Spectroscopic and DFT investigation of interactions between cyclophosphamide and aspirin with lysozyme as binary and ternary systems

Multi-spectroscopic and density functional theory (DFT) calculations was used to study the interaction between cyclophosphamide (CYP) and aspirin (ASA) with lysozyme (LYS). The experimental results showed that fluorescence quenching of LYS by drug was a result of the formation of drug–LYS complex; static quenching was confirmed to result in fluorescence quenching. Modified Stern–Volmer plots of interaction between CYP and ASA with protein in the binary and ternary systems were used to determine the binding parameters. Molecular distances between the donor (LYS) and acceptor (CYP and ASA) for all systems were estimated according to Forster’s theory. The quantitative analysis obtained by CD spectra suggested that the presence of ASA and CYP decreased the α-helical content of LYS and induced the destabilizing of it. Theoretical studies on the interaction between LYS with ASA and CYP have been carried out using DFT at the B3LYP/6-31G level in the solvent phase. Binding energy of the mentioned complexes was calculated. It showed that tryptophan (Trp) 62 had the most affinity toward ASA and CYP. Analyzing the calculated results revealed that the five member ring of Trp has a key role in interaction of LYS with ASA and CYP.     

Normalization of miRNA qPCR high-throughput data: a comparison of methods

Low-density quantitative real-time PCR (qPCR) arrays are often used to profile expression patterns of microRNAs in various biological milieus. To achieve accurate analysis of expression of miRNAs, non-biological sources of variation in data should be removed through precise normalization of data. We have systematically compared the performance of 19 normalization methods on different subsets of a real miRNA qPCR dataset that covers 40 human tissues. After robustly modeling the mean squared error (MSE) in normalized data, we demonstrate lower variability between replicates is achieved using various methods not applied to high-throughput miRNA qPCR data yet. Normalization methods that use splines or wavelets smoothing to estimate and remove Cq dependent non-linearity between pairs of samples best reduced the MSE of differences in Cq values of replicate samples. These methods also retained between-group variability in different subsets of the dataset.     

Gold-deferrioxamine nanometric interface for selective recognition of Fe(III) using square wave voltammetry and electrochemical impedance spectroscopy methods

Deferrioxamine, a bacterial hydroxamic siderophore having high binding affinity for Fe(III), is used in its immobilized form, as self-assembled monolayer on Au, for accumulation and recognition of Fe(III) from the solution phase. The accumulated Fe(III) is detected via both active mode based on faradaic reduction current of Fe(III), and inactive mode based on impedimetric effect of accumulated Fe(III) against redox reaction of a suitable probe. Appropriate electrochemical techniques, square wave voltammetry and electrochemical impedance spectroscopy, are used for the transduction of analytical signals obtained by this sensor. Then, the parameters influencing the sensor response are optimized. In the best conditions, a linear response, from 1.0×10(-10) to 1.0×10(-7)M Fe(III) in logarithmic scale with a detection limit of 2.0×10(-11)M, and mean relative standard deviation of 1.7% for n=4 is observed. The results show that the sensor can be used for determination of Fe(III) in the presence of various inorganic ions and biological species. Validity of the method and applicability of the sensor are successfully tested by determination of Fe(III) in various real samples including plant tissue (corn leaves), industrial alloy (Ferrotitanium), and pharmaceutical samples (Venofer(?) ampoule, Ironorm(?) capsule, and V.M. Protein(?) powder).     

Immunogenicity of Salmonella enterica serovar Enteritidis virulence protein,InvH, and cross-reactivity of its antisera with Salmonella strains

Acellular vaccines containing bacterial immunodominant components such as surface proteins may be potent alternatives to live attenuated vaccines in order to reduce salmonellosis risk to human health. invH gene, an important part of needle complex in type three secretion system (TTSS) plays important role in efficient bacterial adherence and entry into epithelial cells. In this work we hypothesize that use of a 15 kDa recombinant InvH as Salmonella enterica serovar Enteritidis surface protein could provoke antibody production in mouse and would help us study feasibility of its potential for diagnosis and/or a recombinant vaccine. The purified InvH provoked significant rise of IgG in mice. Active protection induced by immunization with InvH against variable doses of S. enterica serovar Enteritidis, indicated that the immunized mice were completely protected against challenge with 10⁴ LD₅₀. The immunoreaction of sera from immunized mice with other Salmonella strains or cross reaction with sera of Salmonella strains inoculated mice is indicative of possessing by Salmonella strains of the surface protein, InvH, that can be employed in both prophylactic and diagnostic measures against S. enterica. Bacteria free spleen and ileum of the immunized mice in this study indicate that the invH gene affects bacterial invasion. Efficacy of the virulence protein, InvH, in shuttling into host cells in injectisome of S. enterica serovar Enteritidis and inhibition of this phenomenon by active immunization was shown in this study. In conclusion immunization with InvH protein can develop protection against S. enterica serovar Enteritidis infections. InvH in Salmonella strains can be exploited in protective measures as well as a diagnostic tool in Salmonella infections.     

A genetic assay of three patients in the same family with Holt-Oram syndrome; a case report

Holt-Oram syndrome (HOS) is a developmental disorder inherited in an autosomal-dominant pattern. Affected organs are the heart and forelimbs with upper extremity skeletal defects and congenital heart malformation. In this study we present three cases of HOS in the same family. In one of these three individuals we detected a transition of C to T (CTG-GTT, V205V) in exon 7 of the TBX5 gene. This nucleotide change causes no amino acid change and potential pathologic effects remain unknown.Key Words: Holt-Oram syndrome, Congenital heart malformation, TBX5 gene     

Effects of the adsorption of alkali metal oxides on the electronic,optical, and thermodynamic properties of the Mg<Subscript>12</Subscript>O<Subscript>12</Subscript>nanocage: a density functional theory study

The effect of alkali metal oxides M _n O (M?=?Li, Na, K; n?=?2, 3, 4) on the geometric, electronic, and linear and nonlinear optical properties of the Mg₁₂O₁₂ nanocage was investigated by density-functional-based methods. According to the computational results, these alkali metal oxides are adsorbed on the Mg₁₂O₁₂ nanocage because this adsorption reduces its energy gap. The static first hyperpolarizability (β ₀) of the nanocage is dramatically increased in the presence of the alkali metal oxides, with the greatest increase seen in the presence of the superalkalis (i.e., M₃O; M?=?Li, Na, and K). The highest first hyperpolarizability (β ₀?≈?600,000 a.u.) was calculated for K₃O@Mg₁₂O₁₂, which was considerably more than that for Mg₁₂O₁₂. The thermodynamic properties and relative stabilities of these inorganic compounds are discussed.

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Graphical Abstract Optimized structure and DOS spectrum of K₃O(e@Mg₁₂O₁₂)

     

Measurement of some Benzylisoquinoline Alkaloids in Different Organs of Persian Poppy during Ontogenetical Stages

Papaver bracteatum, a perennial species, has been known as a rich source of thebaine and a potential alternative to Papaver somniferum for the production of codeine and some semisynthetic antagonist drugs. In this study, ion mobility spectrum (IMS) of the root, leaf, bottom part of stem, upper part of stem, capsule wall, petal, and capsule content during developmental stages of P. bracteatum including annual rosette, perennial rosette, bud initiation, pendulous bud, preflowering, and lancing were investigated. The IMS revealed thebaine, papaverine, and noscapine as the major components of the extracted alkaloids. Based on the results of the study it appears that, at least in part, there is a competition among the biosynthesis pathways of papaverine, noscapine, and morphinan alkaloids from a common source . Root and capsule wall were the most potent organs for extraction of thebaine, while lancing stage was the best developmental stage for thebaine exploitation. However, it seems that total biomass of root and capsule wall plays a key role in the final selection of favorite organ. Although papaverine and noscapine in the stem at preflowering stage had the most quantity, significant amounts were found in the capsule wall. In general, total alkaloid content of leaf was lower than the other plant parts.     

Design and characterization of electrochemical dopamine–aptamer as convenient and integrated sensing platform

Here, an ultrasensitive label-free electrochemical aptasensor was developed for dopamine (DA) detection. Construction of the aptasensor was carried out by electrodeposition of gold–platinum nanoparticles (Au–PtNPs) on glassy carbon (GC) electrode modified with acid-oxidized carbon nanotubes (CNTs–COOH). A designed complementary amine-capped capture probe (ssDNA1) was immobilized at the surface of PtNPs/CNTs–COOH/GC electrode through the covalent amide bonds formed by the carboxyl groups on the nanotubes and the amino groups on the oligonucleotides. DA-specific aptamer was attached onto the electrode surface through hybridization with the ssDNA1. Methylene blue (MB) was used as an electrochemical indicator that was intercalated into the aptamer through the specific interaction with its guanine bases. In the presence of DA, the interaction between aptamer and DA displaced the MB from the electrode surface, rendering a lowered electrochemical signal attributed to a decreased amount of adsorbed MB. This phenomenon can be applied for DA detection. The peak current of probe (MB) linearly decreased over a DA concentration range of 1–30 nM with a detection limit of 0.22 nM.