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PubMed2004

Rapid identification of environmental bacterial strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

In recent years, various mass spectrometry procedures have been developed for bacterial identification. The accuracy and speed with which data can be obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) could make this a powerful tool for environmental monitoring. However, minor variations in the sample preparation can influence the mass spectra significantly. Therefore, the first objectives of this study were the adjustment and the optimization of experimental parameters allowing a rapid identification of whole bacterial cells without laborious sample preparation. The tested experimental parameters were matrix, extraction solvent, salt content, deposition method, culture medium and incubation time. This standardized protocol was applied to identify reference and environmental bacterial strains of Escherichia coli, Salmonella and Acinetobacter. The environmental bacterial strains were isolated from sewage sludge using an original microextraction procedure based on repeated sonications and enzymatic treatments. The bacterial identification was realized by the observation of the respective genus-, species- and strain-specific biomarkers. This bacterial taxonomy could be completed within one hour, with minimal sample preparation, provided that sufficient bacteria had been collected prior to MALDI-TOF analysis.

Actinobacteria↗

PubMed2026

Using high-dimensional environmental covariates to study genotype by environment interaction for reproductive traits in Duroc boars.

We investigated the potential of incorporating grid-cell-based environmental covariates (ECs) in the genetic evaluation of total sperm count (TSC), sperm motility (MOT), and sperm morphology (MOR) for Duroc boars. A total of 188,665 records derived from 3,684 genotyped boars, born between December 2018 and October 2024 and raised in three stud farms located in different U.S. states, were analyzed using multi-trait linear-threshold repeatability models. To account for genotype by environment interactions (GE), we constructed an interaction matrix as the Hadamard product of the genomic relationship matrix and an environmental (co)variance matrix. The environmental groups were defined in three ways: farm, farm-season, and farm-year-season. The (co)variance matrix was constructed based on daily ECs obtained from the NASA POWER database for each environmental group. Of all available ECs, those significantly associated with TSC, MOT, and MOR (temperature, relative humidity, atmospheric pressure, and wind speed and direction) were retained. We evaluated five models with different GE structures: M1 represented the baseline without accounting for GE, in M2 the GE included farm as environmental groups, in M3 the GE included farm-season as environmental groups, in M4 the GE included farm-year-season as environmental groups, and M5 involved M3 with an additional random effect of the farm-season. Estimates of heritability for TSC, MOT, and MOR ranged from 0.03 to 0.04, 0.05 to 0.08, and 0.04 to 0.08, respectively. Corresponding repeatability ranged from 0.15 to 0.23, 0.28 to 0.49, and 0.28 to 0.49. The proportion of phenotypic variance attributed to GE variance ranged from 0.00 to 0.32, 0.00 to 0.44, and 0.00 to 0.44. Lastly, estimates of genetic correlation, TSC-MOT, TSC-MOR, and MOT-MOR ranged from 0.27 to 0.31, 0.24 to 0.31, and 0.98 to 0.99, respectively, with minor differences across models. We assessed the predictive ability of models using the linear regression validation. Across traits and models, bias ranged from -0.05 to 0.02 standard deviations, slope varied from 0.88 to 0.99, the correlation ranged from 0.75 to 0.84, and accuracy from 0.41 to 0.53. Overall, building the GE matrix considering grid-cell-based ECs helped to account for GE, thereby reducing the proportion of phenotypic variance attributed to genetic components; however, it did not improve the validation metrics. Additional on-farm records for ECs may improve the model performance.

Animals↗

PubMed2005

Cholesky problems.

Behavioral geneticists commonly parameterize a genetic or environmental covariance matrix as the product of a lower diagonal matrix postmultiplied by its transpose-a technique commonly referred to as "fitting a Cholesky." Here, simulations demonstrate that this procedure is sometimes valid, but at other times: (1) may not produce fit statistics that are distributed as a chi2; or (2) if the distribution of the fit statistic is chi2, then the degrees of freedom (df) are not always the difference between the number of parameters in the general model less the number of parameters in a constrained model. It is hypothesized that the problem is related to the fact that the Cholesky parameterization requires that the covariance matrix formed by the product be either positive definite or singular. Even though a population covariance matrix may be positive definite, the combination of sampling error and the derived--as opposed to directly observed--nature of genetic and environmental matrices allow matrices that are negative (semi) definite. When this occurs, fitting a Cholesky constrains the numerical area of search and compromises the maximum likelihood theory currently used in behavioral genetics. Until the reasons for this phenomenon are understood and satisfactory solutions are developed, those who fit Cholesky matrices face the burden of demonstrating the validity of their fit statistics and the df for model comparisons. An interim remedy is proposed--fit an unconstrained model and a Cholesky model, and if the two differ, then report the difference in fit statistics and parameter estimates. Cholesky problems are a matter of degree, not of kind. Thus, some Cholesky solutions will differ trivially from the unconstrained solutions, and the importance of the problems must be assessed by how often the two lead to different substantive interpretation of the results. If followed, the proposed interim remedy will develop a body of empirical data to assess the extent to which Cholesky problems are important substantive issues versus statistical curiosities.

Algorithms↗

PubMed2003

Occurrence of toxic cyanobacterial blooms in San Roque Reservoir (Córdoba, Argentina): a field and chemometric study.

We evaluated the presence of cyanobacterial blooms in San Roque Reservoir (Córdoba, Argentina). Cyanobacterial blooms and water samples were collected over 4 years (1998-2002). We confirmed the presence of microcystin-LR and microcystin-RR in 97% of these blooms. The total amount of microcystin (MC) ranged between 5.8 and 2400.0 microg x g(-1) of freeze-dried bloom material. These values suggest that guidelines for safe water consumption and recreational use should be established for this reservoir. Twenty-eight physical and chemical parameters were measured in water samples and evaluated by discriminant analysis (DA). A first DA was used to evaluate the factors promoting cyanobacteria occurrence, identifying nine parameters following three patterns associated with cyanobacterial growth. Inorganic phosphorous was found to promote the presence of blooms, whereas the highest proliferation of cyanobacteria was observed in the presence of smaller amounts of carbonate, bicarbonate, sulfate, and fecal coliform bacteria. The results observed during our fieldwork, analyzed using DA, agreed with the results of other laboratory studies, thus confirming the usefulness of DA to help with the evaluation of a complicated environmental data matrix. A second DA, using only water samples collected during the presence of cyanobacteria blooms, identified another nine parameters. The analysis of these parameters allowed us to identify certain environmental factors that could lead to the dominance of toxic strains, thus increasing the amount of MC. The results showed that, in our case, an increase in the water temperature was associated with higher amounts of MC per dry weight unit, whereas an increase in the concentrations of ammonia-nitrogen and iron were associated with lower amounts of MC, thus disfavoring the dominance of toxic strains.

Argentina↗

PubMed2002

Potential analytical applications of interfacing a GC to an FT-ICR MS: fingerprinting complex sample matrixes.

Details of interfacing a high-pressure gas chromatograph to the internal ion source of a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) are described. We present our preliminary results and potential analytical applications of GC/FT-ICR for analyzing complex biological and environmental sample matrixes, such as petroleum mixtures. Based on GC/FT-ICR data, rapid characterization of various automobile gasoline samples is possible. Comparison between acquired data from the GC/FT-ICR MS (in broadband mode) and a commercial GC quadrupole mass spectrometer (QMS) (over a wide mass range) indicates that sensitivity of the GC/FT-ICR MS is an order of magnitude lower. High mass resolution and mass measurement accuracy of FT-ICR MS can be utilized for unambiguous molecular formula identification of unknown analytes.

Journal Article↗

PubMed2002

Matrix molecular weight cut-off for encapsulation of carbonic anhydrase in polyelectrolyte beads.

The enzyme bovine carbonic anhydrase (BCA) has been immobilized in the chitosan-alginate system for the first time, to catalyze the conversion of CO2 to HCO3-. Chitosan-coated alginate beads are a biodegradable and environmentally benign matrix, chosen for application of the enzyme in a novel biomimetic CO2 sequestration system. The feasibility of the system and immobilization of the enzyme were demonstrated in our earlier studies. Optimization of the matrix to improve the retention time of the enzyme in an encapsulated form is the subject of the present study. The improvement in the molecular weight cut-off of the beads was accomplished by adjusting the cross-linking conditions, coating composition, and molecular weight of the system. The quantity of enzyme released from the system was measured by a Bio-Rad protein assay. Poly-L-lysine was also used as a coating reagent for comparison purposes. The presence of a coating on the alginate beads was verified by Kjeldahl analyses. The difference in the microstructures of alginate and chitosan/alginate beads was demonstrated by SEM studies. Mineralization of the chitosan/alginate matrix in the presence of CaCO3 was also studied by FT-IR, to assess the possibility of using the beads continuously in a bioreactor.

Alginates↗

PubMed2002

Environmental water in a regulated river system: the Murrumbidgee River planning approach to the determination of environmental needs.

The major platform of the Council of Australian Governments (COAG) water reform program is the equitable and sustainable sharing of surface and groundwater resources between the environment and consumptive water users. In the regulated section of the Murrumbidgee River below Burrinjuck Dam, approximately 2,800 GL of the available surface water (4,300 GL) is diverted or extracted for irrigation uses in the Murrumbidgee Irrigation Area and Districts, and in the Coleambally Irrigation Area. Environmental flow rules have been developed for the Murrumbidgee which provide for an allocation of water to the environment but on the basis of no more than a 10% impact on farm-gate income of irrigation farmers. This provision limits the volume of water that can be used for environmental purposes, so the most effective use must be made of it. To identify and quantify the benefits to the environment of this limited additional volume of water and to determine the most effective use of the water, an "environmental spreadsheet matrix" has been developed. This paper outlines the development and use of the matrix in the planned implementation of flow regimes appropriate to the protection and enhancement of riparian and aquatic ecosystems and ecological processes.

Australia↗

PubMed2001

Determination of carbamate, urea, and thiourea pesticides and herbicides in water.

Microbore liquid chromatography and positive ion electrospray mass spectrometry are applied to the determination of 16 carbamate, urea, and thiourea pesticides and herbicides in water. The electrospray mass spectra of the analytes were measured and are discussed and mobile-phase matrix effects were evaluated. Analyte positive ion abundances are generally inversely related to the concentration of acetic acid in the acetonitrile-water mobile phase in the range of 0.001-0.1% (v/v) acetic acid. Using an internal standard for quantitative analyses and no acid in the mobile phase, retention time precision, peak width precision, concentration measurement precision, mean recoveries, and instrument detection limits were determined in reagent water. The 16 analytes were also measured in fortified environmental water samples from a recreational lake, a groundwater well, a cistern, a farm pond, and drinking water. These measurements were at 5 ng/mL of each analyte, which is within the range expected for environmental pesticide and herbicide contaminants. The analytes were separated from the environmental water matrixes with an on-line extraction and concentration to provide rapid sample analyses without a slow off-line liquid-liquid or liquid-solid-liquid extraction and extract concentration. Recoveries of 12 of the analytes from 4 environmental water samples were in the range of 75-124% with relative standard deviations in the range of 11-16%.

Carbamates↗

PubMedDate not supplied

Full conjugate analysis of normal multiple traits with missing records using a generalized inverted Wishart distribution.

A Markov chain Monte Carlo (MCMC) algorithm to sample an exchangeable covariance matrix, such as the one of the error terms (R0) in a multiple trait animal model with missing records under normal-inverted Wishart priors is presented. The algorithm (FCG) is based on a conjugate form of the inverted Wishart density that avoids sampling the missing error terms. Normal prior densities are assumed for the 'fixed' effects and breeding values, whereas the covariance matrices are assumed to follow inverted Wishart distributions. The inverted Wishart prior for the environmental covariance matrix is a product density of all patterns of missing data. The resulting MCMC scheme eliminates the correlation between the sampled missing residuals and the sampled R0, which in turn has the effect of decreasing the total amount of samples needed to reach convergence. The use of the FCG algorithm in a multiple trait data set with an extreme pattern of missing records produced a dramatic reduction in the size of the autocorrelations among samples for all lags from 1 to 50, and this increased the effective sample size from 2.5 to 7 times and reduced the number of samples needed to attain convergence, when compared with the 'data augmentation' algorithm.

Algorithms↗

PubMed2004

Rosacea: I. Etiology, pathogenesis, and subtype classification.

Rosacea is one of the most common conditions dermatologists treat. Rosacea is most often characterized by transient or persistent central facial erythema, visible blood vessels, and often papules and pustules. Based on patterns of physical findings, rosacea can be classified into 4 broad subtypes: erythematotelangiectatic, papulopustular, phymatous, and ocular. The cause of rosacea remains somewhat of a mystery. Several hypotheses have been documented in the literature and include potential roles for vascular abnormalities, dermal matrix degeneration, environmental factors, and microorganisms such as Demodex folliculorum and Helicobacter pylori. This article reviews the current literature on rosacea with emphasis placed on the new classification system and the main pathogenic theories. Learning objective At the conclusion of this learning activity, participants should be acquainted with rosacea's defining characteristics, the new subtype classification system, and the main theories on pathogenesis.

Adrenal Cortex Hormones↗

PubMed1991

Physiology of bone: mineral compartment proteins as candidates for environmental perturbation by lead.

Termine et al. first demonstrated that sequential dissociative extraction and fractionation procedures with protease inhibitors could provide a convenient approach for the study of mineral compartment constituents. The primary extraction regimen used 4 M guanidine HCl to remove most of the protein from the nonmineralized phase of bone. Subsequently, EDTA-guanidine was used to remove the mineral-phase components. These methods discriminate on the basis of physical-chemical association with a mineral phase rather than on the specific gene products of a particular cell. In the present discussion emphasis is directed at a group of divalent cation binding proteins isolated from the mineral compartment of bone. The localization, synthesis, and chemical characteristics of osteonectin, bone sialoproteins I and II, and bone acidic glycoprotein-75 are discussed and offered as possible sites for perturbation by the environment with lead exposure.

Amino Acid Sequence↗

PubMed2005

Formulation and characterization of an experimental PCB mixture designed to mimic human exposure from contaminated fish.

Each environmental exposure matrix contains a unique mixture of PCB congeners. Since several congener types have multiple and distinct biological actions, it is important to characterize congener profiles in exposure sources. The Fox River Environment and Diet Study (FRIENDS) is assessing the human health effects of consumption of PCB-contaminated fish from the Fox River in northeastern Wisconsin. Concurrent laboratory studies required the formulation of a dosing solution which closely mimicked the human PCB exposure from fish. PCB congener profiles from Fox River walleye were compared to profiles for various theoretical mixtures having different relative percentages of Aroclors by weight. The theoretical mixture which provided the best approximation of the Fox River fish PCB profile contained 35% 1242, 35% 1248, 15% 1254, and 15% 1260. A PCB mixture was formulated to match this theoretical construct, and the congener profile for the mixture of Aroclors was determined by capillary column gas chromatography with electron capture detection (GC/ECD). The relative percent of each congener was compared to the PCB congener profile of the theoretical Aroclor mixture and that for Fox River walleye. The specific congeners differed on average by 17% from the theoretical Aroclor mixture predicted values, and the specific congeners measured in the mixture were on average within 71% of those reported for Fox River fish. The mixture was found to have relatively low AhR activity but high RyR activity. Indirect comparisons suggest that in vivo toxicity was slightly greater than that for Aroclor 1254. This illustrates that Aroclor mixtures are useful for formulating dosing solutions which closely approximate actual environmental exposures.

Animals↗

PubMed1998

Excessive synthesis of matrix metalloproteinases in exocrine tissues of NOD mouse models for Sjögren's syndrome.

OBJECTIVE: Matrix metalloproteinases (MMP) and their substrates, components of the extracellular matrix, regulate environmental signals for cellular differentiation and tissue function. Changes in the levels of these enzymes may influence cell survival as well as pathology involving ectopic apoptosis. Using the non-obese diabetic (NOD) mouse model for Sjögren's syndrome, we evaluated the synthesis and expression of MMP in the exocrine target tissues of autoimmunity. METHODS: NOD, immunodeficient NOD-scid, and nondiabetic NOD.B10.H2b mice were evaluated for MMP activity in their saliva and exocrine gland lysates by gelatin zymography and reverse transcriptase-polymerase chain reaction (RT-PCR). In addition, changes in protein content of saliva and gland lysates were determined by specific Western blot and by enzymatic activity of amylase and cysteine proteases. Mice continuously treated with the MMP inhibitor GM6001 were evaluated from 7 to 20 weeks of age for the contribution of MMP activity to development of these hallmark biochemical markers of Sjogren's syndrome-like disease of NOD mice. RESULTS: Gelatin zymography of whole saliva and gland lysates indicated the presence of increased proteolytic activity, corresponding to proteins with a molecular mass ranging from 50 to 95 kDa, in the saliva of older (> 20 weeks of age) NOD mice as well as NOD.B10.H2b and NOD-scid mice compared to BALB/c controls. Elevated steady state levels of mRNA transcripts for the gelatinases MMP-2 and MMP-9 were detected in total RNA extracted from parotid and submandibular glands by RT-PCR. Despite prophylactic injection of the broad spectrum MMP inhibitor GM6001 into mice beginning at 7 weeks of age and continuing to 20 weeks, development of the autoimmune exocrinopathy was neither stopped nor retarded. CONCLUSION: These observations suggest that excessive MMP activity is associated with autoimmune Sjögren's syndrome-like disease in NOD mice. However, a possible contribution by increased MMP activity in initiation and progression of this autoimmune disease is yet to be elucidated.

Animals↗

PubMed2006

Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR-1 in a novel high-throughput mini-bioreactor.

The growth and Cr(VI) reduction by Shewanella oneidensis MR-1 was examined using a mini-bioreactor system that independently monitors and controls pH, dissolved oxygen (DO), and temperature for each of its 24, 10-mL reactors. Independent monitoring and control of each reactor in the cassette allows the exploration of a matrix of environmental conditions known to influence S. oneidensis chromium reduction. S. oneidensis MR-1 grew in minimal medium without amino acid or vitamin supplementation under aerobic conditions but required serine and glycine supplementation under anaerobic conditions. Growth was inhibited by DO concentrations >80%. Lactate transformation to acetate was enhanced by low concentration of DO during the logarithmic growth phase. Between 11 and 35 degrees C, the growth rate obeyed the Arrhenius reaction rate-temperature relationship, with a maximum growth rate occurring at 35 degrees C. S. oneidensis MR-1 was able to grow over a wide range of pH (6-9). At neutral pH and temperatures ranging from 30 to 35 degrees C, S. oneidensis MR-1 reduced 100 microM Cr(VI) to Cr(III) within 20 min in the exponential growth phase, and the growth rate was not affected by the addition of chromate; it reduced chromate even faster at temperatures between 35 and 39 degrees C. At low temperatures (<25 degrees C), acidic (pH < 6.5), or alkaline (pH > 8.5) conditions, 100 microM Cr(VI) strongly inhibited growth and chromate reduction. The mini-bioreactor system enabled the rapid determination of these parameters reproducibly and easily by performing very few experiments. Besides its use for examining parameters of interest to environmental remediation, the device will also allow one to quickly assess parameters for optimal production of recombinant proteins or secondary metabolites.

Biodegradation, Environmental↗

PubMed2001

Development of a reference material for routine performance monitoring of methods measuring polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and dioxin-like polychlorinated biphenyls.

Matrix-matched environmental certified reference materials (CRMs) are one of the most useful tools to validate analytical methods, assess analytical laboratory performance and to assist in the resolution of data conflicts between laboratories. This paper describes the development of a lake sediment as a CRM for polychorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (DLPCBs). The presence of DLPCBs in the environment is of increased concern and analytical methods are being developed internationally for monitoring DLPCBs in the environment. This paper also reports the results of an international interlaboratory study involving thirty-five laboratories from seventeen countries, conducted to characterize and validate levels of a sediment reference material for PCDDs, PCDFs and DLPCBs.

Benzofurans↗

PubMed2006

Leaching behaviour of low level organic pollutants contained in cement-based materials: experimental methodology and modelling approach.

The aim of this paper is the investigation of the leaching behaviour of different porous materials containing organic pollutants (PAH: naphthalene and phenanthrene). The assessment methodology of long term leaching behaviour of inorganic materials was extended to cement solidified organic pollutants. Based on a scenario-approach considering environmental factors, matrix and pollutants specificities, the applied methodology is composed of adapted equilibrium and dynamic leaching tests. The contributions of different physical and chemical mechanisms were identified and the leaching behaviour was modelled. The physical parameters of the analysed reference and polluted materials are similar. A difference in the pore size distribution appears for higher naphthalene content. The solubility of the PAH contained in the material is affected by the ionic strength and by the presence of a co-solvent; the solution pH does not influence PAH solubility. The solubility of the major mineral species is not influenced by the presence of the two PAH nor by the presence of the methanol as co-solvent in the range of the tested material compositions. In the case of the leaching of a monolith material the main transport mechanism is the diffusion in the porous system. For both mineral and organic species we observed at least two dynamic domains. At the beginning of the leaching process the released flux is due to the surface dissolution and to the diffusion of the main quantity dissolved in the initial pore solution. The second period is governed by a stationary regime between dissolution in pore water and diffusion. The model, coupling transport and chemical phenomena in the pore solution, at the monolith surface and in the leachate simulates satisfactory the release for both mineral and organic species.

Adsorption↗

PubMed2003

Evolution of antibiotic occurrence in a river through pristine, urban and agricultural landscapes.

A river along the semi-arid Front Range of Colorado was monitored for antibiotics including five tetracycline and six sulfonamide compounds. Existing analytical methods were adapted to measure these compounds in a surface water matrix at environmentally relevant concentrations (0.05 microg/L). Natural organic matter present in surface waters was confirmed to significantly impact the low-level analysis of tetracyclines (TCs) necessitating the use of standard addition quantification techniques. Five sites along the Cache la Poudre River were monitored for antibiotics encompassing pristine areas without anthropogenic influence, urban areas impacted by wastewater discharges and agricultural areas susceptible to non-point source contaminant runoff. The only site at which no antibiotics were detected was the pristine site in the mountains before the river had encountered urban or agricultural landscapes. By the time the river had exited the urban area, 6 of the 11 antibiotic compounds that were monitored were found in the samples. At Site 5, which had both urban and agricultural influences all five of the TCs monitored were detected indicating both urban and agricultural influences. The concentration of TCs at Site 5 ranged from 0.08 to 0.30 microg/L.

Agriculture↗

PubMed2001

Preconcentration and preseparation procedure for platinum determination at trace levels by neutron activation analysis.

A procedure that simultaneously allows both preconcentration and preseparation of platinum for its determination by neutron activation analysis at trace levels (<0.1 microg x g(-1)) in environmental related matrixes is developed. The method is mainly based on a two-step chemical procedure: (i) a preirradiation concentration/separation based on a column chromatography separation where the platinum is previously retained and subsequently separated from Au, Ca, Na, Br, and P; (ii) a postirradiation separation/purification of the 199Au at 158.4 keV used for the platinum determination via [198Pt (n,gamma)-->199Pt (beta-)-->199Au]. The method eliminates the following radionuclides with the gamma lines in the region of 158 keV: 47Sc (daughter of Ca) at 159.3 keV; 199Au (produced by double neutron capture onto the natural 197Au) at 158.4 keV; 123m Te at 158.8 keV. In addition, the background activity deriving from 24Na, 32p, and 82Br is drastically reduced. The method was tested by the analysis of certified rock material and then applied for platinum determination in airborne particulate matter.

Journal Article↗