Secondary Ion Mass Spectrometry Imaging of Molecular Distributions in Cultured Neurons and Their Processes: Comparative Analysis of Sample Preparation

Neurons often exhibit a complex chemical distribution and topography; therefore, sample preparation protocols that preserve structures ranging from relatively large cell somata to small neurites and growth cones are important factors in secondary ion mass spectrometry (SIMS) imaging studies. Here, SIMS was used to investigate the subcellular localization of lipids and lipophilic species in neurons from Aplysia californica. Using individual neurons cultured on silicon wafers, we compared and optimized several SIMS sampling approaches. After an initial step to remove the high salt culturing media, formaldehyde, paraformaldehyde, and glycerol, and various combinations thereof, were tested for their ability to achieve cell stabilization during and after the removal of extracellular media. These treatments improved the preservation of cellular morphology as visualized with SIMS imaging. For analytes >250?Da, coating the cell surface with a 3.2?nm-thick gold layer increased the ion intensity; multiple analytes previously not observed or observed at low abundance were detected, including intact cholesterol and vitamin E molecular ions. However, once a sample was coated, many of the lower molecular mass (<200?Da) analyte signals were suppressed. The optimum approach depended on the analyte being studied; the approaches evaluated included rinsing with water and cell stabilization with glycerol and 4?% paraformaldehyde. The sample preparation methods described here enhance SIMS imaging of processes of individual cultured neurons over a broad mass range with enhanced image contrast.     

Digital Microfluidics and Magnetic Bead-Based Intact Proteoform Elution for Quantitative Top-down Nanoproteomics of Single C. elegans Nematodes

While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up proteomics workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we established a facile one-pot sample preparation protocol based on protein aggregation on magnetic beads and intact proteoform elution using 40 % formic acid. Performed on a digital microfluidics device, the workflow enabled sensitive analyses of single Caenorhabditis elegans nematodes, thereby increasing the number of proteoform identifications compared to in-tube sample preparation by 46 %. Label-free quantification of single nematodes grown under different conditions allowed to identify changes in the abundance of proteoforms not distinguishable by bottom-up proteomics. The presented workflow will facilitate proteoform-directed analysis on samples of limited availability.     

Effects of soluble fractions from untreated and SiO2-treated subcellular particles of macrophages on nucleic acid metabolism in isolated nuclei of experimental granulation tissue.

Nuclei isolated from proliferating granulation tissue were incubated with 20 000 g supernatants from untreated and SiO2-treated subcellular particles of rat peritoneal macrophages in the presence of radioactive nucleic acid precursors. The supernatant from SiO2-treated subcellular particles increased the incorporation of [3H]CTP into nuclear RNA maximally by 26% at 5 min, and that of [methyl-3H]dTTP into DNA by 16% at 20 min. The release of radioactivity from labeled DNA was suppressed simultaneously. An RNase preparation from rat peritoneal macrophages enhanced the release of radioactivity from labeled DNA similarly as the soluble fraction from untreated subcellular particles of macrophages. The results suggest that the effects of the soluble fractions upon DNA metabolism of granuloma cells are at least partly independent of the effects on RNA metabolism and that the soluble fraction from SiO2-treated subcellular particles of macrophages stabilizes DNA through inhibition of nuclease activity.     

Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review

Sample preparation is an essential step for nearly every type of biochemical analysis in use today. Among the most important of these analyses is the diagnosis of diseases, since their treatment may rely greatly on time and, in the case of infectious diseases, containing their spread within a population to prevent outbreaks. To address this, many different methods have been developed for use in the wide variety of settings for which they are needed. In this work, we have reviewed the literature and report on a broad range of methods that have been developed in recent years and their applications to point-of-care (POC), high-throughput screening, and low-resource and traditional clinical settings for diagnosis, including some of those that were developed in response to the coronavirus disease 2019 (COVID-19) pandemic. In addition to covering alternative approaches and improvements to traditional sample preparation techniques such as extractions and separations, techniques that have been developed with focuses on integration with smart devices, laboratory automation, and biosensors are also discussed.     

Molecular imaging of membrane proteins and microfilaments using atomic force microscopy

Atomic force microscopy (AFM) is an emerging technique for a variety of uses involving the analysis of cells. AFM is widely applied to obtain information about both cellular structural and subcellular events. In particular, a variety of investigations into membrane proteins and microfilaments were performed with AFM. Here, we introduce applications of AFM to molecular imaging of membrane proteins, and various approaches for observation and identification of intracellular microfilaments at the molecular level. These approaches can contribute to many applications of AFM in cell imaging.     

Dried blood spot analysis with liquid chromatography and mass spectrometry: Trends in clinical chemistry

Dried blood spot samples are simple to prepare and transport, enabling safe and accessible diagnostics, both locally and globally. We review dried blood spot samples for clinical analysis, focusing on liquid chromatography-mass spectrometry as a versatile measurement tool for these samples. Dried blood spot samples can provide information for, for example, metabolomics, xenobiotic analysis, and proteomics. Targeted analyses of small molecules are the main application of dried blood spot samples and liquid chromatography-mass spectrometry, but emerging applications include untargeted metabolomics and proteomics. Applications are highly varied, including analyses related to newborn screening, diagnostics and monitoring of disease progression and treatment effects of virtually any disease, as well as studies into the physiology and effects of diet, exercise, xenobiotics, and doping. A range of dried blood spot products and methods are available, and applied liquid chromatography-mass spectrometry instrumentation is varied with regard to liquid chromatography column formats and selectivity. In addition, novel approaches such as on-paper sample preparation (e.g., selective trapping of analytes with paper-immobilized antibodies) are described. We focus on research papers published in the last 5 years.     

Integrating subcellular location for improving machine learning models of remote homology detection in eukaryotic organisms

A significant challenge in homology detection is to identify sequences that share a common evolutionary ancestor, despite significant primary sequence divergence. Remote homologs will often have less than 30% sequence identity, yet still retain common structural and functional properties. We demonstrate a novel method for identifying remote homologs using a support vector machine (SVM) classifier trained by fusing sequence similarity scores and subcellular location prediction. SVMs have been shown to perform well in a variety of applications where binary classification of data is the goal. At the same time, data fusion methods have been shown to be highly effective in enhancing discriminative power of data. Combining these two approaches in the application SVM-SimLoc resulted in identification of significantly more remote homologs (p-value<0.006) than using either sequence similarity or subcellular location independently.     

Towards the proteome of the rhodopsin-bearing post-Golgi compartment of retinal photoreceptor cells

Polarized sorting of rhodopsin in retinal rod photoreceptor cells is mediated by post-Golgi carrier membranes that bud from the trans-Golgi network and fuse with the specialized domain of the plasma membrane in the rod inner segment. The identity of the majority of the resident proteins of this organelle still remains elusive, despite multifaceted approaches to study this compartment. In the present study we have taken a proteomic approach to the analysis of the post-Golgi carriers. First, we modified the previously established fractionation protocols in order to achieve greater purity of the isolated membranes. Specifically, the new fractionation scheme depleted the post-Golgi fraction of cytosolic proteins that were the most abundant contaminants complicating analysis of two-dimensional (2-D) gel profiles in our previous preparations. The isolated membranes were subjected to 2-D gel electrophoresis, immunoblotting and microsequencing. This analysis showed that the improved subcellular fractionation yielded a fraction highly enriched in rhodopsin-bearing post-Golgi carrier membranes. Two-dimensional mapping revealed 29 proteins that are preferentially found in this fraction and therefore represent candidates for post-Golgi membrane-specific proteins. This preparation of rhodopsin-bearing post-Golgi carriers is a first step towards the proteomics of this important organelle.     

Increasing phosphoproteomic coverage through sequential digestion by complementary proteases

Protein phosphorylation is a reversible post-translational modification known to regulate protein function, subcellular localization, complex formation, and protein degradation. Detailed phosphoproteomic information is critical to kinomic studies of signal transduction and for elucidation of cancer biomarkers, such as in non-small-cell lung adenocarcinoma, where phosphorylation is commonly dysregulated. However, the collection and analysis of phosphorylation data remains a difficult problem. The low concentrations of phosphopeptides in complex biological mixtures as well as challenges inherent in their chemical nature have limited phosphoproteomic characterization and some phosphorylation sites are inaccessible by traditional workflows. We developed a sequential digestion method using complementary proteases, Glu-C and trypsin, to increase phosphoproteomic coverage and supplement traditional approaches. The sequential digestion method is more productive than workflows utilizing only Glu-C and we evaluated the orthogonality of the sequential digestion method relative to replicate trypsin-based analyses. Finally, we demonstrate the ability of the sequential digestion method to access new regions of the phosphoproteome by comparison to existing public phosphoproteomic databases. Our approach increases coverage of the human lung cancer phosphoproteome by accessing both new phosphoproteins and novel phosphorylation site information.     

A Mn12 single-molecule magnet [Mn12O12(OAc)12(dpp)4] (dppH = diphenyl phosphate) with no coordinating water molecules

The preparation and physical characterization are reported for a novel single-molecule magnet [Mn(12)O(12)(OAc)(12)(dpp)(4)] (dppH = diphenyl phosphate) with no coordinating water molecules. The crystal structure analysis reveals that there are four five-coordinate Mn(III) ions with Mn.H approaches. Addition of water in CD(2)Cl(2) solution was monitored by (1)H NMR, which showed that H(2)O could coordinate to a vacant site of a five-coordinate Mn(III) ion in solution. The measurements and analyses of magnetization hysteresis and ac magnetic susceptibility indicate that the title complex is a single-molecule magnet with a quantum tunneling behavior, whose ground state was tentatively assigned to S = 10 with g = 1.78 and D = -0.60 K.     

A pseudotargeted method based on sequential window acquisition of all theoretical spectra mass spectrometry acquisition and its application in quality assessment of traditional Chinese medicine preparation-Yuanhu Zhitong tablet

Quality control plays a key role in the application of Chinese materia medica, especially in the preparation of traditional Chinese medicine. A pseudotargeted analysis method using an ultra-high-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry that was operated in the sequential window acquisition of all theoretical spectra mode was proposed to explore the chemical markers of traditional Chinese medicine preparation. Full-scan-based untargeted analysis was applied to extract the target ions. After data preprocessing, 302 target ions were extracted and used for the subsequent sequential window acquisition of all theoretical spectra analyses. The established sequential window acquisition of all theoretical spectra-based pseudotargeted approaches exhibited good repeatability and a wide linear range. The established method was successfully applied to discover analytical markers for the Yuanhu Zhitong tablet. After multivariate statistical analysis, 94 potential markers were identified. Ten markers were annotated by matching accurate m/z and product ion information obtained from previous reports. It is clearly indicated that the pseudotargeted analysis could make a great contribution to the quality assessment of traditional Chinese medicine preparation as a newly emerging technique.     

Evaluation of multidimensional capillary electrophoretic methodologies for determination of amino bisphosphonate pharmaceuticals

Alendronate and pamidronate are amino bisphosphonate analogues of pyrophosphate used for the treatment of a variety of bone diseases. Analysis of these compounds is problematic due to their polar ionic nature, lack of a suitable chromophore and chelation properties and current analytical approaches involve extensive sample preparation and derivatization procedures. The potential of multidimensional capillary electrophoretic methodological approaches, which eliminate sample preparation have been evaluated for the analysis of these compounds both in aqueous and urinary matrices. Capillary isotachophoresis (cITP) was employed as a pre-separation and on-line sample concentration step prior to analytical determination using either cITP or capillary zone electrophoresis (CZE) with conductivity detection. Single cITP, cITP-cITP and cITP-CZE approaches were partially validated with respect to repeatability, recovery and linearity of response for both compounds. The increases in sensitivity achievable through increasing injection volume from 30 to 300muL may render such strategies appropriate for determination of these agents at biologically relevant concentrations with minimal sample work-up.     

Enantioselective chromatography as a powerful alternative for the preparation of drug enantiomers

The preparative separation of enantiomers by chromatography on chiral stationary phases (CSPs) has been recognized as being a useful alternative to the more conventional approaches such as enantioselective synthesis and enzymatically catalyzed transformations. The possible contribution of enantioselective chromatography with respect to the preparation of enantiomerically pure compounds is reviewed in the context of the competitive approaches and depending on the application scale, with a special emphasis on the recent progresses achieved in this particular field of separation.     

Sample preparation with solid phase microextraction and exhaustive extraction approaches: Comparison for challenging cases

In chemical analysis, sample preparation is frequently considered the bottleneck of the entire analytical method. The success of the final method strongly depends on understanding the entire process of analysis of a particular type of analyte in a sample, namely: the physicochemical properties of the analytes (solubility, volatility, polarity etc.), the environmental conditions, and the matrix components of the sample. Various sample preparation strategies have been developed based on exhaustive or non-exhaustive extraction of analytes from matrices. Undoubtedly, amongst all sample preparation approaches, liquid extraction, including liquid–liquid (LLE) and solid phase extraction (SPE), are the most well-known, widely used, and commonly accepted methods by many international organizations and accredited laboratories. Both methods are well documented and there are many well defined procedures, which make them, at first sight, the methods of choice. However, many challenging tasks, such as complex matrix applications, on-site and in vivo applications, and determination of matrix-bound and free concentrations of analytes, are not easily attainable with these classical approaches for sample preparation.     

What do we need for a superhydrophobic surface? A review on the recent progress in the preparation of superhydrophobic surfaces

Superhydrophobic surfaces have drawn a lot of interest both in academia and in industry because of the self-cleaning properties. This critical review focuses on the recent progress (within the last three years) in the preparation, theoretical modeling, and applications of superhydrophobic surfaces. The preparation approaches are reviewed according to categorized approaches such as bottom-up, top-down, and combination approaches. The advantages and limitations of each strategy are summarized and compared. Progress in theoretical modeling of surface design and wettability behavior focuses on the transition state of superhydrophobic surfaces and the role of the roughness factor. Finally, the problems/obstacles related to applicability of superhydrophobic surfaces in real life are addressed. This review should be of interest to students and scientists interested specifically in superhydrophobic surfaces but also to scientists and industries focused in material chemistry in general.     

Composite particles of polyethylene @ silica

Polyethylene (PE) and silica are perhaps the simplest and most common organic and inorganic polymers, respectively. We describe, for the first time, a physically interpenetrating nanocomposite between these two elementary polymers. While polymer-silica composites are well known, the nanometric physical blending of PE and silica has remained a challenge. A method for the preparation of such materials, which is based on the entrapment of dissolved PE in a polymerizing tetraethoxysilane (TEOS) system, has been developed. Specifically, the preparation of submicron particles of low-density PE@silica and high-density PE@silica is detailed, which is based on carrying out a silica sol-gel polycondensation process within emulsion droplets of TEOS dissolved PE, at elevated temperatures. The key to the successful preparation of this new composite has been the identification of a surfactant, PE-b-PEG, that is capable of stabilizing the emulsion and promoting the dissolution of the PE. A mechanism for the formation of the particles as well as their inner structure are proposed, based on a large battery of analyses, including transmission electron microscopy (TEM) and scanning electron microscopies (SEM), surface area and porosity analyses, various thermal analyses including thermal gravimetric analysis (TGA/DTA) and differential scanning calorimetry (DSC) measurements, small-angle X-ray scattering (SAXS) measurements and solid-state NMR spectroscopy.     

Gold-labeled block copolymer micelles reveal gold aggregates at multiple subcellular sites

There is increasing interest in the usefulness of block copolymer micelles as drug delivery vehicles. However, their subcellular distribution has not been explored extensively, mostly because of the lack of adequately labeled block copolymers. In a previous study, we showed that fluorescently labeled block copolymer micelles entered living cells and co-localized with cytoplasmic organelles selectively labeled with fluorescent dyes. The details of the observed co-localizations were, however, limited by the resolution of the fluorescence approach, which is ca. 500 nm. Using transmission electron microscopy (TEM), we established time- and concentration-dependent subcellular distributions of gold-labeled micelles within human embryonic kidney (HEK 293) cells and human lung carcinoma (A549) cells. Gold particles were incorporated into poly(4-vinylpyridine)-block-poly(ethylene oxide) (P4VP21-b-PEO45) micelles. Data from dynamic light scattering (DLS) and TEM analyses revealed that the sizes of the gold particles ranged from 4 to 8 nm. The cells survived up to 24 h in the presence of low gold-labeled micelle concentrations (0.73 microg/mL), but cell death occurred at higher concentrations (i.e., kidney cells are more susceptible than lung cells). Over 24 h periods of equivalent exposure, lung cells internalized significantly more gold-incorporated micelles than kidney cells. Although micelles were added to the cell culture media as dispersed colloidal particles, the presence of serum in these media caused aggregation. These aggregates occurred mainly close to the cell plasma membrane at early times (5-10 min); however, at later times (24 h) aggregated particles were seen inside endosomes and lysozomes. Thus, gold-incorporated (labeled) micelles can serve as a valuable extension of the fluorescence approach to visualizing the localization of micelles in subcellular compartments, improving the resolution by at least 20-fold.     

Imaging of atomic and molecular species in tissue with laser‐SNMS for pharmaceutical studies

Successful anticancer therapies will have the ability to selectively deliver compounds to target cells while sparing normal tissue. Currently, methods to determine the distribution of compounds with very high sensitivity and subcellular resolution are still unavailable. Laser secondary neutral mass spectrometry (laser‐SNMS) and time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) are capable of detecting atoms and molecules with high sensitivity and a spatial resolution of up to 80 nm. The use of such methods requires special preparation techniques that preserve the morphological and chemical integrity of living cells. In this paper, the ability of laser‐SNMS to study transportation processes in animals of boron‐containing compounds for boron neutron capture therapy will be discussed. The data show that with laser‐SNMS it is possible to measure the distribution of these compounds in tissues with subcellular resolution, and that laser‐SNMS is a very powerful tool for locating anticancer drugs in tissues. Copyright © 2006 John Wiley & Sons, Ltd.