No association between polymorphism in the vascular endothelial growth factor gene at position−460 and sporadic prostate cancer in the Turkish population

The development and progression of prostate cancer (PCa) has biologically and genetically remained a mystery. A man’s risk of developing PCa is influenced by both genetic and environmental factors. Angiogenic cytokines like vascular endothelial growth factor (VEGF) play a pivotal role in tumor angiogenesis. Single nucleotide polymorphisms in angiogenesis-dependent genes affect the sensibility of cancer development and progression. Therefore, we hypothesized a potential association between DNA sequence variations in VEGF −460 gene region and sporadic PCa patients in the Turkish population. 133 sporadic PCa patients and 157 healthy controls were studied. Genotypes were determined by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. The distribution of genotype and allele frequencies of the polymorphism did not yield a statistically significant difference between patients and controls (P > 0.05). Furthermore, classification of patients by tumor-lymph nodes-metastasis (TNM), Gleason Scores (GS) and serum prostate-specific antigen (PSA) levels did not show significant differences among the VEGF −460 C>T genotypes (P > 0.05). This is the first demonstration showing that the VEGF −460 C>T polymorphism in men is not associated with sporadic PCa in the Turkish population.     

The activity of antioxidative enzymes in three strawberry cultivars related to salt-stress tolerance

Effects of salt stress on the time course of stomatal behaviors and the activity of antioxidative enzymes such as catalase (CAT) (EC 1.11.1.6), ascorbate peroxidase (APX) (EC 1.11.1.11), and glutathione reductase (GR) (EC. 1.6.4.2) were studied in three strawberry cultivars. The responses of the cultivars ‘Camarosa’, ‘Tioga,’ and ‘Chandler’ were compared when they were irrigated with nutrient solution containing 0, 8.5, 17.0, and 34.0 mM sodium chloride (NaCl) for 30 days. A significant reduction in stomatal conductance (g_s) was seen particularly on the 30th day of the salt treatments only in Camarosa, which is parallel to transpiration rate (E). CAT activities decreased in all of the salt treatments only in Tioga, while it remained almost unchanged or slightly increased depending on the period in Camarosa and Chandler. APX activity sharply increased in 17.0 and 8.5-mM NaCl treatments for 30 days in Camarosa and Tioga, respectively, whereas it linearly increased based on the NaCl treatments in Chandler. On the other hand, only Camarosa demonstrated a sharp increase in GR activity induced by salinity applied for 30 days. All the data indicated that control of the stomatal behavior, the higher salt-stress tolerance (LT₅₀) and higher constitutive activity of antioxidant enzymes made Camarosa and Tioga relatively salt-tolerant cultivars.     

Apoptosis and nitric oxide release induced by thalidomide, gossypol and dexamethasone in cultured human chronic myelogenous leukemic K-562 cells

The effects of different dosages of thalidomide, gossypol and dexamethasone on the levels of apoptosis and nitric oxide (NO) production were studied in a human chronic myelogenous leukemic cell line, K-562. Increases in the levels of apoptosis were induced by both 15 and 30 microM of thalidomide but only 15 microM significantly increased NO production. All dosages of gossypol used increased the production of NO and all dosages except 200 microM raised the level of apoptosis. After dexamethasone treatment the level of NO either decreased or stayed constant. Thus, some dosages of thalidomide and gossypol concomitantly raise the levels of apoptosis and NO production, but dexamethasone, though it induced apoptosis, had no significant effect on NO production.     

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.     

Adaptive evolution of metabolic pathways in Drosophila

The adaptive significance of enzyme variation has been of central interest in population genetics. Yet, how natural selection operates on enzymes in the larger context of biochemical pathways has not been broadly explored. A basic expectation is that natural selection on metabolic phenotypes will target enzymes that control metabolic flux, but how adaptive variation is distributed among enzymes in metabolic networks is poorly understood. Here, we use population genetic methods to identify enzymes responding to adaptive selection in the pathways of central metabolism in Drosophila melanogaster and Drosophila simulans. We report polymorphism and divergence data for 17 genes that encode enzymes of 5 metabolic pathways that converge at glucose-6-phosphate (G6P). Deviations from neutral expectations were observed at five loci. Of the 10 genes that encode the enzymes of glycolysis, only aldolase (Ald) deviated from neutrality. The other 4 genes that were inconsistent with neutral evolution (glucose-6-phosphate dehydrogenase [G6pd]), phosphoglucomutase [Pgm], trehalose-6-phosphate synthetase [Tps1], and glucose-6phosphatase [G6pase] encode G6P branch point enzymes that catalyze reactions at the entry point to the pentose-phosphate, glycogenic, trehalose synthesis, and gluconeogenic pathways. We reconcile these results with population genetics theory and existing arguments on metabolic regulation and propose that the incidence of adaptive selection in this system is related to the distribution of flux control. The data suggest that adaptive evolution of G6P branch point enzymes may have special significance in metabolic adaptation.     

A pilot study evaluating sequential administration of a PPI-amoxicillin followed by a PPI-metronidazole-tetracycline in Turkey

BACKGROUND: There is no effective regimen for the eradication of Helicobacter pylori in our country. It may be due to the increasing prevalence of resistance to antibiotics used for the treatment of H. pylori. Recently, a study from Turkey has revealed that a new treatment scheme consisting of sequential administration of pantoprazole plus amoxicillin for 7 days followed by pantoprazole plus metronidazole, and tetracycline for the remaining 7 days was effective in the first-line treatment of H. pylori. Therefore, we aimed to confirm efficacy of a new therapy scheme in the first-line H. pylori eradication. MATERIAL AND METHODS: This is a prospective, open label, single center, pilot study and included 32 patients infected with H. pylori diagnosed by both histologic examinations, rapid urease test and (13)C-urea breath test (UBT). The patients received a 14-day sequential regimen (pantoprazole 40 mg b.d. plus amoxicillin 1000 mg b.d. for 7 days and pantoprazole 40 mg b.d., metronidazole 500 mg b.d. and tetracycline 500 mg q.d. for the remaining 7 days). Eradication was assessed with (13)C-UBT 4 weeks after completion of the therapy. Intention-to-treat and per-protocol eradication rates were determined. RESULTS: At intention-to-treat analysis, the eradication rate was 50% (16/32). For the per protocol analysis, the eradication rate was 57% (16/28). There were no significant adverse effects and treatment compliance was good. CONCLUSION: A new therapy consisting of sequentially administered drugs for 14 days yielded unacceptably low eradication rates. This scheme was not efficient for H. pylori eradication in our region. Further investigations are needed to determine the effectiveness of this scheme in other regions of Turkey.     

Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes

Apoptosis is a matter of life and death for cells and both inhibited and enhanced apoptosis may be involved in the pathogenesis of human diseases. The structures of protein-protein complexes in the apoptosis signaling pathway are important as the structural pathway helps in understanding the mechanism of the regulation and information transfer, and in identifying targets for drug design. Here, we aim to predict the structures toward a more informative pathway than currently available. Based on the 3D structures of complexes in the target pathway and a protein-protein interaction modeling tool which allows accurate and proteome-scale applications, we modeled the structures of 29 interactions, 21 of which were previously unknown. Next, 27 interactions which were not listed in the KEGG apoptosis pathway were predicted and subsequently validated by the experimental data in the literature. Additional interactions are also predicted. The multi-partner hub proteins are analyzed and interactions that can and cannot co-exist are identified. Overall, our results enrich the understanding of the pathway with interactions and provide structural details for the human apoptosis pathway. They also illustrate that computational modeling of protein-protein interactions on a large scale can help validate experimental data and provide accurate, structural atom-level detail of signaling pathways in the human cell.     

Barbiturate and benzodiazepine modulation of GABA receptor binding and function

The inhibitory neurotransmitter gamma-aminobutyric acid (GABA) acts primarily on receptors that increase chloride permeability in postsynaptic neurons. These receptors are defined by sensitivity to the agonist muscimol and the antagonist bicuculline, and are also subject to indirect allosteric inhibition by picrotoxin-like convulsants and enhancement by the clinically important drugs, the benzodiazepines and the barbiturates. All of these drugs modulate GABA-receptor regulated chloride channels at the cellular level assayed by electrophysiological or radioactive ion tracer techniques. Specific receptor sites for GABA, benzodiazepines, picrotoxin/convulsants, and barbiturates can be assayed in vitro by radioactive ligand binding. Mutual chloride-dependent allosteric interactions between the four receptor sites indicate that they are all coupled in the same membrane macromolecular complex. Indirect effects of barbiturates on the other three binding sites define a pharmacologically specific, stereospecific receptor. All of the activities can be solubilized in the mild detergent 3-[(3-cholamidopropyl)-dimethylammonio]propane sulfonate (CHAPS) and co-purify as a single protein complex.     

NLF2 gene expression in the endometrium of patients with implantation failure after IVF treatment

We developed and evaluated the specificity and sensitivity of a loop-mediated isothermal amplification (LAMP) method for rapid detection of the multidrug-resistance gene cfr. A pair of outer primers and a pair of inner primers and one loop primer were specially designed for recognizing seven distinct sequences on the target cfr gene. The amplification reaction was performed within only 35 min under isothermal conditions at 63 °C in a regular water bath with visual measurement. The LAMP assay showed higher sensitivity than the conventional PCR, with a detection limit of 1 pg per tube of chicken Staphylococcus sciuri genomic DNA. The detection rate of cfr gene for 50 Staphylococcus clinical strains by LAMP assays was 16% and appeared 100% consistence with the result by PCR method. The LAMP method reported here demonstrated a potential and valuable means for detection of the multidrug-resistance gene cfr: easy, rapid, visual, specific, accurate and sensitive, especially useful for on-the-spot investigation.