Bioavailability of Soil-Borne Chemicals: Method Development and Validation

Chemicals present in contaminated soils generally exhibit altered bioavailability compared to other vehicles used in studies of chemical toxicity. Methods used to assess the bioavailability of soil-borne chemicals have generally been modified versions of methods that are widely used in biomedical research. Oral and dermal bioavailability of semivolatile organic chemicals and metals in soil has been assessed by a variety of in vivo and in vitro methods. Due to variations in metabolism and excretion of different chemicals, approaches to measuring bioavailability must be selected with an understanding of disposition of the chemical being studied. Standard methods need to be modified due to constraints associated with doses relevant to environmental concentrations, the need to reflect weathering behavior in soils over time, and the need to generate data applicable to human health risk assessments. Estimates of relative bioavailability for chemicals in soil can be used directly to modify exposure estimates. Application of bioavailability data in a site-specific risk assessment requires regulatory acceptance of the data. Acceptance of the data will generally be dependent on either the use of a validated test method or a careful scientific review of the test method employed. A process for validating newly developed alternative toxicity methods for routine use developed by the Interagency Coordinating Committee on the Validation of Alternative Methods provides relevant guidance for assessing in vitro methods, but method validation should not be the only litmus test for inclusion of bioavailability data in risk assessments.     

International Society for Analytical Cytology biosafety standard for sorting of unfixed cells.

BACKGROUND: Cell sorting of viable biological specimens has become very prevalent in laboratories involved in basic and clinical research. As these samples can contain infectious agents, precautions to protect instrument operators and the environment from hazards arising from the use of sorters are paramount. To this end the International Society of Analytical Cytology (ISAC) took a lead in establishing biosafety guidelines for sorting of unfixed cells (Schmid et al., Cytometry 1997;28:99-117). During the time period these recommendations have been available, they have become recognized worldwide as the standard practices and safety precautions for laboratories performing viable cell sorting experiments. However, the field of cytometry has progressed since 1997, and the document requires an update. METHODS: Initially, suggestions about the document format and content were discussed among members of the ISAC Biosafety Committee and were incorporated into a draft version that was sent to all committee members for review. Comments were collected, carefully considered, and incorporated as appropriate into a draft document that was posted on the ISAC web site to invite comments from the flow cytometry community at large. The revised document was then submitted to ISAC Council for review. Simultaneously, further comments were sought from newly-appointed ISAC Biosafety committee members. RESULTS: This safety standard for performing viable cell sorting experiments was recently generated. The document contains background information on the biohazard potential of sorting and the hazard classification of infectious agents as well as recommendations on (1) sample handling, (2) operator training and personal protection, (3) laboratory design, (4) cell sorter set-up, maintenance, and decontamination, and (5) testing the instrument for the efficiency of aerosol containment. CONCLUSIONS: This standard constitutes an updated and expanded revision of the 1997 biosafety guideline document. It is intended to provide laboratories involved in cell sorting with safety practices that take into account the enhanced hazard potential of high-speed sorting. Most importantly, it states that droplet-based sorting of infectious or hazardous biological material requires a higher level of containment than the one recommended for the risk group classification of the pathogen. The document also provides information on safety features of novel instrumentation, new options for personal protective equipment, and recently developed methods for testing the efficiency of aerosol containment.     

Beyond F<Subscript>ST</Subscript>: Analysis of population genetic data for conservation

Both the ability to generate DNA data and the variety of analytical methods for conservation genetics are expanding at an ever-increasing pace. Analytical approaches are now possible that were unthinkable even five years ago due to limitations in computational power or the availability of DNA data, and this has vastly expanded the accuracy and types of information that may be gained from population genetic data. Here we provide a guide to recently developed methods for population genetic analysis, including identification of population structure, quantification of gene flow, and inference of demographic history. We cover both allele-frequency and sequence-based approaches, with a special focus on methods relevant to conservation genetic applications. Although classical population genetic approaches such as F _st (and its derivatives) have carried the field thus far, newer, more powerful, methods can infer much more from the data, rely on fewer assumptions, and are appropriate for conservation genetic management when precise estimates are needed.     

CONDUCTING PHYLOGENETIC COMPARATIVE STUDIES WHEN THE PHYLOGENY IS NOT KNOWN

A method is proposed to conduct phylogenetic analyses of comparative or interspecific data when the true phylogeny is not known. Standard models of speciation and/or extinction or other methods are used to generate a sample from the set of all possible phylogenies for the measured species. The comparative data are then analyzed on each of the possible trees to obtain a distribution of possible evolutionary statistics for these data. The mean of this distribution is proposed as a reasonable estimate of the true evolutionary statistic of interest. Ways of obtaining confidence intervals and of developing hypothesis tests for this mean statistic are also proposed. The method can be used with any comparative method or phylogenetic analysis technique when phylogenetic relationships among species are not known or when branch lengths for a phylogeny in units of expected character change (as required by most methods) are not available. Computer programs to conduct the analyses are available on request.     

Variable selection and multivariate methods for the identification of microorganisms by flow cytometry.

BACKGROUND: When exploited fully, flow cytometry can be used to provide multiparametric data for each cell in the sample of interest. While this makes flow cytometry a powerful technique for discriminating between different cell types, the data can be difficult to interpret. Traditionally, dual-parameter plots are used to visualize flow cytometric data, and for a data set consisting of seven parameters, one should examine 21 of these plots. A more efficient method is to reduce the dimensionality of the data (e.g., using unsupervised methods such as principal components analysis) so that fewer graphs need to be examined, or to use supervised multivariate data analysis methods to give a prediction of the identity of the analyzed particles. MATERIALS AND METHODS: We collected multiparametric data sets for microbiological samples stained with six cocktails of fluorescent stains. Multivariate data analysis methods were explored as a means of microbial detection and identification. RESULTS: We show that while all cocktails and all methods gave good accuracy of predictions (>94%), careful selection of both the stains and the analysis method could improve this figure (to > 99% accuracy), even in a data set that was not used in the formation of the supervised multivariate calibration model. CONCLUSIONS: Flow cytometry provides a rapid method of obtaining multiparametric data for distinguishing between microorganisms. Multivariate data analysis methods have an important role to play in extracting the information from the data obtained. Artificial neural networks proved to be the most suitable method of data analysis.     

Evaluation of the saccharide content and stability of the first WHO International Standard for Haemophilus influenzae b capsular polysaccharide

Haemophilus influenzae b conjugate vaccines (Hib) are almost entirely evaluated by physico-chemical methods to ensure the consistency of manufacture of batches. As different assays are employed for the quantification of Hib capsular polysaccharide PRP (polyribosyl ribitol phosphate; 5-D-ribitol-(1-->1)-beta-D-ribose-3-phosphate) in final formulations and bulk components, there was deemed a need for an International Standard of Hib PRP polysaccharide to be made available. Ten laboratories from 8 different countries participated in a collaborative study to determine the PRP content and assess the suitability of a candidate International Standard PRP preparation (02/208). The results illustrate that a reduction in between-laboratory variability could be achieved by use of a common reference preparation and data analysis showed no significant differences in the values obtained by the different assays: ribose, phosphorus, and high performance anion exchange chromatography-pulsed amperometric detection (HPAEC-PAD), suggesting the suitability of the proposed reference for use across these assays for quantification of PRP content in Hib vaccines. On the basis of the results of this study, the First International Standard for PRP, NIBSC Code 02/208, has been established by the Expert Committee of Biological Standards of the World Health Organisation, with a content of 4.933+/-0.267mg/ampoule, as determined by the ribose assays carried out by 7 of the participating laboratories.     

Proposed standard for human blood vitamin B1 value using HPLC. The Committee for Vitamin Laboratory Standards, Japan

Standard reference ranges for all laboratory test values are mandatory. This study was designed to establish a reference range for blood vitamin B1 levels, since the normal range has not been determined in the Japanese population. We founded the Japan Committee for Vitamin Laboratory Standards, which was incorporated with the Vitamin Society of Japan and the Japanese Society of Nutrition and Food Science. We standardized whole blood vitamin B1 levels using three HPLC techniques (post-column reverse-phase HPLC, pre-column reverse-phase HPLC, and precolumn GP-HPLC). The reference range was obtained in 54 volunteers administered a 1,800 kcal diet with 2 mg of vitamin B1 (1.74 mg measured) daily to avoid marginal vitamin B1 deficiency in the population. The range for each assay was 26-47, 28-51, and 28-56 ng/ml, respectively. Our data suggest that 26-28 ng/ml is the lower limit of normal for whole blood vitamin B1, but further studies in a larger population are needed in order to obtain more definitive results.     

RAPID DETECTION of STAPHYLOCOCCUS AUREUS IN FOOD BY FLOW CYTOMETRY

This report describes the detection of Staphylococcus aureus in buffer and in several kinds of food by flow cytometry. Fluorescein isothiocyanate conjugated anti-protein A antibodies were used in a 4-h procedure to label cells, 10⁵-10⁶ cells/mL are needed. the use of single parameter, green fluorescence, enabled specific differentiation of S. aureus from other bacteria including 11 Staphylococcus species. the flow cytometric method can detect S. aureus in food samples after 48-h enrichment in trypticase soy broth with 10% NaCl. As low as 2 S. aureus cells present in 10 mL enrichment broth could grow to a population density detectable by the flow cytometric method after enrichment. This method was faster and less laborious than the conventional BAM (Bacteriological Analytical Manual) or AOAC (Association of Official Analytical Chemists) methods, and could be automated for analysis of S. aureus in food.     

Advances in on-line monitoring and control of mammalian cell cultures: Supporting the PAT initiative

In recent years, much attention has been directed towards the development of global methods for on-line process monitoring, especially since the Food and Drug Administration (FDA) launched the Process Analytical Technology (PAT) guidance, stimulating biopharmaceutical companies to update their monitoring tools to ensure a pre-defined final product quality. The ideal technologies for biopharmaceutical processes should operate in situ, be non-invasive and generate on-line information about multiple key bioprocess and/or metabolic variables. A wide range of spectroscopic techniques based on in situ probes have already been tested in mammalian cell cultures, such as near infrared (NIR), mid infrared (MIR), 2D fluorescence and dielectric capacitance spectroscopy; similarly, the electronic nose technique based on chemical array sensors has been tested for in situ off-gas analysis of mammalian cell cultures. All these methods provide series of spectra, from which meaningful information must be extracted. In this sense, data mining techniques such as principal components regression (PCR), partial least squares (PLS) or artificial neural networks (ANN) have been applied to handle the dense flow of data generated from the real-time process analyzers. Furthermore, the implementation of feedback control methods would help to improve process performance and ultimately ensure reproducibility. This review discusses the suitability of several spectroscopic techniques coupled with chemometric methods for improved monitoring and control of mammalian cell processes.     

Calibration and commutability assessment of the 1st International Standard for Diphtheria Antitoxin Human

The 1st International Standard for Diphtheria Antitoxin Human (coded 10/262) was established by the World Health Organization Expert Committee on Biological Standardization in 2012. This paper describes the production, characterization and calibration of the new standard which is intended for use in the standardization of assays used to measure diphtheria antibody responses in human serum. The new standard was calibrated in terms of the International Standard for Diphtheria Antitoxin Equine in an international collaborative study. A total of 8 participants from 8 different countries performed in vivo and/or in vitro toxin neutralization tests and returned data that was used to assign units to the proposed new standard. The new standard has a diphtheria antitoxin potency of 2 IU/ampoule and is predicted to be stable. A follow up study was performed to assess commutability of the new standard. The follow up study was an existing external quality assessment, modified to include the new standard. Results obtained suggest that the new standard is commutable, showing comparable behaviour to native human serum samples in the majority of the assays compared, and is therefore suitable for use as a reference preparation in assays used to measure the level of anti-diphtheria antibodies in human serum.     

EN CORE® Sampler Performance: Storing Soil for VOC Analysis

The En Core® sampler is designed to collect and store soil samples in a manner that minimizes loss of contaminants due to volatilization and/or biodegradation. Use of this device is described in American Society for Testing and Materials (ASTM) Practice D 6418, Standard Practice for Using the Disposable En Core Sampler for Sampling and Storing Soil for Volatile Organic Analysis. Two studies were performed to evaluate the performance of the En Core sampler to store VOC-contaminated soil for analysis. One study involved spiking soil samples with low concentrations of VOCs (less than 200?µg/kg) and storing them under various conditions prior to analysis. Results from this study show that the En Core sampler gives 80% or greater recoveries of low concentrations of VOCs from soil samples stored under a number of conditions. The second study was performed to generate data on the performance of the 25-g En Core sampler to store soil samples spiked with EPA Method 1311, Toxicity Characteristic Leaching Procedure (TCLP), volatile organic analytes. Results show that the En Core device gives 80% or greater recoveries of most of the Method 1311 volatile organic analytes from soil stored under various conditions for 14 days.     

Nonparametric discriminant analysis of phytoplankton species using data from analytical flow cytometry

BACKGROUND: Analytical flow cytometry (AFC) provides rapid and accurate measurement of particles from heterogeneous populations. AFC has been used to classify and identify phytoplankton species, but most methods of discriminant analysis of resulting data have depended on normality assumptions and outcomes have been disappointing. METHODS AND RESULTS: In this study, we consider nonparametric methods based on density estimation. In addition to the familiar kernel method, methods based on wavelets are also implemented. Full five-dimensional wavelet estimation proves to be computationally prohibitive with current workstation power, so we employ projection pursuit for reduction of dimensionality. AFC typically produces very large samples, so we also investigate data simplification through binning. Further modifications to the discrimination strategy are suggested by specific features of phytoplankton data, namely, a hierarchical group structure, the possible presence of many groups, and the likelihood of encountering an aberrant group in a test sample. CONCLUSIONS: We apply all the resultant procedures to appropriate subsets of a very large data set, demonstrate their efficacy, and compare their error rates with those of more conventional methods. We further show that incorporation of the specific features of phytoplankton data into the analysis leads to improved results and provides a general framework for analysis of such data.     

SED88: a Pascal program for the analysis of sedimentation equilibrium data

Analytical ultracentrifugation is commonly used for the determinationof molecular weights (sedimentation equilibrium) and sedimentationcoefficients (sedimentation rate) of biological macromoleculesin solution. A Turbo Pascal program for the analysis of sedimentationequilibrium centrifugation data produced by absorbance opticalsystems is described. The user may enter data from a scan ofabsorbance versus distance from the centre of rotation, viaa graphics tablet (or ASCII file). This is subsequently manipulatedto yield an apparent weight average molecular weight for thegiven sample. Plots of In (absorbance) versus (radius²) mayalso be produced. The method described uses readily availablecomputational equipment requiring only a graphics tablet inaddition to an IBM PC compatible computer. This technique andthe software developed have been used to investigate the molecularweight range of two International Humic Substances Society (IHSS)reference samples from the Suwannee River. Received on October 7, 1988; accepted on December 12, 1988     

The effect of lubricant contamination on ThinPrep® (Cytyc) cervical cytology liquid-based preparations

Objectives:  To assess the extent of lubricant use by smear-takers and the effect of lubricant contamination of ThinPrep^® processed cervical cytology samples.
Methods:  All primary care smear-takers were sent a questionnaire on lubricant type and frequency of use. Fifty cervical cytology samples were then contaminated with incremental amounts of K-Y^® jelly, 50 samples contaminated with incremental amounts of Aquagel^® and ten non-contaminated vials were processed using the ThinPrep^® T2000 processor followed by Papanicolaou staining. The morphological appearances of lubricant contamination were described microscopically and formal cell counts performed on all slides.
Results:  Seventy of 94 (74.5%) primary care smear-takers indicated lubricant use of whom 9/70 (12.8%) used Aquagel^® and 61/70 (87.2%) used K-Y^® jelly. K-Y^® jelly appeared as mucoid blue deposits in the slide background whereas Aquagel^® appeared as pink stringy background material. Cell counting showed a significant difference between Aquagel^® and K-Y^® jelly contaminated slides compared to the original non-contaminated preparations for all fields and the average fields ( P  < 0.001) with a significantly higher count for the original non-contaminated slides than the lubricant contaminated groups.
Conclusion:  Lubricant contamination of ThinPrep^® cervical cytology samples may result in reduced cellularity of the subsequent slide. This study provides evidence-based data to support British Society for Clinical Cytology recommendations for no lubricant use when taking cervical samples.     

Two green and sensitive spectrofluorimetric approaches for determination of Ambroxol and guaifenesin in their single and combined pharmaceutical formulations

Ambroxol hydrochloride (AMX) and guaifenesin (GFN) are approved drugs utilized to treat coughs through their potent mucolytic and expectorant properties. Due to their massive, combined administration in many illnesses, there is a persistent need for their concurrent estimation in different pharmaceutical formulations. Two sensitive, environmentally friendly spectrofluorimetric methods were developed. AMX was determined using the first method (I) without interference from GFN. This method depends on the quenching of Erythrosine B (EB) native fluorescence at 552 nm after excitation at 527 nm due to the formation of a non-fluorescent AMX-EB ion-pair complex in Britton–Robinson buffer (BRB) solution pH (3.5). The concentration plot is linear over the 0.25–5.0 μg/mL range, with a mean percent found value of 99.74%. Method (II) depends on measuring the native fluorescence of aqueous GFN solution at two analytical wavelengths, either 300 or 600 nm, after excitation at 274 nm. Relative fluorescence intensity (RFI)–concentration plots are linear over the ranges of 0.02–0.5 and 0.1–2.0 μg/ml, with mean percent found at 99.96% and 99.91% at dual wavelengths, respectively. The proposed methods were successfully applied to assay both drugs in raw materials and different single and combined pharmaceutical formulations. These methods have been thoroughly validated following International Committee on Harmonisation (ICH) guidelines. National Environmental Methods Index, Analytical Eco-Scale, and Green Analytical Procedure Index were used to prove greenness, thereby enhancing their applicability. The proposed techniques provide straightforward, precise, and cost-effective solutions for routine formulation analysis in quality control laboratories.     

An analysis and revision of Cyclamen L. with emphasis on subgenus Gyrophoebe O. Schwarz

Studies in the areas of comparative morphology and palynology of the genus Cyclamen L. (Primulaceae) are outlined, and used in combination with observations and analyses of past works and publications and of field data (gathered by the Cyclamen Society and others) to generate new data sets. These are subject to cladistic parsimony analysis for the entire genus, and to phenetic ordinal analysis for subgenus Gyrophoebe O.Schwarz, to reach a conclusion on the validity of the latter classification, and the separation of taxa within it. A phylogeny and subgeneric reclassification is proposed with the reinstatement of Cyclamen elegans Boiss. & Buhse at species level based on the results gathered. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 473–481.     

Inferring the evolutionary history of divergence despite gene flow in a lizard species,Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation‐with‐migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration–divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

A test for linkage and association in general pedigrees: the pedigree disequilibrium test

Family-based tests of linkage disequilibrium typically are based on nuclear-family data including affected individuals and their parents or their unaffected siblings. A limitation of such tests is that they generally are not valid tests of association when data from related nuclear families from larger pedigrees are used. Standard methods require selection of a single nuclear family from any extended pedigrees when testing for linkage disequilibrium. Often data are available for larger pedigrees, and it would be desirable to have a valid test of linkage disequilibrium that can use all potentially informative data. In this study, we present the pedigree disequilibrium test (PDT) for analysis of linkage disequilibrium in general pedigrees. The PDT can use data from related nuclear families from extended pedigrees and is valid even when there is population substructure. Using computer simulations, we demonstrated validity of the test when the asymptotic distribution is used to assess the significance, and examined statistical power. Power simulations demonstrate that, when extended pedigree data are available, substantial gains in power can be attained by use of the PDT rather than existing methods that use only a subset of the data. Furthermore, the PDT remains more powerful even when there is misclassification of unaffected individuals. Our simulations suggest that there may be advantages to using the PDT even if the data consist of independent families without extended family information. Thus, the PDT provides a general test of linkage disequilibrium that can be widely applied to different data structures.     

Reductional groupings in cold-treated onion roots

Summary In roots which had been kept for ten days at 5–6°C the observed frequency of metaphase and anaphase reductional groupings (R. G’s) was lower, that of prophase R. G’s higher, than in simultaneously fixed roots kept at 21–22°C. The frequency of R. G’s can undergo considerable changes independent of temperature. It appears highly likely that a process of somatic reduction may start from R. G’s but its successful conclusion would be, at least in onion, a very rare event. In the present material the probability of a mitosis becoming a R. G. that finally leads to a haploid cell with a complete genome is almost certainly less than 10⁻⁵ and more likely less than 10⁻⁶. Contribution from the Programme in Cytology, Department of Botany, University of Wisconsin, Madison, supported by grants to late Dr.C. Leonard Huskins from the American Cancer Society upon recommendation of the Committee on Growth of the National Research Council, from the Rockefeller Foundation and from the Research Committee of the Graduate School with funds supplied by the Wisconsin Alumni Research Foundation.