Sample Preparation Protocol Research Articles

An isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS)-based candidate reference measurement procedure (RMP) for the quantification of lamotrigine in human serum and plasma.

We developed an isotope dilution (ID)-liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based candidate reference measurement procedure (RMP) for lamotrigine in human serum and plasma, using quantitative nuclear magnetic resonance-characterized reference standards to ensure traceability to the International System of Units. A sample preparation protocol based on protein precipitation combined with LC-MS/MS analysis using a C18 column for chromatographic separation was established for the quantification of lamotrigine in human serum and plasma. Assay validation was performed according to current guidelines. Spiked serum and plasma samples were used to assess selectivity and specificity; a post-column infusion experiment and comparison of standard line slopes were performed to ascertain possible matrix effects. Precision and accuracy were determined in a 5days validation experiment. Measurement uncertainty was determined per the Guide to the Expression of Uncertainty in Measurement. The method allowed the quantification of lamotrigine in serum and plasma in a range of 0.600-24.0μg/mL without any observable matrix effects. The relative mean bias (n=6) ranged from 1.7 to 3.7%; intermediate precision, including variances in between-day, -calibration, and -injection, was ≤2.4%, independent of the level and matrix. Total measurement uncertainty for a single measurement was≤2.6%; expanded uncertainty was≤5.2% (coverage factor k=2). This candidate RMP based on ID-LC-MS/MS provides a traceable and reliable platform for the standardization of routine assays and the evaluation of clinical samples.

Elucidating the Metabolism of 2,4-Dibromophenol in Plants.

Crops can be extensively exposed to organic pollutants, since soil is a major sink for pollutants discarded into the environment. This creates potential human exposure through the consumption of pollutant-accumulated foods. Elucidating the uptake and metabolism of xenobiotics in crops is essential for the assessment of dietary exposure risk in humans. However, for such experiments, the use of intact plants requires long-term experiments and complex sample preparation protocols that can be affected by various factors. Plant callus cultures combined with high-resolution mass spectrometry (HRMS) may provide a solution for the accurate and time-saving identification of metabolites of xenobiotics in plants, as it can avoid interference from the microbial or fungal microenvironment, shorten the treatment duration, and simplify the matrix effect of intact plants. 2,4-dibromophenol, a typical flame retardant and endocrine disrupter, was chosen as the model substance due to its widespread occurrence in soil and its uptake potential by plants. Herein, plant callus was generated from asepsis seeds and exposed to sterile 2,4-dibromophenol-containing culture medium. The results showed that eight metabolites of 2,4-dibromophenol were identified in the plant callus tissues after 120 h of incubation. This indicates that 2,4-dibromophenol was rapidly metabolized inthe plant callus tissues. Thus, the plant callus culture platform is an effective method to evaluate the uptake and metabolism of xenobiotics in plants.

Getting Ready for Large-Scale Proteomics in Crop Plants.

Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.

Platelet count, temperature and pH value differentially affect hemostatic and immunomodulatory functions of platelets

Platelets are primarily recognized for their role in hemostasis, but also regulate immune responses by interacting with leukocytes. Their highly sensitive nature enables platelets to rapidly respond to micro-environmental changes, which is crucial under physiological condition but can jeopardize in vitro analyses. Thus, we tested how platelet count and changes in pH and temperatures, which are commonly experienced during inflammation and infection but also affected by ex vivo analyses, influence platelet-leukocyte interaction and immunomodulation.Reducing platelet count by up to 90 % slightly decreased platelet activation and platelet-leukocyte aggregate formation, but did not affect CD11b activation nor CD62L shedding of monocytes or neutrophils. Acidosis (pH 6.9) slightly elevated platelet degranulation and binding to innate leukocytes, though pH changes did not modulate leukocyte activation. While platelet responsiveness was higher at room temperature than at 37 °C, incubation temperature did not affect platelet-leukocyte aggregate formation. In contrast, platelet-mediated CD11b activation and CD62L expression increased with temperature.Our data thus demonstrate the importance of standardized protocols for sample preparation and assay procedure to obtain comparable data. Further, unspecific physiologic responses such as thrombocytopenia, acidosis or temperature changes may contribute to platelet dysfunction and altered platelet-mediated immunomodulation in inflammatory and infectious disease.

Reliable cell preparation protocol for Raman imaging to effectively differentiate normal leukocytes and leukemic blasts

Leukemias are a remarkably diverse group of malignancies originating from abnormal progenitor cells in the bone marrow. Leukemia subtypes are classified according to the cell type that has undergone neoplastic transformation using demanding and time-consuming methods. Alternative is Raman imaging that can be used both for living and fixed cells. However, considering the diversity of leukemic cell types and normal leukocytes, and the availability of different sample preparation protocols, the main objective of this work was to verify them for leukemia and normal blood cell samples for Raman imaging.The effect of glutaraldehyde (GA) fixation in a concentration gradient (0.1 %, 0.5 %, and 2.5 % GA) on the molecular structure of T-cell acute lymphoblastic leukemia (T-ALL) and peripheral blood mononuclear cells (PBMCs) was verified. Changes in the secondary structure of proteins within cells were indicated as the main effect of fixation, as shown by an increase in band intensity at 1041 cm−1, characteristic for in-plane δ(CH) deformation in phenylalanine (Phe).Different sensitivity of mononuclear and leukemic cells to fixation was observed. While the 0.1 % concentration of GA was too low to preserve the cell structure for an extended period of time, a GA concentration of 0.5 % seemed optimal for both normal and malignant cells. Chemical changes in PBMCs samples stored for 11 days were also investigated, which manifested in numerous modifications in the secondary structure of proteins and the content of nucleic acids. The impact of cell preculturing for 72 h after unbanking was verified, and there was no significant effect on the molecular structure of cells fixed with 0.5 % GA. In summary, the developed protocol for the preparation of samples for Raman imaging allows for the effective differentiation of fixed normal leukocytes from malignant T lymphoblasts.

An isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS)-based candidate reference measurement procedure (RMP) for the quantification of gabapentin in human serum and plasma.

To describe and validate a reference measurement procedure (RMP) for gabapentin, employing quantitative nuclear magnetic resonance (qNMR) spectroscopy to determine the absolute content of the standard materials in combination with isotope dilution-liquid chromatograph-tandem mass spectrometry (ID-LC-MS/MS) to accurately measure serum and plasma concentrations. A sample preparation protocol based on protein precipitation in combination with LC-MS/MS analysis using a C8 column for chromatographic separation was established for the quantification of gabapentin. Assay validation anddetermination of measurement uncertainty were performed according to guidance from the Clinical and Laboratory Standards Institute, the International Conference on Harmonization, and the Guide to the expression of uncertainty in measurement. ID-LC-MS/MS parameters evaluated included selectivity, specificity, matrix effects, precision and accuracy, inter-laboratory equivalence, and uncertainty of measurement. The use of qNMR provided traceability to International System (SI) units. The chromatographic assay was highly selective, allowing baseline separation of gabapentin and the gabapentin-lactam impurity, without observable matrix effects. Variability between injections, preparations, calibrations, and days (intermediate precision) was <2.3%, independent of the matrix, while the coefficient of variation for repeatability was 0.9-2.0% across all concentration levels. The relative mean bias ranged from-0.8-1.0% for serum and plasma samples. Passing-Bablok regression analysis indicated very good inter-laboratory agreement; the slope was 1.00 (95% confidence interval [CI] 0.98 to 1.03) and the intercept was-0.05 (95% CI -0.14 to 0.03). Pearson's correlation coefficient was≥0.996. Expanded measurement uncertainties for single measurements were found to be≤5.0% (k=2). This analytical protocol for gabapentin, utilizing traceable and selective qNMR and ID-LC-MS/MS techniques, allows for the standardization of routine tests and the reliable evaluation of clinical samples.

Analysis of Organochlorine Pesticides in a Soil Sample by a Modified QuEChERS Approach Using Ammonium Formate

Currently, the QuEChERS method represents the most widely used sample preparation protocol worldwide for analyzing pesticide residues in a broad variety of matrices both in official and non-official laboratories. The QuEChERS method using ammonium formate has previously proven to be advantageous compared to the original and the two official versions. On the one hand, the simple addition of 0.5 g of ammonium formate per gram of sample is sufficient to induce phase separation and achieve good analytical performance. On the other hand, ammonium formate reduces the need for maintenance in routine analyses. Here, a modified QuEChERS method using ammonium formate was applied for the simultaneous analysis of organochlorine pesticide (OCP) residues in agricultural soil. Specifically, 10 g of the sample was hydrated with 10 mL of water and then extracted with 10 mL of acetonitrile. Next, phase separation was carried out using 5 g of ammonium formate. After centrifugation, the supernatant was subjected to a dispersive solid-phase extraction clean-up step with anhydrous magnesium sulfate, primary-secondary amine, and octadecylsilane. Gas chromatography-mass spectrometry was used as the analytical technique. The QuEChERS method using ammonium formate is demonstrated as a successful alternative for extracting OCP residues from a soil sample.

Improving the routine analysis of siderite for δ13 C and δ18 O in environmental change research.

The carbon (δ13 C) and oxygen (δ18 O) isotope composition of siderite (FeCO3 ) is used widely to understand and quantify geochemical processes to reconstruct past climate and environmental change. However, few laboratories follow precisely the same protocol for the preparation and analysis of siderite-bearing materials, which combined with the absence of international reference materials and mineral-specific acid fractionation factors, leads potentially to significant differences in isotope data generated by individual laboratories. Here we examine procedures for the isotope analysis of siderite and discuss factors potentially contributing to inconsistencies in sample measurement data. Isotope analysis of siderite is first assessed using similar versions of the classical off-line, sealed vessel acid digestion method by comparing data sets obtained from intercomparison materials measured at two participating laboratories. We then compare data from the classical method against those generated using an automated preparation technique using data produced from an independent set of test materials. Measurement of siderite δ13 C is generally both repeatable and reproducible, but measurement of δ18 O may be subject to large (~1‰), method-dependent bias for siderite reacted at differing temperatures (70°C and 100°C) under classical and automated CO2 preparation conditions. The potential for poor oxygen isotope measurement reproducibility is amplified by local differences in sample preparation protocols and procedures used to calibrate measurement data to international reference scales. We offer suggestions for improving the repeatability and reproducibility of δ13 C and δ18 O analysis on siderite. The challenge of producing consistent isotope data from siderite can only be resolved by ensuring the availability of siderite reference materials to facilitate identical treatment as a basis for minimising method-dependent contributions to data inconsistency between laboratories.

Solid-phase microextraction Arrow combined with comprehensive two-dimensional gas chromatography-mass spectrometry for the elucidation of the volatile composition of honey samples.

In this work, a solid-phase microextraction (SPME) Arrow method combined with comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) was developed for the elucidation of the volatile composition of honey samples. The sample preparation protocol was optimized to ensure high extraction efficiency of the volatile organic compounds (VOCs) which are directly associated with the organoleptic properties of honey and its acceptance by the consumers. Following its optimization, SPME Arrow was compared to conventional SPME in terms of sensitivity, precision, and number of extracted VOCs. The utilization of SPME Arrow fibers enabled the determination of 203, 147, and 149 compounds in honeydew honey, flower honey, and pine honey, respectively, while a significantly lower number of compounds (124, 94, and 111 for honeydew honey, flower honey, and pine honey, respectively) was determined using conventional SPME. At the same time, the utilization of SPME Arrow resulted in enhanced sensitivity and precision. All things considered, SPME Arrow and GC × GC-MS can be considered as highly suitable for the elucidation of the volatile composition of complex food samples resulting in high sensitivity and separation efficiency.

Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes

Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals-from three wards and one hospital laboratory-using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1-V2 and V3-V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1-V2 and V3-V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.

IMPRESSÃO 3D DE SEPARADOR MAGNÉTICO: UMA ABORDAGEM ACESSÍVEL PARA O PREPARO DE AMOSTRAS NO DIAGNÓSTICO DA COVID-19

3D PRINTING OF MAGNETIC SEPARATOR: AN AFFORDABLE APPROACH TO SAMPLE PREPARATION IN THE COVID-19 DIAGNOSIS. This report describes the fabrication of a low-cost magnetic separator holder combining 3D printing and compact neodymium blocks for allowing magnetic extraction and purification of RNA from samples collected by nasopharyngeal swab from patients infected by SARS-CoV-2. The device was designed to contain 24 entrances for plastic microtubes in an arrangement like a commercial device. The proof of concept of the proposed device was successfully demonstrated through the sample extraction and purification of swab samples collected from eight patients suspected of SARS-CoV-2 infection. The sample preparation protocol was performed using a commercial kit containing magnetic beads and different solutions. The performance of the printed device was compared to a commercial magnetic separator, usually employed in the golden standard techniques. The fabrication of the 3D printed magnetic separator was completed under optimized printing conditions within 6 h at cost of 4 USD per unit. The RNA extracted from samples using both devices was analyzed by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and the achieved results have indicated no statistical different at confidence level of 95%. Based on the achievements, the use of 3D printing and neodymium blocks have demonstrated an alternative route to be used in routing analysis associated to COVID-19 diagnosis.

An analysis for proteomic profile of NeuroD2 related changes in N2A neuroblastoma cell line

Aim: NeuroD2 transcription factor is a key regulator of neurogenin-NeuroD signaling network and induces neuronal development, differentiation, neurogenesis and calcium dependent signaling. NeuroD2 regulates expression of survival and plasticity related proteins in neurons. Surprisingly, inhibition of NeuroD2 causes an increase in apoptotic cell death. Even though previous studies found out important data about NeuroD2 function, molecular interactions of NeuroD2 behind all of these impacts remains elusive. For this reason, it was aimed to shed light on the proteome profile of NeuroD2 based changes in the N2A cell line. Materials and methods: NeuroD2 over-expression and NeuroD2 inhibition groups were created via lentiviral vectors. Mouse N2A cell line was transfected with the given vectors and incubated for 6 hours. After incubation samples were prepared for proteomic analyses with Filter Aided Sample Preparation (FASP) protocol an LC-MS/MS analysis was carried out. Results: Under conditions of overexpression and inhibition, detected proteins were filtered according to significant cut off values. The filtered proteins were further investigated to exhibit a coherent expression in each situation. Eventually, increased NeuroD2 activity was accompanied by an increase in N-alpha-acetyltransferase 25 (NAA25), and Synaptobrevin homolog (YKT6). On the other hand, when NeuroD2 was suppressed, expression of Cytoplasmic Dynein 1 Light Intermediate Chain 1, Kinesin-Like Protein (KIF-11), Leucine-tRNA Ligase (LARS1), and Ubiquitin-Associated Protein 2 (UBA2) were found to be upregulated with a back action. Conclusion: Up-regulations of the proteins Cytoplasmic Dynein 1, KIF11, LARS1, and UBA2 suggested that these proteins might be controlled by inhibiting NeuroD2. Axonal transport, neuronal signaling, and activity of PI3K/AKT pathway can be indirectly induced by NeuroD2.

Critical evaluation of sample preparation for SP-ICP-MS determination of selenium nanoparticles in microorganisms – focus on yeast

Different sample preparation protocols for the characterization of biogenic SeNPs in yeast by SP-ICP-MS have been critically evaluated.

A low-cost, paper-based hybrid capture assay to detect high-risk HPV DNA for cervical cancer screening in low-resource settings.

Cervical cancer is a leading cause of cancer death for women in low-resource settings. The World Health Organization recommends that cervical cancer screening programs incorporate HPV DNA testing, but available tests are expensive, require laboratory infrastructure, and cannot be performed at the point-of-care. We developed a two-dimensional paper network (2DPN), hybrid-capture, signal amplification assay and a point-of-care sample preparation protocol to detect high-risk HPV DNA from exfoliated cervical cells within an hour. The test does not require expensive equipment and has an estimated cost of <$3 per test without the need for batching. We evaluated performance of the paper HPV DNA assay with short synthetic and genomic HPV DNA targets, HPV positive and negative cellular samples, and two sets of clinical samples. The first set of clinical samples consisted of 16 biobanked, provider-collected cervical samples from a study in El Salvador previously tested with careHPV and subsequently tested in a controlled laboratory environment. The paper HPV DNA test correctly identified eight of eight HPV-negative clinical samples and seven of eight HPV-positive clinical samples. We then performed a field evaluation of the paper HPV DNA test in a hospital laboratory in Mozambique. Cellular controls generated expected results throughout field testing with fully lyophilized sample preparation and 2DPN reagents. When evaluated with 16 residual self-collected cervicovaginal samples previously tested by the GeneXpert HPV assay ("Xpert"), the accuracy of the HPV DNA paper test in the field was reduced compared to testing in the controlled laboratory environment, with positive results obtained for all eight HPV-positive samples as well as seven of eight HPV-negative samples. Further evaluation showed reduction in performance was likely due in part to increased concentration of exfoliated cells in the self-collected clinical samples from Mozambique compared with provider-collected samples from El Salvador. Finally, a formal usability assessment was conducted with users in El Salvador and Mozambique; the assay was rated as acceptable to perform after minimal training. With additional optimization for higher cell concentrations and inclusion of an internal cellular control, the paper HPV DNA assay offers promise as a low-cost, point-of-care cervical cancer screening test in low-resource settings.

Evaluation of the influence of the cultivation medium on the result of identification of microorganisms from the group of acid-resistant bacteria of the order actinomycetales by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Problem with mass spectrometers is the difficulty in identifying some genera of acid-fast bacteria (AFB). Due to the peculiarities of the colony architectonics (the formation of dry colonies with a complex structure) and the structure of the cell wall, the probability of obtaining a sufficient amount of ribosomal proteins is significantly reduced. This problem is partially solved using an extended method of direct application and extraction with formic acid, which can significantly improve the quality of the identification. The study analyzed strains of microorganisms obtained during the examination of patients with suspected tuberculosis. In total, 287 strains of nontuberculous mycobacteria (NTM) were obtained. In addition, 63 strains of the most common bacteria from the AFB group were analyzed. Matrix-assisted laser desorption/ionization (MALDI) was used. Three main methods of sample preparation of microorganisms according to the manufacturer's recommendations for use with the MALDI-time-of-flight (ToF) mass spectrometry method were used in the work: Direct coating method, extended direct coating method, and formic acid extraction method. When evaluating the influence of the cultivation medium on the result of NTM identification by MALDI-ToF mass spectrometry, statistically significant results of the influence of the medium on the result of NTM identification were revealed for all compared parameters. Optimization of sample preparation protocols and assessment of the impact on the identification of new methods of cultivating microorganisms can significantly improve the quality of the identification of both clinically significant microorganisms from the AFB group and saprophytic microflora, the clinical significance of which has not been proven at the moment.

A conventional fixation volume electron microscopy protocol for plants.

Volume electron microscopy techniques play an important role in plant research from understanding organelles and unicellular forms to developmental studies, environmental effects and microbial interactions with large plant structures, to name a few. Due to large air voids central vacuole, cell wall and waxy cuticle, many plant tissues pose challenges when trying to achieve high quality morphology, metal staining and adequate conductivity for high-resolution volume EM studies. Here, we applied a robust conventional chemical fixation strategy to address the special challenges of plant samples and suitable for, but not limited to, serial block-face and focused ion beam scanning electron microscopy. The chemistry of this protocol was modified from an approach developed for improved and uniform staining of large brain volumes. Briefly, primary fixation was in paraformaldehyde and glutaraldehyde with malachite green followed by secondary fixation with osmium tetroxide, potassium ferrocyanide, thiocarbohydrazide, osmium tetroxide and finally uranyl acetate and lead aspartate staining. Samples were then dehydrated in acetone with a propylene oxide transition and embedded in a hard formulation Quetol 651 resin. The samples were trimmed and mounted with silver epoxy, metal coated and imaged via serial block-face scanning electron microscopy and focal charge compensation for charge suppression. High-contrast plant tobacco and duckweed leaf cellular structures were readily visible including mitochondria, Golgi, endoplasmic reticulum and nuclear envelope membranes, as well as prominent chloroplast thylakoid membranes and individual lamella in grana stacks. This sample preparation protocol serves as a reliable starting point for routine plant volume electron microscopy.

Comparison of laboratory methods for identifying members of the family Mycobacteriaceae.

The introduction of a method based on matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF mass spectrometry) into the practice of laboratories significantly increased the identification of acid-resistant bacteria (ARB). Seventy-four nontuberculous mycobacteria (NTM) cultures identified by deoxyribonucleic acid (DNA) hybridization, polymerase chain reaction, Sanger sequencing, and MALDI-ToF mass spectrometry. Analysis of the identification results obtained by the methods of DNA hybridization and Sanger sequencing showed a complete match only for 67.6% of samples of the total number of cultures included in the study. The partial match of the identification results was 68.9%. When comparing the results of the identification of 74 samples obtained by MALDI-ToF mass spectrometry to the results obtained by sequencing, full match of identification of Mycobacterium chimaera/Mycobacterium intracelullare, Mycobacterium porcinum/Mycobacterium peregrinum and Mycobacterium tuberculosis complex was found for 90.5% of the samples; the partial match of the results - for 4.1%.. DNA hybridization as a method for identifying NTM showed acceptable sensitivity and specificity; however, for mass spectrometry, a significantly higher sensitivity with comparable specificity was determined. Mass spectrometry is an important element in the modern system of species identification of microorganisms. The optimization of sample preparation protocols and assessment of the impact on the identification of new techniques of cultivation of microorganisms can significantly improve the quality of identification of microorganisms from the ARB group. In this case, accurate species identification and the development of algorithms for its application will improve the diagnosis of diseases caused by ARB.

Large cell triaxial tests of a partially saturated soil with vegetation

The use of vegetation roots as a nature-based solution against landslides and erosion requires the definition of sample preparation protocols and adoption of equipment that allows testing representative elementary volumes of the whole soil-root system. For this purpose, large cell triaxial compression tests were carried out on fallow and vegetated samples at different degrees of saturation. Samples were prepared by static compaction of a silty sand and seeded with Cynodon dactylon. The hydraulic state during plants growth was controlled and reproduced on bare soil samples. After isotropic compressions, the shearing phase was carried out at very low confining stresses (i.e., below 50 kPa). Tests were deemed to be comparable by assessing the normalised volume of roots with respect to soil, after shearing. For a given confining stress, soil samples with higher matric suction exhibited higher shear strength, furtherly increased by roots. The stress-strain behaviour observed in the vegetated soil systematically changed, when comparing tests at low and high matric suction values, due to the different mechanisms of vegetation reinforcement depending on the hydraulic state at the soil-root interface. The results were successfully interpreted within a failure criterion and skeleton stress framework for partially saturated soils, considering soil suction, degree of saturation, soil microstructure and the normalised volume of roots.

A Robust and Clinically Applicable Sample Preparation Protocol for Urinary Extracellular Vesicle Isolation Suitable for Mass Spectrometry-Based Proteomics.

Urinary extracellular vesicles (uEVs) are a rich source of noninvasive protein biomarkers. However, for translation to clinical applications, an easy-to-use uEV isolation protocol is needed that is compatible with proteomics. Here, we provide a detailed description of a quick and clinical applicable uEV isolation protocol. We focus on the isolation procedure and subsequent in-depth proteome characterization using LC-MS/MS-based proteomics. As an example, we show how differential analyses can be performed using urine samples obtained from prostate cancer patients, compared to urine from controls.

Single-run UHPLC-MS/MS method for simultaneous quantification of endogenous steroids and their phase II metabolites in serum for anti-doping purposes

Anti-doping rule violations related to the abuse of endogenous anabolic androgenic steroids can be currently discovered by the urinary steroidal module of Athlete Biological Passport. Since this powerful tool is still subjected to some limitations due to various confounding factors altering the steroid profile, alternative strategies have been constantly proposed. Among these, the measurement of blood concentrations of endogenous steroid hormones by LC-MS is currently of increasing interest in anti-doping, bringing significant advantages for the detection of testosterone abuse in females and in individuals with deletion of UGT2B17 enzyme. Although various research groups have made significant efforts in method development, there is currently no accepted or harmonized anti-doping method for quantitative analysis of the various testosterone doping markers in blood. In this study we present a UHPLC-MS/MS method for the quantification of major circulating steroid hormones together with an extended panel of glucuro- and sulpho-conjugated phase II metabolites of androgens. Chromatographic setup was optimized by comparing the performance of three different C18 stationary phases and by the careful selection of mobile phases with the aim of separating all the target steroids, including numerous isomeric/isobaric compounds. MS parameters were fine-tuned to obtain the sensitivity needed for measuring the target analytes, that show specific serum concentrations ranging from low pg/mL for less abundant compounds to μg/mL for sulpho-conjugated steroids. Finally, sample preparation protocol was developed for the extraction of steroid hormones from 200 μL of serum and the performance was evaluated in terms of extraction recovery and matrix effect. The final method was then applied to authentic serum samples collected from healthy volunteers (40 males and 40 females) at the Blood Bank of the City of Health and Science University Hospital of Turin. The analysis of these samples allowed to obtain results on serum concentrations of the targeted steroids, with particular emphasis on previously undiscovered phase II metabolites, such as the isomers of 5-androstane-3,17-diol glucuronide. This preliminary application also enabled measuring dihydrotestosterone sulphate in male samples, efficiently separating this analyte from its isomer, epiandrosterone sulphate, which circulates in blood at high concentrations.The promising results of this study are encouraging for the measurement of blood steroid profile markers in serum and plasma samples for Athlete Biological Passport purposes.