Optimized Sample Preparation Research Articles

Suspect Screening of Lupin-Produced Phytotoxins in Environmental Samples

Phytotoxins, secondary metabolites synthesized by plants, are now recognized as a new category of environmental micropollutants. Only a limited number of phytotoxins have been detected and reported in terrestrial and aquatic environments, partially due to analytical challenges. In this article, a robust, reliable, and efficient approach, namely Source Supported Suspect Screening (4S), is introduced for high-throughput analysis of phytotoxins from their plant origin to the downstream environmental compartments. The approach was established on an ultrahigh-performance liquid chromatography–electrospray ionization–quadrupole‑time‑of‑flight-mass spectrometry (UHPLC–ESI–QTOF-MS) analytical platform where optimal sample preparation and chromatographic conditions were investigated and a new suspect screening protocol was suggested.

Evaluating the use of locked nucleic acid capture probes in hybrid LC-MS/MS analysis of siRNA analytes.

Background: Hybrid LC-MS assays for oligonucleotides rely on capture probes to develop assays with high sensitivity and specificity. Locked nucleic acid (LNA) probes are thermodynamically superior to existing capture probes, but are not currently used for hybrid LC-MS assays. Materials & methods: Using two lipid-conjugated double-stranded siRNAcompounds as model analytes, hybrid LC-MS/MS assays using LNA probes were developed. Results: The workflows demonstrated the superiority of the LNA probes, optimized sample preparation conditions to maximize analyte recovery, evaluated the need for analyte-specific internal standards, and demonstrated that advanced mass spectrometric technology can increase assay sensitivity by up to 20-fold. Conclusion: The workflow can be used in future bioanalytical studies to develop effective hybrid LC-MS/MS methods for siRNA analytes.

A magnetic nanoparticle-based microfluidic device fabricated using a 3D-printed mould for separation of Escherichia coli from blood.

Herein, A microfluidic device is described, produced with a 3D-printed master mould that rapidly separates and concentrates Escherichia coli directly from whole blood samples, enabling a reduction in the turnaround time of bloodstream infections (BSIs) diagnosis. Moreover, it promotes the cleansing of the blood samples whose complexity frequently hampers bacterial detection. The device comprises a serpentine mixing channel with two inlets, one for blood samples (spiked with bacteria) and the other for magnetic nanoparticles (MNPs) functionalized with a (bacterio)phage receptor-binding protein (RBP) with high specificity for E. coli. After the magnetic labelling of bacteria throughout the serpentine, the microchannel ends with a trapping reservoir where bacteria-MNPs conjugates are concentrated using a permanent magnet. The optimized sample preparation device successfully recovered E. coli (on average, 66%) from tenfold diluted blood spiked within a wide range of bacterial load (102CFU to 107CFUmL-1). The non-specific trapping, tested with Staphylococcus aureus, was at a negligible level of 12%. The assay was performed in 30min directly from diluted blood thus presenting an advantage over the conventional enrichment in blood cultures (BCs). The device is simple and cheap to fabricate and can be tailored for multiple bacterial separation from complex clinical samples by using RBPs targeting different species. Moreover, the possibility to integrate a biosensing element to detect bacteria on-site can provide a reliable, fast, and cost-effective point-of-care device.

Optimisation of Sample Preparation from Primary Mouse Tissue to Maintain RNA Integrity for Methods Examining Translational Control.

The protein output of different mRNAs can vary by two orders of magnitude; therefore, it is critical to understand the processes that control gene expression operating at the level of translation. Translatome-wide techniques, such as polysome profiling and ribosome profiling, are key methods for determining the translation rates occurring on specific mRNAs. These techniques are now widely used in cell lines; however, they are underutilised in tissues and cancer models. Ribonuclease (RNase) expression is often found to be higher in complex primary tissues in comparison to cell lines. Methods used to preserve RNA during lysis often use denaturing conditions, which need to be avoided when maintaining the interaction and position of the ribosome with the mRNA is required. Here, we detail the cell lysis conditions that produce high-quality RNA from several different tissues covering a range of endogenous RNase expression levels. We highlight the importance of RNA integrity for accurate determination of the global translation status of the cell as determined by polysome gradients and discuss key aspects to optimise for accurate assessment of the translatome from primary mouse tissue.

Abstract P1185: Spatial Transcriptome Profiling In The Mouse Heart With Single-Cell Resolution

Background: The spatial organization of the diverse cells in the heart shapes biological function. For instance, during the inflammatory and fibrotic processes that are central to heart disease, many cells act mainly within their local microenvironment. Recent studies using single-cell RNA sequencing (scRNA-seq) have provided a detailed list of the cell types and states involved in development, homeostasis and in cardiovascular diseases. However, scRNA-seq requires tissue dissociation, which removes spatial information and thereby limits our ability to determine how cells interact with each other to maintain health or cause disease. As a consequence, the precise spatial organization of cell types and states in the mammalian heart remains unknown. We sought to address this knowledge gap by using multiplexed error-robust fluorescence in situ hybridization (MERFISH), a method that enables simultaneous identification and localization of single transcripts from hundreds of different genes in intact tissue sections. Methods/Results: We adapted MERFISH and developed a new single-cell image segmentation method to creating a single-cell atlas of the mouse heart. First, we designed and constructed a 128-gene MERFISH probe library including cell type marker genes and also genes covering a broad range of cardiac signaling pathways. We then optimized sample preparation, including cell boundary staining and tissue clearing. Once optimized, we used this approach to image 10 μm-thick sections from healthy mouse heart, resolving tens of thousands of cells and millions of transcripts. Our data thus constitute the first single-cell spatial transcriptome atlas of the mouse heart. Conclusion: Through our newly developed cardiac MERFISH platform, we identified tens of thousands of cells and labeled millions of individual RNA transcripts in intact sections of mouse heart. Our cellular transcriptome profile maps enable new insights into how the organization of the heart shapes its biological function.

Optimal Diverse Biological Sample Preparation Methods for 2D and 3D Electron Microscopy Imaging.

Optimal Diverse Biological Sample Preparation Methods for 2D and 3D Electron Microscopy Imaging.

Optimization of bioanalysis of dried blood samples

IntroductionPharmacokinetic/pharmacodynamic modelling has emerged as a valuable technique for understanding drug exposure and response relationships in drug development. Pharmacokinetic data are often obtained by taking multiple blood samples, which may disturb physiological parameters and complicate study designs. Wearable automatic blood sampling systems can improve this limitation by collecting dried blood samples at programmable time points without disrupting cardiovascular parameters. It is the objective of this study to evaluate the bioanalysis of DBS in comparison to conventional blood sampling techniques and to optimize the recovery of various compounds spiked into canine blood dried on filter paper tape. MethodsIncubated blood samples from Beagle dogs were spiked with 16 different compounds and half of the whole blood sample was centrifuged to obtain plasma. After the dried blood sample drops were dried, liquid chromatography-mass spectrometry methods were used to analyze the samples. The study explored different anticoagulants, sample preparation methods and technical approaches to best determine the compound concentrations in dried blood samples. ResultsWith the two anticoagulants tested and using the optimized sample preparation methods and technical approaches we employed, the bioanalysis of dried blood samples can provide equivalent results to conventional blood sampling techniques. DiscussionAutomated blood sampling systems have the potential to provide increased numbers of blood samples, providing substantially more Pharmacokinetic data within safety pharmacology studies without disrupting physiological parameters. They can provide a viable alternative to traditional methods of obtaining blood for various other types of studies or analyses.

Visualization of Differential Cardiolipin Profiles in Murine Retinal Cell Layers by High-Resolution MALDI Mass Spectrometry Imaging.

The precise fatty acyl chain configuration of cardiolipin (CL), a tetrameric mitochondrial-specific membrane lipid, exhibits dependence on cell and tissue types. A powerful method to map CL profiles in tissue sections in a spatially resolved manner is matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). To build on and explore this potential, we employed a quadrupole time-of-flight mass spectrometer along with optimized sample preparation protocols. We imaged the CL profiles of individual murine retinal cell layers at a pixel size of 10 μm. In combination with tandem MS, we obtained detailed insights into the CL composition of individual retinal cell layers. In particular, we found differential expression of the polyunsaturated fatty acids (PUFA) linoleic, arachidonic, and docosahexaenoic acids. PUFAs are prone to peroxidation and hence regarded as critical factors in development and progression of retinal pathologies, such as age-related macular degeneration (AMD). The ability of MALDI-MSI to provide cues on the CL composition in neuronal tissue with close to single-cell resolution can provide important insights into retinal physiology in health and disease.

Investigation of snow cover solid phase using total‐reflection x‐ray fluorescence method for an assessment of the environmental pollution

AbstractSnow cover is an important source of data for the study of environmental pollution due to its ability to accumulate atmospheric dust particles. A total reflection x‐ray fluorescence method (TXRF) was applied to assess the concentration levels of potentially toxic elements (As, Pb, Zn, Ni, Cu, Cr, V, Mn, and Sr) in samples of snow cover solid phase collected in suburban areas of the Irkutsk region with industrial activity. Suspension was chosen as an optimal sample preparation procedure for solid phases of snow samples obtained after melting and filtration. Results were compared with those obtained by wavelength‐dispersive x‐ray fluorescence spectrometry and atomic absorption spectrometry. Precision of TXRF results expressed by repeatability values was not exceeded 15% (n = 3) for most of the elements, and the trueness of the TXRF method expressed by recovery values was in the range of 87%–115% for concentration levels of 5.0–350 μg/g. Forty samples of snow cover solid phase were analyzed by TXRF method and results were compared with the background values. The investigation showed low contamination of the studied area by Pb, Cu, V, Mn, and Sr, medium contamination by Ni, As, and Cr, and high contamination by Zn. TXRF is advantageous in being rapid, cost‐efficient, and simple and can be used as a promising method for an assessment of environmental pollution.

A new approach with dried plasma spots: a rapid determination of antidepressants and antipsychotics by fast GC-MS.

Background: The increasing prevalence of poisoning cases related to antidepressants and antipsychotics has raised concerns. Methods: To address this issue, a new adaptation of the dried plasma spot technique was developed using a 24-well plate and fast gas chromatography-mass spectrometry. The method involves the optimization of extraction variables and sample preparation, and was successfully validated. Results: The limits of quantitation ranged from 20 to 60ng/ml, and accuracy ranged from 87.8% to 112.2%. The technique was applied to 102 human plasma samples from suspected poisoning cases, with positivity of 90.2%. Conclusion: This method provides a cheap, easy to implement and fast approach, making it ideal for toxicological emergency laboratories and promoting valuable support for healthcare professionals managing poisoning cases involving antidepressants and antipsychotics.

Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes

Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-min linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Data analysis was performed with DIA-NN using a predicted spectral library. Performance was evaluated according to the number of identified proteins, quantitative precision, throughput, costs, and biological safety. With this rapid workflow, over 40% of all encoded genes were detected per bacterial species. We demonstrated the general applicability of our workflow on a set of 23 taxonomically and physiologically diverse bacterial species. We could confidently identify over 45,000 proteins in the combined dataset, of which 30,000 have not been experimentally validated before. Our work thereby provides a valuable resource for the microbial scientific community. Finally, we grew Escherichia coli and Bacillus cereus in replicates under 12 different cultivation conditions to demonstrate the high-throughput suitability of the workflow. The proteomic workflow we present in this manuscript does not require any specialized equipment or commercial software and can be easily applied by other laboratories to support and accelerate the proteomic exploration of the bacterial kingdom.

Target and non-target analytical method for potential hazardous substances in livestock and pet hair using liquid- and gas chromatography quadrupole time-of-flight mass spectrometry

Extraction using acetonitrile and water and quadrupole time-of-flight mass spectrometry (LC and GC-QTOF/MS) techniques were used to screen for potential hazardous substances in livestock and pet hair. In addition, LC-MS/MS and GC-MS/MS techniques were used for verification of the analytical method and quantitative analysis of pesticides, veterinary drugs, mycotoxins and antioxidants in hair. Optimized sample preparation involves extracting 0.05 g of sample with 0.6 mL of ACN and 0.4 mL of distilled water. In addition, the two layers were separated by adding 0.1 g of NaCl. Then, both the ACN and water layers were analyzed by LC-TOF/MS, and the ACN layer was analyzed by GC-TOF/MS. Most of the matrix effects of livestock and pet hair were less than 50%, but some matrices and components showed high results, so matrix matching correction was applied for more precise quantification. Method validation was performed for 394 constituents (293 pesticides, 93 veterinary drugs, 6 mycotoxins and 2 preservatives) in dog, cat, cow and pig hair and chicken and duck feathers. All components showed good linearity (r2 ≥0.98) in the developed assay. The quantification limit of all compounds was set at 0.02 mg/kg, which is the lowest level that satisfies the recovery rate standard. The recovery experiment was repeated 8 times at 3 concentrations. Most of the components were extracted with the ACN layer, and the recovery rate was 63.35-119.98%. In order to confirm the efficiency of extracting harmful substances from actual samples, 30 hairs of livestock and pets were screened.

Optimization of Mass Spectrometry Imaging for Drug Metabolism and Distribution Studies in the Zebrafish Larvae Model: A Case Study with the Opioid Antagonist Naloxone.

Zebrafish (ZF; Danio rerio) larvae have emerged as a promising in vivo model in drug metabolism studies. Here, we set out to ready this model for integrated mass spectrometry imaging (MSI) to comprehensively study the spatial distribution of drugs and their metabolites inside ZF larvae. In our pilot study with the overall goal to improve MSI protocols for ZF larvae, we investigated the metabolism of the opioid antagonist naloxone. We confirmed that the metabolic modification of naloxone is in high accordance with metabolites detected in HepaRG cells, human biosamples, and other in vivo models. In particular, all three major human metabolites were detected at high abundance in the ZF larvae model. Next, the in vivo distribution of naloxone was investigated in three body sections of ZF larvae using LC-HRMS/MS showing that the opioid antagonist is mainly present in the head and body sections, as suspected from published human pharmacological data. Having optimized sample preparation procedures for MSI (i.e., embedding layer composition, cryosectioning, and matrix composition and spraying), we were able to record MS images of naloxone and its metabolites in ZF larvae, providing highly informative distributional images. In conclusion, we demonstrate that all major ADMET (absorption, distribution, metabolism, excretion, and toxicity) parameters, as part of in vivo pharmacokinetic studies, can be assessed in a simple and cost-effective ZF larvae model. Our established protocols for ZF larvae using naloxone are broadly applicable, particularly for MSI sample preparation, to various types of compounds, and they will help to predict and understand human metabolism and pharmacokinetics.

Recent Progress in Micro- and Nanotechnology-Enabled Sensors for Biomedical and Environmental Challenges

Micro- and nanotechnology-enabled sensors have made remarkable advancements in the fields of biomedicine and the environment, enabling the sensitive and selective detection and quantification of diverse analytes. In biomedicine, these sensors have facilitated disease diagnosis, drug discovery, and point-of-care devices. In environmental monitoring, they have played a crucial role in assessing air, water, and soil quality, as well as ensured food safety. Despite notable progress, numerous challenges persist. This review article addresses recent developments in micro- and nanotechnology-enabled sensors for biomedical and environmental challenges, focusing on enhancing basic sensing techniques through micro/nanotechnology. Additionally, it explores the applications of these sensors in addressing current challenges in both biomedical and environmental domains. The article concludes by emphasizing the need for further research to expand the detection capabilities of sensors/devices, enhance sensitivity and selectivity, integrate wireless communication and energy-harvesting technologies, and optimize sample preparation, material selection, and automated components for sensor design, fabrication, and characterization.

GFP labeling of a Bradyrhizobium strain and an attempt to track the crack entry process during symbiosis with peanuts.

Compared to the well-studied model legumes, where symbiosis is established via root hair entry, the peanut is infected by Bradyrhizobium through the crack entry, which is less common and not fully understood. Crack entry is, however, considered a primitive symbiotic infection pathway, which could be potentially utilized for engineering non-legume species with nitrogen fixation ability. We utilized a fluorescence-labeled Bradyrhizobium strain to help in understanding the crack entry process at the cellular level. A modified plasmid pRJPaph-bjGFP, harboring the codon-optimized GFP gene and tetracycline resistance gene, was created and conjugated into Bradyrhizobium strain Lb8, an isolate from peanut nodules, through tri-parental mating. Microscopic observation and peanut inoculation assays confirmed the successful GFP tagging of Lb8, which is capable of generating root nodules. A marking system for peanut root potential infection sites and an optimized sample preparation protocol for cryostat sectioning was developed. The feasibility of using the GFP-tagged Lb8 for observing crack entry was examined. GFP signal was detected at the nodule primordial stage and the following nodule developmental stages with robust GFP signals observed in infected cells in the mature nodules. Spherical bacteroids in the root tissue were visualized at the nodules' inner cortex under higher magnification, reflecting the trace along the rhizobial infection path. The GFP labeled Lb8 can serve as an essential tool for plant-microbe studies between the cultivated peanut and Bradyrhizobium, which could facilitate further study of the crack entry process during the legume-rhizobia symbiosis.

Quantitative plasma profiling by 1H NMR-based metabolomics: impact of sample treatment.

Introduction: There is evidence that sample treatment of blood-based biosamples may affect integral signals in nuclear magnetic resonance-based metabolomics. The presence of macromolecules in plasma/serum samples makes investigating low-molecular-weight metabolites challenging. It is particularly relevant in the targeted approach, in which absolute concentrations of selected metabolites are often quantified based on the area of integral signals. Since there are a few treatments of plasma/serum samples for quantitative analysis without a universally accepted method, this topic remains of interest for future research. Methods: In this work, targeted metabolomic profiling of 43 metabolites was performed on pooled plasma to compare four methodologies consisting of Carr-Purcell-Meiboom-Gill (CPMG) editing, ultrafiltration, protein precipitation with methanol, and glycerophospholipid solid-phase extraction (g-SPE) for phospholipid removal; prior to NMR metabolomics analysis. The effect of the sample treatments on the metabolite concentrations was evaluated using a permutation test of multiclass and pairwise Fisher scores. Results: Results showed that methanol precipitation and ultrafiltration had a higher number of metabolites with coefficient of variation (CV) values above 20%. G-SPE and CPMG editing demonstrated better precision for most of the metabolites analyzed. However, differential quantification performance between procedures were metabolite-dependent. For example, pairwise comparisons showed that methanol precipitation and CPMG editing were suitable for quantifying citrate, while g-SPE showed better results for 2-hydroxybutyrate and tryptophan. Discussion: There are alterations in the absolute concentration of various metabolites that are dependent on the procedure. Considering these alterations is essential before proceeding with the quantification of treatment-sensitive metabolites in biological samples for improving biomarker discovery and biological interpretations. The study demonstrated that g-SPE and CPMG editing are effective methods for removing proteins and phospholipids from plasma samples for quantitative NMR analysis of metabolites. However, careful consideration should be given to the specific metabolites of interest and their susceptibility to the sample treatment procedures. These findings contribute to the development of optimized sample preparation protocols for metabolomics studies using NMR spectroscopy.

Optimisation and implementation of QuEChERS-based sample preparation for identification and semi-quantification of 694 targeted contaminants in honey, jam, jelly, and syrup by UHPLC-Q/ToF high-resolution mass spectrometry

A screening and semi-quantitative method was developed for the analysis of 694 various contaminants in honey, jam, jelly and syrup samples by ultrahigh-performance liquid chromatography and quadrupole time-of-flight mass spectrometry. Sample preparation, which was optimised using split factorial design, was based on acetate-buffered version of QuEChERS, followed by a clean-up step and a concentration step to enhance sensitivity of analytes. The method was validated according to SANTE/11312/2021 guidelines. The screening detection and limits of identification were established as being less than or equal to 0.05 mg.kg−1 for 89% and 74% of the contaminants, respectively. The validated screening method was applied to 50 concentrated sugary products. Overall, 46% of the samples were positive to pesticide residues. Most of the positive samples (78%) contained mixtures of pesticide residues. Three time-and-cost saving convenient strategies suitable for high-throughput analysis were proposed for the targeted semi-quantification of the previously contaminants identified in samples.

Evaluation of extraction methods for untargeted metabolomic studies for future applications in zebrafish larvae infection models

Sample preparation in untargeted metabolomics should allow reproducible extractions of as many molecules as possible. Thus, optimizing sample preparation is crucial. This study compared six different extraction procedures to find the most suitable for extracting zebrafish larvae in the context of an infection model. Two one-phase extractions employing methanol (I) and a single miscible phase of methanol/acetonitrile/water (II) and two two-phase methods using phase separation between chloroform and methanol/water combinations (III and IV) were tested. Additional bead homogenization was used for methods III and IV (III_B and IV_B). Nine internal standards and 59 molecules of interest (MoInt) related to mycobacterial infection were used for method evaluation. Two-phase methods (III and IV) led to a lower feature count, higher peak areas of MoInt, especially amino acids, and higher coefficients of variation in comparison to one-phase extractions. Adding bead homogenization increased feature count, peak areas, and CVs. Extraction I showed higher peak areas and lower CVs than extraction II, thus being the most suited one-phase method. Extraction III and IV showed similar results, with III being easier to execute and less prone to imprecisions. Thus, for future applications in zebrafish larvae metabolomics and infection models, extractions I and III might be chosen.

The identification and quantification of metal atoms in proteins using microPIXE: A critical evaluation

Around one third of all known protein molecules contain a small number of metal atoms which are often crucial to the biological function of the molecule. Identifying and quantifying these is not possible using commonly available analysis tools and there is a growing awareness that a majority of the metal atoms in the over 38,000 metalloprotein structures deposited in the Protein Data Bank are misidentified, with major consequences for the interpretation of protein function and mechanism. In the 1990s the authors developed a method for the identification and quantification of metals in liquid and crystalline protein samples by combining microbeam Proton Induced X-ray Emission and Rutherford backscattering. This has been used on overexpressed and purified proteins and has addressed many critical metal identification problems in structural biology. The capability has recently been extended to provide high throughput capability.In this paper we give an overview of the methodology and provide a critical evaluation of accuracy and detection limit and provide guidance on the optimisation of sample preparation and analysis conditions for these measurements. The discussion will be illustrated using some recent results illustrating the power of this method to answer biological questions.

Suspect Screening of Lupin-Produced Phytotoxins in Environmental Samples

Phytotoxins, the secondary metabolites synthesized by plants, are now recognized as a new category of environmental micropollutants. So far, only a limited number of phytotoxins have been detected and reported in terrestrial and aquatic environments, partially due to the analytical challenge involved. In this article, a robust, reliable, and efficient approach, namely Source Supported Suspect Screening (4S), is introduced for high-throughput analysis of phytotoxins from their plant origin to the downstream environmental compartments. The approach was established on an ultrahigh-performance liquid chromatography–electrospray ionization–quadrupole‑time‑of‑flight-mass spectrometry (UHPLC–ESI-QTOF-MS) analytical platform where optimal sample preparation and chromatographic conditions were investigated and a new suspect screening protocol was suggested.