Analytical Approach to the Surface Plasmon Resonance Characteristic of Metal Nanoparticle Dimer in Dipole-Dipole Approximation

This theoretical study deals with the effect of bi-particle interaction on the surface plasmon resonance (SPR) in a dimer which includes two identical metal nanoparticles (NPs). Considering the dipole-dipole interaction in a Drude-like model, an appropriate equation is derived for the permittivity of each NP. The restoration force related to the classical confinement originating from the finite size of NPs is considered, and an appropriate adjustment coefficient is considered for this term through analyzing experimental data. Two different polarizations are considered for the laser beam electric field, and it is shown that the orientation of the electric field has an essential role in the linear optical properties of a dimer. Numerical investigation is accomplished for a dimer of gold NPs with two different diameters of 4 nm and 20 nm. For the parallel polarization, dipole-dipole interaction leads to the redshift of SPR wavelength and increase in its peak value, while for the perpendicular polarization, the absolute opposite results are derived. For all cases, it is shown that SPR wavelength functionality with respect to the geometric factor a/d (NP radius to the separation) can be presented by a cubic equation that fits better than an exponential one suggested by the earlier studies which demonstrates the dipole-dipole characteristic of the interaction. Qualitatively, our results are in good agreement with the other experimental studies.

     

Modeling the effects of sodium chloride, acetic acid, and intracellular pH on survival of Escherichia coli O157:H7

Microbiological safety has been a critical issue for acid and acidified foods since it became clear that acid-tolerant pathogens such as Escherichia coli O157:H7 can survive (even though they are unable to grow) in a pH range of 3 to 4, which is typical for these classes of food products. The primary antimicrobial compounds in these products are acetic acid and NaCl, which can alter the intracellular physiology of E. coli O157:H7, leading to cell death. For combinations of acetic acid and NaCl at pH 3.2 (a pH value typical for non-heat-processed acidified vegetables), survival curves were described by using a Weibull model. The data revealed a protective effect of NaCl concentration on cell survival for selected acetic acid concentrations. The intracellular pH of an E. coli O157:H7 strain exposed to acetic acid concentrations of up to 40 mM and NaCl concentrations between 2 and 4% was determined. A reduction in the intracellular pH was observed for increasing acetic acid concentrations with an external pH of 3.2. Comparing intracellular pH with Weibull model predictions showed that decreases in intracellular pH were significantly correlated with the corresponding times required to achieve a 5-log reduction in the number of bacteria.     

Detecting novel SNPs and breed-specific haplotypes at calpastatin gene in Iranian fat- and thin-tailed sheep breeds and their effects on protein structure

Calpastatin has been introduced as a potential candidate gene for growth and meat quality traits. In this study, genetic variability was investigated in the exon 6 and its intron boundaries of ovine CAST gene by PCR-SSCP analysis and DNA sequencing. Also a protein sequence and structural analysis were performed to predict the possible impact of amino acid substitutions on physicochemical properties and structure of the CAST protein. A total of 487 animals belonging to four ancient Iranian sheep breeds with different fat metabolisms, Lori-Bakhtiari and Chall (fat-tailed), Zel-Atabay cross-bred (medium fat-tailed) and Zel (thin-tailed), were analyzed. Eight unique SSCP patterns, representing eight different sequences or haplotypes, CAST-1, CAST-2 and CAST-6 to CAST-11, were identified. Haplotypes CAST-1 and CAST-2 were most common with frequency of 0.365 and 0.295. The novel haplotype CAST-8 had considerable frequency in Iranian sheep breeds (0.129). All the consensus sequences showed 98–99%, 94–98%, 92–93% and 82–83% similarity to the published ovine, caprine, bovine and porcine CAST locus sequences, respectively. Sequence analysis revealed four SNPs in intron 5 (C24T, G62A, G65T and T69-) and three SNPs in exon 6 (c.197A > T, c.282G > T and c.296C > G). All three SNPs in exon 6 were missense mutations which would result in p.Gln 66 Leu, p.Glu 94 Asp and p.Pro 99 Arg substitutions, respectively, in CAST protein. All three amino acid substitutions affected the physicochemical properties of ovine CAST protein including hydrophobicity, amphiphilicity and net charge and subsequently might influence its structure and effect on the activity of Ca2 + channels; hence, they might regulate calpain activity and afterwards meat tenderness and growth rate. The Lori-Bakhtiari population showed the highest heterozygosity in the ovine CAST locus (0.802). Frequency difference of haplotypes CAST-10 and CAST-8 between Lori-Bakhtiari (fat-tailed) and Zel (thin-tailed) breeds was highly significant (P < 0.001), indicating that these two haplotypes might be breed-specific haplotypes that distinguish between fat-tailed and thin-tailed sheep breeds.     

Safe bunker designing for the 18?MV Varian 2100 Clinac: a comparison between Monte Carlo simulation based upon data and new protocol recommendations

Aim

The aim of this study was to compare two bunkers designed by only protocols recommendations and Monte Carlo (MC) based upon data derived for an 18 MV Varian 2100Clinac accelerator.

Background

High energy radiation therapy is associated with fast and thermal photoneutrons. Adequate shielding against the contaminant neutron has been recommended by IAEA and NCRP new protocols.

Materials and methods

The latest protocols released by the IAEA (safety report No. 47) and NCRP report No. 151 were used for the bunker designing calculations. MC method based upon data was also derived. Two bunkers using protocols and MC upon data were designed and discussed.

Results

From designed door''s thickness, the door designed by the MC simulation and Wu–McGinley analytical method was closer in both BPE and lead thickness. In the case of the primary and secondary barriers, MC simulation resulted in 440.11 mm for the ordinary concrete, total concrete thickness of 1709 mm was required. Calculating the same parameters value with the recommended analytical methods resulted in 1762 mm for the required thickness using 445 mm as recommended by TVL for the concrete. Additionally, for the secondary barrier the thickness of 752.05 mm was obtained.

Conclusion

Our results showed MC simulation and the followed protocols recommendations in dose calculation are in good agreement in the radiation contamination dose calculation. Difference between the two analytical and MC simulation methods revealed that the application of only one method for the bunker design may lead to underestimation or overestimation in dose and shielding calculations.     

Sequencing cyclic peptides by multistage mass spectrometry

Some of the most effective antibiotics (e.g. Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of MS-based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage MS, and show its advantages over single-stage MS. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria.     

Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids

Proteins of halophilic organisms, which accumulate molar concentrations of KCl in their cytoplasm, have a much higher content in acidic amino acids than proteins of mesophilic organisms. It has been proposed that this excess is necessary to maintain proteins hydrated in an environment with low water activity, either via direct interactions between water and the carboxylate groups of acidic amino acids or via cooperative interactions between acidic amino acids and hydrated cations. Our simulation study of five halophilic proteins and five mesophilic counterparts does not support either possibility. The simulations use the AMBER ff14SB force field with newly optimized Lennard-Jones parameters for the interactions between carboxylate groups and potassium ions. We find that proteins with a larger fraction of acidic amino acids indeed have higher hydration levels, as measured by the concentration of water in their hydration shell and the number of water/protein hydrogen bonds. However, the hydration level of each protein is identical at low (b_KCl = 0.15 mol/kg) and high (b_KCl = 2 mol/kg) KCl concentrations; excess acidic amino acids are clearly not necessary to maintain proteins hydrated at high salt concentration. It has also been proposed that cooperative interactions between acidic amino acids in halophilic proteins and hydrated cations stabilize the folded protein structure and would lead to slower dynamics of the solvation shell. We find that the translational dynamics of the solvation shell is barely distinguishable between halophilic and mesophilic proteins; if such a cooperative effect exists, it does not have that entropic signature.     

A Randomized Controlled Trial: Efficacy and Safety of Azithromycin,Ofloxacin, Bismuth,and Omeprazole Compared With Amoxicillin,Clarithromycin, Bismuth,and Omeprazole as Second‐Line Therapy in Patients With Helicobacter pylori Infection

Background: Helicobacter pylori infection of the stomach is widespread among human populations and is considered to play a major role in the pathogenesis of various diseases such as peptic ulcer, adenocarcinoma, and mucosa associated lymphoid tissue (MALT) lymphoma of the stomach. To increase H. pylori eradication rate without increasing bacterial resistance, various regimens have been recommended. Commonly the association of at least two antibiotics with a proton‐pump inhibitor is used. The treatment regimens for second‐line therapy, suggested in studies from the western world may not be ideal in Iran. Aim: In this study, we evaluated the safety and efficacy of a new quadruple therapy regimen and compared it with the standard second‐line treatment for H. pylori eradication. Methods: We selected 220 H. pylori positive patients, with a clear indication of eradication therapy, who did not respond to a 2 weeks treatment with metronidazole, amoxicillin, omeprazole, and bismuth. They were randomized into two groups. Group A (n = 110) were treated with azithromycin, ofloxacin, bismuth, and omeprazole and group B (n = 110) with amoxicillin, clarithromycin, bismuth, and omeprazole for 2 weeks. Four weeks after the end of treatment, urea breath test was performed for all subjects to confirm eradication. Results: In intention‐to‐treat analysis, the rate of H. pylori eradication in groups A and B was 77.3% (85/110) and 64.5% (71/110) respectively (p = .027). In per‐protocol analysis, the rate of H. pylori eradication in groups A and B was 86.7 and 74.7%, respectively (p = .026). The incidence of poor compliance was lower, although not significantly so, in group A than group B (3.5 vs 4.3%). No major adverse events occurred in both groups. Conclusion: Two weeks of treatment with ofloxacin, azithromycin, omeprazole, and bismuth is an effective and safe regimen for H. pylori eradication as second‐line therapy.