Health-related monitoring and assessment of airborne particulate matter

Since 1992, the International Atomic Energy Agency (IAEA) has been promoting studies of air pollution using a standard design of air sampler that provides separation on filters into two size fractions with cutoffs of 2.5 and 10 Μm (approximately). These are the size ranges presently considered to have the most important health consequences. Such filter samples are highly amenable to analysis using nuclear and related techniques. After reviewing some of the health effects of airborne particulate matter and current air quality standards and guidelines, this article provides an overview of current and recent IAEA programs in this area, which involve collaborative activities with participants in more than 40 countries.     

Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation

The genetic consequences of small population size and isolation are of central concern in both population and conservation biology. Organisms with a metapopulation structure generally show effective population sizes that are much smaller than the number of mature individuals and this can reduce genetic diversity especially in small sized and isolated subpopulations. Here, we examine the association between heterozygosity and the size and spatial isolation of natal colonies in a metapopulation of lesser kestrels (Falco naumanni). For this purpose, we used capture-mark-recapture data to determine the patterns of immigration into the studied colonies, and 11 highly polymorphic microsatellite markers that allowed us to estimate genetic diversity of locally born individuals. We found that individuals born in smaller and more isolated colonies were genetically less diverse. These colonies received a lower number of immigrants, supporting the idea that both reduced gene flow and small population size are responsible for the genetic pattern observed. Our results are particularly intriguing because the lesser kestrel is a vagile and migratory species with great movement capacity and dispersal potential. Overall, this study provides evidence of the association between individual heterozygosity and the size and spatial isolation of natal colonies in a highly mobile vertebrate showing relatively frequent dispersal and low genetic differentiation among local subpopulations.     

Real-time detection of virus particles and viral protein expression with two-color nanoparticle probes

Respiratory syncytial virus (RSV) mediates serious lower respiratory tract illness in infants and young children and is a significant pathogen of the elderly and immune compromised. Rapid and sensitive RSV diagnosis is important to infection control and efforts to develop antiviral drugs. Current RSV detection methods are limited by sensitivity and/or time required for detection. In this study, we show that antibody-conjugated nanoparticles rapidly and sensitively detect RSV and estimate relative levels of surface protein expression. A major development is use of dual-color quantum dots or fluorescence energy transfer nanobeads that can be simultaneously excited with a single light source.     

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models

SUMMARY: The survcomp package provides functions to assess and statistically compare the performance of survival/risk prediction models. It implements state-of-the-art statistics to (i) measure the performance of risk prediction models; (ii) combine these statistical estimates from multiple datasets using a meta-analytical framework; and (iii) statistically compare the performance of competitive models.     

Comparison of three vegetation monitoring methods: Their relative utility for ecological assessment and monitoring

Vegetation cover and composition are two indicators commonly used to monitor terrestrial ecosystems. These indicators are currently quantified with a number of different methods. The interchangeability and relative benefits of different methods have been widely discussed in the literature, but there are few published comparisons that address multiple criteria across a broad range of grass- and shrub-dominated communities, while keeping sampling effort (time) approximately constant. This study compared the utility of three field sampling methods for ecological assessment and monitoring: line-point intercept, grid-point intercept, and ocular estimates. The criteria used include: (1) interchangeability of data, (2) precision, (3) cost, and (4) value of each method based on its potential to generate multiple indicators. Foliar cover by species was measured for each method in five plant communities in the Chihuahuan Desert. Line- and grid-point intercept provide similar estimates of species richness which were lower than those based on ocular estimates. There were no differences in the precision of the number of species detected. Estimates of foliar cover with line- and grid-point intercept were similar and significantly higher than those based on ocular estimates. Precision of cover estimates with line-point intercept was higher than for ocular estimates. Time requirements for the three methods were similar, despite the fact that the point-based methods included cover estimates for all canopy layers and the soil surface, while the ocular estimates included only the top canopy layer. Results suggest that point-based methods provide interchangeable data with higher precision than ocular estimates. Moreover these methods can be used to generate a much greater number of indicators that are more directly applicable to a variety of monitoring objectives, including soil erosion and wildlife habitat.     

Identification of candidate predictive and surrogate molecular markers for dasatinib in prostate cancer: rationale for patient selection and efficacy monitoring

Background  

Dasatinib is a potent, multi-targeted kinase inhibitor that was recently approved for treatment of chronic myelogenous leukemia resistant to imatinib. To aid the clinical development of dasatinib in prostate cancer, we utilized preclinical models to identify potential molecular markers for patient stratification and efficacy monitoring.     

Application of Salmonella strains with altered nitroreductase and O-acetyltransferase activities to the evaluation of the mutagenicity of airborne particles

The Ames test was applied to evaluation of the mutagenicity of month's samples of airborne particles from the center of Wroc?aw (SW Poland) collected in August and December 1997. The strains used for the study were TA 98, TA 100 and their derivatives: TA 98 NR, YG 1021, YG 1024, YG 1026, YG 1029, YG 1041, YG 1042. Both studied samples were mutagenic for almost all tested strains, with the exception of the August sample which did not influence the strain TA 100 without the metabolic activation with the S9 fraction. The December sample exhibited higher genotoxic activity than the August sample. Mutagenicity ratios of the strains with reduced nitroreductase and O-acetyltransferase activities were higher, and of the strain without the nitroreductase--lower than those of the parent strains. This indicates that nitro and amino derivatives of PAHs are responsible for the significant proportion of total mutagenicity of the studied samples of particulates. Metabolic activation with the S9 fraction caused the increase of the mutagenic activity of the samples, which indicates the presence of promutagens. The GC-MS analysis revealed the presence of known indirect mutagens from the PAHs group.     

Real-time dissolved carbon dioxide monitoring I: Application of a novel in situ sensor for CO2 monitoring and control

Dissolved carbon dioxide (dCO₂) is a well-known critical parameter in bioprocesses due to its significant impact on cell metabolism and on product quality attributes. Processes run at small-scale faces many challenges due to limited options for modular sensors for online monitoring and control. Traditional sensors are bulky, costly, and invasive in nature and do not fit in small-scale systems. In this study, we present the implementation of a novel, rate-based technique for real-time monitoring of dCO₂ in bioprocesses. A silicone sampling probe that allows the diffusion of CO₂ through its wall was inserted inside a shake flask/bioreactor and then flushed with air to remove the CO₂ that had diffused into the probe from the culture broth (sensor was calibrated using air as zero-point calibration). The gas inside the probe was then allowed to recirculate through gas-impermeable tubing to a CO₂ monitor. We have shown that by measuring the initial diffusion rate of CO₂ into the sampling probe we were able to determine the partial pressure of the dCO₂ in the culture. This technique can be readily automated, and measurements can be made in minutes. Demonstration experiments conducted with baker's yeast and Yarrowia lipolytica yeast cells in both shake flasks and mini bioreactors showed that it can monitor dCO₂ in real-time. Using the proposed sensor, we successfully implemented a dCO₂-based control scheme, which resulted in significant improvement in process performance.     

城市生态环境损害鉴定评估监测体系研究

我国城市生态环境损害事件频发,不但造成大气、地表水、地下水、土壤等环境质量下降,也造成城市生态系统结构和功能的退化,推进生态环境损害赔偿制度势在必行。由于城市生态系统的复杂性和特殊性,确认环境损害行为、说清因果关系、判定损害程度和计算赔偿金额等环节难度均比较大,开展城市生态环境损害鉴定评估技术研究迫在眉睫。根据城市地理学和城市生态学相关理论,在分析城市生态环境损害概念和特征基础上,从城市生态系统完整性角度出发,结合实例构建了一套测度城市生态系统损害状态监测的样方体系,通过形成城市生态环境整体水平评估框架为综合判定城市生态环境基线奠定基础;进一步提出充分利用既有生态观测样方、环境监测站点和社会公众参与式数据共享策略,以提高现场勘察效率、降低鉴定评估成本和提高评估结果质量的方法。研究所形成的样方体系、监测策略和方法对我国城市生态环境损害鉴定评估工作业务化具有指导意义。     

Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems

Antibiotic application in plant agriculture is primarily used to control fire blight caused by Erwinia amylovora in pome fruit orchards. In order to facilitate environmental impact assessment for antibiotic applications, we developed and validated culture-independent quantitative real-time PCR multiplex assays for streptomycin (strA, strB, aadA and insertion sequence IS1133) and tetracycline (tetB, tetM and tetW) resistance elements in plant and soil samples. The qPCR were reproducible and consistent whether the DNA was extracted directly from bacteria, plant and soil samples inoculated with bacteria or soil samples prior to and after manure slurry treatment. The genes most frequently identified in soils pre- and post-slurry treatment were strB, aadA, tetB and tetM. All genes tested were detected in soils pre-slurry treatment, and a decrease in relative concentrations of tetB and the streptomycin resistance genes was observed in samples taken post-slurry treatment. These multiplex qPCR assays offer a cost-effective, reliable method for simultaneous quantification of antibiotic resistance genes in complex, environmental sample matrices.     

Depression of mitochondrial respiration during daily torpor of the Djungarian hamster,Phodopus sungorus,is specific for liver and correlates with body temperature

Small mammals actively decrease metabolism during daily torpor and hibernation to save energy. Increasing evidence suggests depression of mitochondrial respiration during daily torpor of the Djungarian hamster but tissue-specificity and relation to torpor depth is unknown. We first confirmed a previous study by Brown and colleagues reporting on the depressed substrate oxidation in isolated liver mitochondria of the Djungarian hamster (Phodopus sungorus) during daily torpor. Next, we show that mitochondrial respiration is not depressed in kidneys, skeletal muscle and heart. In liver mitochondria, we found that state 3 and state 4 respirations correlate with body temperature, suggesting inhibition related to torpor depth and to metabolic rate. We conclude that molecular events leading to depression of mitochondrial respiration during daily torpor are specific to liver and linked to a decrease in body temperature. Different tissue-specificity of mitochondrial depression may assist to compare and identify the molecular nature of mitochondrial alterations during torpor.     

Application of flow cytometry and fluorescent in situ hybridization for assessment of exposures to airborne bacteria.

Current limitations in the methodology for enumeration and identification of airborne bacteria compromise the precision and accuracy of bioaerosol exposure assessment. In this study, flow cytometry and fluorescent in situ hybridization (FISH) were evaluated for the assessment of exposures to airborne bacteria. Laboratory-generated two-component bioaerosols in exposures chambers and complex native bioaerosols in swine barns were sampled with two types of liquid impingers (all-glass impinger-30 and May 3-stage impinger). Aliquots of collection media were processed and enumerated by a standard culture technique, microscopy, or flow cytometry after nucleic acid staining with 4',6-diamidino-2-phenylindole (DAPI) and identified taxonomically by FISH. DAPI-labeled impinger samples yielded comparable estimates of bioaerosol concentrations when enumerated by microscopy or flow cytometry. The standard culture method underestimated bioaerosol concentrations by 2 orders of magnitude when compared to microscopy or flow cytometry. In the FISH method, aliquots of collection media were incubated with a probe universally complementary to eubacteria, a probe specific for several Pseudomonas species, and a probe complementary to eubacteria for detection of nonspecific binding. With these probes, FISH allowed quantitative identification of Pseudomonas aeruginosa and Escherichia coli bioaerosols in the exposure chamber without measurable nonspecific binding. Impinger samples from the swine barn demonstrated the efficacy of the FISH method for the identification of eubacteria in a complex organic dust. This work demonstrates the potential of emerging molecular techniques to complement traditional methods of bioaerosol exposure assessment.     

Imaging of chlorophyll a fluorescence: theoretical and practical aspects of an emerging technique for the monitoring of photosynthetic performance

The development of chlorophyll (Chl) a fluorescence imaging systems has greatly increased the versatility of Chl a fluorometry as a non-invasive technique for the investigation of photosynthesis in plants and algae. For example, systems that image at the microscopic level have made it possible to measure PSII photochemical efficiencies from chloroplasts within intact leaves and from individual algal cells within mixed populations, while systems that image over much larger areas have been used to investigate heterogeneous patterns of photosynthetic performance across leaves and in screening programmes that image tens or even hundreds of plants simultaneously. In addition, it is now practical to use fluorescence imaging systems as real-time, multi-channel fluorometers, which can be used to record continuous fluorescence traces from multiple leaves, plants, or algal cells. This paper discusses some of the theoretical and practical issues associated with the imaging of Chl a fluorescence and with Chl a fluorometry in general. This discussion includes a review of the most commonly used Chl a fluorescence parameters.     

Sensitivity of different endpoints for in vitro measurement of genotoxicity of extractable organic matter associated with ambient airborne particles (PM10)

Sensitivity and correlations among three endpoints were evaluated to assess the genotoxic potential of organic complex mixtures in vitro. This study was focused on DNA adduct formation, DNA single strand break induction and tumour suppressor p53 protein up-regulation produced by extractable organic matter (EOM) absorbed on respirable particulate matter PM₁₀ (particulate matter < 10 μm) collected in three European cities (Prague, Sofia, Košice) during winter and summer period. To compare the sensitivity of particular endpoints for in vitro measurement of complex mixture genotoxicity, the metabolically competent human hepatoma cell line Hep G2 was treated with equivalent EOM concentration of 50 μg/ml. Cell exposure to EOMs resulted in significant DNA adduct formation and DNA strand break induction, however, a lack of protein p53 up-regulation over the steady-state level was found. While the maximum of DNA strand breaks was determined after 2 h cell exposure to EOMs, 24 h treatment interval was optimal for DNA adduct determination.

No substantial location- and season-related differences in EOM genotoxicity were detected using DNA strand break assessment. In agreement with these results no significant variation in DNA adduct levels were found in relation to the locality and season except for the monitoring site in Prague. The Prague EOM sample collected during summer period produced nearly three-fold lower DNA adduct level in comparison to the winter EOM sample.

Comparable results were obtained when the ambient air genotoxicity, based on the concentration of carcinogenic PAHs in cubic meter of air (ng c-PAHs/m³), was elicited using either DNA adduct or strand break determination. In general, at least six-fold higher genotoxicity of the winter air in comparison to the summer air was estimated by each particular endpoint. Moreover, the genotoxic potential of winter air revealed by DNA adduct assessment and DNA strand break measurement increased in the same order: Košice  Prague < Sofia.

Based on these data we suppose that two endpoints DNA breakage and DNA adduction are sensitive in vitro biomarkers for estimation of genotoxic activity of organic complex mixture associated with airborne particles. On the other hand, the measurement of protein p53 up-regulation manifested some limitations; therefore it cannot be used as a reliable endpoint for in vitro genotoxicity assessment.     

Construction and performance of plug-in membrane inlet mass spectrometer for fermentor monitoring

An in situ sterilizable plug-in membrane inlet mass spectrometer for monitoring dissolved gases and volatiles in fermentors was constructed and tested. The design ensured a minimal distance to be traveled by analyte molecules from the bulk of the fermentation broth to the ionization chamber of the mass spectrometer. Apart from the specific cross talk due to overlapping mass peaks from different compounds, we found that carbon dioxide interfered unspecifically with all the mass peaks of other substances, changing them by the same factor. The interference changed slowly with time and could be positive or negative depending on the history of the mass spectrometer. Also, the general sensitivity of the instrument changed slowly with time. These effects can be neglected or corrected for empirically in short-term measurements. When the fermentor was aerated with a three-component gas mixture including carbon dioxide, a rapid change in the partial pressure of carbon dioxide in the gas mixture gave rise to a transient in the signal of a gas whose partial pressure was kept constant. This effect revealed a transient change in the composition of the gas mixture in the bubbles caused by net import or export of carbon dioxide during equilibration with the new gas mixture. An experimental method to determine the effective partial pressures of gases in the bubbles during steady-state transport of carbon dioxide was designed. The plug-in membrane inlet mass spectrometer was tried as a probe for oxygen and ethanol in an oxystatic culture of the yeast Pichia stipitis. We found that it was possible to keep a steady-state concentration of as little as 0.5 muM throughout the lifetime of the culture. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 535-542, 1997.     

A portable sampler (PARTRAP FA 52) for microbiological evaluation of airborne particles: comparison with standard sedimetric and volumetric methods in haemodialysis rooms

Experiments for microbiological evaluation of airborne particles were led in two haemodialysis rooms at the beginning and at the end of activity time (6 h). The efficiency of a new personal and portable aerobiological sampler in comparison with a fixed sampler and a traditional sedimetric method was evaluate. The personal and portable sampler allowed a good evaluation of concentration of bacteria and fungi per cubic metres of sampled air. Since its aspiration flow is equal to Minute Ventilation of an adult; this device provides a quantification of inhaled particles. We propose this device for evaluating the risk for patients and sanitary operators, for monitoring air quality and in implementing adequate environmental prophylaxis and for other applications, e.g. environmental applications.     

Establishment of specific pathogen-free guinea-pig colonies using limited-flora guinea-pigs associated with conventional guinea-pig flora, and monitoring of their cecal flora.

Six groups of limited flora (LF) Hartley guinea-pigs were produced by inoculation of hysterectomy-derived GF guinea-pigs with various combinations of cecal bacteria of conventional (CV) guinea-pigs to determine the effective bacterial cocktails for the establishment of a specific pathogen free (SPF) colony. Bifidobacterium magnum (Bif) isolated from CV guinea-pigs was used for pretreatment. The mortality of LF guinea-pigs inoculated with only Bif was 75%, and that of those inoculated with Bif plus chloroform-treated cecal suspension (CHF) or Bif plus CHF plus 32 isolates from CV guinea-pigs was 40 to 66.7%. These three groups were in an unhealthy condition with mucoid enteritis-like diarrhea. However, the mortality of LF guinea-pigs inoculated with the anaerobic growth on EG plates injected with 10(-5) dilution of cecal contents (CF) or inoculated with Bif plus CF was 6.3 and 15%, respectively. These latter two groups of LF guinea-pigs were transferred to separate barrier rooms and some of the LF guinea-pigs were maintained in isolators as a source of intestinal flora for SPF guinea-pigs. The composition of cecal flora of LF guinea-pigs was stable for a long time, and bacteroidaceae and peptococcaceae were maintained as predominant components. The basic composition of the cecal flora of SPF guinea-pigs originated from LF guinea-pigs, which consists mainly of the anaerobic bacteria, was not changed over a long period, and the flora composition became similar to that in CV guinea-pigs. Guinea-pig-specific pathogens from the SPF colonies were not detected during experiments.     

Reliable gene signatures for microarray classification: assessment of stability and performance

MOTIVATION: Two important questions for the analysis of gene expression measurements from different sample classes are (1) how to classify samples and (2) how to identify meaningful gene signatures (ranked gene lists) exhibiting the differences between classes and sample subsets. Solutions to both questions have immediate biological and biomedical applications. To achieve optimal classification performance, a suitable combination of classifier and gene selection method needs to be specifically selected for a given dataset. The selected gene signatures can be unstable and the resulting classification accuracy unreliable, particularly when considering different subsets of samples. Both unstable gene signatures and overestimated classification accuracy can impair biological conclusions. METHODS: We address these two issues by repeatedly evaluating the classification performance of all models, i.e. pairwise combinations of various gene selection and classification methods, for random subsets of arrays (sampling). A model score is used to select the most appropriate model for the given dataset. Consensus gene signatures are constructed by extracting those genes frequently selected over many samplings. Sampling additionally permits measurement of the stability of the classification performance for each model, which serves as a measure of model reliability. RESULTS: We analyzed a large gene expression dataset with 78 measurements of four different cartilage sample classes. Classifiers trained on subsets of measurements frequently produce models with highly variable performance. Our approach provides reliable classification performance estimates via sampling. In addition to reliable classification performance, we determined stable consensus signatures (i.e. gene lists) for sample classes. Manual literature screening showed that these genes are highly relevant to our gene expression experiment with osteoarthritic cartilage. We compared our approach to others based on a publicly available dataset on breast cancer. AVAILABILITY: R package at http://www.bio.ifi.lmu.de/~davis/edaprakt