Computer simulations of nucleation of nanoparticle superclusters from solution

This paper presents simulation studies of nanoparticle supercluster (NPSC) nucleation from a temperature quenched system. The nanoparticles are represented as 5 nm, spherical gold nanoparticles ligated with alkane thiols. The pair potential accounts for the van der Waals interaction between the metallic cores and ligand-ligand and ligand-solvent interactions. Phenomena well-known for molecular systems are observed including a prenucleation induction period, fluctuating prenucleation clusters that predominately add monomers one at a time, a critical nucleus size, and growth of NPSCs from solution in the presence of an equilibrium supernatant, all consistent with classical nucleation theory. However, only the largest prenucleating clusters are dense, and the cluster size can occasionally range greater than the critical size in the prenucleation regime until a cluster with low enough energy occurs, then nucleation ensues. Late in the nucleation process, the clusters display a crystalline structure that is a random mix of face-centered cubic (fcc) and hexagonal close-packed (hcp) lattices and indistinguishable from a randomized icosahedra structure.

Ethical issues in microbiology

Ethical issues facing microbiologists could be considered in two parts. The first relates to the way the ethical issues during their laboratory work. The second pertains to ethical issues on the data/reports they generate for the patients or in research. In both segments, there is pressure to perform, which is exerted by both, the community, as well as peers. It has therefore become increasingly necessary to recognize the facts that unethical actions might be a frequent reality. Since some of these activities generate serious ethical concerns, both in practice and research, it is necessary for microbiologists to be aware and equipped to meet these issues in a prepared and measured way. In an attempt to highlight this requirement, this article outlines the important ethical issues and guidelines relevant to the field of Microbiology.

Kinetics of nanochain formation in a simplified model of amelogenin biomacromolecules

We show that the kinetics of nanochain formation of amelogenin molecules is well described by a combination of translational and rotational diffusion of a simplified anisotropic bipolar model consisting of hydrophobic spherical colloid particles and a point charge located on each particle surface. The colloid particles interact via a standard depletion attraction whereas the point charges interact through a screened Coulomb repulsion. We study the kinetics via a Brownian dynamics simulation of both translational and rotational motions and show that the anisotropy brought in by the charge dramatically affects the kinetic pathway of cluster formation and our simple model captures the main features of the experimental observations.

Pathways of cluster growth and kinetic slowing down in a model of short-range attractive colloids

We present the results of an extensive 3D Brownian dynamics simulation of the self-assembly of colloidal particles for a short-range attractive model that is quenched below its metastable critical point. In particular, results are obtained in the small-volume-fraction, low-temperature region in which we find so-called sticky beads that diffuse around the system, without reaching a final large cluster on the timescale of our simulation. For larger volume fractions in this low-temperature regime, a gel forms as the result of kinetically slowed down spinodal decomposition, as shown earlier for other short-range attractive models (Foffi, G.; De Michele, C.; Sciortino, F.; Tartaglia, P. Phys. Rev. Lett. 2005, 94, 078301. Zaccarelli, E. J. Phys.: Condens. Matter 2007, 19, 323101). We also show that for quenches below the critical point but above the intersection of the binodal with the glass line, two-step crystallization takes place. For sufficiently small volume fractions, the first step is the nucleation of dense fluid drops, followed by the second step of crystallization within these drops, as first proposed for a model of protein crystallization for quenches just above the metastable critical point (ten Wolde, P. R.; Frenkel, D. Science 1997, 277, 1975). For larger values of the volume fraction, the initial step is spinodal decomposition that leads to the formation of an interconnected network of low- and high-density fluids. The second step is crystallization that takes place within the dense fluid phase.

Elevated levels of redox regulators, membrane-bound globin chains, and cytoskeletal protein fragments in hereditary spherocytosis erythrocyte proteome

OBJECTIVE

Hereditary spherocytosis (HS), a common inherited hemolytic anemia characterized by decreased deformability, reduced surface to volume ratio, and increased osmotic fragility of the spheroidal erythrocytes, is associated with several mutations of α- and β-spectrin, ankyrin, band 3, band 4.2. HS manifests itself with high degrees of clinical heterogeneity and the molecular events leading to premature hemolysis of the spherocytes are unclear. We have employed proteomic techniques to identify differentially regulated proteins in the membrane and hemoglobin-depleted cytosol of HS erythrocytes.

METHODS

We have employed 2-D gel electrophoresis and tandem matrix assisted laser desorption ionization-time of flight/time of flight mass spectrometry to investigate the differential proteome profiling of membrane and hemoglobin-depleted cytosol of erythrocytes isolated from the peripheral blood samples of HS patients and normal volunteers.

RESULTS

Our study showed that redox regulators are up-regulated; while a co-chaperone and a nucleotide kinase are down-regulated in HS erythrocyte cytosol. We observed elevated levels of membrane-associated globin chains and low-molecular weight fragments of several major cytoskeletal proteins.

CONCLUSION

The observed changes in the erythrocyte proteomes indicate altered redox regulation, nucleotide metabolism, protein aggregation and/or degradation, cytoskeletal disorganization, and severe oxidative stress in HS. Taken together, this study could enlighten upon disease progression and pathophysiology of HS.

Effect of Ayurvedic mercury preparation Makaradhwaja on geriatric canine--a preliminary study

Makaradhwaja, an alchemical Ayurvedic mercury preparation is used as stimulant and vitalizer. Towards veterinary practices, the acceptability, tolerability and toxicity studies were undertaken in geriatric pet dogs aged more than 10 years irrespective of breed and sex for future use. Makaradhwaja (2.5 mg/kg) was used with honey once daily for 30 days. Before and after treatment, blood was collected for hematological studies as well as liver, kidney function and anti-oxidant activity. In control group, honey itself showed no appreciable change whereas, Makaradhwaja lowered neutrophil and total leucocyte count. Serum cholesterol, urea, glucose, alanine amino transferase, aspartate amino transferase, sodium, phosphorus and calcium were decreased. Haemoglobin and serum creatinine were significantly increased. There was appreciable physical, behavioral and body weight change including quality of life. The dose was used in replication of human dose (125 mg/50 kg). Anti-oxidant study showed significant increase of lipid per oxidation in experimental group while the values of ABTS radical cation decolorisation assay although decreased but did not show any significant changes. Decrease of serum urea and increase of serum creatinine could not be explained on single dose response. Different dose study could only explain the optimum dose to be required in canine practices.

Endemic fungal infections in the Asia-Pacific region

Endemic mycoses are important fungal infections in their respective habitats. In the Asia-Pacific region, an accurate epidemiological picture of endemic mycoses is elusive; few epidemiological surveys have been performed, and limited laboratory facilities and experience with fungal infections have further hampered recognition of infection. However, pockets of endemicity do indeed exist, and endemic fungal infections can have a significant impact on public health. This article reviews the most common endemic mycoses in the Asia-Pacific region: histoplasmosis, penicilliosis, and sporotrichosis. Blastomycosis, which has been infrequently reported within the region, is also briefly discussed. Certain areas of the Asia-Pacific region are endemic for histoplasmosis; however, the ecologic niche for this infection remains unclear. Penicilliosis is restricted to Southeast and Eastern Asia, whereas sporotrichosis is encountered in tropical areas of the Asia-Pacific region linked to environmental reservoirs distinct from those seen in the Western world. Before the advent of acquired immune deficiency syndrome (AIDS), histoplasmosis and penicilliosis were only occasionally reported; however, the incidence of both mycoses has increased with the rise in the incidence of AIDS. Comprehensive studies are needed to fully assess the areas of endemicity and the impact of endemic mycoses in the Asia-Pacific region.

DNA binding domain of RFX5: interactions with X-box DNA and RFXANK

Regulatory factor X (RFX) is a heterotrimeric protein complex having RFX5, RFXANK and RFXAP as its three subunits. It is involved in the regulation of the transcription of MHCII molecules in antigen presenting cells. The RFX complex binds to X-box DNA, using the DNA binding domain, present in RFX5. The DNA binding domain (DBD) of RFX5 (12kD) and intact RFXANK (35 kD) were subcloned, expressed and purified. The associations of RFX5DBD with the X-box DNA and between RFX5DBD and RFXANK were measured in this study. The interaction of RFX5DBD and X-box DNA was studied using steady state fluorescence quenching and circular dichroism. The binding dissociation constant (K(d)) of the DNA-protein complex was determined from fluorescence measurements. The van't Hoff plot was linear over the temperature range 10-25 degrees C and the binding was found to be entropy-driven and enthalpy-favorable. The effect of electrolytes in RFX5DBD-DNA association was also studied. Molecular association between RFX5DBD and RFXANK has been observed by fluorescence resonance energy transfer (FRET) measurements, changes in the ratio of the two vibronic intensities of pyrene labeled RFX5DBD in presence of RFXANK and chemical cross-linking followed by tandem mass spectrometry. Results showed that the two proteins could interact in the absence of the third subunit RFXAP, in vitro with an apparent dissociation constant (K(d)) of 128 nM.

Coulomb explosion sputtering of selectively oxidized Si

We have studied the sputtering of a unique system comprising of coexisting silicon and silicon oxide surfaces due to the impact of multiply charged Ar(q+) ions. Such surfaces are produced by oblique angle oxygen ion bombardment on Si(100), which results in one side oxidized ripple formation due to preferential oxygen implantation. It is observed by atomic force microscopy and conducting atomic force microscopy studies that the higher the potential energy of the Ar(q+) ion, the higher the sputtering yield of the nonconducting (oxide) side of the ripple as compared to the semiconducting side while ensuring an identical irradiation and measurement condition. It also shows experimentally the potential of highly charged ions in the gentle cleaning or tailoring of nanostructures. The results are explained in terms of the Coulomb explosion model, where potential sputtering depends on the conductivity of the ion impact sites.

Structure and conformational studies on dityrosine formation in the DNA binding domain of RFX5

The DNA binding protein RFX5 is a subunit of RFX complex involved in transcription regulation of MHCII molecules. The RFX complex binds to the X-box DNA through the DNA binding domain of RFX5. We have examined the formation of intramolecular tyrosine cross linking, dityrosine, in RFX5DBD under oxidative stress, through UV irradiation and enzymatic action of H(2)O(2)/peroxidase by fluorescence spectroscopic studies. Dityrosine (DT) was formed predominantly in alkaline condition showing its intense characteristic fluorescence emission. Homology modeling indicated Y(39) and Y(42) could be the potential tyrosine residues undergoing oxidative cross-linking. Conformational changes in RFX5DBD under oxidative stress were observed by CD measurements. The in vitro association of X-box DNA with RFX5DBD increased DT fluorescence significantly and protected RFX5DBD from UV irradiation as observed in SDS-PAGE followed by mass spectrometric analysis. Results indicate cross protection in both RFX5DBD and DNA under oxidative stress playing important role in protein modification.

Design and development of a radio frequency quadrupole linac postaccelerator for the Variable Energy Cyclotron Center rare ion beam project

A four-rod type heavy-ion radio frequency quadrupole (RFQ) linac has been designed, constructed, and tested for the rare ion beam (RIB) facility project at VECC. Designed for cw operation, this RFQ is the first postaccelerator in the RIB beam line. It will accelerate A/q < or = 14 heavy ions coming from the ion source to the energy of around 100 keV/u for subsequent acceleration in a number of Interdigital H-Linac. Operating at a resonance frequency of 37.83 MHz, maximum intervane voltage of around 54 kV will be needed to achieve the final energy over a vane length of 3.12 m for a power loss of 35 kW. In the first beam tests, transmission efficiency of about 90% was measured at the QQ focus after the RFQ for O(5+) beam. In this article the design of the RFQ including the effect of vane modulation on the rf characteristics and results of beam tests will be presented.

Differential regulation of redox proteins and chaperones in HbEβ-thalassemia erythrocyte proteome

PURPOSE

In (hemoglobin, Hb) HbEβ-thalassemia, HbE (β-26 Glu→Lys) interacts with β-thalassemia to produce clinical manifestation of varying severity. This is the first proteomic effort to study changes in protein levels of erythrocytes isolated from HbEβ-thalassemic patients compared to normal.

EXPERIMENTAL DESIGN

We have used 2-DE and MALDI-MS/MS-based techniques to investigate the differential proteome profiling of membrane and Hb-depleted fraction of cytosolic proteins of erythrocytes isolated from the peripheral blood samples of HbEβ-thalassemia patients and normal volunteers.

RESULTS

Our study showed that redox regulators such as peroxiredoxin 2, Cu-Zn superoxide dismutase and thioredoxin and chaperones such as α-hemoglobin stabilizing protein and HSP-70 were upregulated in HbEβ-thalassemia. We have also observed larger amounts of membrane associated globin chains and indications of disruption of spectrin-based junctional complex in the membrane skeleton of HbEβ-thalassemic erythrocytes upon detection of low molecular weight fragments of β-spectrin and decrease in β-actin and dematin content.

CONCLUSION AND CLINICAL RELEVANCE

We have observed interesting changes in the proteomic levels of redox regulators and chaperons in the thalassemic hemolysates and have observed strong correlation or association of the extent of such proteomic changes with HbE levels. This could be important in understanding the role of HbE in disease progression and pathophysiology.

Self-assembly of ligated gold nanoparticles: phenomenological modeling and computer simulations

We study the assembly of ligated gold nanoparticles by both phenomenological modeling and computer simulations for various ligand chain lengths. First, we develop an effective nanoparticle-nanoparticle pair potential by treating the ligands as flexible polymer chains. Besides van der Waals interactions, we incorporate both the free energy of mixing and elastic contributions from compression of the ligands in our effective pair potentials. The separation of the nanoparticles at the potential minimum compares well with experimental results of gold nanoparticle superlattice constants for various ligand lengths. Next, we use the calculated pair potentials as input to Brownian dynamics simulations for studying the formation of nanoparticle assembly in three dimensions. For dodecanethiol ligated nanoparticles in toluene, our model gives a relatively shallower well depth and the clusters formed after a temperature quench are compact in morphology. Simulation results for the kinetics of cluster growth in this case are compared with phase separations in binary mixtures. For decanethiol ligated nanoparticles, the model well depth is found to be deeper, and simulations show hybrid, fractal-like morphology for the clusters. Cluster morphology in this case shows a compact structure at short length scales and a fractal structure at large length scales. Growth kinetics for this deeper potential depth is compared with the diffusion-limited cluster-cluster aggregation (DLCA) model.