The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

Abstract

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.

Communicated by Ramaswamy H. Sarma     

Curcumin ameliorated myocardial infarction by inhibition of cardiotoxicity in the rat model

Cardiovascular diseases are the main cause of death globally. Many attempts have been done to ameliorate the pathological changes after the occurrence of myocardial infarction. Curcumin is touted as a polyphenol phytocompound with appropriate cardioprotective properties. In this study, the therapeutic effect of curcumin was investigated on acute myocardial infarction in the model of rats. Rats were classified into four groups; control, isoproterenol hydrochloride (ISO) (100 mg/kbw), curcumin (50 mg/kbw), and curcumin plus ISO treatment groups. After 9-day administration of curcumin, levels of lactate dehydrogenase (LDH), creatine kinase (CK), and cardiac troponin I (cTnI) were determined. Superoxide dismutase (SOD) and malondialdehyde (MDA) contents were measured to investigate the oxidative status in infarct rats received curcumin. By using H & E staining, tissue inflammation was performed. Masson’s trichrome staining was conducted to show cardiac remodeling and collagen deposition. The number of apoptotic cells was determined by using the terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Data showed the serum decrease of LDH, CK, and cTnI in infarct rats after curcumin intake compared to the rats given (ISO) ( P < 0.05). Curcumin was found to reduce oxidative status by reducing SOD and MDA contents ( P < 0.05). Gross and microscopic examinations revealed that the decrease of infarct area, inflammation response and collagen deposition in rats given ISO plus curcumin ( P < 0.05). We noted the superior effect of curcumin to reduce the number of apoptotic cardiomyocytes after 9 days. Data point the cardioprotective effect of curcumin to diminish the complication of infarction by the reduction of cell necrosis and apoptosis in a rat model of experimental infarction.     

MiRNAs and inflammatory bowel disease: An interesting new story

Inflammatory bowel disease (IBD), as a chronic and recurrent inflammatory disorder, is caused by a dysregulated and aberrant immune response to exposed environmental factors in genetically susceptible individuals. Despite huge efforts in determining the molecular pathogenesis of IBD, an increasing worldwide incidence of IBD has been reported. MicroRNAs (miRNAs) are a set of noncoding RNA molecules that are about 22 nucleotides long, and these molecules are involved in the regulation of the gene expression. By clarifying the important role of miRNAs in a number of diseases, their role was also considered in IBD; numerous studies have been performed on this topic. In this review, we attempt to summarize a number of studies and discuss some of the recent developments in the roles of miRNAs in the pathophysiology, diagnosis, and treatment of IBD.     

Epidemiology of Cholera in the Philippines

Background

Despite being a cholera-endemic country, data on cholera in the Philippines remain sparse. Knowing the areas where cholera is known to occur and the factors that lead to its occurrence will assist in planning preventive measures and disaster mitigation.

Methods

Using sentinel surveillance data, PubMed and ProMED searches covering information from 2008–2013 and event-based surveillance reports from 2010–2013, we assessed the epidemiology of cholera in the Philippines. Using spatial log regression, we assessed the role of water, sanitation and population density on the incidence of cholera.

Results and Discussion

We identified 12 articles from ProMED and none from PubMed that reported on cholera in the Philippines from 2008 to 2013. Data from ProMed and surveillance revealed 42,071 suspected and confirmed cholera cases reported from 2008 to 2013, among which only 5,006 were confirmed. 38 (47%) of 81 provinces and metropolitan regions reported at least one confirmed case of cholera and 32 (40%) reported at least one suspected case. The overall case fatality ratio in sentinel sites was 0.62%, but was 2% in outbreaks. All age groups were affected. Using both confirmed and suspected cholera cases, the average annual incidence in 2010–2013 was 9.1 per 100,000 population. Poor access to improved sanitation was consistently associated with higher cholera incidence. Paradoxically, access to improved water sources was associated with higher cholera incidence using both suspected and confirmed cholera data sources. This finding may have been due to the breakdown in the infrastructure and non-chlorination of water supplies, emphasizing the need to maintain public water systems.

Conclusion

Our findings confirm that cholera affects a large proportion of the provinces in the country. Identifying areas most at risk for cholera will support the development and implementation of policies to minimize the morbidity and mortality due to this disease.     

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.     

Application of water super absorbents in waste air biofiltration

Water super absorbents are low cross-linked hydrophilic polymers that absorb water in amounts up to several hundred times their dry weight. In this study, the effect of adding these materials to the bed of a biofilter was investigated. Two equal size biofilters were used for this purpose. One of the biofilters was packed with a mixture of perlite and a commercial polyacrylamide based super absorbent (2.3% dry weight), and the other was packed with perlite to perform as a control. The biofilters were inoculated with a bacterial culture that was able to grow on n-hexane as the sole source of carbon and energy. Both biofilters removed up to 90% of the entering pollutants when using an inlet n-hexane concentration of 1 g/m³, and an air flow rate of 0.3 L/min (mass loading of 18.34 g/m³/h, and empty bed residence time of 3.27 min). The super absorbent had a positive effect on the performance of the biofilter. While the difference in the performance of the biofilters was marginal when frequent moistening was applied, the difference was considerable when moistening was less frequent.     

Ultrasonographic contrast-agent imaging of sub-millimeter vessel structures with spatial compounding: in vitro analyses.

In clinical diagnostics, ultrasonographic contrast-agent imaging gives access to medical parameters such as perfusion and vascularization. In addition to the artifacts that are typical for ultrasonic imaging, e.g., speckle noise and depth-dependent sensitivity and resolution, contrast-agent imaging shows more pronounced depth dependence and may suffer from shadowing artifacts that arise from high attenuation of the ultrasound waves by the contrast agent at high concentrations. By imaging an object from different viewing angles in one 2D image plane and summing the images obtained (spatial compounding), image quality can be increased and artifacts can be suppressed. In the present study, we combined both techniques to overcome the limitations of contrast-agent imaging. We used a commercially available ultrasound scanner and a custom-made high-precision mechanical system to rotate the ultrasound transducer fully around the object under investigation. Using this set-up, ultrasound data were acquired in reflection mode to generate a 360 degrees compound scan of a flow-mimicking phantom supplied with contrast agent.