Mechanism Of Aggregate Formation Research Articles

α-Synuclein oligomers form by secondary nucleation

Oligomeric species arising during the aggregation of α-synuclein are implicated as a major source of toxicity in Parkinson’s disease, and thus a major potential drug target. However, both their mechanism of formation and role in aggregation are largely unresolved. Here we show that, at physiological pH and in the absence of lipid membranes, α-synuclein aggregates form by secondary nucleation, rather than simple primary nucleation, and that this process is enhanced by agitation. Moreover, using a combination of single molecule and bulk level techniques, we identify secondary nucleation on the surfaces of existing fibrils, rather than formation directly from monomers, as the dominant source of oligomers. Our results highlight secondary nucleation as not only the key source of oligomers, but also the main mechanism of aggregate formation, and show that these processes take place under conditions which recapitulate the neutral pH and ionic strength of the cytosol.

Wild-Type DCTN1 Suppresses the Aggregation of DCTN1 Mutants Associated with Perry Disease.

Perry disease, a rare autosomal dominant neurodegenerative disorder, is characterized by parkinsonism, depression or apathy, unexpected weight loss, and central hypoventilation. Genetic analyses have revealed a strong association between point mutations in the dynactin I gene (DCTN1) coding p150glued and Perry disease. Although previous reports have suggested a critical role of p150glued aggregation in Perry disease pathology, whether and how p150glued mutations affect protein aggregation is not fully understood. In this study, we comprehensively investigated the intracellular distribution of the p150glued mutants in HEK293T cells. We further assessed the effect of co-overexpression of the wild-type p150glued protein with mutants on the formation of mutant aggregates. Notably, overexpression of p150glued mutants identified in healthy controls, which is also associated with amyotrophic lateral sclerosis, showed a thread-like cytoplasmic distribution, similar to the wild-type p150glued. In contrast, p150glued mutants in Perry disease and motor neuron disease caused aggregation. In addition, the co-overexpression of the wild-type protein with p150glued mutants in Perry disease suppressed aggregate formation. In contrast, the p150glued aggregation of motor neuron disease mutants was less affected by the wild-type p150glued. Further investigation of the mechanism of aggregate formation, contents of the aggregates, and biological mechanisms of Perry disease could help develop novel therapeutics.

Calcium carbonate promotes the formation and stability of soil macroaggregates in mining areas of China

We studied changes in the concentrations of aggregate-cementing agents after different reclamation times and with different fertilization regimes, as well as the formation mechanism of aggregates in reclaimed soil, to provide a theoretical basis for rapid reclamation of soil fertility in the subsidence area of coal mines in Shanxi Province, China. In this study, soil samples of 0–20 cm depth were collected from four fertilization treatments of a long-term experiment started in 2008: no fertilizer (CK), inorganic fertilizer (NPK), chicken manure compost (M), and 50% inorganic fertilizer plus 50% chicken manure compost (MNPK). The concentrations of cementing agents and changes in soil aggregate size distribution and stability were analysed. The results showed that the formation of >2 mm aggregates, the aggregate mean weight diameter (MWD), and the proportion of >0.25 mm water-stable aggregates (WR0.25) increased significantly after 6 and 11 years of reclamation. The concentration of organic cementing agents tended to increase with reclamation time, whereas free iron oxide (Fed) and free aluminium oxide (Ald) concentrations initially increased but then decreased. In general, the MNPK treatment significantly increased the concentrations of organic cementing agents and CaCO3, and CaCO3 increased by 60.4% at 11 years after reclamation. Additionally, CaCO3 had the greatest effect on the stability of aggregates, promoting the formation of >0.25 mm aggregates and accounting for 54.4% of the variance in the proportion and stability of the aggregates. It was concluded that long-term reclamation is beneficial for improving soil structure. The MNPK treatment was the most effective measure for increasing maize grain yield and concentration of organic cementing agents and CaCO3.

Acidity rectified aggregation behaviour of colloids in sugarcane juice

SummaryDuring processing and low‐temperature storage, pH change affects the stability of sugarcane juice. This study investigated the colloidal stability and aggregation mechanisms of membrane‐filtered sugarcane juice at the pH range of 2.5–9.5. The mechanisms of aggregate formation were speculated based on the compositional variations in sugarcane juice at different pH. When pH was lower than 6.03, aggregation was driven by the electrostatic effect, wherein proteins, polysaccharides and phenolic compounds interact, hence increase the average particle size and turbidity. The absolute value of the zeta potential of the juice was decreased and found an isoelectric point at the pH range of 3.0–3.5. However, under alkaline conditions, calcium phosphate mesh flocs, which are the dominant components of the aggregate, attract colloidal impurities in the juice, eventually resulting in a sharp increase in turbidity and the rapid formation of enormous precipitates, further increasing particle size. This work provides new clues to control aggregation issues commonly encountered by the sugarcane beverage industry.

Aggregation-Induced Emission in Phenothiazine-Based Fluorophores: An Insight into the Excited State and Aggregate Formation Mechanism

In this study, we report evidence for emissive aggregates of push–pull phenothiazine and phenothiazine dioxide derivatives produced both in water dispersions and in the solid state, highly promising for applications in both biology and material science. An insightful investigation of the aggregation-induced emission (AIE) mechanism was carried out via time-resolved spectroscopies, with nanosecond and femtosecond temporal resolution, coupled with advanced data analysis. Our steady-state and time-resolved spectroscopic results unambiguously show that a significant AIE behavior is activated by the restriction of intramolecular rotations for the phenothiazine derivatives. Investigation of the nonlinear optical properties also revealed that aggregates exhibit notable emission upon two-photon excitation. In particular, the phenothiazine dioxide-based aggregates exhibit remarkable fluorescence efficiencies and large two-photon absorption cross sections, as well as the capability to be internalized in HeLa cells exerting no cytotoxic effect. These aggregate species thus prove to be promising as novel fluorophores for bioimaging.

Study of molecular interactions in aniline and its aqueous solutions: experiment and calculations

In this work, a liquid aniline was studied in a pure and aqueous solution using experimental and theoretical calculations. Using Raman spectra, the region of 100–3200 cm−1 was analyzed, and blue shift and red shift were observed in this region. For the first time, the reasons for this shift were found to be due to the C–H···O nonclassical hydrogen bonding in the complex formation and were confirmed in the results calculated using the theoretical DFT//BL3YP/6-311+G(2d,p) method. Mechanisms of aggregate formation with aniline+(H2O)7 molecules were also analyzed using theoretical calculations. Calculations show that the total energy increases with the increase in the number of water molecules in the formation of aggregates.

The Kinetics of Dye Encapsulation in Single-Walled Carbon Nanotubes Probed By Statistical Raman Imaging

Single-Walled Carbon Nanotubes (SWNTs) are nanosystems with a large aspect ratio that have potential in a wide range of optical applications, such as in biomedical imaging [1]. An important advantage of SWNTs in that context is their capability to support two or more functionalities, for instance detection as well as targeting of molecules of interest. The hollowness of SWNTs interior is therefore particularly interesting since SWNTs can act as a template for the creation of new hybrid nanostructures, while leaving the surface free for further functionalization. It was shown that dyes encapsulated inside carbon nanotubes (CNTs) are protected from degradation and present a strong Raman signature with narrow emission peaks, free of background fluorescence, which could enable their use as Raman optical markers [2]. Further, confinement inside SWNTs was found to largely impact molecular organisation [3], tuning the physical and chemical properties of the encapsulated molecules. However, the kinetics of such a system, as well as the precise mechanism of aggregate formation, is still not completely understood. In this study, we explore the encapsulation mechanism of dye molecules in SWNTs. Sexithiophene (6T) molecules were chosen due to their well-conjugated, rod-like structure and giant Raman signal upon encapsulation, at an excitation of 532 nm.Raman imaging (RIMA, Raman Imaging system, Photon etc.) is used to obtain statistical information from a large number of individual SWNTs (>1000 per data point). The encapsulation is carried out using a liquid-phase protocol, allowing the investigation of the impact of various encapsulation parameters (dye concentration and temperature) on the kinetics of the encapsulation process. Spatially resolved Raman imaging allows the comparison of filling and densification speeds for all encapsulation parameters, showing that, in all studied cases, the filling is faster than densification, which occurs over longer time scales. Raman imaging also enables the tailored analysis of different sub-populations, in order to probe the effect of the length or the diameter of the SWNTs on the encapsulation kinetics. Furthermore, Raman intensity distributions are studied, which provide signatures of single and double aggregation that can be correlated to SWNTs characteristics. Finally, a kinetic model and an encapsulation mechanism are proposed. Based on the intensity distributions and the proposed kinetic model, we predict the apparition of double aggregation for all the encapsulation parameters investigated. These results provide much needed insight on aggregate formation in 1D systems, which is crucial to the development of well-behaved and controlled hybrid materials. [1] Kostarelos, K., Bianco, A., & Prato, M. (2009). Promises, facts and challenges for carbon nanotubes in imaging and therapeutics. Nature nanotechnology, 4(10), 627-633.[2] Gaufrès, E., Tang, N. W., Lapointe, F., Cabana, J., Nadon, M. A., Cottenye, N., ... & Martel, R. (2014). Giant Raman scattering from J-aggregated dyes inside carbon nanotubes for multispectral imaging. Nature Photonics, 8(1), 72-78.[3] Almadori, Y., Alvarez, L., Le Parc, R., Aznar, R., Fossard, F., Loiseau, A., ... & Rahmani, A. (2014). Chromophore ordering by confinement into carbon nanotubes. The Journal of Physical Chemistry C, 118(33), 19462-19468.

Supramolecular self-assemblies formed by co-assembly of carbon dots and tannic acid

In recent years, it is heartening to witness that carbon dots (CDs), a rising star in the family of carbon nanomaterials, have displayed tremendous applications. However, the investigations toward self-assembly of CDs are still in their infancy. Tannic acid (TA) is a naturally derived polyphenolic compound with special molecular structure. Here, the co-assembly of CDs and TA in aqueous solutions has been investigated. The CDs/TA binary mixtures exhibited rich phase behavior, which went through the process of transparent phase-turbid phase-transparent phase. We focus on investigating the morphologies of the samples. As the concentration of TA increases, the aggregates evolve from the network structures to the spherical aggregates, and finally become the vesicles. Through systemic analysis of changes of zeta potential, morphologies and size distributions at varying temperature and pH, the mechanism of aggregate formation is proposed. The effect of adding TA on the fluorescence properties of CDs aqueous solutions was studied. After integration into aggregates, the potential applications of the CDs in biology and life sciences could be significantly expanded.

Basic study of formation of acicular crystals by chemical reactions between RuO2 and NaNO3 in a waste vitrification process

ABSTRACT Aggregates of acicular RuO2 occur in high-level waste glass. Large aggregates may settle rapidly in the glass, providing a more efficient electrical path on the melter bottom and interfering with the Joule heating of the glass. To clarify the formation mechanism of aggregates and to develop countermeasures to such formation, chemical reactions between RuO2 and NaNO3 with/without borosilicate glass were observed. Sodium ruthenates were formed from a RuO2–NaNO3 mixture heated without the glass or on a flat glass. On the flat glass, aggregates of acicular crystals of RuO2 appeared with a decreasing amount of sodium ruthenates at high temperature. Neither sodium ruthenates nor acicular crystals of RuO2 were formed from the RuO2–NaNO3 mixture well mixed with powdery glass and heated. Results of a series of experiments suggest that acicular crystals of RuO2 and their aggregates formed through the formation and decomposition of sodium ruthenate when the dissolution of sodium into the glass was slower than its reaction with RuO2. Promoting the dissolution of sodium into a glass or reducing the amount of sodium in liquid waste is expected to suppress the formation of aggregates and their sedimentation.

Influence of various sodium salt species on formation mechanism of lightweight aggregates made from coal fly ash-based material

To save energy in sintering to produce construction and building materials, alkali compounds are always recognized as a good flux component. We added various sodium salts, to coal fly ash/glass mixture, to investigate the effect of sodium salt species type on formation mechanism of lightweight aggregates. TGA/DTA, and XRD are used in this study. Results indicate that, despite the great similarity in melting point of the salt additives, a change of additive from one sodium salt to another leads to considerably different lightweight aggregate formation mechanism, thereby affecting the aggregate properties. Thermal behavior of sodium salt additives, as revealed in their TGA/DSC curves, might play a critical factor in influencing lightweight aggregate formation. All sodium salts can indirectly, following two-step sequential reactions, form sodium silicate with SiO2 present in coal fly ash/glass mixture. Sodium silicates are suggested as major components of viscous layer during sintering; they can envelope bloating gases to expand the size of lightweight aggregates. The solubility of coal fly ash/glass mixture in melt NaCl during sintering, is not as much as in melt Na2O and Na2SO4, thus requiring higher sintering temperature to prepare lightweight aggregates.As compared with the lightweight aggregates prepared in industry, all sodium salt additives used in present study can effectively reduce sintering energy, from the aspects of lightweight aggregate particle density. Effectiveness for the sodium salt additives to reduce sintering temperature for successful lightweight aggregate preparation is, in increasing order, sodium carbonate < sodium sulfate < sodium chloride. Sintering temperature can be potentially reduced to ≤1050 °C by proper addition of the sodium salts.

Development of “Soft” Cleaning Chemistries for Enhanced STI Post-CMP Cleaning

Due to the emergence of sub-10 nm technologies, limiting device defects has become of utmost importance in maintaining high performing integrated circuits. Shallow trench isolation (STI) chemical mechanical planarization (CMP) uses a synergistic balance of ceria (CeO2) nanoparticles and functional chemistry to modulate critical surface adsorption interactions necessary to remove excess topography. Literature has identified that the surface redox state of the CeO2 nanoparticle (Ce3+/4+) is a critical factor in controlling CMP performance. More specifically, controlling the oxygen vacancies has been shown to directly impact removal rate (Ce3+ state), as well as post-CMP cleaning efficiency (Ce4+ state). Current post-CMP cleaning processes utilize oxidation/reduction reactions, etching, encapsulation, and ultrasonic methods as a means of undercutting the particle from the substrate surface. These methods have proven to be highly effective at particle removal but have shown to potentially induce further defectivity due to the aggressive cleaning conditions. This work aims to develop a post-CMP cleaning chemistry that enhances particle removal via soft encapsulation of undesirable nanoparticle/slurry chemistry non-covalent complexes on the wafer surface. By employing a polyelectrolyte/surfactant (PES) matrix, a surface adsorbing/charge-flipping encapsulation process is proposed as a vehicle to remove slurry contamination at low friction. Investigation into the synergy between slurry chemistry and PES cleaning chemistry, with respect to defect aggregate formation, was correlated to the cleaning efficiency as well as friction. Techniques were developed to study real-time properties such as the defect aggregate formation mechanism via in-line dynamic light scattering (DLS), coefficient of friction (COF), particle removal, and scratch defectivity to draw a correlation between cleaning chemistry structure and post-CMP performance.

Development of “Soft” Cleaning Chemistries for Enhanced STI Post-CMP Cleaning

With the rapid miniaturization of advanced technologies, limiting device defects has become of utmost importance in maintaining high performing integrated circuits. Shallow trench isolation (STI) chemical mechanical planarization (CMP) uses a synergistic balance of ceria (CeO2) nanoparticles and functional chemistry to modulate surface adsorption interactions necessary to remove excess topography. This work aims to develop a post-CMP cleaning chemistry that enhances nanoparticle removal via “soft” encapsulation by employing a polyelectrolyte/surfactant (PES) matrix. A surface adsorbing/charge flipping encapsulation process is proposed as a vehicle to remove slurry contamination at low friction. Investigation into the synergy between slurry chemistry and PES cleaning chemistry, with respect to defect aggregate formation, was correlated to the cleaning efficiency as well as friction. Using a suite of techniques to study the real-time defect aggregate formation mechanism it was determined that the supramolecular structure is critical to balance defect forming events with enhanced cleaning efficiency.

N-cadherin-mediated aggregate formation; cell detachment by Trypsin-EDTA loses N-cadherin and delays aggregate formation

Although cell aggregates/spheroids are useful tools in various fields of cell biology, the mechanism for aggregate formation is not fully resolved yet. Here I show the involvement of N-cadherin in the quick formation of packed aggregates in suspension culture. HEK293T cells detached from substratum by Trypsin alone quickly formed packed aggregates in suspension. This aggregate formation was inhibited by the down-regulation of N-cadherin. Meanwhile, aggregate formation of cells detached by Trypsin-EDTA was significantly delayed. N-cadherin was transiently lost by Trypsin-EDTA-treatment, and the re-expression of N-cadherin corresponded to delayed aggregate formation. Furthermore, packed phenotype was not observed in the absence of N-cadherin. These findings indicate that N-cadherin mediates quick formation of packed aggregates/spheroids in suspension culture.

Structural Version of Ostwald—de Waele Equation: Fractal Treatment

Structural treatment of Ostwald—de Waele equation is proposed. It involves the representations of fractal analysis for describing the rheological properties of the rubber/disperse filler system. It is shown that the magnitude of viscosity and the type of system flow are determined by the filler particle structure (aggregates) characterized by their fractal dimension. In turn, this dimension is determined by the mechanism of aggregate formation. The model proposed makes it possible to predict the viscosity of the rubber/disperse filler systems for different filler contents and shear rates.

Roles of soil organic carbon and iron oxides on aggregate formation and stability in two paddy soils

Knowledges of aggregate stability and formation depending on soil organic carbon (SOC) and iron oxides are essential to the conservation of soil structure. In this work, the effects of SOC and different forms of iron oxides on the stability of aggregates of paddy soils were determined by applying the Le Bissonnais (LB) and extractions method by water, oxalate (OA), dithionite–citrate–bicarbonate (DCB), or hydrogen peroxide (H2O2). Two topsoils (0–20 cm) were selected based on two levels of SOC and iron oxides, high SOC (22.1 g kg−1)–low iron oxides (S1) and low SOC (8.50 g kg−1)–high iron oxides (S2) paddy soils from subtropical China. For the fast-wetting (FW) test, the percentage of 2–0.25 mm (34.0%) and >2 mm (42.2%) aggregate fractions were highest in S1 and S2, respectively. Both the soils had a >2 mm fraction that was above 60% under the slow-wetting (SW) and stirring after prewetting (WS) test. The free Fe oxide (Fe(DCB)) could increase in aggregate stability when SOC contents were low in S2. All three chemical extractions considerably decreased the >2 mm fractions (35.5–87.5%), and consequently increased the <0.053 mm fractions. The S1 soil presented the lower mean weight diameter (MWD) after DCB extractions, whereas it was no significantly different after OA or DCB extraction in S2 soil, indicating that Fe(DCB) had a greater effect on the stability of aggregates than amorphous Fe oxide (Fe(OA)) in the S1 soil, but both had the same effect for S2. The H2O2 treatment destructed>2 mm and 2–0.25 mm aggregates intensively, indicating that SOC was the major binding agent for aggregates of these sizes. The SOC was a key agent influencing soil aggregation not only in macro-aggregates (>0.25 mm) but also in micro-aggregates (0.25–0.053 mm) in the S1. The formation of aggregates in S1 was attributed to its higher content of organo-mineral complexes because the contents of SOC (3.30–11.2 g kg−1) were higher in >0.053 mm aggregates compared with S2 after H2O2 extractions. Fe oxides were the key agents for <0.25 mm aggregates formation. The MWD of the FW treatment was found to have a significant positive correlations with Fe(DCB), and MWD of the WS treatment proved significant positive correlations with SOC and Fe(OA) oxide, indicated that SOC and Fe oxides improved aggregate stability against external force collapse. This implies that the differential roles of SOC and Fe oxides in mechanisms of aggregate formation and stability in two paddy soils.

Salivary gland cell aggregates are derived from self-organization of acinar lineage cells

Objective: The objective of this study was to characterize the mechanism by which salivary gland cells (SGC) aggregate in vitro.Design: Timelapse microscopy was utilized to analyze the process of salivary gland aggregate formation using both primary murine and human salivary gland cells. The role of cell density, proliferation, extracellular calcium, and secretory acinar cells in aggregate formation was investigated. Finally, the ability of cells isolated from irradiated glands to form aggregates was also evaluated.Results: Salivary gland cell self-organization rather than proliferation was the predominant mechanism of aggregate formation in both primary mouse and human salivary gland cultures. Aggregation was found to require extracellular calcium while acinar lineage cells account for ∼80% of the total aggregate cell population. Finally, aggregation was not impaired by irradiation.Conclusions: The data reveal that aggregation occurs as a result of heterogeneous salivary gland cell self-organization rather than from stem cell proliferation and differentiation, contradicting previous dogma. These results suggest a re-evaluation of aggregate formation as a criterion defining salivary gland stem cells.

Effects of land conversion from native shrub to pistachio orchard on soil erodibility in an arid region.

Land-use change through degrading natural vegetation for agricultural production adversely affects many of soil properties particularly organic carbon content of soils. The native shrub land and grassland of Gaziantep-Adiyaman plateau that is an important pistachio growing eco-region have been cleared to convert into pistachio orchard for the last 50 to 60years. In this study, the effects of conversion of natural vegetation into agricultural uses on soil erodibility have been investigated. Soil samples were collected from surface of agricultural fields and adjacent natural vegetation areas, and samples were analyzed for some soil erodibility indices such as dispersion ratio (DR), erosion ratio (ER), structural stability index (SSI), Henin's instability index (I s ), and aggregate size distribution after wet sieving (AggSD). According to the statistical evaluation, these two areas were found as different from each other in terms of erosion indices except for I s index (P<0.001 for DR and ER or P<0.01 for SSI). In addition, native shrub land and converted land to agriculture were found different in terms of AggSD in all aggregate size groups. As a contrary to expectations, correlation tests showed that there were no any interaction between soil organic carbon and measured erodibility indices in two areas. In addition, significant relationships were determined between measured variables and soil textural fractions as statistical. These obtaining findings were attributed to changing of textural component distribution and initial aggregate size distribution results from land-use change in the study area. Study results were explained about hierarchical aggregate formation mechanism.

Acid-induced assembly of a reconstituted silk protein system.

Silk cocoons are reconstituted into an aqueous suspension, and protein stability is investigated by comparing the protein's response to hydrochloric acid and sodium chloride. Aggregation occurs for systems mixed with hydrochloric acid, while sodium chloride over the same range of concentrations does not cause aggregation. We measure the structures present on the protein and aggregate length scales in these solutions using both optical and small-angle neutron scattering, while mass spectrometry techniques shed light on a possible mechanism for aggregate formation. We find that the introduction of acid modulates the aggregate size and pervaded volume of the protein, an effect that is not observed with salt.

Interactome Mapping Guided by Tissue-Specific Phosphorylation in Age-Related Macular Degeneration.

The current study aims to determine the molecular mechanisms of age-related macular degeneration (AMD) using the phosphorylation network. Specifically, we examined novel biomarkers for oxidative stress by protein interaction mapping using in vitro and in vivo models that mimic the complex and progressive characteristics of AMD. We hypothesized that the early apoptotic reactions could be initiated by protein phosphorylation in region-dependent (peripheral retina vs. macular) and tissue-dependent (retinal pigment epithelium vs. retina) manner under chronic oxidative stress. The analysis of protein interactome and oxidative biomarkers showed the presence of tissue- and region-specific post-translational mechanisms that contribute to AMD progression and suggested new therapeutic targets that include ubiquitin, erythropoietin, vitronectin, MMP2, crystalline, nitric oxide, and prohibitin. Phosphorylation of specific target proteins in RPE cells is a central regulatory mechanism as a survival tool under chronic oxidative imbalance. The current interactome map demonstrates a positive correlation between oxidative stress-mediated phosphorylation and AMD progression and provides a basis for understanding oxidative stress-induced cytoskeletal changes and the mechanism of aggregate formation induced by protein phosphorylation. This information could provide an effective therapeutic approach to treat age-related neurodegeneration.

Interdiffusion and crystallization of oppositely charged colloids.

The aggregation of oppositely charged colloids, usually denoted as heteroaggregation, is often used in colloidal processing, for which a precise control of the basic mechanisms of aggregate formation is of crucial importance. A promising way to achieve a better degree of control is to guide heteroaggregation by imposing geometric constraints. Here, we consider this possibility by simulating the heteroaggregation of two oppositely charged suspensions which are initially separated and then put into contact through a planar interface. Our Brownian dynamics simulations show that this type of heteroaggregation allows the formation of mixed films whose thickness can be controlled by tuning the interactions between the particles or by changing the colloidal concentration in the initial suspensions. The dependence of the type of crystalline order in these films on these parameters is also analyzed.