Fabrication of Silver Chevron Arrays as an Efficient and Stable SERS Substrate: Implications in Biological Sensing

Plasmonics - Although glancing angle deposited silver substrates offer an excellent figures for surface enhanced Raman scattering (SERS) sensing, the chemical instability issues of silver...     

Ag Nanostructures Produced by Glancing Angle Deposition with Remarkable Refractive Index Sensitivity

Glancing angle deposition is a powerful method for direct fabrication of nanostructures on various substrates. In this research, GLAD method has been used to fabricate Ag nanostructures with columnar morphology for refractive index sensing applications. The morphology and plasmonic properties of the nanostructures are controlled by changing deposition parameters such as glancing angle, speed of azimuthal rotation of the substrate, and the height of deposited nanostructures. The results show that increasing the deposition thickness from 200 to 500 nm leads to narrowing the plasmonic peak, which mainly relates to increment of the distance between larger nanostructures. By changing the glancing angle between 86° to 80°, the narrowest plasmonic peak corresponding to the greatest sensitivity has been obtained for the film deposited at the angle of 82°. Also, increment of the rotation speed of the samples leads to narrowing of the plasmonic peaks. By measuring the refractive index sensitivity (RIS) of the nanostructures, a best sensitivity of 154 nm/RIU has been obtained. Finally, we investigated the stability of Ag nanostructures in deionized water by introducing a new stabilizing technique in which a thin Au layer is coated on the Ag nanostructures. This technique has the merits of simultaneously protecting the Ag nanostructures against oxidation and keeping their refractive index sensitivity high enough for long time usages.     

Surface Plasmon Resonance in Small Gold Nanoparticles: Introducing a Size-Dependent Plasma Frequency for Nanoparticles in Quantum Regime

Plasmonics - Study of surface plasmon resonance for small nanoparticles (R < 10 nm) has many theoretical complexities due to lack of a simple quantitative model for describing...     

Symmetric bursting behaviors in the generalized FitzHugh–Nagumo model

In the current paper, we have investigated the generalized FitzHugh–Nagumo model. We have shown that symmetric bursting behaviors of different types could be observed in this model with an appropriate recovery term. A modified version of this system is used to construct bursting activities. Furthermore, we have shown some numerical examples of delayed Hopf bifurcation and canard phenomenon in the symmetric bursting of super-Hopf/homoclinic type near its super-Hopf and homoclinic bifurcations, respectively.     

Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics

Protein-protein ligand is one of the most detection methods used in Nano biosensors. Based on the advantage of specific docking between two special 3D structures, they have become a potent candidate in bioanalysis and Nanodiagnostic tools. These tools lease users to do a simple, fast, cost-effective, sensitive, and specific detection of molecular biomarkers in real samples. Recent advantages of using protein-protein ligand Nano-biosensors application is remarkable due to its special docking that refers to each protein unique 3D conformation. However, it challenges different problems such as low rate of docking and hard process for fixation on the basic layer. These challenges make developers to optimize the structure and functions of proteins. The process has different Nano scale calculation that could be done with algorithms and solutions are available as bioinformatics tools. This article aimed to have a short overview of the abilities of bioinformatics tools for modeling and optimization of physiochemical features of proteins in Nano scale.     

Modeling the time dependent biodistribution of Samarium-153 ethylenediamine tetramethylene phosphonate using compartmental analysis

Aim

The main purpose of this work was to develop a pharmacokinetic model for the bone pain palliation agent Samarium-153 ethylenediamine tetramethylene phosphonate ([¹⁵³Sm]-EDTMP) in normal rats to analyze the behavior of the complex.

Background

The use of compartmental analysis allows a mathematical separation of tissues and organs to determine the concentration of activity in each fraction of interest. Biodistribution studies are expensive and difficult to carry out in humans, but such data can be obtained easily in rodents.

Materials and methods

We have developed a physiologically based pharmacokinetic model for scaling up activity concentration in each organ versus time. The mathematical model uses physiological parameters including organ volumes, blood flow rates, and vascular permabilities; the compartments (organs) are connected anatomically. This allows the use of scale-up techniques to predict new complex distribution in humans in each organ.

Results

The concentration of the radiopharmaceutical in various organs was measured at different times. The temporal behavior of biodistribution of ¹⁵³Sm-EDTMP was modeled and drawn as a function of time.

Conclusions

The variation of pharmaceutical concentration in all organs is described with summation of 6–10 exponential terms and it approximates our experimental data with precision better than 2%.     

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

Soils contaminated with crude oil are rich sources of enzymes suitable for both degradation of hydrocarbons through bioremediation processes and improvement of crude oil during its refining steps. Due to the long term selection, crude oil fields are unique environments for the identification of microorganisms with the ability to produce these enzymes. In this metagenomic study, based on Hiseq Illumina sequencing of samples obtained from a crude oil field and analysis of data on MG‐RAST, Actinomycetales (9.8%) were found to be the dominant microorganisms, followed by Rhizobiales (3.3%). Furthermore, several functional genes were found in this study, mostly belong to Actinobacteria (12.35%), which have a role in the metabolism of aliphatic and aromatic hydrocarbons (2.51%), desulfurization (0.03%), element shortage (5.6%), and resistance to heavy metals (1.1%). This information will be useful for assisting in the application of microorganisms in the removal of hydrocarbon contamination and/or for improving the quality of crude oil. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:638–648, 2016     

Substrate recognition and ubiquitination of SCFSkp2/Cks1 ubiquitin-protein isopeptide ligase

p27, an important cell cycle regulator, blocks the G(1)/S transition in cells by binding and inhibiting Cdk2/cyclin A and Cdk2/cyclin E complexes (Cdk2/E). Ubiquitination and subsequent degradation play a critical role in regulating the levels of p27 during cell cycle progression. Here we provide evidence suggesting that both Cdk2/E and phosphorylation of Thr(187) on p27 are essential for the recognition of p27 by the SCF(Skp2/Cks1) complex, the ubiquitin-protein isopeptide ligase (E3). Cdk2/E provides a high affinity binding site, whereas the phosphorylated Thr(187) provides a low affinity binding site for the Skp2/Cks1 complex. Furthermore, binding of phosphorylated p27/Cdk2/E to the E3 complex showed positive cooperativity. Consistently, p27 is also ubiquitinated in a similarly cooperative manner. In the absence of p27, Cdk2/E and Cks1 increase Skp2 phosphorylation. This phosphorylation enhances Skp2 auto-ubiquitination, whereas p27 inhibits both phosphorylation and auto-ubiquitination of Skp2.     

The most reliable surface marker for the identification of colorectal cancer stem-like cells: A systematic review and meta-analysis

Several surface markers have been proposed for the identification and characterization of colorectal cancer stem-like cells (CR-CSLCs). However, their reliability in CR-CSLCs identification remains controversial. This study evaluated the correlation between all candidate surface marker's expression and CSLCs properties (tumorigenicity) through monitoring in vivo tumor incidence and final tumor volume. PubMed, Web of Science, and Scopus databases were systematically searched until November 2017. A total of 27 studies were found that met the inclusion criteria for cluster of differentiation 133 (CD133) and CD44 markers. Results indicated that either CD133 or CD44 positive cells caused about twofold increase in tumor volume compared with the negative cells (p < 0.05). In two groups of cells derived from primary tumors and cell lines, CD133 ⁺ cells had 25 and 1.45 times higher tumor incidence potential than CD133 ⁻ cells, respectively ( p < 0.05). Also, cohort evaluation showed that CD133 overexpression at protein level is a marker of poor overall survival in colorectal cancer (CRC) patients. While CD44 ⁺ cells displayed twofold tumorigenicity compared with the negative cells ( p < 0.05), combination of CD44 and CD133 showed about sevenfold tumorigenicity potential ( p < 0.05). In conclusion, the present meta-analysis suggests that CD133 is a robust biomarker to identify primary tumor CSLCs and can be proposed as a prognostic marker of CRC patient whereas it should be used with caution in cell lines. It seems to be more reliable to use CD133 in combination with CD44 as target biomarkers for the isolation of CR-CSLCs in both cell line and primary tumor cells populations.     

High Level Activity of Recombinant Lysostaphin After Computer Simulation and Additive-Based Refolding

International Journal of Peptide Research and Therapeutics - Lysostaphin is a peptidoglycan hydrolase, produced by Staphylococcus simulans, which has illustrated significant bactericidal activities...