A PCR-independent approach for mtDNA enrichment and next-generation sequencing: comprehensive evaluation and clinical application

BACKGROUND

Sequencing the mitochondrial genome has been increasingly important for the investigation of primary mitochondrial diseases (PMD) and mitochondrial genetics. To overcome the limitations originating from PCR-based mtDNA enrichment, we set out to develop and evaluate a PCR-independent approach in this study, named Pime-Seq (PCR-independent mtDNA enrichment and next generation Sequencing).

RESULTS

By using the optimized mtDNA enrichment procedure, the mtDNA reads ratio reached 88.0 ± 7.9% in the sequencing library when applied on human PBMC samples. We found the variants called by Pime-Seq were highly consistent among technical repeats. To evaluate the accuracy and reliability of this method, we compared Pime-Seq with lrPCR based NGS by performing both methods simultaneously on 45 samples, yielding 1677 concordant variants, as well as 146 discordant variants with low-level heteroplasmic fraction, in which Pime-Seq showed higher reliability. Furthermore, we applied Pime-Seq on 4 samples of PMD patients retrospectively, and successfully detected all the pathogenic mtDNA variants. In addition, we performed a prospective study on 192 apparently healthy pregnant women during prenatal screening, in which Pime-Seq identified pathogenic mtDNA variants in 4 samples, providing extra information for better health monitoring in these cases.

CONCLUSIONS

Pime-Seq can obtain highly enriched mtDNA in a PCR-independent manner for high quality and reliable mtDNA deep-sequencing, which provides us an effective and promising tool for detecting mtDNA variants for both clinical and research purposes.

An LC-ESI-MS/MS method for determination of ondansetron in low-volume plasma and cerebrospinal fluid: Method development, validation, and clinical application

Ondansetron is used in clinical settings as an antiemetic drug. Although the animal studies showed its potential effectiveness also in treating neuropathic pain, the results from humans are inconclusive. The lack of efficacy of ondansetron in a subset of patients might be due to the overexpression of P-glycoprotein, which could result in low concentrations of ondansetron in the central nervous system (CNS). A surrogate of the CNS exposure might be drug concentration in the cerebrospinal fluid (CSF), especially in humans, as assessing the drug disposition directly in the patient's brain would be challenging. The study aimed to develop a sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to determine concentrations of ondansetron in human K3EDTA plasma and CSF. Ondansetron was extracted from biological matrices by liquid-liquid extraction. The quantification was performed on a Sciex QTRAP 6500+ mass spectrometer with labeled ondansetron as an internal standard. The calibration range was 0.25-350 ng/mL in plasma and 0.025-100 ng/mL in CSF; for both matrices, 25 µL of samples was required for the assays. The method was validated according to the FDA and EMA guidelines and showed acceptable results. A pilot study confirmed its suitability for clinical samples: after 4-16 mg of intravenous ondansetron, the determined concentrations in plasma were 1.22-235.90 ng/mL, while in CSF - 0.018-11.93 ng/mL. In conclusion, the developed method fulfilled all validation requirements and can be applied to pharmacokinetic studies assessing the CNS ondansetron exposure in humans. The method's advantages, such as a low volume of matrix and a wide calibration range, support its use in a study in which rich sampling and various drug doses are expected.

Using an age and fibrinogen levels adjusted D-dimer cutoff significantly improves the specificity of two equivalent D-dimer assays for excluding pulmonary embolism

OBJECTIVES

Our single-center prospective study compared two methods of D-dimer determination used in the exclusion of pulmonary embolism: bioMérieux method, VIDAS® D-Dimer Exclusion™ II, and Diagnostica Stago method, STA®-Liatest® D-Di Plus. For each of these two methods, we calculated optimized variable cutoffs based on fibrinogen and/or age to improve the specificity of the methods.

PATIENTS - METHODS

2530 patients admitted to the Emergency Department of the Brest University Hospital for suspected pulmonary embolism were included in this study. The comparison of the two methods was performed by calculating their different characteristics: sensitivity, specificity and negative predictive value for different cutoffs systems: fixed or age-adjusted according to Douma et al. An optimization of the variable cutoff according to age and fibrinogen was then performed.

RESULTS

The two methods VIDAS and STAGO are approximately equivalent in terms of performance even if the STAGO method presents a better specificity (57.1 %) at the fixed cutoff of 0.5 μg/mL. The adoption of age-adjusted, fibrinogen-adjusted or doubly-adjusted (age and fibrinogen) cutoffs, significantly improves the specificity of the tests without affecting their excellent sensitivity. These specificities peak respectively at 75.8 % and 76 % for the VIDAS and STAGO tests when using a doubly-adjusted, age and fibrinogen, cutoff, i.e. a gain in specificity of approximately 10 % compared with the age-adjusted cutoff of Douma et al. and of approximately 20 % compared with the fixed cutoff of 0.5 μg/mL.

CONCLUSION

Adopting an optimized variable cutoff based on fibrinogen and/or age significantly improves specificity of D-dimer methods for pulmonary embolism exclusion.

Comparison of Literature Review, Social Media Listening, and Qualitative Interview Research Methods in Generating Patient-Reported Symptom and Functional Impact Concepts of Presbyopia

INTRODUCTION

To compare the insights obtained about the experience of individuals with presbyopia (age-related impaired near vision) across three different sources of qualitative data: a structured targeted literature review, a social media listening (SML) review, and qualitative concept elicitation (CE) interviews with individuals with presbyopia and healthcare professionals (HCPs). The number of concepts identified, depth of data, cost and time implications, and value of the patient insights generated were explored and compared for each method.

METHODS

Keyword searches in bibliographic databases and review of abstracts identified 120 relevant publications; in-depth targeted literature review of the qualitative studies identified key symptoms/functioning concepts. SML was conducted using publicly accessible social media sources with focus on ophthalmologic diseases using a pre-defined search string. Relevant posts from individuals with presbyopia (n = 270) were analysed and key concepts identified. Semi-structured CE interviews were conducted with individuals with presbyopia (US n = 30, Germany n = 10, France n = 10), and HCPs (US = 3, France n = 2, Germany n = 1, Japan n = 1) who were experienced in treating presbyopia. Verbatim transcripts were coded using thematic analysis. A conceptual model summarised concepts identified across sources RESULTS: Out of the total of 158 concepts identified across the three sources, qualitative CE interviews yielded the highest number of concepts (n = 151/158, 96%), with SML yielding a third of the concepts (n = 51/158, 32%) and the literature review yielding the fewest concepts (n = 33/158, 21%). Qualitative CE interviews provided greater depth of data than SML and literature reviews. SML and literature reviews were less costly and quicker to run than qualitative CE interviews and also were less burdensome for participants.

CONCLUSION

Qualitative CE interviews are considered the gold standard in providing greater depth of understanding of the patient experience, and more robust data. However, research requirements, budget, and available time should be considered when choosing the most appropriate research method. More time and cost-effective SML and literature review methods can be used to supplement qualitative CE interview data and provide early identification of measurement concepts. More research and regulatory guidance into less traditional qualitative methods, however, are needed to increase the value of SML and literature review data.

Comparison of five different methodologies for evaluating ankle-foot orthosis stiffness

BACKGROUND

The mechanical properties of an ankle-foot orthosis (AFO) play an important role in the gait mechanics of the end user. However, testing methodologies for evaluating these mechanical properties are not standardized. The purpose of this study was to compare five different evaluation frameworks to assess AFO stiffness.

METHOD

The same 13 carbon composite AFOs were tested with five different methods. Four previously reported custom test fixtures (the BRUCE, KST, SMApp, and EMPIRE) rotated an AFO into dorsiflexion about a defined axis in the sagittal plane. The fifth method involved quasi-static deflection of AFOs into dorsiflexion by hanging weights (HW) from the footplate. AFO rotational stiffness was calculated as the linear fit of the AFO resistive torque and angular deflection. Differences between methods were assessed using descriptive statistics and a repeated measures Friedman with post-hoc Bonferroni-Holm adjusted Wilcoxon signed-rank tests.

RESULTS

There were significant differences in measured AFO stiffnesses between test methods. Specifically, the BRUCE and HW methods measured lower stiffness than both the EMPIRE and the KST. Stiffnesses measured by the SMApp were not significantly different than any test method. Stiffnesses were lowest in the HW method, where motion was not constrained to a single plane. The median difference in absolute AFO stiffness across methods was 1.03 Nm/deg with a range of [0.40 to 2.35] Nm/deg. The median relative percent difference, measured as the range of measured stiffness from the five methods over the average measured stiffness was 62% [range 13% to 156%]. When the HW method was excluded, the four previously reported test fixtures produced a median difference in absolute AFO stiffness of 0.52 [range 0.38 to 2.17] Nm/deg with a relative percent difference between the methods of 27% [range 13% to 89%].

CONCLUSIONS

This study demonstrates the importance of developing mechanical testing standards, similar to those that exist for lower limb prosthetics. Lacking standardization, differences in methodology can result in large differences in measured stiffness, particularly for different constraints on motion. Non-uniform measurement practices may limit the clinical utility of AFO stiffness as a metric in AFO prescription and future research.

Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation

Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of biodiversity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column samples, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.

Benchmarking UMI-based single-cell RNA-seq preprocessing workflows

BACKGROUND

Single-cell RNA-sequencing (scRNA-seq) technologies and associated analysis methods have rapidly developed in recent years. This includes preprocessing methods, which assign sequencing reads to genes to create count matrices for downstream analysis. While several packaged preprocessing workflows have been developed to provide users with convenient tools for handling this process, how they compare to one another and how they influence downstream analysis have not been well studied.

RESULTS

Here, we systematically benchmark the performance of 10 end-to-end preprocessing workflows (Cell Ranger, Optimus, salmon alevin, alevin-fry, kallisto bustools, dropSeqPipe, scPipe, zUMIs, celseq2, and scruff) using datasets yielding different biological complexity levels generated by CEL-Seq2 and 10x Chromium platforms. We compare these workflows in terms of their quantification properties directly and their impact on normalization and clustering by evaluating the performance of different method combinations. While the scRNA-seq preprocessing workflows compared vary in their detection and quantification of genes across datasets, after downstream analysis with performant normalization and clustering methods, almost all combinations produce clustering results that agree well with the known cell type labels that provided the ground truth in our analysis.

CONCLUSIONS

In summary, the choice of preprocessing method was found to be less important than other steps in the scRNA-seq analysis process. Our study comprehensively compares common scRNA-seq preprocessing workflows and summarizes their characteristics to guide workflow users.

Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey

Background

Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey.

Results

Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method.

Conclusions

Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01947-x.

Comparative study of two immunoassays used for the determination of serum vitamin D

Objectives

The best indicator of vitamin D level is the determination of serum 25-hydroxyvitamin D (25(OH)D). Due to the lack of standardization of the available methods, there are problems of precision and reproducibility in its measurement. The objective of this study was to compare the results of 25(OH)D concentration determined by two different immunoassay methods.

Design

and Methods: 25(OH)D was analyzed in 184 serum samples in an IDS-iSYS Multi-Discipline Automated System Analyzer (Vitro) and in an Alinity i automated Analyzer (Abbott). Then, results were compared. Three groups were considered: group of total patients, group with vitamin D supplements and group without treatment.

Results

Of the total patients, 52.7% received vitamin D supplements. The correlation coefficient of agreement for general group, supplementation group and group without supplementation was 0.92, 0.91 and 0.89, respectively. In all of them, a kappa index>0.75 was obtained.

Conclusions

The assays evaluated are not comparable to each other. Despite this, they show an excellent concordance in the evaluation of the vitamin D status.

•

The best indicator of vitamin D level is the determination of serum 25-hydroxyvitamin D.

•

Due to the lack of standardization, there are problems of precision and reproducibility in its analysis.

•

The serum levels measured with IDS-iSYS Analyzer (Vitro) and Alinity i Analyzer (Abbott) were not comparable.

•

Both methods showed an excellent concordance in the evaluation of the vitamin D status.

A quantitative comparison of towed-camera and diver-camera transects for monitoring coral reefs

Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site—slope, depth and structural complexity—also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.

Sequential rank agreement methods for comparison of ranked lists

The comparison of alternative rankings of a set of items is a general and common task in applied statistics. Predictor variables are ranked according to magnitude of association with an outcome, prediction models rank subjects according to the personalized risk of an event, and genetic studies rank genes according to their difference in gene expression levels. We propose a sequential rank agreement measure to quantify the rank agreement among two or more ordered lists. This measure has an intuitive interpretation, it can be applied to any number of lists even if some are partially incomplete, and it provides information about the agreement along the lists. The sequential rank agreement can be evaluated analytically or be compared graphically to a permutation based reference set in order to identify changes in the list agreements. The usefulness of this measure is illustrated using gene rankings, and using data from two Danish ovarian cancer studies where we assess the within and between agreement of different statistical classification methods.

Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison

BACKGROUND

Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast artifacts making automatic segmentation challenging. The aim of this study was to compare the segmentation efficacy of published steps of segmentation work-flow (image reconstruction, foreground segmentation, cell detection (seed-point extraction) and cell (instance) segmentation) on a dataset of the same cells from multiple contrast microscopic modalities.

RESULTS

We built a collection of routines aimed at image segmentation of viable adherent cells grown on the culture dish acquired by phase contrast, differential interference contrast, Hoffman modulation contrast and quantitative phase imaging, and we performed a comprehensive comparison of available segmentation methods applicable for label-free data. We demonstrated that it is crucial to perform the image reconstruction step, enabling the use of segmentation methods originally not applicable on label-free images. Further we compared foreground segmentation methods (thresholding, feature-extraction, level-set, graph-cut, learning-based), seed-point extraction methods (Laplacian of Gaussians, radial symmetry and distance transform, iterative radial voting, maximally stable extremal region and learning-based) and single cell segmentation methods. We validated suitable set of methods for each microscopy modality and published them online.

CONCLUSIONS

We demonstrate that image reconstruction step allows the use of segmentation methods not originally intended for label-free imaging. In addition to the comprehensive comparison of methods, raw and reconstructed annotated data and Matlab codes are provided.

Gene set analysis methods: a systematic comparison

Background

Gene set analysis is a valuable tool to summarize high-dimensional gene expression data in terms of biologically relevant sets. This is an active area of research and numerous gene set analysis methods have been developed. Despite this popularity, systematic comparative studies have been limited in scope.

Methods

In this study we present a semi-synthetic simulation study using real datasets in order to test and compare commonly used methods.

Results

A software pipeline, Flexible Algorithm for Novel Gene set Simulation (FANGS) develops simulated data based on a prostate cancer dataset where the KRAS and TGF-β pathways were differentially expressed. The FANGS software is compatible with other datasets and pathways. Comparisons of gene set analysis methods are presented for Gene Set Enrichment Analysis (GSEA), Significance Analysis of Function and Expression (SAFE), sigPathway, and Correlation Adjusted Mean RAnk (CAMERA) methods. All gene set analysis methods are tested using gene sets from the MSigDB knowledge base. The false positive rate and power are estimated and presented for comparison. Recommendations are made for the utility of the default settings of methods and each method’s sensitivity towards various effect sizes.

Conclusions

The results of this study provide empirical guidance to users of gene set analysis methods. The FANGS software is available for researchers for continued methods comparisons.

Electronic supplementary material

The online version of this article (10.1186/s13040-018-0166-8) contains supplementary material, which is available to authorized users.

Methods comparison

The current report discusses the process in which a methods comparison study in the National Animal Health Laboratory Network is performed. Specific details are provided for designing and analyzing studies intended to evaluate analytical sensitivity, efficiency, analytical specificity, cross-contamination, repeatability, operator variability, and to compare the performance of methods using diagnostic samples. As an example, a case study is presented comparing the performance of a candidate reverse transcription polymerase chain reaction (RT-PCR) chemistry to the current RT-PCR chemistry in use when the assay was originally validated. The present study revealed that, for all of the validation factors evaluated, the candidate method performed at least as well and generally better than the current method. The candidate method was, therefore, deemed fit for the original intended purpose of the current method and rendered acceptable for use. A discussion of the case study is intended to further motivate consideration of the study designs chosen.

Comparison of gaseous and particulate emissions from a pilot-scale combustor using three varieties of coal

Gaseous and particulate emissions generated from the combustion of coal have been associated with adverse effects on human health and the environment, and have therefore been the subject of regulation by federal and state government agencies. Detailed emission characterizations are needed to better understand the impacts of pre- and post-combustion controls on a variety of coals found in the United States (U.S.). While the U.S. Environmental Protection Agency (EPA) requires industry reporting of emissions for criteria and several hazardous air pollutants (HAPs), many of the methods for monitoring and measuring these gaseous and particulate emissions rely on time-integrated sampling techniques. Though these emissions reports provide an overall representation of day-to-day operations, they represent well-controlled operations and do not encompass real combustion events that occur sporadically. The current study not only characterizes emissions from three coals (bituminous, sub-bituminous, and lignite), but also investigates the use of instrumentation for improved measurement and monitoring techniques that provide real-time, continuous emissions data. Testing was completed using the U.S. EPA's Multi-Pollutant Control Research Facility, a pilot-scale coal-fired combustor using industry-standard emission control technologies, in Research Triangle Park, North Carolina. Emissions were calculated based on measurements from the flue gas (pre- and post-electrostatic precipitator), to characterize gaseous species (CO, CO₂, O₂, NO_X, SO₂, other acid gases, and several organic HAPs) as well as fine and ultrafine particulate (mass, size distribution, number count, elemental carbon, organic carbon, and black carbon). Comparisons of traditional EPA methods to those made via Fourier Transfer Infrared (FTIR) Spectroscopy for CO, NO_X, and SO₂ are also reported.

Assessing coral health and disease from digital photographs and in situ surveys

Methods for monitoring the status of marine communities are increasingly adopting the use of images captured in the field. However, it is not always clear how data collected from photographic images relate to historic data collected using traditional underwater visual census methods. Here, we compare coral health and disease data collected in situ by scuba divers with photographic images collected simultaneously at 12 coral reef sites. Five globally relevant coral diseases were detected on 194 colonies from in situ surveys and 79 colonies from photos, whilst 698 colonies from in situ surveys and 535 colonies from photos exhibited signs of compromised health other than disease. Comparisons of in situ surveys with photographic analyses indicated that the number of disease cases occurring in the examined coral populations (prevalence) was six times higher (4.5 vs. 0.8% of colonies), whilst compromised health was three times higher (14 vs. 4% of colonies) from in situ surveys. Skeletal eroding band disease, sponge overgrowth and presence of Waminoa flatworms were not detected in photographs, though they were identified in situ. Estimates of black band disease and abnormally pigmented coral tissues were similar between the two methods. Estimates of the bleached and healthy colonies were also similar between methods and photographic analyses were a strong predictor of bleached (r ² = 0.8) and healthy (r ² = 0.5) colony prevalence from in situ surveys. Moreover, when data on disease and compromised health states resulting in white or pale coral colony appearance were pooled, the prevalence of 'white' colonies from in situ (14%) and photographic analyses (11%) were statistically similar. Our results indicate that information on coral disease and health collected by in situ surveys and photographic analyses are not directly comparable, with in situ surveys generally providing higher estimates of prevalence and greater ability to identify some diseases and compromised states. Careful sampling of photographs can however identify signs of coral stress, including some coral diseases, which may be used to trigger early-warning management interventions.

Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.

Correspondence between hair cortisol concentrations and 30-day integrated daily salivary and weekly urinary cortisol measures

Characterization of cortisol production, regulation and function is of considerable interest and relevance given its ubiquitous role in virtually all aspects of physiology, health and disease risk. The quantification of cortisol concentration in hair has been proposed as a promising approach for the retrospective assessment of integrated, long-term cortisol production. However, human research is still needed to directly test and validate current assumptions about which aspects of cortisol production and regulation are reflected in hair cortisol concentrations (HCC). Here, we report findings from a validation study in a sample of 17 healthy adults (mean±SD age: 34±8.6 yrs). To determine the extent to which HCC captures cumulative cortisol production, we examined the correspondence of HCC, obtained from the first 1cm scalp-near hair segment, assumed to retrospectively reflect 1-month integrated cortisol secretion, with 30-day average salivary cortisol area-under-the curve (AUC) based on 3 samples collected per day (on awakening, +30min, at bedtime) and the average of 4 weekly 24-h urinary free cortisol (UFC) assessments. To further address which aspects of cortisol production and regulation are best reflected in the HCC measure, we also examined components of the salivary measures that represent: (1) production in response to the challenge of awakening (using the cortisol awakening response [CAR]), and (2) chronobiological regulation of cortisol production (using diurnal slope). Finally, we evaluated the test-retest stability of each cortisol measure. Results indicate that HCC was most strongly associated with the prior 30-day integrated cortisol production measure (average salivary cortisol AUC) (r=0.61, p=0.01). There were no significant associations between HCC and the 30-day summary measures using CAR or diurnal slope. The relationship between 1-month integrated 24-h UFC and HCC did not reach statistical significance (r=0.30, p=0.28). Lastly, of all cortisol measures, test-retest correlations of serial measures were highest for HCC (month-to-month: r=0.84, p<0.001), followed by 24-h UFC (week-to-week: r's between 0.59 and 0.68, ps<0.05) and then integrated salivary cortisol concentrations (week-to-week: r's between 0.38 and 0.61, p's between 0.13 and 0.01). These findings support the contention that HCC provides a reliable estimate of long-term integrated free cortisol production that is aligned with integrated salivary cortisol production measured over a corresponding one-month period.

Comparison of methods used to estimate coral cover in the Hawaiian Islands

Nine coral survey methods were compared at ten sites in various reef habitats with different levels of coral cover in Kāne'ohe Bay, O'ahu, Hawai'i. Mean estimated coverage at the different sites ranged from less than 10% cover to greater than 90% cover. The methods evaluated include line transects, various visual and photographic belt transects, video transects and visual estimates. At each site 25 m transect lines were laid out and secured. Observers skilled in each method measured coral cover at each site. The time required to run each transect, time required to process data and time to record the results were documented. Cost of hardware and software for each method was also tabulated. Results of this investigation indicate that all of the methods used provide a good first estimate of coral cover on a reef. However, there were differences between the methods in detecting the number of coral species. For example, the classic "quadrat" method allows close examination of small and cryptic coral species that are not detected by other methods such as the "towboard" surveys. The time, effort and cost involved with each method varied widely, and the suitability of each method for answering particular research questions in various environments was evaluated. Results of this study support the finding of three other comparison method studies conducted at various geographic locations throughout the world. Thus, coral cover measured by different methods can be legitimately combined or compared in many situations. The success of a recent modeling effort based on coral cover data consisting of observations taken in Hawai'i using the different methods supports this conclusion.

Comparison of results from commercial assays for plasma CTX: The need for harmonization

INTRODUCTION

Plasma C-terminal telopeptide of type I collagen (CTX) is the nominated reference bone resorption marker. We set out to test the agreement of patients' results between the available plasma CTX assays.

METHODS

Samples were collected from patients attending tertiary hospitals and clinics for investigation and management of metabolic bone disease. Plasma (EDTA) samples were collected from fasted patients between 7.00 am and 11.00 am, divided into three portions and stored at -20°C until analysis. Plasma CTX was measured by enzyme-linked immunosorbent assay (ELISA) (Immunodiagnostic Systems plc), E170 (Roche Diagnostics) and IDS-iSYS (Immunodiagnostic Systems plc) methods. Agreement of patient sample results was assessed by Passing and Bablok regression. Commutability of the calibrators in each kit was assessed by assaying each calibrator in the alternate methods and comparing the observed results with those expected based on the relevant patients' samples method comparison; ±8.1% was set as the criterion for commutablity.

RESULTS

161 specimens were analysed. Regression parameters (slope, intercept) were 0.788, 0.2 ng/L for Roche vs ELISA, 1.266 and -109 ng/L for iSYS vs ELISA and 1.605 and -109 ng/L for iSYS vs Roche. Only the ELISA calibrator assayed in the Roche assay gave a result within 8.1% of the expected value.

CONCLUSIONS

There is significant disagreement between the results generated for patient samples by the 3 CTX assays and limited commutability of the currently supplied calibrator materials between assays. Harmonization of the results from the different assays would greatly enhance the value of CTX as the reference bone resorption marker.

American Association of Veterinary Parasitologists' review of veterinary fecal flotation methods and factors influencing their accuracy and use--is there really one best technique?

The principle of fecal flotation is based on the ability of a solution to allow less dense material (including parasite elements) to rise to the top. However, there are numerous factors that will influence the accuracy and use of such a theoretically simple technique. Whether or not centrifugation is used appears to have an impact on the ability to detect some parasites, but not others. Using a flotation solution with a relatively high specific gravity favors the simultaneous flotation of the diagnostic stages of many different parasites while, at the same time, making recognition of some more difficult because of distortion as well as the amount of debris in the preparation. Dilution methods tend to be less accurate because they require extrapolation; however, they are quicker to perform, in part, because of the cleaner preparation. Timing is a critical factor in the success of all flotation methods, as is technical ability of the personnel involved. Thus, simplicity, low costs and time savings have generally favored gravitational flotation techniques (including the McMaster technique and its modifications). How accurate the method needs to be is dependent upon the purpose of its use and choice of method requires an understanding of analytical sensitivity and expected levels of egg excretion. In some instances where the difference between, for example, 0 and 50 eggs per gram is insignificant with regards to management decisions, less accurate methods will suffice. In others, where the presence of a parasite means treatment of the animal regardless of the numbers of eggs present, methods with higher analytical sensitivities will be required, particularly for those parasites that pass few eggs. For other uses, such as the Fecal Egg Count Reduction Test, accuracy may become critical. Therefore, even though recommendations for standardized fecal flotation procedures have been promoted in the past, it is clear that the factors are too numerous to allow for the recommendation of one, or even a few, procedures for all purposes.

Comparison of liquid chromatography-tandem mass spectrometry-based targeted proteomics and conventional analytical methods for the determination of P-glycoprotein in human breast cancer cells

P-glycoprotein (P-gp) is the most frequently proposed factor for multi-drug resistance. It is traditionally measured using antibody-based methods. While these techniques can provide relative quantification values for P-gp levels, the important information that is usually missing is its amount in the biological system. In this study, a novel and advanced liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based targeted proteomics assay was developed and validated for the determination of P-gp in the breast cancer drug sensitive cell line MCF-7/WT and the drug resistant cell line MCF-7/ADR. Three tryptic peptides (434STTVQLMQR442, 674GSQAQDR680 and 368IIDNKPSIDSYSK380) can specifically represent P-gp. Among these peptides, 434STTVQLMQR442 was selected as the surrogate analyte for quantification, and a stable isotope-labeled synthetic peptide with the same sequence was used as an internal standard. The calibration range was validated from 10 to 1000ng/mL. The intra- and inter-day precisions were within 5.9% and 3.7%, respectively. The accuracy for the quality control (QC) samples was within 8.0%. Using this assay, the amounts of P-gp were accurately quantified as 3.53fg/cell (∼2.08×10(-2)amol/cell) in the MCF-7/WT cells and 34.5fg/cell (∼2.02×10(-1)amol/cell) in the MCF-7/ADR cells. This outcome was then compared with those obtained by conventional analytical methods including confocal microscopy, western blotting and flow cytometry. The comparative results show that not only is the LC/MS/MS-based targeted proteomics assay able to monitor the protein levels in a more accurate manner, but the large discrepancy observed between the other methods was most likely due to the lack of specificity and the semi-quantitative nature of the conventional assays.