Effects of the Application of Different Concentrations of NaN3 for Different Times on the Morphological and Cytogenetic Characteristics of Barley (Hordeum vulgare L.) Seedlings

Sodium azide (NaN3) has been used in many biological studies as a mutagen. In the present study, the morphological and cytogenetic effects of NaN3 on barley (Hordeum vulgare L.) seedlings were investigated. Seeds of barley were treated with different concentrations of NaN3 (0.5, 1.0, 1.5, 2.0, 2.5, and3.0 mmol/L) and applied for different periods of time (3 and 4 h). Parameters investigated, except for the mitotic index, were determined on Days 7 and 14. Increasing concentrations of NaN3 affected germination rates on Days 7 and 14 following application for 3 and 4 h. Although the length of the roots and leaves was affected by treatment with NaN3 on Day 14 of the germination period, coleoptile length was affected by NaN3 treatment on Day 7. Increasing concentrations of NaN3 and increased treatment period decreased the mitotic index compared with the untreated control. The inhibitory effects of NaN3 on the mitotic index indicate that NaN3 can have genotoxic and mutagenic effects on barley seedlings.     

Comparison of Two Methods for Purification of Enterocin B,a Bacteriocin Produced by Enterococcus faecium W3

This study aimed to compare two different approaches for the purification of enterocin B from Enterococcus faecium strain W3 based on the observation that the bacteriocin was found both in cell associated form and in culture supernatant. The first approach employed ammonium sulfate precipitation, cation-exchange chromatography, and sequential reverse-phase high-performance liquid chromatography. The latter approach exploited a pH-mediated cell adsorption–desorption method to extract cell-bound bacteriocin, and one run of reverse-phase chromatography. The first method resulted in purification of enterocin B with a recovery of 4% of the initial bacteriocin activity found in culture supernatant. MALDI-TOF MS analysis and de novo peptide sequencing of the purified bacteriocin confirmed that the active peptide was enterocin B. The second method achieved the purification of enterocin B with a higher recovery (16%) and enabled us to achieve pure bacteriocin within a shorter period of time by avoiding time consuming purification protocols. The purity and identity of the active peptide were confirmed again by matrix-assisted laser desorption/ionization time-of flight (MALDI-TOF) mass spectrometry (MS) analysis. Although both approaches were satisfactory to obtain a sufficient amount of enterocin B for use in MS and amino acid sequence analysis, the latter was proved to be applicable in large-scale and rapid purification of enterocin B.     

Assessment of Atrial Electromechanical Delay by Tissue Doppler Echocardiography in Obese Subjects

Our aim was to evaluate whether atrial electromechanical delay measured by tissue Doppler imaging (TDI), which is an early predictor of atrial fibrillation (AF) development, is prolonged in obese subjects. A total of 40 obese and 40 normal‐weight subjects with normal coronary angiograms were included in this study. P‐wave dispersion (PWD) was calculated on the 12‐lead electrocardiogram (ECG). Systolic and diastolic left ventricular (LV) functions, inter‐ and intra‐atrial electromechanical delay were measured by TDI and conventional echocardiography. Inter‐ and intra‐atrial electromechanical delay were significantly longer in the obese subjects compared with the controls (44.08 ± 10.06 vs. 19.35 ± 5.94 ms and 23.63 ± 6.41 vs. 5.13 ± 2.67 ms, P < 0.0001 for both, respectively). PWD was higher in obese subjects (53.40 ± 5.49 vs. 35.95 ± 5.93 ms, P < 0.0001). Left atrial (LA) diameter, LA volume index and LV diastolic parameters were significantly different between the groups. Interatrial electromechanical delay was correlated with PWD (r = 0.409, P = 0.009), high‐sensitivity C‐reactive protein (hsCRP) levels (r = 0.588, P < 0.0001). Interatrial electromechanical delay was positively correlated with LA diameter, LA volume index, and LV diastolic function parameters consisting of mitral early wave (E) deceleration time (DT) and isovolumetric relaxation time (IVRT; r = 0.323, P = 0.042; r = 0.387, P = 0.014; r = 0.339, P = 0.033; r = 0.325, P = 0.041; respectively) and, negatively correlated with mitral early (E) to late (A) wave ratio (E/A) (r = ?0.380, P = 0.016) and myocardial early‐to‐late diastolic wave ratio (E_m/A_m) (r = ?0.326, P = 0.040). This study showed that atrial electromechanical delay is prolonged in obese subjects. Prolonged atrial electromechanical delay is due to provoked low‐grade inflammation as well as LA enlargement and early LV diastolic dysfunction in obese subjects.     

Optimization based tumor classification from microarray gene expression data

Background

An important use of data obtained from microarray measurements is the classification of tumor types with respect to genes that are either up or down regulated in specific cancer types. A number of algorithms have been proposed to obtain such classifications. These algorithms usually require parameter optimization to obtain accurate results depending on the type of data. Additionally, it is highly critical to find an optimal set of markers among those up or down regulated genes that can be clinically utilized to build assays for the diagnosis or to follow progression of specific cancer types. In this paper, we employ a mixed integer programming based classification algorithm named hyper-box enclosure method (HBE) for the classification of some cancer types with a minimal set of predictor genes. This optimization based method which is a user friendly and efficient classifier may allow the clinicians to diagnose and follow progression of certain cancer types.

Methodology/Principal Findings

We apply HBE algorithm to some well known data sets such as leukemia, prostate cancer, diffuse large B-cell lymphoma (DLBCL), small round blue cell tumors (SRBCT) to find some predictor genes that can be utilized for diagnosis and prognosis in a robust manner with a high accuracy. Our approach does not require any modification or parameter optimization for each data set. Additionally, information gain attribute evaluator, relief attribute evaluator and correlation-based feature selection methods are employed for the gene selection. The results are compared with those from other studies and biological roles of selected genes in corresponding cancer type are described.

Conclusions/Significance

The performance of our algorithm overall was better than the other algorithms reported in the literature and classifiers found in WEKA data-mining package. Since it does not require a parameter optimization and it performs consistently very high prediction rate on different type of data sets, HBE method is an effective and consistent tool for cancer type prediction with a small number of gene markers.     

Molecular and clinical evaluation of Turkish patients with lysinuric protein intolerance

Lysinuric protein intolerance is an autosomal recessive metabolic disorder caused by defective transport of the cationic amino acids lysine, arginine and ornithine in the epithelial cells of the basolateral membrane in the small intestine and renal tubules. Mutations in the solute carrier family 7, member 7, SLC7A7, gene cause this multisystemic disease with a variety of clinical symptoms such as hepatosplenomegaly, osteoporosis, hypotonia, developmental delay, pulmonary insufficiency or end-stage renal disease. In the present study, genomic structure of SLC7A7 in six Turkish patients with lysinuric protein intolerance was examined in order to detect disease causing mutations by denaturing high pressure liquid chromatography and direct sequencing. Four novel mutations were identified in SLC7A7: c.223insGTC, p.Val74_Ile75insVal; c.283insTGG, p.Glu94_Thr95insTrp; c.344_347delTTGC, p.Leu115LeufsX53; and c.1099insT, p.Ile367TyrfsX16. Clinical and biochemical findings were evaluated together with these molecular analyses.     

Intraguild predation of Serangium parcesetosum (Coleoptera: Coccinellidae), on whitefly Bemisia tabaci (Homoptera: Aleyrodidae) parasitized by Eretmocerus mundus (Hymenoptera: Aphelinidae)

We studied intraguild predation of Serangium parcesetosum on Eretmocerus mundus, both natural enemies of Bemisia tabaci, on eggplant under laboratory conditions. Fourth instar and adult predators attacked parasitized and unparasitized hosts equally if immature parasitoids were larvae, but avoided predating on parasitized hosts containing pupae.     

Phenotypic and Genotypic Characterization of Bacteriocins in Enterococcal Isolates of Different Sources

A collection of 57 enterococcal isolates from different origin (including river, treatment plant, spring and garbage water, soil, animal, and vegetables from Aydın) was screened for the production of bacteriocins. Enterococci were identified at species levels as Enterococcus faecium (34), E. hirae (6), E. casseliflavus (4), E. durans (4), E. faecalis (4), E. mundtii (3) and E. avium (2). Of the 57 isolates 40 of them inhibited the growth of at least one indicator bacterium. Based on our PCR results 54 strains possesed enterocin genes. The genes of entA and entB were the most frequently detected structural genes among the PCR positive strains (54 and 53 strains, respectively) and the entB gene was always associated with entA gene. The highest combination of enterocin genes (24 of 54 strains) detected was entA, entB, entP and entL50A/B. The enterocins AS-48 and CylL_LS genes were not found. Three enterococcal isolates, 2 E. faecium and 1 E. hirae were not harbour any of tested enterocin genes. No correlation between the presence of enterocin structural genes and the origin of the strain was detected, also no relationship seemed to exist between the tested enterocin genes and the activity spectra of isolates. Genes encoding bacteriocins are widely disseminated among enterocci from different origin and more studies should be done for evaluate industrial potential of bacteriocins.