Characteristics and genetic diversity of bioluminescent Shewanella woodyi strains isolated from the Gulf of Izmir, Turkey

The purpose of this study was to isolate bioluminescent strains and to phenotypically and biochemically identify them based on the 16S rRNA gene sequence. 16S rRNA gene sequence analysis of the 11 isolates revealed that they belonged to Shewanella woodyi. Nevertheless, they were determined to exhibit various growth characteristics, enzymatic activities, assimilation of carbon and nitrogen sources, and different characteristics in antibiotic resistance profiles, and also, it was determined that different growth conditions affect the amount of biofilm. Pulsed-field gel electrophoresis (PFGE) analysis of S. woodyi strains performed with SmaI and NotI restriction enzymes revealed that they exhibited restriction fragment pattern homology ranging from 56 to 89 % and from 82 to 94 %, respectively. As a result, PFGE analysis of the genome S. woodyi (as the first record) revealed that although these strains inhabiting the Gulf of Izmir exhibit common characteristics, they also have high levels of genomic polymorphism.     

Synthesis,characterization and tyrosinase inhibitory properties of benzimidazole derivatives

1-Alkylbenzimidazole and 1,3-dialkyl benzimidazolium salts were synthesized and characterized by the data of IR, ¹H NMR, ¹³C NMR spectra and elemental analyses. These compounds were investigated as tyrosinase inhibitors. Tyrosinase has been purified from banana by affinity chromatography on a Sepharose 4B gel conjugated with L-tyrosine-p-aminobenzoic acid. All the synthesized compounds inhibited the tyrosinase activity. Among the compounds studied, 1,4-di(1H-benzo[d]imidazol-1-yl)butane was found to be the most active tyrosinase inhibitor (IC₅₀ 0.31 mM).     

Typhlonesticus gocmeni sp. n., a new cave-dwelling blind spider species from the Aegean region of Turkey (Araneae,Nesticidae)

A new species of the troglobitic spider genus Typhlonesticus is described from specimens found in Keloğlan Cave (Denizli Province, Dodurgalar Town), Turkey. Typhlonesticus gocmeni sp. n. is described on the basis of both sexes; and its phylogenetic relationships with closely related European genera and species are discussed based on morphological and molecular data (the cox1, rrnL and H3 genes). Three new combinations are proposed: Typhlonesticus idriacus (Roewer, 1931), comb. n., Typhlonesticus morisii (Brignoli, 1975) comb. n. and Typhlonesticus obcaecatus (Simon, 1907), comb. n. all ex Nesticus.     

Nicotine potentiates the neurogenic contractile response of rabbit bladder tissue via nicotinic acetylcholine receptors: nitric oxide and prostaglandins have no role in this process

Nicotine, a nicotinic acetylcholine receptors (nAChRs) agonist, has a role in modulation of the neurotransmitter release following nerve stimulation in both the central and peripheral nervous systems. The aim of this study was to determine whether electrical field stimulation (EFS)-evoked contractions are altered in rabbit bladder in the presence of nicotine and, if an alteration occurs, to investigate the effects of nitric oxide and prostaglandins on nicotine-induced alternation in isolated rabbit bladder. EFS-evoked contractile responses from rabbit bladder obtained were recorded with isometric force displacement transducers. Nicotine was added to preparations at various concentrations. The effects of hexamethonium, cadmium (Cd(2+)), indomethacin and N-nitro-L-arginine methyl ester (L-NAME) were tested on the EFS-evoked contractions in the presence of nicotine. Nicotine led to a dose-dependent increase in the amplitude of the EFS-evoked contractile responses. Cd(2+) and hexamethonium inhibited the nicotine-induced increase in EFS-evoked responses, whereas indomethacin and L-NAME had no effect. In conclusion, nicotine increased the EFS-evoked contractile responses possibly by facilitating release of neurotransmitters from nerve terminals by a mechanism dependent on the influx of Ca(2+) from voltage-gated Ca(2+) channels (VGCCs) via activation of nAChRs in isolated rabbit bladder. Nitric oxide and prostaglandins do not have a physiological role in the regulation of neurotransmitter release.     

Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors

PDEδ is a small protein that binds and controls the trafficking of RAS subfamily proteins. Its inhibition protects initiation of RAS signaling, and it is one of the common targets considered for oncological drug development. In this study, we used solved x-ray structures of inhibitor-bound PDEδ targets to investigate mechanisms of action of six independent all-atom MD simulations. An analysis of atomic simulations combined with the molecular mechanic-Poisson-Boltzmann solvent accessible surface area/generalized Born solvent accessible surface area calculations led to the identification of action mechanisms for a panel of novel PDEδ inhibitors. To the best of our knowledge, this study is one of the first in silico investigations on co-crystallized PDEδ protein. A detailed atomic-scale understanding of the molecular mechanism of PDEδ inhibition may assist in the design of novel PDEδ inhibitors. One of the most common side effects for diverse small molecules/kinase inhibitors is their off-target interactions with cardiac ion channels and human-ether-a-go-go channel specifically. Thus, all of the studied PDEδ inhibitors are also screened in silico at the central cavities of hERG1 potassium channels.     

Identification of potential serodiagnostic and subunit vaccine antigens by antibody profiling of toxoplasmosis cases in Turkey

Toxoplasmosis, caused by infection of the protozoan parasite Toxoplasma gondii, is associated with mild disease in healthy individuals, whereas individuals with depressed immunity may develop encephalitis, neurologic disorders, and other organ diseases. Women who develop acute toxoplasmosis during pregnancy are at risk of transmitting the infection to the fetus, which may lead to fetal damage. A diagnosis is usually confirmed by measuring IgG, or IgM where it is important to determine the onset of infection. A negative IgM result essentially excludes acute infection, whereas a positive IgM test is largely uninterpretable because IgM can persist for up to 18 months after infection. To identify antigens for improved diagnosis of acute infection, we probed protein microarrays displaying the polypeptide products of 1357 Toxoplasma exons with well-characterized sera from Turkey. The sera were classified according to conventional assays into (1) seronegative individuals with no history of T. gondii infection; (2) acute infections defined by clinical symptoms, high IgM titers, and low avidity IgG; (3) chronic/convalescent cases with high avidity IgG but persisting IgM; (iv) true chronic infections, defined by high avidity IgG and no IgM. We have identified 38 IgG target antigens and 108 IgM target antigens that can discriminate infected patients from healthy controls, one or more of which could form the basis of a 'tier-1' test to determine current or previous exposure. Of these, three IgG antigens and five IgM antigens have the potential to discriminate chronic/IgM persisting or true chronics from recent acutely infected patients (a 'tier-2' test). Our analysis of the antigens revealed several enriched features relative to the whole proteome, which include transmembrane domains, signal peptides, or predicted localization at the outer membrane. This is the first protein microarray survey of the antibody response to T. gondii, and will help in the development of improved serodiagnostics and vaccines.     

Standard abdominal wound edge protection with surgical dressings vs coverage with a sterile circular polyethylene drape for prevention of surgical site infections (BaFO): study protocol for a randomized controlled trial

ABSTRACT: BACKGROUND: Postoperative surgical site infections cause substantial morbidity, prolonged hospitalization, costs and even mortality and remain one of the most frequent surgical complications. Approximately 14% to 30% of all patients undergoing elective open abdominal surgery are affected and methods to reduce surgical site infection rates warrant further investigation and evaluation in randomized controlled trials. METHODS: To investigate whether the application of a circular plastic wound protector reduces the rate of surgical site infections in general and visceral surgical patients that undergo midline or transverse laparotomy by 50%. BaFO is a randomized, controlled, patient-blinded and observer-blinded multicenter clinical trial with two parallel surgical groups. The primary outcome measure will be the rate of surgical site infections within 45 days postoperative assessed according to the definition of the Center for Disease Control. Statistical analysis of the primary endpoint will be based on the intention-to-treat population. The global level of significance is set at 5% (2 sided) and sample size (n = 258 per group) is determined to assure a power of 80% with a planned interim analysis for the primary endpoint after the inclusion of 340 patients. DISCUSSION: The BaFO trial will explore if the rate of surgical site infections can be reduced by a single, simple, inexpensive intervention in patients undergoing open elective abdominal surgery. Its pragmatic design guarantees high external validity and clinical relevance. Trial registration http://www.clinicaltrials.gov NCT01181206. Date of registration: 11 August 2010; date of first patient randomized: 8 September 2010.     

Combining optimal control theory and molecular dynamics for protein folding

A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.