Assembly of Human Papillomavirus Type-16 Virus-Like Particles: Multifactorial Study of Assembly and Competing Aggregation

Pentameric capsomeres of human papillomavirus capsid protein L1 expressed in Escherichia coli self-assemble into virus-like particles (VLPs) in vitro. A multifactorial experimental design was used to explore a wide range of solution conditions to optimize the assembly process. The degree of assembly was measured using an enzyme-linked immunosorbent assay, and a high-throughput turbidity assay was developed to monitor competing aggregation. The presence of zinc ions in the assembly buffer greatly increased the incidence of aggregation and had to be excluded from the experiment for meaningful analysis. Assembly of VLPs was optimal at a pH of about 6.5, calcium and sodium ions had no measurable effect, and dithiothreitol and glutathione inhibited assembly. Tryptophan fluorescence spectroscopy demonstrated that an increase in urea concentration reduced the rate of VLP formation but had no effect on the final concentration of assembled VLPs. This study demonstrates the use of the hanging-drop vapor-diffusion crystallization method to screen for conditions that promote aggregation and the use of tryptophan fluorescence spectroscopy for real-time monitoring of the assembly process.

Bile-salt-induced aggregation of poly(N-isopropylacrylamide) and lowering of the lower critical solution temperature in aqueous solutions

The effect of sodium cholate (NaC; concentration 1-16 mM), a biological surfactant, on the aggregation behavior of 1% (w/v, 2.2 × 10(-3) M) poly(N-isopropylacrylamide) (PNIPAM) aqueous solutions was studied as a function of temperature. From turbidity, dynamic light scattering, viscosity, and fluorescence measurements, it was observed that (i) there is NaC-induced nanoscale aggregation of PNIPAM in its sol state and (ii) the lower critical solution temperature corresponding to sol-gel transition shifts to a lower temperature by about 2 °C.

A priori prediction of aggregation efficiency and rate constant for fluidized bed melt granulation

This paper presents a predictive aggregation rate model for spray fluidized bed melt granulation. The aggregation rate constant was derived from probability analysis of particle–droplet contact combined with time scale analysis of droplet solidification and granule–granule collision rates. The latter was obtained using the principles of kinetic theory of granular flow (KTGF). The predicted aggregation rate constants were validated by comparison with reported experimental data for a range of binder spray rate, binder droplet size and operating granulator temperature. The developed model is particularly useful for predicting particle size distributions and growth using population balance equations (PBEs).

Aggregation and caking processes of granular materials:continuum model and simulation with application to sugar

Aggregation and caking of particles are common severe problems in many operations and processing of granular materials, where granulated sugar is an important example. Prevention of aggregation and caking of granular materials requires a good understanding of moisture migration and caking mechanisms. In this paper, the modeling of solid bridge formation between particles is introduced, based on moisture migration of atmospheric moisture into containers packed with granular materials through vapor evaporation and condensation. A model for the caking process is then developed, based on the growth of liquid bridges (during condensation), and their hardening and subsequent creation of solid bridges (during evaporation). The predicted caking strengths agree well with some available experimental data on granulated sugar under storage conditions.

Additive and multiplicative properties of scoring methods for preference aggregation

The paper reviews some additive and multiplicative properties of ranking procedures used for generalized tournaments with missing values and multiple comparisons. The methods analysed are the score, generalised row sum and least squares as well as fair bets and its variants. It is argued that generalised row sum should be applied not with a fixed parameter, but a variable one proportional to the number of known comparisons. It is shown that a natural additive property has strong links to independence of irrelevant matches, an axiom judged unfavourable when players have different opponents.

Mitigating congestion by integrating time forecasting and realtime information aggregation in cellular networks

An iterative travel time forecasting scheme, named the Advanced Multilane Prediction based Real-time Fastest Path (AMPRFP) algorithm, is presented in this dissertation. This scheme is derived from the conventional kernel estimator based prediction model by the association of real-time nonlinear impacts that caused by neighboring arcs’ traffic patterns with the historical traffic behaviors. The AMPRFP algorithm is evaluated by prediction of the travel time of congested arcs in the urban area of Jacksonville City. Experiment results illustrate that the proposed scheme is able to significantly reduce both the relative mean error (RME) and the root-mean-squared error (RMSE) of the predicted travel time. To obtain high quality real-time traffic information, which is essential to the performance of the AMPRFP algorithm, a data clean scheme enhanced empirical learning (DCSEEL) algorithm is also introduced. This novel method investigates the correlation between distance and direction in the geometrical map, which is not considered in existing fingerprint localization methods. Specifically, empirical learning methods are applied to minimize the error that exists in the estimated distance. A direction filter is developed to clean joints that have negative influence to the localization accuracy. Synthetic experiments in urban, suburban and rural environments are designed to evaluate the performance of DCSEEL algorithm in determining the cellular probe’s position. The results show that the cellular probe’s localization accuracy can be notably improved by the DCSEEL algorithm. Additionally, a new fast correlation technique for overcoming the time efficiency problem of the existing correlation algorithm based floating car data (FCD) technique is developed. The matching process is transformed into a 1-dimensional (1-D) curve matching problem and the Fast Normalized Cross-Correlation (FNCC) algorithm is introduced to supersede the Pearson product Moment Correlation Co-efficient (PMCC) algorithm in order to achieve the real-time requirement of the FCD method. The fast correlation technique shows a significant improvement in reducing the computational cost without affecting the accuracy of the matching process.

High-performance liquid chromatography measurement of carotenoids in human serum, etoposide in pig cerebrospinal fluid and measurement of the aggregation of xanthophylls in aqueous solutions

The present study measured a chemotherapy drug, etoposide, in pig cerebrospinal fluid after intraventricular administrations were made directly into the fourth ventricle of the brain; cytotoxic concentrations for a twenty-four hour period after infusions. The analytical method developed validates the potential treatment of malignant brain tumors. The increase in serum carotenoid concentration in 30 healthy individuals was measured after supplementation with lutein. HPLC analysis of serum levels of carotenoids showed an increase in the concentration of lutein and a constant concentration of other major serum carotenoids. An initial attempt to measure the enthalpy of aggregation of xanthophylls was conducted by using ultraviolet-visible spectroscopy. The enthalpy of lutein aggregation and AH range of zeaxanthin disordering of aggregation are reported. Monomethyl ether of lutein did not aggregate in any of the aqueous solutions.

Enzyme-induced Aggregation of Plasmonic Nanoparticles for the Development of Label-free and Ultrasensitive Detection of Bacterial DNA

Sensitive detection of pathogens is critical to ensure the safety of food supplies and to prevent bacterial disease infection and outbreak at the first onset. While conventional techniques such as cell culture, ELISA, PCR, etc. have been used as the predominant detection workhorses, they are however limited by either time-consuming procedure, complicated sample pre-treatment, expensive analysis and operation, or inability to be implemented at point-of-care testing. Here, we present our recently developed assay exploiting enzyme-induced aggregation of plasmonic gold nanoparticles (AuNPs) for label-free and ultrasensitive detection of bacterial DNA. In the experiments, AuNPs are first functionalized with specific, single-stranded RNA probes so that they exhibit high stability in solution even under high electrolytic condition thus exhibiting red color. When bacterial DNA is present in a sample, a DNA-RNA heteroduplex will be formed and subsequently prone to the RNase H cleavage on the RNA probe, allowing the DNA to liberate and hybridize with another RNA strand. This continuously happens until all of the RNA strands are cleaved, leaving the nanoparticles ‘unprotected’. The addition of NaCl will cause the ‘unprotected’ nanoparticles to aggregate, initiating a colour change from red to blue. The reaction is performed in a multi-well plate format, and the distinct colour signal can be discriminated by naked eye or simple optical spectroscopy. As a result, bacterial DNA as low as pM could be unambiguously detected, suggesting that the enzyme-induced aggregation of AuNPs assay is very easy to perform and sensitive, it will significantly benefit to development of fast and ultrasensitive methods that can be used for disease detection and diagnosis.

Temporal aggregation of migration counts can improve accuracy and precision of trends

Temporal replicate counts are often aggregated to improve model fit by reducing zero-inflation and count variability, and in the case of migration counts collected hourly throughout a migration, allows one to ignore nonindependence. However, aggregation can represent a loss of potentially useful information on the hourly or seasonal distribution of counts, which might impact our ability to estimate reliable trends. We simulated 20-year hourly raptor migration count datasets with known rate of change to test the effect of aggregating hourly counts to daily or annual totals on our ability to recover known trend. We simulated data for three types of species, to test whether results varied with species abundance or migration strategy: a commonly detected species, e.g., Northern Harrier, Circus cyaneus; a rarely detected species, e.g., Peregrine Falcon, Falco peregrinus; and a species typically counted in large aggregations with overdispersed counts, e.g., Broad-winged Hawk, Buteo platypterus. We compared accuracy and precision of estimated trends across species and count types (hourly/daily/annual) using hierarchical models that assumed a Poisson, negative binomial (NB) or zero-inflated negative binomial (ZINB) count distribution. We found little benefit of modeling zero-inflation or of modeling the hourly distribution of migration counts. For the rare species, trends analyzed using daily totals and an NB or ZINB data distribution resulted in a higher probability of detecting an accurate and precise trend. In contrast, trends of the common and overdispersed species benefited from aggregation to annual totals, and for the overdispersed species in particular, trends estimating using annual totals were more precise, and resulted in lower probabilities of estimating a trend (1) in the wrong direction, or (2) with credible intervals that excluded the true trend, as compared with hourly and daily counts.

One Person, Many Votes: Divided Majority and Information Aggregation

In elections, majority divisions pave the way to focal manipulations and coordination failures, which can lead to the victory of the wrong candidate. This paper shows how this flaw can be addressed if voter preferences over candidates are sensitive to information. We consider two potential sources of divisions: majority voters may have similar preferences but opposite information about the candidates, or opposite preferences. We show that when information is the source of majority divisions, Approval Voting features a unique equilibrium with full information and coordination equivalence. That is, it produces the same outcome as if both information and coordination problems could be resolved. Other electoral systems, such as Plurality and Two-Round elections, do not satisfy this equivalence. The second source of division is opposite preferences. Whenever the fraction of voters with such preferences is not too large, Approval Voting still satisfies full information and coordination equivalence.

Effect of the synthetic coumarin, ethyl 2-oxo-2H-chromene-3-carboxylate, on activity of Crotalus durissus ruruima sPLA2 as well as on edema and platelet aggregation induced by this factor

We show that ethyl 2-oxo-2H-chromene-3-carboxylate (EOCC), a synthetic coumarin, irreversibly inhibits phospholipase A(2) (sPLA2) from Crotalus durissus ruruima venom (sPLA2r) with an IC(50) of 3.1 +/- 0.06 nmol. EOCC strongly decreased the V(max) and K(m), and it virtually abolished the enzyme activity of sPLA2r as well as sPLA2s from other sources. The edema induced by 5PLA2r + EOCC was less than that induced by 5PLA2r treated with p-bromophenacyl bromide, which was more efficient at neutralizing the platelet aggregation activity of native 5PLA2r. Native 5PLA2r induced platelet aggregation of 91.54 +/- 9.3%, and sPLA2r +/- EOCC induced a platelet aggregation of 18.56 +/- 6.5%. EOCC treatment also decreased the myotoxic effect of sPLA2r. Mass spectrometry showed that EOCC formed a stable complex with sPLA2r, which increased the mass of native 5PLA2r from 14,299.34 da to 14,736.22 Da. Moreover, the formation of this complex appeared to be involved in the loss of 5PLA2r activity. Our results strongly suggest that EOCC can be used as a pharmacological agent against the 5PLA2 in Crotalus durissus sp. venom as well as other sPLA2s. (C) 2010 Elsevier Ltd. All rights reserved.

Harpalycin 2 inhibits the enzymatic and platelet aggregation activities of PrTX-III, a D49 phospholipase A(2) from Bothrops pirajai venom

Background: Harpalycin 2 (HP-2) is an isoflavone isolated from the leaves of Harpalyce brasiliana Benth., a snakeroot found in northeast region of Brazil and used in folk medicine to treat snakebite. Its leaves are said to be anti-inflammatory. Secretory phospholipases A(2) are important toxins found in snake venom and are structurally related to those found in inflammatory conditions in mammals, as in arthritis and atherosclerosis, and for this reason can be valuable tools for searching new anti-phospholipase A(2) drugs.Methods: HP-2 and piratoxin-III (PrTX-III) were purified through chromatographic techniques. The effect of HP-2 in the enzymatic activity of PrTX-III was carried out using 4-nitro-3-octanoyloxy-benzoic acid as the substrate. PrTX-III induced platelet aggregation was inhibited by HP-2 when compared to aristolochic acid and p-bromophenacyl bromide (p-BPB). In an attempt to elucidate how HP-2 interacts with PrTX-III, mass spectrometry, circular dichroism and intrinsic fluorescence analysis were performed. Docking scores of the ligands (HP-2, aristolochic acid and p-BPB) using PrTX-III as target were also calculated.Results: HP-2 inhibited the enzymatic activity of PrTX-III (IC50 11.34 +/- 0.28 mu g/mL) although it did not form a stable chemical complex in the active site, since mass spectrometry measurements showed no difference between native (13,837.34 Da) and HP-2 treated PrTX-III (13,856.12 Da). A structural analysis of PrTX-III after treatment with HP-2 showed a decrease in dimerization and a slight protein unfolding. In the platelet aggregation assay, HP-2 previously incubated with PrTX-III inhibited the aggregation when compared with untreated protein. PrTX-III chemical treated with aristolochic acid and p-BPB, two standard PLA(2) inhibitors, showed low inhibitory effects when compared with the HP-2 treatment. Docking scores corroborated these results, showing higher affinity of HP-2 for the PrTX-III target (PDB code: 1GMZ) than aristolochic acid and p-BPB. HP-2 previous incubated with the platelets inhibits the aggregation induced by untreated PrTX-III as well as arachidonic acid.Conclusion: HP-2 changes the structure of PrTX-III, inhibiting the enzymatic activity of this enzyme. In addition, PrTX-III platelet aggregant activity was inhibited by treatment with HP-2, p-BPB and aristolochic acid, and these results were corroborated by docking scores.

Mathematical models for cellular aggregation: the chemotactic instability and clustering formation

In this thesis we present a mathematical formulation of the interaction between microorganisms such as bacteria or amoebae and chemicals, often produced by the organisms themselves. This interaction is called chemotaxis and leads to cellular aggregation. We derive some models to describe chemotaxis. The first is the pioneristic Keller-Segel parabolic-parabolic model and it is derived by two different frameworks: a macroscopic perspective and a microscopic perspective, in which we start with a stochastic differential equation and we perform a mean-field approximation. This parabolic model may be generalized by the introduction of a degenerate diffusion parameter, which depends on the density itself via a power law. Then we derive a model for chemotaxis based on Cattaneo's law of heat propagation with finite speed, which is a hyperbolic model. The last model proposed here is a hydrodynamic model, which takes into account the inertia of the system by a friction force. In the limit of strong friction, the model reduces to the parabolic model, whereas in the limit of weak friction, we recover a hyperbolic model. Finally, we analyze the instability condition, which is the condition that leads to aggregation, and we describe the different kinds of aggregates we may obtain: the parabolic models lead to clusters or peaks whereas the hyperbolic models lead to the formation of network patterns or filaments. Moreover, we discuss the analogy between bacterial colonies and self gravitating systems by comparing the chemotactic collapse and the gravitational collapse (Jeans instability).