Int. J. Mol. Sci., Volume 9, Issue 4 (April 2008) – 18 articles , Pages 434-678

Aptamers, single stranded DNA or RNA molecules, generated by a method called SELEX (systematic evolution of ligands by exponential enrichment) have been widely used in various biomedical applications. The newly developed Cell-SELEX (cell based-SELEX) targeting whole living cells has raised great expectations for cancer biology, -therapy and regenerative medicine. Combining nanobiotechnology with aptamers, this technology opens the way to more sophisticated applications in molecular diagnosis. This paper gives a review of recent developments in SELEX technologies and new applications of aptamers. Full article

The structural damage of double-stranded DNA under UV radiation was examined using single-molecule fluorescence microscopy. Compared to undamaged DNA, the diffusion coefficient of λ-DNA was significantly increased with 12 min or 20 min of radiation but remained unchanged for 40 min of exposure possibly due to strand crosslinking. The structural damage of DNA was further examined using transmission electron microscopy which revealed kinks and sharp bends along the DNA backbone. Full article

Receptor for advanced glycation end products (RAGE) was studied in different stages of carbon tetrachloride induced hepatic fibrosis (HF), and effect of its gene silencing in the HF development was evaluated in rats. Silencing RAGE expression by specific siRNA effectively suppressed NF-κB activity, hepatic stellate cell activation, and accumulation of extracellular matrix proteins in the fibrotic liver, and also greatly improved the histopathology and the ultra-structure of liver cells. These effects may be partially mediated by the inhibition on IκBα degradation. RAGE gene silencing effectively prevented liver from fibrosis, therefore it offers a potential pharmacological tool for anti-HF gene therapy. Full article

In this study, screw and nail withdrawal resistance of fir (Abies nordmanniana), oak (Quercus robur L.) black pine (Pinus nigra Arnold) and Stone pine (Pinus pinea L.) wood were determined and compared. The data represent the testing of withdrawal resistance of three types of screws as smart, serrated and conventional and common nails. The specimens were prepared according to TS 6094 standards. The dimensions of the specimens were 5x5x15cm and for all of the directions. Moreover, the specimens were conditioned at ambient room temperature and 65±2% relative humidity. The screws and nails were installed according to ASTM-D 1761 standards. Nail dimensions were 2.5mm diameter and 50 mm length, conventional screws were 4x50mm, serrated screws were 4x45mm and smart screws were 4x50mm. Results show that the maximum screw withdrawal resistance value was found in Stone pine for the serrated screw. There were no significant differences between Stone pine and oak regarding screw withdrawal resistance values. Conventional screw yielded the maximum screw withdrawal resistance value in oak, followed by Stone pine, black pine and fir. Oak wood showed the maximum screw withdrawal resistance value for the smart screw, followed by Stone pine, black pine, and fir. Oak wood showed higher nail withdrawal resistances than softwood species. It was also determined that oak shows the maximum nail withdrawal resistance in all types. The nail withdrawal resistances at the longitudinal direction are lower with respect to radial and tangential directions. Full article

The complexes RuCl₂(PCy₃)₂(=CHPh), 1, and RuCl₂(PCy₃)(H₂IMes)(=CHPh), 2, proved to be active catalysts for the self-metathesis of oleate-type fatty compounds containing the ester, hydroxyl, epoxy and carboxylic acid functional groups. At elevated reaction temperatures 2 showed a higher activity, stability and lower selectivity for primary metathesis products compared to 1. A profound influence of organic functional groups on catalyst activity and selectivity was found and from relative activities and selectivities 2 has proved to be more resistant to deactivation by polar functional groups and more inclined to promote double bond isomerisation than 1. The observed catalyst deactivation by oxygen-containing functional groups could be attributed to a phosphine displacement side reaction. Full article

In the present study the phenolic (Folin-Dennis) and flavonoid (colorimetric assay) constituents and the antioxidant activity of Pterodon emarginatus seeds were investigated in several samples prepared with different extraction procedures: essential oil (EO) using a Clevenger-type apparatus; hexanic (HF), ethyl acetate (EAF), buthanolic (BF) and methanolic (MF) fractions using Soxhlet extraction, and extracts (1 g/extract) obtained from different methods: reflux 80°C/30 min, ultrasound/30 min, static maceration/48 h and heating plate 100°C/45 min. These extracts were prepared using water or ethanol/water at 30:70 v/v, 50:50 v/v or 70:30 v/v. Antioxidant activity [2,2-diphenyl-2- picrylhydrazyl hydrate (DPPH)] was tested only in the fractions obtained from Soxhlet extraction. The extract obtained from reflux using ethanol/water (70:30, v/v) showed the highest phenolic constituents level. The EAF, BF and MF showed DPPH scavenging activities with IC₅₀=163.22, 18.89 and 10.15 μg/ml, respectively. Full article

Various etiological factors contributing to the development of mycotoxic nephropathy in farm animals and humans are reviewed. The possible synergistic effect between ochratoxin A (OTA) and other mycotoxins, as penicillic acid (PA) and fumonisin B1 (FB1), contributing to this nephropathy is also considered and discussed. The most convenient ways of prophylaxis and various preventive measures against OTA contamination of feeds or foods are reviewed. A reference is made concerning the most successful methods of veterinary hygiene control in the slaughterhouses in order to prevent the entering of OTA in commercial channels with a view to human health. The economic efficacy of these prophylactic procedures is also considered. An evaluation of human exposure to OTA is made. Full article

The extraction and separation conditions of glycyrrhizic acid and glabridin from licorice were investigated. By changing the different extraction solvents, procedures, times and temperature, the optimum extraction condition was established: the used of ethanol/water (30:70, v/v) as an extraction solvent, and 60 min dipping time under 50°C. The extracts of licorice were separated and determined by reversed-phase high performance liquid chromatography with a methanol/water (70:30, v/v, containing 1% acetic acid) as the mobile phase. Under the optimum extraction condition, 2.39 mg/g of glycyrrhizic acid and 0.92 mg/g of glabridin were extracted from Chinese licorice and the recoveries were 89.7% and 72.5% respectively. Full article

A polymerase chain reaction (PCR) based diagnostic assay was used to develop markers for detection of Fusarium verticillioides (=F. moniliforme), a fumonisin producing fungus in maize tissues. Species-specific primers were designed based on sequence data from the polyketide synthase (PKS) gene (FUM1- previously FUM5) responsible for fumonisin production in fungi. Four sets of oligonucleotide primers were tested for their specificity using 24 strains of F. verticillioides, 10 F. proliferatum, and 12 of other Fusarium species. In addition, 13 species of other fungal genera, from four phyla, were tested as negative controls. Among the four sets, primer set B consistently amplified a 419- bp fragment from the DNA 96% of all F. verticillioides strains and 83% of F. proliferatum. All other fungi tested were negative using primer set B. A total of 38% of the F. verticillioides strains grown on a selective liquid medium produced fumonisin and 92% formed the toxin on standard rice medium. When fumonisin formed in culture, PCR assay using primer set B detected every strain of F. verticillioides, but only amplified 80% of F. proliferatum strains that produced the toxin. PCR detection was consistent at 100 pg/μl concentration of genomic DNA from 4 F. verticillioides strains, but varied at 10 pg/μl. Two duplicate greenhouse tests using artificially inoculated maize plants, had greater levels of F. verticillioides detected after re-evaluting using primer set B than from culturing of the tissues. The molecular protocols described in this study requires only 1 day for completion compared to approximately 10 days for cultural work and morphological determination. In conclusion, conventional PCR assay using primer set B provides a sensitive and accurate detection assay that can be used as a primary or secondary confirmation method for identification and occurrence of F. verticillioides within the maize tissues. However, studies using primer set B for fumonisin production determined by strains of F. verticillioides and F. proliferatum will require further verification. Full article

A model experiment monitoring the fate of total residue oxidant (TRO) in water at a constant temperature and salinity indicated that it decayed exponentially with time, and with TRO decaying faster in seawater than in distilled water. The reduction of TRO by temperature (°K) was found to fit a curvilinear relationship in distilled water (r² = 0.997) and a linear relationship in seawater (r² = 0.996). Based on the decay rate, flow rate, and the length of cooling water flowing through at a given temperature, the TRO level in the cooling water of a power plant could be estimated using the equation developed in this study. This predictive model would provide a benchmark for power plant operators to adjust the addition of chlorine to levels necessary to control bio-fouling of cooling water intake pipelines, but without irritating ambient marine organisms. Full article

The objectives of this study were to identify harmful insect species, understand their biology, assess their damage potential and target plants and define distribution areas. There are a lot of native or cultured ornamental plants in Bartın and its surrounding (Çaycuma, Zonguldak, Karabük, Mengen, Devrek). These plants are herbaceous and woody species. Specimens were collected from various cultured and non-cultured plants. A total of 34 species belonging to 20 families of 5 orders were identified. The order Hemiptera was represented by the highest number of species (19 species), followed by Coleoptera (8), Lepidoptera (4), Orthoptera (2), and Dermaptera (1). Insect samples were collected from plants by net traps, special insect aspirators, and various insect traps. The identified species have been stored in the collection room of the Forest Entomology and Protection Unit, Bartın Forestry Faculty, Zonguldak Karaelmas University (Z.K.U.), Turkey. This is the first detailed study about insect species causing damage on ornamental plants and saplings of Bartin province and its vicinity, although similar studies of different regions exist. This research makes a very important contribution to the insect fauna of Bartin, its environs and Turkey. Twenty four of the identified species were new for Bartın and its vicinity, while the remainder had been previously recorded in different parts of Bartın. Full article

The Thermogravimetric Analysis (TGA) techniques and concretely the study of the burning profile provide information that can be used to estimate the behaviour of the combustion of carbonous materials. Commonly, these techniques have been used for the study of carbons, but are also interesting for the analysis of biomass wastes, due to the different species present on the wastes affect directly to its thermal properties. In this work, techniques of thermal analysis have been applied to compare the behaviour of different wastes coming from olive oil mills. From these results, it is remarkable that the Concentrated Olive Mill Waste Water (COMWW) presents more unfavourable conditions for its combustion. Full article

Quartz crystal microbalance with dissipation (QCM-D) monitoring and atomic force microscopy (AFM) were combined to evaluate the defects created by an ionic liquid anion and a cation in a supported phospholipid bilayer composed of zwitterionic lipids on a silica surface. The cation 1-octyl-3-methyl imidazolium (OMIM⁺) was shown to remove lipids from the bilayer, increase the roughness to approximately 2.8 nm (~0.2 for stable supported bilayer) and possibly redeposit lipids with entrapped water. The anion bis(trifluoromethylsulfonyl)imide (Tf₂N^-) was found to leave distinct defects within the bilayer that had large pore-like interiors which left the surrounding bilayer intact. However, the ionic liquid 1-butyl-1-methyl pyrrolidinium bis(trifluoromethylsulfonyl)imide (BMP-Tf₂N) formed a film over the supported bilayer. This work demonstrates, for the first time, the direct effects common components of ionic liquids have on a supported phospholipids bilayer. Full article

The supramolecular layer-by-layer assembly of 3D multicomponent nanostructures of nanoparticles is demonstrated. Nanoimprint lithography (NIL) was used as the patterning tool for making patterned β-cyclodextrin (CD) self-assembled monolayers (SAMs) and for the confinement of nanoparticles on the substrate. A densely packed and multilayered nanoparticle structure was created by alternating assembly steps of complementary guest- (Fc-SiO₂, 60 nm) and host-functionalized (CD-Au, 3 nm) nanoparticles. The effects induced by the order of the nanoparticle assembly steps, going from large to small and from small to large nanoparticles by using Fc-SiO₂, CD-Au, and CD-SiO₂ (350 nm) nanoparticles, were compared. AFM height profiles revealed that the specific supramolecular assembly of nanoparticles was self-limited, i.e. one nanoparticle layer per assembly step, allowing the control over the thickness of the supramolecular hybrid nanostructure by choosing the size of the nanoparticles, irrespective of the core material of the nanoparticles. The roughness of structure, observed by AFM imaging of the top layer, was directly influenced by the size and packing of the underlying nanoparticle layers. Full article

The long-term durability of varnished wooden surfaces used in either indoors or outdoors environments depends on the resistance of varnish layers on these surfaces against potential physical, mechanical and chemical effects to which they may be exposed. In this study, “Nanolacke ultraviolet varnish”, developed by a Turkish dying and varnish industry company and widely accepted as a 21^st century technology has been compared to other conventional varnish systems widely used in the industry in terms of dry film resistance properties. In this study, cellulosic, polyurethane, polyester, synthetic and Nanolacke ultraviolet varnish have been applied on beech (Fagus orientalis L.) and oak (Quercus robur L.) wood samples which had been prepared according to the industry standards. Then, the hardness and adhesion resistance of these layers have been determined according to ASTM D 4366 and ASTM D 3359-2 standards, respectively. Full article

The present study was undertaken to evaluate the effects of high protein (soybean protein or casein) on the balance between production of free radicals and antioxidant level in digestive organs of mice. For this purpose, male (C57BL/6J) mice were adapted to experimental diets containing soybean protein or casein with 20% (normal protein diets, NPDs) or 60% (high protein diets, HPDs), and HPDs supplemented with 0.06g/kg cysteamine. After two weeks of feeding, oxidative and antioxidative parameters in duodenum, liver and pancreas were measured. The results show that ingestion of high protein markedly increased contents of superoxide anion and malondialdehyde (MDA), decreased activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT) and Na⁺ K⁺-ATPase, and content of reduced glutathione (GSH) in digestive organs of mice (P<0.05). Levels of oxidative parameters were lower and antioxidant capacity of both enzyme and non-enzyme was higher in mice fed with soybean protein than those fed with casein. In groups fed HPDs supplemented with cysteamine, oxidative stress was mitigated. However, oxidative parameter levels were still higher than those of NPD-fed groups. The present study indicates that ingestion of high protein diets could result in an imbalance between oxidant and antioxidant, and thus induce oxidative stress in digestive organs of mice. The oxidative damage was smaller in mice fed with high level of soy protein in comparison with casein. Full article

The mechanical properties of laminated window profiles manufactured using two types of adhesives were determined. The objective of this study is to evaluate the effects of heat treatment on some mechanical properties of laminated window profiles that manufactured from Kosipo (Entandrophragma candollei Harms.) using differenet type adhesives. Commercially produced polyurethane based Macroplast UR 7221 and polyvinyl acetate (PVAc) adhesive were used for experiments. The overall test results were found to be comparable to those obtained in the previous studies. Both types of adhesives resulted in significant differences in their strength characteristics at 95% confidence level. Adhesive UR 7221 improved the overall properties of the samples in contrast to PVAc. Full article

The concentration of five soil heavy metals (Pb, Co, Cr, Cu, Hg) was measured in forty sampling sites in central Transylvania, Romania, regions known as centres of pollution due to the chemical and metallurgical activities. The soil samples were collected from locations where the ground is not sliding and the probability of alluvial deposits is small. The concentration of heavy metals was measured by using the Inductively Coupled Plasma Spectrometry method. Data were verified by using the Neutron Activation Analysis method. In some locations, the concentration for the investigated heavy metals exceeds the concentration admitted by the Romanian guideline. The highest concentration of lead (1521.8 ppm) and copper (1197.6 ppm) was found in Zlatna. The highest concentration of chromium was found in Târnăveni (1080 ppm). The maximum admitted concentrations in the sensitive areas revealed to be exceed from five to forty times. Full article