Two new records of Oribatula (Zygoribatula) species (Acari: Oribatida) from Turkey, with redescriptions

The oribatid mite fauna of Turkey is still relatively poorly known. The present paper adds two species of oribatid mites to the known Turkish fauna viz., Oribatula (Zygoribatula) debilitranslamellata (Kulijev, 1962) and O. (Z.) exilis (Nicolet, 1855). Both species are characterised by large, prominent lamellar cusps, with the lamellar setae inserted apically on the cusps, and by the presence of distinct translamellae. They can be distinguished, however, by the smaller lamellae, absence of cuspidal teeth, narrowly fusiform sensilli and, 13 pairs of thin, smooth, apically almost flagellate notogastral setae, in O. (Z.) debilitranslamellata, and by the wider lamellae, presence of cuspidal teeth, widely fusiform sensilli, and 14 pairs of thin, smooth notogastral setae, with seta c (1) slightly thicker and minutely barbed in O. (Z.) exilis. The following species have been previously reported from Turkey: O. (Z.) cognata (Oudemans, 1902), O. (Z.) undulata (Berlese, 1917), O. (Z.) terricola Van der Hammen, 1952, and O. (Z.) lanceolata Grobler, Bayram & Cobanoglu, 2004.     

Crystallization and preliminary X-ray studies of the liganded lysine, arginine, ornithine-binding protein from Salmonella typhimurium.

The periplasmic binding protein LAO from Salmonella typhimurium, which is involved in lysine, arginine and ornithine transport, has been crystallized together with one of its ligands, arginine (LAO-Arg). Preliminary X-ray diffraction studies of LAO-Arg crystal show that it belongs to the orthorhombic space group P2(1)2(1)2(1) and has the unit cell dimensions of a = 37.65 A, b = 59.45 A, c = 115.91 A. Crystals of the LAO-Arg complex diffract beyond 2.0 A resolution.     

Crystal structure of the lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium at 2.7-A resolution.

A wide variety of sugars, amino acids, peptides, and inorganic ions are transported into bacteria by periplasmic transport systems consisting of substrate-specific receptors (binding proteins) and membrane-bound protein complexes. The crystal structure of the lysine-, arginine-, ornithine-binding protein (LAO) at 2.7-A resolution shows that the molecule has a bi-lobal structure and that its topological structure is different from other amino acid-binding proteins but is similar to the sulfate-binding protein and maltose-binding protein. High sequence homology between LAO and the histidine-binding protein (HisJ) and the fact that LAO and HisJ share the same membrane-bound protein complex allow one to define functional regions responsible for the ligand binding and for the interaction with the membrane complex.     

Crystallization and preliminary X-ray studies of HisJ and LAO periplasmic proteins from Salmonella typhimurium

Two periplasmic binding proteins, HisJ and LAO, which are involved in histidine and arginine transport, respectively, have been crystallized. Preliminary X-ray diffraction studies of the HisJ and LAO crystals show that both belong to the orthorhombic space group P2(1)2(1)2(1) and have unit cell dimensions of a = 39.26 A, b = 66.17 A, c = 88.33 A and a = 36.08 A, b = 78.34 A, c = 102.02 A, respectively. Both HisJ and LAO crystals diffract beyond 2.0 A resolution.     

Genome screen for twinning rate QTL in four North American Holstein families

The objective of this study was to identify twinning rate quantitative trait loci (QTL) by typing pooled samples in a preliminary screening followed by interval mapping to test QTL effects. Four elite North American Holstein half-sib sire families with high twinning rate predicted transmitting abilities (PTA) were used in this study. Chromosomes 5, 7, 19 and 23 were not genotyped as these chromosomes were scanned for QTL in these families in a previous study. DNA was extracted from phenotypically extreme sons in each sire family. Two pools were prepared from sons of sires in each phenotypic tail, two each for high and low PTA levels for twinning rates. Each pool contained DNA from 4 to 15% of all sons of the sire depending on family. A total of 268 fluorescently labelled microsatellite markers were tested for heterozygosity in sires. About 135--170 informative markers per family were genotyped using pooled DNA samples. Based on the preliminary evidence for potential twinning rate QTL from pooled typing, interval mapping was performed subsequently on 12 chromosomal regions by family combinations. Evidence of QTL for twinning rate was found in one family on BTA 21 and 29 at a chromosome-wide P<0.05 and on BTA 8, 10 and 14 with a chromosome-wide P<0.01.     

Comparison of serum DNA,native DNA-binding and deoxyribonuclease levels in ten animal species and man

Circulating levels of DNA, native DNA-binding proteins and deoxyribonuclease were determined for 11 mammalian species. Native DNA-binding proteins constitutive to normal dog and horse serum were able to protect native DNA from hydrolysis by deoxyribonuclease I under conditions approximating serum. Interaction of serum DNA with circulating nucleases and specific binding proteins was discussed with respect to possible metabolic and functional relationships.     

ApicoAMP: The first computational model for identifying apicoplast-targeted transmembrane proteins in Apicomplexa

Background

Computational identification of apicoplast-targeted proteins is important in drug target determination for diseases such as malaria. While there are established methods for identifying proteins with a bipartite signal in multiple species of Apicomplexa, not all apicoplast-targeted proteins possess this bipartite signature. The publication of recent experimental findings of apicoplast membrane proteins, called transmembrane proteins, that do not possess a bipartite signal has made it feasible to devise a machine learning approach for identifying this new class of apicoplast-targeted proteins computationally.

Methodology/principal findings

In this work, we develop a method for predicting apicoplast-targeted transmembrane proteins for multiple species of Apicomplexa, whereby several classifiers trained on different feature sets and based on different algorithms are evaluated and combined in an ensemble classification model to obtain the best expected performance. The feature sets considered are the hydrophobicity and composition characteristics of amino acids over transmembrane domains, the existence of short sequence motifs over cytosolically disposed regions, and Gene Ontology (GO) terms associated with given proteins. Our model, ApicoAMP, is an ensemble classification model that combines decisions of classifiers following the majority vote principle. ApicoAMP is trained on a set of proteins from 11 apicomplexan species and achieves 91% overall expected accuracy.

Conclusions/significance

ApicoAMP is the first computational model capable of identifying apicoplast-targeted transmembrane proteins in Apicomplexa. The ApicoAMP prediction software is available at http://code.google.com/p/apicoamp/ and http://bcb.eecs.wsu.edu.     

In vitro medicinal potentials of Bryum capillare,a moss sample,from Turkey

In this study was conducted the in vitro antimicrobial, antibiofilm, antioxidant, antigenotoxic and anticancer activities investigations on the moss Bryum capillare Hedw (BC). Antimicrobial and antibiofilm activity were tested by MIC and microplate biofilm methods on antibiotic resistant bacteria. While the antioxidant activity of the extract was evaluated by DPPH, metal chelating, plasma lipid peroxidation and total phenolic content, the antigenotoxicity and cytotoxicity were established by Comet test and the WST-1 Cell proliferation assay kit respectively. The MIC values were found to be ≥ 125 µg.mL⁻¹ and a biofilm inhibition of 3–5% against only S. epidermidis was observed. Total phenolic compounds were determined as 23.26 mg/g. The results of DPPH assay, chelating and plasma lipid peroxidation activity were found to be 15%, 3% and 4% respectively. The extract was observed to decrease the affect of H₂O₂ that cause DNA damage. The BC was also determined 60 ± 5% anticancer activity against SKBR 3 and 76 ± 5% anticancer activity against HeLa cells, where this concentration had only 18 ± 5% cytotoxicity against MCF-12A cells. Also, these results have indicated the potential of Bryum capillare for the first time in novel natural compounds search.     

Protective effects of selenium, vitamin C and vitamin E against oxidative stress of cigarette smoke in rats

Cataractous lenses have been found to have an altered distribution of the intracellular ionic environment: the concentrations of potassium and magnesium being decreased and the concentrations of sodium and calcium increased. These changes arise as a result of changes to lens membrane characteristics causing an increase in lens membrane permeability. In this study flame atomic absorption spectroscopy (AAS) was used for calcium, magnesium, iron and zinc determination, and flame atomic emission spectroscopy (AES) was used for sodium and potassium contents in normal and cigarette smoke-exposed rat lenses. The methods are sensitive enough to detect quantitatively all six cations in a single rat lenses. In this work, six elements, including Ca2+, K+, Na+, Zn2+, Fe2+ and Mg2+ in experimental rat eye lenses and normal transparent lenses were determined. It was found that the concentrations of Ca2+, Na+, Zn2+, and Fe2+ were increased dramatically while K+ and Mg2+ decreased in smoke-exposed rat lenses when compared to the control rat lenses. There were no significant changes between 'smoked' rats supplied with vitamin C and control groups. A positive correlation was found also in the other two groups of 'cigarette smoked' animals supplemented with selenium plus vitamin E and selenium when compared with 'cigarette smoked' without any supplements. These data provide support for the hypothesis that cigarette smoking increases the risk of cataract formation. We investigated whether vitamin C is the most important antioxidant in the body. The roles of diet with optimum amounts of antioxidant vitamins C and vitamin E and the antioxidant mineral selenium are discussed.