HingeProt: automated prediction of hinges in protein structures

Proteins are highly flexible molecules. Prediction of molecular flexibility aids in the comprehension and prediction of protein function and in providing details of functional mechanisms. The ability to predict the locations, directions, and extent of molecular movements can assist in fitting atomic resolution structures to low-resolution EM density maps and in predicting the complex structures of interacting molecules (docking). There are several types of molecular movements. In this work, we focus on the prediction of hinge movements. Given a single protein structure, the method automatically divides it into the rigid parts and the hinge regions connecting them. The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins. The output can be used in applications such as flexible protein-protein and protein-ligand docking, flexible docking of protein structures into cryo-EM maps, and refinement of low-resolution EM structures. The web server of HingeProt provides convenient visualization of the results and is available with two mirror sites at http://www.prc.boun.edu.tr/appserv/prc/HingeProt3 and http://bioinfo3d.cs.tau.ac.il/HingeProt/.     

Antibiotic susceptibility patterns of respiratory isolates of Staphylococcus aureus in a Turkish university hospital

A total of 391 respiratory isolates of Staphylococcus aureus in Sivas (Turkey) were studied between January 1999-2002. The organisms were cultured from the following specimens: throat (43%), sputum (28%), transtracheal/endotracheal aspirates (27%), and bronchial lavage (2%). The isolates were tested against 11 different antibiotics by a disk diffusion method or standardized microdilution technique. Methicillin-resistant isolates constituted 76.9% of all isolates. Most of the methicillin-resistant isolates (95.1%) were isolated from inpatients. The rate of methicillin-resistant isolates in throat, sputum, and tracheal aspirates was 17.2%, 60.1%, and 68.9%, respectively. The resistance of methicillin-resistant isolates in throat to teicoplanin was 3.4%. The methicillin-sensitive isolates were susceptible to most agents tested, while most methicillin-resistant isolates were resistant to these agents. Overall resistance to erythromycin was 61.9%, tetracycline 56.6%, gentamicin 50.7%, ofloxacin 42.0%, rifampin 40.8%, clindamycin 38.9%, chloramphenicol 19.0%, co-trimoxazole 10.2%, and vancomycin 0%.     

Application of automatic mutation-gene pair extraction to diseases

To have a better understanding of the mechanisms of disease development, knowledge of mutations and the genes on which the mutations occur is of crucial importance. Information on disease-related mutations can be accessed through public databases or biomedical literature sources. However, information retrieval from such resources can be problematic because of two reasons: manually created databases are usually incomplete and not up to date, and reading through a vast amount of publicly available biomedical documents is very time-consuming. In this paper, we describe an automated system, MuGeX (Mutation Gene eXtractor), that automatically extracts mutation-gene pairs from Medline abstracts for a disease query. Our system is tested on a corpus that consists of 231 Medline abstracts. While recall for mutation detection alone is 85.9%, precision is 95.9%. For extraction of mutation-gene pairs, we focus on Alzheimer's disease. The recall for mutation-gene pair identification is estimated at 91.3%, and precision is estimated at 88.9%. With automatic extraction techniques, MuGeX overcomes the problems of information retrieval from public resources and reduces the time required to access relevant information, while preserving the accuracy of retrieved information.     

Relationship between synovial fluid and plasma manganese,arginase, and nitric oxide in patients with rheumatoid arthritis

Nitric oxide (NO) participates in the pathogenesis of inflammatory reactions in many autoimmune diseases such as rheumatoid arthritis (RA). There is a reciprocal pathway between arginase and nitric oxide synthese (NOS) for NO production, and Mn is required for arginase activity and stability. To investigate whether NO production related with the arginine-nitric oxide pathway in patients with RA, we measured synovial fluid and plasma nitrite (NO_x) levels, arginase activities, and its cofactor manganese (Mn) concentrations in 21 RA patients and 13 healthy control subjects. Plasma albumin levels were measured as an index of nutritional status. NO_x levels were determined after the reduction of nitrates to nitrites using the Griess reaction. Whereas, synovial fluid arginase activities and Mn levels were found to be significantly lower (p<0.001, p<0.001, respectively), plasma arginase activities and Mn levels were similar in patients with RA when compared to the control subjects. Plasma and synovial fluid NO levels were similar in patients with RA and in healthy subjects (p>0.05, p>0.05, respectively). There were significantly positive correlations between synovial fluid and plasma arginase activities vs Mn content (r=0.543, p=0.011; r=0.516, p=0.017, respectively) and significantly negative correlations between synovial fluid and plasma NO levels vs arginase activities (r=−0.497, p=0.022; r=−0.508, p=0.019 respectively) in the patients group. Our results indicate that the lower concentration of synovial fluid Mn could cause lower arginase activity and this could also upregulate NO production by increasing L-arginine content in patients with RA.     

Functions and oxidative stress status of leukocytes in patients with nephrotic syndrome

This study was conducted to establish the functions and oxidative stress status in leukocytes of adult patients with nephrotic syndrome. Thirty adult patients with nephrotic syndrome and 32 controls were included. Phagocytosis ability, the killing ability of the micro-organism phagosited of polymorphonuclear leukocytes (PMNL) and monocytes, along with oxidative stress parameters of PMNLs were assessed. There was no statistically significant difference in phagocytosis function of PMNLs and monocytes of patients when compared to those of controls. PMNL burst activities of the patient and control groups also showed no difference; however, the monocyte burst activities of patients were significant (p = 0.012). The glutathione peroxidase (GSH-Px) activities in PMNLs of the patients with nephrotic syndrome were significantly higher (p = 0.026) when compared to those of controls. In comparison with those of the control subjects, the patients had also higher selenium levels in their PMNLs (p < 0.001). Although PMNL malonyldialdehyde (MDA) levels of the patients seem to be higher than those of controls, the difference had no statistical significance (p = 0.071). Conclusively, in the patients with nephrotic syndrome, PMNLs appear to be exposed to an oxidative stress as indicated by their increased GSH-Px activities and selenium content. However, PMNLs in nephrotic syndrome patients seem to be coping with the insulting oxidative stress, as suggested by their near-normal MDA productions. Furthermore, these data suggest that nephrotic syndrome appears not to have an influence on phagocytosis and killing abilities of granulocytes and monocytes as long as these cells can overcome the oxidative stress to which they are exposed in this disease.     

Simultaneous ex vivo quantification of antigen-specific CD4<Superscript>+</Superscript> and CD8<Superscript>+</Superscript> T cell responses using in vitro transcribed RNA

Assessment of antigen-specific T-cell responses has been greatly facilitated by development of ELISPOT and intracellular cytokine flow cytometry (CFC) assays. The use of autologous antigen presenting cells transfected with in vitro transcribed RNA as stimulators allows in principle quantification of antigen-specific T-cells independent of the knowledge of the epitopes. We describe here a cytokine secretion assay that enables simultaneous assessment of both antigen-specific CD4+ as well as CD8+ T-cells directly from clinical samples without the need for generation of dendritic cells. To this aim, bulk PBMCs were electroporated with RNA encoding the antigen fused to trafficking signal sequences derived from a MHC class I molecule and used as stimulators. With human cytomegalovirus (HCMV) phosphoprotein 65 (pp65) as antigen we show that for measuring ex vivo T-cell responses in ELISPOT and CFC such stimulators are superior or at least equivalent to a pool of overlapping peptides representing the entire pp65 sequence as well as to untagged pp65 encoding RNA. This approach avoids the time consuming generation of dendritic cells as immune stimulators and, in particular when used in the context of the CFC, is robust, broadly applicable and fast.     

Evaluation of four colourimetric susceptibility tests for the rapid detection of multidrug-resistant Mycobacterium tuberculosis isolates

The purpose of this study is to evaluate four rapid colourimetric methods, including the resazurin microtitre assay (REMA), malachite green decolourisation assay (MGDA), microplate nitrate reductase assay (MNRA) and crystal violet decolourisation assay (CVDA), for the rapid detection of multidrug-resistant (MDR) tuberculosis. Fifty Mycobacterium tuberculosis isolates were used in this study. Eighteen isolates were MDR, two isolates were only resistant to isoniazid (INH) and the remaining isolates were susceptible to both INH and rifampicin (RIF). INH and RIF were tested in 0.25 µg/mL and 0.5 µg/mL, respectively. The agar proportion method was used as a reference method. MNRA and REMA were performed with some modifications. MGDA and CVDA were performed as defined in the literature. The agreements of the MNRA for INH and RIF were 96% and 94%, respectively, while the agreement of the other assays for INH and RIF were 98%. In this study, while the specificities of the REMA, MGDA and CVDA were 100%, the specificity of the MNRA was lower than the others (93.3% for INH and 90.9% for RIF). In addition, while the sensitivity of the MNRA was 100%, the sensitivities of the others were lower than that of the MNRA (from 94.1-95%). The results were reported on the seventh-10th day of the incubation. All methods are reliable, easy to perform, inexpensive and easy to evaluate and do not require special equipment.     

Antituberculotic drug resistance in a Turkish state hospital with national data

Antituberculosis drug resistance is a major factor threatening the success of tuberculosis control programmes. The aim of this study was to reveal the patterns of antituberculosis drug resistance in a secondary hospital in Turkey and to compare with national data. The results of BACTEC MGIT 960 system for susceptibility testing were retrospectively analysed on 76 clinical Mycobacterium tuberculosis complex isolates from different patients. The mean age of 48 men (63.2%) and 28 women was 37 and 39, respectively. Overall resistance rate to isoniazid was 14.5%, followed by streptomycin 9.2%, ethambutol 6.9% and rifampin 5.3%. Female sex and diabetes mellitus but not the presence of cavitary lesion or radiological involvement was a risk factor for the development of drug resistance. Anemia, leukocytosis or thrombocytosis was not associated with the drug resistance. In conclusions, further studies should be conducted regularly to monitor drug resistance in Turkey in order to manage effectively national tuberculosis control efforts.