Universal Pretreatment Development for Low-input Proteomics Using Lauryl Maltose Neopentyl Glycol

In recent years, there has been a growing demand for low-input proteomics, particularly in the context of single-cell proteomics (SCP). In this study, we have developed a lauryl maltose neopentyl glycol (LMNG)-assisted sample preparation (LASP) method. This method effectively reduces protein and peptide loss in samples by incorporating LMNG, a surfactant, into the digestion solution and subsequently removing the LMNG simply via reversed phase solid-phase extraction. The advantage of removing LMNG during sample preparation for general proteomic analysis is the prevention of mass spectrometry (MS) contamination. When we applied the LASP method to the low-input SP3 method and on-bead digestion in coimmunoprecipitation-MS, we observed a significant improvement in the recovery of the digested peptides. Furthermore, we have established a simple and easy sample preparation method for SCP based on the LASP method and identified a median of 1175 proteins from a single HEK239F cell using liquid chromatography (LC)-MS/MS with a throughput of 80 samples per day.

Optimization of mRNA extraction from human nasal mucosa biopsies for gene expression profile analysis by qRT-PCR

Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold-standard method for analyzing modifications in gene expression in cells and tissues. However, large quantities of high-quality RNA samples are needed for analyzing the expression of multiple genes from one human tissue sample. Here, we provide an optimized protocol for extracting large amounts of RNA from human nasal mucosal biopsies. The quality and quantity of samples were sufficient for qRT-PCR analyses of the expressions of various genes, in duplicate. In contrast to other protocols, we optimized RNA isolation to increase the amount from nasal biopsy samples for analyses of multiple genes. In most previous publications, expressions of only one or a few genes, including housekeeping genes, were analyzed because the amount of biological material was small. We were able to improve our protocol with respect to the yield and quality of RNA. This is likely to produce better results from molecular analyses of very small biopsy samples of human nasal mucosa.

Increasing the coverage of the N-terminome with LysN amino terminal enrichment (LATE)

The field of N-terminomics has been advancing with the development of novel methods that provide a comprehensive and unbiased view of the N-terminome. Negative selection N-terminomics enables the identification of free and naturally modified protein N-termini. Here, we present a streamlined protocol that combines two negative selection N-terminomics methods, LATE and HYTANE, to increase N-terminome coverage by 1.5-fold compared to using a single methodology. Our protocol includes sample preparation and data analysis of both methods and can be applied to studying the N-terminome of diverse samples. The suggested approach enables researchers to achieve a more detailed and accurate understanding of the N-terminome.

GdClean: removal of Gadolinium contamination in mass cytometry data

MOTIVATION

Mass cytometry (Cytometry by Time-Of-Flight, CyTOF) is a single-cell technology that is able to quantify multiplex biomarker expressions and is commonly used in basic life science and translational research. However, the widely used Gadolinium (Gd)-based contrast agents (GBCAs) in magnetic resonance imaging (MRI) scanning in clinical practice can lead to signal contamination on the Gd channels in the CyTOF analysis. This Gd contamination greatly affects the characterization of the real signal from Gd-isotope-conjugated antibodies, severely impairing the CyTOF data quality and ruining downstream single-cell data interpretation.

RESULTS

We first in-depth characterized the signals of Gd isotopes from a control sample that was not stained with Gd-labeled antibodies but was contaminated by Gd isotopes from GBCAs, and revealed the collinear intensity relationship across Gd contamination signals. We also found that the intensity ratios of detected Gd contamination signals to the reference Gd signal were highly correlated with the natural abundance ratios of corresponding Gd isotopes. We then developed a computational method named by GdClean to remove the Gd contamination signal at the single-cell level in the CyTOF data. We further demonstrated that the GdClean effectively cleaned up the Gd contamination signal while preserving the real Gd-labeled antibodies signal in Gd channels. All of these shed lights on the promising applications of the GdClean method in preprocessing CyTOF datasets for revealing the true single-cell information.

AVAILABILITY AND IMPLEMENTATION

The R package GdClean is available on GitHub at https://github.com/JunweiLiu0208/GdClean.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Sample Preparation of Secreted Mammalian Host Cell Proteins and Their Characterization by Two-Dimensional Electrophoresis and Western Blotting

The manufacturing and purification of therapeutic recombinant proteins expressed by cultivated mammalian cells into the cell culture medium leaves the potential for contamination by host cell proteins (HCPs). Validation and quality control testing of any therapeutic protein needs to include a test to show that HCP contamination is at a minimal level. The presence of residual mammalian HCPs during purification and in the final drug product is typically determined using enzyme linked immunosorbent assay (ELISA), which is regarded as the gold standard. The complexity and heterogeneity of HCPs, which include proteins with significant differences in molecular weight (MW), isoelectric point (pI) and hydrophobicity, poses a challenge to detection and quantitation. Two-dimensional gel electrophoresis (2-DE) is one of the most powerful technologies for studying complex protein profiles and is a valuable analytical method in biologics manufacturing. In the purification process, it is very important to know the nature and composition of HCPs, and this information can be used in a rational process design in order to minimize HCPs from the product. Additionally, 2-DE in combination with western blotting can support ELISA development and quality control for the comprehensive immunochemical detection of HCPs by estimating the recognition capacity of the polyclonal serum used in those assays. Here, we present a standardized 2-DE western blotting protocol which takes into account the latest developments in sample preparation of HCPs, protein electrophoresis, protein transfer, immunostaining, and imaging.

Bead-Based Multiplex Immunoassays: Procedures, Tips, and Tricks

Multiplex immunoassays enable the measurement of multiple proteins in a small volume of sample in a single well, enhancing discovery and profiling of multiple biomarkers when compared to singleplex immunoassays. In order to ensure optimal results are generated, it is important to know what critical actions and assay steps can adversely affect results. This chapter covers best practices for sample collection and storage, to important considerations during the assay run, and ways to ensure optimal data generation and efficient data analysis. When these practices are applied, the potential to generate actionable and quality results accelerates the research and discovery process.

Released N-Glycan Analysis for Biotherapeutic Development Using Liquid Chromatography and Mass Spectrometry

In this chapter, we describe an LC-fluorescence (FLR)/MS-based method for released N-glycan analysis in the development of biotherapeutic proteins. The method includes enzymatic release and labeling of N-glycans with a signal-enhancing tag, LC-MS data collection, and data interpretation. Using the given protocol, up to 24 glycan samples can be prepared within 1 h, while the LC-FLR/MS data can be collected and analyzed using an established data processing method in a semi-automated manner.

A Protocol for Isolation, Purification, Characterization, and Functional Dissection of Exosomes

Extracellular vesicles (EVs) are membrane-enclosed vesicles released by cells. They carry proteins, nucleic acids, and metabolites which can be transferred to a recipient cell, locally or at a distance, to elicit a functional response. Since their discovery over 30 years ago, the functional repertoire of EVs in both physiological (e.g., organ morphogenesis, embryo implantation) and pathological (e.g., cancer, neurodegeneration) conditions has cemented their crucial role in intercellular communication. Moreover, because the cargo encapsulated within circulating EVs remains protected from degradation, their diagnostic as well as therapeutic (such as drug delivery tool) applications have garnered vested interest. Global efforts have been made to purify EV subtypes from biological fluids and in vitro cell culture media using a variety of strategies and techniques, with a major focus on EVs of endocytic origin called exosomes (30-150 nm in size). Given that the secretome comprises of soluble secreted proteins, protein aggregates, RNA granules, and EV subtypes (such as exosomes, shed microvesicles, apoptotic bodies), it is imperative to purify exosomes to homogeneity if we are to perform biochemical and biophysical characterization and, importantly, functional dissection. Besides understanding the composition of EV subtypes, defining molecular bias of how they reprogram target cells also remains of paramount importance in this area of active research. Here, we outline a systematic "how to" protocol (along with useful insights/tips) to obtain highly purified exosomes and perform their biophysical and biochemical characterization. This protocol employs a mass spectrometry-based proteomics approach to characterize the protein composition of exosomes. We also provide insights on different isolation strategies and their usefulness in various downstream applications. We outline protocols for lipophilic labeling of exosomes to study uptake by a recipient cell, investigating cellular reprogramming using proteomics and studying functional response to exosomes in the Transwell-Matrigel™ Invasion assay.

Improved Immunoprecipitation to Mass Spectrometry Method for the Enrichment of Low-Abundant Protein Targets

Immunoprecipitation (IP) is commonly used upstream of mass spectrometry (MS) as an enrichment tool for low-abundant protein targets. However, several aspects of the classical IP procedure such as nonspecific protein binding to the isolation matrix, detergents or high salt concentrations in wash and elution buffers, and antibody chain contamination in elution fractions render it incompatible with downstream mass spectrometry analysis. Here, we discuss an improved IP-MS workflow that is designed to minimize sample prep time and these contaminants. The method employs biotinylated antibodies to the targets of interest and streptavidin magnetic beads that exhibit low background binding. In addition, alterations in the elution protocol and subsequent MS sample prep were made to reduce time and antibody leaching in the eluent, minimizing potential ion suppression effects and thereby maximizing detection of multiple target antigens and interacting proteins.

Sample Preparation for Metabolic Profiling using MALDI Mass Spectrometry Imaging

Metabolomics, the study to identify and quantify small molecules and metabolites present in an experimental sample, has emerged as an important tool to investigate the biological activities during development and diseases. Metabolomics approaches are widely employed in the study of cancer, nutrition/diet, diabetes, and other physiological and pathological conditions involving metabolic processes. An advantageous tool that aids in metabolomic profiling advocated in this paper is matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI). Its ability to detect metabolites in situ without labeling, structural modifications, or other specialized reagents, such as those used in immunostaining, makes MALDI MSI a unique tool in advancing methodologies relevant in the field of metabolomics. An appropriate sample preparation process is critical to yield optimal results and will be the focus of this paper.

Non-chromatographic Speciation of As by HG Technique-Analysis of Samples with Different Matrices

The applicability of the hydride generation (HG) sample introduction technique combined with different spectrochemical detection methods for non-chromatographic speciation of toxic As species, i.e., As(III), As(V), dimethylarsinate (DMA) and monomethylarsonate (MMA), in waters and other environmental, food and biological matrices is presented as a promising tool to speciate As by obviating chromatographic separation. Different non-chromatographic procedures along with speciation protocols reported in the literature over the past 20 year are summarized. Basic rules ensuring species selective generation of the corresponding hydrides are presented in detail. Common strategies and alternative approaches are highlighted. Aspects of proper sample preparation before analysis and the selection of adequate strategies for speciation purposes are emphasized.

Investigations into the Effects of pH on Quantitative Measurements of Lactate in Biological Media Using ATR-FTIR Spectroscopy

Quantification of lactate/lactic acid in critical care environments is essential as lactate serves as an important biochemical marker for the adequacy of the haemodynamic circulation in shock and of cell respiration at the onset of sepsis/septic shock. Hence, in this study, ATR-FTIR was explored as a potential tool for lactate measurement, as the current techniques depend on sample preparation and fails to provide rapid response. Moreover, the effects of pH on PBS samples (7.4, 7, 6.5 and 6) and change in solution conditions (PBS to whole blood) on spectral features were also investigated. A total 189 spectra from five sets of lactate containing media were obtained. Results suggests that lactate could be measured with more than 90% accuracy in the wavenumber range of 1500–600 cm−1. The findings of this study further suggest that there exist no effects of change in pH or media, when estimating lactate concentration changes in this range of the Mid-IR spectral region.

Covalent Organic Frameworks in Sample Preparation

Covalent organic frameworks (COFs) can be classified as emerging porous crystalline polymers with extremely high porosity and surface area size, and good thermal stability. These properties have awakened the interests of many areas, opening new horizons of research and applications. In the Analytical Chemistry field, COFs have found an important application in sample preparation approaches since their inherent properties clearly match, in a good number of cases, with the ideal characteristics of any extraction or clean-up sorbent. The review article is meant to provide a detailed overview of the different COFs that have been used up to now for sample preparation (i.e., solid-phase extraction in its most relevant operational modes-conventional, dispersive, magnetic/solid-phase microextraction and stir-bar sorptive extraction); the extraction devices/formats in which they have been applied; and their performances and suitability for this task.

Biocompatible chitosan-zinc oxide nanocomposite based dispersive micro-solid phase extraction coupled with HPLC-UV for the determination of rosmarinic acid in the extracts of medical plants and water sample

In the present research, a procedure was described for the recovery of rosmarinic acid (RA) from medical extract samples using chitosan‑zinc oxide nanoparticles as a biocompatible nanocomposite (CS-ZnO-NC). The dispersive micro-solid phase extraction (D-μ-SPE) of RA from the medical extract samples was investigated by using the prepared biocompatible composite as a solid phase. The HPLC-UV method was used for measuring the extracted RA. The important variables (pH, biocompatible composite mass, contact time, and volume of eluent) associated with the extraction process were analyzed by the application of central composite design (CCD). The achieved optimum values for the mentioned variables were 7.0, 10 mg, 4 min, and 180 μL, respectively. The extraction recovery (99.68%) obtained from the predicted model was in agreement with the experimental data (98.22 ± 1.33%). In addition, under the obtained optimum conditions and over the concentration in the range of 2-3500 ng mL-1, a linear calibration curve was obtained with R2 > 0.993. The limit of detection (LOD) and quantification (LOQ) values were computed, and the obtained ranges were respectively from 0.060 to 0.089 ng mL-1 and 0.201 to 0.297 ng mL-1. In addition, the enrichment factors were obtained in the range of 93.7-110.5 with preconcentration factor of 83.3. Therefore, the D-μ-SPE-HPLC-UV method could be used for analyzing RA in the samples of the extracts obtained from the medical plants and water with the recovery values of the analyte in the range of 96.6%-105.4% and the precision with relative standard deviation <5.7%.

A novel approach to remove interference of therapeutic monoclonal antibody with serum protein electrophoresis

OBJECTIVES

Multiple myeloma (MM) is characterized by malignant growth of plasma cells, usually producing a monoclonal antibody (mAb). New treatments for MM include therapeutic monoclonal antibodies (tmAbs), but patients treated with tmAb demonstrate interference on serum electrophoresis (SPE) and immunoprecipitation electrophoresis (IEP). Evaluation of treatment efficacy and determination of MM remission include SPE and IEP which identifies mAb, but cannot differentiate between disease associated mAb and tmAb. We hypothesized that tmAb could be removed from patient sera before testing by SPE and IEP to provide accurate diagnoses for clinicians.

DESIGN AND METHODS

We developed the Antigen Specific therapeutic monoclonal Antibody Depletion Assay (ASADA), that utilizes magnetic beads coated with the cognate antigen of the tmAbs, to deplete two different tmAb (daratumumab, elotuzumab) from saline and patient sera and assessed for complete removal of tmAb by SPE and IEP.

RESULTS

We found that tmAb could be efficiently removed from saline and patient sera. ASADA demonstrated acceptable analytical specificity and sensitivity in IEP. Recovery of appropriate quantitative values by SPE was demonstrated with clinically acceptable precision. A single bead cocktail could be used to treat both daratumumab and elotuzumab.

CONCLUSIONS

This demonstrates proof of principle that ASADA can be used to remove current and future tmAb from patient sera, regardless of platform. This research provides for accurate diagnosis, disease monitoring, and remission status in MM patients being treated with tmAb.

Investigating pre-analytical requirements for serum and plasma based infrared spectro-diagnostic

Infrared spectroscopy is a rapid, easy-to-operate, label-free and therefore cost-effective technique. Many studies performed on biofluids (eg, serum, plasma, urine, sputum, bile and cerebrospinal fluid) have demonstrated its promising application as a clinical diagnostic tool. Given all these characteristics, infrared spectroscopy appears to be an ideal candidate to be implemented into the clinics. However, before considering its translation, a clear effort is needed to standardise protocols for biofluid spectroscopic analysis. To reach this goal, careful investigations to identify and track errors that can occur during the pre-analytical phase is a crucial step. Here, we report for the first time, results of investigations into pre-analytical factors that can affect the quality of the spectral data acquired on serum and plasma, such as the impact of long-term freezing time storage of samples as well as the month-to-month reproducibility of the spectroscopic analysis. The spectral data discrimination has revealed to be majorly impacted by a residual water content variation in serum and plasma dried samples.

Simultaneous determination of intracellular concentrations of tenofovir, emtricitabine, and dolutegravir in human brain microvascular endothelial cells using liquid chromatography-tandem mass spectrometry (LC-MS/MS)

Combination antiretroviral therapy (cART) regimens are recommended for HIV patients to better achieve and maintain plasma viral suppression. Despite adequate plasma viral suppression, HIV persists inside the brain, which is, in part thought to result from poor brain penetration of antiretroviral drugs. In this study, a simple and ultra-sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for simultaneous determination of tenofovir, emtricitabine, and dolutegravir in cell lysates of an immortalized human brain microvascular endothelial cell line (hCMEC/D3) was developed and validated. Analytes were separated on a reverse phase C18 column using water and 0.1% formic acid in acetonitrile as mobile phases. The analytes were detected using positive electrospray ionization mode with multiple reaction monitoring (MRM). The assay was linear in the concentration range of 0.1-100 ng mL-1 for all analytes. Intra- and inter-assay precision and accuracy were within ±13.33% and ±10.53%, respectively. This approach described herein was used to determine the intracellular accumulation of tenofovir, emtricitabine, dolutegravir simultaneously in hCMEC/D3 cells samples.

High-throughput quantification of carboxymethyl lysine in serum and plasma using high-resolution accurate mass Orbitrap mass spectrometry

BACKGROUND

Carboxymethyl lysine is an advanced glycation end product of interest as a potential biomarker of cardiovascular and other diseases. Available methods involve ELISA, with potential interference, or isotope dilution mass spectrometry (IDMS), with low-throughput sample preparation.

METHODS

A high-throughput sample preparation method based on 96-well plates was developed. Protein-bound carboxymethyl lysine and lysine were quantified by IDMS using reversed phase chromatography coupled to a high-resolution accurate mass Orbitrap Exactive mass spectrometer. The carboxymethyl lysine concentration (normalized to lysine concentration) was measured in 1714 plasma samples from the British Regional Heart Study (BRHS).

RESULTS

For carboxymethyl lysine, the lower limit of quantification (LLOQ) was estimated at 0.16 μM and the assay was linear between 0.25 and 10 μM. For lysine, the LLOQ was estimated at 3.79 mM, and the assay was linear between 2.5 and 100 mM. The intra-assay coefficient of variation was 17.2% for carboxymethyl lysine, 9.3% for lysine and 10.5% for normalized carboxymethyl lysine. The inter-assay coefficient of variation was 18.1% for carboxymethyl lysine, 14.8 for lysine and 16.2% for normalized carboxymethyl lysine. The median and inter-quartile range of all study samples in each batch were monitored. A mean carboxymethyl lysine concentration of 2.7 μM (IQR 2.0-3.2 μM, range 0.2-17.4 μM) and a mean normalized carboxymethyl lysine concentration of 69 μM/M lysine (IQR 54-76 μM/M, range 19-453 μM/M) were measured in the BRHS.

CONCLUSION

This high-throughput sample preparation method makes it possible to analyse large cohorts required to determine the potential of carboxymethyl lysine as a biomarker.

Detection of the tuberculosis biomarker mannose-capped lipoarabinomannan in human serum: Impact of sample pretreatment with perchloric acid

The development of an accurate and rapid diagnostic test for tuberculosis (TB) to use at point of need is vital to efforts aimed at reducing the global burden from this disease. This paper builds on our previous studies of mannose-capped lipoarabinomannan (ManLAM) as a serum biomarker for active TB infection by means of a heterogeneous immunoassay. That work found that complexation with components in serum (e.g., proteins) sterically hindered the capture and/or labeling of ManLAM in an immunoassay at levels <10 ng mL-1, compromising the clinical utility of this biomarker for detection of active TB infection. We also showed that the acidification of ManLAM-containing serum samples with perchloric acid improved the detectability of ManLAM by 250× by complex disruption when compared to measurements of untreated serum. The present study examined what effects the PCA treatment of serum samples may have on the recovery and structural integrity of ManLAM, owing to its potential susceptibility to acid hydrolysis. Recovery was assessed with an enzyme-linked immunosorbent assay (ELISA). The possible impact of acid hydrolysis on the ManLAM structure was investigated by gas chromatography-mass spectrometry and carbohydrate chemical degradation methods. The ELISA study indicated that while the signal strength for ManLAM in the serum spike-in experiments was significantly stronger after PCA pretreatment when compared to untreated human serum, it was only ∼20% of the ManLAM measured in physiological buffer. This loss in detectability was shown by structural analysis to arise mainly from the acid-induced degradation of the arabinan domains of ManLAM that are targeted by antibodies used for antigen capture and/or tagging. The implications of these findings in terms of the detection of this important biomarker for TB are also discussed.

Versatile exclusion-based sample preparation platform for integrated rare cell isolation and analyte extraction

Rare cell populations provide a patient-centric tool to monitor disease treatment, response, and resistance. However, understanding rare cells is a complex problem, which requires cell isolation/purification and downstream molecular interrogation - processes challenged by non-target populations, which vary patient-to-patient and change with disease. As such, cell isolation platforms must be amenable to a range of sample types while maintaining high efficiency and purity. The multiplexed technology for automated extraction (mTAE) is a versatile magnetic bead-based isolation platform that facilitates positive, negative, and combinatorial selection with integrated protein staining and nucleic acid isolation. mTAE is validated by isolating circulating tumor cells (CTCs) - a model rare cell population - from breast and prostate cancer patient samples. Negative selection yielded high efficiency capture of CTCs while positive selection yielded higher purity with an average of only 95 contaminant cells captured per milliliter of processed whole blood. With combinatorial selection, an overall increase in capture efficiency was observed, highlighting the potential significance of integrating multiple capture approaches on a single platform. Following capture (and staining), on platform nucleic acid extraction enabled the detection of androgen receptor-related transcripts from CTCs isolated from prostate cancer patients. The flexibility (e.g. negative, positive, combinatorial selection) and capabilities (e.g. isolation, protein staining, and nucleic acid extraction) of mTAE enable users to freely interrogate specific cell populations, a capability required to understand the potential of emerging rare cell populations and readily adapt to the heterogeneity presented across clinical samples.

Detection of Glyphosate in Drinking Water: A Fast and Direct Detection Method without Sample Pretreatment

Glyphosate (Gly) is one of the most problematic pesticides that repeatedly appears in drinking water. Continuous on-site detection of Gly in water supplies can provide an early warning in incidents of contamination, before the pesticide reaches the drinking water. Here, we report the first direct detection of Gly in tap water with electrochemical sensing. Gold working electrodes were used to detect the pesticide in spiked tap water without any supporting electrolyte, sample pretreatment or electrode modifications. Amperometric measurements were used to quantify Gly to a limit of detection of 2 μM, which is below the regulation limit of permitted contamination of drinking water in the United States. The quantification of Gly was linearly proportional with the measured signal. The selectivity of this method was evaluated by applying the same technique on a Gly Metabolite, AMPA, and on another pesticide, omethoate, with a chemical structure similar to Gly. The testing revealed no interfering electrochemical activity at the potential range used for Gly detection. The simple detection of Gly presented in this work may lead to direct on-site monitoring of Gly contamination at drinking water sources.

Validated UPLC-MS/MS method for the quantification of dasatinib in plasma: Application to pharmacokinetic interaction studies with nutraceuticals in Wistar rats

Dasatinib (DAS) is a tyrosine kinase inhibitor (TKI) used in the treatment of chronic myeloid leukemia and in the management of ulcerative colitis (UC). Since some nutraceuticals (e.g. curcumin, olive oil, and cocoa extract) could alter the function of ABC transporters and /or CYP450 enzymes, DAS bioavailability could potentially be affected following their co-administration. This work aims at studying the possibility of PK interaction between DAS and the selected nutraceuticals in UC rats using UPLC- MS/MS. Chromatographic analysis was carried out using BEH C 18 column (Waters) with a mobile phase consisting of acetonitrile and 50% aqueous methanol, 65:35, v/v, each with 0.1% formic acid and using erlotinib (ERL) as an internal standard (IS). DAS quantitation was carried out using multiple reaction monitoring (MRM) with positive ionization of the transitions at m/z 488.03 > 400.92 (DAS), and m/z 394.29 > 278.19 (ERL). Method validation was assessed as per the FDA guidelines for bioanalytical methods for DAS determination within the concentration range 1–500 ng/mL. No significant effect on the oral bioavailability of DAS was reported with any of the studied nutraceuticals. Thus, the concomitant administration of these nutraceuticals with DAS could be considered safe with a necessity to perform more detailed clinical investigations.

Rapid and safe one-step extraction method for the identification of Brucella strains at genus and species level by MALDI-TOF mass spectrometry

Brucellosis is essentially a disease of domesticated livestock; however, humans can also be infected via the consumption of contaminated meat or dairy products, underlying the need for rapid and accurate identification methods. Procedures for microbiological identification and typing of Brucella spp. are expensive, time-consuming, and must be conducted in biohazard containment facilities to minimize operator risk. The development of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based assay has reduced the processing time while maintaining performance standards. In this study, to improve the identification accuracy and suitability of the MALDI-TOF-based assay for routine diagnosis, we developed a new protein extraction protocol and generated a custom reference database containing Brucella strains representative of the most widespread species. The reference library was then challenged with blind-coded field samples isolated from infected animals. The results indicated that the database could be used to correctly identify 99.5% and 97% of Brucella strains at the genus and species level, respectively, indicating that the performance of the assay was not affected by the different culture conditions used for microbial isolation. Moreover, the inactivated samples were stored and shipped to reference laboratories with no ill effect on protein stability, thus confirming the reliability of our method for routine diagnosis. Finally, we evaluated the epidemiological value of the protocol by comparing the clustering analysis results of Brucella melitensis strains obtained via multiple locus variable-number tandem repeat analysis or MALDI-TOF MS. The results showed that the MALDI-TOF assay could not decipher the true phylogenetic tree, suggesting that the protein profile did not correspond with the genetic evolution of Brucella.

Assessment of Mycotoxin Exposure in Breastfeeding Mothers with Celiac Disease

OBJECTIVE

To assess the risk of mycotoxin exposure (aflatoxin M1, ochratoxin A, and zearalenone) in celiac disease (CD) breastfeeding mothers and healthy control mothers, as well as in their offspring, by quantifying these contaminants in breast milk.

STUDY DESIGN

Thirty-five breastfeeding women with CD on a gluten-free diet and 30 healthy breastfeeding controls were recruited. Milk sampling was performed three times per day for three consecutive days. Mycotoxin content was investigated by an analytical method using immunoaffinity column clean-up and high-performance liquid chromatography (HPLC) with fluorometric detection.

RESULTS

Aflatoxin M1 (AFM1) was detected in 37% of CD group samples (mean ± SD = 0.012 ± 0.011 ng/mL; range = 0.003-0.340 ng/mL). The control group showed lower mean AFM1 concentration levels in 24% of the analyzed samples (0.009 ± 0.007 ng/mL; range = 0.003-0.067 ng/mL, ANOVA on ranks, p-value < 0.01). Ochratoxin A and zearalenone did not differ in both groups.

CONCLUSION

Breast milk AFM1 contamination for both groups is lower than the European safety threshold. However, the estimated exposures of infants from CD mothers and control mothers was much higher (≃15 times and ≃11 times, respectively) than the threshold set by the joint FAO/WHO Expert Committee on Food Additives (JECFA). Since incongruities exist between JECFA and the European Union standard, a novel regulatory review of the available data on this topic is desirable. Protecting babies from a neglected risk of high AFM1 exposure requires prompt regulatory and food-control policies.

A new approach in separating microplastics from environmental samples based on their electrostatic behavior

Numerous studies on microplastics (MPs; Ø < 5 mm) in the aquatic environment have been published, but knowledge about the occurrence and ecological risks of MPs is limited. This is in part because current data on the distribution of MPs are comparable only to a limited extent, due to the many different methods of investigation. In addition, sample preparation is often difficult such that standard procedures are lacking. The aim of this work was to simplify the preparation of different kinds of MP samples. Our method makes use of the electrostatic behavior of plastic particles to facilitate their separation from sample matter, with up to 99% of the original sample mass removed without any loss of MPs. To determine the efficacy of this approach, four different materials (quartz sand, freshwater suspended particulate matter, freshwater sediment, and beach sand) were spiked with MPs (size: 0.063-5 mm from the seven most common types of plastics, one bioplastic type, polyethylene fibers, and tire wear. A modified electrostatic metal/plastic separator was used to reduce the sample mass and concentrate the plastics based on their physical separation. The recovery achieved with this method was as high as nearly 100% for each type of material. The method was then tested on plastic particles of different shapes and types isolated from the Rhine River. These were successfully electroseparated from the four materials, which demonstrated the utility of this method. Its advantages include the simplified handling and preparation of different field samples as well as a much shorter processing time, because after the last separation step there is hardly any biological material remaining in the sample fraction.