) and 3,000 cells, respectively. Conventional detection of PCR products by gel electrophoresis was the most sensitive method (300-cell limit), and in the present environmental survey, neurotoxin B genes only were detected in 94% of the samples. Images PMID:7989554

Investigation of Legionella Contamination in Bath Water Samples by Culture, Amoebic Co-Culture, and Real-Time Quantitative PCR Methods

PubMed Central

Edagawa, Akiko; Kimura, Akio; Kawabuchi-Kurata, Takako; Adachi, Shinichi; Furuhata, Katsunori; Miyamoto, Hiroshi

2015-01-01

We investigated Legionella contamination in bath water samples, collected from 68 bathing facilities in Japan, by culture, culture with amoebic co-culture, real-time quantitative PCR (qPCR), and real-time qPCR with amoebic co-culture. Using the conventional culture method, Legionella pneumophila was detected in 11 samples (11/68, 16.2%). Contrary to our expectation, the culture method with the amoebic co-culture technique did not increase the detection rate of Legionella (4/68, 5.9%). In contrast, a combination of the amoebic co-culture technique followed by qPCR successfully increased the detection rate (57/68, 83.8%) compared with real-time qPCR alone (46/68, 67.6%). Using real-time qPCR after culture with amoebic co-culture, more than 10-fold higher bacterial numbers were observed in 30 samples (30/68, 44.1%) compared with the same samples without co-culture. On the other hand, higher bacterial numbers were not observed after propagation by amoebae in 32 samples (32/68, 47.1%). Legionella was not detected in the remaining six samples (6/68, 8.8%), irrespective of the method. These results suggest that application of the amoebic co-culture technique prior to real-time qPCR may be useful for the sensitive detection of Legionella from bath water samples. Furthermore, a combination of amoebic co-culture and real-time qPCR might be useful to detect viable and virulent Legionella because their ability to invade and multiply within free-living amoebae is considered to correlate with their pathogenicity for humans. This is the first report evaluating the efficacy of the amoebic co-culture technique for detecting Legionella in bath water samples. PMID:26492259

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

Treesearch

Taylor M. Wilcox; Kevin S. McKelvey; Michael K. Young; Adam J. Sepulveda; Bradley B. Shepard; Stephen F. Jane; Andrew R. Whiteley; Winsor H. Lowe; Michael K. Schwartz

2016-01-01

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive...

Ground-water quality data in the north San Francisco Bay hydrologic provinces, California, 2004: Results from the California Ground-water Ambient Monitoring and Assessment (GAMA) program

USGS Publications Warehouse

Kulongoski, Justin T.; Belitz, Kenneth; Dawson, Barbara J.

2006-01-01

Ground-water samples were analyzed for major and minor ions, trace elements, nutrients, volatile organic compounds, pesticides and pesticide degradates, waste-water indicators, dissolved methane, nitrogen, carbon dioxide and noble gases (in collaboration with Lawrence Livermore National Laboratory). Naturally occurring isotopes (tritium, carbon-14, oxygen-18, deuterium and helium-4) also were measured in the samples to help identify the source and age of the ground water. Results show that no anthropogenic constituents were detected at concentrations higher than those levels set for regulatory purposes, and relatively few naturally-occurring constituents were detected at concentrations greater than regulatory levels. In this study, 21 of the 88 volatile organic compounds (VOCs) and gasoline additives and (or) oxygenates investigated were detected in ground-water samples, however, detected concentrations were one-half to one-forty-thousandth the maximum contaminant levels (MCL). Thirty-two percent of the randomized wells sampled had at least a single detection of a VOC or gasoline additive and (or) oxygenate. The most frequently detected compounds were chloroform, found in 12 of the 84 randomized wells; carbon disulfide, found in 8 of the 84 randomized wells; and toluene, found in 4 of the 84 randomized wells. Trihalomethanes were the most frequently detected class of VOCs. Nine of the 122 pesticides and (or) pesticide degradates investigated were detected in ground-water samples, however, concentrations were one-seventieth to one-eight-hundredth the MCLs. Seventeen percent of the randomized wells sampled had at least a single detection of pesticide and pesticide degradate. Herbicides were the most frequently detected class of pesticides. The most frequently detected compound was simazine, found in 8 of the 84 of the randomized wells. Chlordiamino-s-triazine and deisopropyl atrazine were both found in 2 of the 84 randomized wells sampled. Thirteen out of 63 compounds that may be indicative of the prescence of waste-water were detected in ground-water samples. Twenty-six percent of the randomized wells sampled for waste-water indicators had at least one detection. Isophorone was the most frequently detected in 6 of the 84 randomized wells. Bisphenol-A, caffeine, and indole each were detected in 3 of the 84 randomized wells. Major and minor ions and dissolved solids (DS) samples were collected at 33 public-supply wells; 3 samples had DS concentrations above the secondary maximum contaminant level (SMCL) of 500 mg/L. Ground-water samples from 32 public-supply wells were analyzed for trace elements. Arsenic concentrations above the MCL of 10 μg/L were measured at 4 public-supply wells, boron concentrations above the detection level for the purpose of reporting (DLR) of 100 μg/L were measured at 19 wells. Iron concentrations above the SMCL of 300 μg/L were measured at 7 wells, a lead concentration above the California notification level (NL) of 15 μg/L at one well, and manganese concentrations above the SMCL of 50 μg/L were measured at 17 wells. Vanadium concentrations above the DLR of 3 μg/L were measured at 9 public-supply wells; and chromium(VI) concentrations above the DLR of 1 μg/L were measured at 48 public-supply wells. Major and minor ions and dissolved solids (DS) samples were collected at 33 public-supply wells; 3 samples had DS concentrations above the secondary maximum contaminant level (SMCL) of 500 mg/L. Ground-water samples from 32 public-supply wells were analyzed for trace elements. Arsenic concentrations above the MCL of 10 μg/L were measured at 4 public-supply wells, boron concentrations above the detection level for the purpose of reporting (DLR) of 100 μg/L were measured at 19 wells. Iron concentrations above the SMCL of 300 μg/L were measured at 7 wells, a lead concentration above the California notification level (NL) of 15 μg/L at one well, and manganese concentrations above the SMCL of 50 μg/L were measured at 17 wells. Vanadium concentrations above the DLR of 3 μg/L were measured at 9 public-supply wells; and chromium(VI) concentrations above the DLR of 1 μg/L were measured at 48 public-supply wells. Microbial constituents were analyzed in 22 ground-water samples. Total coliform was detected in three wells. Counts ranged from 2 colonies per 100 mL to 20 colonies per 100 mL. MCLs for microbial constituents are based on reoccurring detection, and will be monitored during future sampling.

Detection of alpha radiation in a beta radiation field

DOEpatents

Mohagheghi, Amir H.; Reese, Robert P.

2001-01-01

An apparatus and method for detecting alpha particles in the presence of high activities of beta particles utilizing an alpha spectrometer. The apparatus of the present invention utilizes a magnetic field applied around the sample in an alpha spectrometer to deflect the beta particles from the sample prior to reaching the detector, thus permitting detection of low concentrations of alpha particles. In the method of the invention, the strength of magnetic field required to adequately deflect the beta particles and permit alpha particle detection is given by an algorithm that controls the field strength as a function of sample beta energy and the distance of the sample to the detector.

A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus).

PubMed

Kistler, Whitney M; Parlos, Julie A; Peper, Steven T; Dunham, Nicholas R; Kendall, Ronald J

2016-01-01

Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53-0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population.

A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus)

PubMed Central

Kistler, Whitney M.; Parlos, Julie A.; Peper, Steven T.; Dunham, Nicholas R.; Kendall, Ronald J.

2016-01-01

Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53–0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population. PMID:27893772

Residual Agar Determination in Bacterial Spores by Electrospray Ionization Mass Spectrometry

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

Wahl, Karen L.; Colburn, Heather A.; Wunschel, David S.

2010-02-15

Presented here is an analytical method to detect residual agar from a bacterial spore sample as an indication of culturing on an agar plate. This method is based on the resolubilization of agar polysaccharide from a bacterial spore sample, enzymatic digestion, followed by electrospray ionization tandem mass spectrometry (ESI-MSn) analysis for detection of a specific agar fragment ion. A range of Bacillus species and strains were selected to demonstrate the effectiveness of this approach. The characteristic agar fragment ion was detected in the spores grown on agar that were washed from 1 to 5 times, irradiated or non-irradiated and notmore » in the spores grown in broth. A sample containing approximately 108 spores is currently needed for confident detection of residual agar from culture on agar plates in the presence of bacterial spores with a limit of detection of approximately 1 ppm agar spiked into a broth-grown spore sample. The results of a proficiency test with 42 blinded samples are presented demonstrating the utility of this method with no false positives and only 3 false negatives for samples that were below the detection level of the method as documented.« less

Compressive Sensing of Roller Bearing Faults via Harmonic Detection from Under-Sampled Vibration Signals

PubMed Central

Tang, Gang; Hou, Wei; Wang, Huaqing; Luo, Ganggang; Ma, Jianwei

2015-01-01

The Shannon sampling principle requires substantial amounts of data to ensure the accuracy of on-line monitoring of roller bearing fault signals. Challenges are often encountered as a result of the cumbersome data monitoring, thus a novel method focused on compressed vibration signals for detecting roller bearing faults is developed in this study. Considering that harmonics often represent the fault characteristic frequencies in vibration signals, a compressive sensing frame of characteristic harmonics is proposed to detect bearing faults. A compressed vibration signal is first acquired from a sensing matrix with information preserved through a well-designed sampling strategy. A reconstruction process of the under-sampled vibration signal is then pursued as attempts are conducted to detect the characteristic harmonics from sparse measurements through a compressive matching pursuit strategy. In the proposed method bearing fault features depend on the existence of characteristic harmonics, as typically detected directly from compressed data far before reconstruction completion. The process of sampling and detection may then be performed simultaneously without complete recovery of the under-sampled signals. The effectiveness of the proposed method is validated by simulations and experiments. PMID:26473858

Prevalence, quantification and typing of adenoviruses detected in river and treated drinking water in South Africa.

PubMed

van Heerden, J; Ehlers, M M; Heim, A; Grabow, W O K

2005-01-01

Human adenoviruses (HAds), of which there are 51 serotypes, are associated with gastrointestinal, respiratory, urinary tract and eye infections. The importance of water in the transmission of HAds and the potential health risks constituted by HAds in these environments are widely recognized. Adenoviruses have not previously been quantified in river and treated drinking water samples. In this study, HAds in river water and treated drinking water sources in South Africa were detected, quantified and typed. Adenoviruses were recovered from the water samples using a glass wool adsorption-elution method followed by polyethylene glycol/NaCl precipitation for secondary concentration. The sensitivity and specificity of two nested PCR methods were compared for detection of HAds in the water samples. Over a 1-year period (June 2002 to July 2003), HAds were detected in 5.32% (10/188) of the treated drinking water and 22.22% (10/45) of river water samples using the conventional nested PCR method. The HAds detected in the water samples were quantified using a real-time PCR method. The original treated drinking water and river water samples had an estimate of less than one copy per litre of HAd DNA present. The hexon-PCR products used for typing HAds were directly sequenced or cloned into plasmids before sequencing. In treated drinking water samples, species D HAds predominated. In addition, adenovirus serotypes 2, 40 and 41 were each detected in three different treated drinking water samples. Most (70%) of the HAds detected in river water samples analysed were enteric HAds (serotypes 40 and 41). One HAd serotype 2 and two species D HAds were detected in the river water. Adenoviruses detected in river and treated drinking water samples were successfully quantified and typed. The detection of HAds in drinking water supplies treated and disinfected by internationally recommended methods, and which conform to quality limits for indicator bacteria, warrants an investigation of the risk of infection constituted by these viruses. The risk of infection may have implications for the management of drinking water quality. This study is unique as it is the first report on the quantification and typing of HAds in treated drinking water and river water. This baseline data is necessary for the meaningful assessment of the potential risk of infection constituted by these viruses.

Chemical amplification based on fluid partitioning in an immiscible liquid

DOEpatents

Anderson, Brian L.; Colston, Bill W.; Elkin, Christopher J.

2010-09-28

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

THE CHALLENGE OF DETECTING CLASSICAL SWINE FEVER VIRUS CIRCULATION IN WILD BOAR (SUS SCROFA): SIMULATION OF SAMPLING OPTIONS.

PubMed

Sonnenburg, Jana; Schulz, Katja; Blome, Sandra; Staubach, Christoph

2016-10-01

Classical swine fever (CSF) is one of the most important viral diseases of domestic pigs ( Sus scrofa domesticus) and wild boar ( Sus scrofa ). For at least 4 decades, several European Union member states were confronted with outbreaks among wild boar and, as it had been shown that infected wild boar populations can be a major cause of primary outbreaks in domestic pigs, strict control measures for both species were implemented. To guarantee early detection and to demonstrate freedom from disease, intensive surveillance is carried out based on a hunting bag sample. In this context, virologic investigations play a major role in the early detection of new introductions and in regions immunized with a conventional vaccine. The required financial resources and personnel for reliable testing are often large, and sufficient sample sizes to detect low virus prevalences are difficult to obtain. We conducted a simulation to model the possible impact of changes in sample size and sampling intervals on the probability of CSF virus detection based on a study area of 65 German hunting grounds. A 5-yr period with 4,652 virologic investigations was considered. Results suggest that low prevalences could not be detected with a justifiable effort. The simulation of increased sample sizes per sampling interval showed only a slightly better performance but would be unrealistic in practice, especially outside the main hunting season. Further studies on other approaches such as targeted or risk-based sampling for virus detection in connection with (marker) antibody surveillance are needed.

Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations

PubMed Central

PIÑEYRO-NELSON, A; VAN HEERWAARDEN, J; PERALES, H R; SERRATOS-HERNÁNDEZ, J A; RANGEL, A; HUFFORD, M B; GEPTS, P; GARAY-ARROYO, A; RIVERA-BUSTAMANTE, R; ÁLVAREZ-BUYLLA, E R

2009-01-01

A possible consequence of planting genetically modified organisms (GMOs) in centres of crop origin is unintended gene flow into traditional landraces. In 2001, a study reported the presence of the transgenic 35S promoter in maize landraces sampled in 2000 from the Sierra Juarez of Oaxaca, Mexico. Analysis of a large sample taken from the same region in 2003 and 2004 could not confirm the existence of transgenes, thereby casting doubt on the earlier results. These two studies were based on different sampling and analytical procedures and are thus hard to compare. Here, we present new molecular data for this region that confirm the presence of transgenes in three of 23 localities sampled in 2001. Transgene sequences were not detected in samples taken in 2002 from nine localities, while directed samples taken in 2004 from two of the positive 2001 localities were again found to contain transgenic sequences. These findings suggest the persistence or re-introduction of transgenes up until 2004 in this area. We address variability in recombinant sequence detection by analyzing the consistency of current molecular assays. We also present theoretical results on the limitations of estimating the probability of transgene detection in samples taken from landraces. The inclusion of a limited number of female gametes and, more importantly, aggregated transgene distributions may significantly lower detection probabilities. Our analytical and sampling considerations help explain discrepancies among different detection efforts, including the one presented here, and provide considerations for the establishment of monitoring protocols to detect the presence of transgenes among structured populations of landraces. PMID:19143938

Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations.

PubMed

Piñeyro-Nelson, A; Van Heerwaarden, J; Perales, H R; Serratos-Hernández, J A; Rangel, A; Hufford, M B; Gepts, P; Garay-Arroyo, A; Rivera-Bustamante, R; Alvarez-Buylla, E R

2009-02-01

A possible consequence of planting genetically modified organisms (GMOs) in centres of crop origin is unintended gene flow into traditional landraces. In 2001, a study reported the presence of the transgenic 35S promoter in maize landraces sampled in 2000 from the Sierra Juarez of Oaxaca, Mexico. Analysis of a large sample taken from the same region in 2003 and 2004 could not confirm the existence of transgenes, thereby casting doubt on the earlier results. These two studies were based on different sampling and analytical procedures and are thus hard to compare. Here, we present new molecular data for this region that confirm the presence of transgenes in three of 23 localities sampled in 2001. Transgene sequences were not detected in samples taken in 2002 from nine localities, while directed samples taken in 2004 from two of the positive 2001 localities were again found to contain transgenic sequences. These findings suggest the persistence or re-introduction of transgenes up until 2004 in this area. We address variability in recombinant sequence detection by analyzing the consistency of current molecular assays. We also present theoretical results on the limitations of estimating the probability of transgene detection in samples taken from landraces. The inclusion of a limited number of female gametes and, more importantly, aggregated transgene distributions may significantly lower detection probabilities. Our analytical and sampling considerations help explain discrepancies among different detection efforts, including the one presented here, and provide considerations for the establishment of monitoring protocols to detect the presence of transgenes among structured populations of landraces.

Microbial Quality, Safety, and Pathogen Detection by Using Quantitative PCR of Raw Salad Vegetables Sold in Dhanbad City, India.

PubMed

Mritunjay, Sujeet K; Kumar, Vipin

2017-01-01

Consumption of ready-to-eat fresh vegetables has increased worldwide, with a consequent increase in outbreaks caused by foodborne pathogens. In the Indian subcontinent, raw fresh vegetables are usually consumed without washing or other decontamination procedures, thereby leading to new food safety threats. In this study, the microbiological quality and pathogenic profile of raw salad vegetables was evaluated through standard protocols. In total, 480 samples (60 each of eight different salad vegetables) of cucumber, tomato, carrot, coriander, cabbage, beetroot, radish, and spinach were collected from different locations in Dhanbad, a city famous for its coal fields and often called the "Coal Capital of India." The samples were analyzed for total plate count, total coliforms, Escherichia coli , E. coli O157:H7, Listeria monocytogenes , and Salmonella spp. Incidences of pathogens were detected through quantitative PCR subsequent to isolation. Results showed that 46.7% (for total plate counts) and 30% (for total coliforms) of samples were unacceptable for consumption per the Food Safety and Standards Authority of India. Pathogenic microorganisms were detected in 3.7% of total samples. E. coli O157:H7 was detected in three samples of spinach (2) and beetroot ( 1 ); L. monocytogenes was detected in 14 samples of spinach ( 8 ), tomato ( 3 ), cucumber ( 2 ), and radish ( 1 ); and Salmonella spp. were detected in 16 samples of spinach ( 7 ), tomato ( 3 ), beetroot ( 2 ), cucumber ( 2 ), carrot ( 1 ), and radish ( 1 ). Pathogens were not detected in any of the cabbage and coriander samples.

Influence of Soap Characteristics and Food Service Facility Type on the Degree of Bacterial Contamination of Open, Refillable Bulk Soaps.

PubMed

Schaffner, Donald W; Jensen, Dane; Gerba, Charles P; Shumaker, David; Arbogast, James W

2018-02-01

Concern has been raised regarding the public health risks from refillable bulk-soap dispensers because they provide an environment for potentially pathogenic bacteria to grow. This study surveyed the microbial quality of open refillable bulk soap in four different food establishment types in three states. Two hundred ninety-six samples of bulk soap were collected from food service establishments in Arizona, New Jersey, and Ohio. Samples were tested for total heterotrophic viable bacteria, Pseudomonas, coliforms and Escherichia coli, and Salmonella. Bacteria were screened for antibiotic resistance. The pH, solids content, and water activity of all soap samples were measured. Samples were assayed for the presence of the common antibacterial agents triclosan and parachlorometaxylenol. More than 85% of the soap samples tested contained no detectable microorganisms, but when a sample contained any detectable microorganisms, it was most likely contaminated at a very high level (∼7 log CFU/mL). Microorganisms detected in contaminated soap included Klebsiella oxytoca, Serratia liquefaciens, Shigella sonnei, Enterobacter gergoviae, Serratia odorifera, and Enterobacter cloacae. Twenty-three samples contained antibiotic-resistant organisms, some of which were resistant to two or more antibiotics. Every sample containing less than 4% solids had some detectable level of bacteria, whereas no samples with greater than 14% solids had detectable bacteria. This finding suggests the use of dilution and/or low-cost formulations as a cause of bacterial growth. There was a statistically significant difference ( P = 0.0035) between the fraction of bacteria-positive samples with no detected antimicrobial agent (17%) and those containing an antimicrobial agent (7%). Fast food operations and grocery stores were more likely to have detectable bacteria in bulk-soap samples compared with convenience stores ( P < 0.05). Our findings underscore the risk to public health from use of refillable bulk-soap dispensers in food service establishments.

Quality of malaria diagnosis and molecular confirmation of Plasmodium ovale curtisi in a rural area of the southeastern region of Ethiopia.

PubMed

Díaz, Pedro Berzosa; Lozano, Patricia Mula; Rincón, Jose Manuel Ramos; García, Luz; Reyes, Francisco; Llanes, Agustín Benito

2015-09-18

Approximately 50 million people (60 %) live in malaria risk areas in Ethiopia, at altitudes below 2000 m. According to official data, 60-70 % of malaria cases are due to Plasmodium falciparum, and 40-30 % by Plasmodium vivax. The species Plasmodium ovale was detected in 2013 in the northwest of the country, being the first report of the presence of this species in Ethiopia since the 60 s. The aim of this study was to assess the diagnosis by microscopy and PCR, and demonstrate the presence of other Plasmodium species in the country. The survey was conducted in Bulbula, situated in the Rift Valley (West Arsi Province, Oromia Region). From December 2010 to October 2011, 3060 samples were collected from patients with symptoms of malaria; the diagnosis of malaria was done by microscopy and confirmation by PCR. 736 samples were positive for malaria by microscopy. After removing the 260 samples (109 positives and 151 negatives) for which it was not possible to do PCR, there were a total of 2800 samples, 1209 are used for its confirmation by PCR and quality control (627 are positives and 582 negatives by microscopy). From the 627 positive samples, 604 were confirmed as positive by PCR, 23 false positives were detected, and the group of 582 negative samples, 184 were positive by PCR (false negatives), which added to the previous positive samples is a total of 788, positive samples for some species of Plasmodium sp. 13.3 % more positives were detected with the PCR than the microscopy. Importantly, 23 samples were detected by PCR as P. ovale, after the sequencing of these samples was determined as P. ovale curtisi. The PCR detected more positive samples than the microscopy; in addition, P. ovale and P. ovale/P. vivax were detected that had not been detected by microscopy, which can affect in the infection control.

Anthropogenic constituents in shallow ground water in the Upper Illinois River Basin

USGS Publications Warehouse

Morrow, William S.

2003-01-01

The potential for anthropogenic effects on ground water is becoming of increasing concern as land throughout the Nation becomes more urbanized. The possible contamination of water resources by volatile organic compounds (VOCs), pesticides (including transformation products), and nitrate, from current urban land use and past agricultural land use, is of particular concern. As part of the U.S. Geological Survey's National Water-Quality Assessment program, water samples for analysis of VOCs, pesticides, and nitrate were collected from 43 wells in shallow (175 feet deep or less) ground water in glacial deposits overlying a major bedrock aquifer in recently urbanized areas in the Chicago, Ill. and Milwaukee, Wis. metropolitan counties.Constituents were reported using two reporting levels. For the laboratory reporting level, the risk of a false positive or false negative detection is less than or equal to 1 percent. For the information-rich method level, estimated concentrations are identified positively and are qualified to be present on the basis of quality-control criteria, but have a higher risk of false positive detections.VOCs were detected in 32 percent (12 of 38) of the well samples with 15 detections of 7 VOCs, based on laboratory reporting levels. Concentrations ranged from 0.03 (estimated) to 4.6 micrograms per liter (?g/L), with a median concentration of 0.13 ?g/L. Methyl tert-butyl ether (MTBE) and trichloromethane (chloroform) were the most common with detections in 10 percent (4 of 38) of the well samples. Using information-rich method reporting levels, VOCs were detected in 74 percent of the wells with 37 detections of 15 VOCs. Chloroform was most common with detections in 24 percent (9 of 38) of the well samples.Pesticides were detected in 62 percent (26 of 42) of the well samples with 83 detections of 20 pesticides, based on laboratory reporting levels for the respective constituent. Concentrations ranged from 0.003 (estimated) to 3.6 (estimated) ?g/L, with a median concentration of 0.06 ?g/L. Deethylatrazine was most common with detections in 43 percent (18 of 42) of the well samples. Using information-rich method reporting levels, pesticides were detected in 74 percent (31 of 42) of the well samples with 134 detections of 29 pesticides. Deethylatrazine was most common with detections in 45 percent (19 of 42) of the well samples.Nitrate concentrations ranged from less than 0.047 to 12.5 milligrams per liter (mg/L) with a median concentration of 0.068 mg/L. Nitrate concentrations were greater than 2 mg/L in 30 percent (13 of 43) of the wells sampled. Total VOC detections did not correlate well (less than Spearman Rank correlation value of plus or minus 0.10) with well depth, age, or dissolved oxygen. Total pesticide detections did correlate with dissolved oxygen and negatively correlated with well depth. Nitrate concentrations correlated with dissolved oxygen and apparent recharge date.No VOC or pesticide concentrations exceeded U.S. Environmental Protection Agency drinking-water standards and only one nitrate 2 Anthropogenic Constituents in Shallow Ground Water in the Upper Illinois River Basin detection exceeded the standards. However, of the 43 wells sampled for VOCs or pesticides using information-rich methods, or nitrate at laboratory reporting levels, 40 of 43 (93 percent) well samples had at least one detection of a VOC or pesticide, or a detection of nitrate above 2.0 mg/L. This result indicates that most of these wells are anthropogenically affected, but presently not at U.S. Environmental Protection Agency drinking-water regulation levels of concern. The wells sampled were not public drinking-water supplies; therefore, these wells were not subject to U.S. Environmental Protection Agency drinking-water regulations.

Comparison of culture and biochemical tests with PCR for detection of Brachyspira hyodysenteriae and Brachyspira pilosicoli.

PubMed

Råsbäck, T; Fellström, C; Gunnarsson, A; Aspán, A

2006-08-01

Traditional culture and biochemical tests (CBT) were compared with PCR for sensitivity and detection of Brachyspira hyodysenteriae and Brachyspira pilosicoli in seeded faeces and clinical samples from diarrhoeic pigs. A duplex PCR system was developed based on primers detecting the tlyA-gene of B. hyodysenteriae and the 16S rRNA-gene of B. pilosicoli. Sensitivities for the PCR system were determined on seeded faeces, using DNA that had been recovered from primary cultures or extracted directly from faeces. Compared to CBT, PCR applied to DNA extracted directly from faeces lowered the sensitivity by a factor of 1000 to 10,000. B. hyodysenteriae and B. pilosicoli detection was compared for CBT and PCR using 200 clinical samples. CBT detected more B. hyodysenteriae isolates in the clinical samples than PCR, but fewer B. pilosicoli positive samples. An atypical strongly haemolytic isolate was detected only by CBT.

Evaluation of a microbiological indicator test for antibiotic detection in ewe and goat milk.

PubMed

Comunian, R; Paba, A; Dupré, I; Daga, E S; Scintu, M F

2010-12-01

Antibiotics are widely used for therapeutic and prophylactic purposes in dairy animals. The presence of residual antibiotics in milk could cause potentially serious problems in human health and have technological implication in the manufacturing of dairy products. The aim of this study was to evaluate Delvotest Accelerator (DSM Food Specialties, Delft, the Netherlands), a new system for a fully automated microbial test to detect antibiotic residues in ewe and goat milk. Forty-three samples of raw, whole, refrigerated bulk-tank milk samples (22 of ewe milk and 21 of goat milk) were analyzed during the whole lactation period. Four concentrations of 4 antibiotics were diluted in milk: penicillin G at 1, 2, 3, and 4 μg/L; sulfadiazine at 25, 50, 100, and 200 μg/L; tetracycline at 50, 100, 200, and 400 μg/L; and gentamicin at 25, 50, 100, and 200 μg/L. The detection limit of the Delvotest Accelerator was calculated as the range of antibiotic concentrations within which 95% of positive result lie. The range of detection limit of penicillin G and sulfadiazine was easily detected by Delvotest Accelerator at or below the European Union maximum residue limits, both for ewe and goat milk samples. In contrast, the system showed a lower ability to detect tetracycline and gentamicin both for ewe and goat milk samples. Very low percentages of false-positive outcomes were obtained. Lactation phase did not seem to be a crucial factor affecting the ability of the Delvotest Accelerator to detect spiked milk samples. A higher detection ability was observed for goat milk samples compared with ewe milk samples. A negative correlation between the percentage of positive milk samples detected and milk fat, protein, and lactose contents was observed for gentamicin only. Copyright © 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Detection of Zaire Ebola virus by real-time reverse transcription-polymerase chain reaction, Sierra Leone, 2014.

PubMed

Liu, Licheng; Sun, Yang; Kargbo, Brima; Zhang, Chuntao; Feng, Huahua; Lu, Huijun; Liu, Wenseng; Wang, Chengyu; Hu, Yi; Deng, Yongqiang; Jiang, Jiafu; Kang, Xiaoping; Yang, Honglei; Jiang, Yongqiang; Yang, Yinhui; Kargbo, David; Qian, Jun; Chen, Weijun

2015-09-15

During the 2014 Ebola virus disease (EVD) outbreak, a real-time quantitative polymerase chain reaction was established to detect and identify the Zaire Ebola virus. We describe the use of this assay to screen 315 clinical samples from EVD suspected person in Sierra Leone. The detection rate in blood samples was 77.81% (207/266), and there were relatively higher detection rate (79.32% and 81.42%, respectively) during the first two weeks after onset of symptoms. In the two weeks that followed, the detection rate declined to 66.67% and 25.00%, respectively. There was the highest virus load at the first week and then decreased. The detection rate in swab samples was 89.79% (44/49). This may be benefit from the included patients. 46 of 49 swab samples were collected from died patients. Taken together, the results presented here indicate that the assay specifically and sensitively detects Zaire Ebola virus. Copyright © 2015 Elsevier B.V. All rights reserved.

[Detection of human parvovirus B19, human bocavirus and human parvovirus 4 infections in blood samples among 95 patients with liver disease in Nanjing by nested PCR].

PubMed

Tong, Rui; Zhou, Wei-Min; Liu, Xi-Jun; Wang, Yue; Lou, Yong-Liang; Tan, Wen-Jie

2013-04-01

To analyze the infection of human parvovirus B19, human bocavirus (HBoV) and human parvovirus 4 (PARV4) in blood samples among patients with liver disease in Nanjing by molecular detection. Nested PCR assays were designed and validated to detect B19, HBoV and PARV4, respectively. The assays were used to screen three parvoviruses in blood samples from 95 patients with different liver disease in Nanjing. The parvovirus infection was analyzed statistically. The detection limits were 10 copies of genomic DNA equivalents per reaction for each assays and the good specificity were observed. The frequency of B19 and HBoV were 2/95 (2.1%) and 9/95 (9.5%) in blood samples respectively. No PARV4 was detected. HBoV was detected in 3/5 patients with drug-induced hepatitis. Both B19 and HBoV infection were detected in blood from patients with liver disease.

Polymerase chain reaction detection of Propionibacterium propionicus and Actinomyces radicidentis in primary and persistent endodontic infections.

PubMed

Siqueira, José F; Rôças, Isabela N

2003-08-01

Propionibacterium propionicus and the recently described species Actinomyces radicidentis have been isolated from infections of endodontic origin; nevertheless, the possibility exists that their actual prevalence may have been underestimated by culture. The purpose of our study was to assess the occurrence of these 2 species in different types of endodontic infections by using the sensitive 16S rDNA-based nested polymerase chain reaction approach. To detect these 2 species, nested polymerase chain reaction was performed directly in samples taken from primary endodontic infections associated with asymptomatic periradicular lesions, acute apical periodontitis, or acute periradicular abscesses and in samples from patients in whom endodontic therapy had failed. DNA was extracted from the samples and initially amplified by using universal 16S rDNA primers. In the second round of amplification, the first polymerase chain reaction products were used to detect a specific 16S rDNA fragment of either P propionicus or A radicidentis. P propionicus was detected in 6/21 (29%) root canal samples from teeth with chronic periradicular lesions, in 5/10 (50%) cases diagnosed as acute apical periodontitis, and in 7/19 (37%) pus samples aspirated from acute periradicular abscesses. Overall, this species was found in 18/50 (36%) samples taken from primary endodontic infections. Of the root canal samples obtained from root-filled teeth with chronic periradicular lesions, P propionicus was detected in 7/12 (58%) cases. A radicidentis was detected in 1/21 (5%) root canal samples from teeth with chronic periradicular lesions and in 1/10 (10%) cases of acute apical periodontitis. No pus sample yielded this species. In general, A radicidentis was detected in 2/50 (4%) samples taken from primary endodontic infections and in 1/12 (8%) root canal samples taken from patients in whom endodontic treatment had failed. P propionicus was found in a relatively large number of patients with primary and persistent endodontic infections. This strengthens the assumption that this bacterial species is an endodontic pathogen associated with different forms of periradicular diseases. In contrast, A radicidentis was only occasionally detected in the patients examined. The role played by this species in endodontic infections remains to be clarified.

Pesticides in Wyoming Groundwater, 2008-10

USGS Publications Warehouse

Eddy-Miller, Cheryl A.; Bartos, Timothy T.; Taylor, Michelle L.

2013-01-01

Groundwater samples were collected from 296 wells during 1995-2006 as part of a baseline study of pesticides in Wyoming groundwater. In 2009, a previous report summarized the results of the baseline sampling and the statistical evaluation of the occurrence of pesticides in relation to selected natural and anthropogenic (human-related) characteristics. During 2008-10, the U.S. Geological Survey, in cooperation with the Wyoming Department of Agriculture, resampled a subset (52) of the 296 wells sampled during 1995-2006 baseline study in order to compare detected compounds and respective concentrations between the two sampling periods and to evaluate the detections of new compounds. The 52 wells were distributed similarly to sites used in the 1995-2006 baseline study with respect to geographic area and land use within the geographic area of interest. Because of the use of different types of reporting levels and variability in reporting-level values during both the 1995-2006 baseline study and the 2008-10 resampling study, analytical results received from the laboratory were recensored. Two levels of recensoring were used to compare pesticides—a compound-specific assessment level (CSAL) that differed by compound and a common assessment level (CAL) of 0.07 microgram per liter. The recensoring techniques and values used for both studies, with the exception of the pesticide 2,4-D methyl ester, were the same. Twenty-eight different pesticides were detected in samples from the 52 wells during the 2008-10 resampling study. Pesticide concentrations were compared with several U.S. Environmental Protection Agency drinking-water standards or health advisories for finished (treated) water established under the Safe Drinking Water Act. All detected pesticides were measured at concentrations smaller than U.S. Environmental Protection Agency drinking-water standards or health advisories where applicable (many pesticides did not have standards or advisories). One or more pesticides were detected at concentrations greater than the CAL in water from 16 of 52 wells sampled (about 31 percent) during the resampling study. Detected pesticides were classified into one of six types: herbicides, herbicide degradates, insecticides, insecticide degradates, fungicides, or fungicide degradates. At least 95 percent of detected pesticides were classified as herbicides or herbicide degradates. The number of different pesticides detected in samples from the 52 wells was similar between the 1995-2006 baseline study (30 different pesticides) and 2008-2010 resampling study (28 different pesticides). Thirteen pesticides were detected during both studies. The change in the number of pesticides detected (without regard to which pesticide was detected) in groundwater samples from each of the 52 wells was evaluated and the number of pesticides detected in groundwater did not change for most of the wells (32). Of those that did have a difference between the two studies, 17 wells had more pesticide detections in groundwater during the 1995-2006 baseline study, whereas only 3 wells had more detections during the 2008-2010 resampling study. The difference in pesticide concentrations in groundwater samples from each of the 52 wells was determined. Few changes in concentration between the 1995-2006 baseline study and the 2008-2010 resampling study were seen for most detected pesticides. Seven pesticides had a greater concentration detected in the groundwater from the same well during the baseline sampling compared to the resampling study. Concentrations of prometon, which was detected in 17 wells, were greater in the baseline study sample compared to the resampling study sample from the same well 100 percent of the time. The change in the number of pesticides detected (without regard to which pesticide was detected) in groundwater samples from each of the 52 wells with respect to land use and geographic area was calculated. All wells with land use classified as agricultural had the same or a smaller number of pesticides detected in the resampling study compared to the baseline study. All wells in the Bighorn Basin geographic area also had the same or a smaller number of pesticides detected in the resampling study compared to the baseline study.

Levels of pesticides residues in the White Nile water in the Sudan.

PubMed

Nesser, Gibreel A A; Abdelbagi, Azhari O; Hammad, Ahmed Mohammed Ali; Tagelseed, Mirghani; Laing, Mark D

2016-06-01

Twenty-two commonly used pesticides were monitored during autumn, winter, and summer of 2004-2005 in 27 water samples from three sites along the White Nile in Sudan (former Sudan). Sites were selected to reflect pesticides gathered from drainage canals in central Sudan and from upstream sources. Collected samples were extracted and subjected to gas chromatographic analysis. Pesticides levels were measured in nanograms per liter. Pesticides residues were detected in 96 % of the samples with a total residue burden of 4132.6 ng L(-1), and an overall mean concentration and range of 50.99 and not detected-1570 ng L(-1), respectively. Ororganochlorines were the most frequently detected contaminants, which were found in 70 % of the samples, causing a total burden of 2852.8 ng L(-1), followed by pyrethroids 15 % of the samples, with a total burden of 926.5 ng L(-1). The tested herbicides were detected in ˂4 % of the samples with a total burden of 353.3 ng L(-1), while organophosphorus levels were below the detection limit. The most frequent contaminants were the following: heptachlor and its epoxide (52 % of samples), followed by DDTs (dichlorodiphenyltrichloroethanes) (DDT and DDE, in 19 % of the samples), cypermethrin and fenvalerate (in 11 % of the samples), and pendimethalin (in <4 % of the samples). Residues of hexachlorocyclohexane (HCH) isomers (α, β, γ and δ), endosulfan (α and β), p, p-DDD, λ cyhalothrin, deltamethrin, and oxyfluorfen were not detected in the analyzed samples. Generally, levels were least in autumn, and followed by summer and winter. Sources of contamination might include agricultural lands in central Sudan and upstream sources. Both recent and old contaminations were indicated.

Comparison of potentially pathogenic free-living amoeba hosts by Legionella spp. in substrate-associated biofilms and floating biofilms from spring environments.

PubMed

Hsu, Bing-Mu; Huang, Chin-Chun; Chen, Jung-Sheng; Chen, Nai-Hsiung; Huang, Jen-Te

2011-10-15

This study compares five genera of free-living amoebae (FLA) hosts by Legionella spp. in the fixed and floating biofilm samples from spring environments. Detection rate of Legionella spp. was 26.9% for the floating biofilms and 3.1% for the fixed biofilms. Acanthamoeba spp., Hartmanella vermiformis, and Naegleria spp. were more frequently detected in floating biofilm than in fixed biofilm samples. The percentage of pathogenic Acanthamoeba spp. among all the genus Acanthamoeba detected positive samples was 19.6%. The potential pathogenic Naegleria spp. (for example, Naegleria australiensis, Naegleria philippinensis, and Naegleria italica) was 54.2% to all the Naegleria detected positive samples. In the study, 12 serotypes of possible pneumonia causing Legionella spp. were detected, and their percentage in all the Legionella containing samples was 42.4%. The FLA parasitized by Legionella included unnamed Acanthamoeba genotype, Acanthamoeba griffini, Acanthamoeba jacobsi, H. vermiformis, and N. australiensis. Significant differences were also observed between the presence/absence of H. vermiformis and Legionella parasitism in FLA. Comparisons between the culture-confirmed method and the PCR-based detection method for detecting FLA and Legionella in biofilms showed great variation. Therefore, using these analysis methods together to detect FLA and Legionella is recommended. Copyright © 2011 Elsevier Ltd. All rights reserved.

Highly Sensitive Bacteriophage-Based Detection of Brucella abortus in Mixed Culture and Spiked Blood

PubMed Central

Sergueev, Kirill V.; Filippov, Andrey A.; Nikolich, Mikeljon P.

2017-01-01

For decades, bacteriophages (phages) have been used for Brucella species identification in the diagnosis and epidemiology of brucellosis. Traditional Brucella phage typing is a multi-day procedure including the isolation of a pure culture, a step that can take up to three weeks. In this study, we focused on the use of brucellaphages for sensitive detection of the pathogen in clinical and other complex samples, and developed an indirect method of Brucella detection using real-time quantitative PCR monitoring of brucellaphage DNA amplification via replication on live Brucella cells. This assay allowed the detection of single bacteria (down to 1 colony-forming unit per milliliter) within 72 h without DNA extraction and purification steps. The technique was equally efficient with Brucella abortus pure culture and with mixed cultures of B. abortus and α-proteobacterial near neighbors that can be misidentified as Brucella spp., Ochrobactrum anthropi and Afipia felis. The addition of a simple short sample preparation step enabled the indirect phage-based detection of B. abortus in spiked blood, with the same high sensitivity. This indirect phage-based detection assay enables the rapid and sensitive detection of live B. abortus in mixed cultures and in blood samples, and can potentially be applied for detection in other clinical samples and other complex sample types. PMID:28604602

Self-sampling is appropriate for detection of Staphylococcus aureus: a validation study

PubMed Central

2012-01-01

Background Studies frequently use nasal swabs to determine Staphylococcus aureus carriage. Self-sampling would be extremely useful in an outhospital research situation, but has not been studied in a healthy population. We studied the similarity of self-samples and investigator-samples in nares and pharynxes of healthy study subjects (hospital staff) in the Netherlands. Methods One hundred and five nursing personnel members were sampled 4 times in random order after viewing an instruction paper: 1) nasal self-sample, 2) pharyngeal self-sample, 3) nasal investigator-sample, and 4) pharyngeal investigator-sample. Results For nasal samples, agreement is 93% with a kappa coefficient of 0.85 (95% CI 0.74-0.96), indicating excellent agreement, for pharyngeal samples agreement is 83% and the kappa coefficient is 0.60 (95% CI 0.43-0.76), indicating good agreement. In both sampling sites self-samples even detected more S. aureus than investigator-samples. Conclusions This means that self-samples are appropriate for detection of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus. PMID:23137281

Detection of solar events

DOEpatents

Fischbach, Ephraim; Jenkins, Jere

2013-08-27

A flux detection apparatus can include a radioactive sample having a decay rate capable of changing in response to interaction with a first particle or a field, and a detector associated with the radioactive sample. The detector is responsive to a second particle or radiation formed by decay of the radioactive sample. The rate of decay of the radioactive sample can be correlated to flux of the first particle or the field. Detection of the first particle or the field can provide an early warning for an impending solar event.

Detection of neutrinos

DOEpatents

Fischbach, Ephraim; Jenkins, Jere

2016-05-10

A flux detection apparatus can include a radioactive sample having a decay rate capable of changing in response to interaction with a first particle or a field, and a detector associated with the radioactive sample. The detector is responsive to a second particle or radiation formed by decay of the radioactive sample. The rate of decay of the radioactive sample can be correlated to flux of the first particle or the field. Detection of the first particle or the field can provide an early warning for an impending solar event.

Detection of neutrinos

DOEpatents

Fischbach, Ephraim; Jenkins, Jere

2014-02-04

A flux detection apparatus can include a radioactive sample having a decay rate capable of changing in response to interaction with a first particle or a field, and a detector associated with the radioactive sample. The detector is responsive to a second particle or radiation formed by decay of the radioactive sample. The rate of decay of the radioactive sample can be correlated to flux of the first particle or the field. Detection of the first particle or the field can provide an early warning for an impending solar event.

Anthropogenic organic compounds in source water of selected community water systems that use groundwater, 2002-05

USGS Publications Warehouse

Hopple, Jessica A.; Delzer, Gregory C.; Kingsbury, James A.

2009-01-01

Source water, defined as groundwater collected from a community water system well prior to water treatment, was sampled from 221 wells during October 2002 to July 2005 and analyzed for 258 anthropogenic organic compounds. Most of these compounds are unregulated in drinking water and include pesticides and pesticide degradates, gasoline hydrocarbons, personal-care and domestic-use products, and solvents. The laboratory analytical methods used in the study have detection levels that commonly are 100 to 1,000 times lower than State and Federal standards and guidelines for protecting water quality. Detections of anthropogenic organic compounds do not necessarily indicate a concern to human health but rather help to identify emerging issues and track changes in occurrence and concentrations over time. Less than one-half (120) of the 258 compounds were detected in at least one source-water sample. Chloroform, in 36 percent of samples, was the most commonly detected of the 12 compounds that were in about 10 percent or more of source-water samples. The herbicides atrazine, metolachlor, prometon, and simazine also were among the commonly detected compounds. The commonly detected degradates of atrazine - deethylatrazine and deisopropylatrazine - as well as degradates of acetochlor and alachlor, generally were detected at concentrations similar to or greater than concentrations of the parent herbicide. The compounds perchloroethene, trichloroethene, 1,1,1-trichloroethane, methyl tert-butyl ether, and cis-1,2-dichloroethene also were detected commonly. The most commonly detected compounds in source-water samples generally were among those detected commonly across the country and reported in previous studies by the U.S. Geological Survey's National Water-Quality Assessment Program. Relatively few compounds were detected at concentrations greater than human-health benchmarks, and 84 percent of the concentrations were two or more orders of magnitude less than benchmarks. Five compounds (perchloroethene, trichloroethene, 1,2-dibromoethane, acrylonitrile, and dieldrin) were detected at concentrations greater than their human-health benchmark. The human-health benchmarks used for comparison were U.S. Environmental Protection Agency Maximum Contaminant Levels (MCLs) for regulated compounds and Health-Based Screening Levels developed by the U.S. Geological Survey in collaboration with the U.S. Environmental Protection Agency and other agencies for unregulated compounds. About one-half of all detected compounds do not have human-health benchmarks or adequate toxicity information to evaluate results in a human-health context. Ninety-four source-water and finished-water (water that has passed through all the treatment processes but prior to distribution) sites were sampled at selected community water systems during June 2004 to September 2005. Most of the samples were analyzed for compounds that were detected commonly or at relatively high concentrations during the initial source-water sampling. The majority of the finished-water samples represented water blended with water from one or more other wells. Thirty-four samples were from water systems that did not blend water from sampled wells with water from other wells prior to distribution. The comparison of source- and finished-water samples represents an initial assessment of whether compounds present in source water also are present in finished water and is not intended as an evaluation of water-treatment efficacy. The treatment used at the majority of the community water systems sampled is disinfection, which, in general, is not designed to remove the compounds monitored in this study. Concentrations of all compounds detected in finished water were less than their human-health benchmarks. Two detections of perchloroethene and one detection of trichloroethene in finished water had concentrations within an order of magnitude of the MCL. Concentrations of disinfection by-products were

Early detection of nonnative alleles in fish populations: When sample size actually matters

USGS Publications Warehouse

Croce, Patrick Della; Poole, Geoffrey C.; Payne, Robert A.; Gresswell, Bob

2017-01-01

Reliable detection of nonnative alleles is crucial for the conservation of sensitive native fish populations at risk of introgression. Typically, nonnative alleles in a population are detected through the analysis of genetic markers in a sample of individuals. Here we show that common assumptions associated with such analyses yield substantial overestimates of the likelihood of detecting nonnative alleles. We present a revised equation to estimate the likelihood of detecting nonnative alleles in a population with a given level of admixture. The new equation incorporates the effects of the genotypic structure of the sampled population and shows that conventional methods overestimate the likelihood of detection, especially when nonnative or F-1 hybrid individuals are present. Under such circumstances—which are typical of early stages of introgression and therefore most important for conservation efforts—our results show that improved detection of nonnative alleles arises primarily from increasing the number of individuals sampled rather than increasing the number of genetic markers analyzed. Using the revised equation, we describe a new approach to determining the number of individuals to sample and the number of diagnostic markers to analyze when attempting to monitor the arrival of nonnative alleles in native populations.

Lab-on-a-chip modules for detection of highly pathogenic bacteria: from sample preparation to detection

NASA Astrophysics Data System (ADS)

Julich, S.; Kopinč, R.; Hlawatsch, N.; Moche, C.; Lapanje, A.; Gärtner, C.; Tomaso, H.

2014-05-01

Lab-on-a-chip systems are innovative tools for the detection and identification of microbial pathogens in human and veterinary medicine. The major advantages are small sample volume and a compact design. Several fluidic modules have been developed to transform analytical procedures into miniaturized scale including sampling, sample preparation, target enrichment, and detection procedures. We present evaluation data for single modules that will be integrated in a chip system for the detection of pathogens. A microfluidic chip for purification of nucleic acids was established for cell lysis using magnetic beads. This assay was evaluated with spiked environmental aerosol and swab samples. Bacillus thuringiensis was used as simulant for Bacillus anthracis, which is closely related but non-pathogenic for humans. Stationary PCR and a flow-through PCR chip module were investigated for specific detection of six highly pathogenic bacteria. The conventional PCR assays could be transferred into miniaturized scale using the same temperature/time profile. We could demonstrate that the microfluidic chip modules are suitable for the respective purposes and are promising tools for the detection of bacterial pathogens. Future developments will focus on the integration of these separate modules to an entire lab-on-a-chip system.

Concentrations of selected pharmaceuticals and antibiotics in south-central Pennsylvania waters, March through September 2006

USGS Publications Warehouse

Loper, Connie A.; Crawford, J. Kent; Otto, Kim L.; Manning, Rhonda L.; Meyer, Michael T.; Furlong, Edward T.

2007-01-01

This report presents environmental and quality-control data from analyses of 15 pharmaceutical and 31 antibiotic compounds in water samples from streams and wells in south-central Pennsylvania. The analyses are part of a study by the U.S. Geological Survey (USGS) in cooperation with the Pennsylvania Department of Environmental Protection (PADEP) to define concentrations of selected emerging contaminants in streams and well water in Pennsylvania. Sampling was conducted at 11 stream sites and at 6 wells in 9 counties of south-central Pennsylvania. Five of the streams received municipal wastewater and 6 of the streams received runoff from agricultural areas dominated by animal-feeding operations. For all 11 streams, samples were collected at locations upstream and downstream of the municipal effluents or animal-feeding operations. All six wells were in agricultural settings. A total of 120 environmental samples and 21 quality-control samples were analyzed for the study. Samples were collected at each site in March/April, May, July, and September 2006 to obtain information on changes in concentration that could be related to seasonal use of compounds.For streams, 13 pharmaceuticals and 11 antibiotics were detected at least 1 time. Detections included analytical results that were estimated or above the minimum reporting limits. Seventy-eight percent of all detections were analyzed in samples collected downstream from municipal-wastewater effluents. For streams receiving wastewater effluents, the pharmaceuticals caffeine and para-xanthine (a degradation product of caffeine) had the greatest concentrations, 4.75 μg/L (micrograms per liter) and 0.853 μg/L, respectively. Other pharmaceuticals and their respective maximum concentrations were carbamazepine (0.516 μg/L) and ibuprofen (0.277 μg/L). For streams receiving wastewater effluents, the antibiotic azithromycin had the greatest concentration (1.65 μg/L), followed by sulfamethoxazole (1.34 μg/L), ofloxacin (0.329 μg/L), and trimethoprim (0.256 μg/L).For streams receiving runoff from animal-feeding operations, the only pharmaceuticals detected were acetaminophen, caffeine, cotinine, diphenhydramine, and carbamazepine. The maximum concentration for pharmaceuticals was 0.053 μg/L. Three streams receiving runoff from animal-feeding operations had detections of one or more antibiotic compound--oxytetracycline, sulfadimethoxine, sulfamethoxazole, and tylosin. The maximum concentration for antibiotics was 0.157 μg/L. The average number of compounds (pharmaceuticals and antibiotics) detected in sites downstream from animal-feeding operations was three. The average number of compounds detected downstream from municipal-wastewater effluents was 13.For wells used to supply livestock, four compounds were detected--two pharmaceuticals (cotinine and diphenhydramine) and two antibiotics (tylosin and sulfamethoxazole). There were five detections in all the well samples. The maximum concentration detected in well water was for cotinine, estimated to be 0.024 μg/L.Seasonal occurrence of pharmaceutical and antibiotic compounds in stream water varied by compound and site type. At four stream sites, the same compounds were detected in all four seasonal samples. At other sites, pharmaceutical or antibiotic compounds were detected only one time in seasonal samples. Winter samples collected in streams receiving municipalwastewater effluent had the greatest number of compounds detected (21). Research analytical methods were used to determine concentrations for pharmaceuticals and antibiotics. To assist in evaluating the quality of the analyses, detailed information is presented on laboratory methodology and results from qualitycontrol samples. Quality-control data include results for nine blanks, nine duplicate environmental sample pairs, and three laboratory-spiked environmental samples as well as the recoveries of compounds in laboratory surrogates and laboratory reagent spikes.

Measurement of metallic contaminants in food with a high-Tc SQUID

NASA Astrophysics Data System (ADS)

Tanaka, Saburo; Natsume, Miyuki; Uchida, Masashi; Hotta, Naoki; Matsuda, Takemasa; Spanut, Zarina A.; Hatsukade, Yoshimi

2004-04-01

We have proposed and demonstrated a high-Tc SQUID system for detecting metallic contaminants in foodstuffs. There is a demand for the development of systems for detecting not only magnetic materials but also non-magnetic materials such as Cu and aluminium in foodstuffs to ensure food safety. The system consists of a SQUID magnetometer, an excitation coil and a permanent magnet. For a non-magnetic sample, an AC magnetic field is applied during detection to induce an eddy current in the sample. For a magnetizable sample, a strong magnetic field is applied to the sample prior to the detection attempt. We were able to detect a stainless steel ball with a diameter of 0.1 mm and a Cu ball less than 1 mm in diameter, for example.

Efficient method of image edge detection based on FSVM

NASA Astrophysics Data System (ADS)

Cai, Aiping; Xiong, Xiaomei

2013-07-01

For efficient object cover edge detection in digital images, this paper studied traditional methods and algorithm based on SVM. It analyzed Canny edge detection algorithm existed some pseudo-edge and poor anti-noise capability. In order to provide a reliable edge extraction method, propose a new detection algorithm based on FSVM. Which contains several steps: first, trains classify sample and gives the different membership function to different samples. Then, a new training sample is formed by increase the punishment some wrong sub-sample, and use the new FSVM classification model for train and test them. Finally the edges are extracted of the object image by using the model. Experimental result shows that good edge detection image will be obtained and adding noise experiments results show that this method has good anti-noise.

Presence of Cryptosporidium parvum and Giardia lamblia in water samples from Southeast Asia: towards an integrated water detection system.

PubMed

Kumar, Thulasi; Abd Majid, Mohamad Azlan; Onichandran, Subashini; Jaturas, Narong; Andiappan, Hemah; Salibay, Cristina C; Tabo, Hazel A L; Tabo, Norbel; Dungca, Julieta Z; Tangpong, Jitbanjong; Phiriyasamith, Sucheep; Yuttayong, Boonyaorn; Polseela, Raxsina; Do, Binh Nhu; Sawangjaroen, Nongyao; Tan, Tian-Chye; Lim, Yvonne A L; Nissapatorn, Veeranoot

2016-01-13

Access to clean and safe drinking water that is free from pathogenic protozoan parasites, especially Cryptosporidium parvum and Giardia lamblia that cause gastrointestinal illness in humans, is still an issue in Southeast Asia (SEA). This study is the first attempt to detect the aforementioned protozoan parasites in water samples from countries in SEA, using real-time polymerase chain reaction (qPCR) assays. A total of 221 water samples of 10 l each were collected between April and October 2013 from Malaysia (53), Thailand (120), the Philippines (33), and Vietnam (15). A physicochemical analysis was conducted. The water samples were processed in accordance with the US Environmental Protection Agency's methods 1622/1623.1, microscopically observed and subsequently screened using qPCR assays. Cryptosporidium oocysts were detected in treated water samples from the Philippines (1/10), with a concentration of 0.06 ± 0.19 oocyst/L, and untreated water samples from Thailand (25/93), Malaysia (17/44), and the Philippines (11/23), with concentrations ranging from 0.13 ± 0.18 to 0.57 ± 1.41 oocyst/L. Giardia cysts were found in treated water samples from the Philippines (1/10), with a concentration of 0.02 ± 0.06 cyst/L, and in untreated water samples from Thailand (20/93), Vietnam (5/10), Malaysia (22/44), and the Philippines (16/23), with concentrations ranging from 0.12 ± 0.3 to 8.90 ± 19.65 cyst/L. The pathogens C. parvum and G. lamblia were detected using using qPCR assays by targeting the 138-bp fragment and the small subunit gene, respectively. C. parvum was detected in untreated water samples from the Philippines (1/23) and Malaysia (2/44), whilst, G. lamblia detected was detected in treated water samples from the Philippines (1/10) and in untreated water samples from Thailand (21/93), Malaysia (12/44), and the Philippines (17/23). Nitrate concentration was found to have a high positive correlation with (oo)cyst (0.993). The presence of (oo)cysts in the water samples means that there is potential risk for zoonotic disease transmission in the studied countries. Detection using qPCR is feasible for quantifying both pathogenic C. parvum and G. lamblia in large water samples.

Threshold-dependent sample sizes for selenium assessment with stream fish tissue

USGS Publications Warehouse

Hitt, Nathaniel P.; Smith, David R.

2015-01-01

Natural resource managers are developing assessments of selenium (Se) contamination in freshwater ecosystems based on fish tissue concentrations. We evaluated the effects of sample size (i.e., number of fish per site) on the probability of correctly detecting mean whole-body Se values above a range of potential management thresholds. We modeled Se concentrations as gamma distributions with shape and scale parameters fitting an empirical mean-to-variance relationship in data from southwestern West Virginia, USA (63 collections, 382 individuals). We used parametric bootstrapping techniques to calculate statistical power as the probability of detecting true mean concentrations up to 3 mg Se/kg above management thresholds ranging from 4 to 8 mg Se/kg. Sample sizes required to achieve 80% power varied as a function of management thresholds and Type I error tolerance (α). Higher thresholds required more samples than lower thresholds because populations were more heterogeneous at higher mean Se levels. For instance, to assess a management threshold of 4 mg Se/kg, a sample of eight fish could detect an increase of approximately 1 mg Se/kg with 80% power (given α = 0.05), but this sample size would be unable to detect such an increase from a management threshold of 8 mg Se/kg with more than a coin-flip probability. Increasing α decreased sample size requirements to detect above-threshold mean Se concentrations with 80% power. For instance, at an α-level of 0.05, an 8-fish sample could detect an increase of approximately 2 units above a threshold of 8 mg Se/kg with 80% power, but when α was relaxed to 0.2, this sample size was more sensitive to increasing mean Se concentrations, allowing detection of an increase of approximately 1.2 units with equivalent power. Combining individuals into 2- and 4-fish composite samples for laboratory analysis did not decrease power because the reduced number of laboratory samples was compensated for by increased precision of composites for estimating mean conditions. However, low sample sizes (<5 fish) did not achieve 80% power to detect near-threshold values (i.e., <1 mg Se/kg) under any scenario we evaluated. This analysis can assist the sampling design and interpretation of Se assessments from fish tissue by accounting for natural variation in stream fish populations.

High throughput, real-time detection of Naegleria lovaniensis in natural river water using LED-illuminated Fountain Flow Cytometry.

PubMed

Johnson, P E; Deromedi, A J; Lebaron, P; Catala, P; Havens, C; Pougnard, C

2007-09-01

To test Fountain Flow Cytometry (FFC) for the rapid and sensitive detection of Naegleria lovaniensis amoebae (an analogue for Naegleria fowleri) in natural river waters. Samples were incubated with one of two fluorescent labels to facilitate detection: ChemChrome V6, a viability indicator, and an R-phycoerytherin (RPE) immunolabel to detect N. lovaniensis specifically. The resulting aqueous sample was passed as a stream in front of a light-emitting diode, which excited the fluorescent labels. The fluorescence was detected with a digital camera as the sample flowed toward the imager. Detections of N. lovaniensis were made in inoculated samples of natural water from eight rivers in France and the United States. FFC enumeration yielded results that are consistent with other counting methods: solid-phase cytometry, flow cytometry, and hemocytometry, down to concentrations of 0.06 amoebae ml(-1), using a flow rate of 15 ml min(-1). This study supports the efficacy of using FFC for the detection of viable protozoa in natural waters and indicates that use of RPE illuminated at 530 nm and detected at 585 nm provides a satisfactory means of attenuating background. Because of the severe global public health issues with drinking water and sanitation, there is an urgent need to develop a technique for the real-time detection of viable pathogens in environmental samples at low concentrations. FFC addresses this need.

Nitrate and pesticides in ground water in the eastern San Joaquin Valley, California : occurrence and trends

USGS Publications Warehouse

Burow, Karen R.; Stork, Sylvia V.; Dubrovsky, N.M.

1998-01-01

The occurrence of nitrate and pesticides in ground water in California's eastern San Joaquin Valley may be greatly influenced by the long history of intensive farming and irrigation and the generally permeable sediments. This study, which is part of the U.S. Geological Survey National Water-Quality Assessment Program, was done to assess the quality of the ground water and to do a preliminary evaluation of the temporal trends in nitrate and pesticides in the alluvial fans of the eastern San Joaquin Valley. Ground-water samples were collected from 30 domestic wells in 1995 (each well was sampled once during 1995). The results of the analyses of these samples were related to various physical and chemical factors in an attempt to understand the processes that control the occurrence and the concentrations of nitrate and pesticides. A preliminary evaluation of the temporal trends in the occurrence and the concentration of nitrate and pesticides was done by comparing the results of the analyses of the 1995 ground-water samples with the results of the analyses of the samples collected in 1986-87 as part of the U.S. Geological Survey Regional Aquifer-System Analysis Program. Nitrate concentrations (dissolved nitrate plus nitrite, as nitrogen) in ground water sampled in 1995 ranged from less than 0.05 to 34 milligrams per liter, with a median concentration of 4.6 milligrams per liter. Nitrate concentrations exceeded the maximum contaminant level of 10 milligrams per liter (as nitrogen) in 5 of the 30 ground-water samples (17 percent), whereas 12 of the 30 samples (40 percent) had nitrate concentrations less than 3.0 milligrams per liter. The high nitrate concentrations were associated with recently recharged, well-oxygenated ground water that has been affected by agriculture (indicated by the positive correlations between nitrate, dissolved-oxygen, tritium, and specific conductance). Twelve pesticides were detected in 21 of the 30 ground-water samples (70 percent) in 1995, although only 5 pesticides were detected in more than 10 percent of the ground-water samples. All 12 pesticides were detected at concentrations below the maximum contaminant levels, except the banned soil fumigants 1,2-dibromo-3-chloropropane (3 detections) and 1,2-dibromoethane (1 detection). Atrazine and desethyl atrazine (a transformation product of atrazine) were the most frequently detected pesticides; they were detected in 11 ground-water samples. The frequent detections of atrazine and desethyl atrazine may be related either to past applications of atrazine or to recent application on rights-of-way. Simazine was detected in 10 ground-water samples and diuron was detected in 4 ground-water samples. The detections of simazine and diuron are generally consistent with their reported applications on the crops near the wells where they were detected. 1,2,3-trichloropropane, a manufacturing by-product of 1,2-dichloropropane and 1,3- dichloropropene formulations, was detected in 4 ground-water samples. The occurrence of 1,2,3-trichloropropane, 1,2-dibromo-3-chloropropane, and 1,2-dibromoethane is probably related to past use. Similar to nitrate concentrations, pesticide occurrence was positively correlated to dissolved-oxygen concentrations, indicating that areas with high dissolved-oxygen concentrations may be vulnerable to contamination by nitrate and pesticides. High dissolved-oxygen concentrations may be associated with water that has been rapidly recharged. A comparison of the concentrations and the occurrence of nitrate and pesticides between 1986-87 and 1995 indicates that nitrate concentrations may pose a greater threat to the quality of the ground-water resource in this region than pesticides, in the context of current drinking-water standards. Nitrate concentrations were significantly higher in the 1995 ground-water samples than in the 1986-87 samples collected from the same wells. Although the number of pesticide detections in 1995 is higher than the numb

Methods, compounds and systems for detecting a microorganism in a sample

DOEpatents

Colston, Jr, Bill W.; Fitch, J. Patrick; Gardner, Shea N.; Williams, Peter L.; Wagner, Mark C.

2016-09-06

Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.

Detection of image structures using the Fisher information and the Rao metric.

PubMed

Maybank, Stephen J

2004-12-01

In many detection problems, the structures to be detected are parameterized by the points of a parameter space. If the conditional probability density function for the measurements is known, then detection can be achieved by sampling the parameter space at a finite number of points and checking each point to see if the corresponding structure is supported by the data. The number of samples and the distances between neighboring samples are calculated using the Rao metric on the parameter space. The Rao metric is obtained from the Fisher information which is, in turn, obtained from the conditional probability density function. An upper bound is obtained for the probability of a false detection. The calculations are simplified in the low noise case by making an asymptotic approximation to the Fisher information. An application to line detection is described. Expressions are obtained for the asymptotic approximation to the Fisher information, the volume of the parameter space, and the number of samples. The time complexity for line detection is estimated. An experimental comparison is made with a Hough transform-based method for detecting lines.

Application of loop-mediated isothermal amplification assay in the detection of herpesvirus of turkey (FC 126 strain) from chicken samples in Nigeria

PubMed Central

Adedeji, A. J.; Abdu, P. A.; Luka, P. D.; Owoade, A. A.; Joannis, T. M.

2017-01-01

Aim: This study was designed to optimize and apply the use of loop-mediated isothermal amplification (LAMP) as an alternative to conventional polymerase chain reaction (PCR) for the detection of herpesvirus of turkeys (HVT) (FC 126 strain) in vaccinated and non-vaccinated poultry in Nigeria. Materials and Methods: HVT positive control (vaccine) was used for optimization of LAMP using six primers that target the HVT070 gene sequence of the virus. These primers can differentiate HVT, a Marek’s disease virus (MDV) serotype 3 from MDV serotypes 1 and 2. Samples were collected from clinical cases of Marek’s disease (MD) in chickens, processed and subjected to LAMP and PCR. Results: LAMP assay for HVT was optimized. HVT was detected in 60% (3/5) and 100% (5/5) of the samples analyzed by PCR and LAMP, respectively. HVT was detected in the feathers, liver, skin, and spleen with average DNA purity of 3.05-4.52 μg DNA/mg (A260/A280) using LAMP. Conventional PCR detected HVT in two vaccinated and one unvaccinated chicken samples, while LAMP detected HVT in two vaccinated and three unvaccinated corresponding chicken samples. However, LAMP was a faster and simpler technique to carry out than PCR. Conclusion: LAMP assay for the detection of HVT was optimized. LAMP and PCR detected HVT in clinical samples collected. LAMP assay can be a very good alternative to PCR for detection of HVT and other viruses. This is the first report of the use of LAMP for the detection of viruses of veterinary importance in Nigeria. LAMP should be optimized as a diagnostic and research tool for investigation of poultry diseases such as MD in Nigeria. PMID:29263603

Factors Affecting Detection of Hepatitis E Virus on Canadian Retail Pork Chops and Pork Livers Assayed Using Real-Time RT-PCR.

PubMed

Wilhelm, B J; Leblanc, D; Avery, B; Pearl, D L; Houde, A; Rajić, A; McEwen, S A

2016-03-01

We collected 599 Canadian retail pork chops and 283 pork livers routinely (usually weekly) from April 2011 to March 2012 using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) retail sampling platform. Samples were assayed using validated real-time (q) reverse transcriptase polymerase chain reaction (RT-PCR) and nested classical RT-PCR for the detection of hepatitis E virus (HEV), porcine enteric calicivirus (PEC) and rotavirus (RV). The presence of Escherichia coli, Salmonella spp. and Campylobacter spp. was measured on a subset of our samples. Exact logistic regression models were fitted for predictors for HEV detection, for each assay. For both assays, sample type (pork chop versus liver) was a significant predictor for HEV RNA detection. For nested classical RT-PCR but not qRT-PCR, region of sample collection was a significant predictor (P = 0.008) of HEV detection. Odds of HEV detection were greatest in spring relative to other seasons. E. coli was a significant predictor for HEV RNA detection using the qRT-PCR (P = 0.03). Overall, the prevalence of E. coli, Salmonella spp. and Campylobacter spp. was significantly greater than HEV, PEC or RV on our retail pork samples. Our sparse data set for the detection of PEC and RV precluded modelling of risk factors for the detection of these viruses. © 2015 Zoonoses and Public Health © 2015 Her Majesty the Queen in Right of Canada Reproduced with the permission of the Minister of the Public Health Agency of Canada.

[Isolation and identification of Cronobacter (Enterobacter sakazakii) strains from food].

PubMed

Dong, Xiaohui; Li, Chengsi; Wu, Qingping; Zhang, Jumei; Mo, Shuping; Guo, Weipeng; Yang, Xiaojuan; Xu, Xiaoke

2013-05-04

This study aimed to detect and quantify Cronobacter in 300 powdered milk samples and 50 non-powdered milk samples. Totally, 24 Cronobacter (formerly Enterobacter sakazakii) strains isolated from powdered milk and other foods were identified and confirmed. Cronobacter strains were detected quantitatively using most probable number (MPN) method and molecular detection method. We identified 24 Cronobacter strains using biochemical patterns, including indole production and dulcitol, malonate, melezitose, turanose, and myo-Inositol utilization. Of the 24 strains, their 16S rRNA genes were sequenced, and constructed phylogenetic tree by N-J (Neighbour-Joining) with the 16S rRNA gene sequences of 17 identified Cronobacter strains and 10 non-Cronobacter strains. Quantitative detection showed that Cronobacter strains were detected in 23 out of 350 samples yielding 6.6% detection rate. Twenty-four Cronobacter strains were isolated from 23 samples and the Cronobacter was more than 100 MPN/100g in 4 samples out of 23 samples. The 24 Cronobacter spp. isolates strains were identified and confirmed, including 19 Cronobacter sakazakii strains, 2 C. malonaticus strains, 2 C. dubliensis subsp. lactaridi strains, and 1 C. muytjensii strain. The combination of molecular detection method and most probable number (MPN) method could be suitable for the detection of Cronobacter in powdered milk, with low rate of contamination and high demand of quantitative detection. 24 isolated strains were confirmed and identified by biochemical patterns and molecular technology, and C. sakazakii could be the dominant species. The problem of Cronobacter in powdered milk should be a hidden danger to nurseling, and should catch the government and consumer's attention.

Sensitivity of the ViroSeq HIV-1 Genotyping System for Detection of the K103N Resistance Mutation in HIV-1 Subtypes A, C, and D

PubMed Central

Church, Jessica D.; Jones, Dana; Flys, Tamara; Hoover, Donald; Marlowe, Natalia; Chen, Shu; Shi, Chanjuan; Eshleman, James R.; Guay, Laura A.; Jackson, J. Brooks; Kumwenda, Newton; Taha, Taha E.; Eshleman, Susan H.

2006-01-01

The US Food and Drug Administration-cleared ViroSeq HIV-1 Genotyping System (ViroSeq) and other population sequencing-based human immunodeficiency virus type 1 (HIV-1) genotyping methods detect antiretroviral drug resistance mutations present in the major viral population of a test sample. These assays also detect some mutations in viral variants that are present as mixtures. We compared detection of the K103N nevirapine resistance mutation using ViroSeq and a sensitive, quantitative point mutation assay, LigAmp. The LigAmp assay measured the percentage of K103N-containing variants in the viral population (percentage of K103N). We analyzed 305 samples with HIV-1 subtypes A, C, and D collected from African women after nevirapine administration. ViroSeq detected K103N in 100% of samples with >20% K103N, 77.8% of samples with 10 to 20% K103N, 71.4% of samples with 5 to 10% K103N, and 16.9% of samples with 1 to 5% K103N. The sensitivity of ViroSeq for detection of K103N was similar for subtypes A, C, and D. These data indicate that the ViroSeq system reliably detects the K103N mutation at levels above 20% and frequently detects the mutation at lower levels. Further studies are needed to compare the sensitivity of different assays for detection of HIV-1 drug resistance mutations and to determine the clinical relevance of HIV-1 minority variants. PMID:16931582

Pesticides in the atmosphere of the Mississippi River Valley, part II - Air

USGS Publications Warehouse

Foreman, W.T.; Majewski, M.S.; Goolsby, D.A.; Wiebe, F.W.; Coupe, R.H.

2000-01-01

Weekly composite air samples were collected from early April through to mid-September 1995 at three paired urban and agricultural sites along the Mississippi River region of the Midwestern United States. The paired sampling sites were located in Mississippi, Iowa, and Minnesota. A background site, removed from dense urban and agricultural areas, was located on the shore of Lake Superior in Michigan. Each sample was analyzed for 49 compounds; of these, 21 of 26 herbicides, 13 of 19 insecticides, and 4 of 4 related transformation products were detected during the study, with most pesticides detected in more than one sample. The maximum number of pesticides detected in an air sample was 18. Herbicides were the predominant type of pesticide detected at every site. Detection frequencies of most herbicides were similar at the urban and agricultural sites in Iowa and Minnesota. In Mississippi, herbicides generally were detected more frequently at the agricultural site. The insecticides chlorpyrifos, diazinon, and carbaryl, which are used in agricultural and non-agricultural settings, were detected more frequently in urban sites than agricultural sites in Mississippi and Iowa. Methyl parathion was detected in 70% of the samples from the Mississippi agricultural site and at the highest concentration (62 ng/m3 air) of any insecticide measured in the study. At the background site, dacthal (100%), atrazine (35%), cyanazine (22%), and the (primarily atrazine) triazine transformation products CIAT (35%) and CEAT (17%) were detected most frequently, suggesting their potential for long-range atmospheric transport. Copyright (C) 2000 Elsevier Science B.V.

Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health.

PubMed

King, Dawn N; Donohue, Maura J; Vesper, Stephen J; Villegas, Eric N; Ware, Michael W; Vogel, Megan E; Furlong, Edward F; Kolpin, Dana W; Glassmeyer, Susan T; Pfaller, Stacy

2016-08-15

An occurrence survey was conducted on selected pathogens in source and treated drinking water collected from 25 drinking water treatment plants (DWTPs) in the United States. Water samples were analyzed for the protozoa Giardia and Cryptosporidium (EPA Method 1623); the fungi Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus (quantitative PCR [qPCR]); and the bacteria Legionella pneumophila (qPCR), Mycobacterium avium, M. avium subspecies paratuberculosis, and Mycobacterium intracellulare (qPCR and culture). Cryptosporidium and Giardia were detected in 25% and in 46% of the source water samples, respectively (treated waters were not tested). Aspergillus fumigatus was the most commonly detected fungus in source waters (48%) but none of the three fungi were detected in treated water. Legionella pneumophila was detected in 25% of the source water samples but in only 4% of treated water samples. M. avium and M. intracellulare were both detected in 25% of source water, while all three mycobacteria were detected in 36% of treated water samples. Five species of mycobacteria, Mycobacterium mucogenicum, Mycobacterium phocaicum, Mycobacterium triplex, Mycobacterium fortuitum, and Mycobacterium lentiflavum were cultured from treated water samples. Although these DWTPs represent a fraction of those in the U.S., the results suggest that many of these pathogens are widespread in source waters but that treatment is generally effective in reducing them to below detection limits. The one exception is the mycobacteria, which were commonly detected in treated water, even when not detected in source waters. Published by Elsevier B.V.

Pharmaceuticals and other organic wastewater contaminants within a leachate plume downgradient of a municipal landfill

USGS Publications Warehouse

Barnes, Kimberlee K.; Christenson, Scott C.; Kolpin, Dana W.; Focazio, Michael J.; Furlong, Edward T.; Zaugg, Steven D.; Meyer, Michael T.; Barber, Larry B.

2004-01-01

Ground water samples collected from the Norman Landfill research site in central Oklahoma were analyzed as part of the U.S. Geological Survey (USGS) Toxic Substances Hydrology Program's national reconnaissance of pharmaceuticals and other organic waste water contaminants (OWCs) in ground water. Five sites, four of which are located downgradient of the landfill, were sampled in 2000 and analyzed for 76 OWCs using four research methods developed by the USGS. OWCs were detected in water samples from all of the sites sampled, with 22 of the 76 OWCs being detected at least once. Cholesterol (a plant and animal steroid), was detected at all five sites and was the only compound detected in a well upgradient of the landfill. N,Ndiethyltoluamide (DEET used in insect repellent) and tri(2-chloroethyl) phosphate (fire-retardant) were detected in water samples from all four sites located within the landfill-derived leachate plume. The sites closest to the landfill had more detections and greater concentrations of each of the detected compounds than sites located farther away. Detection of multiple OWCs occurred in the four sites located within the leachate plume, with a minimum of four and a maximum of 17 OWCs detected. Because the landfill was established in the 1920s and closed in 1985, many compounds detected in the leachate plume were likely disposed of decades ago. These results indicate the potential for long-term persistence and transport of some OWCs in ground water.

Digital Holographic Microscopy, a Method for Detection of Microorganisms in Plume Samples from Enceladus and Other Icy Worlds

PubMed Central

Bedrossian, Manuel; Lindensmith, Chris

2017-01-01

Abstract Detection of extant microbial life on Earth and elsewhere in the Solar System requires the ability to identify and enumerate micrometer-scale, essentially featureless cells. On Earth, bacteria are usually enumerated by culture plating or epifluorescence microscopy. Culture plates require long incubation times and can only count culturable strains, and epifluorescence microscopy requires extensive staining and concentration of the sample and instrumentation that is not readily miniaturized for space. Digital holographic microscopy (DHM) represents an alternative technique with no moving parts and higher throughput than traditional microscopy, making it potentially useful in space for detection of extant microorganisms provided that sufficient numbers of cells can be collected. Because sample collection is expected to be the limiting factor for space missions, especially to outer planets, it is important to quantify the limits of detection of any proposed technique for extant life detection. Here we use both laboratory and field samples to measure the limits of detection of an off-axis digital holographic microscope (DHM). A statistical model is used to estimate any instrument's probability of detection at various bacterial concentrations based on the optical performance characteristics of the instrument, as well as estimate the confidence interval of detection. This statistical model agrees well with the limit of detection of 103 cells/mL that was found experimentally with laboratory samples. In environmental samples, active cells were immediately evident at concentrations of 104 cells/mL. Published estimates of cell densities for Enceladus plumes yield up to 104 cells/mL, which are well within the off-axis DHM's limits of detection to confidence intervals greater than or equal to 95%, assuming sufficient sample volumes can be collected. The quantitative phase imaging provided by DHM allowed minerals to be distinguished from cells. Off-axis DHM's ability for rapid low-level bacterial detection and counting shows its viability as a technique for detection of extant microbial life provided that the cells can be captured intact and delivered to the sample chamber in a sufficient volume of liquid for imaging. Key Words: In situ life detection—Extant microorganisms—Holographic microscopy—Ocean Worlds—Enceladus—Imaging. Astrobiology 17, 913–925. PMID:28708412

A comparison of passive and active acoustic sampling for a bat community impacted by White-nose syndrome

USGS Publications Warehouse

Coleman, Laci S.; Ford, W. Mark; Dobony, Christopher A.; Britzke, Eric R.

2014-01-01

In the summers of 2011 and 2012, we compared passive and active acoustic sampling for bats at 31 sites at Fort Drum Military Installation, New York. We defined active sampling as acoustic sampling that occurred in 30-min intervals between the hours of sunset and 0200 with a user present to manipulate the directionality of the microphone. We defined passive sampling as acoustic sampling that occurred over a 12-h period (1900–0700 hours) without a user present and with the microphone set in a predetermined direction. We detected seven of the nine possible species at Fort Drum, including the federally endangered Indiana bat Myotis sodalis, the proposed-for-listing northern bat M. septentrionalis, the little brown bat M. lucifugus, and the big brown bat Eptesicus fuscus, which are impacted by white-nose syndrome (WNS); and the eastern red bat Lasiurus borealis, the hoary bat L. cinereus, and the silver-haired bat Lasionycteris noctivagans, which are not known to be impacted by WNS. We did not detect two additional WNS-impacted species known to historically occur in the area: the eastern small-footed bat Myotis leibii and the tri-colored bat Perimyotis subflavus. Single-season occupancy models revealed lower detection probabilities of all detected species using active sampling versus passive sampling. Additionally, overall detection probabilities declined in detected WNS-impacted species between years. A paired t-test of simultaneous sampling on 21 occasions revealed that overall recorded foraging activity per hour was greater using active than passive sampling for big brown bats and greater using passive than active sampling for little brown bats. There was no significant difference in recorded activity between methods for other WNS-impacted species, presumably because these species have been so reduced in number that their “apparency” on the landscape is lower. Finally, a cost analysis of standard passive and active sampling protocols revealed that passive sampling is substantially more cost-effective than active sampling per hour of data collection. We recommend passive sampling over active sampling methodologies as they are defined in our study for detection probability and/or occupancy studies focused on declining bat species in areas that have experienced severe WNS-associated impacts.

Salmonella enteritidis surveillance by egg immunology: impact of the sampling scheme on the release of contaminated table eggs.

PubMed

Klinkenberg, Don; Thomas, Ekelijn; Artavia, Francisco F Calvo; Bouma, Annemarie

2011-08-01

Design of surveillance programs to detect infections could benefit from more insight into sampling schemes. We address the effect of sampling schemes for Salmonella Enteritidis surveillance in laying hens. Based on experimental estimates for the transmission rate in flocks, and the characteristics of an egg immunological test, we have simulated outbreaks with various sampling schemes, and with the current boot swab program with a 15-week sampling interval. Declaring a flock infected based on a single positive egg was not possible because test specificity was too low. Thus, a threshold number of positive eggs was defined to declare a flock infected, and, for small sample sizes, eggs from previous samplings had to be included in a cumulative sample to guarantee a minimum flock level specificity. Effectiveness of surveillance was measured by the proportion of outbreaks detected, and by the number of contaminated table eggs brought on the market. The boot swab program detected 90% of the outbreaks, with 75% fewer contaminated eggs compared to no surveillance, whereas the baseline egg program (30 eggs each 15 weeks) detected 86%, with 73% fewer contaminated eggs. We conclude that a larger sample size results in more detected outbreaks, whereas a smaller sampling interval decreases the number of contaminated eggs. Decreasing sample size and interval simultaneously reduces the number of contaminated eggs, but not indefinitely: the advantage of more frequent sampling is counterbalanced by the cumulative sample including less recently laid eggs. Apparently, optimizing surveillance has its limits when test specificity is taken into account. © 2011 Society for Risk Analysis.

Ground-water-quality data for selected wells in the Beaver Creek watershed, West Tennessee

USGS Publications Warehouse

Williams, S.D.

1996-01-01

In 1993 the U.S. Geological Survey, in cooperation with the Tennessee Department of Environment and Conservation (TDEC), began an investigation of the quality of ground water in the Beaver Creek watershed in West Tennessee. A total of 408 water samples were collected from 91 wells during 5 sampling periods in 1994. Water samples were analyzed for selected water-quality properties, fecal coliform and streptococci bacteria, nutrients, and major inorganic constituents. Selected well- construction data and information on potential sources of contamination were also collected for the 91 wells sampled. Nitrate concentrations (measured as NO3) ranged from a detection limit of 0.1 to 91 milligrams per liter (mg/L). Nitrate concentrations exceeding 13 mg/L were detected in 71 of the samples collected. Nitrate concentrations in water samples collected from three wells exceeded the TDEC primary drinking water standard of 44 mg/L for nitrate (measured as NO3). Nitrite (measured as NO2), ammonium (measured as NH4), and orthophosphate (measured as PO4) concentrations in samples were generally less than 0.1 mg/L (detection limit). Fecal coliform bacteria were detected in 33 of the 408 water samples collected. Samples from 21 of the 91 wells contained fecal coliform bacteria during one or more of the five sampling periods. Fecal streptococci bacteria were detected in 123 of the 408 samples. Samples from 59 wells contained fecal streptococci bacteria during one or more of the five sampling periods.

Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.

PubMed

Kageyama, A; Benno, Y

2001-01-01

PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species-specific primers, would allow rapid detection of Eubacterium species in human feces.

Feasibility and acceptance of cervicovaginal self-sampling within the German National Cohort (Pretest 2).

PubMed

Castell, Stefanie; Krause, G; Schmitt, M; Pawlita, M; Deleré, Y; Obi, N; Flesch-Janys, D; Kemmling, Y; Kaufmann, A M

2014-11-01

Within the German National Cohort (GNC) 100,000 adult women in Germany will be comprehensively interviewed and examined. While women's health is addressed in the basic interview, direct detection of cervicovaginal microbial colonisation or infection is not part of the examination protocol. In a pilot project the feasibility of female study participants of the GNC collecting a cervicovaginal lavage at home without having to involve a gynecologist or other medical personnel was thus investigated. The ability of the procedure to detect vaginal microbes and conditions including human papillomavirus (HPV), Chlamydia trachomatis and bacterial vaginosis (BV) were also explored. This cross-sectional study was conducted in two study centers (Hamburg and Hanover) of the GNC during Pretest 2 in 2012 as an add-on module to the main program of the National Cohort. Participants were randomly selected through the population registration office. After providing written informed consent at the study center, participants self-collected a cervicovaginal lavage (Delphi Screener™) at home following written instructions. Participants mailed samples and acceptability questionnaires to the laboratory and the study center, respectively. Acceptability of self-sampling was categorized as consent, partial consent and rejection. The samples were analyzed by multiplex HPV genotyping for the presence of 27 mucosal HPV subtypes. To detect other pathogens "Sexually Transmitted Infection Profiling" (STIP) was used, a novel multiplex polymerase chain reaction (PCR) for various vaginally occurring pathogens/conditions coupled with subsequent bead-based Luminex(®) hybridization. Human beta-globin and DNA polymerase alpha (PolA) sequences were used as positive controls for the detection of human DNA during HPV detection and STIP, respectively. The participation based on the proportion of all women in Pretest 2 who could take part in the add-on Pretest 2 was 67.3 % (109 out of 162). The age of participants ranged from 20 to 69 years. The self-reported median duration of the collection of the lavage was 5 min. Analysis of the questionnaires (n = 108) revealed that the self-sampling of a cervicovaginal lavage was acceptable to 98 % of women (106 out of 108), and considered to be easy by 89 % (96 out of 108) as well as user-friendly by 96 % of the women (104 out of 108). Human beta-globin and PolA as markers for human DNA and sample quality were detected in all samples analyzed while HPV as a marker for pathogen detectability was identified in 18 out of 109 samples. Of the 107 samples tested with STIP as a second marker for pathogen detectability, 5 samples were excluded from statistical analyses on bacterial colonization because of signs in the laboratory results of the use of antibiotics. For the computation of the possible occurrence of bacterial vaginosis and candidiasis 7 and 8 samples, respectively, were excluded because of low signal intensities resulting in an evaluation of 95 or 94 samples, respectively. Ureaplasma parvum was detected in 22 out of 102 samples, BV in 14 out of 95 samples and candidiasis in 13 out of 94 samples. Chlamydia trachomatis was not detected in any sample. The feasibility study on cervicovaginal self-sampling indicates that this form of biosampling was very well accepted within the framework of the GNC and feasible in terms of pathogen detection. Its further application in the GNC would allow investigation of transience and persistence, or long-term effects of vaginal (co)infections and colonization.

Use of the ecf1 gene to detect Shiga toxin-producing Escherichia coli in beef samples.

PubMed

Livezey, Kristin W; Groschel, Bettina; Becker, Michael M

2015-04-01

Escherichia coli O157:H7 and six serovars (O26, O103, O121, O111, O145, and O45) are frequently implicated in severe clinical illness worldwide. Standard testing methods using stx, eae, and O serogroup-specific gene sequences for detecting the top six non-O157 STEC bear the disadvantage that these genes may reside, independently, in different nonpathogenic organisms, leading to false-positive results. The ecf operon has previously been identified in the large enterohemolysin-encoding plasmid of eae-positive Shiga toxin-producing E. coli (STEC). Here, we explored the utility of the ecf operon as a single marker to detect eae-positive STEC from pure broth and primary meat enrichments. Analysis of 501 E. coli isolates demonstrated a strong correlation (99.6%) between the presence of the ecf1 gene and the combined presence of stx, eae, and ehxA genes. Two large studies were carried out to determine the utility of an ecf1 detection assay to detect non-O157 STEC strains in enriched meat samples in comparison to the results using the U. S. Department of Agriculture Food Safety and Inspection Service (FSIS) method that detects stx and eae genes. In ground beef samples (n = 1,065), the top six non-O157 STEC were detected in 4.0% of samples by an ecf1 detection assay and in 5.0% of samples by the stx- and eae-based method. In contrast, in beef samples composed largely of trim (n = 1,097), the top six non-O157 STEC were detected at 1.1% by both methods. Estimation of false-positive rates among the top six non-O157 STEC revealed a lower rate using the ecf1 detection method (0.5%) than using the eae and stx screening method (1.1%). Additionally, the ecf1 detection assay detected STEC strains associated with severe illness that are not included in the FSIS regulatory definition of adulterant STEC.

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

PubMed Central

Jun, Goo; Flickinger, Matthew; Hetrick, Kurt N.; Romm, Jane M.; Doheny, Kimberly F.; Abecasis, Gonçalo R.; Boehnke, Michael; Kang, Hyun Min

2012-01-01

DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies. PMID:23103226

Detection of oral HPV infection - Comparison of two different specimen collection methods and two HPV detection methods.

PubMed

de Souza, Marjorie M A; Hartel, Gunter; Whiteman, David C; Antonsson, Annika

2018-04-01

Very little is known about the natural history of oral HPV infection. Several different methods exist to collect oral specimens and detect HPV, but their respective performance characteristics are unknown. We compared two different methods for oral specimen collection (oral saline rinse and commercial saliva kit) from 96 individuals and then analyzed the samples for HPV by two different PCR detection methods (single GP5+/6+ PCR and nested MY09/11 and GP5+/6+ PCR). For the oral rinse samples, the oral HPV prevalence was 10.4% (GP+ PCR; 10% repeatability) vs 11.5% (nested PCR method; 100% repeatability). For the commercial saliva kit samples, the prevalences were 3.1% vs 16.7% with the GP+ PCR vs the nested PCR method (repeatability 100% for both detection methods). Overall the agreement was fair or poor between samples and methods (kappa 0.06-0.36). Standardizing methods of oral sample collection and HPV detection would ensure comparability between future oral HPV studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Point detection of bacterial and viral pathogens using oral samples

NASA Astrophysics Data System (ADS)

Malamud, Daniel

2008-04-01

Oral samples, including saliva, offer an attractive alternative to serum or urine for diagnostic testing. This is particularly true for point-of-use detection systems. The various types of oral samples that have been reported in the literature are presented here along with the wide variety of analytes that have been measured in saliva and other oral samples. The paper focuses on utilizing point-detection of infectious disease agents, and presents work from our group on a rapid test for multiple bacterial and viral pathogens by monitoring a series of targets. It is thus possible in a single oral sample to identify multiple pathogens based on specific antigens, nucleic acids, and host antibodies to those pathogens. The value of such a technology for detecting agents of bioterrorism at remote sites is discussed.

BEVACIZUMAB LEVELS IN BREAST MILK AFTER LONG-TERM INTRAVITREAL INJECTIONS.

PubMed

McFarland, Trevor J; Rhoads, Andrew D; Hartzell, Matthew; Emerson, Geoffrey G; Bhavsar, Abdhish R; Stout, J Timothy

2015-08-01

The purpose of this study is to determine whether bevacizumab is detectable in the breast milk of nursing mothers. Breast milk samples were collected from 2 patients receiving monthly intravitreal bevacizumab injections for choroidal neovascularization over the course of 16 months. Enzyme-linked immunosorbent assay and Western blot analysis was used to determine the levels of bevacizumab in the milk samples. An enzyme-linked immunosorbent assay was developed using antibodies specific to bevacizumab in which the sensitivity threshold was 3 ng/mL. All breast milk samples assayed from the two patients actively undergoing treatment did not have detectable levels of bevacizumab. Samples collected 1.5 hours and 7 hours after an injection and 2 randomly chosen samples were negative by Western blot analysis. A sensitive assay to detect bevacizumab in breast milk samples assayed suggests that intravitreal injections do not result in detectable bevacizumab in breast milk.

Apparatus for chemical amplification based on fluid partitioning in an immiscible liquid

DOEpatents

Anderson, Brian L [Lodi, CA; Colston, Bill W [San Ramon, CA; Elkin, Christopher J [San Ramon, CA

2012-05-08

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

Method for chemical amplification based on fluid partitioning in an immiscible liquid

DOEpatents

Anderson, Brian L.; Colston, Bill W.; Elkin, Christopher J.

2015-06-02

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

Method for chemical amplification based on fluid partitioning in an immiscible liquid

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

Anderson, Brian L.; Colston, Bill W.; Elkin, Christopher J.

A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

Pesticides in rain in four agricultural watersheds in the United States

USGS Publications Warehouse

Vogel, J.R.; Majewski, M.S.; Capel, P.D.

2008-01-01

Rainfall samples were collected during the 2003 and 2004 growing seasons at four agricultural locales across the USA in Maryland, Indiana, Nebraska, and California. The samples were analyzed for 21 insecticides, 18 herbicides, three fungicides, and 40 pesticide degradates. Data from all sites combined show that 7 of the 10 most frequently detected pesticides were herbicides, with atrazine (70%) and metolachlor (83%) detected at every site. Dacthal, acetochlor, simazine, alachlor, and pendimethalin were detected in more than 50% of the samples. Chlorpyrifos, carbaryl, and diazinon were the only insecticides among the 10 most frequently detected compounds. Of the remaining pesticide parent compounds, 18 were detected in fewer than 30% of the samples, and 13 were not detected. The most frequently detected degradates were deethylatrazine; the oxygen analogs (OAs) of the organophosphorus insecticides chlorpyrifos, diazinon, and malathion; and 1-napthol (degradate of carbaryl). Deethylatrazine was detected in nearly 70% of the samples collected in Maryland, Indiana, and Nebraska but was detected only once in California. The OAs of chlorpyrifos and diazinon were detected primarily in California. Degradates of the acetanilide herbicides were rarely detected in rain, indicating that they are not formed in the atmosphere or readily volatilized from soils. Herbicides accounted for 91 to 98% of the total pesticide mass deposited by rain except in California, where insecticides accounted for 61% in 2004. The mass of pesticides deposited by rainfall was estimated to be less than 2% of the total applied in these agricultural areas. Copyright ?? 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Effects of Sampling and Spatio/Temporal Granularity in Traffic Monitoring on Anomaly Detectability

NASA Astrophysics Data System (ADS)

Ishibashi, Keisuke; Kawahara, Ryoichi; Mori, Tatsuya; Kondoh, Tsuyoshi; Asano, Shoichiro

We quantitatively evaluate how sampling and spatio/temporal granularity in traffic monitoring affect the detectability of anomalous traffic. Those parameters also affect the monitoring burden, so network operators face a trade-off between the monitoring burden and detectability and need to know which are the optimal paramter values. We derive equations to calculate the false positive ratio and false negative ratio for given values of the sampling rate, granularity, statistics of normal traffic, and volume of anomalies to be detected. Specifically, assuming that the normal traffic has a Gaussian distribution, which is parameterized by its mean and standard deviation, we analyze how sampling and monitoring granularity change these distribution parameters. This analysis is based on observation of the backbone traffic, which exhibits spatially uncorrelated and temporally long-range dependence. Then we derive the equations for detectability. With those equations, we can answer the practical questions that arise in actual network operations: what sampling rate to set to find the given volume of anomaly, or, if the sampling is too high for actual operation, what granularity is optimal to find the anomaly for a given lower limit of sampling rate.

Methods for simultaneous detection of the cyanotoxins BMAA, DABA, and anatoxin-a in environmental samples.

PubMed

Al-Sammak, Maitham Ahmed; Hoagland, Kyle D; Snow, Daniel D; Cassada, David

2013-12-15

Blue-green algae, also known as cyanobacteria, can produce several different groups of toxins in the environment including hepatotoxins (microcystins), neurotoxic non-protein amino acids β-methylamino-l-alanine (BMAA), and 2,4-diaminobutyric (DABA), as well as the bicyclic amine alkaloid anatoxin-a. Few studies have addressed the methods necessary for an accurate determination of cyanotoxins in environmental samples, and none have been published that can detect these cyanotoxins together in a single sample. Cyanotoxins occur in a wide range of environmental samples including water, fish, and aquatic plant samples. Using polymeric cation exchange solid phase extraction (SPE) coupled with liquid chromatography and fluorescence detection (HPLC/FD), and liquid chromatography ion trap tandem mass spectrometry (LC/MS/MS), these compounds can for the first time be simultaneously quantified in a variety of environmental sample types. The extraction method for biological samples can distinguish bound and free cyanotoxins. Detection limits for water ranged from 5 to 7 μg/L using HPLC/FD, while detection limits for and LC/MS were in the range of 0.8-3.2 μg/L. Copyright © 2013 Elsevier Ltd. All rights reserved.

Comparison of traditional and molecular analytical methods for detecting biological agents in raw and drinking water following ultrafiltration

USGS Publications Warehouse

Francy, D.S.; Bushon, R.N.; Brady, A.M.G.; Bertke, E.E.; Kephart, C.M.; Likirdopulos, C.A.; Mailot, B.E.; Schaefer, F. W.; Lindquist, H.D. Alan

2009-01-01

Aims: To compare the performance of traditional methods to quantitative polymerase chain reaction (qPCR) for detecting five biological agents in large-volume drinking-water samples concentrated by ultrafiltration (UF). Methods and Results: Drinking-water samples (100 l) were seeded with Bacillus anthracis, Cryptospordium parvum, Francisella tularensis, Salmonella Typhi, and Vibrio cholerae and concentrated by UF. Recoveries by traditional methods were variable between samples and between some replicates; recoveries were not determined by qPCR. Francisella tularensis and V. cholerae were detected in all 14 samples after UF, B. anthracis was detected in 13, and C. parvum was detected in 9 out of 14 samples. Numbers found by qPCR after UF were significantly or nearly related to those found by traditional methods for all organisms except for C. parvum. A qPCR assay for S. Typhi was not available. Conclusions: qPCR can be used to rapidly detect biological agents after UF as well as traditional methods, but additional work is needed to improve qPCR assays for several biological agents, determine recoveries by qPCR, and expand the study to other areas. Significance and Impact of the Study: To our knowledge, this is the first study to compare the use of traditional and qPCR methods to detect biological agents in large-volume drinking-water samples. ?? 2009 The Society for Applied Microbiology.

Sensitivity of seven PCRs for early detection of koi herpesvirus in experimentally infected carp, Cyprinus carpio L., by lethal and non-lethal sampling methods.

PubMed

Monaghan, S J; Thompson, K D; Adams, A; Bergmann, S M

2015-03-01

Koi herpesvirus (KHV) causes an economically important, highly infectious disease in common carp and koi, Cyprinus carpio L. Since the occurrence of mass mortalities worldwide, highly specific and sensitive molecular diagnostic methods have been developed for KHV detection. The sensitivity and reliability of these assays have essentially focused at the detection of low viral DNA copy numbers during latent or persistent infections. However, the efficacy of these assays has not been investigated with regard to low-level viraemia during acute infection stages. This study was conducted to compare the sensitivity of seven different polymerase chain reaction (PCR) assays to detect KHV during the first hours and days post-infection (hpi; dpi), using lethal and non-lethal sampling methods. The results highlight the limitations of the assays for detecting virus during the first 4 dpi despite rapid mortality in experimentally infected carp. False-negative results were associated with time post-infection and the tissue sampled. Non-lethal sampling appears effective for KHV screening, with efficient detection in mucus samples obtained from external swabs during this early infection period (<5 dpi), while biopsies from gills and kidney were negative using the same PCR assays. Non-lethal sampling may improve the reliability of KHV detection in subclinical, acutely infected carp. © 2014 John Wiley & Sons Ltd.

Performance of polymerase chain reaction for the diagnosis of cystic echinococcosis using serum, urine, and cyst fluid samples

PubMed Central

Chaya, DR; Parija, Subhash Chandra

2014-01-01

Introduction: Cystic echinococcosis (CE) is a chronic zoonosis which presents with variable clinical manifestations. Currently the diagnosis of this disease is based on radiological findings and serological tests which lack specificity. Although antigen detection from the cyst fluid is the most specific, it is seldom done due to the complications involved. Detecting the presence of Echinococcus granulosus specific deoxyribonucleic acid (DNA) by the polymerase chain reaction (PCR) could provide a definitive diagnosis of CE. Materials and Methods: An in-house PCR assay was devised to detect E. granulosus specific DNA in serum, urine and hydatid cyst fluid. The ability of the PCR to detect E. granulosus in the above mentioned samples were observed in comparison with other antigen and antibody detection tests. Results: Serum samples from surgically confirmed patients of CE with ruptured cysts contained the corresponding DNA while the in the majority of cases who had an intact cyst had no DNA of E. granulosus in their serum. DNA of E. granulosus was not found to be excreted in urine. PCR performed equal to antigen detection ELISA while testing hydatid cyst fluid samples. Conclusions: Serum and urine might not serve as useful samples for the molecular diagnosis of cystic echinococcosis. However, PCR can be useful on serum samples to detect ruptured hydatid cysts and on hydatid cyst fluid to confirm the parasitic diagnosis. PMID:24754027

Performance of polymerase chain reaction for the diagnosis of cystic echinococcosis using serum, urine, and cyst fluid samples.

PubMed

Chaya, Dr; Parija, Subhash Chandra

2014-01-01

Cystic echinococcosis (CE) is a chronic zoonosis which presents with variable clinical manifestations. Currently the diagnosis of this disease is based on radiological findings and serological tests which lack specificity. Although antigen detection from the cyst fluid is the most specific, it is seldom done due to the complications involved. Detecting the presence of Echinococcus granulosus specific deoxyribonucleic acid (DNA) by the polymerase chain reaction (PCR) could provide a definitive diagnosis of CE. An in-house PCR assay was devised to detect E. granulosus specific DNA in serum, urine and hydatid cyst fluid. The ability of the PCR to detect E. granulosus in the above mentioned samples were observed in comparison with other antigen and antibody detection tests. Serum samples from surgically confirmed patients of CE with ruptured cysts contained the corresponding DNA while the in the majority of cases who had an intact cyst had no DNA of E. granulosus in their serum. DNA of E. granulosus was not found to be excreted in urine. PCR performed equal to antigen detection ELISA while testing hydatid cyst fluid samples. Serum and urine might not serve as useful samples for the molecular diagnosis of cystic echinococcosis. However, PCR can be useful on serum samples to detect ruptured hydatid cysts and on hydatid cyst fluid to confirm the parasitic diagnosis.

The atmosphere can be a source of certain water soluble volatile organic compounds in urban streams

USGS Publications Warehouse

Kenner, Scott J.; Bender, David A.; Zogorski, John S.; ,; James F. Pankow,

2014-01-01

Surface water and air volatile organic compound (VOC) data from 10 U.S. Geological Survey monitoring sites were used to evaluate the potential for direct transport of VOCs from the atmosphere to urban streams. Analytical results of 87 VOC compounds were screened by evaluating the occurrence and detection levels in both water and air, and equilibrium concentrations in water (Cws) based on the measured air concentrations. Four compounds (acetone, methyl tertiary butyl ether, toluene, and m- & p-xylene) were detected in more than 20% of water samples, in more than 10% of air samples, and more than 10% of detections in air were greater than long-term method detection levels (LTMDL) in water. Benzene was detected in more than 20% of water samples and in more than 10% of air samples. Two percent of benzene detections in air were greater than one-half the LTMDL in water. Six compounds (chloroform, p-isopropyltoluene, methylene chloride, perchloroethene, 1,1,1-trichloroethane, and trichloroethene) were detected in more than 20% of water samples and in more than 10% of air samples. Five VOCs, toluene, m- & p-xylene, methyl tert-butyl ether (MTBE), acetone, and benzene were identified as having sufficiently high concentrations in the atmosphere to be a source to urban streams. MTBE, acetone, and benzene exhibited behavior that was consistent with equilibrium concentrations in the atmosphere.

Detection of Mycoplasma hyopneumoniae by Air Sampling with a Nested PCR Assay

PubMed Central

Stärk, Katharina D. C.; Nicolet, Jacques; Frey, Joachim

1998-01-01

This article describes the first successful detection of airborne Mycoplasma hyopneumoniae under experimental and field conditions with a new nested PCR assay. Air was sampled with polyethersulfone membranes (pore size, 0.2 μm) mounted in filter holders. Filters were processed by dissolution and direct extraction of DNA for PCR analysis. For the PCR, two nested pairs of oligonucleotide primers were designed by using an M. hyopneumoniae-specific DNA sequence of a repeated gene segment. A nested PCR assay was developed and used to analyze samples collected in eight pig houses where respiratory problems had been common. Air was also sampled from a mycoplasma-free herd. The nested PCR was highly specific and 104 times as sensitive as a one-step PCR. Under field conditions, the sampling system was able to detect airborne M. hyopneumoniae on 80% of farms where acute respiratory disease was present. No airborne M. hyopneumoniae was detected on infected farms without acute cases. The chance of successful detection was increased if air was sampled at several locations within a room and at a lower air humidity. PMID:9464391

Adaptive detection of noise signal according to Neumann-Pearson criterion

NASA Astrophysics Data System (ADS)

Padiryakov, Y. A.

1985-03-01

Optimum detection according to the Neumann-Pearson criterion is considered in the case of a random Gaussian noise signal, stationary during measurement, and a stationary random Gaussian background interference. Detection is based on two samples, their statistics characterized by estimates of their spectral densities, it being a priori known that sample A from the signal channel is either the sum of signal and interference or interference alone and sample B from the reference interference channel is an interference with the same spectral density as that of the interference in sample A for both hypotheses. The probability of correct detection is maximized on the average, first in the 2N-dimensional space of signal spectral density and interference spectral density readings, by fixing the probability of false alarm at each point so as to stabilize it at a constant level against variation of the interference spectral density. Deterministic decision rules are established. The algorithm is then reduced to equivalent detection in the N-dimensional space of the ratio of sample A readings to sample B readings.

Steroidal hormones and other endocrine active compounds in shallow groundwater in nonagricultural areas of Minnesota—Study design, methods, and data, 2009–10

USGS Publications Warehouse

Erickson, Melinda L.

2012-01-01

The U.S. Geological Survey, in cooperation with the Minnesota Pollution Control Agency, completed a study on the occurrence of steroidal hormones and other endocrine active compounds in shallow groundwater in nonagricultural areas of Minnesota during 2009–10. This report describes the study design and methods, and presents the data collected on steroidal hormones and other related compounds. Environmental and quality-control samples were collected from 40 wells as part of this study. Samples were analyzed by the U.S. Geological Survey National Water Quality Laboratory for 16 steroidal hormones and 4 other related compounds, of which all but 2 compounds are endocrine active compounds. Most of the water samples did not contain detectable concentrations of any of the 20 compounds analyzed. Water samples from three wells had detectable concentrations of one or more compounds. Bisphenol A was detected in samples from three wells, and trans-diethylstilbestrol was detected in one of the samples in which bisphenol A also was detected.

Detection of Toxoplasma gondii DNA in Brazilian oysters (Crassostrea rhizophorae).

PubMed

Ribeiro, L A; Santos, L K N S S; Brito, P A; Maciel, B M; Da Silva, A V; Albuquerque, G R

2015-05-04

The aim of this study was to detect evidence of Toxoplasma gondii using polymerase chain reaction (PCR)-based techniques in oysters (Crassostrea rhizophorae) obtained from the southern coastal region of Bahia, Brazil. A total of 624 oysters were collected, and the gills and digestive glands were dissected. Each tissue sample was separated into pools containing tissues (of the same type) from three animals, leading to a total of 416 experimental samples for analysis (208 samples each from the gills and digestive glands). Molecular analysis using PCR-based detection of the T. gondii AF 146527 repetitive fragment yielded negative results for all samples. However, when nested-PCR was used for detection of the T. gondii SAG-1 gene, 17 samples were positive, with the gills being the tissue with maximal detection of the parasite. These positive results were confirmed by sample sequencing. It is therefore suggested that C. rhizophorae oysters are capable of filtering and retaining T. gondii oocysts in their tissue. This represents a risk to public health because they are traditionally ingested in natura.

THE SCREENING AND RANKING ALGORITHM FOR CHANGE-POINTS DETECTION IN MULTIPLE SAMPLES

PubMed Central

Song, Chi; Min, Xiaoyi; Zhang, Heping

2016-01-01

The chromosome copy number variation (CNV) is the deviation of genomic regions from their normal copy number states, which may associate with many human diseases. Current genetic studies usually collect hundreds to thousands of samples to study the association between CNV and diseases. CNVs can be called by detecting the change-points in mean for sequences of array-based intensity measurements. Although multiple samples are of interest, the majority of the available CNV calling methods are single sample based. Only a few multiple sample methods have been proposed using scan statistics that are computationally intensive and designed toward either common or rare change-points detection. In this paper, we propose a novel multiple sample method by adaptively combining the scan statistic of the screening and ranking algorithm (SaRa), which is computationally efficient and is able to detect both common and rare change-points. We prove that asymptotically this method can find the true change-points with almost certainty and show in theory that multiple sample methods are superior to single sample methods when shared change-points are of interest. Additionally, we report extensive simulation studies to examine the performance of our proposed method. Finally, using our proposed method as well as two competing approaches, we attempt to detect CNVs in the data from the Primary Open-Angle Glaucoma Genes and Environment study, and conclude that our method is faster and requires less information while our ability to detect the CNVs is comparable or better. PMID:28090239

Microbiological Detection Systems for Molecular Analysis of Environmental Water and Soil Samples

EPA Science Inventory

Multiple detection systems are being targeted to track various species and genotypes of pathogens found in environmental samples with the overreaching goal of developing analytical separation and detection techniques for Salmonella enterica Serovars Typhi, Cryptosporidium parvum,...

Hepatitis A and E Viruses in Wastewaters, in River Waters, and in Bivalve Molluscs in Italy.

PubMed

Iaconelli, M; Purpari, G; Della Libera, S; Petricca, S; Guercio, A; Ciccaglione, A R; Bruni, R; Taffon, S; Equestre, M; Fratini, M; Muscillo, M; La Rosa, Giuseppina

2015-12-01

Several studies have reported the detection of hepatitis A (HAV) and E (HEV) virus in sewage waters, indicating a possibility of contamination of aquatic environments. The objective of the present study was to assess the occurrence of HAV and HEV in different water environments, following the route of contamination from raw sewage through treated effluent to the surface waters receiving wastewater discharges . Bivalve molluscan shellfish samples were also analyzed, as sentinel of marine pollution. Samples were tested by RT-PCR nested type in the VP1/2A junction for HAV, and in the ORF1 and ORF2 regions for HEV. Hepatitis A RNA was detected in 12 water samples: 7/21 (33.3%) raw sewage samples, 3/21 (14.3%) treated sewage samples, and 2/27 (7.4%) river water samples. Five sequences were classified as genotype IA, while the remaining 7 sequences belonged to genotype IB. In bivalves, HAV was detected in 13/56 samples (23.2%), 12 genotype IB and one genotype IA. Whether the presence of HAV in the matrices tested indicates the potential for waterborne and foodborne transmission is unknown, since infectivity of the virus was not demonstrated. HEV was detected in one raw sewage sample and in one river sample, both belonging to genotype 3. Sequences were similar to sequences detected previously in Italy in patients with autochthonous HEV (no travel history) and in animals (swine). To our knowledge, this is the first detection of HEV in river waters in Italy, suggesting that surface water can be a potential source for exposure .

Chemical and radiochemical constituents in water from wells in the vicinity of the naval reactors facility, Idaho National Engineering and Environmental Laboratory, Idaho, 1997-98

USGS Publications Warehouse

Bartholomay, Roy C.; Knobel, LeRoy L.; Tucker, Betty J.; Twining, Brian V.

2000-01-01

The U.S. Geological Survey, in response to a request from the U.S. Department of Energy?s Phtsburgh Naval Reactors Ofilce, Idaho Branch Office, sampled water from 13 wells during 1997?98 as part of a long-term project to monitor water quality of the Snake River Plain aquifer in the vicinity of the Naval Reactors Facility, Idaho National Engineering and Environmental Laboratory, Idaho. Water samples were analyzed for naturally occurring constituents and man-made contaminants. A totalof91 samples were collected from the 13 monitoring wells. The routine samples contained detectable concentrations of total cations and dissolved anions, and nitrite plus nitrate as nitrogen. Most of the samples also had detectable concentrations of gross alpha- and gross beta-particle radioactivity and tritium. Fourteen qualityassurance samples also were collected and analyze~ seven were field-blank samples, and seven were replicate samples. Most of the field blank samples contained less than detectable concentrations of target constituents; however, some blank samples did contain detectable concentrations of calcium, magnesium, barium, copper, manganese, nickel, zinc, nitrite plus nitrate, total organic halogens, tritium, and selected volatile organic compounds.

Molecular detection of Toxoplasma gondii in water samples from Scotland and a comparison between the 529bp real-time PCR and ITS1 nested PCR.

PubMed

Wells, Beth; Shaw, Hannah; Innocent, Giles; Guido, Stefano; Hotchkiss, Emily; Parigi, Maria; Opsteegh, Marieke; Green, James; Gillespie, Simon; Innes, Elisabeth A; Katzer, Frank

2015-12-15

Waterborne transmission of Toxoplasma gondii is a potential public health risk and there are currently no agreed optimised methods for the recovery, processing and detection of T. gondii oocysts in water samples. In this study modified methods of T. gondii oocyst recovery and DNA extraction were applied to 1427 samples collected from 147 public water supplies throughout Scotland. T. gondii DNA was detected, using real time PCR (qPCR) targeting the 529bp repeat element, in 8.79% of interpretable samples (124 out of 1411 samples). The samples which were positive for T. gondii DNA originated from a third of the sampled water sources. The samples which were positive by qPCR and some of the negative samples were reanalysed using ITS1 nested PCR (nPCR) and results compared. The 529bp qPCR was the more sensitive technique and a full analysis of assay performance, by Bayesian analysis using a Markov Chain Monte Carlo method, was completed which demonstrated the efficacy of this method for the detection of T. gondii in water samples. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Occurrence of antibiotics in hospital, residential, and dairy effluent, municipal wastewater, and the Rio Grande in New Mexico.

PubMed

Brown, Kathryn D; Kulis, Jerzy; Thomson, Bruce; Chapman, Timothy H; Mawhinney, Douglas B

2006-08-01

This study had three objectives: 1) determine occurrence of antibiotics in effluent from hospitals, residential facilities, and dairies, and in municipal wastewater 2) determine antibiotic removal at a large wastewater treatment plant (WWTP) in Albuquerque, NM, and 3) determine concentrations of antibiotics in the Rio Grande, which receives wastewater from the Albuquerque WWTP. Twenty-three samples of wastewater and 3 samples of Rio Grande water were analyzed for the presence of 11 antibiotics. Fifty-eight percent of samples had at least one antibiotic present while 25% had three or more. Hospital effluent had detections of sulfamethoxazole, trimethoprim, ciprofloxacin, ofloxacin, lincomycin, and penicillin G, with 4 of 5 hospital samples having at least one antibiotic detected and 3 having four or more. At the residential sampling sites, ofloxacin was found in effluent from assisted living and retirement facilities, while the student dormitory had no detects. Only lincomycin was detected in dairy effluent (in 2 of 8 samples, at 700 and 6600 ng/L). Municipal wastewater had detections of sulfamethoxazole, trimethoprim, ciprofloxacin, and ofloxacin, with 4 of 6 samples having at least one antibiotic present and 3 having 3 or more. The relatively high concentrations (up to 35,500 ng/L) of ofloxacin found in hospital and residential effluent may be of concern due to potential genotoxic effects and development of antibiotic resistance. At the Albuquerque WWTP, both raw wastewater and treated effluent had detections of sulfamethoxazole, trimethoprim, and ofloxacin, at concentrations ranging from 110 to 470 ng/L. However, concentrations in treated effluent were reduced by 20% to 77%. No antibiotics were detected in the Rio Grande upstream of the Albuquerque WWTP discharge, and only one antibiotic, sulfamethoxazole, was detected in the Rio Grande (300 ng/L) below the WWTP.

Molecular Diagnosis of Invasive Aspergillosis and Detection of Azole Resistance by a Newly Commercialized PCR Kit

PubMed Central

Gabriel, Frédéric; Gaboyard, Manuel; Lagardere, Gaëlle; Audebert, Lucile; Quesne, Gilles; Godichaud, Sandrine; Verweij, Paul E.; Accoceberry, Isabelle

2017-01-01

ABSTRACT Aspergillus fumigatus is the main species responsible for aspergillosis in humans. The diagnosis of aspergillosis remains difficult, and the rapid emergence of azole resistance in A. fumigatus is worrisome. The aim of this study was to validate the new MycoGENIE A. fumigatus real-time PCR kit and to evaluate its performance on clinical samples for the detection of A. fumigatus and its azole resistance. This multiplex assay detects DNA from the A. fumigatus species complex by targeting the multicopy 28S rRNA gene and specific TR34 and L98H mutations in the single-copy-number cyp51A gene of A. fumigatus. The specificity of cyp51A mutation detection was assessed by testing DNA samples from 25 wild-type or mutated clinical A. fumigatus isolates. Clinical validation was performed on 88 respiratory samples obtained from 62 patients and on 69 serum samples obtained from 16 patients with proven or probable aspergillosis and 13 patients without aspergillosis. The limit of detection was <1 copy for the Aspergillus 28S rRNA gene and 6 copies for the cyp51A gene harboring the TR34 and L98H alterations. No cross-reactivity was detected with various fungi and bacteria. All isolates harboring the TR34 and L98H mutations were accurately detected by quantitative PCR (qPCR) analysis. With respiratory samples, qPCR results showed a sensitivity and specificity of 92.9% and 90.1%, respectively, while with serum samples, the sensitivity and specificity were 100% and 84.6%, respectively. Our study demonstrated that this new real-time PCR kit enables sensitive and rapid detection of A. fumigatus DNA and azole resistance due to TR34 and L98H mutations in clinical samples. PMID:28814586

Evaluation of the Roche LightMix Gastro parasites multiplex PCR assay detecting Giardia duodenalis, Entamoeba histolytica, cryptosporidia, Dientamoeba fragilis, and Blastocystis hominis.

PubMed

Friesen, J; Fuhrmann, J; Kietzmann, H; Tannich, E; Müller, M; Ignatius, R

2018-03-23

Multiplex PCR assays offer highly sensitive and specific tools for the detection of enteric pathogens. This prospective study aimed at comparing the novel Roche LightMix Modular Assay Gastro Parasites (LMAGP) detecting Giardia duodenalis, Entamoeba histolytica, Cryptosporidium spp., Blastocystishominis, and Dientamoebafragilis with routine laboratory procedures. Stool specimens (n = 1062 from 1009 patients) were consecutively examined by LMAGP, R-Biopharm Ridascreen enzyme immunoassays (EIAs) detecting G. duodenalis or E. histolytica/dispar, and microscopy of wet mounts. Discrepant results were analysed by in-house PCR. D. fragilis or B. hominis were detected by LMAGP in 131 (14.4%) and 179 (19.9%; 16 samples positive by microscopy; p < 0.0001) of 909 samples, respectively. Of 918 samples analysed for Cryptosporidium spp., six were positive by LMAGP (three could be confirmed by Kinyoun staining and one by in-house PCR). G. duodenalis was detected by LMAGP, EIA, or microscopy in 20, 16, or 9 of 1039 stool samples, respectively; all four samples missed by EIA were confirmed by in-house PCR. In total, 938 stool samples were analysed for E. histolytica/dispar. Nine of ten EIA-positive samples were negative by LMAGP but positive by in-house PCR for E. dispar. One E. histolytica infection (positive by both LMAGP and in-house PCR) was missed by EIA and microscopy. Parasites only detected by microscopy included Enterobius vermicularis eggs (n = 3) and apathogenic amoebae (n = 27). The data call for routine use of multiplex PCR assays for the detection of enteric protozoan parasites in laboratory diagnostics. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Comparison of Human Papillomavirus Detections in Urine, Vulvar, and Cervical Samples from Women Attending a Colposcopy Clinic

PubMed Central

Gravitt, Patti E.; Dunn, S. Terence; Brown, David; Allen, Richard A.; Eby, Yolanda J.; Smith, Katie; Zuna, Rosemary E.; Zhang, Roy R.; Gold, Michael A.; Schiffman, Mark; Walker, Joan L.; Castle, Philip E.; Wentzensen, Nicolas

2014-01-01

While urine-based sampling for human papillomavirus (HPV) is being explored as a simple and noninvasive approach for cervical cancer screening, data comparing HPV genotyping in urine and those in cellular sampling of the cervix and vulva, and their correlation with rigorously confirmed cervical disease status, are sparse. We performed HPV genotyping on voided-urine and clinician-collected vulvar and cervical samples from 72 women undergoing colposcopy. Although urine-based HPV carcinogenic HPV detection was lower (58.3%) than cervical (73.6%) and vulvar (72.1%) detection (P = 0.05 and 0.07, respectively), the agreement of urine HPV with cervical and vulvar HPV was moderate (kappa = 0.55) and substantial (kappa = 0.62), respectively. Urine-based carcinogenic HPV detection had a clinical sensitivity of 80.8% (95% confidence interval [CI] = 60.7 to 93.5) and a specificity of 53.3% (95% CI = 37.9 to 68.3) for diagnosing cervical intraepithelial neoplasia grades 2/3 (CIN2/3) on histology; 90.0% of CIN3 was positive for urine HPV. The corresponding sensitivity and specificity values for vulvar sampling were 92% (95% CI = 74 to 99) and 40.5% (95% CI = 25.6 to 56.7), and those for cervical sampling were 96.2% (95% CI = 80.4 to 99.9) and 40% (95% CI = 25.7 to 55.7), respectively. HPV16 was the most common carcinogenic genotype detectable in 25% of urine, 33.8% of vulvar, and 31.9% of cervical samples overall, with prevalence increasing with cervical disease grade, regardless of the sampling method. Stronger cervical HPV PCR signal strengths were associated with increased frequency of urine HPV detection. In summary, the relatively lower detection rates but comparable clinical performance of urine-based HPV sampling underscore the need for larger studies to evaluate urine-based sampling for cervical cancer screening, epidemiologic studies, and postvaccination HPV disease surveillance. PMID:24197879

Comparative evaluation of PCR amplification of RLEP, 16S rRNA, rpoT and Sod A gene targets for detection of M. leprae DNA from clinical and environmental samples.

PubMed

Turankar, Ravindra P; Pandey, Shradha; Lavania, Mallika; Singh, Itu; Nigam, Astha; Darlong, Joydeepa; Darlong, Fam; Sengupta, Utpal

2015-03-01

PCR assay is a highly sensitive, specific and reliable diagnostic tool for the identification of pathogens in many infectious diseases. Genome sequencing Mycobacterium leprae revealed several gene targets that could be used for the detection of DNA from clinical and environmental samples. The PCR sensitivity of particular gene targets for specific clinical and environmental isolates has not yet been established. The present study was conducted to compare the sensitivity of RLEP, rpoT, Sod A and 16S rRNA gene targets in the detection of M. leprae in slit skin smear (SSS), blood, soil samples of leprosy patients and their surroundings. Leprosy patients were classified into Paucibacillary (PB) and Multibacillary (MB) types. Ziehl-Neelsen (ZN) staining method for all the SSS samples and Bacteriological Index (BI) was calculated for all patients. Standard laboratory protocol was used for DNA extraction from SSS, blood and soil samples. PCR technique was performed for the detection of M. leprae DNA from all the above-mentioned samples. RLEP gene target was able to detect the presence of M. leprae in 83% of SSS, 100% of blood samples and in 36% of soil samples and was noted to be the best out of all other gene targets (rpoT, Sod A and 16S rRNA). It was noted that the RLEP gene target was able to detect the highest number (53%) of BI-negative leprosy patients amongst all the gene targets used in this study. Amongst all the gene targets used in this study, PCR positivity using RLEP gene target was the highest in all the clinical and environmental samples. Further, the RLEP gene target was able to detect 53% of blood samples as positive in BI-negative leprosy cases indicating its future standardization and use for diagnostic purposes. Copyright © 2015 Asian African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

Pesticide Occurrence and Distribution in the Lower Clackamas River Basin, Oregon, 2000-2005

USGS Publications Warehouse

Carpenter, Kurt D.; Sobieszczyk, Steven; Arnsberg, Andrew J.; Rinella, Frank A.

2008-01-01

Pesticide occurrence and distribution in the lower Clackamas River basin was evaluated in 2000?2005, when 119 water samples were analyzed for a suite of 86?198 dissolved pesticides. Sampling included the lower-basin tributaries and the Clackamas River mainstem, along with paired samples of pre- and post-treatment drinking water (source and finished water) from one of four drinking water-treatment plants that draw water from the lower river. Most of the sampling in the tributaries occurred during storms, whereas most of the source and finished water samples from the study drinking-water treatment plant were obtained at regular intervals, and targeted one storm event in 2005. In all, 63 pesticide compounds were detected, including 33 herbicides, 15 insecticides, 6 fungicides, and 9 pesticide degradation products. Atrazine and simazine were detected in about half of samples, and atrazine and one of its degradates (deethylatrazine) were detected together in 30 percent of samples. Other high-use herbicides such as glyphosate, triclopyr, 2,4-D, and metolachlor also were frequently detected, particularly in the lower-basin tributaries. Pesticides were detected in all eight of the lower-basin tributaries sampled, and were also frequently detected in the lower Clackamas River. Although pesticides were detected in all of the lower basin tributaries, the highest pesticide loads (amounts) were found in Deep and Rock Creeks. These medium-sized streams drain a mix of agricultural land (row crops and nurseries), pastureland, and rural residential areas. The highest pesticide loads were found in Rock Creek at 172nd Avenue and in two Deep Creek tributaries, North Fork Deep and Noyer Creeks, where 15?18 pesticides were detected. Pesticide yields (loads per unit area) were highest in Cow and Carli Creeks, two small streams that drain the highly urban and industrial northwestern part of the lower basin. Other sites having relatively high pesticide yields included middle Rock Creek and upper Noyer Creek, which drain basins having nurseries, pasture, and rural residential land. Some concentrations of insecticides (diazinon, chlorpyrifos, azinphos-methyl, and p,p?-DDE) exceeded U.S. Environmental Protection Agency (USEPA) aquatic-life benchmarks in Carli, Sieben, Rock, Noyer, Doane, and North Fork Deep Creeks. One azinphos-methyl concentration in Doane Creek (0.21 micrograms per liter [?g/L]) exceeded Federal and State of Oregon benchmarks for the protection of fish and benthic invertebrates. Concentrations of several other pesticide compounds exceeded non-USEPA benchmarks. Twenty-six pesticides or degradates were detected in the Clackamas River mainstem, typically at much lower concentrations than those detected in the lower-basin tributaries. At least 1 pesticide was detected in 65 percent of 34 samples collected from the Clackamas River, with an average of 2?3 pesticides per sample. Pesticides were detected in 9 (or 60 percent) of the 15 finished water samples collected from the study water-treatment plant during 2003?2005. These included 10 herbicides, 1 insecticide, 1 fungicide, 1 insect repellent, and 2 pesticide degradates. The herbicides diuron and simazine were the most frequently detected (four times each during the study), at concentrations far below human-health benchmarks?USEPA Maximum Contaminant Levels or U.S. Geological Survey human Health-Based Screening Levels (HBSLs). The highest pesticide concentration in finished drinking water was 0.18 ?g/L of diuron, which was 11 times lower than its low HBSL benchmark. Although 0?2 pesticides were detected in most finished water samples, 9 and 6 pesticides were detected in 2 storm-associated samples from May and September 2005, respectively. Three of the unregulated compounds detected in finished drinking water (diazinon-oxon, deethylatrazine [CIAT], and N, N-diethyl-m-toluamide [DEET]) do not have human-health benchmarks available for comparison. Although most of the 51 curren

The detection of Giardia muris and Giardia lamblia cysts by immunofluorescence in animal tissues and fecal samples subjected to cycles of freezing and thawing.

PubMed

Erlandsen, S L; Sherlock, L A; Bemrick, W J

1990-04-01

The effects of freezing and thawing on the detection of selected Giardia spp. cysts were investigated using immunofluorescence, bright field microscopy, and low voltage scanning electron microscopy (SEM). Giardia muris cysts were obtained from either animal carcasses, fecal pellets, or isolated cyst preparations, whereas Giardia lamblia cysts were isolated from fecal samples. These samples were stained using an immunofluorescence technique after 1-3 freezing (-16 C) and thawing (20 C) cycles. Cysts were detected successfully by immunofluorescence in all samples. However, in those samples subjected to freeze-thawing, the cyst walls often became distorted and then were not detectable by bright field microscopy. Low voltage SEM demonstrated that the filaments in the distorted cyst wall underwent rearrangements of interfilament spacing. Quantitation of cyst recovery after freezing and thawing demonstrated that a substantial loss occurred after 1 cycle of alternating temperature when low concentrations of cysts were used, but not with high concentrations of cysts. Cyst recovery, after 3 freezing and thawing cycles, was dramatically lowered irrespective of the initial cyst concentration. These results demonstrated that immunofluorescence was an effective technique for the detection of Giardia spp. cysts in frozen samples and would suggest that freezing and thawing of fecal samples could prevent the detection of cysts when only bright field microscopy was employed.

Evaluation of different fluids for detection of Clostridium perfringens type D epsilon toxin in sheep with experimental enterotoxemia.

PubMed

Layana, Jorge E; Fernandez Miyakawa, Mariano E; Uzal, Francisco A

2006-08-01

Enterotoxemia caused by Clostridium perfringens type D is a highly lethal disease of sheep, goats and other ruminants. The diagnosis of this condition is usually confirmed by detection of epsilon toxin, a major exotoxin produced by C. perfringens types B and D, in the intestinal content of affected animals. It has been suggested that other body fluids can also be used for detection of epsilon toxin. This study was performed to evaluate the usefulness of intestinal content versus other body fluids in detecting epsilon toxin in cases of sheep enterotoxemia. Samples of duodenal, ileal and colon contents, pericardial and abdominal fluids, aqueous humor and urine from 15 sheep with experimentally induced enterotoxemia, were analysed for epsilon toxin using a capture ELISA. Epsilon toxin was detected in 92% of the samples of ileal content, 64% of the samples of duodenal content, 57% of the samples of colon content and in 7% of the samples of pericardial fluid and aqueous humor. No epsilon toxin was found in samples of abdominal fluid or urine from the animals with enterotoxemia or in any samples from six clinically healthy sheep used as negative controls. The results of this study indicate that with the diagnostic capture ELISA used, intestinal content (preferably ileum) should be used for C. perfringens type D epsilon toxin detection in suspected cases of sheep enterotoxemia.

Multi-scale occupancy estimation and modelling using multiple detection methods

USGS Publications Warehouse

Nichols, James D.; Bailey, Larissa L.; O'Connell, Allan F.; Talancy, Neil W.; Grant, Evan H. Campbell; Gilbert, Andrew T.; Annand, Elizabeth M.; Husband, Thomas P.; Hines, James E.

2008-01-01

Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method.We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site.We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber. For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species.Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be viewed as another variation of Pollock's robust design and may be applicable to a wide variety of scenarios where species occur in an area but are not always near the sampled locations. The estimation approach is likely to be especially useful in multispecies conservation programmes by providing efficient estimates using multiple detection devices and by providing device-specific detection probability estimates for use in survey design.

Occurrence of antibiotic compounds in source water and finished drinking water from the upper Scioto River Basin, Ohio, 2005-6

USGS Publications Warehouse

Finnegan, Dennis P.; Simonson, Laura A.; Meyer, Michael T.

2010-01-01

The occurrence of antibiotics in surface water and groundwater in urban basins has become a topic of increasing interest in recent years. Little is known about the occurrence, fate, or transport of these compounds and the possible health effects in humans and aquatic life. The U.S. Geological Survey, in cooperation with the City of Columbus, Division of Power and Water, did a study to provide a synoptic view of the occurrence of antibiotics in source and finished waters in the upper Scioto River Basin. Water samples were collected seasonally-winter (December 2005), spring (May 2006), summer (August 2006) and fall (October 2006)-at five surface-water sites, one groundwater site, and three water-treatment plants (WTPs). Within the upper Scioto River Basin, sampling at each WTP involved two sampling sites: a source-water intake site and a finished-water site. One or more antibiotics were detected at 11 of the 12 sampling sites. Of the 49 targeted antibiotic compounds, 12 (24 percent) were detected at least one time for a total of 61 detections overall. These compounds were azithromycin, tylosin, erythromycin-H2O, erythromycin, roxithromycin, ciprofloxacin, ofloxacin, sulfamethazine, sulfamethoxazole, iso-chlorotetracycline, lincomycin, and trimethoprim. Detection results were at low levels, with an overall median of 0.014 (u or mu)g/L. Hap Cremean WTP had the fewest detections, with two source-water detections of sulfamethoxazole and azithromycin and no detections in the finished water. Of the total of 61 detections, 31 were in the winter sample run. Sulfamethoxazale and azithromycin detections represent 41 percent of all antibiotic detections. Azithromycin was detected only in the winter sample. Some antibiotics, such as those in the quinoline and tetracycline families, dissipate more quickly in warm water, which may explain why they were detected in the cool months (winter, spring, and fall) and not in the summer. Antibiotic data collected during this study were compared to antibiotic data collected in previous national, regional, and local studies. Many of the same antibiotic compounds detected in the upper Scioto River Basin also were detected in those investigations.

Ground-water quality in northeastern St. Joseph County, Indiana

USGS Publications Warehouse

Fenelon, J.M.; Bayless, E. Randall; Watson, Lee R.

1995-01-01

No industrial organic compounds were detected in the water samples. Four pesticides - alachlor, carbofuran, metolachlor, and triazines - were detected in water samples; the highest pesticide concentration in a water sample was 1.0 microgram per liter of alachlor.

Assumptions of acceptance sampling and the implications for lot contamination: Escherichia coli O157 in lots of Australian manufacturing beef.

PubMed

Kiermeier, Andreas; Mellor, Glen; Barlow, Robert; Jenson, Ian

2011-04-01

The aims of this work were to determine the distribution and concentration of Escherichia coli O157 in lots of beef destined for grinding (manufacturing beef) that failed to meet Australian requirements for export, to use these data to better understand the performance of sampling plans based on the binomial distribution, and to consider alternative approaches for evaluating sampling plans. For each of five lots from which E. coli O157 had been detected, 900 samples from the external carcass surface were tested. E. coli O157 was not detected in three lots, whereas in two lots E. coli O157 was detected in 2 and 74 samples. For lots in which E. coli O157 was not detected in the present study, the E. coli O157 level was estimated to be <12 cells per 27.2-kg carton. For the most contaminated carton, the total number of E. coli O157 cells was estimated to be 813. In the two lots in which E. coli O157 was detected, the pathogen was detected in 1 of 12 and 2 of 12 cartons. The use of acceptance sampling plans based on a binomial distribution can provide a falsely optimistic view of the value of sampling as a control measure when applied to assessment of E. coli O157 contamination in manufacturing beef. Alternative approaches to understanding sampling plans, which do not assume homogeneous contamination throughout the lot, appear more realistic. These results indicate that despite the application of stringent sampling plans, sampling and testing approaches are inefficient for controlling microbiological quality.

Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations▿ †

PubMed Central

Mitsuya, Yumi; Varghese, Vici; Wang, Chunlin; Liu, Tommy F.; Holmes, Susan P.; Jayakumar, Prerana; Gharizadeh, Baback; Ronaghi, Mostafa; Klein, Daniel; Fessel, W. Jeffrey; Shafer, Robert W.

2008-01-01

T215 revertant mutations such as T215C/D/E/S that evolve from the nucleoside reverse transcriptase (RT) inhibitor mutations T215Y/F have been found in about 3% of human immunodeficiency virus type 1 (HIV-1) isolates from newly diagnosed HIV-1-infected persons. We used a newly developed sequencing method—ultradeep pyrosequencing (UDPS; 454 Life Sciences)—to determine the frequency with which T215Y/F or other RT inhibitor resistance mutations could be detected as minority variants in samples from untreated persons that contain T215 revertants (“revertant” samples) compared with samples from untreated persons that lack such revertants (“control” samples). Among the 22 revertant and 29 control samples, UDPS detected a mean of 3.8 and 4.8 additional RT amino acid mutations, respectively. In 6 of 22 (27%) revertant samples and in 4 of 29 control samples (14%; P = 0.4), UDPS detected one or more RT inhibitor resistance mutations. T215Y or T215F was not detected in any of the revertant or control samples; however, 4 of 22 revertant samples had one or more T215 revertants that were detected by UDPS but not by direct PCR sequencing. The failure to detect viruses with T215Y/F in the 22 revertant samples in this study may result from the overwhelming replacement of transmitted T215Y variants by the more fit T215 revertants or from the primary transmission of a T215 revertant in a subset of persons with T215 revertants. PMID:18715933

Multiplex Real-Time PCR for Detection of Staphylococcus aureus, mecA and Panton-Valentine Leukocidin (PVL) Genes from Selective Enrichments from Animals and Retail Meat

PubMed Central

Velasco, Valeria; Sherwood, Julie S.; Rojas-García, Pedro P.; Logue, Catherine M.

2014-01-01

The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL) genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat). The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus), mecA (associated with methicillin resistance) and PVL (virulence factor), and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68–0.88 (from substantial to almost perfect agreement) and 0.29–0.77 (from fair to substantial agreement) for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0–0.49 (from no agreement beyond that expected by chance to moderate agreement) for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA) using the standard culture method. PMID:24849624

Multiplex real-time PCR for detection of Staphylococcus aureus, mecA and Panton-Valentine Leukocidin (PVL) genes from selective enrichments from animals and retail meat.

PubMed

Velasco, Valeria; Sherwood, Julie S; Rojas-García, Pedro P; Logue, Catherine M

2014-01-01

The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL) genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat). The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus), mecA (associated with methicillin resistance) and PVL (virulence factor), and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68-0.88 (from substantial to almost perfect agreement) and 0.29-0.77 (from fair to substantial agreement) for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0-0.49 (from no agreement beyond that expected by chance to moderate agreement) for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA) using the standard culture method.

Detection of sex chromosome aneuploidies using quantitative fluorescent PCR in the Hungarian population.

PubMed

Nagy, Balint; Nagy, Richard Gyula; Lazar, Levente; Schonleber, Julianna; Papp, Csaba; Rigo, Janos

2015-05-20

Aneuploidies are the most frequent chromosomal abnormalities at birth. Autosomal aneuploidies cause serious malformations like trisomy 21, trisomy 18 and trisomy 13. However sex chromosome aneuploidies are causing less severe syndromes. For the detection of these aneuploidies, the "gold standard" method is the cytogenetic analysis of fetal cells, karyograms show all numerical and structural abnormalities, but it takes 2-4 weeks to get the reports. Molecular biological methods were developed to overcome the long culture time, thus, FISH and quantitative fluorescent PCR were introduced. In this work we show our experience with a commercial kit for the detection of sex chromosome aneuploidies. We analyzed 20.173 amniotic fluid samples for the period of 2006-2013 in our department. A conventional cytogenetic analysis was performed on the samples. We checked the reliability of quantitative fluorescent PCR and DNA fragment analysis on those samples where sex chromosomal aneuploidy was diagnosed. From the 20.173 amniotic fluid samples we found 50 samples with sex chromosome aneuploidy. There were 19 samples showing 46, XO, 17 samples with 46, XXY, 9 samples with 47, XXX and 5 samples with 47, XYY karyotypes. The applied quantitative fluorescent PCR and DNA fragment analyses method are suitable to detect all abnormal sex chromosome aneuploidies. Quantitative fluorescent PCR is a fast and reliable method for detection of sex chromosome aneuploidies. Copyright © 2015. Published by Elsevier B.V.

Nationwide reconnaissance of contaminants of emerging ...

EPA Pesticide Factsheets

Mobile and persistent chemicals that are present in urban wastewater, such as pharmaceuticals, may survive on-site or municipal wastewater treatment and post-discharge environmental processes. These pharmaceuticals have the potential to reach surface and groundwaters, essential drinking-water sources. A joint, two-phase U.S. Geological Survey-U.S. Environmental Protection Agency study examined source and treated waters from 25 drinking-water treatment plants from across the United States. Treatment plants that had probable wastewater inputs to their source waters were selected to assess the prevalence of pharmaceuticals in such source waters, and to identify which pharmaceuticals persist through drinking-water treatment. All samples were analyzed for 24 pharmaceuticals in Phase I and for 118 in Phase II. In Phase I, 11 pharmaceuticals were detected in all source-water samples, with a maximum of nine pharmaceuticals detected in any one sample. The median number of pharmaceuticals for all 25 samples was five. Quantifiable pharmaceutical detections were fewer, with a maximum of five pharmaceuticals in any one sample and a median for all samples of two. In Phase II, 47 different pharmaceuticals were detected in all source-water samples, with a maximum of 41 pharmaceuticals detected in any one sample. The median number of pharmaceuticals for all 25 samples was eight. For 37 quantifiable pharmaceuticals in Phase II, median concentrations in source water were below 11

Mid-infrared spectroscopy combined with chemometrics to detect Sclerotinia stem rot on oilseed rape (Brassica napus L.) leaves.

PubMed

Zhang, Chu; Feng, Xuping; Wang, Jian; Liu, Fei; He, Yong; Zhou, Weijun

2017-01-01

Detection of plant diseases in a fast and simple way is crucial for timely disease control. Conventionally, plant diseases are accurately identified by DNA, RNA or serology based methods which are time consuming, complex and expensive. Mid-infrared spectroscopy is a promising technique that simplifies the detection procedure for the disease. Mid-infrared spectroscopy was used to identify the spectral differences between healthy and infected oilseed rape leaves. Two different sample sets from two experiments were used to explore and validate the feasibility of using mid-infrared spectroscopy in detecting Sclerotinia stem rot (SSR) on oilseed rape leaves. The average mid-infrared spectra showed differences between healthy and infected leaves, and the differences varied among different sample sets. Optimal wavenumbers for the 2 sample sets selected by the second derivative spectra were similar, indicating the efficacy of selecting optimal wavenumbers. Chemometric methods were further used to quantitatively detect the oilseed rape leaves infected by SSR, including the partial least squares-discriminant analysis, support vector machine and extreme learning machine. The discriminant models using the full spectra and the optimal wavenumbers of the 2 sample sets were effective for classification accuracies over 80%. The discriminant results for the 2 sample sets varied due to variations in the samples. The use of two sample sets proved and validated the feasibility of using mid-infrared spectroscopy and chemometric methods for detecting SSR on oilseed rape leaves. The similarities among the selected optimal wavenumbers in different sample sets made it feasible to simplify the models and build practical models. Mid-infrared spectroscopy is a reliable and promising technique for SSR control. This study helps in developing practical application of using mid-infrared spectroscopy combined with chemometrics to detect plant disease.

Concordance of human papillomavirus types detected on the surface and in the tissue of genital lesions in men.

PubMed

Anic, Gabriella M; Messina, Jane L; Stoler, Mark H; Rollison, Dana E; Stockwell, Heather; Villa, Luisa L; Lazcano-Ponce, Eduardo; Gage, Christine; Silva, Roberto Jose C; Baggio, Maria L; Salmerón, Jorge; Giuliano, Anna R

2013-09-01

Swabbing the surface of a genital lesion to obtain a sample for HPV DNA testing is less invasive than a biopsy, but may not represent HPV types present in the lesion tissue. The objective of this study was to examine the concordance of HPV types detected in swab and biopsy samples from 165 genital lesions from men ages 18-70. Lesions included 90 condyloma, 10 penile intraepithelial neoplasia (PeIN), 23 non-condyloma with a known histology, and 42 lesions with an undetermined histology. All lesions were sampled by swabbing the surface of the lesion with a pre-wetted Dacron swab and taking a shave biopsy. HPV genotyping was performed using Linear Array for swab samples and INNO-LiPA for biopsy samples. The kappa and McNemar statistics were used to compare the concordance of detecting HPV types in swab and biopsy samples. Both sampling methods had high agreement for detection of HPV DNA in condyloma (87.8% agreement) and PeIN (100% agreement). There was also high concordance for detection of HPV16 (kappa = 1.00) and HPV18 (kappa = 1.00) in PeIN, however, agreement was low to moderate for detecting HPV6 (kappa = 0.31) and HPV11 (kappa = 0.56) in condyloma. Low to moderate agreement was also observed between sampling methods for detecting individual HPV types in the non-condyloma and lesions with an indefinite histology. The results suggest that obtaining a biopsy in addition to swabbing the surface of a lesion may provide additional information about specific HVP types associated with male genital lesions. Copyright © 2013 Wiley Periodicals, Inc.

Occurrence and status of volatile organic compounds in ground water from rural, untreated, self-supplied domestic wells in the United States, 1986-99

USGS Publications Warehouse

Moran, Michael J.; Lapham, Wayne W.; Rowe, Barbara L.; Zogorski, John S.

2002-01-01

Samples of untreated ground water from 1,926 rural, self-supplied domestic wells were analyzed for volatile organic compounds (VOCs) during 1986-99. This information was used to characterize the occurrence and status of VOCs in domestic well water. The samples were either collected as part of the U.S. Geological Survey?s National Water-Quality Assessment (NAWQA) Program occurrence-assessment studies or were compiled by NAWQA from existing ambient ground-water or source-water-quality monitoring programs conducted by local, State, and other Federal agencies. Water samples were collected at the wellhead prior to treatment or storage. In most samples, 55 target VOCs were analyzed, and occurrence and status information generally was computed at an assessment level of 0.2 mg/L (microgram per liter). At least one VOC was detected in 12 percent of samples (232 samples) at an assessment level of 0.2 mg/L. This detection frequency is relatively low compared to the 26 percent detection frequency of at least one VOC in public sup-ply wells sampled by NAWQA, and the difference may be due, in part, to the higher pumping rates, pumping stress factors, and larger contributing areas of public supply wells. Samples with detections of at least one VOC were collected from wells located in 31 of 39 States. Solvents were the most frequently detected VOC group with detections in 4.6 percent of samples (89 samples) at an assessment level of 0.2 mg/L. The geographic distribution of detections of some VOC groups, such as fumigants and oxygenates, relates to the use pattern of com-pounds in that group. With the exception of com-pounds used in organic synthesis, detection frequencies of VOCs by group are proportional to the average half-life of compounds in the group. When the organic synthesis group is excluded from the analysis, a good correlation exists between the detection frequency of VOCs by group and average half-life of compounds in the group. Individually, VOCs were not commonly detected at an assessment level of 0.2 mg/L, with the seven most frequently detected VOCs found in only 1 to 5 percent of samples. Mixtures (two or more compounds) were a common mode of occurrence for VOCs when no assessment level was applied, and mixtures occurred in one-half of all samples that contained at least one VOC. Only 1.4 percent of samples (27 samples) had one or more VOC concentrations that exceeded a federally established drinking-water standard or health criterion. Only 0.1 percent of samples (2 samples) had one or more VOC concentrations that exceeded a taste/odor threshold. Potential point sources of VOCs near domestic wells are numerous. Leaks from under-ground storage tanks and aboveground storage tanks that hold gasoline, diesel fuel, or heating oil have the potential to be major point sources of contaminants to domestic wells. Shock chlorination may be a source of trichloromethane and other trihalomethanes in some domestic wells. Septic systems are believed to be an important source of contaminants to domestic wells, but extensive research on this subject does not exist. VOCs frequently are ingredients in household products such as cleansers and insecticides, and some VOCs have been found in septic systems.

Aqueous geochemical data from the analysis of stream water samples collected in August 2004--Taylor Mountains 1:250,000 scale Quadrangle, Alaska

USGS Publications Warehouse

Wang, Bronwen; Mueller, Seth; Bailey, Elizabeth; Lee, Greg

2006-01-01

We report on the chemical analysis of water samples collected from the Taylor Mountains 1:250,000 quadrangle. Samples were collected as part of the multi-year U.S. Geological Survey's project -- Geologic and Mineral Deposit Data for Alaskan Economic Development. Data presented here are from water samples collected primarily in the northeastern part of the Taylor Mountains quadrangle. The data include samples taken from the Taylor Mountains C1, C2, D1, D2, and D4 1:63,360 scale quadrangles. The data are being released at this time with minimal interpretation. Site selection was based on a regional sampling strategy that focused on first and second order drainages. Water sampling site selection was based on landscape parameters that included physiography, wetland extent, lithological changes, and the cursory field review of the mineralogy from the pan concentrates. Stream water in the Taylor Mountians quadrangle is dominated by bicarbonate (HCO3-), though in a few samples more than 50% of the anionic charge can be attibuted to sulfate ( SO42-). The major-cation chemistry range from Ca/Mg dominated to a mix of Ca/Mg/Na+K. Good agreement was found between the major cation and anions in the duplicate samples. Many trace elements were at or near the method detection limit in these samples but good agreement was found between duplicate samples for elements with detectable concentrations. Major ion concentrations were below detection in all field blanks and the trace elements concentrations generally were below detection. However, Ta (range 0.9 -.1 ug/L) and Zn (1 to 3.5 ug/L) were detected in all blanks and Ba ( 0.24 ug/L) and Th (0.2 ug/L) were detected in one blank. There was good agreement between dupilicate total- and methyl- mercury and DOC samples; however, total mercury, methyl-mercury and dissolve organic carbon (DOC) were detected in the blank at 2.35 ng/L, 0.07 ng/L and 0.57 mg/L, respectively.

Efficiency of Airborne Sample Analysis Platform (ASAP) bioaerosol sampler for pathogen detection

PubMed Central

Sharma, Anurag; Clark, Elizabeth; McGlothlin, James D.; Mittal, Suresh K.

2015-01-01

The threat of bioterrorism and pandemics has highlighted the urgency for rapid and reliable bioaerosol detection in different environments. Safeguarding against such threats requires continuous sampling of the ambient air for pathogen detection. In this study we investigated the efficacy of the Airborne Sample Analysis Platform (ASAP) 2800 bioaerosol sampler to collect representative samples of air and identify specific viruses suspended as bioaerosols. To test this concept, we aerosolized an innocuous replication-defective bovine adenovirus serotype 3 (BAdV3) in a controlled laboratory environment. The ASAP efficiently trapped the surrogate virus at 5 × 103 plaque-forming units (p.f.u.) [2 × 105 genome copy equivalent] concentrations or more resulting in the successful detection of the virus using quantitative PCR. These results support the further development of ASAP for bioaerosol pathogen detection. PMID:26074900

Compressed sensing: Radar signal detection and parameter measurement for EW applications

NASA Astrophysics Data System (ADS)

Rao, M. Sreenivasa; Naik, K. Krishna; Reddy, K. Maheshwara

2016-09-01

State of the art system development is very much required for UAVs (Unmanned Aerial Vehicle) and other airborne applications, where miniature, lightweight and low-power specifications are essential. Currently, the airborne Electronic Warfare (EW) systems are developed with digital receiver technology using Nyquist sampling. The detection of radar signals and parameter measurement is a necessary requirement in EW digital receivers. The Random Modulator Pre-Integrator (RMPI) can be used for matched detection of signals using smashed filter. RMPI hardware eliminates the high sampling rate analog to digital computer and reduces the number of samples using random sampling and detection of sparse orthonormal basis vectors. RMPI explore the structural and geometrical properties of the signal apart from traditional time and frequency domain analysis for improved detection. The concept has been proved with the help of MATLAB and LabVIEW simulations.

Organochlorine compounds in streambed sediment and in biological tissue from streams and their relations to land use, central Arizona

USGS Publications Warehouse

Gebler, Joseph B.

2000-01-01

Streambed-sediment samples from 13 sites and biological-tissue samples from 11 sites in the Gila River Basin in central Arizona were analyzed for 32 organochlorine compounds in streambed sediment and 28 compounds in biological tissue during 1996 as part of the U.S. Geological Survey's National Water-Quality Assessment program. The objectives of the study were to determine the occurrence and distribution of organochlorine compounds and their relation to land use. Sampling sites were categorized on the basis of major land uses in the basin or the source of water in the stream. Because land uses were mixed or had changed over time, some land-use categories were combined. Sites were categorized as forest/rangeland (6), forest/urban (1), urban (4), or agricultural/urban (2). Thirteen organochlorine compounds were detected in streambed-sediment samples, and 10 were detected in tissue samples. The number of compounds found in streambed-sediment samples from individual sites ranged from 0 to 10, and the range for individual tissue samples was 0 to 7. Comparison of the number of detections in streambed-sediment samples to the number of detections in tissue samples from particular sites where both were sampled yielded five instances where more compounds were detected in streambed sediment, six instances where more compounds were detected in tissue, and five instances where the number of detections in streambed sediment and tissue were equal. The frequency of detection of particular compounds for sites where both streambed sediment and tissue were sampled resulted in five compounds being detected more frequently in streambed sediment, five more frequently in tissue, and three compounds that were equally frequent in streambed sediment and in tissue. Few contaminants were detected in samples from the forest/rangeland sites; greater numbers of compounds were detected at the urban sites and at the forest/urban site. The greatest number of compounds and the highest concentrations of many contaminants were detected at agriculture/urban sites. The compound detected most frequently in streambed-sediment and tissue samples was p,p'-DDE. Streambed-sediment guideline values for the protection of aquatic life for p,p'-DDE and total DDT were exceeded at both agricultural/urban sites, The streambed-sediment guideline value for the protection of aquatic life for total chlordane was exceeded at one agricultural/urban site, one urban site, and the forest/urban site. The streambed-sediment guideline value for the protection of aquatic life for total PCB’s was exceeded at one agricultural/urban site. Guideline values for the protection of fish-eating wildlife for total DDT and for toxaphene were exceeded only in samples from the two agricultural/urban sites. The guideline value for the protection of fish-eating wildlife for total PCB’s was equaled or exceeded in samples from two sites—one urban and one agricultural/urban site. Screening values established by the U.S. Environmental Protection Agency for the protection of human health for edible portions of fish were exceeded by total DDT and by toxaphene in fish-tissue samples from both agricultural/urban sites. The human-health criterion for total PCB’s was exceeded in two fish-tissue samples from an agricultural site and from an urban site. Tissue samples analyzed in this study were for whole fish, and thus, concentration data are not entirely comparable to the screening values of the U.S. Environmental Protection Agency. Because these exceedences were an order of magnitude above the criteria, however, it is possible that concentrations in the edible portions of fish from these locations could present a human- health risk. Analyses of samples of edible portions of fish from these locations would be needed to adequately assess the presence or absence of a human-health risk. The similarity of the results of this study to the results of other studies of organochlorine compounds in the environment suggests that there is a correlation between contaminants in sediment and biological-tissue samples and land uses. As with other studies of the occurrence and distribution of organochlorine contaminants in streambed sediments and biological tissue, this study shows that many organochlorine compounds continue to persist in the environment and thus could pose a threat to aquatic life, fish-eating wildlife, and possibly to humans who consume contaminated fish.

Water column and bed-sediment core samples collected from Brownlee Reservoir near Oxbow, Oregon, 2012

USGS Publications Warehouse

Fosness, Ryan L.; Naymik, Jesse; Hopkins, Candice B.; DeWild, John F.

2013-01-01

The U.S. Geological Survey, in cooperation with Idaho Power Company, collected water-column and bed-sediment core samples from eight sites in Brownlee Reservoir near Oxbow, Oregon, during May 5–7, 2012. Water-column and bed-sediment core samples were collected at each of the eight sites and analyzed for total mercury and methylmercury. Additional bed-sediment core samples, collected from three of the eight sites, were analyzed for pesticides and other organic compounds, trace metals, and physical characteristics, such as particle size. Total mercury and methylmercury were detected in each of the water column and bed-sediment core samples. Only 17 of the 417 unique pesticide and organic compounds were detected in bed-sediment core samples. Concentrations of most organic wastewater compounds detected in bed sediment were less than the reporting level. Trace metals detected were greater than the reporting level in all the bed-sediment core samples submitted for analysis. The particle size distribution of bed-sediment core samples was predominantly clay mixed with silt.

Effects of sample injection amount and time-of-flight mass spectrometric detection dynamic range on metabolome analysis by high-performance chemical isotope labeling LC-MS.

PubMed

Zhou, Ruokun; Li, Liang

2015-04-06

The effect of sample injection amount on metabolome analysis in a chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) platform was investigated. The performance of time-of-flight (TOF) mass spectrometers with and without a high-dynamic-range (HD) detection system was compared in the analysis of (12)C2/(13)C2-dansyl labeled human urine samples. An average of 1635 ± 21 (n = 3) peak pairs or putative metabolites was detected using the HD-TOF-MS, compared to 1429 ± 37 peak pairs from a conventional or non-HD TOF-MS. In both instruments, signal saturation was observed. However, in the HD-TOF-MS, signal saturation was mainly caused by the ionization process, while in the non-HD TOF-MS, it was caused by the detection process. To extend the MS detection range in the non-HD TOF-MS, an automated switching from using (12)C to (13)C-natural abundance peaks for peak ratio calculation when the (12)C peaks are saturated has been implemented in IsoMS, a software tool for processing CIL LC-MS data. This work illustrates that injecting an optimal sample amount is important to maximize the metabolome coverage while avoiding the sample carryover problem often associated with over-injection. A TOF mass spectrometer with an enhanced detection dynamic range can also significantly increase the number of peak pairs detected. In chemical isotope labeling (CIL) LC-MS, relative metabolite quantification is done by measuring the peak ratio of a (13)C2-/(12)C2-labeled peak pair for a given metabolite present in two comparative samples. The dynamic range of peak ratio measurement does not need to be very large, as only subtle changes of metabolite concentrations are encountered in most metabolomic studies where relative metabolome quantification of different groups of samples is performed. However, the absolute concentrations of different metabolites can be very different, requiring a technique to provide a wide detection dynamic range to allow the detection of as many peak pairs as possible. In this work, we demonstrated that controlling the sample injection amount into LC-MS was critical to achieve the optimal detectability while avoiding sample carry-over problem. In addition, the use of a high-dynamic-range TOF system increased the number of peak pairs detected, compared to a conventional TOF system. We also investigated the ionization and detection saturation factors limiting the dynamic range of detection. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras. Copyright © 2014 Elsevier B.V. All rights reserved.

Annual INTEC Groundwater Monitoring Report for Group 5 - Snake River Plain Aquifer (2001)

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

Roddy, Michael Scott

2002-02-01

This report describes the monitoring activities conducted and presents the results of groundwater sampling and water-level measurements from October 2000 to September 2001. Groundwater samples were initially collected from 41 wells from the Idaho Nuclear Technology and Engineering Center and the Central Facilities Area and analyzed for iodine-129, strontium-90, tritium, gross alpha, gross beta, technetium-99, uranium isotopes, plutonium isotopes, neptunium-237, americium-241, gamma spectrometry, and mercury. Samples from 41 wells were collected in April and May 2001. Additional sampling was conducted in August 2001 and included the two CFA production wells, the CFA point of compliance for the production wells, onemore » well that was previously sampled and five additional monitoring wells. Iodine-129 and strontium-90 were the only analytes above their respective maximum contaminant levels. Iodine-129 was detected just above its maximum contaminant level of 1 pCi/L at two of the Central Facilities Area landfill wells. Iodine-129 was detected in the CFA production wells at 0.35±0.083 pCi/L in CFA-1, but was below detectable activity in CFA-2. Strontium-90 was above its maximum contaminant level of 8 pCi/L in several wells near the Idaho Nuclear Technology and Engineering Center but was below its maximum contaminant level in the downgradient wells at the Central Facilities Area landfills. Sr-90 was not detected in the CFA production wells. Gross beta results generally mirrored the results for strontium-90 and technetium-99. Plutonium isotopes and neptunium-237 were not detected. Uranium-233/234 and uranium-238 isotopes were detected in all samples. Concentrations of background and site wells were similar and are within background limits for total uranium determined by the USGS, suggesting that the concentrations are background. Uranium-235/236 was detected in 11 samples, but all the detected concentrations were similar and near the minimum detectable activity. Americium-241 was detected at three locations near the minimum detectable activity of approximately 0.07 pCi/L. The gamma spectrometry results detected cesium-137 in three samples, potassium-40 at eight locations, and radium-226 at one location. Mercury was below its maximum contaminant level of 2 µg/L in all samples. Gamma spectrometry results for the CFA production wells did not detect any analytes. Water-level measurements were taken from wells in the Idaho Nuclear Technology and Engineering Center, Central Facilities Area, and the area south of Central Facilities Area to evaluate groundwater flow directions. Water-level measurements indicated groundwater flow to the south-southwest from the Idaho Nuclear Technology and Engineering Center.« less

Direct and long-term detection of gene doping in conventional blood samples.

PubMed

Beiter, T; Zimmermann, M; Fragasso, A; Hudemann, J; Niess, A M; Bitzer, M; Lauer, U M; Simon, P

2011-03-01

The misuse of somatic gene therapy for the purpose of enhancing athletic performance is perceived as a coming threat to the world of sports and categorized as 'gene doping'. This article describes a direct detection approach for gene doping that gives a clear yes-or-no answer based on the presence or absence of transgenic DNA in peripheral blood samples. By exploiting a priming strategy to specifically amplify intronless DNA sequences, we developed PCR protocols allowing the detection of very small amounts of transgenic DNA in genomic DNA samples to screen for six prime candidate genes. Our detection strategy was verified in a mouse model, giving positive signals from minute amounts (20 μl) of blood samples for up to 56 days following intramuscular adeno-associated virus-mediated gene transfer, one of the most likely candidate vector systems to be misused for gene doping. To make our detection strategy amenable for routine testing, we implemented a robust sample preparation and processing protocol that allows cost-efficient analysis of small human blood volumes (200 μl) with high specificity and reproducibility. The practicability and reliability of our detection strategy was validated by a screening approach including 327 blood samples taken from professional and recreational athletes under field conditions.

Methicillin-Resistant Staphylococcus aureus (MRSA) Detection: Comparison of Two Molecular Methods (IDI-MRSA PCR Assay and GenoType MRSA Direct PCR Assay) with Three Selective MRSA Agars (MRSA ID, MRSASelect, and CHROMagar MRSA) for Use with Infection-Control Swabs▿

PubMed Central

van Hal, S. J.; Stark, D.; Lockwood, B.; Marriott, D.; Harkness, J.

2007-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing problem. Rapid detection of MRSA-colonized patients has the potential to limit spread of the organism. We evaluated the sensitivities and specificities of MRSA detection by two molecular methods (IDI-MRSA PCR assay and GenoType MRSA Direct PCR assay) and three selective MRSA agars (MRSA ID, MRSASelect, and CHROMagar MRSA), using 205 (101 nasal, 52 groin, and 52 axillary samples) samples from consecutive known MRSA-infected and/or -colonized patients. All detection methods had higher MRSA detection rates for nasal swabs than for axillary and groin swabs. Detection of MRSA by IDI-MRSA was the most sensitive method, independent of the site (94% for nasal samples, 80% for nonnasal samples, and 90% overall). The sensitivities of the GenoType MRSA Direct assay and the MRSA ID, MRSASelect, and CHROMagar MRSA agars with nasal swabs were 70%, 72%, 68%, and 75%, respectively. All detection methods had high specificities (95 to 99%), independent of the swab site. Extended incubation for a further 24 h with selective MRSA agars increased the detection of MRSA, with a corresponding decline in specificity secondary to a significant increase in false-positive results. There was a noticeable difference in test performance of the GenoType MRSA Direct assay in detection of MRSA (28/38 samples [74%]) compared with detection of nonmultiresistant MRSA (17/31 samples [55%]) (susceptible to two or more non-β-lactam antibiotics). This was not observed with selective MRSA agar plates or IDI-MRSA. Although it is more expensive, in addition to rapid turnaround times of 2 to 4 h, IDI-MRSA offers greater detection of MRSA colonization, independent of the swab site, than do conventional selective agars and GenoType MRSA Direct. PMID:17537949

Sensitive and Rapid Detection of Viable Giardia Cysts and Cryptosporidium parvum Oocysts in Large-Volume Water Samples with Wound Fiberglass Cartridge Filters and Reverse Transcription-PCR

PubMed Central

Kaucner, Christine; Stinear, Timothy

1998-01-01

We recently described a reverse transcription-PCR (RT-PCR) for detecting low numbers of viable Cryptosporidium parvum oocysts spiked into clarified environmental water concentrates. We have now modified the assay for direct analysis of primary sample concentrates with simultaneous detection of viable C. parvum oocysts, Giardia cysts, and a novel type of internal positive control (IPC). The IPC was designed to assess both efficiency of mRNA isolation and potential RT-PCR inhibition. Sensitivity testing showed that low numbers of organisms, in the range of a single viable cyst and oocyst, could be detected when spiked into 100-μl packed pellet volumes of concentrates from creek and river water samples. The RT-PCR was compared with an immunofluorescence (IF) assay by analyzing 29 nonspiked environmental water samples. Sample volumes of 20 to 1,500 liters were concentrated with a wound fiberglass cartridge filter. Frequency of detection for viable Giardia cysts increased from 24% by IF microscopy to 69% by RT-PCR. Viable C. parvum oocysts were detected only once by RT-PCR (3%) in contrast to detection of viable Cryptosporidium spp. in four samples by IF microscopy (14%), suggesting that Cryptosporidium species other than C. parvum were present in the water. This combination of the large-volume sampling method with RT-PCR represents a significant advance in terms of protozoan pathogen monitoring and in the wider application of PCR technology to this field of microbiology. PMID:9572946

Short communication: Ability of dogs to detect cows in estrus from sniffing saliva samples.

PubMed

Fischer-Tenhagen, C; Tenhagen, B-A; Heuwieser, W

2013-02-01

Efficient estrus detection in high-producing dairy cows is a permanent challenge for successful reproductive performance. In former studies, dogs have been trained to identify estrus-specific odor in vaginal fluid, milk, urine, and blood samples under laboratory conditions with an accuracy of more than 80%. For on-farm utilization of estrus-detection dogs it would be beneficial in terms of hygiene and safety if dogs could identify cows from the feed alley. The objective of this proof of concept study was to test if dogs can be trained to detect estrus-specific scent in saliva of cows. Saliva samples were collected from cows in estrus and diestrus. Thirteen dogs of various breeds and both sexes were trained in this study. Five dogs had no experience in scent detection, whereas 8 dogs had been formerly trained for detection of narcotics or cancer. In the training and test situation, dogs had to detect 1 positive out of 4 samples. Dog training was based on positive reinforcement and dogs were rewarded with a clicker and food for indicating saliva samples of cows in estrus. A false indication was ignored and documented in the test situation. Dogs with and without prior training were trained for 1 and 5 d, respectively. For determining the accuracy of detection, the position of the positive sample was unknown to the dog handler, to avoid hidden cues to the dog. The overall percentage of correct positive indications was 57.6% (175/304), with a range from 40 (1 dog) to 75% (3 dogs). To our knowledge, this is the first indication that dogs are able to detect estrus-specific scent in saliva of cows. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Evaluation of a polymerase chain reaction-based system for detection of Salmonella enteritidis, Escherichia coli O157:H7, Listeria spp., and Listeria monocytogenes on fresh fruits and vegetables.

PubMed

Shearer, A E; Strapp, C M; Joerger, R D

2001-06-01

A polymerase chain reaction (PCR)-based detection system, BAX, was evaluated for its sensitivity in detecting Salmonella Enteritidis, Escherichia coli O157:H7, Listeria sp., and Listeria monocytogenes on fresh produce. Fifteen different types of produce (alfalfa sprouts, green peppers, parsley, white cabbage, radishes, onions, carrots, mushrooms, leaf lettuce, tomatoes, strawberries, cantaloupe, mango, apples, and oranges) were inoculated, in separate studies, with Salmonella Enteritidis, E. coli O157:H7, and L. monocytogenes down to the predicted level of 1 CFU per 25-g sample. Detection by BAX was compared to recovery of the inoculated bacteria by culture methods according to the Food and Drug Administration's (FDA) Bacteriological Analytical Manual (BAM). BAX was essentially as sensitive as the culture-based method in detecting Salmonella Enteritidis and L. monocytogenes and more sensitive than the culture-based method for the detection of E. coli O157:H7 on green pepper, carrot, radish, and sprout samples. Detection of the pathogenic bacteria in samples spiked with a predicted number of less than 10 CFU was possible for most produce samples, but both methods failed to detect L. monocytogenes on carrot samples and one of two mushroom and onion samples spiked with less than 100 CFU. Both BAX and the culture method were also unable to consistently recover low numbers of E. coli O157:H7 from alfalfa sprouts. The PCR method allowed detection of Salmonella Enteritidis, E. coli O157:H7, and L. monocytogenes at least 2 days earlier than the conventional culture methods.

A simple, rapid, cost-effective and sensitive method for detection of Salmonella in environmental and pecan samples.

PubMed

Dobhal, S; Zhang, G; Rohla, C; Smith, M W; Ma, L M

2014-10-01

PCR is widely used in the routine detection of foodborne human pathogens; however, challenges remain in overcoming PCR inhibitors present in some sample matrices. The objective of this study was to develop a simple, sensitive, cost-effective and rapid method for processing large numbers of environmental and pecan samples for Salmonella detection. This study was also aimed at validation of a new protocol for the detection of Salmonella from in-shell pecans. Different DNA template preparation methods, including direct boiling, prespin, multiple washing and commercial DNA extraction kits, were evaluated with pure cultures of Salmonella Typhimurium and with enriched soil, cattle feces and in-shell pecan each spiked individually with Salmonella Typhimurium. PCR detection of Salmonella was conducted using invA and 16S rRNA gene (internal amplification control) specific primers. The effect of amplification facilitators, including bovine serum albumin (BSA), polyvinylpyrrolidone (PVP), polyethylene glycol (PEG) and gelatin on PCR sensitivity, was also evaluated. Conducting a prespin of sample matrices in combination with the addition of 0·4% (w/v) BSA and 1% (w/v) PVP in PCR mix was the simplest, most rapid, cost-effective and sensitive method for PCR detection of Salmonella, with up to 40 CFU Salmonella per reaction detectable in the presence of over 10(9 ) CFU ml(-1) of background micro-organisms from enriched feces soil or pecan samples. The developed method is rapid, cost-effective and sensitive for detection of Salmonella from different matrices. This study provides a method with broad applicability for PCR detection of Salmonella in complex sample matrices. This method has a potential for its application in different research arenas and diagnostic laboratories. © 2014 The Society for Applied Microbiology.

Rapid Waterborne Pathogen Detection with Mobile Electronics.

PubMed

Wu, Tsung-Feng; Chen, Yu-Chen; Wang, Wei-Chung; Kucknoor, Ashwini S; Lin, Che-Jen; Lo, Yu-Hwa; Yao, Chun-Wei; Lian, Ian

2017-06-09

Pathogen detection in water samples, without complex and time consuming procedures such as fluorescent-labeling or culture-based incubation, is essential to public safety. We propose an immunoagglutination-based protocol together with the microfluidic device to quantify pathogen levels directly from water samples. Utilizing ubiquitous complementary metal-oxide-semiconductor (CMOS) imagers from mobile electronics, a low-cost and one-step reaction detection protocol is developed to enable field detection for waterborne pathogens. 10 mL of pathogen-containing water samples was processed using the developed protocol including filtration enrichment, immune-reaction detection and imaging processing. The limit of detection of 10 E. coli O157:H7 cells/10 mL has been demonstrated within 10 min of turnaround time. The protocol can readily be integrated into a mobile electronics such as smartphones for rapid and reproducible field detection of waterborne pathogens.

Organic compounds and trace elements in fish tissue and bed sediment from streams in the Yellowstone River basin, Montana and Wyoming, 1998

USGS Publications Warehouse

Peterson, David A.; Boughton, Gregory K.

2000-01-01

A comprehensive water-quality investigation of the Yellowstone River Basin began in 1997, under the National Water-Quality Assessment (NAWQA) Program. Twenty-four sampling sites were selected for sampling of fish tissue and bed sediment during 1998. Organic compounds analyzed included organochlorine insecticides and their metabolites and total polychlorinated biphenyls (PCBs) from fish-tissue and bed-sediment samples, and semivolatile organic compounds from bed-sediment samples. A broad suite of trace elements was analyzed from both fish-tissue and bed-sediment samples, and a special study related to mercury also was conducted. Of the 12 organochlorine insecticides and metabolites detected in the fish-tissue samples, the most compounds per site were detected in samples from integrator sites which represent a mixture of land uses. The presence of DDT, and its metabolites DDD and DDE, in fish collected in the Yellowstone Park area likely reflects long-term residual effects from historical DDT-spraying programs for spruce budworm. Dieldrin, chlordane, and other organic compounds also were detected in the fish-tissue samples. The compound p, p'-DDE was detected at 71 percent of the sampling sites, more than any other compound. The concentrations of total DDT in fish samples were low, however, compared to concentrations from historical data from the study area, other NAWQA studies in the Rocky Mountains, and national baseline concentrations. Only 2 of the 27 organochlorine insecticides and metabolites and total PCBs analyzed in bed sediment were detected. Given that 12 of the compounds were detected in fish-tissue samples, fish appeared to be more sensitive indicators of contamination than bed sediment.Concentrations of some trace elements in fish and bed sediment were higher at sites in mineralized areas than at other sites. Concentrations of selenium in fish tissue from some sites were above background levels. Concentrations of arsenic, chromium, copper, and lead in some of the bed-sediment samples potentially exceeded criteria for the protection of aquatic life.

Detection of epidermal growth factor receptor gene T790M mutation in cytology samples using the cobas® EGFR mutation test.

PubMed

Satouchi, Miyako; Tanaka, Hiroshi; Yoshioka, Hiroshige; Shimokawaji, Tadasuke; Mizuno, Keiko; Takeda, Koji; Yoshino, Ichiro; Seto, Takashi; Kurata, Takayasu; Tashiro, Naoki; Hagiwara, Koichi

2017-09-01

Detection of epidermal growth factor receptor (EGFR) gene mutations is essential in deciding therapeutic strategy in non-small cell lung cancer (NSCLC) patients at initial diagnosis. Moreover, in EGFR mutation-positive (EGFRm) NSCLC patients, re-biopsy at disease progression to clarify resistance mechanisms is also important. However, collecting histology samples is often difficult because of inaccessibility and invasiveness. In some cases, only cytology samples can be collected, and studies have reported that cytology samples are appropriate for EGFR gene mutation testing. The cobas ® EGFR Mutation Test (Roche Molecular Systems Inc., Branchburg, New Jersey, USA) is approved as a companion diagnostic for osimertinib, a third-generation EGFR-tyrosine kinase inhibitor approved in Japan. However, it is not clear whether the EGFR T790M mutation can be detected in cytology samples using this test. The primary objective of this study was to assess concordance of EGFR T790M gene mutation detection between histology and matched cytology samples using the cobas ® EGFR Mutation Test. We conducted a multicenter, observational study in Japan. Overall, 41 EGFRm NSCLC patients who had both histology and cytology samples collected at the same time at re-biopsy and with the results of EGFR mutation test using histology samples were enrolled. The EGFR mutation status of both sample types was tested using the cobas ® EGFR Mutation Test and the concordance rates were calculated. The EGFR T790M mutation detection rate in histology and cytology samples was 42.5% and 37.5%, respectively. The overall percent agreement between the histology and cytology samples was 91.7%. These data demonstrate that the cobas ® EGFR Mutation Test can detect the EGFR T790M mutation in both cytology and histology samples. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

A Method for Choosing the Best Samples for Mars Sample Return

PubMed Central

Gordon, Peter R.

2018-01-01

Abstract Success of a future Mars Sample Return mission will depend on the correct choice of samples. Pyrolysis-FTIR can be employed as a triage instrument for Mars Sample Return. The technique can thermally dissociate minerals and organic matter for detection. Identification of certain mineral types can determine the habitability of the depositional environment, past or present, while detection of organic matter may suggest past or present habitation. In Mars' history, the Theiikian era represents an attractive target for life search missions and the acquisition of samples. The acidic and increasingly dry Theiikian may have been habitable and followed a lengthy neutral and wet period in Mars' history during which life could have originated and proliferated to achieve relatively abundant levels of biomass with a wide distribution. Moreover, the sulfate minerals produced in the Theiikian are also known to be good preservers of organic matter. We have used pyrolysis-FTIR and samples from a Mars analog ferrous acid stream with a thriving ecosystem to test the triage concept. Pyrolysis-FTIR identified those samples with the greatest probability of habitability and habitation. A three-tier scoring system was developed based on the detection of (i) organic signals, (ii) carbon dioxide and water, and (iii) sulfur dioxide. The presence of each component was given a score of A, B, or C depending on whether the substance had been detected, tentatively detected, or not detected, respectively. Single-step (for greatest possible sensitivity) or multistep (for more diagnostic data) pyrolysis-FTIR methods informed the assignments. The system allowed the highest-priority samples to be categorized as AAA (or A*AA if the organic signal was complex), while the lowest-priority samples could be categorized as CCC. Our methods provide a mechanism with which to rank samples and identify those that should take the highest priority for return to Earth during a Mars Sample Return mission. Key Words: Mars—Astrobiology—Search for Mars' organics—Infrared spectroscopy—Planetary habitability and biosignatures. Astrobiology 18, 556–570. PMID:29443541

A Method for Choosing the Best Samples for Mars Sample Return.

PubMed

Gordon, Peter R; Sephton, Mark A

2018-05-01

Success of a future Mars Sample Return mission will depend on the correct choice of samples. Pyrolysis-FTIR can be employed as a triage instrument for Mars Sample Return. The technique can thermally dissociate minerals and organic matter for detection. Identification of certain mineral types can determine the habitability of the depositional environment, past or present, while detection of organic matter may suggest past or present habitation. In Mars' history, the Theiikian era represents an attractive target for life search missions and the acquisition of samples. The acidic and increasingly dry Theiikian may have been habitable and followed a lengthy neutral and wet period in Mars' history during which life could have originated and proliferated to achieve relatively abundant levels of biomass with a wide distribution. Moreover, the sulfate minerals produced in the Theiikian are also known to be good preservers of organic matter. We have used pyrolysis-FTIR and samples from a Mars analog ferrous acid stream with a thriving ecosystem to test the triage concept. Pyrolysis-FTIR identified those samples with the greatest probability of habitability and habitation. A three-tier scoring system was developed based on the detection of (i) organic signals, (ii) carbon dioxide and water, and (iii) sulfur dioxide. The presence of each component was given a score of A, B, or C depending on whether the substance had been detected, tentatively detected, or not detected, respectively. Single-step (for greatest possible sensitivity) or multistep (for more diagnostic data) pyrolysis-FTIR methods informed the assignments. The system allowed the highest-priority samples to be categorized as AAA (or A*AA if the organic signal was complex), while the lowest-priority samples could be categorized as CCC. Our methods provide a mechanism with which to rank samples and identify those that should take the highest priority for return to Earth during a Mars Sample Return mission. Key Words: Mars-Astrobiology-Search for Mars' organics-Infrared spectroscopy-Planetary habitability and biosignatures. Astrobiology 18, 556-570.

Detection of Salmonella invA gene in shrimp enrichment culture by polymerase chain reaction.

PubMed

Upadhyay, Bishnu Prasad; Utrarachkij, Fuangfa; Thongshoob, Jarinee; Mahakunkijcharoen, Yuvadee; Wongchinda, Niracha; Suthienkul, Orasa; Khusmith, Srisin

2010-03-01

Contamination of seafood with salmonellae is a major public health concern. Detection of Salmonella by standard culture methods is time consuming. In this study, an enrichment culture step prior to polymerase chain reaction (PCR) was applied to detect 284 bp fragment of Salmonella invA in comparison with the conventional culture method in 100 shrimp samples collected from four different shrimp farms and fresh food markets around Bangkok. Samples were pre-enriched in non-selective lactose broth (LB) and selective tetrathionate broth (TTB). PCR detection limit was 10 pg and 10(4) cfu/ml of viable salmonellae with 100% specificity. PCR assay detected 19 different Salmonella serovars belonging to 8 serogroups (B, C1, C2-C3, D1, E1, E4 and K) commonly found in clinical and environmental samples in Thailand. The detection rate of PCR following TTB enrichment (24%) was higher than conventional culture method (19%). PCR following TTB, but not in LB enrichment allowed salmonella detection with 84% sensitivity, 90% specificity and 89% accuracy. Shrimp samples collected from fresh food markets had higher levels of contaminated salmonellae than those from shrimp farms. The results indicated that incorporation of an enrichment step prior to PCR has the potential to be applied for detection of naturally contaminated salmonellae in food, environment and clinical samples.

Paper-based archiving of biological samples from fish for detecting betanodavirus.

PubMed

Navaneeth Krishnan, A; Bhuvaneswari, T; Ezhil Praveena, P; Jithendran, K P

2016-07-01

This study was carried out to evaluate the efficiency of the Flinders Technology Associates (FTA(®)) card (Whatman(®)) as a sampling device and storage platform for RNA from betanodavirus-infected biological samples (viz., larvae, broodstock, cell culture supernatants and rearing seawater spiked with infected materials). The study showed that FTA cards can be used to detect betanodaviruses by reverse transcription-polymerase chain reaction (RT-PCR). The diagnostic efficiency of RT-PCR from all sample types on FTA cards decreased after 21 days of storage at 4 °C, although the virus could be detected up to 28 days by nested RT-PCR. The FTA card protocol thus provides a supplementary method for quick and easy collection of samples, preservation of RNA on a dry storage basis, and detection of betanodavirus-infected fish.

Rapid detection of food-borne Salmonella contamination using IMBs-qPCR method based on pagC gene.

PubMed

Wang, Jiashun; Li, Yi; Chen, Jia; Hua, Deping; Li, Yi; Deng, Hui; Li, Ying; Liang, Zhixuan; Huang, Jinhai

Detection of Salmonella is very important to minimize the food safety risk. In this study, the recombinant PagC protein and PagC antibody were prepared and coupled with immunomagnetic beads (IMBs) to capture Salmonella cells from pork and milk samples. And then the SYBR Green qualitative PCR was developed to detect the pathogenic Salmonella. The results showed that the PagC polyclonal antiserum is of good specificity and the capture rate of 0.1mg IMBs for Salmonella tended to be stable at the range of 70-74% corresponding to the concentrations between 10 1 and 10 4 CFU/mL. The method developed demonstrated high specificity for the positive Salmonella samples when compared to non-specific DNA samples, such as Escherichia coli, Staphylococcus aureus, Yersinia enterocolitica, and Yersinia pseudotuberculosis. The limit of detection of this assay was 18CFU/mL. Detection and quantitative enumeration of Salmonella in samples of pork or milk shows good recoveries of 54.34% and 52.07%. In conclusion, the polyclonal antibody of recombinant PagC protein is effective to capture Salmonella from detected samples. The developed pagC antibody IMBs-qPCR method showed efficiency, sensitivity and specificity for 30 Salmonella detection, enabling detection within 10h, which is a promising rapid method to detect Salmonella in emergency. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Immunoblotting assays for keratan sulfate.

PubMed

Yoon, Jung Hae; Brooks, Randolph; Halper, Jaroslava

2002-07-15

The detection of microquantities of glycosaminoglycans (GAGs) in biological samples has been hampered by the lack of sensitive methods. In this paper we describe the modification and development of three sensitive assays capable of detecting nanogram quantities of GAGs in biological samples. The first assay detects total GAGs. It is a modified Alcian blue dye precipitation assay in which the dye binds to the negatively charged GAGs in CsCl-fractionated extracts from chicken tendons. This assay compares favorably with the widely used uronic acid assay in terms of its sensitivity and ability to detect all classes of GAGs, including keratan sulfate (KS). Two other assays, dot-blotting and immunoblotting, detect KS in complex mixtures and can be easily adapted for the detection of other GAGs. Both take advantage of binding of carboxyl and sulfate groups of GAGs to trivalent neodymium. In dot-blotting, samples were directly blotted onto nitrocellulose membrane soaked in Nd(2)(SO(4))(3) buffer, and KS was detected with the monoclonal anti-KS 5-D-4 antibody and an avidin-biotin complex detection system. In immunoblotting, the samples were first separated in 28% polyacrylamide gels, transferred onto a Nd(2)(SO(4))(3)-soaked nitrocellulose membrane using a phosphate buffer system, and stained and developed using the same protocol as in dot-blotting. Whereas dot-blotting allows the use of very low quantities of samples because of its high sensitivity (lower detection limit was 5 ng), immunoblotting provides more specificity.

Evaluation of blood and muscle tissues for molecular detection and characterization of hematozoa infections in northern pintails (Anas acuta) wintering in California

USGS Publications Warehouse

Ramey, Andy M.; Schmutz, Joel A.; Fleskes, Joseph P.; Yabsley, Michael J.

2013-01-01

Information on the molecular detection of hematozoa from different tissue types and multiple years would be useful to inform sample collection efforts and interpret results of meta-analyses or investigations spanning multiple seasons. In this study, we tested blood and muscle tissue collected from northern pintails (Anas acuta) during autumn and winter of different years to evaluate prevalence and genetic diversity ofLeucocytozoon, Haemoproteus, and Plasmodium infections in this abundant waterfowl species of the Central Valley of California. We first compared results for paired blood and wing muscle samples to assess the utility of different tissue types for molecular investigations of haemosporidian parasites. Second, we explored inter-annual variability of hematozoa infection in Central Valley northern pintails and investigated possible effects of age, sex, and sub-region of sample collection on estimated parasite detection probability and prevalence. We found limited evidence for differences between tissue types in detection probability and prevalence ofLeucocytozoon, Haemoproteus, and Plasmodium parasites, which supports the utility of both sample types for obtaining information on hematozoan infections. However, we detected 11 haemosporidian mtDNA cyt bhaplotypes in blood samples vs. six in wing muscle tissue collected during the same sample year suggesting an advantage to using blood samples for investigations of genetic diversity. Estimated prevalence ofLeucocytozoon parasites was greater during 2006–2007 as compared to 2011–2012 and four unique haemosporidian mtDNA cyt b haplotypes were detected in the former sample year but not in the latter. Seven of 15 mtDNA cyt b haplotypes detected in northern pintails had 100% identity with previously reported hematozoa lineages detected in waterfowl (Haemoproteus and Leucocytozoon) or other avian taxa (Plasmodium) providing support for lack of host specificity for some parasite lineages.

Reconnaissance investigations of potential ground-water and sediment contamination at three former underground storage tank locations, Fort Jackson, South Carolina, 1994

USGS Publications Warehouse

Robertson, J.F.; Nagle, Douglas D.; Rhodes, Liesl C.

1994-01-01

Investigations to provide initial qualitative delineation of petroleum hydrocarbon contamination at three former underground storage tank locations at Fort Jackson, South Carolina, were made during March 1994. Ground-water and sediment samples were collected using direct-push technology and analyzed on-site with a gas chromatograph, which provided real-time, semi-quantitative data. In addition, ground-water and sediment samples were collected at selected sites for laboratory analyses to provide a confirmation of the on-site data. These analyses provided qualitative data on the lateral distri- bution of petroleum hydrocarbons. Petroleum hydrocarbons were detected by on-site analysis in ground-water samples from nine locations at Site 1062, suggesting the presence of a contaminant plume. Concentrations ranged from less than the minimum detection limit to 4,511 mg/L (micrograms per liter) for benzene, 15,594 mg/L for toluene, 16,501 mg/L for ethylbenzene, and 19,391 mg/L for total xylenes. Concentrations of Total Petroleum Hydrocarbons-Gasoline Range Organics ranged from 323 mg/L to 3,364 mg/L; Total Petroleum Hydrocarbons-Diesel Range Organics were not detected. Three samples from this site were analyzed for benzene, toluene, ethylbenzene, and total xylenes at a laboratory and results showed concentrations ranging from less than the minimum detection limit to 1,070 mg/L for benzene, 7,930 mg/L for toluene, 6,890 mg/L for ethylbenzene, and 1,524 mg/L for total xylenes. Petroleum hydro- carbons were detected by on-site analysis in only one sample at Site 2438. A concentration of 131,000 micrograms per kilogram Total Petroleum Hydrocarbons-Diesel Range Organics was detected in sample number GP-2-4-13.5. Petroleum hydrocarbons were detected by on-site analysis in only one ground-water sample from Site 2444. A concentration of 3,145 mg/L Total Petroleum Hydrocarbons-Gasoline Range Organics was detected at sampling location GP-3-2.

Immunological detection of small organic molecules in the presence of perchlorates: relevance to the life marker chip and life detection on Mars.

PubMed

Rix, Catherine S; Sims, Mark R; Cullen, David C

2011-11-01

The proposed ExoMars mission, due to launch in 2018, aims to look for evidence of extant and extinct life in martian rocks and regolith. Previous attempts to detect organic molecules of biological or abiotic origin on Mars have been unsuccessful, which may be attributable to destruction of these molecules by perchlorate salts during pyrolysis sample extraction techniques. Organic molecules can also be extracted and measured with solvent-based systems. The ExoMars payload includes the Life Marker Chip (LMC) instrument, capable of detecting biomarker molecules of extant and extinct Earth-like life in liquid extracts of martian samples with an antibody microarray assay. The aim of the work reported here was to investigate whether the presence of perchlorate salts, at levels similar to those at the NASA Phoenix landing site, would compromise the LMC extraction and detection method. To test this, we implemented an LMC-representative sample extraction process with an LMC-representative antibody assay and used these to extract and analyze a model sample that consisted of a Mars analog sample matrix (JSC Mars-1) spiked with a representative organic molecular target (pyrene, an example of abiotic meteoritic infall targets) in the presence of perchlorate salts. We found no significant change in immunoassay function when using pyrene standards with added perchlorate salts. When model samples spiked with perchlorate salts were subjected to an LMC-representative liquid extraction, immunoassays functioned in a liquid extract and detected extracted pyrene. For the same model sample matrix without perchlorate salts, we observed anomalous assay signals that coincided with yellow coloration of the extracts. This unexpected observation is being studied further. This initial study indicates that the presence of perchlorate salts, at levels similar to those detected at the NASA Phoenix landing site, is unlikely to prevent the LMC from extracting and detecting organic molecules from martian samples.

New biosensors for food safety screening solutions

NASA Astrophysics Data System (ADS)

Dyer, Maureen A.; Oberholtzer, Jennifer A.; Mulligan, David C.; Hanson, William P.

2009-05-01

Hanson Technologies has developed the automated OmniFresh 1000 system to sample large volumes of produce wash water, collect the pathogens, and detect their presence. By collecting a continuous sidestream of wash water, the OmniFresh uses a sample that represent the entire lot of produce being washed. The OmniFresh does not require bacterial culture or enrichment, and it detects both live and dead bacteria in the collected sample using an in-line sensor. Detection occurs in an array biosensor capable of handling large samples with complex matrices. Additionally, sample can be sent for traditional confirming tests after the screening performed by the OmniFresh.

Optimal sampling strategies for detecting zoonotic disease epidemics.

PubMed

Ferguson, Jake M; Langebrake, Jessica B; Cannataro, Vincent L; Garcia, Andres J; Hamman, Elizabeth A; Martcheva, Maia; Osenberg, Craig W

2014-06-01

The early detection of disease epidemics reduces the chance of successful introductions into new locales, minimizes the number of infections, and reduces the financial impact. We develop a framework to determine the optimal sampling strategy for disease detection in zoonotic host-vector epidemiological systems when a disease goes from below detectable levels to an epidemic. We find that if the time of disease introduction is known then the optimal sampling strategy can switch abruptly between sampling only from the vector population to sampling only from the host population. We also construct time-independent optimal sampling strategies when conducting periodic sampling that can involve sampling both the host and the vector populations simultaneously. Both time-dependent and -independent solutions can be useful for sampling design, depending on whether the time of introduction of the disease is known or not. We illustrate the approach with West Nile virus, a globally-spreading zoonotic arbovirus. Though our analytical results are based on a linearization of the dynamical systems, the sampling rules appear robust over a wide range of parameter space when compared to nonlinear simulation models. Our results suggest some simple rules that can be used by practitioners when developing surveillance programs. These rules require knowledge of transition rates between epidemiological compartments, which population was initially infected, and of the cost per sample for serological tests.

Rapid detection of Naegleria fowleri in water distribution pipeline biofilms and drinking water samples.

PubMed

Puzon, Geoffrey J; Lancaster, James A; Wylie, Jason T; Plumb, Iason J

2009-09-01

Rapid detection of pathogenic Naegleria fowler in water distribution networks is critical for water utilities. Current detection methods rely on sampling drinking water followed by culturing and molecular identification of purified strains. This culture-based method takes an extended amount of time (days), detects both nonpathogenic and pathogenic species, and does not account for N. fowleri cells associated with pipe wall biofilms. In this study, a total DNA extraction technique coupled with a real-time PCR method using primers specific for N. fowleri was developed and validated. The method readily detected N. fowleri without preculturing with the lowest detection limit for N. fowleri cells spiked in biofilm being one cell (66% detection rate) and five cells (100% detection rate). For drinking water, the detection limit was five cells (66% detection rate) and 10 cells (100% detection rate). By comparison, culture-based methods were less sensitive for detection of cells spiked into both biofilm (66% detection for <10 cells) and drinking water (0% detection for <10 cells). In mixed cultures of N. fowleri and nonpathogenic Naegleria, the method identified N. fowleri in 100% of all replicates, whereastests with the current consensus primers detected N. fowleri in only 5% of all replicates. Application of the new method to drinking water and pipe wall biofilm samples obtained from a distribution network enabled the detection of N. fowleri in under 6 h, versus 3+ daysforthe culture based method. Further, comparison of the real-time PCR data from the field samples and the standard curves enabled an approximation of N. fowleri cells in the biofilm and drinking water. The use of such a method will further aid water utilities in detecting and managing the persistence of N. fowleri in water distribution networks.

Consistently Sampled Correlation Filters with Space Anisotropic Regularization for Visual Tracking

PubMed Central

Shi, Guokai; Xu, Tingfa; Luo, Jiqiang; Li, Yuankun

2017-01-01

Most existing correlation filter-based tracking algorithms, which use fixed patches and cyclic shifts as training and detection measures, assume that the training samples are reliable and ignore the inconsistencies between training samples and detection samples. We propose to construct and study a consistently sampled correlation filter with space anisotropic regularization (CSSAR) to solve these two problems simultaneously. Our approach constructs a spatiotemporally consistent sample strategy to alleviate the redundancies in training samples caused by the cyclical shifts, eliminate the inconsistencies between training samples and detection samples, and introduce space anisotropic regularization to constrain the correlation filter for alleviating drift caused by occlusion. Moreover, an optimization strategy based on the Gauss-Seidel method was developed for obtaining robust and efficient online learning. Both qualitative and quantitative evaluations demonstrate that our tracker outperforms state-of-the-art trackers in object tracking benchmarks (OTBs). PMID:29231876

Validation of a new HPV self-sampling device for cervical cancer screening: The Cervical and Self-Sample In Screening (CASSIS) study.

PubMed

El-Zein, Mariam; Bouten, Sheila; Louvanto, Karolina; Gilbert, Lucy; Gotlieb, Walter; Hemmings, Robert; Behr, Marcel A; Franco, Eduardo L

2018-04-17

We compared the self-sampling performance of the newly designed HerSwab™ device with a physician-collected cervical sample and another self-sample using the cobas® PCR Female swab for the detection of cervical intraepithelial neoplasia (CIN) and cancer. Women referred for colposcopy at McGill University affiliated hospital clinics collected two consecutive self-samples, one with HerSwab™ and one with cobas® swab, after receiving instructions. The order of sampling was randomized. The colposcopist then collected a cervical sample and conducted a colposcopic examination. Samples were tested for human papillomavirus (HPV) DNA. Sensitivity and specificity to detect CIN2+ and respective 95% confidence intervals (CI) were calculated to compare sampling approaches. The HPV testing agreement between samples was measured using the Kappa statistic. Of 1217 women enrolled, 1076 had complete results for HPV and cytology; 148 (13.8%) had CIN1, 147 (13.7%) had CIN2/3, and 5 (0.5%) had cancer. There was very good agreement between methods for HPV detection (HerSwab™ versus physician: kappa=0.84; cobas® swabs versus physician: kappa=0.81; HerSwab™ versus cobas® swabs: kappa=0.87). The sensitivity of HPV detection for CIN2+ was 87.6% (95%CI: 79.8-93.2) with self-sampling using HerSwab™, 88.6% (95%CI: 80.9-94.0) with self-sampling using the cobas® swab, and 92.4% (95%CI: 85.5-96.7) with physician sampling. Corresponding estimates of specificity were 58.1% (95%CI: 54.1-62.1), 55.0% (95%CI: 50.9-59.0) and 58.7% (95%CI: 54.6-62.6). Cytology (ASC-US or more severe) done on the physician-collected specimen was 80.2% (95%CI: 70.8-87.6) sensitive and 61.4% (95%CI: 57.2-65.5) specific for CIN2+. The HerSwab™ had good agreement with physician sampling in detecting HPV, and adequate performance in detecting high-grade lesions among women referred to colposcopy for abnormal cytology. Copyright © 2018 Elsevier Inc. All rights reserved.

An empirical probability model of detecting species at low densities.

PubMed

Delaney, David G; Leung, Brian

2010-06-01

False negatives, not detecting things that are actually present, are an important but understudied problem. False negatives are the result of our inability to perfectly detect species, especially those at low density such as endangered species or newly arriving introduced species. They reduce our ability to interpret presence-absence survey data and make sound management decisions (e.g., rapid response). To reduce the probability of false negatives, we need to compare the efficacy and sensitivity of different sampling approaches and quantify an unbiased estimate of the probability of detection. We conducted field experiments in the intertidal zone of New England and New York to test the sensitivity of two sampling approaches (quadrat vs. total area search, TAS), given different target characteristics (mobile vs. sessile). Using logistic regression we built detection curves for each sampling approach that related the sampling intensity and the density of targets to the probability of detection. The TAS approach reduced the probability of false negatives and detected targets faster than the quadrat approach. Mobility of targets increased the time to detection but did not affect detection success. Finally, we interpreted two years of presence-absence data on the distribution of the Asian shore crab (Hemigrapsus sanguineus) in New England and New York, using our probability model for false negatives. The type of experimental approach in this paper can help to reduce false negatives and increase our ability to detect species at low densities by refining sampling approaches, which can guide conservation strategies and management decisions in various areas of ecology such as conservation biology and invasion ecology.

Next-Generation Genotyping by Digital PCR to Detect and Quantify the BRAF V600E Mutation in Melanoma Biopsies.

PubMed

Lamy, Pierre-Jean; Castan, Florence; Lozano, Nicolas; Montélion, Cécile; Audran, Patricia; Bibeau, Frédéric; Roques, Sylvie; Montels, Frédéric; Laberenne, Anne-Claire

2015-07-01

The detection of the BRAF V600E mutation in melanoma samples is used to select patients who should respond to BRAF inhibitors. Different techniques are routinely used to determine BRAF status in clinical samples. However, low tumor cellularity and tumor heterogeneity can affect the sensitivity of somatic mutation detection. Digital PCR (dPCR) is a next-generation genotyping method that clonally amplifies nucleic acids and allows the detection and quantification of rare mutations. Our aim was to evaluate the clinical routine performance of a new dPCR-based test to detect and quantify BRAF mutation load in 47 paraffin-embedded cutaneous melanoma biopsies. We compared the results obtained by dPCR with high-resolution melting curve analysis and pyrosequencing or with one of the allele-specific PCR methods available on the market. dPCR showed the lowest limit of detection. dPCR and allele-specific amplification detected the highest number of mutated samples. For the BRAF mutation load quantification both dPCR and pyrosequencing gave similar results with strong disparities in allele frequencies in the 47 tumor samples under study (from 0.7% to 79% of BRAF V600E mutations/sample). In conclusion, the four methods showed a high degree of concordance. dPCR was the more-sensitive method to reliably and easily detect mutations. Both pyrosequencing and dPCR could quantify the mutation load in heterogeneous tumor samples. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

[New methodological advances: algorithm proposal for management of Clostridium difficile infection].

PubMed

González-Abad, María José; Alonso-Sanz, Mercedes

2015-06-01

Clostridium difficile infection (CDI) is considered the most common cause of health care-associated diarrhea and also is an etiologic agent of community diarrhea. The aim of this study was to assess the potential benefit of a test that detects glutamate dehydrogenase (GDH) antigen and C. difficile toxin A/B, simultaneously, followed by detection of C. difficile toxin B (tcdB) gene by PCR as confirmatory assay on discrepant samples, and to propose an algorithm more efficient. From June 2012 to January 2013 at Hospital Infantil Universitario Niño Jesús, Madrid, the stool samples were studied for the simultaneous detection of GDH and toxin A/B, and also for detection of toxin A/B alone. When results between GDH and toxin A/B were discordant, a single sample for patient was selected for detection of C. difficile toxin B (tcdB) gene. A total of 116 samples (52 patients) were tested. Four were positive and 75 negative for toxigenic C. difficile (Toxin A/B, alone or combined with GDH). C. difficile was detected in the remaining 37 samples but not toxin A/B, regardless of the method used, except one. Twenty of the 37 specimens were further tested for C. difficile toxin B (tcdB) gene and 7 were positive. The simultaneous detection of GDH and toxin A/B combined with PCR recovered undiagnosed cases of CDI. In accordance with our data, we propose a two-step algorithm: detection of GDH and PCR (in samples GDH positive). This algorithm could provide a superior cost-benefit ratio in our population.

Electrochemical sample matrix elimination for trace-level potentiometric detection with polymeric membrane ion-selective electrodes.

PubMed

Chumbimuni-Torres, Karin Y; Calvo-Marzal, Percy; Wang, Joseph; Bakker, Eric

2008-08-01

Potentiometric sensors are today sufficiently well understood and optimized to reach ultratrace level (subnanomolar) detection limits for numerous ions. In many cases of practical relevance, however, a high electrolyte background hampers the attainable detection limits. A particularly difficult sample matrix for potentiometric detection is seawater, where the high saline concentration forms a major interfering background and reduces the activity of most trace metals by complexation. This paper describes for the first time a hyphenated system for the online electrochemically modulated preconcentration and matrix elimination of trace metals, combined with a downstream potentiometric detection with solid contact polymeric membrane ion-selective microelectrodes. Following the preconcentration at the bismuth-coated electrode, the deposited metals are oxidized and released to a medium favorable to potentiometric detection, in this case calcium nitrate. Matrix interferences arising from the saline sample medium are thus circumvented. This concept is successfully evaluated with cadmium as a model trace element and offers potentiometric detection down to low parts per billion levels in samples containing 0.5 M NaCl background electrolyte.

Electrochemical Sample Matrix Elimination for Trace Level Potentiometric Detection with Polymeric Membrane Ion-Selective Electrodes

PubMed Central

Chumbimuni-Torres, Karin Y.; Calvo-Marzal, Percy; Wang, Joseph; Bakker, Eric

2008-01-01

Potentiometric sensors are today sufficiently well understood and optimized to reach ultra-trace level (sub-nanomolar) detection limits for numerous ions. In many cases of practical relevance, however, a high electrolyte background hampers the attainable detection limits. A particularly difficult sample matrix for potentiometric detection is seawater, where the high saline concentration forms a major interfering background and reduces the activity of most trace metals by complexation. This paper describes for the first time a hyphenated system for the online electrochemically modulated preconcentration and matrix elimination (EMPM) of trace metals, combined with a downstream potentiometric detection with solid contact polymeric membrane ion-selective microelectrodes. Following the preconcentration at the bismuth coated electrodes, the deposited metals are oxidized and released to a medium favorable to potentiometric detection, in this case calcium nitrate. Matrix interferences arising from the saline sample medium are thus circumvented. This concept is successfully evaluated with cadmium as a model trace element and offers potentiometric detection down to low parts per billion levels in samples containing 0.5 M NaCl background electrolyte. PMID:18570385

Detection of Salmonella enterica Serovar Typhimurium by Using a Rapid, Array-Based Immunosensor

PubMed Central

Taitt, Chris Rowe; Shubin, Yura S.; Angel, Roselina; Ligler, Frances S.

2004-01-01

The multianalyte array biosensor (MAAB) is a rapid analysis instrument capable of detecting multiple analytes simultaneously. Rapid (15-min), single-analyte sandwich immunoassays were developed for the detection of Salmonella enterica serovar Typhimurium, with a detection limit of 8 × 104 CFU/ml; the limit of detection was improved 10-fold by lengthening the assay protocol to 1 h. S. enterica serovar Typhimurium was also detected in the following spiked foodstuffs, with minimal sample preparation: sausage, cantaloupe, whole liquid egg, alfalfa sprouts, and chicken carcass rinse. Cross-reactivity tests were performed with Escherichia coli and Campylobacter jejuni. To determine whether the MAAB has potential as a screening tool for the diagnosis of asymptomatic Salmonella infection of poultry, chicken excretal samples from a private, noncommercial farm and from university poultry facilities were tested. While the private farm excreta gave rise to signals significantly above the buffer blanks, none of the university samples tested positive for S. enterica serovar Typhimurium without spiking; dose-response curves of spiked excretal samples from university-raised poultry gave limits of detection of 8 × 103 CFU/g. PMID:14711637

Detection of Adulterated Vegetable Oils Containing Waste Cooking Oils Based on the Contents and Ratios of Cholesterol, β-Sitosterol, and Campesterol by Gas Chromatography/Mass Spectrometry.

PubMed

Zhao, Haixiang; Wang, Yongli; Xu, Xiuli; Ren, Heling; Li, Li; Xiang, Li; Zhong, Weike

2015-01-01

A simple and accurate authentication method for the detection of adulterated vegetable oils that contain waste cooking oil (WCO) was developed. This method is based on the determination of cholesterol, β-sitosterol, and campesterol in vegetable oils and WCO by GC/MS without any derivatization. A total of 148 samples involving 12 types of vegetable oil and WCO were analyzed. According to the results, the contents and ratios of cholesterol, β-sitosterol, and campesterol were found to be criteria for detecting vegetable oils adulterated with WCO. This method could accurately detect adulterated vegetable oils containing 5% refined WCO. The developed method has been successfully applied to multilaboratory analysis of 81 oil samples. Seventy-five samples were analyzed correctly, and only six adulterated samples could not be detected. This method could not yet be used for detection of vegetable oils adulterated with WCO that are used for frying non-animal foods. It provides a quick method for detecting adulterated edible vegetable oils containing WCO.

Detection probabilities of electrofishing, hoop nets, and benthic trawls for fishes in two western North American rivers

USGS Publications Warehouse

Smith, Christopher D.; Quist, Michael C.; Hardy, Ryan S.

2015-01-01

Research comparing different sampling techniques helps improve the efficiency and efficacy of sampling efforts. We compared the effectiveness of three sampling techniques (small-mesh hoop nets, benthic trawls, boat-mounted electrofishing) for 30 species in the Green (WY, USA) and Kootenai (ID, USA) rivers by estimating conditional detection probabilities (probability of detecting a species given its presence at a site). Electrofishing had the highest detection probabilities (generally greater than 0.60) for most species (88%), but hoop nets also had high detectability for several taxa (e.g., adult burbot Lota lota, juvenile northern pikeminnow Ptychocheilus oregonensis). Benthic trawls had low detection probabilities (<0.05) for most taxa (84%). Gear-specific effects were present for most species indicating large differences in gear effectiveness among techniques. In addition to gear effects, habitat characteristics also influenced detectability of fishes. Most species-specific habitat relationships were idiosyncratic and reflected the ecology of the species. Overall findings of our study indicate that boat-mounted electrofishing and hoop nets are the most effective techniques for sampling fish assemblages in large, coldwater rivers.

Short-term Natural History of High-Risk Human Papillomavirus Infection in Mid-Adult Women Sampled Monthly (Short title: Short-term HPV Natural History in Mid-Adult Women)

PubMed Central

Fu, Tsung-chieh (Jane); Xi, Long Fu; Hulbert, Ayaka; Hughes, James P.; Feng, Qinghua; Schwartz, Stephen M.; Hawes, Stephen E.; Koutsky, Laura A.; Winer, Rachel L.

2015-01-01

Characterizing short-term HPV detection patterns and viral load may inform HPV natural history in mid-adult women. From 2011–2012, we recruited women aged 30–50 years. Women submitted monthly self-collected vaginal samples for high-risk HPV DNA testing for 6 months. Positive samples were tested for type-specific HPV DNA load by real-time PCR. HPV type-adjusted linear and Poisson regression assessed factors associated with 1) viral load at initial HPV detection and 2) repeat type-specific HPV detection. One-hundred thirty-nine women (36% of 387 women with ≥4 samples) contributed 243 type-specific HR HPV infections during the study; 54% of infections were prevalent and 46% were incident. Incident (versus prevalent) detection and past pregnancy were associated with lower viral load, whereas current smoking was associated with higher viral load. In multivariate analysis, current smoking was associated with a 40% (95%CI:5%–87%) increase in the proportion of samples that were repeatedly positive for the same HPV type, whereas incident (versus prevalent) detection status and past pregnancy were each associated with a reduction in the proportion of samples repeatedly positive (55%,95%CI:38%–67% and 26%,95%CI:10%–39%, respectively). In a separate multivariate model, each log10 increase in viral load was associated with a 10% (95%CI:4%–16%) increase in the proportion of samples repeatedly positive. Factors associated with repeat HPV detection were similar to those observed in longer-term studies, suggesting that short-term repeat detection may relate to long-term persistence. The negative associations between incident HPV detection and both viral load and repeat detection suggest that reactivation or intermittent persistence was more common than new acquisition. PMID:25976733

Rapid diagnosis of common deletional α-thalassemia in the Chinese population by qPCR based on identical primer homologous fragments.

PubMed

Long, Ju

2016-05-01

In China, -(SEA), -α(3.7) and -α(4.2) are common deletional α-thalassemia alleles. Gap-PCR is the currently used detection method for these alleles, whose disadvantages include time-consuming procedure and increased potential for PCR product contamination. Therefore, this detection method needs to be improved. Based on identical-primer homologous fragments, a qPCR system was developed for deletional α-thalassemia genotyping, which was composed of a group of quantitatively-related primers and their corresponding probes plus two groups of qualitatively-related primers and their corresponding probes. In order to verify the accuracy of the qPCR system, known genotype samples and random samples are employed. The standard curve result demonstrated that designed primers and probes all yielded good amplification efficiency. In the tests of known genotype samples and random samples, sample detection results were consistent with verification results. In detecting αα, -(SEA), -α(3.7) and -α(4.2) alleles, deletional α-thalassemia alleles are accurately detected by this method. In addition, this method is provided with a wider detection range, greater speed and reduced PCR product contamination risk when compared with current common gap-PCR detection reagents. Copyright © 2016 Elsevier B.V. All rights reserved.

Immunochromatographic strip assay for the rapid and sensitive detection of Salmonella Typhimurium in artificially contaminated tomato samples.

PubMed

Shukla, Shruti; Leem, Hyerim; Lee, Jong-Suk; Kim, Myunghee

2014-06-01

This study was designed to confirm the applicability of a liposome-based immunochromatographic assay for the rapid detection of Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella Typhimurium) in artificially contaminated tomato samples. To determine the detection limit and pre-enrichment incubation time (10, 12, and 18 h pre-enrichment in 1% buffered peptone water), the tests were performed with different cell numbers of Salmonella Typhimurium (3 × 10(0), 3 × 10(1), 3 × 10(2), and 3 × 10(3) CFU·mL(-1)) inoculated into 25 g of crushed tomato samples. The assay was able to detect as few as 30 Salmonella Typhimurium cells per 25 g of tomato samples (1.2 cells·g(-1)) after 12 h pre-enrichment incubation. Moreover, when the developed assay was compared with traditional morphological and biochemical culture-based methods as well as colloidal gold nanoparticle-based commercial test strips, the developed assay yielded positive results for the detection of Salmonella Typhimurium within a shorter period time. These findings confirm that the developed assay may have practical application for the sensitive detection of Salmonella Typhimurium in various food samples, including raw vegetables, with a relatively low detection limit and shorter analysis time.

A Unimodal Model for Double Observer Distance Sampling Surveys.

PubMed

Becker, Earl F; Christ, Aaron M

2015-01-01

Distance sampling is a widely used method to estimate animal population size. Most distance sampling models utilize a monotonically decreasing detection function such as a half-normal. Recent advances in distance sampling modeling allow for the incorporation of covariates into the distance model, and the elimination of the assumption of perfect detection at some fixed distance (usually the transect line) with the use of double-observer models. The assumption of full observer independence in the double-observer model is problematic, but can be addressed by using the point independence assumption which assumes there is one distance, the apex of the detection function, where the 2 observers are assumed independent. Aerially collected distance sampling data can have a unimodal shape and have been successfully modeled with a gamma detection function. Covariates in gamma detection models cause the apex of detection to shift depending upon covariate levels, making this model incompatible with the point independence assumption when using double-observer data. This paper reports a unimodal detection model based on a two-piece normal distribution that allows covariates, has only one apex, and is consistent with the point independence assumption when double-observer data are utilized. An aerial line-transect survey of black bears in Alaska illustrate how this method can be applied.

Occurrence and distribution of organic chemicals and nutrients and comparison of water-quality data from public drinking-water supplies in the Columbia aquifer in Delaware, 2000-08

USGS Publications Warehouse

Reyes, Betzaida

2010-01-01

The U.S. Geological Survey, in cooperation with the Delaware Department of Natural Resources and Environmental Control and the Delaware Geological Survey, conducted a groundwater-quality investigation to (a) describe the occurrence and distribution of selected contaminants, and (b) document any changes in groundwater quality in the Columbia aquifer public water-supply wells in the Coastal Plain in Delaware between 2000 and 2008. Thirty public water-supply wells located throughout the Columbia aquifer of the Delaware Coastal Plain were sampled from August through November of 2008. Twenty-two of the wells in the sampling network for this project were previously sampled in 2000. Eight new wells were selected to replace wells no longer in use. Groundwater collected from the wells was analyzed for the occurrence and distribution of selected pesticides, pesticide degradates, volatile organic compounds, nutrients, and major inorganic ions. Nine of the wells were analyzed for radioactive elements (radium-226, radium-228, and radon). Groundwater-quality data were compared for sites sampled in both 2000 and 2008 to document any changes in water quality. One or more pesticides were detected in samples from 29 of the 30 wells. There were no significant differences in pesticide and pesticide degradate concentrations and similar compounds were detected when comparing sampling results from 2000 and 2008. Pesticide and pesticide degradate concentrations were generally less than 1 microgram per liter. Twenty-four compounds, 14 pesticides, and 10 pesticide degradates were detected in at least one sample; the pesticide degradates, metolachlor ethanesulfonic acid, deethylatrazine, and alachlor ethanesulfonic acid were the most frequently detected compounds, each found in more than 50 percent of samples. Almost 80 percent of the detected pesticides were agricultural herbicides, which reflects the prevalence and wide distribution of agriculture in sampled areas, as well the dominance of agricultural pesticides among the target analytes for this study. No concentration of a pesticide or pesticide degradate exceeded any regulatory standard. Dieldrin, an insecticide that has been banned for several decades, was detected at a concentration that exceeded a non-regulatory health-based screening level of 0.002 micrograms per liter at nine sites. Volatile organic compounds (VOCs) were generally detected at concentrations of less than 1 microgram per liter, although 7 of the 31 detected VOCs had concentrations greater than 1 microgram per liter. There were no significant differences in VOC concentrations from 2000 to 2008; however, among the resampled wells, the mean number of VOCs detected per well was significantly different over the 8-year period. The number of VOCs detected per well decreased in 73 percent of the resampled wells; the decrease ranged from one to eight fewer detections in 2008 than in 2000. Chloroform and methyl tert-butyl ether were the most frequently detected VOCs, at 90 percent and 63 percent, respectively, among the 30 wells. Solvents were the most frequently detected class of VOCs. All measured concentrations of VOCs in groundwater were below established standards for drinking water and below other health-based guidelines. There were no significant differences in nutrient or major-ion concentrations between 2000 and 2008, however, the medians of two field measurements, pH and dissolved oxygen, were significantly higher in 2008 than in 2000 in the resampled wells. Although pH and dissolved oxygen were higher, water was still acidic and predominantly oxic. Nitrate was the predominant nutrient species in the Columbia aquifer, with a 90-percent detection frequency. The median nitrate concentration in groundwater was 4.88 milligrams per liter, which was slightly lower than, but not significantly different from, the median of 5.23 milligrams per liter for the 2000 samples. Concentrations of nitrate exceeded the U.S. Environmental Protection Agency's Maximum Contaminant Level or Federal drinking-water standard of 10 milligrams per liter as nitrogen in samples from two wells. Eight of the 30 wells sampled had iron or manganese concentrations that exceeded the U.S. Environmental Protection Agency's Secondary Maximum Contaminant Level; nine samples exceeded the Health Advisory Limit set by the Delaware Division of Public Health of 20 milligrams per liter for sodium in drinking water. Two radiochemical isotopes, radium-226 and radon-222, were detected in all nine groundwater samples analyzed; five samples had detectable levels of radium-228 activity. None of the samples exceeded the U.S Environmental Protection Agency's Maximum Contaminant Level for radium or radon in drinking water. Although radioactive elements were more frequently detected in 2008 than in 2000, this increased detection frequency is more likely due to lower detection levels in 2008 than 2000. The average age of groundwater entering the screens of the production wells sampled in 2008 ranged from 6 to 35 years, with a median groundwater age of 22 years. Groundwater age was positively correlated with well depth and negatively correlated with dissolved oxygen. Data from the 22 resampled wells indicate a significant positive difference in the average modeled groundwater-sample-age results. The average groundwater age from samples collected in 2008 was generally 7 years older than the average groundwater age from samples collected in 2000.

Groundwater Quality in Central New York, 2007

USGS Publications Warehouse

Eckhardt, David A.V.; Reddy, J.E.; Shaw, Stephen B.

2009-01-01

Water samples were collected from 7 production wells and 28 private residential wells in central New York from August through December 2007 and analyzed to characterize the chemical quality of groundwater. Seventeen wells are screened in sand and gravel aquifers, and 18 are finished in bedrock aquifers. The wells were selected to represent areas of greatest groundwater use and to provide a geographical sampling from the 5,799-square-mile study area. Samples were analyzed for 6 physical properties and 216 constituents, including nutrients, major inorganic ions, trace elements, radionuclides, pesticides, volatile organic compounds, phenolic compounds, organic carbon, and 4 types of bacteria. Results indicate that groundwater used for drinking supply is generally of acceptable quality, although concentrations of some constituents or bacteria exceeded at least one drinking-water standard at several wells. The cations detected in the highest concentrations were calcium, magnesium, and sodium; anions detected in the highest concentrations were bicarbonate, chloride, and sulfate. The predominant nutrients were nitrate and ammonia, but no nutrients exceeded Maximum Contaminant Levels (MCLs). The trace elements barium, boron, lithium, and strontium were detected in every sample; the trace elements present in the highest concentrations were barium, boron, iron, lithium, manganese, and strontium. Fifteen pesticides, including seven pesticide degradates, were detected in water from 17 of the 35 wells, but none of the concentrations exceeded State or Federal MCLs. Sixteen volatile organic compounds were detected in water from 15 of the 35 wells. Nine analytes and three types of bacteria were detected in concentrations that exceeded Federal and State drinking-water standards, which typically are identical. One sample had a water color that exceeded the U.S. Environmental Protection Agency (USEPA) Secondary Maximum Contaminant Level (SMCL) and the New York State MCL of 10 color units. Sulfate concentrations exceeded the USEPA SMCL and the New York State MCL of 250 milligrams per liter (mg/L) in two samples, and chloride concentrations exceeded the USEPA SMCL and the New York State MCL of 250 mg/L in two samples. Sodium concentrations exceeded the USEPA Drinking Water Health Advisory of 60 mg/L in eight samples. Iron concentrations exceeded the USEPA SMCL and the New York State MCL of 300 micrograms per liter (ug/L) in 10 filtered samples. Manganese exceeded the USEPA SMCL of 50 ug/L in 10 filtered samples and the New York State MCL of 300 ug/L in 1 filtered sample. Barium exceeded the MCL of 2,000 ug/L in one sample, and aluminum exceeded the SMCL of 50 ug/L in three samples. Radon-222 exceeded the proposed USEPA MCL of 300 picocuries per liter in 12 samples. One sample from a private residential well had a trichloroethene concentration of 50.8 ug/L, which exceeded the MCL of 5 ug/L. Any detection of coliform bacteria indicates a potential violation of New York State health regulations; total coliform bacteria were detected in 19 samples, and fecal coliform bacteria were detected in one sample. The plate counts for heterotrophic bacteria exceeded the MCL (500 colony-forming units per milliliter) in three samples.

The Effects of Sample Matrices on Immunoassays to Detect Microcystin-LR in Water

EPA Science Inventory

Abstract: Immunoassays are widely used biochemical techniques to detect microcystins in environmental samples. The use of immunoassays for the detection of microcystins is vulnerable to matrix components and other interferents. This study is an evaluation of the effects of interf...

Assessment of soil and water contaminants from selected locations in and near the Idaho Army National Guard Orchard Training Area, Ada County, Idaho, 2001-2003

USGS Publications Warehouse

Parliman, D.J.

2004-01-01

In 2001, the National Guard Bureau and the U.S. Geological Survey began a project to compile hydrogeologic data and determine presence or absence of soil, surface-water, and ground-water contamination at the Idaho Army National Guard Orchard Training Area in southwestern Idaho. Between June 2002 and April 2003, a total of 114 soil, surface-water, ground-water, precipitation, or dust samples were collected from 68 sample sites (65 different locations) in the Orchard Training Area (OTA) or along the vehicle corridor to the OTA. Soil and water samples were analyzed for concentrations of selected total trace metals, major ions, nutrients, explosive compounds, semivolatile organics, and petroleum hydrocarbons. Water samples also were analyzed for concentrations of selected dissolved trace metals and major ions. Distinguishing naturally occurring large concentrations of trace metals, major ions, and nutrients from contamination related to land and water uses at the OTA was difficult. There were no historical analyses for this area to compare with modern data, and although samples were collected from 65 locations in and near the OTA, sampled areas represented only a small part of the complex OTA land-use areas and soil types. For naturally occurring compounds, several assumptions were made?anomalously large concentrations, when tied to known land uses, may indicate presence of contamination; naturally occurring concentrations cannot be separated from contamination concentrations in mid- and lower ranges of data; and smallest concentrations may represent the lowest naturally occurring range of concentrations and (or) the absence of contaminants related to land and water uses. Presence of explosive, semivolatile organic (SVOC), and petroleum hydrocarbon compounds in samples indicates contamination from land and water uses. In areas along the vehicle corridor and major access roads within the OTA, most trace metal, major ion, and nutrient concentrations in soil samples were not in the upper 10th percentile of data, but concentrations of 25 metals, ions, or nutrients were in the upper 10th percentile in a puddle sample near the heavy equipment maneuvering area, MPRC-H. The largest concentrations of tin, ammonia, and nitrite plus nitrate (as nitrogen) in water from the OTA were detected in a sample from this puddle. Petroleum hydrocarbons were the most common contaminant, detected in all soil and surface-water samples. An SVOC, bis (2-ethylhexyl) phthalate, a plasticizer, was detected at a site along the vehicle corridor. In Maneuver Areas within the OTA, many soil samples contained at least one trace metal, major ion, or nutrient in the upper 10th percentile of data, and the largest concentrations of cobalt, iron, mercury, titanium, sodium, ammonia, or total phosphorus were detected in 6 of 13 soil samples outside the Tadpole Lake area. The largest concentrations of aluminum, arsenic, beryllium, nickel, selenium, silver, strontium, thallium, vanadium, chloride, potassium, sulfate, and nitrite plus nitrate were detected in soil samples from the Tadpole Lake area. Water from Tadpole Lake contained the largest total concentrations of 19 trace metals, 4 major ions, and 1 nutrient. Petroleum hydrocarbons were detected in 5 soil samples and water from Tadpole Lake. SVOCs related to combustion of fuel or plasticizers were detected in 1 soil sample. Explosive compounds were detected in 1 precipitation sample.In the Impact Area within the OTA, most soil samples contained at least one trace metal, major ion, or nutrient in the upper 10th percentile of data, and the largest concentrations of barium, chromium, copper, manganese, lead, or orthophosphate were detected in 6 of the 18 soil samples. Petroleum hydrocarbons were detected in 4 soil samples, SVOCs in 6 samples, and explosive compounds in 4 samples. In the mobilization and training equipment site (MATES) compound adjacent to the OTA, all soil and water samples contained at lea

The Detection Method of Escherichia coli in Water Resources: A Review

NASA Astrophysics Data System (ADS)

Nurliyana, M. R.; Sahdan, M. Z.; Wibowo, K. M.; Muslihati, A.; Saim, H.; Ahmad, S. A.; Sari, Y.; Mansor, Z.

2018-04-01

This article reviews several approaches for Escherichia coli (E. coli) bacteria detection from conventional methods, emerging method and goes to biosensor-based techniques. Detection and enumeration of E. coli bacteria usually required long duration of time in obtaining the result since laboratory-based approach is normally used in its assessment. It requires 24 hours to 72 hours after sampling to process the culturing samples before results are available. Although faster technique for detecting E. coli in water such as Polymerase Chain Reaction (PCR) and Enzyme-Linked Immunosorbent Assay (ELISA) have been developed, it still required transporting the samples from water resources to the laboratory, high-cost, complicated equipment usage, complex procedures, as well as the requirement of skilled specialist to cope with the complexity which limit their wide spread practice in water quality detection. Recently, development of biosensor device that is easy to perform, portable, highly sensitive and selective becomes indispensable in detecting extremely lower consolidation of pathogenic E. coli bacteria in water samples.

Production of a monoclonal antibody and development of an immunoassay for detection of Cr(III) in water samples.

PubMed

Zhou, Y; Li, Y S; Meng, X Y; Zhang, Y Y; Yang, L; Li, Z H; Zhang, J H; Wang, X R; Liu, J Q; Lu, S Y; Ren, H L; Hu, P; Liu, Z S

2013-11-01

In this study we report the production of a monoclonal antibody (Mab) specific for Cr(III)-chelate and the development of a competitive immunoassay for detection of Cr(III) in water samples. In the assay, the complete antigen (Cr(III)-ITCBE-BSA) was used as coating antigen, and Cr(III)-ITCBE as competitor competes with coating antigen to bind with Mab. Using this approach, the spiked water samples with Cr(III) were detected. The linear range of the detection was 0.7-12.4 ng mL(-1). The limit of the detection (LOD) was 0.51 ng mL(-1). The spiked results were also confirmed by ICP-MS, which showed a good correlation (R(2)=0.997) between the two methods. The results indicated that the developed assay was reliable and suitable for the detection of Cr(III) in water samples. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Development of a SPA-ELISA method for detecting anti-coronavirus IgG antibodies in serum samples from fulvous fruit bats].

PubMed

Zhou, Jie; Liao, Yu-xue; Chen, Zhong; Li, Yu-chun; Gao, Lu-Lu; Chen, Yi-xiong; Cai, Lian-gong; Chen, Qing; Yu, Shou-yi

2008-05-01

To develop an simple and sensitive method for detecting anti-coronavirus IgG antibodies in bat sera based on enzyme-linked immunosorbent assay (ELISA). A commercial ELISA kit for detecting SARS-CoV antibody was modified for detecting coronavirus antibodies in bat serum samples. The second antibody in the kit was replaced with horseradish peroxidase-conjugated protein-A (HRP-SPA) based on the characteristics of binding between Staphylococcus aureus protein A (SPA) and mammal IgG Fc fragment. The sera of 55 fulvous fruit bats (Rousettus dasymallus) were tested using the SPA-ELISA. The test results of the positive and negative controls in the kit and the serum samples from convalescent ;patient were consistent with expectation. Coronavirus antibody was detected in 2 out of the 55 bat serum samples. Serum neutralization test confirmed the validity of the SPA-ELISA method. This SPA-ELISA method is applicable for detecting coronavirus antibody in bat sera.

Quantifying seining detection probability for fishes of Great Plains sand‐bed rivers

USGS Publications Warehouse

Mollenhauer, Robert; Logue, Daniel R.; Brewer, Shannon K.

2018-01-01

Species detection error (i.e., imperfect and variable detection probability) is an essential consideration when investigators map distributions and interpret habitat associations. When fish detection error that is due to highly variable instream environments needs to be addressed, sand‐bed streams of the Great Plains represent a unique challenge. We quantified seining detection probability for diminutive Great Plains fishes across a range of sampling conditions in two sand‐bed rivers in Oklahoma. Imperfect detection resulted in underestimates of species occurrence using naïve estimates, particularly for less common fishes. Seining detection probability also varied among fishes and across sampling conditions. We observed a quadratic relationship between water depth and detection probability, in which the exact nature of the relationship was species‐specific and dependent on water clarity. Similarly, the direction of the relationship between water clarity and detection probability was species‐specific and dependent on differences in water depth. The relationship between water temperature and detection probability was also species dependent, where both the magnitude and direction of the relationship varied among fishes. We showed how ignoring detection error confounded an underlying relationship between species occurrence and water depth. Despite imperfect and heterogeneous detection, our results support that determining species absence can be accomplished with two to six spatially replicated seine hauls per 200‐m reach under average sampling conditions; however, required effort would be higher under certain conditions. Detection probability was low for the Arkansas River Shiner Notropis girardi, which is federally listed as threatened, and more than 10 seine hauls per 200‐m reach would be required to assess presence across sampling conditions. Our model allows scientists to estimate sampling effort to confidently assess species occurrence, which maximizes the use of available resources. Increased implementation of approaches that consider detection error promote ecological advancements and conservation and management decisions that are better informed.

Stability optimization of microbial surface-enhanced Raman spectroscopy detection with immunomagnetic separation beads

NASA Astrophysics Data System (ADS)

Uusitalo, Sanna; Kögler, Martin; Välimaa, Anna-Liisa; Petäjä, Jarno; Kontturi, Ville; Siitonen, Samuli; Laitinen, Riitta; Kinnunen, Matti; Viitala, Tapani; Hiltunen, Jussi

2017-03-01

Immunomagnetic separation (IMS) beads with antibody coating are an interesting option for biosensing applications for the identification of biomolecules and biological cells, such as bacteria. The paramagnetic properties of the beads can be utilized with optical sensing by migrating and accumulating the beads and the bound analytes toward the focus depth of the detection system by an external magnetic field. The stability of microbial detection with IMS beads was studied by combining a flexible, inexpensive, and mass producible surface-enhanced Raman spectroscopy (SERS) platform with gold nanoparticle detection and antibody recognition by the IMS beads. Listeria innocua ATCC 33090 was used as a model sample and the effect of the IMS beads on the detected Raman signal was studied. The IMS beads were deposited into a hydrophobic sample well and accumulated toward the detection plane by a neodymium magnet. For the first time, it was shown that the spatial stability of the detection could be improved up to 35% by using IMS bead capture and sample well placing. The effect of a neodymium magnet under the SERS chip improved the temporal detection and significantly reduced the necessary time for sample stabilization for advanced laboratory testing.

Rapid detection of mecA and spa by the loop-mediated isothermal amplification (LAMP) method.

PubMed

Koide, Y; Maeda, H; Yamabe, K; Naruishi, K; Yamamoto, T; Kokeguchi, S; Takashiba, S

2010-04-01

To develop a detection assay for staphylococcal mecA and spa by using loop-mediated isothermal amplification (LAMP) method. Staphylococcus aureus and other related species were subjected to the detection of mecA and spa by both PCR and LAMP methods. The LAMP successfully amplified the genes under isothermal conditions at 64 degrees C within 60 min, and demonstrated identical results with the conventional PCR methods. The detection limits of the LAMP for mecA and spa, by gel electrophoresis, were 10(2) and 10 cells per tube, respectively. The naked-eye inspections were possible with 10(3) and 10 cells for detection of mecA and spa, respectively. The LAMP method was then applied to sputum and dental plaque samples. The LAMP and PCR demonstrated identical results for the plaque samples, although frequency in detection of mecA and spa by the LAMP was relatively lower for the sputum samples when compared to the PCR methods. Application of the LAMP enabled a rapid detection assay for mecA and spa. The assay may be applicable to clinical plaque samples. The LAMP offers an alternative detection assay for mecA and spa with a great advantage of the rapidity.

40 CFR 86.109-94 - Exhaust gas sampling system; Otto-cycle vehicles not requiring particulate emission measurements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... detection for the HPLC analyzer. Sampling systems for all phases shall be identical. (iii) The methanol and... detection for the HPLC analyzer. Sampling systems for all phases shall be identical. (iii) The methanol and...

40 CFR 86.109-94 - Exhaust gas sampling system; Otto-cycle vehicles not requiring particulate emission measurements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... detection for the HPLC analyzer. Sampling systems for all phases shall be identical. (iii) The methanol and... detection for the HPLC analyzer. Sampling systems for all phases shall be identical. (iii) The methanol and...

40 CFR 86.109-94 - Exhaust gas sampling system; Otto-cycle vehicles not requiring particulate emission measurements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... detection for the HPLC analyzer. Sampling systems for all phases shall be identical. (iii) The methanol and... detection for the HPLC analyzer. Sampling systems for all phases shall be identical. (iii) The methanol and...

Fresh vs Frozen Samples and Ambient Temperature Have Little Effect on Detection of Colorectal Cancer or Adenomas by a Fecal Immunochemical Test in a Colorectal Cancer Screening Cohort in Germany.

PubMed

Chen, Hongda; Werner, Simone; Brenner, Hermann

2017-10-01

Fecal immunochemical tests (FITs) are used in colorectal cancer (CRC) screening. We compared detection of CRCs and colorectal neoplasms by FITs using fresh samples (collected into buffer-filled tubes) vs frozen samples, and we assessed the effects of seasonal variations in ambient temperature on test performance. We performed a prospective study of 3466 individuals (50% male; mean age, 62 years) undergoing screening colonoscopies at 20 gastroenterology practices in southern Germany from November 2008 through September 2014. Frozen stool samples (collected and frozen by patients through February 2012, n = 1644) and fresh stool samples (collected by patients into buffer-filled tubes after February 2012, n = 1822) were obtained; hemoglobin (Hgb) concentrations were measured by using a commercial, quantitative FIT (cutoff value for positive result, 17 μg Hgb/g feces). Colonoscopy results were used as the gold standard, with results categorized as CRC, advanced adenoma, non-advanced adenoma, or no colorectal neoplasm. Differences in detection of colorectal neoplasms with fresh vs frozen samples were compared by using Wilcoxon rank sum test (continuous variables) and Fisher exact test (categorical variables). We also compared test performance when samples were collected during different seasons (based on outdoor temperature less than 8°, 8°-15°, or more than 15°). Of the samples analyzed by FIT, 12.8% of frozen stool samples (95% confidence interval [CI], 11.3%-14.5%) and 8.7% of fresh stool samples (95% CI, 7.5%-10.1%) had positive results (P value for difference < .001). When adjusting the Hgb cutoff value to produce the same percentage of positive results for fresh and frozen samples (10% and 5%), FIT with frozen vs fresh samples detected colorectal neoplasms with similar levels of sensitivity and specificity. For example, at cutoff values that produced 5% positive results for each sample type, FIT detected advanced neoplasms with 27.8% sensitivity when frozen samples were used (95% CI, 21.4%-35.1%) and 25.6% sensitivity when fresh samples were used (95% CI, 19.8%-32.1%). Specificity values were 97.7% when frozen samples were used (95% CI, 96.8%-98.4%) and 97.6% when fresh samples were used (95% CI, 96.7%-98.3%). We did not observe any differences in detection of neoplasms during different seasons that were based on outdoor temperature. In a prospective study of 3466 individuals who underwent screening colonoscopies and received FITs, we found that use of fresh vs frozen samples slightly affected positivity rates and the proportions of CRCs or adenomas detected at the recommended Hgb cutoff value. However, after we adjusted Hgb cutoff values to produce equal proportions of positive results for fresh vs frozen samples, the performance of the FIT was similar with each sample type. Season of sample collection (based on outdoor temperature) did not affect detection of CRC using either sample type in this study from Middle Europe. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Occurrence of Chlorothalonil, Its Transformation Products, and Selected Other Pesticides in Texas and Oklahoma Streams, 2003-2004

USGS Publications Warehouse

Battaglin, William A.; Kuivila, Kathryn; Winton, Kim; Meyer, Michael

2008-01-01

The primary purpose of the study described in this report was to determine if the fungicide chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile), three of its transformation products, or selected other pesticides are transported to surface water after use on peanuts or other crops in Texas and Oklahoma. The results summarized here are part of a larger study that includes data from sites in Alabama, Florida, and Georgia. Chlorothalonil is classified as a probable carcinogen, and the 4-hydroxy of chlorothalonil transformation product is more soluble, more stable, and, for some species, more toxic than its parent compound. In 2003, water samples were collected from three surface-water sites in Texas and two surface-water sites in Oklahoma; in 2004, samples were collected from the two Oklahoma sites. Chlorothalonil was not detected in any of the 20 samples analyzed. The 4-hydroxy of chlorothalonil transformation product was detected in three samples collected in 2004, with a maximum concentration of 0.018 microgram per liter (?g/L); the other two transformation products (diamide chlorothalonil and 1-amide-4-hydroxy chlorothalonil) were not detected in any sample. In addition, 19 samples were analyzed for as many as 109 other pesticides and transformation products. Atrazine was detected in 13 samples and had a maximum concentration of 0.122 ?g/L. Deethylatrazine was detected in 10 samples and had a maximum concentration of 0.04 ?g/L. Metolachlor was detected in eight samples and had a maximum concentration of 0.019 ?g/L. Fifteen other pesticides or pesticide transformation products also were detected. In general, concentrations of pesticides were less than concentrations that are commonly observed in Midwestern streams. The results indicate that the use of chlorothalonil on peanut crops has not resulted in substantial contamination of the studied streams in Texas and Oklahoma.

[Purity Detection Model Update of Maize Seeds Based on Active Learning].

PubMed

Tang, Jin-ya; Huang, Min; Zhu, Qi-bing

2015-08-01

Seed purity reflects the degree of seed varieties in typical consistent characteristics, so it is great important to improve the reliability and accuracy of seed purity detection to guarantee the quality of seeds. Hyperspectral imaging can reflect the internal and external characteristics of seeds at the same time, which has been widely used in nondestructive detection of agricultural products. The essence of nondestructive detection of agricultural products using hyperspectral imaging technique is to establish the mathematical model between the spectral information and the quality of agricultural products. Since the spectral information is easily affected by the sample growth environment, the stability and generalization of model would weaken when the test samples harvested from different origin and year. Active learning algorithm was investigated to add representative samples to expand the sample space for the original model, so as to implement the rapid update of the model's ability. Random selection (RS) and Kennard-Stone algorithm (KS) were performed to compare the model update effect with active learning algorithm. The experimental results indicated that in the division of different proportion of sample set (1:1, 3:1, 4:1), the updated purity detection model for maize seeds from 2010 year which was added 40 samples selected by active learning algorithm from 2011 year increased the prediction accuracy for 2011 new samples from 47%, 33.75%, 49% to 98.89%, 98.33%, 98.33%. For the updated purity detection model of 2011 year, its prediction accuracy for 2010 new samples increased by 50.83%, 54.58%, 53.75% to 94.57%, 94.02%, 94.57% after adding 56 new samples from 2010 year. Meanwhile the effect of model updated by active learning algorithm was better than that of RS and KS. Therefore, the update for purity detection model of maize seeds is feasible by active learning algorithm.

Pressurized liquid extraction using water/isopropanol coupled with solid-phase extraction cleanup for semivolatile organic compounds, polycyclic aromatic hydrocarbons (PAH), and alkylated PAH homolog groups in sediment

USGS Publications Warehouse

Burkhardt, M.R.; Zaugg, S.D.; Burbank, T.L.; Olson, M.C.; Iverson, J.L.

2005-01-01

Polycyclic aromatic hydrocarbons (PAH) are recognized as environmentally relevant for their potential adverse effects on human and ecosystem health. This paper describes a method to determine the distribution of PAH and alkylated homolog groups in sediment samples. Pressurized liquid extraction (PLE), coupled with solid-phase extraction (SPE) cleanup, was developed to decrease sample preparation time, to reduce solvent consumption, and to minimize background interferences for full-scan GC-MS analysis. Recoveries from spiked Ottawa sand, environmental stream sediment, and commercially available topsoil, fortified at 1.5-15 ??g per compound, averaged 94.6 ?? 7.8%, 90.7 ?? 5.8% and 92.8 ?? 12.8%, respectively. Initial method detection limits for single-component compounds ranged from 20 to 302 ??g/kg, based on 25 g samples. Results from 28 environmental sediment samples, excluding homologs, show 35 of 41 compounds (85.4%) were detected in at least one sample with concentrations ranging from 20 to 100,000 ??g/kg. The most frequently detected compound, 2,6-dimethylnaphthalene, was detected in 23 of the 28 (82%) environmental samples with a concentration ranging from 15 to 907 ??g/kg. The results from the 28 environmental sediment samples for the homolog series showed that 27 of 28 (96%) samples had at least one homolog series present at concentrations ranging from 20 to 89,000 ??g/kg. The most frequently detected homolog series, C2-alkylated naphthalene, was detected in 26 of the 28 (93%) environmental samples with a concentration ranging from 25 to 3900 ??g/kg. Results for a standard reference material using dichloromethane Soxhlet-based extraction also are compared. ?? 2005 Elsevier B.V. All rights reserved.

A near full-length open reading frame next generation sequencing assay for genotyping and identification of resistance-associated variants in hepatitis C virus.

PubMed

Pedersen, M S; Fahnøe, U; Hansen, T A; Pedersen, A G; Jenssen, H; Bukh, J; Schønning, K

2018-06-01

The current treatment options for hepatitis C virus (HCV), based on direct acting antivirals (DAA), are dependent on virus genotype and previous treatment experience. Treatment failures have been associated with detection of resistance-associated substitutions (RASs) in the DAA targets of HCV, the NS3, NS5A and NS5 B proteins. To develop a next generation sequencing based method that provides genotype and detection of HCV NS3, NS5A, and NS5 B RASs without prior knowledge of sample genotype. In total, 101 residual plasma samples from patients with HCV covering 10 different viral subtypes across 4 genotypes with viral loads of 3.84-7.61 Log IU/mL were included. All samples were de-identified and consequently prior treatment status for patients was unknown. Almost full open reading frame amplicons (∼ 9 kb) were generated using RT-PCR with a single primer set. The resulting amplicons were sequenced with high throughput sequencing and analysed using an in-house developed script for detecting RASs. The method successfully amplified and sequenced 94% (95/101) of samples with an average coverage of 14,035; four of six failed samples were genotype 4a. Samples analysed twice yielded reproducible nucleotide frequencies across all sites. RASs were detected in 21/95 (22%) samples at a 15% threshold. The method identified one patient infected with two genotype 2b variants, and the presence of subgenomic deletion variants in 8 (8.4%) of 95 successfully sequenced samples. The presented method may provide identification of HCV genotype, RASs detection, and detect multiple HCV infection without prior knowledge of sample genotype. Copyright © 2018 Elsevier B.V. All rights reserved.

Detection of Listeria monocytogenes in ready-to-eat food by Step One real-time polymerase chain reaction.

PubMed

Pochop, Jaroslav; Kačániová, Miroslava; Hleba, Lukáš; Lopasovský, L'ubomír; Bobková, Alica; Zeleňáková, Lucia; Stričík, Michal

2012-01-01

The aim of this study was to follow contamination of ready-to-eat food with Listeria monocytogenes by using the Step One real time polymerase chain reaction (PCR). We used the PrepSEQ Rapid Spin Sample Preparation Kit for isolation of DNA and MicroSEQ® Listeria monocytogenes Detection Kit for the real-time PCR performance. In 30 samples of ready-to-eat milk and meat products without incubation we detected strains of Listeria monocytogenes in five samples (swabs). Internal positive control (IPC) was positive in all samples. Our results indicated that the real-time PCR assay developed in this study could sensitively detect Listeria monocytogenes in ready-to-eat food without incubation.

Concentrations of organic contaminants detected during managed flow conditions, San Joaquin River and Old River, California, 2001

USGS Publications Warehouse

Orlando, James L.; Kuivila, Kathryn

2005-01-01

Concentrations of organic contaminants were determined in water samples collected at six surface-water sites located along the San Joaquin and Old Rivers during April through June 2001. Water samples were collected, coincident with salmon smolt caging studies conducted by researchers from the Bodega Marine Laboratory at the University of California at Davis to characterize exposure of the salmon smolt to organic contaminants. Sampling occurred prior to, during, and following the implementation of managed streamflow conditions on the San Joaquin and Old Rivers as part of the Vernalis Adaptive Management Plan. Thirteen pesticides were detected in water samples collected during this study, and at least five pesticides were detected in each sample. The total number of pesticide detections varied little between river systems and between sites, but the maximum concentrations of most pesticides occurred in San Joaquin River samples. The total number of pesticides detected varied little over the three time periods. However, during the period of managed streamflow, the fewest number of pesticides were detected at their absolute maximum concentration. Nine wastewater compounds were detected during this study. Suspended-sediment concentrations were similar for the San Joaquin and Old Rivers except during the period of managed streamflow conditions, when suspended-sediment concentration was higher at sites on the San Joaquin River than at sites on the Old River. Values for water parameters (pH, specific conductance, and hardness) were lowest during the period of managed flows.

Detection and Separation of Inorganic Cations in Natural, Potable, and Wastewater Samples Using Capillary Zone Electrophoresis with Indirect UV Detection

PubMed Central

Varden, Lara; Bou-Abdallah, Fadi

2017-01-01

Capillary zone electrophoresis (CZE) is a sensitive and rapid technique for determining traces of inorganic cations in water samples. CZE with indirect UV-diode array detection (CZE-DAD) was utilized to identify several inorganic cations in natural, potable, and wastewater samples. A pH 4.35 background electrolyte system was employed and consisted of 15 mM imidazole, 8 mM malonic acid, 2 mM 18-crown-6 ether as complexing agents, 10% v/v methanol as an organic modifier with indirect absorbance reference at 214 nm. The CZE method involved electromigration injection at 5 kV for 5 s, a separation voltage of 20 kV at 25°C, and a detection wavelength of 280 nm. Six main cations (ammonium NH4+, potassium K+, calcium Ca2+, sodium Na+, magnesium Mg2+, and lead Pb2+) were tested, and all but lead, were detected in the water samples at concentrations between 0.03 and 755 ppm with a detection limit ranging between 0.023 and 0.084 ppm. The successful evaluation of the proposed methodology allowed us to reliably detect and separate six metal ions in different water samples without any pretreatment. All water samples were collected from Northern New York towns and the Raquette River water system, the third longest river in New York State and the largest watershed of the central and western Adirondacks. PMID:29057144

CTP (Cochlin-tomoprotein) detection in the profuse fluid leakage (gusher) from cochleostomy.

PubMed

Ikezono, Tetsuo; Sugizaki, Kazuki; Shindo, Susumu; Sekiguchi, Satomi; Pawankar, Ruby; Baba, Shunkichi; Yagi, Toshiaki

2010-08-01

By testing 125 samples, we confirmed that Cochlin-tomoprotein (CTP) is present in the perilymph, not in cerebrospinal fluid (CSF). Perilymph and CSF exist in two distinct compartments, even in the case of a malformed inner ear with a bony defect in the lamina cribrosa, as described here. Cochleostomy might have suddenly decreased the perilymph pressure, allowing the influx of CSF into the inner ear resulting in profuse fluid leakage, first perilymph then CSF. The first purpose of this study was to further confirm the specificity of the perilymph-specific protein CTP that we reported recently. Secondly, we assessed the nature of the fluid leakage from the cochleostomy using the CTP detection test. A standardized CTP detection test was performed on 65 perilymph and 60 CSF samples. Samples of profuse fluid leakage collected from cochleostomy during cochlear implantation surgery of one patient with branchio-oto-renal (BOR) syndrome were also tested by the CTP detection test. CTP was detected in 60 of 65 perilymph samples but not in any of the CSF samples. The leaked fluid was shown to contain CTP, i.e. perilymph, at the outset, and then the CTP detection signals gradually disappeared as time elapsed.

Detection of respiratory viruses on air filters from aircraft.

PubMed

Korves, T M; Johnson, D; Jones, B W; Watson, J; Wolk, D M; Hwang, G M

2011-09-01

To evaluate the feasibility of identifying viruses from aircraft cabin air, we evaluated whether respiratory viruses trapped by commercial aircraft air filters can be extracted and detected using a multiplex PCR, bead-based assay. The ResPlex II assay was first tested for its ability to detect inactivated viruses applied to new filter material; all 18 applications of virus at a high concentration were detected. The ResPlex II assay was then used to test for 18 respiratory viruses on 48 used air filter samples from commercial aircraft. Three samples tested positive for viruses, and three viruses were detected: rhinovirus, influenza A and influenza B. For 33 of 48 samples, internal PCR controls performed suboptimally, suggesting sample matrix effect. In some cases, influenza and rhinovirus RNA can be detected on aircraft air filters, even more than 10 days after the filters were removed from aircraft. With protocol modifications to overcome PCR inhibition, air filter sampling and the ResPlex II assay could be used to characterize viruses in aircraft cabin air. Information about viruses in aircraft could support public health measures to reduce disease transmission within aircraft and between cities. © The MITRE corporation. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Application of tetraplex PCR for detection of Vibrio cholerae, V. parahaemolyticus, V. vulnificus and V. mimicus in cockle.

PubMed

Senachai, Pachara; Chomvarin, Chariya; Namwat, Wises; Wongboot, Warawan; Wongwajana, Suwin; Tangkanakul, Waraluk

2013-03-01

A tetraplex PCR method was developed for simultaneous detection of Vibrio cholerae, V. parahaemolyticus, V. vulnificus and V. mimicus in cockle samples in comparison with conventional culture method. Specific primers targeting ompW of V. cholerae, tl of V. parahaemolyticus, hsp60 of V. vulnificus and sodB of V. mimicus were employed in the same PCR. Detection limit of the tetraplex PCR assay was 104 cfu/ml (400 cfu/PCR reaction) for pure cultures of all four species of Vibrio. In Vibrio spiked cockle samples, the limit of detection after 6 hours enrichment in alkaline peptone water was 1 cfu/10 g of cockle tissue for three Vibrio spp, except for V. mimicus that was 102 cfu/10 g of cockle tissue. When the tetraplex PCR and culture methods were applied to 100 cockle samples, V. parahaemolyticus, V. vulnificus, V. cholerae and V. mimicus were detected in 100, 98, 80 and 9% of the samples by tetraplex PCR and in 76, 42, 0 and 0% by the culture method, respectively. This developed tetraplex PCR method should be suitable for simultaneous and rapid detection of Vibrio species in food samples and for food safety assessment.

Differences in detection of Aeromonas salmonicida in covertly infected salmonid fishes by the stress-inducible furunculosis test and culture-based assays

USGS Publications Warehouse

Cipriano, R.C.; Ford, L.A.; Smith, D.R.; Schachte, J.H.; Petrie, C.J.

1997-01-01

Accurate detection of Aeromonas salmonicida subsp. salmonicida (the cause of furunculosis disease) in covertly infected salmonids is difficult and is a cause of concern for those involved in fish health inspection and resource management programs. In this study, we examined populations of brook trout Salvelinus fontinalis, Atlantic salmon Salmo salar, and lake trout Salvelinus namaycush that previously sustained natural episodes of furunculosis. Consequently, the sampled fish were presumed to harbor latent infections. Mucus, gill, liver, kidney, heart, spleen, and intestine samples (N = 100 fish per group sampled) were processed and examined by (1) direct dilution counts and (2) quadrant streaking after a 48-h pre-enrichment in trypticase soy broth (TSB). Another subsample of fish from each group was then subjected to stress-inducible furunculosis tests. Stress tests detected A. salmonicida in three of four groups of fish that were examined whereas the pathogen was detected in only two of the groups analyzed with culture-based assays. Although pre-enrichment in TSB enhanced detection within internal sampling sites including the liver, heart, spleen, and kidney, enrichment did not enhance detection from mucus, gill, or intestinal samples.

Comparison of Membrane Filtration and Multiple-Tube Fermentation by the Colilert and Enterolert Methods for Detection of Waterborne Coliform Bacteria, Escherichia coli, and Enterococci Used in Drinking and Bathing Water Quality Monitoring in Southern Sweden

PubMed Central

Eckner, Karl F.

1998-01-01

A total of 338 water samples, 261 drinking water samples and 77 bathing water samples, obtained for routine testing were analyzed in duplicate by Swedish standard methods using multiple-tube fermentation or membrane filtration and by the Colilert and/or Enterolert methods. Water samples came from a wide variety of sources in southern Sweden (Skåne). The Colilert method was found to be more sensitive than Swedish standard methods for detecting coliform bacteria and of equal sensitivity for detecting Escherichia coli when all drinking water samples were grouped together. Based on these results, Swedac, the Swedish laboratory accreditation body, approved for the first time in Sweden use of the Colilert method at this laboratory for the analysis of all water sources not falling under public water regulations (A-krav). The coliform detection study of bathing water yielded anomalous results due to confirmation difficulties. E. coli detection in bathing water was similar by both the Colilert and Swedish standard methods as was fecal streptococcus and enterococcus detection by both the Enterolert and Swedish standard methods. PMID:9687478

Sampling guidelines for oral fluid-based surveys of group-housed animals.

PubMed

Rotolo, Marisa L; Sun, Yaxuan; Wang, Chong; Giménez-Lirola, Luis; Baum, David H; Gauger, Phillip C; Harmon, Karen M; Hoogland, Marlin; Main, Rodger; Zimmerman, Jeffrey J

2017-09-01

Formulas and software for calculating sample size for surveys based on individual animal samples are readily available. However, sample size formulas are not available for oral fluids and other aggregate samples that are increasingly used in production settings. Therefore, the objective of this study was to develop sampling guidelines for oral fluid-based porcine reproductive and respiratory syndrome virus (PRRSV) surveys in commercial swine farms. Oral fluid samples were collected in 9 weekly samplings from all pens in 3 barns on one production site beginning shortly after placement of weaned pigs. Samples (n=972) were tested by real-time reverse-transcription PCR (RT-rtPCR) and the binary results analyzed using a piecewise exponential survival model for interval-censored, time-to-event data with misclassification. Thereafter, simulation studies were used to study the barn-level probability of PRRSV detection as a function of sample size, sample allocation (simple random sampling vs fixed spatial sampling), assay diagnostic sensitivity and specificity, and pen-level prevalence. These studies provided estimates of the probability of detection by sample size and within-barn prevalence. Detection using fixed spatial sampling was as good as, or better than, simple random sampling. Sampling multiple barns on a site increased the probability of detection with the number of barns sampled. These results are relevant to PRRSV control or elimination projects at the herd, regional, or national levels, but the results are also broadly applicable to contagious pathogens of swine for which oral fluid tests of equivalent performance are available. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Optimization of a Viability PCR Method for the Detection of Listeria monocytogenes in Food Samples.

PubMed

Agustí, Gemma; Fittipaldi, Mariana; Codony, Francesc

2018-06-01

Rapid detection of Listeria and other microbial pathogens in food is an essential part of quality control and it is critical for ensuring the safety of consumers. Culture-based methods for detecting foodborne pathogens are time-consuming, laborious and cannot detect viable but non-culturable microorganism, whereas viability PCR methodology provides quick results; it is able to detect viable but non-culturable cells, and allows for easier handling of large amount of samples. Although the most critical point to use viability PCR technique is achieving the complete exclusion of dead cell amplification signals, many improvements are being introduced to overcome this. In the present work, the yield of dead cell DNA neutralization was enhanced by incorporating two new sample treatment strategies: tube change combined with a double light treatment. This procedure was successfully tested using artificially contaminated food samples, showing improved neutralization of dead cell DNA.

Detection of human papillomavirus DNA in urine. A review of the literature.

PubMed

Vorsters, A; Micalessi, I; Bilcke, J; Ieven, M; Bogers, J; Van Damme, P

2012-05-01

The detection of human papillomavirus (HPV) DNA in urine, a specimen easily obtained by a non-invasive self-sampling method, has been the subject of a considerable number of studies. This review provides an overview of 41 published studies; assesses how different methods and settings may contribute to the sometimes contradictory outcomes; and discusses the potential relevance of using urine samples in vaccine trials, disease surveillance, epidemiological studies, and specific settings of cervical cancer screening. Urine sampling, storage conditions, sample preparation, DNA extraction, and DNA amplification may all have an important impact on HPV DNA detection and the form of viral DNA that is detected. Possible trends in HPV DNA prevalence in urine could be inferred from the presence of risk factors or the diagnosis of cervical lesions. HPV DNA detection in urine is feasible and may become a useful tool but necessitates further improvement and standardization.

Monitoring the Presence of 13 Active Compounds in Surface Water Collected from Rural Areas in Northwestern Spain

PubMed Central

Iglesias, Alejandra; Nebot, Carolina; Vázquez, Beatriz I.; Coronel-Olivares, Claudia; Franco Abuín, Carlos M.; Cepeda, Alberto

2014-01-01

Drug residues are considered environmental contaminants, and their occurrence has recently become a matter of concern. Analytical methods and monitoring systems are therefore required to control the continuous input of these drug residues into the environment. This article presents a suitable HPLC-ESI-MS/MS method for the simultaneous extraction, detection and quantification of residues of 13 drugs (antimicrobials, glucocorticosteroids, anti-inflammatories, anti-hypertensives, anti-cancer drugs and triphenylmethane dyes) in surface water. A monitoring study with 549 water samples was carried out in northwestern Spain to detect the presence of drug residues over two sampling periods during 2010, 2011 and 2012. Samples were collected from rural areas with and without farming activity and from urban areas. The 13 analytes were detected, and 18% of the samples collected showed positive results for the presence of at least one analyte. More collection sites were located in rural areas than in urban areas. However, more positive samples with higher concentrations and a larger number of analytes were detected in samples collected from sites located after the discharge of a WWTP. Results indicated that the WWTPs seems to act as a concentration point. Positive samples were also detected at a site located near a drinking water treatment plant. PMID:24837665

Comparison of ELISA and Microscopy for detection of Cryptosporidium in stool

PubMed Central

Sharma, Madhu; Chaudhary, Uma; Yadav, Aparna

2014-01-01

Background: Cryptosporidiosis, a diarrheal disease caused by the protozoan parasite Cryptosporidium spp. has become recognized as one of the most common causes of water borne diseases in humans. Aims and Objectives: To compare the sensitivity of ELISA and Microscopy for detection of Cryptosporidium in stool samples Materials and Methods: The study was conducted in the Department of Microbiology of PT. B.D. Sharma PGIMS Rohtak, between January 2011 to june 2011 on 50 stool samples, which were processed for detection of cryptosporidial antigen by ELISA and detection of cysts by microscopy (Modified Ziehl and Nelsen staining). Study and Design: This was a prospective study conducted in the Department of Microbiology in PT. BD Sharma, PGIMS, Rohtak, India. Result: Out of total, 50 stool samples eighteen (36%) samples were found positive for Cryptosporidium cysts by microscopy in comparison to 3(6%) stool samples which were found positive for cryptosporidial antigen by ELISA. Samples found positive with ELISA were also positive with microscopy. Sensitivity, specificity, positive predictive value and negative predictive value for ELISA was 16.7%, 100%, 100% and 68% respectively. Conclusion: The study concludes that stool microscopic Modified acid fast staining is more sensitive method than ELISA for detection of Cryptosporidium in stool samples but the specificity of ELISA was more than microscopy. PMID:25584216

Monitoring the presence of 13 active compounds in surface water collected from rural areas in northwestern Spain.

PubMed

Iglesias, Alejandra; Nebot, Carolina; Vázquez, Beatriz I; Coronel-Olivares, Claudia; Abuín, Carlos M Franco; Cepeda, Alberto

2014-05-15

Drug residues are considered environmental contaminants, and their occurrence has recently become a matter of concern. Analytical methods and monitoring systems are therefore required to control the continuous input of these drug residues into the environment. This article presents a suitable HPLC-ESI-MS/MS method for the simultaneous extraction, detection and quantification of residues of 13 drugs (antimicrobials, glucocorticosteroids, anti-inflammatories, anti-hypertensives, anti-cancer drugs and triphenylmethane dyes) in surface water. A monitoring study with 549 water samples was carried out in northwestern Spain to detect the presence of drug residues over two sampling periods during 2010, 2011 and 2012. Samples were collected from rural areas with and without farming activity and from urban areas. The 13 analytes were detected, and 18% of the samples collected showed positive results for the presence of at least one analyte. More collection sites were located in rural areas than in urban areas. However, more positive samples with higher concentrations and a larger number of analytes were detected in samples collected from sites located after the discharge of a WWTP. Results indicated that the WWTPs seems to act as a concentration point. Positive samples were also detected at a site located near a drinking water treatment plant.

Validation of High Resolution Melting Analysis (HRM) of the Amplified ITS2 Region for the Detection and Identification of Yeasts from Clinical Samples: Comparison with Culture and MALDI-TOF Based Identification.

PubMed

Duyvejonck, Hans; Cools, Piet; Decruyenaere, Johan; Roelens, Kristien; Noens, Lucien; Vermeulen, Stefan; Claeys, Geert; Decat, Ellen; Van Mechelen, Els; Vaneechoutte, Mario

2015-01-01

Candida species are known as opportunistic pathogens, and a possible cause of invasive infections. Because of their species-specific antimycotic resistance patterns, reliable techniques for their detection, quantification and identification are needed. We validated a DNA amplification method for direct detection of Candida spp. from clinical samples, namely the ITS2-High Resolution Melting Analysis (direct method), by comparing it with a culture and MALDI-TOF Mass Spectrometry based method (indirect method) to establish the presence of Candida species in three different types of clinical samples. A total of 347 clinical samples, i.e. throat swabs, rectal swabs and vaginal swabs, were collected from the gynaecology/obstetrics, intensive care and haematology wards at the Ghent University Hospital, Belgium. For the direct method, ITS2-HRM was preceded by NucliSENS easyMAG DNA extraction, directly on the clinical samples. For the indirect method, clinical samples were cultured on Candida ID and individual colonies were identified by MALDI-TOF. For 83.9% of the samples there was complete concordance between both techniques, i.e. the same Candida species were detected in 31.1% of the samples or no Candida species were detected in 52.8% of the samples. In 16.1% of the clinical samples, discrepant results were obtained, of which only 6.01% were considered as major discrepancies. Discrepancies occurred mostly when overall numbers of Candida cells in the samples were low and/or when multiple species were present in the sample. Most of the discrepancies could be decided in the advantage of the direct method. This is due to samples in which no yeast could be cultured whereas low amounts could be detected by the direct method and to samples in which high quantities of Candida robusta according to ITS2-HRM were missed by culture on Candida ID agar. It remains to be decided whether the diagnostic advantages of the direct method compensate for its disadvantages.

Detection of viable Helicobacter pylori inside free-living amoebae in wastewater and drinking water samples from Eastern Spain.

PubMed

Moreno-Mesonero, Laura; Moreno, Yolanda; Alonso, José Luis; Ferrús, M Antonia

2017-10-01

Helicobacter pylori is one of the most concerning emerging waterborne pathogens. It has been suggested that it could survive in water inside free-living amoebae (FLA), but nobody has studied this relationship in the environment yet. Thus, we aimed to detect viable H. pylori cells from inside FLA in water samples. Sixty-nine wastewater and 31 drinking water samples were collected. FLA were purified and identified by PCR and sequencing. For exclusively detecting H. pylori inside FLA, samples were exposed to sodium hypochlorite and assayed by specific PMA-qPCR, DVC-FISH and culture. FLA were detected in 38.7% of drinking water and 79.7% of wastewater samples, even after disinfection. In wastewater, Acanthamoeba spp. and members of the family Vahlkampfiidae were identified. In drinking water, Acanthamoeba spp. and Echinamoeba and/or Vermamoeba were present. In 39 (58.2%) FLA-positive samples, H. pylori was detected by PMA-qPCR. After DVC-FISH, 21 (31.3%) samples harboured viable H. pylori internalized cells. H. pylori was cultured from 10 wastewater samples. To our knowledge, this is the first report that demonstrates that H. pylori can survive inside FLA in drinking water and wastewater, strongly supporting the hypothesis that FLA could play an important role in the transmission of H. pylori to humans. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparison of loop-mediated isothermal amplification (LAMP) and nested-PCR assay targeting the RE and B1 gene for detection of Toxoplasma gondii in blood samples of children with leukaemia.

PubMed

Fallahi, Shirzad; Seyyed Tabaei, Seyyed Javad; Pournia, Yadollah; Zebardast, Nozhat; Kazemi, Bahram

2014-07-01

Toxoplasmosis diagnosis constitutes an important measure for disease prevention and control. In this paper, a newly described DNA amplification technique, loop-mediated isothermal amplification (LAMP), and nested-PCR targeting the repeated element (RE) and B1 gene, were compared to each other for the detection of Toxoplasma gondii DNA in blood samples of children with leukaemia. One hundred ten blood samples from these patients were analyzed by LAMP and nested-PCR. Out of 50 seropositive samples (IgM+, IgG+), positive results were obtained with 92% and 86% on RE, B1-LAMP and 82% and 68% on RE, B1-nested PCR analyses, respectively. Of the 50 seronegative samples, three, two and one samples were detected positive by RE-LAMP, B1-LAMP and RE-nested PCR assays, respectively, while none were detected positive by B1-nested PCR. None of the 10 IgM-, IgG+ samples was detected positive after testing LAMP and nested-PCR assays in duplicate. This is the first report of a study in which the LAMP method was applied with high sensitivity and efficacy for the diagnosis of T. gonii in blood samples of children with leukaemia. Copyright © 2014 Elsevier Inc. All rights reserved.

Occurrence and sources of antibiotics and their metabolites in river water, WWTPs, and swine wastewater in Jiulongjiang River basin, south China.

PubMed

Jiang, Hongyou; Zhang, Dandan; Xiao, Shichang; Geng, Chunnv; Zhang, Xian

2013-12-01

In this study, the occurrence and sources of five cataloged antibiotics and metabolites were studied in Jiulongjiang River basin, south China. Nineteen antibiotics and 13 metabolites were detected in water samples from 16 river sampling sites, wastewater from 5 swine-raising facilities, and effluent from 5 wastewater treatment plants (WWTPs). The results showed that 12 antibiotics and 6 metabolites were detected in river water samples. Sulfonamides (SAs) and their metabolites were detected at high concentrations (8.59-158.94 ng/L). Tetracyclines (TCs) and their metabolites were frequently detected in swine wastewater, and the maximum concentration was up to the level in milligram per liter. Macrolides (MLs) and β-lactams (β-Ls) were found in all WWTP effluent samples and some river samples, while they were never found in any of the swine wastewater samples. SAs and quinolones (QNs) were detected in all samples. Hierarchical cluster analysis of 16 surface water samples was applied to achieve the spatial distribution characteristics of antibiotics in the Jiulongjiang River. As a result, two categories were obviously obtained. Principal component analysis and redundancy analysis showed that TCs and SAs as well as their metabolites were the major antibiotics in Jiulongjiang River, and they mainly originated from swine wastewater, while the QNs, MLs, and β-Ls in the Jiulongjiang River came from WWTP effluent.

Analysis of pesticides in surface water, stemflow, and throughfall in an agricultural area in South Georgia, USA.

PubMed

Glinski, Donna A; Purucker, S Thomas; Van Meter, Robin J; Black, Marsha C; Henderson, W Matthew

2018-06-18

To study spray drift contributions to non-targeted habitats, pesticide concentrations in stemflow (water flowing down the trunk of a tree during a rain event), throughfall (water from tree canopy only), and surface water in an agriculturally impacted wetland area near Tifton, Georgia, USA were measured (2015-2016). Agricultural fields and sampling locations were on the University of Georgia's Gibbs Research Farm, Tifton, GA. Samples were screened for more than 160 pesticides, and cumulatively, 32 different pesticides were detected across matrices. Data indicate that herbicides and fungicides were present in all types of environmental samples analyzed while insecticides were only detected in surface water samples. The highest pesticide concentration observed was 10.50 μg/L of metolachlor in an August 2015 surface water sample. Metolachlor, tebuconazole, and fipronil were the most frequently detected herbicide, fungicide, and insecticide, respectively, regardless of sample origin. The most frequently detected pesticide in surface water and stemflow samples was metolachlor (0.09-10.5 μg/L), however, the most commonly detected pesticide in throughfall samples was biphenyl (0.02-0.07 μg/L). These data help determine the importance of indirect chemical exposures to non-targeted habitats by assessing inputs from stemflow and throughfall into surface waters. Copyright © 2018 Elsevier Ltd. All rights reserved.

Large sample area and size are needed for forest soil seed bank studies to ensure low discrepancy with standing vegetation.

PubMed

Shen, You-xin; Liu, Wei-li; Li, Yu-hui; Guan, Hui-lin

2014-01-01

A large number of small-sized samples invariably shows that woody species are absent from forest soil seed banks, leading to a large discrepancy with the seedling bank on the forest floor. We ask: 1) Does this conventional sampling strategy limit the detection of seeds of woody species? 2) Are large sample areas and sample sizes needed for higher recovery of seeds of woody species? We collected 100 samples that were 10 cm (length) × 10 cm (width) × 10 cm (depth), referred to as larger number of small-sized samples (LNSS) in a 1 ha forest plot, and placed them to germinate in a greenhouse, and collected 30 samples that were 1 m × 1 m × 10 cm, referred to as small number of large-sized samples (SNLS) and placed them (10 each) in a nearby secondary forest, shrub land and grass land. Only 15.7% of woody plant species of the forest stand were detected by the 100 LNSS, contrasting with 22.9%, 37.3% and 20.5% woody plant species being detected by SNLS in the secondary forest, shrub land and grassland, respectively. The increased number of species vs. sampled areas confirmed power-law relationships for forest stand, the LNSS and SNLS at all three recipient sites. Our results, although based on one forest, indicate that conventional LNSS did not yield a high percentage of detection for woody species, but SNLS strategy yielded a higher percentage of detection for woody species in the seed bank if samples were exposed to a better field germination environment. A 4 m2 minimum sample area derived from power equations is larger than the sampled area in most studies in the literature. Increased sample size also is needed to obtain an increased sample area if the number of samples is to remain relatively low.

Sampling Methods for Detection and Monitoring of the Asian Citrus Psyllid (Hemiptera: Psyllidae).

PubMed

Monzo, C; Arevalo, H A; Jones, M M; Vanaclocha, P; Croxton, S D; Qureshi, J A; Stansly, P A

2015-06-01

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama is a key pest of citrus due to its role as vector of citrus greening disease or "huanglongbing." ACP monitoring is considered an indispensable tool for management of vector and disease. In the present study, datasets collected between 2009 and 2013 from 245 citrus blocks were used to evaluate precision, sensitivity for detection, and efficiency of five sampling methods. The number of samples needed to reach a 0.25 standard error-mean ratio was estimated using Taylor's power law and used to compare precision among sampling methods. Comparison of detection sensitivity and time expenditure (cost) between stem-tap and other sampling methodologies conducted consecutively at the same location were also assessed. Stem-tap sampling was the most efficient sampling method when ACP densities were moderate to high and served as the basis for comparison with all other methods. Protocols that grouped trees near randomly selected locations across the block were more efficient than sampling trees at random across the block. Sweep net sampling was similar to stem-taps in number of captures per sampled unit, but less precise at any ACP density. Yellow sticky traps were 14 times more sensitive than stem-taps but much more time consuming and thus less efficient except at very low population densities. Visual sampling was efficient for detecting and monitoring ACP at low densities. Suction sampling was time consuming and taxing but the most sensitive of all methods for detection of sparse populations. This information can be used to optimize ACP monitoring efforts. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Proportional counter device for detecting electronegative species in an air sample

DOEpatents

Allman, Steve L.; Chen, Fang C.; Chen, Chung-Hsuan

1994-01-01

Apparatus for detecting an electronegative species comprises an analysis chamber, an inlet communicating with the analysis chamber for admitting a sample containing the electronegative species and an ionizable component, a radioactive source within the analysis chamber for emitting radioactive energy for ionizing a component of the sample, a proportional electron detector within the analysis chamber for detecting electrons emitted from the ionized component, and a circuit for measuring the electrons and determining the presence of the electronegative species by detecting a reduction in the number of available electrons due to capture of electrons by the electronegative species.

Proportional counter device for detecting electronegative species in an air sample

DOEpatents

Allman, S.L.; Chen, F.C.; Chen, C.H.

1994-03-08

Apparatus for detecting an electronegative species comprises an analysis chamber, an inlet communicating with the analysis chamber for admitting a sample containing the electronegative species and an ionizable component, a radioactive source within the analysis chamber for emitting radioactive energy for ionizing a component of the sample, a proportional electron detector within the analysis chamber for detecting electrons emitted from the ionized component, and a circuit for measuring the electrons and determining the presence of the electronegative species by detecting a reduction in the number of available electrons due to capture of electrons by the electronegative species. 2 figures.

The trace analysis of microorganisms in real samples by combination of a filtration microcartridge and capillary isoelectric focusing.

PubMed

Horká, Marie; Horký, Jaroslav; Kubesová, Anna; Zapletalová, Eva; Slais, Karel

2011-07-01

Trace analysis of microorganisms in real biological samples needs very sensitive methods for their detection. Most procedures for detecting and quantifying pathogens require a sample preparation step including concentrating microorganisms from large sample volumes with high and reproducible efficiency. Electromigration techniques have great potential to include the preconcentration, separation, and detection of whole cells and therefore they can rapidly indicate the presence of pathogens. The preconcentration and separation of microorganisms from real suspensions utilising a combination of filtration and capillary isoelectric focusing was developed and the possibility for its application to real samples was verified. For our experiments, spores of Monilinia species and of Penicillium expansum were selected as model bioparticles, as they cause major losses in agrosystems. The isoelectric points of the spores of M. laxa, M. fructigena, M. fruticola, and P. expansum were determined and the method was verified using real samples taken directly from infected apples. The coupling of a filtration cartridge with a separation capillary can improve the detection limit of isoelectric focusing with UV detection by at least 4 orders of magnitude. Spores of M. fructigena and of M. laxa in numbers of hundreds of particles per milliliter were detected on a visually noninfected apple surface which was cross-contaminated during handling and storage. The efficiency of preconcentration and a preliminary identification was verified by the phenotyping technique after cultivation of the spores sampled from the apple surface.

Emerging contaminants at a closed and an operating landfill in Oklahoma

USGS Publications Warehouse

Andrews, William J.; Masoner, Jason R.; Cozzarelli, Isabelle M.

2012-01-01

Landfills are the final depositories for a wide range of solid waste from both residential and commercial sources, and therefore have the potential to produce leachate containing many organic compounds found in consumer products such as pharmaceuticals, plasticizers, disinfectants, cleaning agents, fire retardants, flavorings, and preservatives, known as emerging contaminants (ECs). Landfill leachate was sampled from landfill cells of three different age ranges from two landfills in Central Oklahoma. Samples were collected from an old cell containing solid waste greater than 25 years old, an intermediate age cell with solid waste between 16 and 3 years old, and operating cell with solid waste less than 5 years old to investigate the chemical variability and persistence of selected ECs in landfill leachate of differing age sources. Twenty-eight of 69 analyzed ECs were detected in one or more samples from the three leachate sources. Detected ECs ranged in concentration from 0.11 to 114 μg/L and included 4 fecal and plant sterols, 13 household\\industrial, 7 hydrocarbon, and 4 pesticide compounds. Four ECs were solely detected in the oldest leachate sample, two ECs were solely detected in the intermediate leachate sample, and no ECs were solely detected in the youngest leachate sample. Eleven ECs were commonly detected in all three leachate samples and are an indication of the contents of solid waste deposited over several decades and the relative resistance of some ECs to natural attenuation processes in and near landfills.

Development of LAMP assays for the molecular detection of taeniid infection in canine in Tibetan rural area.

PubMed

Feng, Kai; Li, Wei; Guo, Zhihong; Duo, Hong; Fu, Yong; Shen, Xiuying; Tie, Cheng; E, Rijie; Xiao, Changqin; Luo, Yanhong; Qi, Guo; Ni, Ma; Ma, Qingmei; Yamazaki, Wataru; Yoshida, Ayako; Horii, Yoichiro; Yagi, Kinpei; Nonaka, Nariaki

2017-12-22

For field-identification of taeniid cestodes in canine animals in Tibetan area, loop-mediated isothermal amplification (LAMP) assays for Echinococcus multilocularis, E. shiquicus, Taenia hydatigena, T. multiceps, T. pisiformis and T. crassiceps were developed and evaluated along with the reported assay for E. granulosus. The LAMP assays showed specific reaction with their corresponding target species DNA with the detection limit of 1 to 10 pg. Moreover, the assays for E. granulosus, E. multilocularis, T. hydatigena and T. multiceps could detect DNA extracted from 3 or more eggs of their corresponding target species. Then, the LAMP assays were applied on samples containing 3 to 35 taeniid eggs obtained from 61 field-collected canine feces in Qinghai, and the result was compared with a reported multiplex PCR and sequence analysis. The LAMP assays and the PCR detected single species DNA of E. granulosus, E. shiquicus, T. hydatigena and T. multiceps in 5, 2, 44 and 2 samples, respectively. In the rest 8 samples, DNA of both E. granulosus and T. hydatigena were detected by the PCR but the LAMP assays detected those DNAs in 2 samples and only T. hydatigena DNA in 6 samples. It was assumed that less than 3 E. granulosus eggs were mixed in the samples although the samples contained 21 to 27 eggs in total. In conclusion, the LAMP assays were less sensitive than the multiplex PCR, but would have adequate sensitivity for field use in Tibetan area.

Random phase detection in multidimensional NMR.

PubMed

Maciejewski, Mark W; Fenwick, Matthew; Schuyler, Adam D; Stern, Alan S; Gorbatyuk, Vitaliy; Hoch, Jeffrey C

2011-10-04

Despite advances in resolution accompanying the development of high-field superconducting magnets, biomolecular applications of NMR require multiple dimensions in order to resolve individual resonances, and the achievable resolution is typically limited by practical constraints on measuring time. In addition to the need for measuring long evolution times to obtain high resolution, the need to distinguish the sign of the frequency constrains the ability to shorten measuring times. Sign discrimination is typically accomplished by sampling the signal with two different receiver phases or by selecting a reference frequency outside the range of frequencies spanned by the signal and then sampling at a higher rate. In the parametrically sampled (indirect) time dimensions of multidimensional NMR experiments, either method imposes an additional factor of 2 sampling burden for each dimension. We demonstrate that by using a single detector phase at each time sample point, but randomly altering the phase for different points, the sign ambiguity that attends fixed single-phase detection is resolved. Random phase detection enables a reduction in experiment time by a factor of 2 for each indirect dimension, amounting to a factor of 8 for a four-dimensional experiment, albeit at the cost of introducing sampling artifacts. Alternatively, for fixed measuring time, random phase detection can be used to double resolution in each indirect dimension. Random phase detection is complementary to nonuniform sampling methods, and their combination offers the potential for additional benefits. In addition to applications in biomolecular NMR, random phase detection could be useful in magnetic resonance imaging and other signal processing contexts.

Evaluation of Trapper-Collected Nobuto Filter-Paper Blood Samples for Distemper and Parvovirus Antibody Detection in Coyotes (Canis latrans) and Raccoons (Procyon lotor).

PubMed

Kamps, Amanda J; Dubay, Shelli A; Langenberg, Julie; Maes, Roger K

2015-07-01

Blood samples are often collected from free-ranging wildlife for antibody detection. However, filter-paper (FP) strips are more cost efficient and easy to collect and store. We evaluated trapper-collected FP strips and body-cavity blood for canine distemper (CDV) and parvovirus (CPV-2) antibody detection in raccoons (Procyon lotor) and coyotes (Canis latrans). From 2008 to 2010, licensed trappers near Madison and Milwaukee, Wisconsin, US collected paired samples from harvested animals. Canine distemper antibodies were detected using virus neutralization and parvovirus antibodies were detected using hemagglutination inhibition. Titers ≥ 1:32 for CDV and ≥ 1:25 for CPV-2 were considered evidence of exposure. Using Cohen's kappa test of agreement, FP strip titers agreed with sera for CDV in coyotes (n = 28, K = 0.772) and raccoons (n = 29, K = 0.858) and for CPV-2 in coyotes (n = 40, K = 0.775) and raccoons (n = 70, K = 0.646). However, raccoons determined to be exposed to CPV-2 from sera were unexposed by FP strips in 35% of the samples. Titer results may be affected by quality and volume of blood samples, interval between collection and processing, small sample sizes, and diagnostic testing procedures. Filter-paper strips can be useful for detecting CDV and CPV-2 exposure in coyotes and raccoons with correct field sample collection and appropriate diagnostic testing procedures.

40 CFR 92.103 - Test procedures; overview.

Code of Federal Regulations, 2011 CFR

2011-07-01

... organics (i.e., hydrocarbons, alcohols, and aldehydes); diesel-fueled and biodiesel-fueled locomotives... sampling and detection systems, and aldehyde sampling and detection systems. Necessary equipment and...

40 CFR 92.103 - Test procedures; overview.

Code of Federal Regulations, 2012 CFR

2012-07-01

... organics (i.e., hydrocarbons, alcohols, and aldehydes); diesel-fueled and biodiesel-fueled locomotives... sampling and detection systems, and aldehyde sampling and detection systems. Necessary equipment and...

40 CFR 92.103 - Test procedures; overview.

Code of Federal Regulations, 2014 CFR

2014-07-01

... organics (i.e., hydrocarbons, alcohols, and aldehydes); diesel-fueled and biodiesel-fueled locomotives... sampling and detection systems, and aldehyde sampling and detection systems. Necessary equipment and...

40 CFR 92.103 - Test procedures; overview.

Code of Federal Regulations, 2010 CFR

2010-07-01

... organics (i.e., hydrocarbons, alcohols, and aldehydes); diesel-fueled and biodiesel-fueled locomotives... sampling and detection systems, and aldehyde sampling and detection systems. Necessary equipment and...

40 CFR 92.103 - Test procedures; overview.

Code of Federal Regulations, 2013 CFR

2013-07-01

... organics (i.e., hydrocarbons, alcohols, and aldehydes); diesel-fueled and biodiesel-fueled locomotives... sampling and detection systems, and aldehyde sampling and detection systems. Necessary equipment and...

Comparison of culture and a multiplex probe PCR for identifying Mycoplasma species in bovine milk, semen and swab samples

PubMed Central

Parker, Alysia M.; House, John K.; Hazelton, Mark S.; Bosward, Katrina L.; Sheehy, Paul A.

2017-01-01

Mycoplasma spp. are a major cause of mastitis, arthritis and pneumonia in cattle, and have been associated with reproductive disorders in cows. While culture is the traditional method of identification the use of PCR has become more common. Several investigators have developed PCR protocols to detect M. bovis in milk, yet few studies have evaluated other sample types or other important Mycoplasma species. Therefore the objective of this study was to develop a multiplex PCR assay to detect M. bovis, M. californicum and M. bovigenitalium, and evaluate its analytical performance against traditional culture of bovine milk, semen and swab samples. The PCR specificity was determined and the limit of detection evaluated in spiked milk, semen and swabs. The PCR was then compared to culture on 474 field samples from individual milk, bulk tank milk (BTM), semen and swab (vaginal, preputial, nose and eye) samples. Specificity analysis produced appropriate amplification for all M. bovis, M. californicum and M. bovigenitalium isolates. Amplification was not seen for any of the other Mollicutes or eubacterial isolates. The limit of detection of the PCR was best in milk, followed by semen and swabs. When all three Mycoplasma species were present in a sample, the limit of detection increased. When comparing culture and PCR, overall there was no significant difference in the proportion of culture and PCR positive samples. Culture could detect significantly more positive swab samples. No significant differences were identified for semen, individual milk or BTM samples. PCR identified five samples with two species present. Culture followed by 16S-23S rRNA sequencing did not enable identification of more than one species. Therefore, the superior method for identification of M. bovis, M. californicum and M. bovigenitalium may be dependent on the sample type being analysed, and whether the identification of multiple target species is required. PMID:28264012

Pesticides in the nation's rivers, 1975-1980, and implications for future monitoring

USGS Publications Warehouse

Gilliom, Robert J.; Alexander, Richard B.; Smith, Richard A.

1985-01-01

Water samples were taken four times per year and bed-sediment samples two times per year during 1975-80 at 160 to 180 stations on major rivers of the United States. Samples were analyzed for 18 insecticides and 4 herbicides, which together accounted for about one-third of the total amount of all pesticides applied to major crops during 1975-80. Fewer than 10 percent of almost 3,000 water samples and fewer than 20 percent of almost 1,000 bed-sediment samples contained reportable concentrations of any of the compounds. The patterns of detection result from a combination of widely variable detection capabilities, chemical properties, and use. Most detections in water samples were of relatively persistent yet soluble compounds: atrazine (4.8 percent of samples), diazinon (1.2), and lindane (1.1). Most detections in bed-sediment samples were of the hydrophobic and persistent insecticides: DDE (17 percent of samples), DDD (12), dieldrin (12), chlordane (9.9), and DDT (8.5). Only for atrazine in water, and for DDE, DDD, DDT, and chlordane in bed sediments, were geographic patterns of detection correlated (pH<0.10) with use on farms. Detections of organochlorine insecticides in both water and bed sediments appear to have erratically but gradually decreased during 1975-80. For the 1975-79 period, more stations had downtrends than had uptrends in bed-sediment levels of organochlorines. No clear trends were evident in concentrations of organophosphate insecticides or herbicides in either water or bed sediments. Findings suggest that future pesticide monitoring efforts must be responsive to changes in pesticides used and to geographic patterns of use. Different types of monitoring approaches are necesssary for chemicals having different chemical and physical properties. Before an effective dynamic monitoring effort can be designed, however, selected case studies are needed to characterize and refine sampling and analytical capabilities for different types of chemicals, river environments, and sample types.

Detection of Salmonella spp. from chevon, mutton and its environment in retail meat shops in Anand city (Gujarat), India

PubMed Central

Makwana, P. P.; Nayak, J. B.; Brahmbhatt, M. N.; Chaudhary, J. H.

2015-01-01

Aim: The aim of this study was (i) To attempt isolation and identification of Salmonella species from samples. (ii) Serotyping of Salmonella isolates. (iii) Detection of virulence factor associated genes by polymerase chain reaction (PCR). Materials and Methods: A total of 284 samples comprised of chevon and mutton (112 samples each) as well as 60 samples (20 each of retail meat shops environment samples viz. Butchers’ hands, knives and log swabs) were collected from the retail meat shops in and around Anand City under aseptic precautions. Rappaport-vassiliadis soy bean meal broth and tetrathionate broth was used for the enrichment of all the samples and inoculation was done on brilliant green agar and xylose lysine deoxycholate agar. This was followed by the confirmation of isolates using biochemical tests. For the serotyping, isolates were sent to the National Salmonella and Escherichia Centre, Central Research Institute, Kasauli, Himachal Pradesh. Detection of virulence genes was performed by PCR technique using previously reported primer. Result: Of 284 meats and retail meat shops environment samples, 13 (4.58%) samples were found positive for Salmonella. It was interesting to know that incidence of Salmonella was more in mutton (6.25%) than chevon (3.57%). In case of meat shop environmental samples 1 (5.00%) sample observed positive for Salmonella separately among the butchers’ hands and knives swabs (Each of 20 samples) examined. Out of 13, eleven isolates detected as Salmonella Typhimurium, whereas only two isolates were detected as Salmonella Enteritidis. All Salmonella isolates possess invA and stn genes, whereas nine isolates had a presence of spvR gene while only five of the isolates revealed the presence of spvC gene as shown by in vitro detection of virulence genes by PCR. Conclusion: Therefore, might be suggested that the good hygiene practices and effective control measures should be taken to encourage clean meat production with prolonged shelf-life. PMID:27047102

Detection and genome characterization of bovine polyomaviruses in beef muscle and ground beef samples from Germany.

PubMed

Gräfe, Donina; Ehlers, Bernhard; Mäde, Dietrich; Ellerbroek, Lüppo; Seidler, Tassilo; Johne, Reimar

2017-01-16

Polyomaviruses are small, non-enveloped, circular double-stranded DNA viruses. Some polyomaviruses can induce tumors and cancer under certain circumstances. The bovine polyomaviruses (BPyV) 1-3 have been only scarcely analyzed so far. It was hypothesized that the consumption of beef meat containing polyomaviruses could contribute to the development of cancer in humans. In order to assess the distribution of the BPyV genome in meat from Germany, 101 beef muscle samples and 10 ground beef samples were analyzed here. A specific sample preparation method combined with or without rolling circle amplification (RCA), and BPyV-specific PCRs were developed and applied. BPyV-1 DNA was detected in 1/101 (1%) samples from beef meat and in 2/10 (20%) ground beef samples. BPyV-2 DNA was detected in 3/10 (30%) ground beef samples, whereas BPyV-3 was not detected in the samples. Application of RCA did not increase the detection rate in ground beef samples. Sequence analysis of the PCR products indicated the presence of BPyV-1, BPyV-2a and BPyV-2b. The whole genome of a BPyV-1 strain from ground beef meat showed 97.8% sequence identity to the BPyV-1 reference strain and that of a BPyV-2a strain from ground beef meet showed 99.9% sequence identity to strain 2aS11. It can be concluded that BPyV genomes can be frequently detected in ground beef samples, although higher sample numbers should be investigated in future to confirm this finding. Further studies should focus on the infectivity, tumorigenicity and heat resistance of the contained viruses in order to assess the risk of cancer induction through consumption of BPyVs present in beef products. Copyright © 2016 Elsevier B.V. All rights reserved.

Preanalytical considerations in detection of colorectal cancer in blood serum using Raman molecular imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Treado, Patrick J.; Stewart, Shona D.; Smith, Aaron; Kirschner, Heather; Post, Christopher; Overholt, Bergein F.

2016-03-01

Colorectal cancer (CRC) is the third most common cancer in men and women in the United States. Raman Molecular Imaging (RMI) is an effective technique to evaluate human tissue, cells and bodily fluids, including blood serum for disease diagnosis. ChemImage Corporation, in collaboration with clinicians, has been engaged in development of an in vitro diagnostic Raman assay focused on CRC detection. The Raman Assay for Colorectal Cancer (RACC) exploits the high specificity of Raman imaging to distinguish diseased from normal dried blood serum droplets without additional reagents. Pilot Study results from testing of hundreds of biobank patient samples have demonstrated that RACC detects CRC with high sensitivity and specificity. However, expanded clinical trials, which are ongoing, are revealing a host of important preanalytical considerations associated with sample collection, sample storage and stability, sample shipping, sample preparation and sample interferents, which impact detection performance. Results from recent clinical studies will be presented.

[Detection of leptospira in the vitreous body of horses without ocular diseases and of horses with equine recurrent uveitis (ERU) using transmission-electron microscopy].

PubMed

Niedermaier, G; Wollanke, B; Hoffmann, R; Brem, S; Gerhards, H

2006-11-01

Equine recurrent uveitis (ERU) is caused by persistent intraocular leptospira, which appear to use the vitreous body as a refuge. The detection of leptospira in the vitreous body of horses with spontaneous ERU by histological methods has not yet been described. Thirty eight vitreous body samples from 36 horses with ERU (collected during vitrectomy), and 10 vitreous body samples obtained from 5 horses without ocular disease (control group) were examined by transmission electron microscopy. Prior to sample collection, 2 ml of a leptospira culture suspension were injected into the vitreous body of 2 eyes enucleated from horses of the control group. The detection of leptospira in samples, experimentally inoculated with these bacteria was uncomplicated; in vitreous body samples from horses with spontaneous ERU the detection was successful in only a few cases (3/38). The morphologically varying envelope of leptospira in vitreous body samples of horses which developed ERU spontaneously suggests the existence of a bacterial masquerade in vivo.

Exploring revictimization risk in a community sample of sexual assault survivors.

PubMed

Chu, Ann T; Deprince, Anne P; Mauss, Iris B

2014-01-01

Previous research points to links between risk detection (the ability to detect danger cues in various situations) and sexual revictimization in college women. Given important differences between college and community samples that may be relevant to revictimization risk (e.g., the complexity of trauma histories), the current study explored the link between risk detection and revictimization in a community sample of women. Community-recruited women (N = 94) reported on their trauma histories in a semistructured interview. In a laboratory session, participants listened to a dating scenario involving a woman and a man that culminated in sexual assault. Participants were instructed to press a button "when the man had gone too far." Unlike in college samples, revictimized community women (n = 47) did not differ in terms of risk detection response times from women with histories of no victimization (n = 10) or single victimization (n = 15). Data from this study point to the importance of examining revictimization in heterogeneous community samples where risk mechanisms may differ from college samples.

Occurrence of Campylobacter spp. in raw and ready-to-eat foods and in a Canadian food service operation.

PubMed

Medeiros, Diane T; Sattar, Syed A; Farber, Jeffrey M; Carrillo, Catherine D

2008-10-01

The occurrence of Campylobacter spp. in a variety of foods from Ottawa, Ontario, Canada, and raw milk samples from across Canada was determined over a 2-year period. The samples consisted of 55 raw foods (chicken, pork, and beef), 126 raw milk samples from raw milk cheese manufacturers, and 135 ready-to-eat foods (meat products, salads, and raw milk cheeses). Campylobacter jejuni was detected in 4 of the 316 samples analyzed: 1 raw beef liver sample and 3 raw chicken samples. An isolation rate of 9.7% was observed among the raw chicken samples tested. This study also investigated the role of cross-contamination in disseminating Campylobacter from raw poultry within a food service operation specializing in poultry dishes. Accordingly, kitchen surfaces within a restaurant in Ottawa, Ontario, were sampled between March and August 2001. Tests of the sampling method indicated that as few as 100 Campylobacter cells could be detected if sampling was done within 45 min of inoculation; however, Campylobacter spp. were not detected in 125 swabs of surfaces within the kitchens of this food service operation. Despite the reported high prevalence of Campylobacter spp. in raw poultry, this organism was not detected on surfaces within a kitchen of a restaurant specializing in poultry dishes.

Targeted and non-targeted detection of lemon juice adulteration by LC-MS and chemometrics.

PubMed

Wang, Zhengfang; Jablonski, Joseph E

2016-01-01

Economically motivated adulteration (EMA) of lemon juice was detected by LC-MS and principal component analysis (PCA). Twenty-two batches of freshly squeezed lemon juice were adulterated by adding an aqueous solution containing 5% citric acid and 6% sucrose to pure lemon juice to obtain 30%, 60% and 100% lemon juice samples. Their total titratable acidities, °Brix and pH values were measured, and then all the lemon juice samples were subject to LC-MS analysis. Concentrations of hesperidin and eriocitrin, major phenolic components of lemon juice, were quantified. The PCA score plots for LC-MS datasets were used to preview the classification of pure and adulterated lemon juice samples. Results showed a large inherent variability in the chemical properties among 22 batches of 100% lemon juice samples. Measurement or quantitation of one or several chemical properties (targeted detection) was not effective in detecting lemon juice adulteration. However, by using the LC-MS datasets, including both chromatographic and mass spectrometric information, 100% lemon juice samples were successfully differentiated from adulterated samples containing 30% lemon juice in the PCA score plot. LC-MS coupled with chemometric analysis can be a complement to existing methods for detecting juice adulteration.

Pesticides in surface water, bed sediment, and ground water adjacent to commercial cranberry bogs, Lac du Flambeau Reservation, Vilas County, Wisconsin

USGS Publications Warehouse

Saad, David A.

2005-01-01

In samples from the Trout River, which is used as a source of water to maintain lake levels in the Corn Lakes, the only pesticides detected were the non-targeted compounds atrazine and deethyl atrazine, indicating it was not a source of targeted compounds detected in the Corn Lakes. Only two pesticides (chlorpyrifos and metolachlor) were detected in bed-sediment samples collected from the lakes; chlorpyrifos from Little Trout Lake and metolachlor from the Corn Lakes. Four pesticides (the targeted compounds napropamide and norflurazon and the non-targeted compounds atrazine and deethyl atrazine) were detected in ground-water samples from two of four sampled monitor wells. The highest ground-water concentrations (up to 0.14 ?g/L napropamide and 0.56 ?g/L norflurazon) were measured in samples from the monitoring well located directly downgradient from the Corn Lakes and commercial cranberry operations. No pesticides were detected in samples from the reference well located upgradient from the Corn Lakes and cranberry operations. Further study is needed to identify additional pesticides as well as chronic effects on aquatic organisms to determine whether cranberry-related pesticides affect the lake ecosystems of the Lac du Flambeau Reservation.

Enteric Viruses in Raw Vegetables and Groundwater Used for Irrigation in South Korea▿

PubMed Central

Cheong, Sooryun; Lee, Cheonghoon; Song, Sung Won; Choi, Weon Cheon; Lee, Chan Hee; Kim, Sang-Jong

2009-01-01

Raw vegetables irrigated with groundwater that may contain enteric viruses can be associated with food-borne viral disease outbreaks. In this study, we performed reverse transcription-PCR (RT-PCR) and cell culture-PCR to monitor the occurrence of enteric viruses in groundwater samples and in raw vegetables that were cultivated using that groundwater in South Korea. Samples were collected 10 times from three farms located in Gyeonggi Province, South Korea. RT-PCR and cell culture-PCR were performed to detect adenoviruses (AdVs), enteroviruses (EVs), noroviruses (NoVs), and rotaviruses, followed by sequence analyses of the detected strains. Of the 29 groundwater samples and the 30 vegetable samples, five (17%) and three (10%) were positive for enteric viruses, respectively. AdVs were the most frequently detected viruses in four groundwater and three vegetable samples. EVs and NoVs were detected in only one groundwater sample and one spinach sample, respectively. The occurrence of enteric viruses in groundwater and vegetable samples was not correlated with the water temperature and the levels of indicator bacteria, respectively. Phylogenetic analysis indicated that most of the detected AdVs were temporally distributed, irrespective of sample type. Our results indicate that raw vegetables may be contaminated with a broad range of enteric viruses, which may originate from virus-infected farmers and virus-contaminated irrigation water, and these vegetables may act as a potential vector of food-borne viral transmission. PMID:19854919

Overview of pesticide residues in stored pollen and their potential effect on bee colony (Apis mellifera) losses in Spain.

PubMed

Bernal, J; Garrido-Bailón, E; Del Nozal, M J; González-Porto, A V; Martín-Hernández, R; Diego, J C; Jiménez, J J; Bernal, J L; Higes, M

2010-12-01

In the last decade, an increase in honey bee (Apis mellifera L.) colony losses has been reported in several countries. The causes of this decline are still not clear. This study was set out to evaluate the pesticide residues in stored pollen from honey bee colonies and their possible impact on honey bee losses in Spain. In total, 1,021 professional apiaries were randomly selected. All pollen samples were subjected to multiresidue analysis by gas chromatography-mass spectrometry (MS) and liquid chromatography-MS; moreover, specific methods were applied for neonicotinoids and fipronil. A palynological analysis also was carried out to confirm the type of foraging crop. Pesticide residues were detected in 42% of samples collected in spring, and only in 31% of samples collected in autumn. Fluvalinate and chlorfenvinphos were the most frequently detected pesticides in the analyzed samples. Fipronil was detected in 3.7% of all the spring samples but never in autumn samples, and neonicotinoid residues were not detected. More than 47.8% of stored pollen samples belonged to wild vegetation, and sunflower (Heliantus spp.) pollen was only detected in 10.4% of the samples. A direct relation between pesticide residues found in stored pollen samples and colony losses was not evident accordingly to the obtained results. Further studies are necessary to determine the possible role of the most frequent and abundant pesticides (such as acaricides) and the synergism among them and with other pathogens more prevalent in Spain.

FT-IR standoff detection of thermally excited emissions of trinitrotoluene (TNT) deposited on aluminum substrates.

PubMed

Castro-Suarez, John R; Pacheco-Londoño, Leonardo C; Vélez-Reyes, Miguel; Diem, Max; Tague, Thomas J; Hernandez-Rivera, Samuel P

2013-02-01

A standoff detection system was assembled by coupling a reflecting telescope to a Fourier transform infrared spectrometer equipped with a cryo-cooled mercury cadmium telluride detector and used for detection of solid-phase samples deposited on substrates. Samples of highly energetic materials were deposited on aluminum substrates and detected at several collector-target distances by performing passive-mode, remote, infrared detection measurements on the heated analytes. Aluminum plates were used as support material, and 2,4,6-Trinitrotoluene (TNT) was used as the target. For standoff detection experiments, the samples were placed at different distances (4 to 55 m). Several target surface temperatures were investigated. Partial least squares regression analysis was applied to the analysis of the intensities of the spectra obtained. Overall, standoff detection in passive mode was useful for quantifying TNT deposited on the aluminum plates with high confidence up to target-collector distances of 55 m.

Universal explosive detection system for homeland security applications

NASA Astrophysics Data System (ADS)

Lee, Vincent Y.; Bromberg, Edward E. A.

2010-04-01

L-3 Communications CyTerra Corporation has developed a high throughput universal explosive detection system (PassPort) to automatically screen the passengers in airports without requiring them to remove their shoes. The technical approach is based on the patented energetic material detection (EMD) technology. By analyzing the results of sample heating with an infrared camera, one can distinguish the deflagration or decomposition of an energetic material from other clutters such as flammables and general background substances. This becomes the basis of a universal explosive detection system that does not require a library and is capable of detecting trace levels of explosives with a low false alarm rate. The PassPort is a simple turnstile type device and integrates a non-intrusive aerodynamic sampling scheme that has been shown capable of detecting trace levels of explosives on shoes. A detailed description of the detection theory and the automated sampling techniques, as well as the field test results, will be presented.

Air National Guard Installation Restoration Protram. Site Investigation Report: Georgia Air National Guard, Savannah, Georgia

DTIC Science & Technology

1992-01-01

except TPH, which was detected at 0.06 mg/l in Monitor Well 01-MW-02. Some metals (arsenic, cadmium , chromium, lead, silver, and zinc ) were detected at...extraction. Trace quantities of some priority pollutant metals were detected in the surface water samples. Arsenic, cadmium , and zinc were detected at...storage tank. TPH was detected in all five groundwater samples. Arsenic, beryllium, cadmium , chromium, copper, lead, nickel, silver, and zinc were also

DNA Microarray for Detection of Gastrointestinal Viruses

PubMed Central

Martínez, Miguel A.; Soto-del Río, María de los Dolores; Gutiérrez, Rosa María; Chiu, Charles Y.; Greninger, Alexander L.; Contreras, Juan Francisco; López, Susana; Arias, Carlos F.

2014-01-01

Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 103 virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals. PMID:25355758

Optical biosensor system with integrated microfluidic sample preparation and TIRF based detection

NASA Astrophysics Data System (ADS)

Gilli, Eduard; Scheicher, Sylvia R.; Suppan, Michael; Pichler, Heinz; Rumpler, Markus; Satzinger, Valentin; Palfinger, Christian; Reil, Frank; Hajnsek, Martin; Köstler, Stefan

2013-05-01

There is a steadily growing demand for miniaturized bioanalytical devices allowing for on-site or point-of-care detection of biomolecules or pathogens in applications like diagnostics, food testing, or environmental monitoring. These, so called labs-on-a-chip or micro-total analysis systems (μ-TAS) should ideally enable convenient sample-in - result-out type operation. Therefore, the entire process from sample preparation, metering, reagent incubation, etc. to detection should be performed on a single disposable device (on-chip). In the early days such devices were mainly fabricated using glass or silicon substrates and adapting established fabrication technologies from the electronics and semiconductor industry. More recently, the development focuses on the use of thermoplastic polymers as they allow for low-cost high volume fabrication of disposables. One of the most promising materials for the development of plastic based lab-on-achip systems are cyclic olefin polymers and copolymers (COP/COC) due to their excellent optical properties (high transparency and low autofluorescence) and ease of processing. We present a bioanalytical system for whole blood samples comprising a disposable plastic chip based on TIRF (total internal reflection fluorescence) optical detection. The chips were fabricated by compression moulding of COP and microfluidic channels were structured by hot embossing. These microfluidic structures integrate several sample pretreatment steps. These are the separation of erythrocytes, metering of sample volume using passive valves, and reagent incubation for competitive bioassays. The surface of the following optical detection zone is functionalized with specific capture probes in an array format. The plastic chips comprise dedicated structures for simple and effective coupling of excitation light from low-cost laser diodes. This enables TIRF excitation of fluorescently labeled probes selectively bound to detection spots at the microchannel surface. The fluorescence of these detection arrays is imaged using a simple set-up based on a digital consumer camera. Image processing for spot detection and intensity calculation is accomplished using customized software. Using this combined TIRF excitation and imaging based detection approach allowes for effective suppression of background fluorescence from the sample, multiplexed detection in an array format, as well as internal calibration and background correction.

Anthropogenic Organic Compounds in Source and Finished Groundwater of Community Water Systems in the Piedmont Physiographic Province, Potomac River Basin, Maryland and Virginia, 2003-04

USGS Publications Warehouse

Banks, William S.L.; Reyes, Betzaida

2009-01-01

A source- and finished-water-quality assessment of groundwater was conducted in the Piedmont Physiographic Province of Maryland and Virginia in the Potomac River Basin during 2003-04 as part of the U.S. Geological Survey's National Water-Quality Assessment Program. This assessment used a two-phased approach to sampling that allowed investigators to evaluate the occurrence of more than 280 anthropogenic organic compounds (volatile organic compounds, pesticides and pesticide degradates, and other anthropogenic organic compounds). Analysis of waters from 15 of the largest community water systems in the study area were included in the assessment. Source-water samples (raw-water samples collected prior to treatment) were collected at the well head. Finished-water samples (raw water that had been treated and disinfected) were collected after treatment and prior to distribution. Phase one samples, collected in August and September 2003, focused on source water. Phase two analyzed both source and finished water, and samples were collected in August and October of 2004. The results from phase one showed that samples collected from the source water for 15 community water systems contained 92 anthropogenic organic compounds (41 volatile organic compounds, 37 pesticides and pesticide degradates, and 14 other anthropogenic organic compounds). The 5 most frequently occurring anthropogenic organic compounds were detected in 11 of the 15 source-water samples. Deethylatrazine, a degradate of atrazine, was present in all 15 samples and metolachlor ethanesulfonic acid, a degradate of metolachlor, and chloroform were present in 13 samples. Atrazine and metolachlor were present in 12 and 11 samples, respectively. All samples contained a mixture of compounds with an average of about 14 compounds per sample. Phase two sampling focused on 10 of the 15 community water systems that were selected for resampling on the basis of occurrence of anthropogenic organic compounds detected most frequently during the first phase. A total of 48 different anthropogenic organic compounds were detected in samples collected from source and finished water. There were a similar number of compounds detected in finished water (41) and in source water (39). The most commonly detected group of anthropogenic organic compounds in finished water was trihalomethanes - compounds associated with the disinfection of drinking water. This group of compounds accounted for 30 percent of the detections in source water and 44 percent of the detections in finished water, and were generally found in higher concentrations in finished water. Excluding trihalomethanes, the number of total detections was about the same in source-water samples (33) as it was in finished-water samples (35). During both phases of the study, two measurements for human-health assessment were used. The first, the Maximum Contaminant Level for drinking water, is set by the U.S. Environmental Protection Agency and represents a legally enforceable maximum concentration of a contaminant permitted in drinking water. The second, the Health-Based Screening Level, was developed by the U.S. Geological Survey, is not legally enforceable, and represents a limit for more chronic exposures. Maximum concentrations for each detected compound were compared with either the Maximum Contaminant Level or the Health-Based Screening Level when available. More than half of the compounds detected had either a Maximum Contaminant Level or a Health-Based Screening Level. A benchmark quotient was set at 10 percent (greater than or equal to 0.1) of the ratio of the detected concentration of a particular compound to its Maximum Contaminant Level, or Health-Based Screening Level. This was considered a threshold for further monitoring. During phase one, when only source water was sampled, seven compounds (chloroform, benzene, acrylonitrile, methylene chloride, atrazine, alachlor, and dieldrin) met or exceeded a benchmark quotient. No de

Levels of organophosphorus pesticides in medicinal plants commonly consumed in Iran

PubMed Central

2012-01-01

The frequent occurrence of pesticide residues in herbal materials was indicated by previous studies. In this study, the concentration of some of the organophosphorus pesticides including parathion, malathion, diazinon and pirimiphos methyl in different kinds of medicinal plants were determined. The samples were collected randomly from ten local markets of different areas of Iran. At the detection limit of 0.5 ng g-1, parathion and pirimiphos methyl were not detected in any of the samples. Some amounts of malathion and diazinon were found in Zataria, Matricaria chamomile, Spearmint and Cumin Seed samples while, the concentrations of target organophosphorus pesticides in Borage samples were below the detection limits of the methods which could be a result of intensive transformation of organophosphorus pesticides by Borage. In addition the organophosphorus pesticides were detected in all of the samples below the maximum residue levels (MRLs) proposed by the international organizations. PMID:23351610

A survey of the use of soy in processed Turkish meat products and detection of genetic modification.

PubMed

Ulca, Pelin; Balta, Handan; Senyuva, Hamide Z

2014-01-01

To screen for possible illegal use of soybeans in meat products, the performance characteristics of a commercial polymer chain reaction (PCR) kit for detection of soybean DNA in raw and cooked meat products were established. Minced chicken and beef products containing soybean at levels from 0.1% to 10.0% were analysed by real-time PCR to amplify the soybean lectin gene. The PCR method could reliably detect the addition of soybean at a level of 0.1%. A survey of 38 Turkish processed meat products found only six samples to be negative for the presence of soybean. In 32 (84%) positive samples, 13 (34%) contained levels of soy above 0.1%. Of soybean positive samples, further DNA analysis was conducted by real-time PCR to detect whether genetically modified (GM) soybean had been used. Of 32 meat samples containing soybean, two samples were positive for GM modification.

Detection and Quantification of Nitrogen Compounds in the First Drilled Martian Solid Samples by the Sample Analysis at Mars (SAM) Instrument Suite on the Mars Science Laboratory (MSL)

NASA Technical Reports Server (NTRS)

Stern, J. C.; Navarro-Gonzales, R.; Freissinet, C.; McKay, C. P.; Archer, P. D., Jr.; Buch, A.; Brunner, A. E.; Coll, P.; Eigenbrode, J. L.; Franz, H. B.;

Determination of ammonium in river water and sewage samples by capillary zone electrophoresis with direct UV detection.

PubMed

Fukushi, Keiichi; Ito, Hideyuki; Kimura, Kenichi; Yokota, Kuriko; Saito, Keiitsu; Chayama, Kenji; Takeda, Sahori; Wakida, Shin-ichi

2006-02-17

We developed capillary zone electrophoresis (CZE) with direct UV detection for determination of ammonium in environmental water samples. Ammonium in the samples was partly converted into ammonia in the alkaline background electrolyte (BGE) during migration and was detected by molecular absorption of ammonia at 190 nm in approximately 7 min. The limit of detection (LOD) for ammonium was 0.24 mg/l (as nitrogen) at a signal-to-noise ratio of three. The respective values of the relative standard deviation (RSD) of peak area, peak height, and migration time for ammonium were 2.1, 1.8, and 0.46%. Major alkali and alkaline earth metal ions coexisting in the samples did not interfere with ammonium determination by the proposed method. The proposed method determined ammonium in surface water and sewage samples. The results were compared to those obtained using ion chromatography (IC).

Excretion and detection of SARS coronavirus and its nucleic acid from digestive system

PubMed Central

Wang, Xin-Wei; Li, Jin-Song; Guo, Ting-Kai; Zhen, Bei; Kong, Qing-Xin; Yi, Bin; Li, Zhong; Song, Nong; Jin, Min; Wu, Xiao-Ming; Xiao, Wen-Jun; Zhu, Xiu-Mei; Gu, Chang-Qing; Yin, Jing; Wei, Wei; Yao, Wei; Liu, Chao; Li, Jian-Feng; Ou, Guo-Rong; Wang, Min-Nian; Fang, Tong-Yu; Wang, Gui-Jie; Qiu, Yao-Hui; Wu, Huai-Huan; Chao, Fu-Huan; Li, Jun-Wen

2005-01-01

AIM: To study whether severe acute respiratory syndrome coronavirus (SARS-CoV) could be excreted from digestive system. METHODS: Cell culture and semi-nested RT-PCR were used to detect SARS-CoV and its RNA from 21 stool and urine samples, and a kind of electropositive filter media particles was used to concentrate the virus in 10 sewage samples from two hospitals receiving SARS patients in Beijing in China. RESULTS: It was demonstrated that there was no live SARS-CoV in all samples collected, but the RNA of SARS-CoV could be detected in seven stool samples from SARS patients with any one of the symptoms of fever, malaise, cough, or dyspnea, in 10 sewage samples before disinfection and 3 samples after disinfection from the two hospitals. The RNA could not be detected in urine and stool samples from patients recovered from SARS. CONCLUSION: Nucleic acid of SARS-CoV can be excreted through the stool of patients into sewage system, and the possibility of SARS-CoV transmitting through digestive system cannot be excluded. PMID:16038039

Detecting chaos in irregularly sampled time series.

PubMed

Kulp, C W

2013-09-01

Recently, Wiebe and Virgin [Chaos 22, 013136 (2012)] developed an algorithm which detects chaos by analyzing a time series' power spectrum which is computed using the Discrete Fourier Transform (DFT). Their algorithm, like other time series characterization algorithms, requires that the time series be regularly sampled. Real-world data, however, are often irregularly sampled, thus, making the detection of chaotic behavior difficult or impossible with those methods. In this paper, a characterization algorithm is presented, which effectively detects chaos in irregularly sampled time series. The work presented here is a modification of Wiebe and Virgin's algorithm and uses the Lomb-Scargle Periodogram (LSP) to compute a series' power spectrum instead of the DFT. The DFT is not appropriate for irregularly sampled time series. However, the LSP is capable of computing the frequency content of irregularly sampled data. Furthermore, a new method of analyzing the power spectrum is developed, which can be useful for differentiating between chaotic and non-chaotic behavior. The new characterization algorithm is successfully applied to irregularly sampled data generated by a model as well as data consisting of observations of variable stars.

Infrared trace element detection system

DOEpatents

Bien, F.; Bernstein, L.S.; Matthew, M.W.

1988-11-15

An infrared trace element detection system includes an optical cell into which the sample fluid to be examined is introduced and removed. Also introduced into the optical cell is a sample beam of infrared radiation in a first wavelength band which is significantly absorbed by the trace element and a second wavelength band which is not significantly absorbed by the trace element for passage through the optical cell through the sample fluid. The output intensities of the sample beam of radiation are selectively detected in the first and second wavelength bands. The intensities of a reference beam of the radiation are similarly detected in the first and second wavelength bands. The sensed output intensity of the sample beam in one of the first and second wavelength bands is normalized with respect to the other and similarly, the intensity of the reference beam of radiation in one of the first and second wavelength bands is normalized with respect to the other. The normalized sample beam intensity and normalized reference beam intensity are then compared to provide a signal from which the amount of trace element in the sample fluid can be determined. 11 figs.

Infrared trace element detection system

DOEpatents

Bien, Fritz; Bernstein, Lawrence S.; Matthew, Michael W.

1988-01-01

An infrared trace element detection system including an optical cell into which the sample fluid to be examined is introduced and removed. Also introduced into the optical cell is a sample beam of infrared radiation in a first wavelength band which is significantly absorbed by the trace element and a second wavelength band which is not significantly absorbed by the trace element for passage through the optical cell through the sample fluid. The output intensities of the sample beam of radiation are selectively detected in the first and second wavelength bands. The intensities of a reference beam of the radiation are similarly detected in the first and second wavelength bands. The sensed output intensity of the sample beam in one of the first and second wavelength bands is normalized with respect to the other and similarly, the intensity of the reference beam of radiation in one of the first and second wavelength bands is normalized with respect to the other. The normalized sample beam intensity and normalized reference beam intensity are then compared to provide a signal from which the amount of trace element in the sample fluid can be determined.

Detection of Legionella by quantitative-polymerase chain reaction (qPCR) for monitoring and risk assessment.

PubMed

Krøjgaard, Louise H; Krogfelt, Karen A; Albrechtsen, Hans-Jørgen; Uldum, Søren A

2011-11-21

Culture and quantitative polymerase chain reaction (qPCR) assays for the detection of Legionella were compared on samples from a residential area before and after two interventions. A total of 84 samples were collected from shower hoses and taps as first flush samples and at constant temperature. Samples were grouped according to the origin of the sample, a) circulation water b) water from empty apartments c) water from shower hoses. The aims were to investigate the usefulness of qPCR compared to culture for monitoring remedial actions for elimination of Legionella bacteria and as a tool for risk assessment. In water collected from the apartments Legionella spp were detected by qPCR in the concentration range from LOQ to 9.6*105GU/L while L. pneumophila were detected in a range from LOQ to 6.8*105 GU/L. By culturing, the legionellae were detected in the range from below detection limit (> 10 CFU/L) to 1.6*106 CFU/L. In circulating water and in first flush water from shower hoses, culture and qPCR showed the same tendencies. The overall correlation between the bacteria number detected by culture and the two developed qPCR assays (L. spp and L. pneumophila) was relatively poor (r2 = 0.31 for culture and Legionella spp. assay, r2 = 0.20 for culture and L. pneumophila assay). Detection by qPCR was suitable for monitoring changes in the concentration of Legionella but the precise determination of bacteria is difficult. Risk assessment by qPCR only on samples without any background information regarding treatment, timing, etc is dubious. However, the rapid detection by qPCR of high concentrations of Legionella - especially Legionella pneumophila - is valuable as an indicator of risk, although it may be false positive compared to culture results. On the other hand, the detection of a low number of bacteria by qPCR is a strong indication for the absence of risk.

Occurrence of Selected Nutrients, Trace Elements, and Organic Compounds in Streambed Sediment in the Lower Chena River Watershed near Fairbanks, Alaska, 2002-03

USGS Publications Warehouse

Kennedy, Ben W.; Hall, Cassidee C.

2009-01-01

In 2002-03, the U.S. Geological Survey collected samples of streambed sediment at 18 sites in the lower Chena River watershed for analysis of selected nutrients, traces elements, and organic compounds. The purpose of the project was to provide Federal, State, and local agencies as well as neighborhood committees, with information for consideration in plans to improve environmental conditions in the watershed. The exploratory sampling program included analysis of streambed sediment from the Chena River and Chena Slough, a tributary to the Chena River. Results were compared to streambed-sediment guidelines for the protection of aquatic life and to 2001-02 sediment data from Noyes Slough, a side channel of the lower Chena River. The median total phosphorus concentration in Chena Slough sediment samples, 680 milligrams per kilogram (mg/kg), was two orders of magnitude greater than median total phosphorus concentration in Chena River sediment samples of 5.2 mg/kg. Median concentrations of chloride and sulfate also were greater in Chena Slough samples. Low concentrations of nitrate were detected in most of the Chena Slough samples; nitrate concentrations were below method reporting limits or not detected in Chena River sediment samples. Streambed-sediment samples were analyzed for 24 trace elements. Arsenic, nickel, and zinc were the only trace elements detected in concentrations that exceeded probable-effect levels for the protection of aquatic life. Concentrations of arsenic in Chena Slough samples ranged from 11 to 70 mg/kg and concentrations in most of the samples exceeded the probable-effect guideline for arsenic of 17 mg/kg. Arsenic concentrations in samples from the Chena River ranged from 9 to 12 mg/kg. The background level for arsenic in the lower Chena River watershed is naturally elevated because of significant concentrations of arsenic in local bedrock and ground water. Sources of elevated concentrations of zinc in one sample, and of nickel in two samples, are unknown. With the exception of elevated arsenic levels in samples from Chena Slough, the occurrence and concentration of trace elements in the streambed sediments of Chena Slough and Chena River were similar to those in Noyes Slough sediment. Sediment samples were analyzed for 78 semivolatile organic compounds and 32 organochlorine pesticides and polychlorinated biphenyls (PCBs). Low concentrations of dimethylnaphthalene and p-Cresol were detected in most Chena Slough and Chena River sediment samples. The number of semivolatile organic compounds detected ranged from 5 to 21 in most Chena Slough sediment samples. In contrast, three or fewer semivolatile organic compounds were detected in Chena River sediment samples, most likely because chemical-matrix interference resulted in elevated reporting limits for organochlorine compounds in the Chena River samples. Low concentrations of fluoranthene, pyrene, and phenanthrene were detected in Chena Slough sediment. Relatively low concentrations of DDT or its degradation products, DDD and DDE, were detected in all Chena Slough samples. Concentrations of total DDT (DDT+DDD+DDE) in two Chena Slough sediment samples exceeded the effectsrange median aquatic-life criteria of 46.1 micrograms per kilogram (ug/kg). DDT concentrations in Chena River streambed-sediment samples were less than 20 ug/kg. Low concentrations of PCB were detected in two Chena Slough streambed-sediment samples. None of the concentrations of the polychlorinated biphenyls or semivolatile organic compounds for which the samples were analyzed exceeded available guidelines for the protection of aquatic life. With the exception of elevated total DDT in two Chena Slough samples, the occurrence and concentration of organochlorine compounds in Chena Slough and Chena River sediment were similar to those in samples collected from Noyes Slough in 2001-02.

Quality of volatile organic compound data from groundwater and surface water for the National Water-Quality Assessment Program, October 1996–December 2008

USGS Publications Warehouse

Bender, David A.; Zogorski, John S.; Mueller, David K.; Rose, Donna L.; Martin, Jeffrey D.; Brenner, Cassandra K.

2011-01-01

This report describes the quality of volatile organic compound (VOC) data collected from October 1996 to December 2008 from groundwater and surface-water sites for the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program. The VOC data described were collected for three NAWQA site types: (1) domestic and public-supply wells, (2) monitoring wells, and (3) surface-water sites. Contamination bias, based on the 90-percent upper confidence limit (UCL) for the 90th percentile of concentrations in field blanks, was determined for VOC samples from the three site types. A way to express this bias is that there is 90-percent confidence that this amount of contamination would be exceeded in no more than 10 percent of all samples (including environmental samples) that were collected, processed, shipped, and analyzed in the same manner as the blank samples. This report also describes how important native water rinsing may be in decreasing carryover contamination, which could be affecting field blanks. The VOCs can be classified into four contamination categories on the basis of the 90-percent upper confidence limit (90-percent UCL) concentration distribution in field blanks. Contamination category 1 includes compounds that were not detected in any field blanks. Contamination category 2 includes VOCs that have a 90-percent UCL concentration distribution in field blanks that is about an order of magnitude lower than the concentration distribution of the environmental samples. Contamination category 3 includes VOCs that have a 90-percent UCL concentration distribution in field blanks that is within an order of magnitude of the distribution in environmental samples. Contamination category 4 includes VOCs that have a 90-percent UCL concentration distribution in field blanks that is at least an order of magnitude larger than the concentration distribution of the environmental samples. Fifty-four of the 87 VOCs analyzed in samples from domestic and public-supply wells were not detected in field blanks (contamination category 1), and 33 VOC were detected in field blanks. Ten of the 33 VOCs had a 90-percent UCL concentration distribution in field blanks that was at least an order of magnitude lower than the concentration distribution in environmental samples (contamination category 2). These 10 VOCs may have had some contamination bias associated with the environmental samples, but the potential contamination bias was negligible in comparison to the environmental data; therefore, the field blanks were assumed to be representative of the sources of contamination bias affecting the environmental samples for these 10 VOCs. Seven VOCs had a 90-percent UCL concentration distribution of the field blanks that was within an order of magnitude of the concentration distribution of the environmental samples (contamination category 3). Sixteen VOCs had a 90-percent UCL concentration distribution in the field blanks that was at least an order of magnitude greater than the concentration distribution of the environmental samples (contamination category 4). Field blanks for these 16 VOCs appear to be nonrepresentative of the sources of contamination bias affecting the environmental samples because of the larger concentration distributions (and sometimes higher frequency of detection) in field blanks than in environmental samples. Forty-three of the 87 VOCs analyzed in samples from monitoring wells were not detected in field blanks (contamination category 1), and 44 VOCs were detected in field blanks. Eight of the 44 VOCs had a 90-percent UCL concentration distribution in field blanks that was at least an order of magnitude lower than concentrations in environmental samples (contamination category 2). These eight VOCs may have had some contamination bias associated with the environmental samples, but the potential contamination bias was negligible in comparison to the environmental data; therefore, the field blanks were assumed to be representative. Seven VOCs had a 90-percent UCL concentration distribution in field blanks that was of the same order of magnitude as the concentration distribution of the environmental samples (contamination category 3). Twenty-nine VOCs had a 90-percent UCL concentration distribution in the field blanks that was an order of magnitude greater than the distribution of the environmental samples (contamination category 4). Field blanks for these 29 VOCs appear to be nonrepresentative of the sources of contamination bias to the environmental samples. Fifty-four of the 87 VOCs analyzed in surface-water samples were not detected in field blanks (category 1), and 33 VOC were detected in field blanks. Sixteen of the 33 VOCs had a 90-percent UCL concentration distribution in field blanks that was at least an order of magnitude lower than the concentration distribution in environmental samples (contamination category 2). These 16 VOCs may have had some contamination bias associated with the environmental samples, but the potential contamination bias was negligible in comparison to the environmental data; therefore, the field blanks were assumed to be representative. Ten VOCs had a 90-percent UCL concentration distribution in field blanks that was similar to the concentration distribution of environmental samples (contamination category 3). Seven VOCs had a 90-percent UCL concentration distribution in the field blanks that was greater than the concentration distribution in environmental samples (contamination category 4). Field-blank samples for these seven VOCs appear to be nonrepresentative of the sources of contamination bias to the environmental samples. The relation between the detection of a compound in field blanks and the detection in subsequent environmental samples appears to be minimal. The median minimum percent effectiveness of native water rinsing is about 79 percent for the 19 VOCs detected in more than 5 percent of field blanks from all three site types. The minimum percent effectiveness of native water rinsing (10 percent) was for toluene in surface-water samples, likely because of the large detection frequency of toluene in surface-water samples (about 79 percent) and in the associated field-blank samples (46.5 percent). The VOCs that were not detected in field blanks (contamination category 1) from the three site types can be considered free of contamination bias, and various interpretations for environmental samples, such as VOC detection frequency at multiple assessment levels and comparisons of concentrations to benchmarks, are not limited for these VOCs. A censoring level for making comparisons at different assessment levels among environmental samples could be applied to concentrations of 9 VOCs in samples from domestic and public-supply wells, 16 VOCs in samples from monitoring wells, and 9 VOCs in surface-water samples to account for potential low-level contamination bias associated with these selected VOCs. Bracketing the potential contamination by comparing the detection and concentration statistics with no censoring applied to the potential for contamination bias on the basis of the 90-percent UCL for the 90th-percentile concentrations in field blanks may be useful when comparisons to benchmarks are done in a study. The VOCs that were not detected in field blanks (contamination category 1) from the three site types can be considered free of contamination bias, and various interpretations for environmental samples, such as VOC detection frequency at multiple assessment levels and comparisons of concentrations to benchmarks, are not limited for these VOCs. A censoring level for making comparisons at different assessment levels among environmental samples could be applied to concentrations of 9 VOCs in samples from domestic and public-supply wells, 16 VOCs in samples from monitoring wells, and 9 VOCs in surface-water samples to account for potential low-level contamination bias associated with these selected VOCs. Bracketing the potential contamination by comparing the detection and concentration statistics with no censoring applied to the potential for contamination bias on the basis of the 90-percent UCL for the 90th-percentile concentrations in field blanks may be useful when comparisons to benchmarks are done in a study.

Methods for the selective detection of alkyne-presenting molecules and related compositions and systems

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

Valdez, Carlos A.; Vu, Alexander K.

Provided herein are methods for selectively detecting an alkyne-presenting molecule in a sample and related detection reagents, compositions, methods and systems. The methods include contacting a detection reagent with the sample for a time and under a condition to allow binding of the detection reagent to the one or more alkyne-presenting molecules possibly present in the matrix to the detection reagent. The detection reagent includes an organic label moiety presenting an azide group. The binding of the azide group to the alkyne-presenting molecules results in emission of a signal from the organic label moiety.

Evaluation of genotype MTBDRplus VER 2.0 line probe assay for the detection of MDR-TB in smear positive and negative sputum samples.

PubMed

Meaza, Abyot; Kebede, Abebaw; Yaregal, Zelalem; Dagne, Zekarias; Moga, Shewki; Yenew, Bazezew; Diriba, Getu; Molalign, Helina; Tadesse, Mengistu; Adisse, Desalegn; Getahun, Muluwork; Desta, Kassu

2017-04-17

Multi drug resistant tuberculosis (MDR-TB) poses formidable challenges to TB control due to its complex diagnostic and treatment challenges and often associated with a high rate of mortality. Accurate and rapid detection of MDR-TB is critical for timely initiation of treatment. Line Probe Assay (LPA) is a qualitative in vitro diagnostic test based on DNA-STRIP technology for the identification of the M. tuberculosis complex and its resistance to rifampicin (RMP) and/or isoniazid (INH). Hain Lifescience, GmbH, Germany has improved the sensitivity of Genotype MTBDRplus VER 2.0 LPA for the detection of MDR-TB; with the possibility of applying the tool in smear negative sputum samples. A cross sectional study was conducted on 274 presumptive MDR-TB patients referred to the National TB Reference Laboratory (NTRL), Ethiopian Public Health Institute (EPHI) who submitted sputum samples for laboratory diagnosis of drug resistant-TB testing. Seventy-two smear and culture positive samples processed in smear positive direct LPA category and 197 smear negative sputum samples were processed for direct LPA. Among the smear negative samples 145 (73.6%) were culture negative and 26 (13.2%) were culture positive. All specimens were processed using NALC-NaOH method and ZN smear microscopy done from sediments. Genotype MTBDRplus VER 2.0 done from processed sputum sediments and the result was compared against the reference, BACTEC MGIT 960 culture and DST. Sensitivity, specificity, PPV and NPV of Genotype MTBDRplus VER 2.0 assay was determined and P-value <0.05 was considered as statistically significant. The sensitivity, specificity, PPV and NPV of Genotype MTBDRplus VER 2.0 LPA were 96.4, 100, 100 and 96.9%, respectively for the detection of MDR-TB from direct smear positive sputum samples. The sensitivity, specificity, PPV and NPV of Genotype MTBDR plus VER 2.0 LPA were 77.8, 97.2, 82.4 and 97.2%, respectively, for the detection of M. tuberculosis from direct smear negative sputum samples. Fourteen (53.8%) samples had valid results with LPA among the 26 smear negative culture positive samples. The remaining 8 (30.8%) and 4 (15.4%) were invalid and negative with LPA, respectively. The sensitivity and specificity of Genotype MTBDRplus VER 2.0 LPA were 100% for the detection of MDR-TB among 14 direct smear negative and culture positive sputum samples. The most common mutations associated with RMP and INH resistance were S531L and S315TL, respectively. A single rare mutation (C15T/A16G) was detected for INH resistance. The diagnostic performance of Genotype MTBDRplus VER 2.0 LPA in direct smear positive sputum sample was highly sensitive and specific for early detection of MDR-TB. However, the diagnostic performance of this molecular assay in direct smear negative sputum sample was low and showed a high level of invalid results for detection of M. tuberculosis and its resistance to RMP and/or INH so it is unlikely to implement Genotype MTBDRplus VER 2.0 for the detection of MDR-TB in direct smear negative sample in our routine settings. The sensitivity of the assay should be improved for detection of MDR-TB in direct smear negative sputum specimens.

Detection system of capillary array electrophoresis microchip based on optical fiber

NASA Astrophysics Data System (ADS)

Yang, Xiaobo; Bai, Haiming; Yan, Weiping

2009-11-01

To meet the demands of the post-genomic era study and the large parallel detections of epidemic diseases and drug screening, the high throughput micro-fluidic detection system is needed urgently. A scanning laser induced fluorescence detection system based on optical fiber has been established by using a green laser diode double-pumped solid-state laser as excitation source. It includes laser induced fluorescence detection subsystem, capillary array electrophoresis micro-chip, channel identification unit and fluorescent signal processing subsystem. V-shaped detecting probe composed with two optical fibers for transmitting the excitation light and detecting induced fluorescence were constructed. Parallel four-channel signal analysis of capillary electrophoresis was performed on this system by using Rhodamine B as the sample. The distinction of different samples and separation of samples were achieved with the constructed detection system. The lowest detected concentration is 1×10-5 mol/L for Rhodamine B. The results show that the detection system possesses some advantages, such as compact structure, better stability and higher sensitivity, which are beneficial to the development of microminiaturization and integration of capillary array electrophoresis chip.

How do we know if plants in our nursery have Phytophthora? Detection methods and an integrated approach to monitoring

Treesearch

Christa Conforti

2017-01-01

A Phytophthora cactorum-infected nursery crop of Ceanothus thyrsiflorus was used to evaluate three Phytophthora monitoring methods. The Phytophthora detection level of three non-destructive sampling methods was quantified and compared to the detection level of destructive sampling. Non-...

Occurrence of Endocrine Active Compounds and Biological Responses in the Mississippi River - Study Design and Data, June through August 2006

USGS Publications Warehouse

Lee, Kathy E.; Yaeger, Christine S.; Jahns, Nathan D.; Schoenfuss, Heiko L.

2008-01-01

Concern that selected chemicals in the environment may act as endocrine active compounds in aquatic ecosystems is widespread; however, few studies have examined the occurrence of endocrine active compounds and identified biological markers of endocrine disruption such as intersex occurrence in fish longitudinally in a river system. This report presents environmental data collected and analyzed by the U.S. Geological Survey, Minnesota Pollution Control Agency and St. Cloud State University as part of an integrated biological and chemical study of endocrine disruption in fish in the Mississippi River. Data were collected from water, bed sediment, and fish at 43 sites along the river from the headwaters at Lake Itasca to 14 miles downstream from Brownsville, Minnesota during June through August 2006. Twenty-four individual compounds were detected in water samples, with cholesterol, atrazine, N,N-diethyl-meta-toluamide, metolachlor, and hexahydrohexamethylcyclopentabenzopyran detected most frequently (in at least 10 percent of the samples). The number of compounds detected in water per site ranged from 0 to 8. Forty individual compounds were detected in bed-sediment samples. The most commonly detected compounds (in at least 50 percent of the samples) were indole, beta-sitosterol, cholesterol, beta-stigmastanol, 3-methyl-1H-indole, p-cresol, pyrene, phenol, fluoranthene, 3-beta coprostanol, benzo[a]pyrene, acetophenone, and 2,6-dimethylnaphthalene. The total number of detections in bed sediment (at a site) ranged from 3 to 31. The compounds NP1EO, NP2EO, and 4-nonylphenol were detected in greater than 10 percent of the samples. Most (80 percent) female fish collected had measurable concentrations of vitellogenin. Vitellogenin also was detected in 62, 63, and 33 percent of male carp, smallmouth bass, and redhorse, respectively. The one male walleye sample plasma sample analyzed had a vitellogenin detection. Vitellogenin concentrations were lower in male fish (not detected to 10.80 micrograms per milliliter) than female fish (0.04 to 248,079 micrograms per milliliter). Gonadosomatic Index values ranged from 0.02 to 7.49 percent among all male fish and were greater for male carp than for the other three species. No intersex (oocytes present in testes tissue) was found in any male fish sampled.

Sample size and power calculations for detecting changes in malaria transmission using antibody seroconversion rate.

PubMed

Sepúlveda, Nuno; Paulino, Carlos Daniel; Drakeley, Chris

2015-12-30

Several studies have highlighted the use of serological data in detecting a reduction in malaria transmission intensity. These studies have typically used serology as an adjunct measure and no formal examination of sample size calculations for this approach has been conducted. A sample size calculator is proposed for cross-sectional surveys using data simulation from a reverse catalytic model assuming a reduction in seroconversion rate (SCR) at a given change point before sampling. This calculator is based on logistic approximations for the underlying power curves to detect a reduction in SCR in relation to the hypothesis of a stable SCR for the same data. Sample sizes are illustrated for a hypothetical cross-sectional survey from an African population assuming a known or unknown change point. Overall, data simulation demonstrates that power is strongly affected by assuming a known or unknown change point. Small sample sizes are sufficient to detect strong reductions in SCR, but invariantly lead to poor precision of estimates for current SCR. In this situation, sample size is better determined by controlling the precision of SCR estimates. Conversely larger sample sizes are required for detecting more subtle reductions in malaria transmission but those invariantly increase precision whilst reducing putative estimation bias. The proposed sample size calculator, although based on data simulation, shows promise of being easily applicable to a range of populations and survey types. Since the change point is a major source of uncertainty, obtaining or assuming prior information about this parameter might reduce both the sample size and the chance of generating biased SCR estimates.

Ultratrace level determination and quantitative analysis of kidney injury biomarkers in patient samples attained by zinc oxide nanorods

NASA Astrophysics Data System (ADS)

Singh, Manpreet; Alabanza, Anginelle; Gonzalez, Lorelis E.; Wang, Weiwei; Reeves, W. Brian; Hahm, Jong-In

2016-02-01

Determining ultratrace amounts of protein biomarkers in patient samples in a straightforward and quantitative manner is extremely important for early disease diagnosis and treatment. Here, we successfully demonstrate the novel use of zinc oxide nanorods (ZnO NRs) in the ultrasensitive and quantitative detection of two acute kidney injury (AKI)-related protein biomarkers, tumor necrosis factor (TNF)-α and interleukin (IL)-8, directly from patient samples. We first validate the ZnO NRs-based IL-8 results via comparison with those obtained from using a conventional enzyme-linked immunosorbent method in samples from 38 individuals. We further assess the full detection capability of the ZnO NRs-based technique by quantifying TNF-α, whose levels in human urine are often below the detection limits of conventional methods. Using the ZnO NR platforms, we determine the TNF-α concentrations of all 46 patient samples tested, down to the fg per mL level. Subsequently, we screen for TNF-α levels in approximately 50 additional samples collected from different patient groups in order to demonstrate a potential use of the ZnO NRs-based assay in assessing cytokine levels useful for further clinical monitoring. Our research efforts demonstrate that ZnO NRs can be straightforwardly employed in the rapid, ultrasensitive, quantitative, and simultaneous detection of multiple AKI-related biomarkers directly in patient urine samples, providing an unparalleled detection capability beyond those of conventional analysis methods. Additional key advantages of the ZnO NRs-based approach include a fast detection speed, low-volume assay condition, multiplexing ability, and easy automation/integration capability to existing fluorescence instrumentation. Therefore, we anticipate that our ZnO NRs-based detection method will be highly beneficial for overcoming the frequent challenges in early biomarker development and treatment assessment, pertaining to the facile and ultrasensitive quantification of hard-to-trace biomolecules.Determining ultratrace amounts of protein biomarkers in patient samples in a straightforward and quantitative manner is extremely important for early disease diagnosis and treatment. Here, we successfully demonstrate the novel use of zinc oxide nanorods (ZnO NRs) in the ultrasensitive and quantitative detection of two acute kidney injury (AKI)-related protein biomarkers, tumor necrosis factor (TNF)-α and interleukin (IL)-8, directly from patient samples. We first validate the ZnO NRs-based IL-8 results via comparison with those obtained from using a conventional enzyme-linked immunosorbent method in samples from 38 individuals. We further assess the full detection capability of the ZnO NRs-based technique by quantifying TNF-α, whose levels in human urine are often below the detection limits of conventional methods. Using the ZnO NR platforms, we determine the TNF-α concentrations of all 46 patient samples tested, down to the fg per mL level. Subsequently, we screen for TNF-α levels in approximately 50 additional samples collected from different patient groups in order to demonstrate a potential use of the ZnO NRs-based assay in assessing cytokine levels useful for further clinical monitoring. Our research efforts demonstrate that ZnO NRs can be straightforwardly employed in the rapid, ultrasensitive, quantitative, and simultaneous detection of multiple AKI-related biomarkers directly in patient urine samples, providing an unparalleled detection capability beyond those of conventional analysis methods. Additional key advantages of the ZnO NRs-based approach include a fast detection speed, low-volume assay condition, multiplexing ability, and easy automation/integration capability to existing fluorescence instrumentation. Therefore, we anticipate that our ZnO NRs-based detection method will be highly beneficial for overcoming the frequent challenges in early biomarker development and treatment assessment, pertaining to the facile and ultrasensitive quantification of hard-to-trace biomolecules. Electronic supplementary information (ESI) available: Typical SEM images of the ZnO NRs used in the biomarker assays are provided in Fig. S1. See DOI: 10.1039/c5nr08706f

Seasonal distribution of Legionella spp. and L. pneumophila in a river in Taiwan evaluated with culture-confirmed and direct DNA extraction methods

NASA Astrophysics Data System (ADS)

Tung, Min-Che; Chang, Tien-Yu; Hsu, Bing-Mu; Shen, Shu-Min; Huang, Jen-Te; Kao, Po-Min; Chiu, Yi-Chou; Fan, Cheng-Wei; Huang, Yu-Li

2013-07-01

In this study, we evaluated the presence and amount of Legionella in along a river in Taiwan, and the relations between seasonal distribution of Legionella spp. and geographic characteristics in the watershed were also evaluated. Water samples were pre-treated and analyzed with culture-confirmed and direct DNA extraction methods. For culture-confirmed method, water samples were cultivated through a series of selective media, and candidate colonies were confirmed by PCR. For direct DNA extraction method, direct DNA extraction was performed from pre-treated water samples. The DNA extracts were analyzed with PCR and DNA sequence analysis for species determination, quantitative PCR (qPCR) was performed to quantify Legionella concentration in the water sample. In all, 150 water samples were included in this study, with 73 (48.6%) water samples detected with Legionella spp., and 17 with L. pneumophila. Over 80% Legionella spp. detections were through direct DNA extraction method, but more than 80% L. pneumophila detections were through culture-confirmed method. While detection of Legionella spp. was done with two methods, positive results were found through only one method. Legionella spp. was detected in all seasons with detection rate ranging between 34.3-58.8% and seasonal average concentration from 1.9 × 102 to 7.1 × 103 CFU/L. Most of the L. pneumophila detections were from samples collected in fall (38.2%) and summer (6.0%), which also coincided with increased cases of Legionellosis reported through Center of Disease Control in Taiwan. The high prevalence and concentration of Legionella spp. and L. pneumophila in the surface waters should be further evaluated for potential health risks.

Influence of enrichment and isolation media on the detection of Campylobacter spp. in naturally contaminated chicken samples.

PubMed

Repérant, E; Laisney, M J; Nagard, B; Quesne, S; Rouxel, S; Le Gall, F; Chemaly, M; Denis, M

2016-09-01

Investigating Campylobacter epidemiology requires adequate technique and media to ensure optimal culturing and accurate detection and isolation of Campylobacter strains. In the present study, we investigated the performances of three enrichment durations in Bolton broth (0, 24 and 48h) and compared four isolation media (mCCDA, Karmali, Butzler no. 2 and CampyFood agar (CFA)) for the detection of Campylobacter positive samples and the identification of Campylobacter species, from naturally contaminated broiler chicken samples (caeca, neck skin from carcasses, and skin from thighs). We compared our local results to those we obtained with samples from a European survey (caeca and neck skin) and a national survey (neck skin, thigh skin, and breast). Direct plating favored the detection of positive samples highly contaminated by Campylobacter (caeca and neck skin from carcasses) whatever the media. A longer enrichment reduced the rates of Campylobacter recovery except when using Butzler no. 2, more particularly for neck skin which background microflora was less important than in caeca. As a matter of fact, enrichment allowed a higher detection rate of positive samples with low Campylobacter contamination levels (breast, thigh skin), this detection being enhanced when using Butzler no. 2. When comparing the 3 other selective media, CFA was the 2nd most efficient media prior to mCCDA and Karmali. Interestingly, enrichment promoted the growth of Campylobacter coli but this promotion was least with Butzler no. 2 agar. Our study has confirmed the need to adapt the method to the types of samples for improving the detection of Campylobacter and that the method may affect the prevalence of the species. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection limit of Mycobacterium chimaera in water samples for monitoring medical device safety: insights from a pilot experimental series.

PubMed

Schreiber, P W; Köhler, N; Cervera, R; Hasse, B; Sax, H; Keller, P M

2018-07-01

A growing number of Mycobacterium chimaera infections after cardiosurgery have been reported by several countries. These potentially fatal infections were traced back to contaminated heater-cooler devices (HCDs), which use water as a heat transfer medium. Aerosolization of water contaminated with M. chimaera from HCDs enables airborne transmission to patients undergoing open chest surgery. Infection control teams test HCD water samples for mycobacterial growth to guide preventive measures. The detection limit of M. chimaera in water samples, however, has not previously been investigated. To determine the detection limit of M. chimaera in water samples using laboratory-based serial dilution tests. An M. chimaera strain representative of the international cardiosurgery-associated M. chimaera outbreak was used to generate a logarithmic dilution series. Two different water volumes, 50 and 1000mL, were inoculated, and, after identical processing (centrifugation, decantation, and decontamination), seeded on mycobacteria growth indicator tube (MGIT) and Middlebrook 7H11 solid media. MGIT consistently showed a lower detection limit than 7H11 solid media, corresponding to a detection limit of ≥1.44 × 10 4 cfu/mL for 50mL and ≥2.4cfu/mL for 1000mL water samples. Solid media failed to detect M. chimaera in 50mL water samples. Depending on water volume and culture method, major differences exist in the detection limit of M. chimaera. In terms of sensitivity, 1000mL water samples in MGIT media performed best. Our results have important implications for infection prevention and control strategies in mitigation of the M. chimaera outbreak and healthcare water safety in general. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Serum biochemical profile and molecular detection of pathogens in semen of infertile male dromedary camels (Camelus dromedarius).

PubMed

Al-Busadah, Khaled A; El-Bahr, Sabry M; Khalafalla, Abdelmalik I

2017-05-01

Detection of pathogens in the semen of camels has not been completely elucidated. Therefore, the current study aimed to determine the association of some economically important pathogens with infertility in 94 male infertile camels through molecular detection and estimation of selected biochemical parameters in serum of these animals compared with a control non infected fertile animals (n=40). PCR analysis of semen samples of infertile camels indicated that, four potential pathogens namely Mycoplasma spp., Leptospira spp., Brucella melitensis, and Bovine viral diarrhea virus (BVDV) were detected in 50 semen samples of infertile camels whereas, 44 semen samples of infertile camels were free of pathogens and all tested semen samples were negative for bovine herpes virus 1, Salmonella spp. and Trypanosoma evansi. Single and mixed infection was detected in 88% and 12% of the infected semen samples, respectively. Mycoplasma spp., Leptospira spp., Brucella and Bovine viral diarrhea virus infection represented 66%, 27.2%, 4.5% and 2.3% of the single infected semen samples. Mycoplasma spp.+Leptospira spp. and Mycoplasma spp.+Brucella spp. were detected in 83.3% and 16.7% of mixed infected semen samples, respectively. Testosterone concentration decreased significantly in infertile infected camels compare to both control and infertile non infected animals that remained comparable. The current findings reported the molecular detection of mixed infection in camel semen for the first time. Mycoplasma spp. is the most widely recognized microorganism in the present study and together with Leptospira spp., Brucella spp. and Bovine viral diarrhea virus, might be associated with infertility in dromedary camels. Copyright © 2017 Elsevier B.V. All rights reserved.

Occupancy models for monitoring marine fish: a bayesian hierarchical approach to model imperfect detection with a novel gear combination.

PubMed

Coggins, Lewis G; Bacheler, Nathan M; Gwinn, Daniel C

2014-01-01

Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors influencing fish population distribution and dynamics.

Occupancy Models for Monitoring Marine Fish: A Bayesian Hierarchical Approach to Model Imperfect Detection with a Novel Gear Combination

PubMed Central

Coggins, Lewis G.; Bacheler, Nathan M.; Gwinn, Daniel C.

2014-01-01

Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors influencing fish population distribution and dynamics. PMID:25255325

Monitoring for contaminants of emerging concern in drinking water using POCIS passive samplers.

PubMed

Metcalfe, Chris; Hoque, M Ehsanul; Sultana, Tamanna; Murray, Craig; Helm, Paul; Kleywegt, Sonya

2014-03-01

Contaminants of emerging concern (CEC) have been detected in drinking water world-wide. The source of most of these compounds is generally attributed to contamination from municipal wastewater. Traditional water sampling methods (grab or composite) often require the concentration of large amounts of water in order to detect trace levels of these contaminants. The Polar Organic Compounds Integrative Sampler (POCIS) is a passive sampling technology that has been developed to concentrate trace levels of CEC to provide time-weighted average concentrations for individual compounds in water. However, few studies to date have evaluated whether POCIS is suitable for monitoring contaminants in drinking water. In this study, the POCIS was evaluated as a monitoring tool for CEC in drinking water over a period of 2 and 4 weeks with comparisons to typical grab samples. Seven "indicator compounds" which included carbamazepine, trimethoprim, sulfamethoxazole, ibuprofen, gemfibrozil, estrone and sucralose, were monitored in five drinking water treatment plants (DWTPs) in Ontario. All indicator compounds were detected in raw water samples from the POCIS in comparison to six from grab samples. Similarly, four compounds were detected in grab samples of treated drinking water, whereas six were detected in the POCIS. Sucralose was the only compound that was detected consistently at all five plants. The POCIS technique provided integrative exposures of CECs in drinking water at lower detection limits, while episodic events were captured via traditional sampling methods. There was evidence that the accumulation of target compounds by POCIS is a dynamic process, with adsorption and desorption on the sorbent occurring in response to ambient levels of the target compounds in water. CECs in treated drinking water were present at low ng L(-1) concentrations, which are not considered to be a threat to human health.

Development of a Highly Sensitive Nested-PCR Procedure Using a Single Closed Tube for Detection of Erwinia amylovora in Asymptomatic Plant Material

PubMed Central

Llop, Pablo; Bonaterra, Anna; Peñalver, Javier; López, María M.

2000-01-01

A novel method, which involves a nested PCR in a single closed tube, was developed for the sensitive detection of Erwinia amylovora in plant material. The external and internal primer pairs used had different annealing temperatures and directed the amplification of a specific DNA fragment from plasmid pEA29. The procedure involved two consecutive PCRs, the first of which was performed at a higher annealing temperature that allowed amplification only by the external primer pair. Using pure cultures of E. amylovora, the sensitivity of the nested PCR in one tube was similar to that of a standard nested PCR in two tubes. The specificity and sensitivity were greater than those of standard PCR procedures that used a single primer pair. The presence of inhibitors in plant material, very common in E. amylovora hosts, is overcome with this system in combination with a simple DNA extraction protocol because it eliminates many of the inhibitory compounds. In addition, it needs a very small sample volume (1 μl of DNA extracted). With 83 samples of naturally infected material, this method achieved better results than any other PCR technique: standard PCR detected 55% of positive samples, two-tube nested PCR detected 71% of positive samples, and nested PCR in a single closed tube detected 78% of positive samples. When analyzing asymptomatic plant material, the number of positive samples detected by the developed nested PCR was also the highest, compared with the PCR protocols indicated previously (17, 20, and 25% of 251 samples analyzed, respectively). This method is proposed for the detection of endophytic and epiphytic populations of E. amylovora in epidemiological studies and for routine use in quarantine surveys, due to its high sensitivity, specificity, speed, and simplicity. PMID:10788384

Simple and Sensitive Paper-Based Device Coupling Electrochemical Sample Pretreatment and Colorimetric Detection.

PubMed

Silva, Thalita G; de Araujo, William R; Muñoz, Rodrigo A A; Richter, Eduardo M; Santana, Mário H P; Coltro, Wendell K T; Paixão, Thiago R L C

2016-05-17

We report the development of a simple, portable, low-cost, high-throughput visual colorimetric paper-based analytical device for the detection of procaine in seized cocaine samples. The interference of most common cutting agents found in cocaine samples was verified, and a novel electrochemical approach was used for sample pretreatment in order to increase the selectivity. Under the optimized experimental conditions, a linear analytical curve was obtained for procaine concentrations ranging from 5 to 60 μmol L(-1), with a detection limit of 0.9 μmol L(-1). The accuracy of the proposed method was evaluated using seized cocaine samples and an addition and recovery protocol.

Gas-phase detection of solid-state fission product complexes for post-detonation nuclear forensic analysis

DOE PAGES

Stratz, S. Adam; Jones, Steven A.; Oldham, Colton J.; ...

2016-06-27

This study presents the first known detection of fission products commonly found in post-detonation nuclear debris samples using solid sample introduction and a uniquely coupled gas chromatography inductively-coupled plasma time-of-flight mass spectrometer. Rare earth oxides were chemically altered to incorporate a ligand that enhances the volatility of the samples. These samples were injected (as solids) into the aforementioned instrument and detected for the first time. Repeatable results indicate the validity of the methodology, and this capability, when refined, will prove to be a valuable asset for rapid post-detonation nuclear forensic analysis.

Power of tests of normality for detecting contaminated normal samples

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

Thode, H.C. Jr.; Smith, L.A.; Finch, S.J.

1981-01-01

Seventeen tests of normality or goodness of fit were evaluated for power at detecting a contaminated normal sample. This study used 1000 replications each of samples of size 12, 17, 25, 33, 50, and 100 from six different contaminated normal distributions. The kurtosis test was the most powerful over all sample sizes and contaminations. The Hogg and weighted Kolmogorov-Smirnov tests were second. The Kolmogorov-Smirnov, chi-squared, Anderson-Darling, and Cramer-von-Mises tests had very low power at detecting contaminated normal random variables. Tables of the power of the tests and the power curves of certain tests are given.

Gas-phase detection of solid-state fission product complexes for post-detonation nuclear forensic analysis

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

Stratz, S. Adam; Jones, Steven A.; Oldham, Colton J.

This study presents the first known detection of fission products commonly found in post-detonation nuclear debris samples using solid sample introduction and a uniquely coupled gas chromatography inductively-coupled plasma time-of-flight mass spectrometer. Rare earth oxides were chemically altered to incorporate a ligand that enhances the volatility of the samples. These samples were injected (as solids) into the aforementioned instrument and detected for the first time. Repeatable results indicate the validity of the methodology, and this capability, when refined, will prove to be a valuable asset for rapid post-detonation nuclear forensic analysis.

Concentrations of nutrients, pesticides, and suspended sediment in the karst terrane of the Sinking Creek basin, Kentucky, 2004

USGS Publications Warehouse

Crain, Angela S.

2006-01-01

Water samples were collected in streams and springs in the karst terrane of the Sinking Creek Basin in 2004 as part of study in cooperation with the Kentucky Department of Agriculture. A total of 48 water samples were collected at 7 sites (4 springs, 2 streams, and 1 karst window) from April through November 2004. The karst terrane of the Sinking Creek Basin (also known as Boiling Spring Basin) encompasses about 125 square miles in Breckinridge County and portions of Meade and Hardin Counties in Kentucky. Fourteen pesticides were detected of the 52 pesticides analyzed in the stream and spring samples. Of the 14 detected pesticides, 12 were herbicides and 2 were insecticides. The most commonly detected pesticides?atrazine, simazine, metolachlor, and acetochlor?were those most heavily used on crops during the study. Atrazine was detected in 100 percent of all samples; simazine, metolachlor, and acetochlor were detected in more than 35 percent of all samples. The pesticide-transformation compound, deethylatrazine, was detected in 98 percent of the samples. Only one nonagricultural herbicide, prometon, was detected in more than 30 percent of the samples. Malathion, the most commonly detected insecticide, was found in 4 percent of the samples, which was followed by carbofuran (2 percent). Most of the pesticides were present in low concentrations; however, atrazine was found in springs exceeding the U.S. Environmental Protection Agency?s (USEPA) standards for drinking water. Atrazine exceeded the USEPA?s maximum contaminant level 2 times in 48 detections. Concentrations of nitrate greater than 10 milligrams per liter (mg/L) were not found in water samples from any of the sites. Concentrations of nitrite plus nitrate ranged from 0.21 to 3.9 mg/L at the seven sites. The median concentration of nitrite plus nitrate for all sites sampled was 1.5 mg/L. Concentrations of nitrite plus nitrate generally were higher in the springs than in the main stem of Sinking Creek. Forty-two percent of the concentrations of total phosphorus at all seven sites exceeded the USEPA?s recommended maximum concentration of 0.1 mg/L. The median concentration of total phosphorus for all sites sampled was 0.09 mg/L. The highest median concentrations of total phosphorus were found in the springs. Median concentrations of orthophosphate followed the same pattern as concentrations of total phosphorus in the springs. Concentrations of orthophosphate ranged from <0.006 to 0.192 mg/L. Concentrations of suspended sediment generally were low throughout the basin; the median concentration of suspended sediment for all sites sampled was 23 mg/L. The highest concentration of suspended sediment (1,486 mg/L) was measured following a storm event at Sinking Creek near Lodiburg, Ky.

Development of a Rapid, Simple Method for Detecting Naegleria fowleri Visually in Water Samples by Loop-Mediated Isothermal Amplification (LAMP)

PubMed Central

Mahittikorn, Aongart; Mori, Hirotake; Popruk, Supaluk; Roobthaisong, Amonrattana; Sutthikornchai, Chantira; Koompapong, Khuanchai; Siri, Sukhontha; Sukthana, Yaowalark; Nacapunchai, Duangporn

2015-01-01

Naegleria fowleri is the causative agent of the fatal disease primary amebic meningoencephalitis. Detection of N. fowleri using conventional culture and biochemical-based assays is time-consuming and laborious, while molecular techniques, such as PCR, require laboratory skills and expensive equipment. We developed and evaluated a novel loop-mediated isothermal amplification (LAMP) assay targeting the virulence-related gene for N. fowleri. Time to results is about 90 min and amplification products were easily detected visually using hydroxy naphthol blue. The LAMP was highly specific after testing against related microorganisms and able to detect one trophozoite, as determined with spiked water and cerebrospinal fluid samples. The assay was then evaluated with a set of 80 water samples collected during the flooding crisis in Thailand in 2011, and 30 natural water samples from border areas of northern, eastern, western, and southern Thailand. N. fowleri was detected in 13 and 10 samples using LAMP and PCR, respectively, with a Kappa coefficient of 0.855. To the best of our knowledge, this is the first report of a LAMP assay for N. fowleri. Due to its simplicity, speed, and high sensitivity, the LAMP method described here might be useful for quickly detecting and diagnosing N. fowleri in water and clinical samples, particularly in resource-poor settings. PMID:25822175

Development of a rapid, simple method for detecting Naegleria fowleri visually in water samples by loop-mediated isothermal amplification (LAMP).

PubMed

Mahittikorn, Aongart; Mori, Hirotake; Popruk, Supaluk; Roobthaisong, Amonrattana; Sutthikornchai, Chantira; Koompapong, Khuanchai; Siri, Sukhontha; Sukthana, Yaowalark; Nacapunchai, Duangporn

2015-01-01

Naegleria fowleri is the causative agent of the fatal disease primary amebic meningoencephalitis. Detection of N. fowleri using conventional culture and biochemical-based assays is time-consuming and laborious, while molecular techniques, such as PCR, require laboratory skills and expensive equipment. We developed and evaluated a novel loop-mediated isothermal amplification (LAMP) assay targeting the virulence-related gene for N. fowleri. Time to results is about 90 min and amplification products were easily detected visually using hydroxy naphthol blue. The LAMP was highly specific after testing against related microorganisms and able to detect one trophozoite, as determined with spiked water and cerebrospinal fluid samples. The assay was then evaluated with a set of 80 water samples collected during the flooding crisis in Thailand in 2011, and 30 natural water samples from border areas of northern, eastern, western, and southern Thailand. N. fowleri was detected in 13 and 10 samples using LAMP and PCR, respectively, with a Kappa coefficient of 0.855. To the best of our knowledge, this is the first report of a LAMP assay for N. fowleri. Due to its simplicity, speed, and high sensitivity, the LAMP method described here might be useful for quickly detecting and diagnosing N. fowleri in water and clinical samples, particularly in resource-poor settings.

Comparison of methods for the detection of coliphages in recreational water at two California, United States beaches.

PubMed

Rodríguez, Roberto A; Love, David C; Stewart, Jill R; Tajuba, Julianne; Knee, Jacqueline; Dickerson, Jerold W; Webster, Laura F; Sobsey, Mark D

2012-04-01

Methods for detection of two fecal indicator viruses, F+ and somatic coliphages, were evaluated for application to recreational marine water. Marine water samples were collected during the summer of 2007 in Southern California, United States from transects along Avalon Beach (n=186 samples) and Doheny Beach (n=101 samples). Coliphage detection methods included EPA method 1601 - two-step enrichment (ENR), EPA method 1602 - single agar layer (SAL), and variations of ENR. Variations included comparison of two incubation times (overnight and 5-h incubation) and two final detection steps (lysis zone assay and a rapid latex agglutination assay). A greater number of samples were positive for somatic and F+ coliphages by ENR than by SAL (p<0.01). The standard ENR with overnight incubation and detection by lysis zone assay was the most sensitive method for the detection of F+ and somatic coliphages from marine water, although the method takes up to three days to obtain results. A rapid 5-h enrichment version of ENR also performed well, with more positive samples than SAL, and could be performed in roughly 24h. Latex agglutination-based detection methods require the least amount of time to perform, although the sensitivity was less than lysis zone-based detection methods. Rapid culture-based enrichment of coliphages in marine water may be possible by further optimizing culture-based methods for saline water conditions to generate higher viral titers than currently available, as well as increasing the sensitivity of latex agglutination detection methods. Copyright © 2012 Elsevier B.V. All rights reserved.

Rapid detection of the Klebsiella pneumoniae carbapenemase (KPC) gene by loop-mediated isothermal amplification (LAMP).

PubMed

Nakano, Ryuichi; Nakano, Akiyo; Ishii, Yoshikazu; Ubagai, Tsuneyuki; Kikuchi-Ueda, Takane; Kikuchi, Hirotoshi; Tansho-Nagakawa, Shigeru; Kamoshida, Go; Mu, Xiaoqin; Ono, Yasuo

2015-03-01

Klebsiella pneumoniae carbapenemases (KPC), which are associated with resistance to carbapenem, have recently spread worldwide and have become a global concern. It is necessary to detect KPC-producing organisms in clinical settings to be able to control the spread of this resistance. We have developed a loop-mediated isothermal amplification (LAMP) method for rapid detection of KPC producers. LAMP primer sets were designed to recognize the homologous regions of blaKPC-2 to blaKPC-17 and could amplify blaKPC rapidly. The specificity and sensitivity of the primers in the LAMP reactions for blaKPC detection were determined. This LAMP assay was able to specifically detect KPC producers at 68 °C, and no cross-reactivity was observed for other types of β-lactamase (class A, B, C, or D) producers. The detection limit for this assay was found to be 10(0) CFU per tube, in 25 min, which was 10-fold more sensitive than a PCR assay for blaKPC detection. Then, the sensitivity of the LAMP reactions for blaKPC detection in human specimens (sputum samples, urine samples, fecal samples and blood samples) was analyzed; it was observed that the LAMP assay had almost the same sensitivity in these samples as when using purified DNA. The LAMP assay is easy to perform and rapid. It may therefore be routinely applied for detection of KPC producers in the clinical laboratory. Copyright © 2014 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Nutrients and pesticides in ground water of the Ozark Plateaus in Arkansas, Kansas, Missouri, and Oklahoma

USGS Publications Warehouse

Adamski, James C.

1997-01-01

A total of 229 ground-water samples were collected from 215 sites as part of the Ozark Plateaus study unit of the National Water-Quality Assessment Program. These samples were collected from 1993 through 1995 using a network of springs and wells with three scale-dependent components. The first component, the study-unit survey, consisted of 99 randomly selected springs and domestic wells in the Springfield Plateau and Ozark aquifers. The second component, two land-use studies, consisted of 42 springs and domestic wells in a poultry-dominated agricultural area and 40 springs and domestic wells in a cattle-dominated agricultural area overlying the Springfield Plateau aquifer. The third component, the small-watershed study, consisted of 4 springs, 18 domestic wells, and 11 monitoring wells in a small basin within the poultry land-use study area. Samples were analyzed for major ions, nutrients, dissolved organic carbon, methylene blue active substances, tritium, and 88 pesticides and metabolites.The water-quality data from these samples were analyzed with descriptive and statistical methods. Nitrite plus nitrate, which was detected more often and in greater concentrations than any of the other nutrients, ranged from less than 0.05 to 25 milligrams per liter as nitrogen. Nitrite plus nitrate concentrations positively correlated to percent agricultural land use around each site. Median nitrite plus nitrate concentrations generally were greater in samples from springs than in samples from wells. Concentrations of nitrite, ammonia, and ammonia plus organic nitrogen were also affected by land use and also by concentrations of dissolved oxygen in the ground water. Concentrations of phosphorus and orthophosphate probably were affected by land use and also by phosphorus solubility. Pesticides were detected in 80 of 229 samples from 73 of 215 sites. A total of 20 pesticides were detected with a maximum of 5 pesticides detected in any 1 sample. The most commonly detected pesticides were tebuthiuron, atrazine, prometon, desethylatrazine, and simazine. Maximum concentrations ranged from 0.003 to 1.0 microgram per liter. The occurrence and distribution of pesticides were related to land use. Percent agricultural land use was greater for samples with pesticides detected than for samples with no pesticides detected. Pesticides were detected more often in samples from springs than in samples from wells. The occurrence of pesticides also was related to seasonality and chemical characteristics, such as solubility and persistence, of the compounds.