Test of molecular dynamics force fields in gramicidin A

The force fields commonly used in molecular dynamics simulations of proteins are optimized under bulk conditions. Whether the same force fields can be used in simulations of membrane proteins is not well established, although they are increasingly being used for such purposes. Here we consider ion permeation in the gramicidin A channel as a test of the AMBER force field in a membrane environment. The potentials of mean force for potassium ions are calculated along the channel axis and compared with the one deduced from the experimental conductance data. The calculated result indicates a rather large central barrier similar to those obtained from other force fields, which are incompatible with the conductance data. We suggest that lack of polarizability is the most likely cause of this problem, and, therefore, urge development of polarizable force fields for simulations of membrane proteins.     

The protective role of erdosteine on testicular tissue after testicular torsion and detorsion

Testicular torsion and detorsion are important clinical problems for infertile man and oxidative stress may have a role in this clinical situation. The aim of this study was to investigate the protective role of erdosteine, an antioxidant, on unilateral testicular reperfusion injury in rats. The rats were divided into four groups including seven rats in each group: control, torsion, torsion/detorsion and torsion/detorsion+erdosteine. Rats, except the sham operation group, were subjected to left unilateral torsion (720^∘ rotation in the clockwise direction) without including the epididymis. The experiments were finished after sham operation time for control, 120 min torsion for torsion group and 120 min torsion and 240 min detorsion for torsion/detorsion groups. Bilateral orchiectomy was performed for all groups of rats. The ipsilateral and controlateral testis were divided into two pieces to analyse biochemical parameters and to investigate the light microscopic view. Malondialdehyde level of ipsilateral testis was increased in torsion and torsion/detorsion groups in comparison with the other groups (p < 0.05). Erdosteine treatment ameliorated lipid peroxidation after torsion/detorsion in ipsilateral testis (p < 0.05). Also, xanthine oxidase activity of ipsilateral testis was increased in torsion/detorsion group in comparison with the others (p < 0.05). Nitric oxide (NO) level of ipsilateral testis was higher in all experimental groups than sham operated control group (p < 0.05). Also, NO level of torsion group was increased in comparison with detorsion groups (p < 0.05). Erdosteine treatment caused increased glutathione peroxidase activity in comparison with torsion and torsion/detorsion groups and catalase activity in comparison with the other groups in ipsilateral testis (p < 0.05). Superoxide dismutase activity of ipsilateral testis was higher in torsion/detorsion and torsion/detorsion+erdosteine groups than control and torsion groups (p < 0.05). The biochemical parameters were not affected in controlateral testis in all groups. Torsion, torsion/detorsion and torsion/detorsion+erdosteine groups showed ipsilateral testicular damage in the histological examination, but the specimens from torsion/detorsion had a significantly greater histological injury than those from the other groups (p < 0.05). Control rats showed normal seminiferous tubule morphology. Rats in torsion group had slight-to-moderate disruption of the seminiferous epithelium. Rats in torsion/detorsion group displayed moderate-to-severe disruption of the seminiferous epithelium. In all animals from torsion/detorsion+erdosteine group, the testicular tissues were affected with slight-to-moderate degenerative changes of the seminiferous epithelium. Administration of erdosteine resulted in a significantly reduced histological damage associated with torsion of the spermatic cord compared with torsion/detorsion. In all groups, the contralateral testes were histologically normal. In conclusion, the results clearly displayed that erdosteine treatment may have a protective role on testicular torsion/detorsion injury. (Mol Cell Biochem xxx: 193–199, 2005)     

Attitude toward genetic testing for cancer risk in Istanbul

To identify attitudes toward genetic testing, and the effects of this information on decisions regarding issues such as pregnancy, abortion, and prophylactic surgery, several subsets of the Turkish population were surveyed in hospital settings. Individuals (n = 179) chosen arbitrarily from four different subsets of a Turkish population were asked to participate in a confidential 23-question survey. Survey participants were familiar with the concept of cancer being a familial disease (85.5%), and 84.7% of them expressed interest in genetic testing to determine cancer risk, 83.9% would have their fetuses tested for such cancer risk, 65.1% would terminate their pregnancies, 92.2% would have their children tested if they were determined to have an increased cancer risk, 71.9% would agree to undergo prophylactic oophorectomy or orchiectomy and 67.6% would have mastectomy/prostatectomy should there be an increased cancer risk to these organs. It appears that at least the sampled segment of a Turkish population is willing to undergo genetic testing to determine if they are at increased risk for cancer. The feasibility and acceptance of genetic testing and the influence of education and genetic counseling in the Turkish people should further be evaluated with a larger stratified sample of the population.     

Protective Effects of Valproic Acid,a Histone Deacetylase Inhibitor,against Hyperoxic Lung Injury in a Neonatal Rat Model

ObjectiveHistone acetylation and deacetylation may play a role in the pathogenesis of inflammatory lung diseases. We evaluated the preventive effect of valproic acid (VPA), a histone deacetylase (HDAC) inhibitor, on neonatal hyperoxic lung injury.MethodsForty newborn rat pups were randomized in normoxia, normoxia+VPA, hyperoxia and hyperoxia+VPA groups. Pups in the normoxia and normoxia+VPA groups were kept in room air and received daily saline and VPA (30 mg/kg) injections, respectively, while those in hyperoxia and hyperoxia+VPA groups were exposed to 95% O₂ and received daily saline and VPA (30 mg/kg) injections for 10 days, respectively. Growth, histopathological, biochemical and molecular biological indicators of lung injury, apoptosis, inflammation, fibrosis and histone acetylation were evaluated.ResultsVPA treatment during hyperoxia significantly improved weight gain, histopathologic grade, radial alveolar count and lamellar body membrane protein expression, while it decreased number of TUNEL(+) cells and active Caspase-3 expression. Expressions of TGFβ3 and phospho-SMAD2 proteins and levels of tissue proinflammatory cytokines as well as lipid peroxidation biomarkers were reduced, while anti-oxidative enzyme activities were enhanced by VPA treatment. VPA administration also reduced HDAC activity while increasing acetylated H3 and H4 protein expressions.ConclusionsThe present study shows for the first time that VPA treatment ameliorates lung damage in a neonatal rat model of hyperoxic lung injury. The preventive effect of VPA involves HDAC inhibition.     

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.