Use of Rep‐PCR for Genetic Diversity Analyses in Fusarium culmorum

Fusarium culmorum is a pathogen of economically important grain crops. In this work, Rep‐PCR was used to identify genetic diversity in F. culmorum isolates which have been collected from wheat fields in Turkey. Reproducible genomic fingerprints were amplified in each strain by PCRs of prokaryotic repetitive extragenic palindromic (REP), enterobacterial repetitive intergenic consensus (ERIC) and BOX sequences. Totally 104 molecular markers were evaluated and similarity comparisons were shown as a dendrogram. The average genetic diversity was 52.3% ranging from 15.8% to 88.7% according to the Rep‐PCR data. Cluster analysis showed agreement with the distance of sampling locations. The highest genetic similarity (84.2%) was determined between two F. culmorum isolates (F1 and F2) originated from the same agro‐ecological region. Our results showed that Rep‐PCR is convenient and rapid for genetic diversity analyses and strain differentiation in F. culmorum.     

Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase

ADP-glucose pyrophosphorylase, a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Current evidence indicates that the two subunit types play distinct roles in enzyme function. The LS is involved in mainly allosteric regulation through its interaction with the catalytic SS. Recently the crystal structure of the SS homotetramer has been solved, but no crystal structure of the native heterotetrameric enzyme is currently available. In this study, we first modeled the three-dimensional structure of the LS to construct the heterotetrameric enzyme. Because the enzyme has a 2-fold symmetry, six different dimeric (either up-down or side-by-side) interactions were possible. Molecular dynamics simulations were carried out for each of these possible dimers. Trajectories obtained from molecular dynamics simulations of each dimer were then analyzed by the molecular mechanics/Poisson-Boltzmann surface area method to identify the most favorable dimers, one for up-down and the other for side-by-side. Computational results combined with site directed mutagenesis and yeast two hybrid experiments suggested that the most favorable heterotetramer is formed by LS-SS (side-by-side), and LS-SS (up-down). We further determined the order of assembly during the heterotetrameric structure formation. First, side-by-side LS-SS dimers form followed by the up-down tetramerization based on the relative binding free energies.     

7′,8′-Dihydroobolactone,a typanocidal α-pyrone from the rainforest tree Cryptocarya obovata

Mass-directed isolation of the CH₂Cl₂/MeOH extract from the leaves of Cryptocarya obovata resulted in the purification of a new trypanocidal α-pyrone, 7′,8′-dihydroobolactone (1). The chemical structure of 1 was determined by 1D/2D NMR, MS and CD data analysis. 7′,8′-Dihydroobolactone was shown to inhibit Trypanosoma brucei brucei with an IC₅₀ of 2.8 μM.     

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs. PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately, PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/.     

The structural basis of Akt PH domain interaction with calmodulin

Akt plays a key role in the Ras/PI3K/Akt/mTOR signaling pathway. In breast cancer, Akt translocation to the plasma membrane is enabled by the interaction of its pleckstrin homology domain (PHD) with calmodulin (CaM). At the membrane, the conformational change promoted by PIP₃ releases CaM and facilitates Thr308 and Ser473 phosphorylation and activation. Here, using modeling and molecular dynamics simulations, we aim to figure out how CaM interacts with Akt’s PHD at the atomic level. Our simulations show that CaM-PHD interaction is thermodynamically stable and involves a β-strand rather than an α-helix, in agreement with NMR data, and that electrostatic and hydrophobic interactions are critical. The PHD interacts with CaM lobes; however, multiple modes are possible. IP₄, the polar head of PIP₃, weakens the CaM-PHD interaction, implicating the release mechanism at the plasma membrane. Recently, we unraveled the mechanism of PI3Kα activation at the atomistic level and the structural basis for Ras role in the activation. Here, our atomistic structural data clarify the mechanism of how CaM interacts, delivers, and releases Akt—the next node in the Ras/PI3K pathway—at the plasma membrane.     

Temporal Variation in Drug Interaction Between Lithium and Morphine‐Induced Analgesia

The administration‐time‐dependent aspects of the drug interaction between lithium and morphine‐induced analgesia were studied using the mouse hot‐plate test at six different times of day, each scheduled at 4 h intervals. Lithium treatment alone, in doses of 1 to 10 mmol/kg administered intraperitoneally (i.p.) did not significantly alter test latencies compared to the corresponding clock‐time in saline‐injected controls. Basal pain sensitivity and morphine‐induced antinociceptive activity displayed significant circadian rhythms as assessed by the hot‐plate response latencies, with higher values occurring during the nocturnal activity than during the daytime rest span. Acute administration of lithium, in a dose of 3 mmol/kg, 30 min prior to morphine dosing did not influence morphine‐induced analgesia compared to all the clock‐time test‐matched morphine groups, except the 9 HALO (Hours After Lights On) one. There was a prominent potentiation of the morphine‐induced antinociception at this biological time during combined drug treatment. The latter finding demonstrates that administration‐time‐dependent differences in drug‐drug interactions need to be considered in both experimental designs and clinical settings.     

Effectiveness of different cleaning agents on the adherence of Candida albicans to acrylic denture base resin

doi: 10.1111/j.1741‐2358.2010.00379.x
Effectiveness of different cleaning agents on the adherence of Candida albicans to acrylic denture base resin Objective:  To evaluate the ability of three alkaline peroxide‐type (Polident, Efferdent, Fittydent) and two mouth rinse cleaning agents (CloSYSII and Corsodyl) to inhibit Candida albicans on acrylic denture base resin. Background:  Appropriate routine cleaning of dentures is necessary to prevent denture stomatitis and maintenance of healthy supporting tissues. Materials and methods:  A total of 180 acrylic resin specimens (10 × 10 × 2 mm) were prepared and divided into six groups. Candida albicans was incubated on Sabouraud dextrose agar (SDA) at 37°C for 48 h. After dilution, a final yeast suspension of approximately 10 6 C. albicans per millimetre was prepared. Ten acrylic resin specimens for each group were placed in a sterile Petri dish covered with 20 ml of fungal suspension and incubated at 37°C for 90 min. Then, the specimens were immersed in 40 ml of the test solution at 37°C for 15, 30 and 60 min. Fungal cells adhering to acrylic resin surfaces were fixed in formaldehyde and counted microscopically. Results:  Mouth rinses showed the highest removal activity for all the treatment times and completely eliminated the adherence of C. albicans. Conclusions:  The use of mouth rinse may be a suitable method for cleaning dentures.     

Cyclooxygenase-2 gene and epithelial ovarian carcinoma risk

In this study, we aimed to investigate a possible association of the COX-2 polymorphisms (−765G→C and −1195A→G) and with the risk of developing epithelial ovarian carcinoma (EOC). COX-2 gene polymorphisms was investigated in 111 healthy women and 57 patients with EOC. Individuals who had −765 CG, −1195 AA genotype, and −765 C allele had increased risk for ovarian carcinoma (P < 0.01) and individuals with −765 GG, −1195 AG genotypes and −1195 G allele seem to be protected from ovarian carcinoma (P < 0.01). Haplotype analysis confirmed the association of COX-2 gene variants with ovarian carcinoma and revealed that the frequencies of −765C: −1195A haplotype frequencies was significantly higher in patients as compared with those of controls (P = 0.048). We state that there appears to be a modulating role for the COX-2 −1195A→G and −765G→C polymorphisms in the development of EOC. To the best of our knowledge, this is the first study to show such an association.     

Effects of red wine consumption on serum paraoxonase/arylesterase activities and on lipoprotein oxidizability in healthy-men

Although there is a general consensus concerning the lower risk for cardiovascular disease in moderate drinkers, the mechanisms responsible for the cardioprotective effect of red wine remain unknown. It has been proposed that increased serum paraoxonase activity may be a mechanism of action underlying reduced cardiovascular disease risk in moderate drinkers, since paraoxonase inhibits lipoprotein oxidation. The aim of this study was to investigate the effects of red wine consumption on serum paraoxonase/arylesterase activities and on lipoprotein oxidizability in healthy-men. Fourteen healthy-men were included in the study. The subjects consumed 0.375 g alcohol / kg body weight for 3 weeks. Paraoxonase and arylesterase activities were studied spectrophotometrically. Oxidizability of apolipoprotein B-containing lipoproteins were determined, after separating them with precipitation method, by incubating with copper-sulfate. Paraoxonase activity did not change, however arylesterase activity significantly decreased after red wine consumption (P < 0.01). There was a reduced susceptibility of apolipoprotein B-containing lipoproteins to copper-sulfate induced oxidation after red wine consumption (P < 0.01). Our results support that red wine protects lipoproteins against oxidation, however there was not any significant change in serum paraoxonase activity after red wine consumption.KEY WORDS: Red wine; Paraoxonase; Arylesterase; Lipoprotein oxidation