Cryo-EM image alignment based on nonuniform fast Fourier transform

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.     

Dynamic spectrum access in terrestrial TV band: assessment of prospects in Kenya

Wireless connectivity has become a significant part of human life all over the world, both in developing and developed countries. In order to provide sufficient coverage without the densification of cellular networks, relatively low carrier frequencies should be used. This paper considers the reuse of the digital terrestrial television (DTT) band for cellular system operation in Kenya, while protecting incumbent TV signal reception according to the Dynamic Spectrum Alliance (DSAL) rules. A state of the art model for DTT coverage and allowed cellular system power calculation is tested using real data for Kenya. Suggestions regarding future DSAL rules amendments are provided. Moreover, the amount of spectrum resources available for cellular system operation in the DTT band in Kenya is estimated against varying system parameters.

     

Effect of thermal and mechanical factors on rheological properties of high performance inulin gels and spreads

The aim of this study was analysis of a number of factors affecting the rheological properties of high performance inulin gels and spreads in comparison with commercial products. Inulin gels (20%, 25%, 30%), commercial and inulin model spread (20% canola oil, 20% inulin, 3% emulsifier) were analysed. Inulin particles in water environment absorbed water which caused an increase in viscosity of the inulin suspensions. Different temperatures of preparation, cooling rates and viscosity increase which appeared during the stirring of inulin suspensions did not significantly change the rheological parameters of the final gels in contrast to heating rates (p ? 0.05). In spite of rigid laboratory conditions high standard deviation for hardness and apparent viscosity showed how difficult the process of an inulin crystallization is to control. Rheological properties of inulin model spread exhibited thixotropic and shear thinning behaviour which made it similar to commercial spread. The applied structure destruction step in the manufacturing process should be applied to make inulin model spread comparable to commercial spreads.     

Isolation and structure elucidation of phenolic compounds from Cyclopia subternata Vogel (honeybush) intact plant and in vitro cultures

In the presented work, an insight was made into the polyphenolic composition of intact plant material and in vitro cultures of indigenous South African plant Cyclopia subternata Vogel (honeybush). Ethyl acetate fractions of methanol extracts were separated by means of gravity column chromatography and/or semipreparative HPLC on two serially connected monolithic RP-18 columns. The structures of the isolated compounds were determined by means of 1D and 2D NMR techniques and additionally confirmed by LC-DAD-ESI-MS. Apart from the previously described honeybush components, that is mangiferin (1), scolymoside (2), hesperidin (3) and narirutin (4), three additional compounds: iriflophenone 3-C-β-glucoside (benzophenone) (5), phloretin 3′,5′-di-C-β-glucoside (dihydrochalcone) (6), and isorhoifolin (flavone) (7) were identified for the first time in the herb of C. subternata. Additionally, three isoflavone glucosides, namely calycosin 7-O-β-glucoside (8), rothindin (9) and ononin (10), which had not been previously reported in Cyclopia plants, were identified in the callus of the above species. As far as the authors are concerned, this is the first report on the presence of benzophenone and dihydrochalcone derivatives in Cyclopia genus.     

Use of Lactobacillus paracasei isolated from whey for silver nanocomposite synthesis: Antiradical and antimicrobial properties against selected pathogens

The present research emphasizes the use of safe, inexpensive, and available whey using Lactobacillus paracasei as a source in silver nanocomposite synthesis as an alternative bioactive agent for dairy and biomedical applications. Through the multiinstrumental approach used in this study based on spectroscopic and microscopic methods as well as spectrometric techniques, the characterization and evaluation of silver composites and their antimicrobial and antiradical properties were enabled. Synthesized silver nanocomposites have been found in form of nanocrystals, naturally coated by an organic surface with high antimicrobial and antiradical properties. Furthermore, this work also presents an innovative approach regarding the organic surface (naturally secreted by the bacteria isolated from whey) of the core of nanoparticles, which has already been explored and therefore is starting to supplement the scientific approach concerning biologically synthesized nanoparticles. This work also presents a general frame on the resistance subject by performing the trial interaction of commercially available antibiotics (kanamycin and ampicillin) with new bioactive compounds that can create novel knowledge on complementing their action. Moreover, synthesized silver nanocomposites have shown great antioxidant and antimicrobial effects against various foodborne pathogens from dairy products and drug resistance pathogens found in the medical area to rank on the top of mortality rate.     

Copper oxide nanoparticle mediated DNA damage in terrestrial plant models

Engineered nanoparticles, due to their unique electrical, mechanical, and catalytic properties, are presently found in many commercial products and will be intentionally or inadvertently released at increasing concentrations into the natural environment. Metal- and metal oxide-based nanomaterials have been shown to act as mediators of DNA damage in mammalian cells, organisms, and even in bacteria, but the molecular mechanisms through which this occurs are poorly understood. For the first time, we report that copper oxide nanoparticles induce DNA damage in agricultural and grassland plants. Significant accumulation of oxidatively modified, mutagenic DNA lesions (7,8-dihydro-8-oxoguanine; 2,6-diamino-4-hydroxy-5-formamidopyrimidine; 4,6-diamino-5-formamidopyrimidine) and strong plant growth inhibition were observed for radish (Raphanus sativus), perennial ryegrass (Lolium perenne), and annual ryegrass (Lolium rigidum) under controlled laboratory conditions. Lesion accumulation levels mediated by copper ions and macroscale copper particles were measured in tandem to clarify the mechanisms of DNA damage. To our knowledge, this is the first evidence of multiple DNA lesion formation and accumulation in plants. These findings provide impetus for future investigations on nanoparticle-mediated DNA damage and repair mechanisms in plants.     

Different Aspects of the Elemental Analysis of Honey by Flame Atomic Absorption and Emission Spectrometry: A Review

The elemental composition of honey is correlated with the botanical provenience of nectar, pollen, and honeydew that are collected and ripened by bees. In addition to this, the geographical origin related to the locality of an apiary, the soil composition, and climatic conditions may contribute to the origin of elements in honey. The environmental pollution or other anthropogenic processes and activities also have an effect on the quality and the safety of honey since they may be accompanying sources that lead to its contamination and the presence of various trace elements (Cd, Cr, Cu, Fe, Ni, Pb, and Zn). This review article covers the literature devoted to the analysis of honey carried out by the most popular and commonly utilized flame atomic absorption and emission spectrometry, which was published from 1999 to 2011. Various aspects of such analysis are treated in detail, including ways of the sample preparation, the calibration, and the quality assurance of results. In addition, methods and results related to the fractionation analysis of elements in honey by means of chromatographic and non-chromatographic approaches are described.     

Solution process of suspension poly(vinyl chloride) in cyclohexanone by means of a viscometer

To study the structure of grains of suspension poly(vinyl chloride) (PVC), the authors applied a capillary viscometer for cyclic measurements of viscosity of the PVC–cyclohexanone solution during dissolution of the polymer. Final concentration of the solution was 0.5–1.0 g/100 cm³ and the measurements were made at temperatures of 313, 333, 353, and 373 K. It was found that at 353 K, a temperature close to the glass transition temperature of PVC, the curve describing changes of viscosity vs. the dissolution time has a pronounced maximum. It follows from a preliminary analysis of the obtained results that this maximum corresponds to the viscosity of a PVC solution in which average apparent mass is many times larger than true average molecular mass of the studied sample. It mans that into the solution enter single chains and some formations, called microdomains in the literature, that are composed of tens of macromolecules. The microdomains disintegrate later to single macromolecules.     

Polymerization of chlorophenyl glycidyl ethers. VI

Summary Polymerization of p-chlorophenyl glycidyl ether initiated by potassium glycolates (ethylene, propylene and 2-methyl propylene glycolatea) in DMSO containing some 18-crown-6 ether or glycol was investigated. For the reaction system containing the propylene glycolate asymmetrically substituted with a methyl group, relatively high polymerization rates were obtained as compared with those found for the other systems studied, the resultant polymers also having higher molecular weights and comparatively low polydispersities. Aliphatic double bonds were found to be absent in the polymers synthesized, which would suggest that in the anionic polymerization process studied the growing chain is not transferred to the monomer.Dedicated to Prof. C.I. Simionescu on the occasion of the 60th anniversary of his birthday