Protein Biomarker Discovery Studies on Urinary sEV Fractions Separated with UF-SEC for the First Diagnosis and Detection of Recurrence in Bladder Cancer Patients

Urinary extracellular vesicles (EVs) are an attractive source of bladder cancer biomarkers. Here, a protein biomarker discovery study was performed on the protein content of small urinary EVs (sEVs) to identify possible biomarkers for the primary diagnosis and recurrence of non-muscle-invasive bladder cancer (NMIBC). The sEVs were isolated by ultrafiltration (UF) in combination with size-exclusion chromatography (SEC). The first part of the study compared healthy individuals with NMIBC patients with a primary diagnosis. The second part compared tumor-free patients with patients with a recurrent NMIBC diagnosis. The separated sEVs were in the size range of 40 to 200 nm. Based on manually curated high quality mass spectrometry (MS) data, the statistical analysis revealed 69 proteins that were differentially expressed in these sEV fractions of patients with a first bladder cancer tumor vs. an age- and gender-matched healthy control group. When the discriminating power between healthy individuals and first diagnosis patients is taken into account, the biomarkers with the most potential are MASP2, C3, A2M, CHMP2A and NHE-RF1. Additionally, two proteins (HBB and HBA1) were differentially expressed between bladder cancer patients with a recurrent diagnosis vs. tumor-free samples of bladder cancer patients, but their biological relevance is very limited.

Variation of antlers in individual red deer (Cervus elaphus) stags: repeatability, age and side effects

Antlers are formed anew each year to realise an optimal relationship between their size and weight and the physical body condition in Cervidae. This results in the objective to match fighting abilities with size and mechanical performance of the antlers, as well as to advertise these correlated abilities to other males and females. The resulting variation in individual antler characteristics from year to year can show considerable differences. To characterise and understand these differences is important in hunting, game management and deer breeding, as well as potentially to assess the habitat quality. However, relatively few traits of the antler have been scientifically tested for this purpose, and only a few studies were conducted on the same individual in free-ranging red deer over the years. The objective of the present study was to quantify the influence of the individual (repeatability), the age and the site on the expression of 125 antler characteristics. For this purpose, we collected 35 stags with an average of about 10 consecutive antlers per individual (confirmed by genetic analysis), a total of 355 antlers. The antlers were scanned 3-dimensionally and measured semi-automatically. Numbers, lengths, distances, circumferences, bending, curvatures, angles, forms and CIC (International Council for Game and Wildlife Conservation) characteristics were compiled and evaluated in a generalised linear mixed model adapted to the distribution of the characteristics. The complete model explained 1.6 to 83% of character variation. Mean repeatability of the characteristics varied between 2.7 and 74.4%. The stags’ age explained 0 to 36.4%, and the side explained 0 to 2.5% of the variability. Some characteristics of burr, signet, beam and the lower tines reached the highest repeatability; the highest variability was found in characteristics of the crown. Values of 11 features that are frequently used in other studies corresponded very well with the present study. However, some features reached higher repeatability every year, whereas others varied more closely with age. Such characteristics might be selectively included into further research or practical applications to increase informative value.

Human-driven genetic differentiation in a managed red deer population

Nineteen red deer areas in a densely populated region with a huge network of fenced motorways and the division into administrative management units (AMUs) with restricted ecological connectivity were investigated. In the season 2018/2019, a total of 1291 red deer samples (on average 68 per area) were collected and genotyped using 16 microsatellite markers. The results show a clear genetic differentiation between most of the AMUs. Fourteen AMUs may be combined into four regions with a considerable internal genetic exchange. Five areas were largely isolated or showed only a limited gene flow with neighbouring areas. Ten of the 19 AMUs had an effective population size below 100. Effective population sizes greater than 500–1000, required to maintain the evolutionary potential and a long-term adaptation potential, were not achieved by any of the studied AMUs, even when AMUs with an appreciable genetic exchange were aggregated. Substantial genetic differentiation between areas can be associated with the presence of landscape barriers hindering gene flow, but also with the maintenance of ‘red deer–free’ areas. Efforts to sustainably preserve the genetic diversity of the entire region should therefore focus on measures ensuring genetic connectivity. Opportunities for this goal arise from the establishment of game bridges over motorways and from the protection of young male stags migrating through the statutory ‘red deer–free’ areas.

FACS-Based Proteomics Enables Profiling of Proteins in Rare Cell Populations

Understanding disease pathology often does not require an overall proteomic analysis of clinical samples but rather the analysis of different, often rare, subpopulations of cells in a heterogeneous mixture of cell types. For the isolation of pre-specified cellular subtypes, fluorescence activated cell sorting (FACS) is commonly used for its ability to isolate the required cell populations with high purity, even of scarce cell types. The proteomic analysis of a limited number of FACS-sorted cells, however, is very challenging as both sample preparation inefficiencies and limits in terms of instrument sensitivity are present. In this study, we used CD14+CD15+ immune cells sorted out of peripheral blood mononuclear cells isolated from whole blood to improve and evaluate FACS-based proteomics. To optimize both the protein extraction protocol and the mass spectrometry (MS) data acquisition method, PBMCs as well as commercialized HeLa digest were used. To reflect the limited number of sorted cells in some clinical samples, different numbers of sorted cells (1000, 5000, 10,000, or 50,000) were used. This allowed comparing protein profiles across samples with limited protein material and provided further insights in the benefits and limitations of using a very limited numbers of cells.

Improving Quality in Nanoparticle-Induced Cytotoxicity Testing by a Tiered Inter-Laboratory Comparison Study

The quality and relevance of nanosafety studies constitute major challenges to ensure their key role as a supporting tool in sustainable innovation, and subsequent competitive economic advantage. However, the number of apparently contradictory and inconclusive research results has increased in the past few years, indicating the need to introduce harmonized protocols and good practices in the nanosafety research community. Therefore, we aimed to evaluate if best-practice training and inter-laboratory comparison (ILC) of performance of the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay for the cytotoxicity assessment of nanomaterials among 15 European laboratories can improve quality in nanosafety testing. We used two well-described model nanoparticles, 40-nm carboxylated polystyrene (PS-COOH) and 50-nm amino-modified polystyrene (PS-NH2). We followed a tiered approach using well-developed standard operating procedures (SOPs) and sharing the same cells, serum and nanoparticles. We started with determination of the cell growth rate (tier 1), followed by a method transfer phase, in which all laboratories performed the first ILC on the MTS assay (tier 2). Based on the outcome of tier 2 and a survey of laboratory practices, specific training was organized, and the MTS assay SOP was refined. This led to largely improved intra- and inter-laboratory reproducibility in tier 3. In addition, we confirmed that PS-COOH and PS-NH2 are suitable negative and positive control nanoparticles, respectively, to evaluate impact of nanomaterials on cell viability using the MTS assay. Overall, we have demonstrated that the tiered process followed here, with the use of SOPs and representative control nanomaterials, is necessary and makes it possible to achieve good inter-laboratory reproducibility, and therefore high-quality nanotoxicological data.

Adolescent suicide behaviour profiles: comparing unplanned attempts, planned attempts and ideation

Background

Suicide is the second leading cause of death for young people worldwide. A significant amount of suicide attempts is known to be unplanned, but research on unplanned attempts among adolescents is limited. As knowledge on the profile of unplanned suicide attempts is crucial for effective prevention efforts, this study aims to characterize and compare three suicide behaviour profiles among adolescents: planned attempts, unplanned attempts and ideation without attempt.

Methods

Data from the 2014 Luxembourgish Health Behaviour in School-aged Children study was used. 879 adolescents aged 12 to 18 years old are included in this study. Data was gathered using paper questionnaires. ANOVAs with Games-Howell post-hoc tests were conducted for 18 independent variables, using the suicide behaviour variable as the dependent variable.

Results

Unplanned attempters report higher levels of parental and classmate support (p < 0.01), fewer health complaints (p < 0.001), higher life satisfaction (p < 0.01) and a more positive body image (p < 0.01) than planned attempters and ideators. Unplanned and planned attempters are younger than ideators (p < 0.01) and report more substance use and physical fighting than ideators (p < 0.01).

Conclusions

Unplanned attempters report better health (behaviour) and more social support than planned attempters and ideators. Unplanned attempters and planned attempters have higher levels of risk behaviour than ideators. Prevention efforts should be mindful of similarities and differences between the behaviours, and identify and address at risk adolescents accordingly.

Key messages

Unplanned attempters have better health (behaviour) and more social support than planned attempters and ideators. Results are incorporated in the Luxembourgish national plan for suicide prevention.

Using data from the HBSC study for evidence-based suicide prevention in Luxembourg

Issue

As suicide is the second leading cause of death for young people, WHO aims to reduce the suicide rate with 10% by 2020 worldwide. In Luxembourg, organization D’Ligue coordinates suicide prevention. Since suicide research has been carried out in the country for a few years only, data on adolescent suicidal ideation is lacking. Therefore, D’Ligue has contacted the Luxembourg team of the international Health Behaviour in School-aged Children (HBSC) study, to identify risk factors for suicide behaviour and derive recommendations from them.

Description of the problem

First, our practice partner wanted us to provide them with basic data on the suicidal ideation of adolescents: How many adolescents are suicidal and what are risk factors? Second, recommendations for practice should be derived from the results. To this end, the HBSC data (2014) of 5262 pupils aged 12-18 were analysed.

Results

15.1% of adolescents thought about suicide last year and 7% attempted suicide. Of the 24 risk factors examined, 12 were found to be significant, with three being particularly important: multiple health complaints (OR: 1.3 for each health complaint, p < 0.001, CI: 1.18 - 1.33), lower life satisfaction (OR: 1.3 for the loss of each life satisfaction point, p < 0.001, CI: 1.17 - 1.33) and frequent physical fighting (OR: 2.4, p < 0.001, CI: 1.57 - 3.74).

Lessons

Risk factors for suicide behaviour known from research have been confirmed for Luxembourg. What is new is that the number of health complaints is the most important risk factor for Luxembourgish adolescents. Therefore, a list of 8 health complaints was validated as a screening tool for suicidal thoughts. In a further step, this tool could be used, for example, by school nurses. The HBSC data can be used to update the national suicide prevention plan.

Main messages

HBSC data are used to: update the Luxembourgish national plan for suicide prevention.investigate a screening tool for adolescents at risk for suicide.

Determination of variability due to biological and technical variation in urinary extracellular vesicles as a crucial step in biomarker discovery studies

Urinary extracellular vesicles (EVs) are an attractive source of biomarkers for urological diseases. A crucial step in biomarker discovery studies is the determination of the variation parameters to perform a sample size calculation. In this way, a biomarker discovery study with sufficient statistical power can be performed to obtain biologically significant biomarkers. Here, a variation study was performed on both the protein and lipid content of urinary EVs of healthy individuals, aged between 52 and 69 years. Ultrafiltration (UF) in combination with size exclusion chromatography (SEC) was used to isolate the EVs from urine. Different experimental variation set-ups were used in this variation study. The calculated standard deviations (SDs) of the 90% least variable peptides and lipids did not exceed 2 and 1.2, respectively. These parameters can be used in a sample size calculation for a well-designed biomarker discovery study at the cargo of EVs.

Saturable elimination of piperacillin in critically ill patients: implications for continuous infusion

The study aimed to evaluate saturation of piperacillin elimination in critically ill adult patients. Seventeen critically ill adult patients received continuous and intermittent infusion of piperacillin/tazobactam. Piperacillin plasma concentrations (n = 217) were analysed using population pharmacokinetic (PopPK) modelling. Post-hoc simulations were performed to evaluate the type I error rate associated with the study. Unseen data were used to validate the final model. The mean error (ME) and root mean square error (RMSE) were calculated as a measure of bias and imprecision, respectively. A PopPK model with parallel linear and non-linear elimination best fitted the data. The median and 95% confidence interval (CI) for the model parameters drug clearance (CL), volume of central compartment (V), volume of peripheral compartment (V_p) and intercompartmental clearance (Q) were 9 (7.69-11) L/h, 6.18 (4.93-11.2) L, 11.17 (7.26-12) L and 15.61 (12.66-23.8) L/h, respectively. The Michaelis-Menten constant (K_m) and the maximum elimination rate for Michaelis-Menten elimination (V_max) were estimated without population variability in the model to avoid overfitting and inflation of the type I error rate. The population estimates for K_m and V_max were 37.09 mg/L and 353.57 mg/h, respectively. The bias (ME) was -20.8 (95% CI -26.2 to -15.4) mg/L, whilst imprecision (RMSE) was 49.2 (95% CI 41.2-56) mg/L. In conclusion, piperacillin elimination is (partially) saturable. Moreover, the population estimate for K_m lies within the therapeutic window and therefore saturation of elimination should be accounted for when defining optimum dosing regimens for piperacillin in critically ill patients.

Multiple solvent elution, a method to counter the effects of coelution and ion suppression in LC-MS analysis in bottom up proteomics

On average a human cell type expresses around 10,000 different protein coding genes synthesizing all the different molecular forms of the protein product (proteoforms) found in a cell. In a typical shotgun bottom up proteomic approach, the proteins are enzymatically cleaved, producing several 100,000 s of different peptides that are analyzed with liquid chromatography-tandem mass spectrometry (LC-MSMS). One of the major consequences of this high sample complexity is that coelution of peptides cannot be avoided. Moreover, low abundant peptides are difficult to identify as they have a lower chance of being selected for fragmentation due to ion-suppression effects and the semi-stochastic nature of the precursor selection in data-dependent shotgun proteomic analysis where peptides are selected for fragmentation analysis one-by-one as they elute from the column. In the current study we explore a simple novel approach that has the potential to counter some of the effect of coelution of peptides and improves the number of peptide identifications in a bottom-up proteomic analysis. In this method, peptides from a HeLa cell digest were eluted from the reverse phase column using three different elution solvents (acetonitrile, methanol and acetone) in three replicate reversed phase LC-MS/MS shotgun proteomic analysis. Results were compared with three technical replicates using the same solvent, which is common practice in proteomic analysis. In total, we see an increase of up to 10% in unique protein and up to 30% in unique peptide identifications from the combined analysis using different elution solvents when compared to the combined identifications from the three replicates of the same solvent. In addition, the overlap of unique peptide identifications common in all three LC-MS analyses in our approach is only 23% compared to 50% in the replicates using the same solvent. The method presented here thus provides an easy to implement method to significantly reduce the effects of coelution and ion suppression of peptides and improve protein coverage in shotgun proteomics. Data are available via ProteomeXchange with identifier PXD011908.

MALDI Mass Spectrometry Imaging Linked with Top-Down Proteomics as a Tool to Study the Non-Small-Cell Lung Cancer Tumor Microenvironment

Advanced non-small-cell lung cancer (NSCLC) is generally linked with a poor prognosis and is one of the leading causes of cancer-related deaths worldwide. Since only a minority of the patients respond well to chemotherapy and/or targeted therapies, immunotherapy might be a valid alternative in the lung cancer treatment field, as immunotherapy attempts to strengthen the body’s own immune response to recognize and eliminate malignant tumor cells. However, positive response patterns to immunotherapy remain unclear. In this study, we demonstrate how immune-related factors could be visualized from single NSCLC tissue sections (Biobank@UZA) while retaining their spatial information by using matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), in order to unravel the molecular profile of NSCLC patients. In this way, different regions in lung cancerous tissues could be discriminated based on the molecular composition. In addition, we linked visualization (MALDI MSI) and identification (based on liquid chromatography higher resolution mass spectrometry) of the molecules of interest for the correct biological interpretation of the observed molecular differences within the area in which these molecules are detected. This is of major importance to fully understand the underlying molecular profile of the NSCLC tumor microenvironment.

Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization

In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (<5%) of drug-resistant Mtb was possible.

Ultrafiltration and size exclusion chromatography combined with asymmetrical-flow field-flow fractionation for the isolation and characterisation of extracellular vesicles from urine

Extracellular vesicles (EVs) have a great potential in clinical applications. However, their isolation from different bodily fluids and their characterisation are currently not optimal or standardised. Here, we report the results of examining the performance of ultrafiltration combined with size exclusion chromatography (UF-SEC) to isolate EVs from urine. The results reveal that UF-SEC is an efficient method and provides high purity. Furthermore, we introduce asymmetrical-flow field-flow fractionation coupled with a UV detector and multi-angle light-scattering detector (AF4/UV-MALS) as a characterisation method and compare it with current methods. We demonstrate that AF4/UV-MALS is a straightforward and reproducible method for determining size, amount and purity of isolated urinary EVs.

Prävalenzen porziner Circoviren in ausgewählten deutschen Wildschweinpopulationen

Gegenstand und Ziel: Porzine Circoviren vom Typ II zählen weltweit zu den ökonomisch bedeutsamsten Krankheitserregern beim Schwein. In Wechselwirkung mit verschiedensten Haltungs- und Hygienefaktoren werden sie als Auslöser des Postweaning Multisystemic Wasting Syndrome (PMWS) angesehen. Sie können eine Rolle beim porzinen Dermatitis-Nephropathie-Syndrom (PDNS) spielen und werden mit proliferativen interstitiellen Pneumonien (PNP) und Fruchtbarkeitsstörungen assoziiert. Porzine Circoviren vom Typ I gelten hingegen als apathogen. Circoviren sind in den Hausschweinepopulationen weit verbreitet, kommen aber auch beim Wildschwein vor. Epidemiologische Studien aus Belgien und Spanien sowie Einzelbefunde aus Deutschland sprechen für eine potenzielle Rolle von Wildschweinen als Multiplikator und Reservoir für den Erreger. Epidemiologische Daten zur Verbreitung porziner Circoviren bei Wildschweinen in Deutschland zur Abschätzung des Übertragungsrisikos auf Hausschweinpopulationen fehlen bislang. Diese Informationslücke soll mit vorliegender Studie geschlossen werden. Material und Methoden: Mittels PCRAnalyse wurden Milzproben von 238 Wildschweinen aus den Regionen Westerwald, Hunsrück, Rheingau und Odenwald auf PCV-1– und PCV-2-spezifische Nukleinsäuren untersucht und die Befunde mit Alter und körperlicher Entwicklung der Tiere verglichen. Ergebnisse: Bei 61,8% der Tiere konnte weder PCV-1 noch PCV-2 nachgewiesen werden, 21,9% waren positiv für PCV-1 und 18,1% für PCV-2. Die Prävalenzen differierten zwischen den einzelnen Revieren und Regionen signifikant. Im Vergleich zu Ergebnissen aus anderen Ländern waren porzine Circoviren vom Typ II stärker und solche vom Typ I weniger stark verbreitet. Jüngere Tiere erwiesen sich signifikant stärker betroffen als ältere, ein Einfluss auf die Entwicklung der Tiere konnte jedoch nicht festgestellt werden. Klinische Relevanz: Die Daten belegen an ausgewählten Beispielpopulationen, dass in Deutschland von einer flächendeckenden Infektion von Wildschweinpopulationen auszugehen ist. Damit können auch Wildschweine einen Risikofaktor für PCV-assoziierte Erkrankungen von Hausschweinpopulationen darstellen.

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine.

Interpreting biomarker data from the COPHES/DEMOCOPHES twin projects: Using external exposure data to understand biomarker differences among countries

In 2011 and 2012, the COPHES/DEMOCOPHES twin projects performed the first ever harmonized human biomonitoring survey in 17 European countries. In more than 1800 mother-child pairs, individual lifestyle data were collected and cadmium, cotinine and certain phthalate metabolites were measured in urine. Total mercury was determined in hair samples. While the main goal of the COPHES/DEMOCOPHES twin projects was to develop and test harmonized protocols and procedures, the goal of the current paper is to investigate whether the observed differences in biomarker values among the countries implementing DEMOCOPHES can be interpreted using information from external databases on environmental quality and lifestyle. In general, 13 countries having implemented DEMOCOPHES provided high-quality data from external sources that were relevant for interpretation purposes. However, some data were not available for reporting or were not in line with predefined specifications. Therefore, only part of the external information could be included in the statistical analyses. Nonetheless, there was a highly significant correlation between national levels of fish consumption and mercury in hair, the strength of antismoking legislation was significantly related to urinary cotinine levels, and we were able to show indications that also urinary cadmium levels were associated with environmental quality and food quality. These results again show the potential of biomonitoring data to provide added value for (the evaluation of) evidence-informed policy making.

Assessment of human exposure to environmental sources of nickel in Europe: Inhalation exposure

The paper describes the inhalation nickel (Ni) exposure of humans via the environment for the regional scale in the EU, together with a tiered approach for assessing additional local exposure from industrial emissions. The approach was designed, in the context of REACH, for the purpose of assessing and controlling emissions and air quality in the neighbourhood of Ni producers and downstream users. Two Derived No Effect Level (DNEL) values for chronic inhalation exposure to total Ni in PM10 (20 and 60ngNi/m(3)) were considered. The value of 20ngNi/m(3) is the current EU air quality guidance value. The value of 60ngNi/m(3) is derived here based on recently published Ni data (Oller et al., 2014). Both values are protective for respiratory toxicity and carcinogenicity but differ in the application of toxicokinetic adjustments and cancer threshold considerations. Estimates of air Ni concentrations at the European regional scale were derived from the database of the European Environment Agency. The 50th and 90th percentile regional exposures were below both DNEL values. To assess REACH compliance at the local scale, measured ambient air data are preferred but are often unavailable. A tiered approach for the use of modelled ambient air concentrations was developed, starting with the application of the default EUSES model and progressing to more sophisticated models. As an example, the tiered approach was applied to 33 EU Ni sulphate producers' and downstream users' sites. Applying the EUSES model demonstrates compliance with a DNEL of 60ngNi/m(3) for the majority of sites, while the value of the refined modelling is demonstrated when a DNEL of 20ngNi/m(3) is considered. The proposed approach, applicable to metals in general, can be used in the context of REACH, for refining the risk characterisation and guiding the selection of risk management measures.

iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring

Over the past few years, awareness has risen that for mass-spectrometry-based proteomics methods to mature into everyday analytical and clinical practices, extensive quality assessment is mandatory. A currently overlooked source of qualitative information originates from the mass spectrometer itself. Apart from the actual mass spectral data, raw-data objects also contain parameter settings and sensory information about the mass instrument. This information gives a detailed account of the operation of the instrument, which eventually can be related to observations in mass spectral data. The advantage of instrument information at the lowest level is the high sensitivity to detect emerging defects in a timely fashion. To this end, we introduce the Instrument MONitoring DataBase (iMonDB), which allows us to automatically extract, store, and manage the instrument parameters from raw-data objects into a highly efficient database structure. This enables us to monitor the instrument parameters over a considerable time period. Time course information about the instrument performance is necessary to define the normal range of operation and to detect anomalies that may correlate with instrument failure. The proposed tools foster an additional handle on quality control and are released as open source under the permissive Apache 2.0 license. The tools can be downloaded from https://bitbucket.org/proteinspector/imondb.

First steps toward harmonized human biomonitoring in Europe: demonstration project to perform human biomonitoring on a European scale

BACKGROUND

For Europe as a whole, data on internal exposure to environmental chemicals do not yet exist. Characterization of the internal individual chemical environment is expected to enhance understanding of the environmental threats to health.

OBJECTIVES

We developed and applied a harmonized protocol to collect comparable human biomonitoring data all over Europe.

METHODS

In 17 European countries, we measured mercury in hair and cotinine, phthalate metabolites, and cadmium in urine of 1,844 children (5-11 years of age) and their mothers. Specimens were collected over a 5-month period in 2011-2012. We obtained information on personal characteristics, environment, and lifestyle. We used the resulting database to compare concentrations of exposure biomarkers within Europe, to identify determinants of exposure, and to compare exposure biomarkers with health-based guidelines.

RESULTS

Biomarker concentrations showed a wide variability in the European population. However, levels in children and mothers were highly correlated. Most biomarker concentrations were below the health-based guidance values.

CONCLUSIONS

We have taken the first steps to assess personal chemical exposures in Europe as a whole. Key success factors were the harmonized protocol development, intensive training and capacity building for field work, chemical analysis and communication, as well as stringent quality control programs for chemical and data analysis. Our project demonstrates the feasibility of a Europe-wide human biomonitoring framework to support the decision-making process of environmental measures to protect public health.

A semi-probabilistic modelling approach for the estimation of dietary exposure to phthalates in the Belgian adult population

In this study, a semi-probabilistic modelling approach was applied for the estimation of the long-term human dietary exposure to phthalates--one of world's most used families of plasticisers. Four phthalate compounds were considered: diethyl phthalate (DEP), di-n-butyl phthalate (DnBP), benzylbutyl phthalate (BBP) and di(2-ethylhexyl) phthalate (DEHP). Intake estimates were calculated for the Belgian adult population and several subgroups of this population for two considered scenarios using an extended version of the EN-forc model. The highest intake rates were found for DEHP, followed by DnBP, BBP and DEP. In the Belgian adult population, men and young adults generally had the highest dietary phthalate intake estimates. Nevertheless, predicted dietary intake rates for all four investigated phthalates were far below the corresponding tolerable daily intake (TDI) values (i.e. P99 intake values were 6.4% of the TDI at most), which is reassuring because adults are also exposed to phthalates via other contamination pathways (e.g. dust ingestion and inhalation). The food groups contributing most to the dietary exposure were grains and grain-based products for DEP, milk and dairy products for DnBP, meat and meat products or grains and grain-based products (depending on the scenario) for BBP and meat and meat products for DEHP. Comparison of the predicted intake results based on modelled phthalate concentrations in food products with intake estimates from other surveys (mostly based on measured concentrations) showed that the extended version of the EN-forc model is a suitable semi-probabilistic tool for the estimation and evaluation of the long-term dietary intake of phthalates in humans.

Influence of altitude on vitamin D and bone metabolism of lactating sheep and goats

This study investigated the influence of alpine grazing on vitamin D (vitD) and bone metabolism in sheep and goats. Two groups of five adult lactating East Friesian milk sheep and Saanen dairy goats were kept on pastures at 2,000 to 2,600 m a.s.l. (SA: sheep alpine; GA: goats alpine) and 400 m a.s.l. (SL: sheep lowland; GL: goats lowland). The animals were milked twice daily and the milk yield was measured. Blood, milk, skin, and forage samples were collected and the left metatarsi were measured with peripheral quantitative computed tomography. The relative humidity and air temperature were recorded and the ultraviolet B (UVB) radiation was measured with a solar meter at both research stations. In addition, animals from the alpine group were equipped with a global positioning system receiver. The UVB radiation was higher at the alpine station (P<0.05) compared to the lowland station. In contrast, both the relative humidity and the air temperature were higher at the lowland station (P<0.04). The group GA produced more milk than GL (P<0.043). No differences in milk production between SA and SL were detected. Only minor differences between the alpine and lowland species groups were found in the total 25-hydroxyvitamin D (25(OH)D) and 1,25-dihydroxyvitamin D serum concentration and in the 25(OH)D milk concentration. 25-hydroxyvitamin D2 concentration in serum was higher in sheep compared to goats and the 25(OH)D3 concentration in serum increased in all four groups but was higher in the alpine groups during the experiment. In addition, no differences in 7-dehydrocholesterol (7-DHC) concentrations in the skin at high altitude and lowland groups were detectable. However the 7-DHC concentrations in the skin of sheep were less than a tenth of the concentrations in the skin of goats and were nearly not detectable. In both groups SA and SL bone strength index increased during the trial (P=0.043). Bone strength index was lower in GA compared to GL at wk 12 (P=0.047). Mean serum Ca concentrations were higher and P concentrations were lower in the alpine groups than in the lowland groups (P=0.047). In both groups SA and GA the distance travelled increased during the trial. In conclusion, no effect of altitude on vitD status, vitD milk concentration and bone strength could be detected. Both sheep and goats are able to produce vitD in the skin, but sheep depend more on vitD intake with feedstuff, whereas goats rely more on cutaneous vitD production.

Transfer of eight phthalates through the milk chain--a case study

This survey determined the levels of eight phthalates - i.e. dimethyl phthalate (DMP), diethyl phthalate (DEP), diisobutyl phthalate (DiBP), di-n-butyl phthalate (DnBP), benzylbutyl phthalate (BzBP), di(2-ethylhexyl) phthalate (DEHP), dicyclohexyl phthalate (DCHP) and di-n-octyl phthalate (DnOP) - in several Belgian milk and dairy products. Samples were obtained from various farms, a dairy factory and from different shops in order to investigate phthalate contamination "from farm to fork". At several stages in the milk chain, product contamination with phthalates - mostly DiBP, DnBP, BzBP and DEHP - was observed. At farm level, the mechanical milking process and the intake of phthalate containing feed by the cattle were found to be possible contamination sources. At industry and retail level, contact materials including packaging materials were additional contamination sources for phthalates in milk and dairy products.

Stable carbon isotope composition of perirenal adipose tissue fatty acids from Engadine sheep grazing either mountain or lowland pasture

To provide further insights into ruminant lipid digestion and metabolism, and into cis-9,trans-11 18:2 synthesis, 12 growing Engadine lambs grazing either mountain pasture (2,250 m above sea level; n = 6) or lowland pasture (400 m above sea level; n = 6) were studied. Both pastures consisted exclusively of C(3) plants. Before the experiment, all animals grazed a common pasture for 6 wk. Grasses and perirenal adipose tissues of the sheep were analyzed for fatty acids by gas chromatography. Stable C-isotope ratios (δ(13)C values in ‰ vs. the Vienna Pee Dee Belemnite standard) were determined in the composite samples by elemental analysis-isotope ratio mass spectrometry. The δ(13)C of the individual fatty acids were measured by gas chromatography-combustion-isotope ratio mass spectrometry. The δ(13)C value of the entire mountain pasture grass was -27.5‰ (SD 0.31), whereas that of the lowland pasture grass was -30.0‰ (SD 0.07). This difference was reflected in the perirenal adipose tissues of the corresponding sheep (P < 0.05), even though the δ(13)C values were less in the animals than in the grass. The δ(13)C values for cis-9 16:1 and cis-9 18:1 in perirenal fat differed between mountain and lowland lambs (P < 0.05). The 16:0 in the adipose tissue was enriched in (13)C by 5‰ compared with the dietary 16:0, likely as a result of partly endogenous synthesis. The δ(13)C values of cis-9,trans-11 18:2 (cis-9,trans-11 CLA) in the adipose tissue were smaller than those of its dietary precursors, cis-9,cis-12 18:2 and cis-9,cis-12,cis-15 18:3; conversely, the δ(13)C values of trans-11 18:1 were not, suggesting that large proportions of perirenal cis-9,trans-11 18:2 were of endogenous origin and discrimination against (13)C occurred during Δ(9)-desaturation. The same discrimination was indicated by the isotopic shift between 16:0 and cis-9 16:1 in the mountain grazing group. Furthermore, the δ(13)C values of cis-9,trans-11 18:2 were smaller relative to the precursor fatty acids in the mountain lambs compared with the lowland group. This result suggests a reduced extent of biohydrogenation in lambs grazing on mountain grass in comparison with those grazing on lowland grass. This was supported by the smaller cis-9,trans-11 18:2 concentrations in total fatty acids found in the adipose tissues of the lowland lambs (P < 0.001). The results of this study demonstrate that natural differences between δ(13)C values of swards from different pastures and the adipose tissue fatty acids could be used as tracers in studies of lipid metabolism in ruminants.

An intronic polymorphism in the porcine IRF7 gene is associated with better health and immunity of the host during Sarcocystis infection, and affects interferon signalling

Interferon regulatory factor 7 (IRF7), as a key regulator of type I interferon response, plays an important role during innate response against viral infection. Although well conserved across species, the structure of IRF7 and its function during parasite infection are not well documented in farm animals, such as the pig. To bridge this gap, we have determined the porcine IRF7 gene structure and identified two intronic single nucleotide polymorphisms (SNPs), SNP g.748G>C and SNP g.761A>G, in commercial pig breeds. The distribution of SNP g.761A>G in multiple breeds suggested that it was in Hardy-Weinberg equilibrium and allowed us to map it at the top of SSC2. We found that during Sarcocystis miescheriana infection, the G allele was associated with high lymphocyte levels (P < 0.02), reduced drop in platelet levels (P < 0.002) and IgG1-Th2-dominated response (P < 0.05). This suggests that the G allele was associated with better health and immunity of the host during Sarcocystis infection. Furthermore, we have also provided suggestive evidence that the G allele of SNPc.761A>G enhances the transactivation activity of IRF7, possibly by improving IRF7 transcript splicing of intron-3. These findings would suggest that IRF7, as a transcriptional regulator, is involved in the defence mechanism against a larger spectrum of pathogens, and in more host species, than initially anticipated.

Commuting by bike in Belgium, the costs of minor accidents

Minor bicycle accidents are defined as "bicycle accidents not involving death or heavily injured persons, implying that possible hospital visits last less than 24 hours". Statistics about these accidents and related injuries are very poor, because they are mostly not reported to police, hospitals or insurance companies. Yet, they form a major share of all bicycle accidents. Official registrations underestimate the number of minor accidents and do not provide cost data, nor the distance cycled. Therefore related policies are hampered by a lack of accurate data. This paper provides more insight into the importance of minor bicycle accidents and reports the frequency, risk and resulting costs of minor bicycle accidents. Direct costs, including the damage to bike and clothes as well as medical costs and indirect costs such as productivity loss and leisure time lost are calculated. We also estimate intangible costs of pain and psychological suffering and costs for other parties involved in the accident. Data were collected during the SHAPES project using several electronic surveys. The weekly prospective registration that lasted a year, covered 1187 persons that cycled 1,474,978 km. 219 minor bicycle accidents were reported. Resulting in a frequency of 148 minor bicycle accidents per million kilometres. We analyzed the economic costs related to 118 minor bicycle accidents in detail. The average total cost of these accidents is estimated at 841 euro (95% CI: 579-1205) per accident or 0.125 euro per kilometre cycled. Overall, productivity loss is the most important component accounting for 48% of the total cost. Intangible costs, which in past research were mostly neglected, are an important burden related to minor bicycle accidents (27% of the total cost). Even among minor accidents there are important differences in the total cost depending on the severity of the injury.

Variation in resistance to the porcine reproductive and respiratory syndrome virus (PRRSV) in Pietrain and Miniature pigs

Porcine reproductive and respiratory syndrome (PRRS) is one of the economically most important diseases of swine. Viraemia and the prolonged persistence of the virus are among the most critical factors. Virus replication and severity of disease vary with virus isolates, and there is rising evidence for a genetic component of the host susceptibility. Dissecting the genetic basis of resistance/susceptibility to PRRS virus (PRRSV) might lead to improved knowledge on the molecular mechanisms of PRRS and the establishment of genetic markers for future disease control. The aim of this study was to establish a porcine model with emphasized genetic differences in PRRSV susceptibility. Seven 'Wiesenauer Miniature' pigs (MI), a local German breed and eight commercial Pietrain (PI) pigs were challenged with 10(5) TCID(50) of an attenuated PRRSV strain (Ingelvac PRRSV MLV). Clinical status, viraemia and seroconversion of the pigs were compared. No clinical signs were observed during the experiment. Viraemia peaked on day 6 p.i., with 100% of viraemic pigs in PI and on day 12 p.i with 87% of viraemic MI. Viraemia lasted for up to 35 days in MI and for at least 72 days in PI. This surprising result was confirmed by a second study with another four MI. MI and PI showed maximum virus titres of 10(2.5) TCID(50)/ml of serum and 10(4.5) TCID(50)/ml, respectively, indicating a virus replication in MI of approximately 3.3% that of PI over the complete period. MI were more efficient in antibody production. With such pronounced breed differences, the model is of high relevance for the genetic dissection of PRRS pathogenesis and susceptibility.

SNPs in the porcine GOT1 gene improve a QTL for serum aspartate aminotransferase activity on SSC14

Clinical-chemical traits are essential parameters to quantify the health status of individuals and herds, but the knowledge about their genetic architecture is sparse, especially in swine. We have recently described three QTL for serum aspartate aminotransferase activity (sAST), and one of these maps to a region on SSC14 where the aspartate aminotransferase coding gene GOT1 is located. This QTL was only apparent under the acute burden of a model disease. The aim of the present study was to characterize GOT1 as a candidate gene and to test the effects of different GOT1 SNPs as potential quantitative trait nucleotides (QTNs) for sAST. Nine SNPs within GOT1 were identified, and SNP c.-793C>G significantly increased the QTL effects and narrowed the confidence interval from 90 to 15 cM. Additionally, we found a significant association of SNP c.-793C>G in a commercial outbred line, but with reversed phase. We conclude that GOT1 is a putative candidate gene for the sAST QTL on SSC14, and that SNP c.-793C>G is close to the responsible QTN.

Quantitative trait loci for white blood cell numbers in swine

Differential white blood cell counts are essential diagnostic parameters in veterinary practice but knowledge on the genetic architecture controlling variability of leucocyte numbers and relationships is sparse, especially in swine. Total leucocyte numbers (Leu) and the differential leucocyte counts, i.e. the fractions of lymphocytes (Lym), polymorphonuclear leucocytes [neutrophils (Neu), eosinophils (Eos) and basophils (Bas)] and monocytes (Mon) were measured in 139 F(2) pigs from a Meishan/Pietrain family, before and after challenge with the protozoan pathogen Sarcocystis miescheriana for genome-wide quantitative trait loci (QTL) analysis. After infection, the pigs passed through three stages representing acute disease, reconvalescence and chronic disease. Nine genome-wide significant and 29 putative, single QTL controlling leucocyte traits were identified on 15 chromosomes. Because leucocyte traits varied with health and disease status, QTL influencing the leucocyte phenotypes showed specific health/disease patterns. Regions on SSC1, 8 and 12 contained QTL for baseline leucocyte traits. Other QTL regions reached control on leucocyte traits only at distinct stages of the disease model. Two-thirds of the QTL have not been described before. Single QTL explained up to 19% of the phenotypic variance in the F(2) animals. Related traits were partly under common genetic influence. Our analysis confirms that leucocyte trait variation is associated with multiple chromosomal regions.

Quantitative trait loci for red blood cell traits in swine

Haematological traits are essential diagnostic parameters in veterinary practice but knowledge on the genetic architecture controlling variability of erythroid traits is sparse, especially in swine. To identify QTL for erythroid traits in the pig, haematocrit (HCT), haemoglobin (HB), erythrocyte counts (RBC) and mean corpuscular haemoglobin content (MCHC) were measured in 139 F(2) pigs from a Meishan/Pietrain family, before and after challenge with the protozoan pathogen Sarcocystis miescheriana. The pigs passed through three stages representing acute disease, reconvalescence and chronic disease. Forty-three single QTL controlling erythroid traits were identified on 16 chromosomes. Twelve of the QTL were significant at the genome-wide level while 31 were significant at a chromosome-wide level. Because erythroid traits varied with health and disease status, QTL influencing the erythroid phenotypes showed specific health/disease patterns. Regions on SSC5, 7, 8, 12 and 13 contained QTL for baseline erythroid traits, while the other QTL regions affected distinct stages of the disease model. Single QTL explained 9-17% of the phenotypic variance in the F(2) animals. Related traits were partly under common genetic influence. Our analysis confirms that erythroid trait variation differs between Meishan and Pietrain breeds and that this variation is associated with multiple chromosomal regions.

Clinical, morphological, cytogenetic, and prognostic features of patients with myelodysplastic syndromes and del(5q) including band q31

We analyzed data of 76 consecutive patients with myelodysplastic syndrome (MDS) and isolated del(5q) (n=66) or del(5q) plus one additional chromosomal abnormality (n=10) included in our MDS database over the last 26 years. The median age of our patient population was 66.8 years. The male to female ratio was 1:1.7. In all, 14 patients (18%) had advanced MDS with an increased medullary blast count. A total of 17 patients (22%) had significant dysplasia in the nonmegakaryocytic cell lines. Nearly half of the study population showed erythroid hypoplasia in the bone marrow. The projected median survival of patients with isolated del(5q) is 146 months for a median follow-up of 67 months. Patients with an increased medullary blast count and those with an additional chromosomal abnormality have a significantly shorter overall survival (24 and 45 months, respectively) than patients with isolated del(5q). We did not find survival differences for different cytogenetic breakpoints, nor did the amount of dysplasia have an impact on survival in our population. In total, 29 patients have died. Deaths occurred primarily due to transformation into acute leukemia, infection, or cardiac failure. Our data support the current definition of a separate entity of MDS with del(5q) that has been suggested by the World Health Organization.

Orthopithonella collaris sp. nov., a new calcareous dinoflagellate cyst from the K/T boundary (Fish Clay, Stevns Klint/Denmark)

A new calcareous dinoflagellate cyst species, Orthopithonella collaris sp. nov., is described from the Cretaceous/Tertiary (K/T) boundary clay (Fish Clay) of Stevns Klint, Denmark, on the basis of SEM studies and light-microscopic analyses of thin sections of single specimens. The species has been found exclusively in the Fish Clay and as such may be a potential marker for the K/T boundary. Its pulse-like occurrence is thought to be due to the abrupt, relatively short-term ecological catastrophe associated with the K/T boundary event.

Organic-walled dinoflagellate cysts in western equatorial Atlantic surface sediments: distributions and their relation to environment

In contrast to the wide range of studies carried out in temperate and high-latitude oceanic regions, only a few studies have focused on recent and Holocene organic-walled dinoflagellate cyst assemblages from the tropics. This information is, however, essential for fully understanding the ability of species to adapt to different oceanographic regimes, and ultimately their potential application to local and regional palaeoenvironmental and palaeoceanographic reconstructions. Surface sediment samples of the western equatorial Atlantic Ocean north of Brazil, an area greatly influenced by Amazon River discharge waters, were therefore analysed in detail for their organic-walled dinoflagellate cyst content. A diverse association of 43 taxa was identified, and large differences in cyst distribution were observed. The cyst thanatocoenosis in bottom sediments reflects the seasonal advection of Amazon River discharge water through the Guyana Current and the North Equatorial Countercurrent well into the North Atlantic. To establish potential links between cyst distribution and the environmental conditions of the upper water column, distribution patterns were compared with mean temperature, salinity, density and stratification gradients within the upper water column (0-100m) over different times of the year, using correspondence analysis and canonical correspondence analysis. The analyses show that differences in these parameters only play a subordinate role in determining species distribution. Instead, nutrient availability, or related factors, dominates the distribution pattern. The only possible indicators of slightly reduced salinities are Trinovantedinium applanatum and Lingulodinium machaerophorum. Four assemblage groups of cyst taxa with similar environmental affinities related to specific water masses/currents can be distinguished and have potential for palaeoenvironmental reconstruction.

Multiplex-PCR-based differentiation and characterization of Candida-isolates derived from tortoises (Testudinidae)

Candida isolates (n=23) derived from Testudinidae were investigated by multiplex-polymerase chain reaction (PCR). The isolates comprised 13 Candida (C.) tropicalis, nine C. albicans and one C. parapsilosis. In addition, five reference strains C. albicans (ATCC 10231), C. tropicalis (DSM 4238), C. parapsilosis (DSM 4237), C. glabrata (ATCC 70614) and C. krusei (ATCC 70075) were investigated. PCR revealed easily distinguishable species-specific amplicons of the chs1-gene and resulted in a clear identification in all cases. No discrepancies between conventional identification techniques and the PCR-based system were seen. The described PCR offers a rapid alternative to conventional techniques for the identification of C. albicans, C. glabrata, C. tropicalis, C. parapsilosis and C. krusei.

Spatial distribution of calcareous dinoflagellate cysts in surface sediments of the Atlantic Ocean between 13 degrees N and 36 degrees S

To enhance the limited information available about the palaeo-ecological significance of calcareous dinoflagellates, we have studied their lateral distribution in surface sediments of the equatorial and south Atlantic between 13 degrees N and 36 degrees S. Calcareous dinoflagellate cysts appear to be widely distributed throughout the studied area. In the surface sediments, concentrations (cyst per gram dry sediment) of the vegetative stage Thoracosphaera heimii are generally higher than that of the (presumably) calcareous resting cysts. Distribution patterns in surface sediments of Orthopithonella granifera (Fütterer) Keupp and Versteegh, Rhabdothorax spp. Kamptner., Sphaerodinella albatrosiana (Kamptner) Keupp and Versteegh S. albatrosiana praratabulated, Sphaerodinella tuberosa var. 1 (Kamptner) Keupp and Versteegh and S. tuberosa var. 2 and the ratios between these species have been compared with temperature, salinity, density and stratification gradients in the upper water column. Rhabdothorax spp. is characteristically present in sediments of more temperate regions characterized by high seasonality. Dinoflagellates producing these cysts are able to tolerate high nutrient concentrations, and mixing of the water column. S. albatrosiana is abundant in regions characterized by high sea surface temperatures and oligotrophic surface water conditions. In contrast, the distribution of S. tuberosa var. 2 is negatively related to temperature. The other cyst species did not show a characteristic pattern in relation to the studied environmental gradients.The ratio of Sphaerodinella tuberosa var. 2 to Orthopithonella granifera can be used for reconstructing the presence of stratification in the upper 50m of the water column, whereas the ratios of S. tuberosa var. 2 to Sphaerodinella albatrosiana and of O. granifera to Rhabdothorax spp. might be used for palaeotemperature reconstructions. Calcareous dinoflagellate cysts are abundant in oligotrophic areas and may be useful for the reconstruction of palaeoenvironmental conditions.

Sequencing and characterization of the cryptic plasmid QpRS from Coxiella burnetii

Plasmid QpRS from Coxiella burnetii, isolate Priscilla Q177, phase I, has been completely sequenced. DNA for sequencing was amplified with "extra-long" (XL) PCR. The size of the QpRS plasmid sequence was determined to be 39,280 bp, with a G + C content of 39.3%. Putative proteins associated with replication and recombination were identified. The sequence of QpRS plasmid was analyzed for shared and unique regions among C. burnetii plasmids.