Single Particle Analysis Method Research Articles

Thermodynamic solubility measurement without chemical analysis

In this work, the optical imaging based single particle analysis (SPA) and the gold standard shake-flask (SF) solubility methods are compared. We show that to analyze pharmaceutical compounds spanning 7 log units in solubility and a diverse chemical space with limited resources, several analytical techniques are required (HPLC-UV, LC-MS, refractometry and UV–Vis spectrometry), whereas solely the SPA method is able to analyze all the same compounds. SPA experiments take only minutes, while for SF, it may take days to reach thermodynamic equilibration. This decreases the time span needed for the solubility experiment from initial preparations to obtaining the result from roughly three days to less than three hours. The optimal particle size for SPA ranges from approximately one to hundreds of microns. Challenges include measuring large particles, very fast dissolving compounds and handling small sample sizes. Inherent exclusion of density from the SPA measurement is a potential source of error for compounds with very low or high density values. The average relative difference of 37 % between the two methods is very good in the realm of solubility, where 400 % interlaboratory reproducibility can be expected.

A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction.

Cryo-Electron Microscopy (cryo-EM) is a widely used and effective method for determining the three-dimensional (3D) structure of biological molecules. For ab-initio Cryo-EM 3D reconstruction using single particle analysis (SPA), estimating the projection direction of the projection image is a crucial step. However, the existing SPA methods based on common lines are sensitive to noise. The error in common line detection will lead to a poor estimation of the projection directions and thus may greatly affect the final reconstruction results. To improve the reconstruction results, multiple candidate common lines are estimated for each pair of projection images. The key problem then becomes a combination optimization problem of selecting consistent common lines from multiple candidates. To solve the problem efficiently, a physics-inspired method based on a kinetic model is proposed in this work. More specifically, hypothetical attractive forces between each pair of candidate common lines are used to calculate a hypothetical torque exerted on each projection image in the 3D reconstruction space, and the rotation under the hypothetical torque is used to optimize the projection direction estimation of the projection image. This way, the consistent common lines along with the projection directions can be found directly without enumeration of all the combinations of the multiple candidate common lines. Compared with the traditional methods, the proposed method is shown to be able to produce more accurate 3D reconstruction results from high noise projection images. Besides the practical value, the proposed method also serves as a good reference for solving similar combinatorial optimization problems.

Multimodal OF2i-Raman – A novel high-throughput, single particle analysis method in liquids

Multimodal OF2i-Raman – A novel high-throughput, single particle analysis method in liquids

Investigation of the Efficacy of Lanthanoid Heavy Metal Acetates as Electron Staining Reagents for Biomembrane Vesicles.

Transmission electron microscopy (TEM) has revolutionized our understanding of protein structures by enabling atomic-resolution visualization without the need for crystallography, thanks to advancements in cryo-TEM and single particle analysis methods. However, conventional electron microscopy remains relevant for studying stained samples, as it allows the practical determination of optimal conditions through extensive experimentation. TEM also facilitates the examination of supramolecular complexes encompassing proteins, lipids, and nucleic acids. In this study, we investigated the applicability of lanthanoid reagents as electron-staining alternatives to uranyl acetate, which is globally regulated as a nuclear fuel material. We focus on a model biomembrane vesicle system, the chromatophores from the purple photosynthetic eubacterium Rhodospirillum rubrum, which integrate proteins and lipids. Through density distribution analysis of electron micrographs, we evaluated the efficacy of various lanthanoid acetates and found that triacetates of neodymium, samarium, and gadolinium exhibited similar staining effectiveness to uranyl acetate. Additionally, triacetates of praseodymium, erbium, and lutetium, followed by europium show promising results as secondary candidates. Our findings suggest that lanthanoid transition heavy metal acetates could serve as viable alternatives for electron staining in TEM, offering potential advantages over uranyl acetate.

Acidification of blood plasma facilitates the separation and analysis of extracellular vesicles

BackgroundBlood plasma is available with minimal invasive sampling, it has significant diagnostic utility, and it is a valuable source of extracellular vesicles (EVs). Nevertheless, rich protein content, the presence of lipoproteins (LPs) that share similar biophysical properties, and relatively low abundance of EVs, especially those of rare subpopulations, make any downstream application a very challenging task. The growing evidence of the intricate surface interactome of EVs, and the association of EVs with LPs, impose further challenges during EV purification, detection, and biomarker analyses. ObjectivesIn this study, we tackled the fundamental issues of plasma EV yield and LP co-isolation and their implications in the subsequent marker analyses. MethodsModerate acidification of plasma was combined with size exclusion chromatography (SEC) and/or differential centrifugation (DC) to disrupt LPs and improve recovery of EVs and their subsequent detection by immunoassays and single-particle analysis methods. ResultsOur results demonstrate a surprisingly efficient enrichment of EVs (up to 3.3-fold higher than at pH 7) and partial depletion of LPs (up to 61.2%). Acidification of blood plasma samples enabled a quick single-step isoelectric precipitation of up to 20.4% of EVs directly from plasma, upon short low-speed centrifugation. ConclusionThus, acidification holds potential as a simple and inexpensive methodological step, which improves the efficacy of plasma EV enrichment and may have implications in future biomarker discoveries.

Quantification of placental extracellular vesicles in different pregnancy status via single particle analysis method

BackgroundThe nano-sized, lipid bilayer-delimited placental extracellular vesicles (PEVs) released by the placenta are now regarded as important mediators involved in various physiological and pathological processes of pregnant women. The number and contents of PEVs are significantly altered in preeclampsia and are considered as potential biomarkers. However, the distribution pattern of PEVs in the maternal circulation in different pregnancy status is still unclear for the limitation of the traditional method with low sensitivity. MethodsIn this work, we recruited 561 pregnant women with different pregnancy status and investigated the distribution pattern of PEVs in the maternal circulation based on a single extracellular vesicle analysis method and placental alkaline phosphatase (PLAP), a placenta-specific marker. ResultsThe concentration of PEVs in pregnant women increased with the progression of gestational age, while the ratio of PEVs decreased to about 10% in the third trimester. Surprisingly, the PLAP+ EVs also presented in the plasma of non-pregnant women and normal male about 5%. The change in the ratio of PEVs can reflect the pregnancy status and also had a better diagnostic value in severe preeclampsia (AUC = 0.7811). ConclusionsOur study not only reveals the distribution pattern of PEVs, but also identifies the diagnostic potential of PEVs as biomarkers.

Novel Single-Particle Analytical Technique for Submicron Atmospheric Aerosols: Combined Use of Dark-Field Scattering and Surface-Enhanced Raman Spectroscopy.

Raman microspectrometry (RMS) is a useful single particle analysis method that can provide information on the mixing states, molecular species, and chemical functional groups of individual aerosol particles, which are difficult to determine by bulk analysis techniques. On the other hand, drawbacks, such as low Raman cross-section, spatial resolution (∼1 μm), and optical diffraction limit, make the analysis of atmospheric particles in the submicron size range difficult using conventional RMS. This study developed a new strategy to detect individual submicron-size atmospheric particles by combining dark-field (DF) microscopy and surface-enhanced Raman spectroscopy (SERS). The DF technique overcomes optical spatial diffraction limit by contrast enhancement, allowing the visualization of submicron particles. SERS facilitates spectroscopic characterization (obtaining information on molecular fingerprints and mixing states) of trace amounts of analyte by increasing the Raman scattering cross-section at the hot spot. SERS-active silver substrates sputter-coated on a Si wafer efficiently provided a clear background in the dark-field image and uniform hot spots over a large area, which were suitable for single-particle analysis. Various functional groups in individual particles and their heterogeneous mixing states were investigated, demonstrating the potential of this method to provide improved information on submicron atmospheric particles of femtogram-level masses. DF-SERS may elucidate the detailed physicochemical characteristics of individual submicron particles, providing new information on the formation mechanisms and fates of atmospheric particles.

Fast imaging-based single particle analysis method for solubility determination

The solubility and dissolution rates of chemical compounds are crucial properties in several fields of industry and research. However, accurate, rapid and green methods for their measurement, which only consume micrograms of compound, are lacking. Here, the unique approach of non-specific, image-based single particle analysis (SPA) for solubility testing is directly compared to and thus validated on the mid-solubility range with the current gold standard shake-flask method with UV–Vis spectroscopy employed for determining sample concentrations. Five biologically active compounds representing a range of physicochemical properties including pKa and logP were analyzed with both methods. The comparison of SPA and the shake-flask (SF) analysis shows excellent linear correlation (R2 = 0.99). Higher variability of the SPA method is attributed to variability between the properties of individual particles, which cannot be detected with traditional methods. Due to the similar average solubility values compared to those produced with SF, it is concluded that the SPA method has great potential as an analytical tool for small-scale solubility studies. It also has several practical advantages over the current gold standard shake-flask method, such as speed, low consumables consumption, and no requirement for prior knowledge of compound chemistry.

Identification of incorrectly oriented particles in cryo-EM single particle analysis

The quality of a 3D map produced by the single-particle analysis method is highly dependent on an accurate assignment of orientations to the many experimental images. However, the problem’s complexity implies the presence of several local minima in the optimized goal functions. Consequently, validation methods to confirm the angular assignment are very useful to yield higher-resolution 3D maps. In this work, we present a graph-signal-processing-based methodology that analyzes the correlation landscape as a function of the orientation, an approach allowing the estimation of the assigned orientations’ reliability. Using this method, we may identify low-reliability images that probably incorrectly contribute to the final 3D reconstruction.

Machine-Vision-Enabled Salt Dissolution Analysis.

Salt formation is a well-established method to increase the solubility of ionizable drug candidates. However, possible conversion of salt to its original form of free acid or base—disproportionation—can have a drastic effect on the solubility and consequently the bioavailability of a drug. Therefore, during the salt selection process, the salt dissolution behavior should be well understood. Improved understanding could be achieved by a method that enables simultaneous screening of small sample amounts and detailed dissolution process analysis. Here, we use a machine-vision-based single-particle analysis (SPA) method to successfully determine the pH-solubility profile, intrinsic solubility, common-ion effect, pKa, pHmax, and Ksp values of three model compounds in a fast and low sample consumption (<1 mg) manner. Moreover, the SPA method enables, with a particle-scale resolution, in situ observation of the disproportionation process and its immediate effect on the morphology and solubility of dissolving species. In this study, a potentially higher energy thermodynamic solid-state form of diclofenac free acid and an intriguing conversion to liquid verapamil free base were observed upon disproportionation of the respective salts. As such, the SPA method offers a low sample consumption platform for fast yet elaborate characterization of the salt dissolution behavior.

Direct Measurement of Amorphous Solubility.

Amorphous materials exhibit distinct physicochemical properties compared to their respective crystalline counterparts. One of these properties, the increased solubility of amorphous materials, is exploited in the pharmaceutical industry as a way of increasing bioavailability of poorly water-soluble drugs. Despite the increasing interest in drug amorphization, the analytical physicochemical toolbox is lacking a reliable method for direct amorphous solubility assessment. Here, we show, for the first time, a direct approach to measure the amorphous solubility of diverse drugs by combining optics with fluidics, the single particle analysis (SPA) method. Moreover, a comparison was made to a theoretical estimation based on thermal analysis and to a standardized supersaturation and precipitation method. We have found a good level of agreement between the three methods. Importantly, the SPA method allowed for the first experimental measurement of the amorphous solubility for griseofulvin, a fast crystallizing drug, without the use of a crystallization inhibitor. In conclusion, the SPA approach enables rapid and straightforward determination of the supersaturation potential for amorphous materials of less than 0.1 mg, which could prove highly beneficial in the fields of materials science, analytical chemistry, physical chemistry, food science, pharmaceutical science, and others.

Sulfate–nitrate–ammonium as double salts in PM2.5: Direct observations and implications for haze events

Obtaining detailed information on sulfate–nitrate–ammonium (SNA) is fundamentally important to explain the formation of haze in China, since it is a dominant component of fine particulate matter (PM2.5) and plays a critical role in the deterioration of air quality. Several single-particle analysis methods have been applied to study and explain SNA formation; however, determining its mixture state remains a challenge. This study describes a direct observation of the SNA components in atmospheric particles on a single-particle scale, and details the first use of a non-destructive surface-enhanced Raman scattering (SERS) technique for SNA analysis. We studied PM2.5 collected at a site on the premises of Tsinghua University in Beijing, China, during a winter haze episode (12.15.2016–12.23.2016). The on-line data show that the SNA component accounted for 9.4% to 68.2% of the total mass of PM2.5, becoming dominant on heavy haze days, and the sulfate concentration increased with the nitrate concentration (R2 = 0.72). Furthermore, the off-line SERS and scanning electron microscopy-energy dispersive X ray analysis (SEM-EDS) results for the single particles collected also indicated that SNA increase with increasing haze pollution. The existing state of the SNA component on each haze day was observed directly in a non-destructive manner mainly in the form of double salts such as 3(NH4NO3)·(NH4)2SO4 and 2(NH4NO3)·(NH4)2SO4. A Raman mapping experiment further confirmed that the SNA was internally mixed. Our data also show that SNA can evaporate under high-vacuum scanning electron microscopy conditions, suggesting that SERS is an effective method to directly observe SNA without sample loss and may represent a promising single-particle technique to supplement traditional electron microscopy methods. This work will provide evidence for the SNA formation, particularly during haze events.

Lipid environment of membrane proteins in cryo-EM based structural analysis.

Cryoelectron microscopy (cryo-EM) in association with a single particle analysis method (SPA) is now a promising tool to determine the structures of proteins and their macromolecular complexes. The development of direct electron detection cameras and image processing technologies has allowed the structures of many important proteins to be solved at near-atomic resolution or, in some cases, at atomic resolution, by overcoming difficulties in crystallization or low yield of protein production. In the case of membrane-integrated proteins, the proteins were traditionally solubilized and stabilized with various kind of detergents. However, the density of detergent micelles diminished the contrast of membrane proteins in cryo-EM studies and made it difficult to obtain high-resolution structures. To improve the resolution of membrane protein structures in cryo-EM studies, major improvements have been made both in sample preparation techniques and in hardware and software developments. The focus of our review is on improvements which have been made in the various techniques for sample preparation for cryo-EM studies, with a specific interest placed on techniques for mimicking the lipid environment of membrane proteins.

Analysis of exosome purification methods using a model liposome system and tunable-resistive pulse sensing.

Exosomes are vesicles which have garnered interest due to their diagnostic and therapeutic potential. Isolation of pure yields of exosomes from complex biological fluids whilst preserving their physical characteristics is critical for downstream applications. In this study, we use 100 nm-liposomes from 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and cholesterol as a model system as a model system to assess the effect of exosome isolation protocols on vesicle recovery and size distribution using a single-particle analysis method. We demonstrate that liposome size distribution and ζ-potential are comparable to extracted exosomes, making them an ideal model for comparison studies. Four different purification protocols were evaluated, with liposomes robustly isolated by three of them. Recovered yields varied and liposome size distribution was unaltered during processing, suggesting that these protocols do not induce particle aggregation. This leads us to conclude that the size distribution profile and characteristics of vesicles are stably maintained during processing and purification, suggesting that reports detailing how exosomes derived from tumour cells differ in size to those from normal cells are reporting a real phenomenon. However, we hypothesize that larger particles present in most purified exosome samples represent co-purified contaminating non-exosome debris. These isolation techniques are therefore likely nonspecific and may co-isolate non-exosome material of similar physical properties.

Characterization of the Molecular Architecture of Human Caveolin-3 and Interaction with the Skeletal Muscle Ryanodine Receptor

Caveolin-3 facilitates both caveolae formation and a range of cell signaling pathways, including Ca(2+) homeostasis. Caveolin-3 forms a disc-shaped nonamer that binds the Ca(2+)-release channel, RyR1. Multiple caveolin-3 nonamers bind to a single RyR1 homotetramer. First three-dimensional structural insights into caveolin-3 assembly, interactions with RyR1 suggest a novel role in muscle contraction and/or for channel localization within the membrane. Caveolin-3 (cav-3), an integral membrane protein, is a building block of caveolae as well as a regulator of a number of physiological processes by facilitating the formation of multiprotein signaling complexes. We report that the expression of cav-3 in insect (Sf9) cells induces caveola formation, comparable in size with those observed in native tissue. We have also purified the recombinant cav-3 determining that it forms an oligomer of ∼220 kDa. We present the first three-dimensional structure for cav-3 (using transmission electron microscopy and single particle analysis methods) and show that nine cav-3 monomers assemble to form a complex that is toroidal in shape, ~16.5 nm in diameter and ~ 5.5 nm in height. Labeling experiments and reconstitution of the purified cav-3 into liposomes have allowed a proposal for the orientation of the protein with respect to the membrane. We have identified multiple caveolin-binding motifs within the ryanodine receptor (RyR1) sequence employing a bioinformatic analysis. We have then shown experimentally that there is a direct interaction between recombinant cav-3 nonamers and purified RyR1 homotetramers that would imply that at least one of the predicted cav-3-binding sites is exposed within the fully assembled RyR1 structure. The cav-3 three-dimensional model provides new insights as to how a cav-3 oligomer can bind multiple partners in close proximity to form signaling complexes. Furthermore, a direct interaction with RyR1 suggests a possible role for cav-3 as a modifier of muscle excitation-contraction coupling and/or for localization of the receptor to regions of the sarcoplasmic reticulum.

Size-resolved source apportionment of aerosol particles using polycapillary X-ray lens with a plateau in its focal spot

A laboratory micro X-ray fluorescence spectrometer based on a special polycapillary X-ray lens (PXRL) was used to carry out the source apportionment of aerosol particles. In the curve of the distribution of the X-ray intensity in the focal spot of the special PXRL, there was a plateau with a diameter of 21.3 μm in which the distribution of the X-ray intensity was homogeneous. The gain in flux density in the plateau of the PXRL is 1490. The uniformity of this plateau was 2.9%. This was helpful for the quantitative X-ray fluorescence analysis of a single aerosol particle with smaller size than that of the plateau of the PXRL. The fingerprint database of aerosol particles with given sizes from various air pollution sources was established with the single particle analysis method. The size-resolved source apportionment of aerosol particles in haze in Beijing city was performed with this fingerprint database.

Three-dimensional Structure of CaV3.1: COMPARISON WITH THE CARDIAC L-TYPE VOLTAGE-GATED CALCIUM CHANNEL MONOMER ARCHITECTURE

Calcium entry through voltage-gated calcium channels has widespread cellular effects upon a host of physiological processes including neuronal excitability, muscle excitation-contraction coupling, and secretion. Using single particle analysis methods, we have determined the first three-dimensional structure, at 23 Å resolution, for a member of the low voltage-activated voltage-gated calcium channel family, CaV3.1, a T-type channel. CaV3.1 has dimensions of ∼115 × 85 × 95 Å, composed of two distinct segments. The cytoplasmic densities form a vestibule below the transmembrane domain with the C terminus, unambiguously identified by the presence of a His tag being ∼65 Å long and curling around the base of the structure. The cytoplasmic assembly has a large exposed surface area that may serve as a signaling hub with the C terminus acting as a “fishing rod” to bind regulatory proteins. We have also determined a three-dimensional structure, at a resolution of 25 Å, for the monomeric form of the cardiac L-type voltage-gated calcium (high voltage-activated) channel with accessory proteins β and α2δ bound to the ion channel polypeptide CaV1.2. Comparison with the skeletal muscle isoform finds a good match particularly with respect to the conformation, size, and shape of the domain identified as that formed by α2. Furthermore, modeling of the CaV3.1 structure (analogous to CaV1.2 at these resolutions) into the heteromeric L-type voltage-gated calcium channel complex volume reveals multiple interaction sites for β-CaV1.2 binding and for the first time identifies the size and organization of the α2δ polypeptides.

Single-particle characterization of aerosol samples collected before and during an Asian dust storm in Chuncheon, Korea

Low- Z particle electron probe X-ray microanalysis, a single-particle analysis method, was used to characterize aerosol samples collected in Chuncheon, Korea, before and during a dust storm that occurred between 10 and 12 March, 2004. Four different samples were analyzed: just before the storm, peak time of the storm, late stage of the storm, and end of the storm. All four of the samples were found to have experienced chemical modifications during long-range transport due to elevated levels of nitrate and sulfate that resulted from atmospheric reactions with CaCO 3 and sea-salt particles. The sample collected just before the storm underwent the most extensive chemical modification during transport. For this particular sample, the overall relative abundances of reacted CaCO 3 and sea-salt particles were 9.8% and 44.2%, respectively. The sample collected at the peak time of the storm also experienced extensive chemical modification with overall relative abundances of reacted CaCO 3 and sea-salt particles at 4.3% and 23.3%, respectively. The backward trajectory analysis for this particular sample revealed two different types of air-masses arriving at the sampling site in Korea; one is high-altitude air-masses moving rapidly and carrying Asian dust particles and the other a slow-moving low-altitude air-mass from eastern China coastal areas. The single-particle characterization of this same sample showed that the Asian dust particles were mixed with sea-salts entrained over the Yellow Sea, as well as air pollutants from the eastern China coastal areas. However, as the Asian dust storm continued, soil-derived mineral particles became dominant in the samples that were collected at the late stage of the storm and at the end. For this specific Asian dust storm, the mixing of sea-salts and pollution with Asian dust particles was observed to occur just at the early stage of the storm.

Characterization of small particles by micro X-ray fluorescence

Micro X-ray fluorescence was used to study both homogeneous and heterogeneous particle systems. Specifically, homogeneous glass microspheres and heterogeneous soil particle samples were prepared by both bulk and single particle sample preparation methods for evaluation by micro X-ray fluorescence. Single particle sample preparation methods allow for single particles from a collected sample to be isolated and individually presented to the micro X-ray fluorescence instrument for analysis. Various particle dispersion methods, including immobilization onto Tacky Dot™ slides, mounting onto double-sided sticky tape affixed to polypropylene film, or attachment to polypropylene film using 3M Artist's Adhesive, were used to separate the sample particles for single particle analysis. These methods were then compared and evaluated for their ability to disperse the particles into an array of single separated particles for optimal micro X-ray fluorescence characterization with minimal background contribution from the particle mounting surface. Bulk methods of particle sample preparation, which included pellet preparation and aerosol impaction, used a large quantity of collected single particles to make a single homogeneous specimen for presentation to the instrument for analysis. It was found that single particle elemental analysis by micro X-ray fluorescence can be performed if the particles are well separated (minimum separation distance = excitation source beam diameter) down to a particle mass of ∼ 0.04 ng and a mean particle diameter of ∼ 0.06 μm. Homogeneous particulates can be adequately characterized by micro X-ray fluorescence using either bulk or single particle analysis methods, with no loss of analytical information. Heterogeneous samples are much harder to characterize, and both single particle as well as bulk analyses must be performed on the sample to insure full elemental characterization by micro X-ray fluorescence.

L-type voltage-gated calcium channels: understanding function through structure

L-type voltage-gated calcium channels (VGCCs) are multisubunit membrane proteins that regulate calcium influx into excitable cells. Within the last two years there have been four separate reports describing the structure of the skeletal muscle VGCC determined by electron microscopy and single particle analysis methods. There are some discrepancies between the structures, as well as reports for both monomeric and dimeric forms of the channel. This article considers each of the VGCC structures in terms of similarities and differences with an emphasis upon translation of data into a biological context.