Influence of solvent and counter ion on copper complexes with N-alkyl-pyridine-2-carboxamides as studied by electrospray ionization mass spectrometry

The interactions of copper(II) with N-alkyl-pyridine-2-carboxamides (M) were studied by electrospray ionization mass spectrometry. The influence of solvent and counter ion (Cl-, ClO4-) on the type of ions (complexes) observed was discussed. By cone voltage increase, the fragmentation "in source" of the ions discussed was achieved. In methanol solution containing N-alkyl-pyridine-2-carboxamide (M) and CuCl2 the singly- and doubly charged-ions [M+CuCl]+ and [M2+Cu]+2 were detected. In acetonitrile solution containing N-alkyl-pyridine-2-carboxamide and CuCl2, the copper(I)-containing ions [M+CH3CN+Cu]+ were formed. The use of Cu(ClO4)2 instead of CuCl2 resulted in more abundant doubly-charged ions in both methanol and acetonitrlile solutions and, for the former solution, the ions containing methoxyl anion, namely [M+CuOCH3]+, were observed. When water was used as a solvent, the abundant ions corresponding to the protonated ligands were formed, while the ions corresponding to copper complexes were characterised by low abundances.     

Dealing with repetitions in sequencing by hybridization

DNA sequencing by hybridization (SBH) induces errors in the biochemical experiment. Some of them are random and disappear when the experiment is repeated. Others are systematic, involving repetitions in the probes of the target sequence. A good method for solving SBH problems must deal with both types of errors. In this work we propose a new hybrid genetic algorithm for isothermic and standard sequencing that incorporates the concept of structured combinations. The algorithm is then compared with other methods designed for handling errors that arise in standard and isothermic SBH approaches. DNA sequences used for testing are taken from GenBank. The set of instances for testing was divided into two groups. The first group consisted of sequences containing positive and negative errors in the spectrum, at a rate of up to 20%, excluding errors coming from repetitions. The second group consisted of sequences containing repeated oligonucleotides, and containing additional errors up to 5% added into the spectra. Our new method outperforms the best alternative procedures for both data sets. Moreover, the method produces solutions exhibiting extremely high degree of similarity to the target sequences in the cases without repetitions, which is an important outcome for biologists. The spectra prepared from the sequences taken from GenBank are available on our website http://bio.cs.put.poznan.pl/.     

Functionalization of carbon nanotubes with silver clusters

In this paper, an advanced method of one-step functionalization of single and multi walled carbon nanotubes (SWCNTs and MWCNTs) using γ-irradiation was described. Two synthesis procedures, related with different reduction species, were employed. For the first time, poly(vinyl alcohol) PVA is successfully utilized as a source to reduce silver (Ag) metal ions without having any additional reducing agents to obtain Ag nanoparticles on CNTs. The decoration of carbon nanotubes with Ag nanoparticles takes place through anchoring of (PVA) on nanotube's surface. Optical properties of as-prepared samples and mechanism responsible for the functionalization of carbon nanotubes were investigated using UV-vis and FTIR spectroscopy, respectively. Decorated carbon nanotubes were visualized using microscopic techniques: transmission electron microscopy and scanning tunneling microscopy. Also, the presence of Ag on the nanotubes was confirmed using energy dispersive X-ray spectroscopy. This simple and effective method of making a carbon nanotube type of composites is of interest not only for an application in various areas of technology and biology, but for investigation of the potential of radiation technology for nanoengineering of materials.     

Graph algorithms for DNA sequencing – origins,current models and the future

With the ubiquitous presence of next-generation sequencing in modern biological, genetic, pharmaceutical and medical research, not everyone pays attention to the underlying computational methods. Even fewer researchers know what were the origins of the current models for DNA assembly. We present original graph models used in DNA sequencing by hybridization, discuss their properties and connections between them. We also explain how these graph models evolved to adapt to the characteristics of next-generation sequencing. Moreover, we present a practical comparison of state-of-the-art DNA de novo assembly tools representing these transformed models, i.e. overlap and decomposition-based graphs. Even though the competition is tough, some assemblers perform better and certainly large differences may be observed in hardware resources utilization. Finally, we outline the most important trends in the sequencing field, and try to predict their impact on the computational models in the future.     

On diagonal resolvable spheres

In this paper we give the complete answer to a question posed by A. Arhangel?skii and prove that the sphere Sⁿ$S^n$ is diagonal resolvable if and only if Sⁿ$S^n$ is an H  -space if and only if n∈{0,1,3,7}$n\in \{0,1,3,7\}$. Moreover, we prove that any upper half even dimensional Q$\mathbb{Q}$-sphere cannot be diagonal resolvable.     

Convergence of a finite difference method for the time-fractional diffusion equation with concentrated capacity

We investigate the convergence of difference scheme for the time-fractional differential equation with fractional derivative of an order with the coefficient at the time derivative containing Dirac delta distribution. Convergence order of is proved. A numerical example demonstrates the theoretical results. (© 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Targeting Inflammation by Anthocyanins as the Novel Therapeutic Potential for Chronic Diseases: An Update

Low-grade chronic inflammation (LGCI) and oxidative stress act as cooperative and synergistic partners in the pathogenesis of a wide variety of diseases. Polyphenols, including anthocyanins, are involved in regulating the inflammatory state and activating the endogenous antioxidant defenses. Anthocyanins’ effects on inflammatory markers are promising and may have the potential to exert an anti-inflammatory effect in vitro and in vivo. Therefore, translating these research findings into clinical practice would effectively contribute to the prevention and treatment of chronic disease. The present narrative review summarizes the results of clinical studies from the last 5 years in the context of the anti-inflammatory and anti-oxidative role of anthocyanins in both health and disease. There is evidence to indicate that anthocyanins supplementation in the regulation of pro-inflammatory markers among the healthy and chronic disease population. Although the inconsistencies between the result of randomized control trials (RCTs) and meta-analyses were also observed. Regarding anthocyanins’ effects on inflammatory markers, there is a need for long-term clinical trials allowing for the quantifiable progression of inflammation. The present review can help clinicians and other health care professionals understand the importance of anthocyanins use in patients with chronic diseases.