Publications by authors named "Patrick Lambert"

34 Publications

Application of gas chromatography-high resolution quadrupole time-of-flight mass spectrometry in fingerprinting analysis of polycyclic aromatic sulfur heterocycles.

J Chromatogr A 2020 Sep 21;1630:461577. Epub 2020 Sep 21.

Emergencies Science and Technology Section, Science and Technology Branch, Environment and Climate Change Canada, 335 River Road, Ottawa, ON, Canada.

Polycyclic aromatic sulfur heterocycles (PASHs), as a group of major sulfur-containing compounds, widely occur in crude oil and its refined products. Accurate analyses of these petrochemical components play an important role in monitoring oil quality, forensic source identification, and assessment of environmental impact of an oil spill. PASHs occur at relatively lower abundances in most crude oils and refined petroleum products than their corresponding aromatic hydrocarbons and are co-eluted together with some petroleum hydrocarbons in chromatographic analysis, resulting in high uncertainty for their quantitation. Capillary gas chromatography coupled with a quadrupole time-of-flight mass spectrometry (GC-QTOF-MS) provides high resolution and high mass accuracy, which facilitates discrimination of the delicate mass defects of isobaric compounds with the same nominal mass and external matrix material. In this work, GC-QTOF-MS was applied to analyze bicyclic to pentacyclic PASHs including benzothiophenes, dibenzothiophenes, benzonaphthothiophenes, dinaphthothiophenes and their C- to C- alkylated homologues in a number of crude oils, refined petroleum products, and environmental samples. GC-QTOF-MS analysis substantially improved the identification confidence and reduced quantitation uncertainty of PASHs and polycyclic aromatic hydrocarbons (PAHs) by eliminating the interferences presented in nominal mass chromatograms.
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http://dx.doi.org/10.1016/j.chroma.2020.461577DOI Listing
September 2020

An innovative bivariate approach to detect joint temporal trends in environmental conditions: Application to large French rivers and diadromous fish.

Sci Total Environ 2020 Dec 2;748:141260. Epub 2020 Aug 2.

INRAE, Unité EABX - Écosystèmes Aquatiques et Changements Globaux, HYNES (Irstea-EDF R&D), 50 avenue de Verdun, 33612 Cestas Cedex, France.

Most key life-events of organisms are synchronized by complex interactions of several environmental cues to ensure optimal survival and growth of individuals and their offspring. However, global change is known to affect multiple components of ecosystems and cues at the same time. Therefore, detecting joint trends in covariate time series is a crucial challenge in global change ecology that has rarely been addressed so far. In this context, we designed an innovative combination of kernel density estimations and Mann-Kendall trend tests to detect joint temporal trends in a pair of environmental variables. This methodological framework was tested on >30 years (1976-2019) of water temperature and discharge data for 6 large French rivers (the Garonne, Dordogne, Rhône, Rhine, Loire and Vienne rivers). The implications of such trends in both temperature and discharge for diadromous species key life-cycle processes were then explored by checking if significant bivariate environmental changes occurred during seasons of upstream and downstream migration, and reproductive activities. Results were contrasted between rivers and seasons: many rivers displayed an increase in the number of days with high water temperature and low river discharge, but local discharge regulation measures could have mitigated the trend in discharge. Our findings showed that species migrating or spawning in spring were likely to be strongly impacted by the new environmental conditions in the Garonne, Loire and Rhône rivers, given the marked changes in water temperature and discharge associations detected by our new method. Conditions experienced by fall-running and spawning species have been strongly affected in all the rivers studied. This innovative methodology was implemented in a new R package, ChocR, for application to other environments and ecosystems.
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http://dx.doi.org/10.1016/j.scitotenv.2020.141260DOI Listing
December 2020

Occurrence, characterization, and ecological assessment of petroleum-related hydrocarbons in intertidal marine sediments of Burrard Inlet, Vancouver, British Columbia, Canada.

Mar Pollut Bull 2020 Aug 29;157:111304. Epub 2020 May 29.

Emergencies Science and Technology Section (ESTS), Environment & Climate Change Canada, Ottawa, ON, Canada.

Total petroleum hydrocarbons (TPH), n-alkanes, petroleum biomarkers, and polycyclic aromatic hydrocarbons (PAHs) were analyzed in the intertidal sediments of Burrard Inlet, Vancouver, British Columbia, Canada. Most of the sampling sites had low TPH (<40 μg/g). Only 10% of sampling sites, located nearby a harbour and densely populated areas, had relatively high TPH (<260 μg/g). Main biogenic n-alkanes were present in all the sites, except for the main petrogenic input in the sample from the upper intertidal zone (UIZ) of the Maplewood Mudflats. Most sites had trace amounts of petroleum biomarkers. Mixed pyrogenic and petrogenic inputs contributed to PAHs at most sites. PAHs did not show potential toxicity to benthic organisms at most sites; however, possible negative effects from some of the detected PAHs were found for the samples from the UIZs of the Maplewood Mudflats and Labour View Park, and from the lower intertidal zone (LIZ) of Gates Park.
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http://dx.doi.org/10.1016/j.marpolbul.2020.111304DOI Listing
August 2020

Prioritizing river basins for intensive monitoring and assessment by the US Geological Survey.

Environ Monit Assess 2020 Jun 27;192(7):458. Epub 2020 Jun 27.

US Geological Survey, Lawrence, KS, USA.

The US Geological Survey (USGS) is currently (2020) integrating its water science programs to better address the nation's greatest water resource challenges now and into the future. This integration will rely, in part, on data from 10 or more intensively monitored river basins from across the USA. A team of USGS scientists was convened to develop a systematic, quantitative approach to prioritize candidate basins for this monitoring investment to ensure that, as a group, the 10 basins will support the assessment and forecasting objectives of the major USGS water science programs. Candidate basins were the level-4 hydrologic units (HUC04) with some of the smaller HUC04s being combined; median candidate-basin area is 46,600 km. Candidate basins for the contiguous United States (CONUS) were grouped into 18 hydrologic regions. Ten geospatial variables representing land use, climate change, water use, water-balance components, streamflow alteration, fire risk, and ecosystem sensitivity were selected to rank candidate basins within each of the 18 hydrologic regions. The two highest ranking candidate basins in each of the 18 regions were identified as finalists for selection as "Integrated Water Science Basins"; final selection will consider input from a variety of stakeholders. The regional framework, with only one basin selected per region, ensures that as a group, the basins represent the range in major drivers of the hydrologic cycle. Ranking within each region, primarily based on anthropogenic stressors of water resources, ensures that settings representing important water-resource challenges for the nation will be studied.
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http://dx.doi.org/10.1007/s10661-020-08403-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320945PMC
June 2020

Occurrence and weathering of petroleum hydrocarbons deposited on the shoreline of the North Saskatchewan River from the 2016 Husky oil spill.

Environ Pollut 2020 Mar 9;258:113769. Epub 2019 Dec 9.

Emergencies Science and Technology Section, Science and Technology Branch, Environment and Climate Change Canada, Ottawa, ON, K1A0H3, Canada.

Following the 16TAN Husky oil spill along the North Saskatchewan River (NSR), the occurrence and natural attenuation of the petroleum hydrocarbons were assessed by analyzing the littoral zone sediments/oil debris collected from July 2016 to October 2017. Husky oil-free, mixed sediment-Husky oil, and Husky oil debris samples were identified for all the collected samples. Shoreline sediments were contaminated by mixed biogenic, pyrogenic and petrogenic inputs prior to the spill. Oil stranded on the shoreline of NSR was moved or buried due to the very dynamic conditions of the shoreline, or cleaned through a series of cleanup activities after the spill. Most normal alkanes were naturally weathered, whereas most of the branched alkanes and all of the saturated petroleum biomarkers remained. Some lighter molecular weight (e.g., 2 to 3-ring) polycyclic aromatic hydrocarbons (PAHs) were lost rapidly after the spill, whereas sulfur containing components, e.g., dibenzothiophenes and benzonaphthothiiophenes, and those having a heavier molecular weight did not change markedly even 15 months post-spill. Similarly, some light hydrocarbons (e.g.,
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http://dx.doi.org/10.1016/j.envpol.2019.113769DOI Listing
March 2020

Monitoring of polycyclic aromatic hydrocarbon contamination at four oil spill sites using fluorescence spectroscopy coupled with parallel factor-principal component analysis.

Environ Sci Process Impacts 2019 Mar;21(3):413-426

Emergencies Science and Technology Section, Environment and Climate Change Canada, 335 River Rd., Ottawa, K1A0H3, Canada.

Fluorescence spectroscopy analysis of oil and environmental samples collected from four oil spill incidents in Canada-a 2016 pipeline spill into the North Saskatchewan River (NSR), Saskatchewan; a 2015 train derailment in Gogama, Ontario; the 1970 sinking of the SS Arrow ship in Chedabucto Bay, Nova Scotia; and the 1970 sinking of the Irving Whale barge in the Gulf of St. Lawrence-permitted assessment of the PAH content of environmentally weathered samples. A recently developed fluorescence fingerprinting model based on excitation-emission matrix-parallel factor analysis-principal component analysis (EEM-PARAFAC-PCA) was applied to (i) evaluate the intensity of the abundant PAH groups in the samples, (ii) investigate changes in the PAH composition of environmental samples over time due to weathering, and (iii) classify the original spilled oil and environmental samples within the already established classes of the fingerprinting PCA model. The environmental sediment samples collected from the Husky Energy spill site show loss of PAHs occurring over the course of 15 months post-spill. However, the extent of weathering depends on several environmental factors rather than solely the time of weathering, the PAH loss was maximum at 15 months. There was a decrease in the PAH content of the environmental samples of Gogama spill collected 20 months post-spill. Almost all of Gogama environmental sediment samples underwent substantial weathering, making PCA classification impractical. The SS Arrow and Irving Whale samples fell within adjacent PCA groups, as they both had a similar type of spilled oil (Bunker C) with similarity in chemical composition.
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http://dx.doi.org/10.1039/c8em00493eDOI Listing
March 2019

Characterization of Nitrogen-Containing Polycyclic Aromatic Heterocycles in Crude Oils and Refined Petroleum Products.

Adv Mar Biol 2018;81:59-96. Epub 2018 Nov 7.

Emergencies Science and Technology Section, Science and Technology Branch, Environment and Climate Change Canada, Ottawa, ON, Canada.

A large amount of polycyclic aromatic hydrocarbons (PAHs) and their heterocyclic analogues (N, S, O) are released to the marine environment from natural oil seeps, oil spills, bilge discharges and input of land-based sources. Many of these compounds are toxic and have a deleterious effect on marine biota. Nitrogen-containing compounds in crude oils are typically present as cyclic compounds such as polycyclic aromatic nitrogen heterocycles (PANHs) and are generally classified into the two categories of nonbasic (N-PANHs) and basic compounds (B-PANHs). Chromatographic analyses of PANHs are easily to be interfered by other oil components without proper sample preparation prior to instrumental analysis. In this work, dual solid phase extraction columns of 3-(isocyanato)propyl-functionalized silica gel (Si-NCO) and silica gel were employed to efficiently separate both N-PANHs and B-PANHs from saturated and aromatic petroleum hydrocarbons, which enable simultaneous accurate analyses of these groups with single sample preparation. Crude oils studied contain various concentrations of N-PANHs including carbazole, benzocarbazole and B-PANHs including quinolone, acridine and benzoacridine as well as their alkylated homologues. These compounds in light fuel and lubricating oil are generally not detected or are only in trace concentration, but have considerable abundance in heavy fuel oils. Crude oils from different sources and various petroleum products have their unique absolute concentrations and relative distribution patterns of PANHs. Chemical fingerprints of PANHs can provide valuable information for forensic oil spill identification and improve the understanding of the fate, behaviour and chemical degradation of spilled crude oil.
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http://dx.doi.org/10.1016/bs.amb.2018.09.006DOI Listing
March 2019

Retrotransposon methylation and activity in wild fish (A. anguilla): A matter of size.

Environ Pollut 2019 Feb 12;245:494-503. Epub 2018 Nov 12.

Univ. Bordeaux, CNRS, EPOC, 5805, Talence, France.

Understanding how organisms cope with global change is a major question in many fields of biology. Mainly, understanding the molecular mechanisms supporting rapid phenotypic changes of organisms in response to stress and linking stress-induced molecular events to adaptive or adverse outcomes at the individual or population levels remain a major challenge in evolutionary biology, ecology or ecotoxicology. In this view, the present study aimed to test (i) whether environmental factors, especially pollutants, can trigger changes in the activity of retrotransposons (RTs) in wild fish and (ii) if changes in RT DNA methylation or transcription levels can be linked to modifications at the individual level. RTs are genetic elements that have the ability to replicate and integrate elsewhere in the genome. Although RTs are mainly quiescent during normal development, they can be experimentally activated under life-threatening conditions, affecting the fitness of their host. Wild eels were collected in four sampling sites presenting differing levels of contamination. The methylation level and the transcriptional activity of two RTs and two genes involved in development and cell differentiation were analyzed in fish liver in addition to the determination of fish contaminants levels and diverse growth and morphometric indices. An up-regulation of RTs associated to lower methylation levels and lower growth indices were observed in highly contaminated fish. Our results suggest that RT activation in fish experiencing stress conditions could have both detrimental and beneficial implications, affecting fish growth but promoting resistance to environmental stressors such as pollutants.
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http://dx.doi.org/10.1016/j.envpol.2018.11.014DOI Listing
February 2019

Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae.

Plant J 2018 10 14;96(2):358-371. Epub 2018 Sep 14.

Università degli Studi di Milano - DiSAA, Via Celoria 2, 20133, Milano, Italy.

Double flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants, including Prunus persica (peach), a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in five segregating progenies delimited Di2 to an interval spanning 150 858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic resequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait, and we showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co-segregated with the phenotype in 621 progenies, accounting for the dominant inheritance of the Di2 locus. Further corroborating the results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double-flower roses. Phylogenetic analysis showed that these two genes belong to a TARGET OF EAT (TOE)-type clade not represented in Arabidopsis, indicating a divergence of gene functions between AP2-type and TOE-type factors in Arabidopsis and other species. The identification of orthologous candidate genes for the double-flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.
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http://dx.doi.org/10.1111/tpj.14036DOI Listing
October 2018

Occurrence, source and ecological assessment of petroleum related hydrocarbons in intertidal marine sediments of the Bay of Fundy, New Brunswick, Canada.

Mar Pollut Bull 2018 Aug 22;133:799-807. Epub 2018 Jun 22.

Emergencies Science and Technology Section (ESTS), Environment & Climate Change Canada, Ottawa, ON, Canada.

Total petroleum hydrocarbons (TPH), n-alkanes, petroleum-related biomarkers of terpanes and steranes, and polycyclic aromatic hydrocarbons (PAHs) were analyzed in the intertidal sediments in the Bay of Fundy, Nova Scotia/New Brunswick, Canada. Sites close to the harbour and more densely populated areas had higher TPH levels than other pristine areas. n-Alkanes presented a typical single bell-shape in n-C to n-C range and an obvious odd to even carbon preference. Most sites had trace amounts of petroleum biomarkers. Abundant non-alkylated PAHs and lower amounts of alkylated PAHs represented the major input of the incomplete combustion of solid (e.g., coal, coke, biomass, and coal tar) and liquid fuels. The toxicity estimation for PAHs indicates that they did not have potential toxicity to benthic organisms at most sampling sites. However, possible to probable negative effects from the measured PAH concentrations were found for the two samples from Courtenay Bay and Saint Andrews.
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http://dx.doi.org/10.1016/j.marpolbul.2018.06.047DOI Listing
August 2018

Fate of oxygenated intermediates in solar irradiated diluted bitumen mixed with saltwater.

Environ Pollut 2017 Dec 29;231(Pt 1):622-634. Epub 2017 Aug 29.

Emergencies Science and Technology Section, Science and Technology Branch, Environment and Climate Change Canada, Ottawa, ON, K1A0H3, Canada.

Two types of diluted bitumen (dilbit) and a light crude oil spiked onto the surface of saltwater were irradiated with natural solar light in Ottawa to assess the impact of sunlight to the fate of oxygenated intermediates. Oxygenated components, including carbonyl polycyclic aromatic hydrocarbons (PAHs) and acidic polar fractions (naphthenic acid fraction compounds, NAFCs), were identified after periods of solar exposure under both winter and summer conditions. Carbonyl PAHs and NAFCs were formed in both seasons; however, light crude and summer irradiation produced higher abundance of them than dilbits and winter exposure. The formed NAFCs were abundant with the congeners containing a heteroatom of oxygen only (O species), accompanied by the minor amounts of sulfur- and nitrogen-containing acids. The produced O species were predominant with the congeners with light molecular weight, high degree of saturation and heavy oxygen numbers. For both carbonyl PAHs and NAFCs, their abundance continually increased throughout the period of winter exposure. In the summer, some carbonyl PAHs and all O species increased during the early exposure period; then they decreased with continued exposure for most oils, illustrating their transitional nature. Oxygenated intermediates thus appear to have been created through the photo-oxidation of non-to medium-polar petroleum hydrocarbons or the intermediates of aldehydes or ketones (O). Oil properties, the duration of exposure, exposure season and the chemical structure of these intermediates are critical factors controlling their fate through photo-oxidation. The observed chemical changes highlight the effects of sunlight on the potential behavior, fate and impact of spilled oil, with the creation of new resin group compounds and the reduction of aromatics and saturates. These results also imply that the ecological effects of spilled oil, after ageing in sunlight, depend on the specific oil involved and the environmental conditions.
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http://dx.doi.org/10.1016/j.envpol.2017.08.043DOI Listing
December 2017

Characterization of chemical fingerprints of unconventional Bakken crude oil.

Environ Pollut 2017 Nov 12;230:609-620. Epub 2017 Jul 12.

Emergencies Science and Technology Section, Science and Technology Branch, Environment and Climate Change Canada, Ottawa, Ontario, Canada.

The ability to characterize the composition of emerging unconventional Bakken tight oil is essential to better prepare for potential spills and to assess associated environmental concerns. The present work measured and compared the physical and chemical properties of Bakken crudes with conventional crude oils from various regions and different types of refined petroleum products. The physicochemical properties of Bakken crude are overall similar to those of conventional light crudes. The Bakken crude consists of high concentrations of monoaromatic hydrocarbons and alkylated PAHs with a clear dominance of the alkylated naphthalene homologues followed by the phenanthrene series. Its pyrogenic index (PI) values are considerably lower than typical conventional crude oils. The Bakken crude oils in this study exhibit a low abundance of petroleum biomarker such as terpanes, steranes and diamondoids and bicyclic sesquiterpanes. Since tight oil from the Bakken region is produced from low-permeability formations, variations in abundance and diagnostic ratios of common target petroleum hydrocarbons were found among these oils.
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http://dx.doi.org/10.1016/j.envpol.2017.07.011DOI Listing
November 2017

Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies.

BMC Genomics 2017 06 6;18(1):432. Epub 2017 Jun 6.

PTP Science Park, Via Einstein - Loc. Cascina Codazza, Lodi, Italy.

Background: Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach.

Results: A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3-5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average).

Conclusions: This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes.
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http://dx.doi.org/10.1186/s12864-017-3781-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460546PMC
June 2017

Integrated QTL detection for key breeding traits in multiple peach progenies.

BMC Genomics 2017 06 6;18(1):404. Epub 2017 Jun 6.

IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain.

Background: Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability.

Results: Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value.

Conclusions: The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.
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http://dx.doi.org/10.1186/s12864-017-3783-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460339PMC
June 2017

Occurrence, source and ecological assessment of baseline hydrocarbons in the intertidal marine sediments along the shoreline of Douglas Channel to Hecate Strait in British Columbia.

Mar Pollut Bull 2017 Sep 25;122(1-2):450-455. Epub 2017 May 25.

Emergencies Science and Technology Section (ESTS), Environment & Climate Change Canada, Ottawa, ON, Canada.

The occurrence, source and ecological assessment of baseline hydrocarbons in the intertidal zone along the northern British shoreline were evaluated based on analyzing total petroleum hydrocarbons (TPH), n-alkanes, petroleum related biomarkers such as terpanes and steranes, and polycyclic aromatic hydrocarbons (PAHs) including non-alkylated and alkylated homologues (APAHs). The TPH levels, n-alkanes, petroleum biomarkers and PAHs in all the sampling sites, except for Masset Harbor/York Point at Gil Island were low, without obvious unresolved complex mixture (UCM) and petroleum contamination input. Specifically, n-alkanes showed a major terrestrial plants input; PAHs with abundant non-alkylated PAHs but minor APAHs showed a major pyrogenic input. However, obvious petroleum-derived hydrocarbons have impacted Masset Harbor. A historical petroleum input was found in York Point at Gil Island, due to the presence of the low level of petroleum biomarkers. Ecological assessment of 13 non-alkylated PAHs in Masset Harbor indicated no potential toxicity to the benthic organisms.
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http://dx.doi.org/10.1016/j.marpolbul.2017.05.053DOI Listing
September 2017

Toward a phenological mismatch in estuarine pelagic food web?

PLoS One 2017 29;12(3):e0173752. Epub 2017 Mar 29.

Irstea, UR EABX, Cestas, FRANCE.

Alterations of species phenology in response to climate change are now unquestionable. Until now, most studies have reported precocious occurrence of life cycle events as a major phenological response. Desynchronizations of biotic interactions, in particular predator-prey relationships, are however assumed to strongly impact ecosystems' functioning, as formalized by the Match-Mismatch Hypothesis (MMH). Temporal synchronicity between juvenile fish and zooplankton in estuaries is therefore of essential interest since estuaries are major nursery grounds for many commercial fish species. The Gironde estuary (SW France) has suffered significant alterations over the last three decades, including two Abrupt Ecosystem Shifts (AES), and three contrasted intershift periods. The main objective of this study was to depict modifications in fish and zooplankton phenology among inter-shift periods and discuss the potential effects of the resulting mismatches at a community scale. A flexible Bayesian method was used to estimate and compare yearly patterns of species abundance in the estuary among the three pre-defined periods. Results highlighted (1) an earlier peak of zooplankton production and entrance of fish species in the estuary and (2) a decrease in residence time of both groups in the estuary. Such species-specific phenological changes led to changes in temporal overlap between juvenile fish and their zooplanktonic prey. This situation questions the efficiency and potentially the viability of nursery function of the Gironde estuary, with potential implications for coastal marine fisheries of the Bay of Biscay.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173752PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371289PMC
August 2017

Gene transcription profiling in wild and laboratory-exposed eels: Effect of captivity and in situ chronic exposure to pollution.

Sci Total Environ 2016 Nov 25;571:92-102. Epub 2016 Jul 25.

Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400 Talence, France; CNRS, EPOC, UMR 5805, F-33400 Talence, France.

Aquatic ecosystems are subjected to a variety of man-induced stressors but also vary spatially and temporally due to variation in natural factors. In such complex environments, it remains difficult to detect, dissociate and evaluate the effects of contaminants in wild organisms. In this context, the aim of this study was to test whether the hepatic transcriptome profile of fish may be used to detect in situ exposure to a particular contaminant. Transcriptomic profiles from laboratory-exposed and wild eels sampled along a contamination gradient were compared. During laboratory experiments, fish were exposed during 45days to different pollutants (Hg, PCBs, OCPs or Cd) or natural factors (temperature, salinity or low food supply) at levels close to those found in the sampling sites. A strong difference was observed between the transcriptomic profiles obtained from wild and laboratory-exposed animals (whatever the sites or experimental conditions), suggesting a general stress induced by captivity in the laboratory. Among the biological functions that were up-regulated in laboratory eels in comparison to wild eels, histone modification was the most represented. This finding suggests that laboratory conditions could affect the epigenome of fish and thus modulate the transcriptional responses developed by fish in response to pollutant exposure. Among experimental conditions, only the transcription profiles of laboratory animals exposed to cold temperature were correlated with those obtained from wild fish, and more significantly with fish from contaminated sites. Common regulated genes were mainly involved in cell differentiation and liver development, suggesting that stem/progenitor liver cells could be involved in the adaptive response developed by fish chronically exposed to pollutant mixtures.
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http://dx.doi.org/10.1016/j.scitotenv.2016.07.131DOI Listing
November 2016

Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development.

J Exp Bot 2016 05 25;67(11):3419-31. Epub 2016 Apr 25.

Génétique et Amélioration des Fruits et Légumes, INRA, 84000 Avignon, France

Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs controlling metabolite concentrations were observed and discussed. These co-locations raise hypotheses regarding the functional regulation of sugar metabolism and pave the way for further analyses to enable the identification of the underlying genes. In conclusion, we identified the potential impact on fruit breeding of the modification of QTL effect close to maturity.
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http://dx.doi.org/10.1093/jxb/erw169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892732PMC
May 2016

Detecting the exposure to Cd and PCBs by means of a non-invasive transcriptomic approach in laboratory and wild contaminated European eels (Anguilla anguilla).

Environ Sci Pollut Res Int 2016 Mar 14;23(6):5431-41. Epub 2015 Nov 14.

Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400, Talence, France.

Detecting and separating specific effects of contaminants in a multi-stress field context remain a major challenge in ecotoxicology. In this context, the aim of this study was to assess the usefulness of a non-invasive transcriptomic method, by means of a complementary DNA (cDNA) microarray comprising 1000 candidate genes, on caudal fin clips. Fin gene transcription patterns of European eels (Anguilla anguilla) exposed in the laboratory to cadmium (Cd) or a polychloro-biphenyl (PCBs) mixture but also of wild eels from three sampling sites with differing contamination levels were compared to test whether fin clips may be used to detect and discriminate the exposure to these contaminants. Also, transcriptomic profiles from the liver and caudal fin of eels experimentally exposed to Cd were compared to assess the detection sensitivity of the fin transcriptomic response. A similar number of genes were differentially transcribed in the fin and liver in response to Cd exposure, highlighting the detection sensitivity of fin clips. Moreover, distinct fin transcription profiles were observed in response to Cd or PCB exposure. Finally, the transcription profiles of eels from the most contaminated site clustered with those from laboratory-exposed fish. This study thus highlights the applicability and usefulness of performing gene transcription assays on non-invasive tissue sampling in order to detect the in situ exposure to Cd and PCBs in fish.
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http://dx.doi.org/10.1007/s11356-015-5754-2DOI Listing
March 2016

The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species.

PLoS One 2015 1;10(10):e0139194. Epub 2015 Oct 1.

Irstea, EABX, Aquatic Ecosystems and Global Changes research unit, 50 avenue de Verdun, Gazinet Cestas, F-33612, Cestas, France.

Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold temperatures deserved more attention in terms of modelling, but further in conservation planning as well.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139194PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4591278PMC
May 2016

Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca).

New Phytol 2016 Jan 10;209(2):773-84. Epub 2015 Sep 10.

UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.

In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.
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http://dx.doi.org/10.1111/nph.13627DOI Listing
January 2016

Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm.

PLoS One 2015 9;10(9):e0136803. Epub 2015 Sep 9.

IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.

Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136803PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564248PMC
May 2016

Gonadal transcriptome analysis of wild contaminated female European eels during artificial gonad maturation.

Chemosphere 2015 Nov 6;139:303-9. Epub 2015 Jul 6.

Univ. Bordeaux, UMR EPOC CNRS 5805, F-33400 Talence, France; CNRS, EPOC, UMR 5805, F-33400 Talence, France.

Since the early 1980s, the population of European eels (Anguilla anguilla) has dramatically declined. Nowadays, the European eel is listed on the red list of threatened species (IUCN Red List) and is considered as critically endangered of extinction. Pollution is one of the putative causes for the collapse of this species. Among their possible effects, contaminants gradually accumulated in eels during their somatic growth phase (yellow eel stage) would be remobilized during their reproductive migration leading to potential toxic events in gonads. The aim of this study was to investigate the effects of organic and inorganic contaminants on the gonad development of wild female silver eels. Female silver eels from two sites with differing contamination levels were artificially matured. Transcriptomic analyses by means of a 1000 candidate gene cDNA microarray were performed on gonads after 11weeks of maturation to get insight into the mechanisms of toxicity of contaminants. The transcription levels of several genes, that were associated to the gonadosomatic index (GSI), were involved in mitotic cell division but also in gametogenesis. Genes associated to contaminants were mainly involved in the mechanisms of protection against oxidative stress, in DNA repair, in the purinergic signaling pathway and in steroidogenesis, suggesting an impairment of gonad development in eels from the polluted site. This was in agreement with the fact that eels from the reference site showed a higher gonad growth in comparison to contaminated fish.
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http://dx.doi.org/10.1016/j.chemosphere.2015.06.007DOI Listing
November 2015

Abnormal ovarian DNA methylation programming during gonad maturation in wild contaminated fish.

Environ Sci Technol 2014 Oct 19;48(19):11688-95. Epub 2014 Sep 19.

University of Bordeaux, EPOC, UMR 5805 , F-33400 Talence, France.

There is increasing evidence that pollutants may cause diseases via epigenetic modifications. Epigenetic mechanisms such as DNA methylation participate in the regulation of gene transcription. Surprisingly, epigenetics research is still limited in ecotoxicology. In this study, we investigated whether chronic exposure to contaminants experienced by wild female fish (Anguilla anguilla) throughout their juvenile phase can affect the DNA methylation status of their oocytes during gonad maturation. Thus, fish were sampled in two locations presenting a low or a high contamination level. Then, fish were transferred to the laboratory and artificially matured. Before hormonal treatment, the DNA methylation levels of the genes encoding for the aromatase and the receptor of the follicle stimulating hormone were higher in contaminated fish than in fish from the clean site. For the hormone receptor, this hypermethylation was positively correlated with the contamination level of fish and was associated with a decrease in its transcription level. In addition, whereas gonad growth was associated with an increase in DNA methylation in fish from the clean site, no changes were observed in contaminated fish in response to hormonal treatment. Finally, a higher gonad growth was observed in fish from the reference site in comparison to contaminated fish.
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http://dx.doi.org/10.1021/es503712cDOI Listing
October 2014

PDE-based enhancement of color images in RGB space.

IEEE Trans Image Process 2012 May 1;21(5):2500-12. Epub 2011 Dec 1.

Department of Electronics, Faculty of Electronics and Electrical Engineering, University of Sciences and Technology of Oran, Oran, Algeria.

A novel method for color image enhancement is proposed as an extension of the scalar-diffusion-shock-filter coupling model, where noisy and blurred images are denoised and sharpened. The proposed model is based on using the single vectors of the gradient magnitude and the second derivatives as a manner to relate different color components of the image. This model can be viewed as a generalization of the Bettahar-Stambouli filter to multivalued images. The proposed algorithm is more efficient than the mentioned filter and some previous works at color images denoising and deblurring without creating false colors.
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http://dx.doi.org/10.1109/TIP.2011.2177844DOI Listing
May 2012

Horizontal transmission of Candida albicans and evidence of a vaccine response in mice colonized with the fungus.

PLoS One 2011 19;6(7):e22030. Epub 2011 Jul 19.

Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America.

Disseminated candidiasis is the third leading nosocomial blood stream infection in the United States and is often fatal. We previously showed that disseminated candidiasis was preventable in normal mice by immunization with either a glycopeptide or a peptide synthetic vaccine, both of which were Candida albicans cell wall derived. A weakness of these studies is that, unlike humans, mice do not have a C. albicans GI flora and they lack Candida serum antibodies. We examined the influence of C. albicans GI tract colonization and serum antibodies on mouse vaccination responses to the peptide, Fba, derived from fructose bisphosphate aldolase which has cytosolic and cell wall distributions in the fungus. We evaluated the effect of live C. albicans in drinking water and antimicrobial agents on establishment of Candida colonization of the mouse GI tract. Body mass, C. albicans in feces, and fungal-specific serum antibodies were monitored longitudinally. Unexpectedly, C. albicans colonization occurred in mice that received only antibiotics in their drinking water, provided that the mice were housed in the same room as intentionally colonized mice. The fungal strain in unintentionally colonized mice appeared identical to the strain used for intentional GI-tract colonization. This is the first report of horizontal transmission and spontaneous C. albicans colonization in mice. Importantly, many Candida-colonized mice developed serum fungal-specific antibodies. Despite the GI-tract colonization and presence of serum antibodies, the animals made antibodies in response to the Fba immunogen. This mouse model has potential for elucidating C. albicans horizontal transmission and for exploring factors that induce host defense against disseminated candidiasis. Furthermore, a combined protracted GI-tract colonization with Candida and the possibility of serum antibody responses to the presence of the fungus makes this an attractive mouse model for testing the efficacy of vaccines designed to prevent human disseminated candidiasis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022030PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139608PMC
December 2011

Intestinal barrier dysfunction, endotoxemia, and gastrointestinal symptoms: the 'canary in the coal mine' during exercise-heat stress?

Med Sport Sci 2008 ;53:61-73

Department of Exercise Science, Creighton University, Omaha, Nebr., USA.

Reduced intestinal blood flow and high intestinal temperatures during exercise-heat stress can lead to intestinal barrier dysfunction. Such dysfunction may increase intestinal permeability to endotoxin. During exercise-heat stress, intestinal barrier dysfunction and endotoxemia can produce gastrointestinal symptoms and increased production of pro-inflammatory cytokines. Such problems may be a warning sign ('canary in the coal mine') for the onset of exertional heat stroke. Failure to heed such a warning may culminate in problems indicative of exertional heat stroke such as circulatory collapse and multiple organ failure. Prior exposure to exercise-heat stress may, however, be a protective mechanism.
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http://dx.doi.org/10.1159/000151550DOI Listing
March 2009

Effect of exercise intensity on active and passive glucose absorption.

Int J Sport Nutr Exerc Metab 2006 Oct;16(5):485-93

Dept of Exercise Science and Athletic Training, Creighton University, Omaha, NE 68178, USA.

The purpose of this study was to determine the effects of exercise intensity on active and passive intestinal glucose absorption. Eight trained runners (age = 23 +/- 2 y; VO2max = 62.1 +/- 5.8 mL x kg(-1) x min(-1)) performed a 1 h resting experiment and three 1 h treadmill experiments at 30, 50, or 70% VO2max in a thermoneutral environment. Immediately prior to each experiment, euhydrated subjects ingested a solution containing two non-metabolizable glucose analogs, 3-O-methyl-D-glucose (3MG; actively absorbed; 5 g) and D-xylose (passively absorbed; 5 g). During the following 5 h, all urine was collected and the amount of 3MG and D-xylose in the urine was determined. Using repeated measures ANOVA, a significant (P < 0.05) reduction in urinary excretion of each carbohydrate was observed at 70% VO2max compared to the other intensities suggesting that both active and passive intestinal absorption of glucose may be reduced during prolonged running at this intensity.
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http://dx.doi.org/10.1123/ijsnem.16.5.485DOI Listing
October 2006

Gastric emptying and intestinal absorption of a low-carbohydrate sport drink during exercise.

Int J Sport Nutr Exerc Metab 2005 Jun;15(3):220-35

Department of Exercise Sciences, the University of Iowa, Iowa City, IA 68178, USA.

The purpose of this study was to determine if lowering carbohydrate (CHO) concentration in a sport drink influences gastric emptying, intestinal absorption, or performance during cycle ergometry (85 min, 60% VO(2peak)). Five subjects (25 +/- 1 y, 61.5 +/- 2.1 mL . kg(-1) . min(-1) VO(2peak)) ingested a 3% CHO, 6% CHO, or a water placebo (WP) beverage during exercise. Gastric emptying was determined by repeated double sampling and intestinal absorption by segmental perfusion. Total solute absorption and plasma glucose was greater for 6% CHO; however, neither gastric emptying, intestinal water absorption, or 3-mi time trial performance (7:58 +/- 0:33 min, 8:13 +/- 0:25 min, and 8:25 +/- 0:29 min, respectively, for 6% CHO, 3% CHO, and WP) differed among solutions. These results indicate lowering the CHO concentration of a sport drink from 6% CHO does not enhance gastric emptying, intestinal water absorption, or time trial performance, but reduces CHO and total solute absorption.
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http://dx.doi.org/10.1123/ijsnem.15.3.220DOI Listing
June 2005

Tumor necrosis factor-alpha hyper-responsiveness to endotoxin in whole blood is associated with chronic bronchitis in farmers.

J Agromedicine 2005 ;10(1):39-44

Department of Exercise Science and Athletic Training, Creighton University, Omaha, NE 68178, USA.

Many farmers experience chronic bronchitis, airflow obstruction, and asthma. It is thought that these respiratory problems may be related to workplace inhalation of organic dust containing endotoxin. The purpose of this study was to determine whether whole blood cytokine responsiveness to endotoxin is associated with airflow disorders (i.e., airflow obstruction, chronic bronchitis, and doctor-diagnosed asthma). Farmers (N = 95) were recruited from a rural cohort study and completed a respiratory symptom and history questionnaire, spirometry, and blood sampling. Blood was incubated 24 hours in the presence and absence of endotoxin and supernatants were analyzed for TNF-alpha, IL-1beta, IL-6, and IL-8. Hypo- or hyper-responsiveness to endotoxin was based on whether cytokine values were in the lower or upper 10% of the group range, respectively. A significant association existed between TNF-alpha hyper-responsiveness and chronic bronchitis. These results indicate that the whole blood cytokine assay may be useful to identify individual responsiveness to endotoxin, and may provide an additional diagnostic tool to evaluate persons potentially at risk for developing chronic bronchitis following exposure to organic dust in the workplace.
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http://dx.doi.org/10.1300/J096v10n01_05DOI Listing
September 2005