Recognition of functional genetic polymorphism using ESE motif definition: a conservative evolutionary approach to CYP2D6/CYP2C19 gene variants

Genetica - Although predicting the effects of variants near intron-exon boundaries is relatively straightforward, predicting the functional Exon Splicing Enhancers (ESEs) and the possible effects...     

Estimates of economic values for traits of Arabic sheep in village system

A deterministic bio-economic model was used to estimate the economic values of different traits in Arabic sheep native to the Khuzestan province of Iran. In the studied system, variable costs accounted for about 98.5% of the total costs and among variable costs, feed costs had the highest proportion with 70.7%. Revenue sources included meat, wool, and manure, where meat was the most important one and formed 95.5% of total revenues. Economic value for a trait was estimated as the amount of change in the profit of system as its mean increased by one unit, while the means of other traits were constant. The most important trait in this system was litter size, followed by ewe survival, dressing percentage, and wool weight, respectively. Birth weight had a negative economic value but weight at older ages especially weaning weight and 12-month weight had positive economic values. The sensitivity of economic values of traits was investigated by changing feed and non-feed costs, meat and wool prices by ±10%. Results showed that economic values for dressing percentage and wool weight are not sensitive to change in costs. In addition, changes in marketing and management costs had no effect on the economic value for traits related to body weight in different ages. In general, the economic value for traits which showed sensitivity to the changes of costs, except ewe survival, decreased due to an increase in costs. The economic value for all traits, except birth and wool weight, changed because of a change in meat price. Increasing meat price meant a higher economic importance. Among different factors, meat price fluctuations had the most effect on the economic value of traits.     

Safe bunker designing for the 18?MV Varian 2100 Clinac: a comparison between Monte Carlo simulation based upon data and new protocol recommendations

Aim

The aim of this study was to compare two bunkers designed by only protocols recommendations and Monte Carlo (MC) based upon data derived for an 18 MV Varian 2100Clinac accelerator.

Background

High energy radiation therapy is associated with fast and thermal photoneutrons. Adequate shielding against the contaminant neutron has been recommended by IAEA and NCRP new protocols.

Materials and methods

The latest protocols released by the IAEA (safety report No. 47) and NCRP report No. 151 were used for the bunker designing calculations. MC method based upon data was also derived. Two bunkers using protocols and MC upon data were designed and discussed.

Results

From designed door''s thickness, the door designed by the MC simulation and Wu–McGinley analytical method was closer in both BPE and lead thickness. In the case of the primary and secondary barriers, MC simulation resulted in 440.11 mm for the ordinary concrete, total concrete thickness of 1709 mm was required. Calculating the same parameters value with the recommended analytical methods resulted in 1762 mm for the required thickness using 445 mm as recommended by TVL for the concrete. Additionally, for the secondary barrier the thickness of 752.05 mm was obtained.

Conclusion

Our results showed MC simulation and the followed protocols recommendations in dose calculation are in good agreement in the radiation contamination dose calculation. Difference between the two analytical and MC simulation methods revealed that the application of only one method for the bunker design may lead to underestimation or overestimation in dose and shielding calculations.     

Biotransformation of methyl tert-butyl ether by human cytochrome P450 2A6

Methyl tert-butyl ether (MTBE) is widely used as gasoline oxygenate and octane number enhancer for more complete combustion in order to reduce the air pollution caused by motor vehicle exhaust. The possible adverse effects of MTBE on human health are of major public concern. However, information on the metabolism of MTBE in human tissues is scarce. The present study demonstrates that human cytochrome P450 2A6 is able to metabolize MTBE to tert-butyl alcohol (TBA), a major circulating metabolite and marker for exposure to MTBE. As CYP2A6 is known to be constitutively expressed in human livers, we infer that it may play a significant role in metabolism of gasoline ethers in liver tissue.     

Prediction of GABAA receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine

The amino acid gamma-aminobutyric-acid receptors (GABA_ARs) belong to the ligand-gated ion channels (LGICs) superfamily. GABA_ARs are highly diverse in the central nervous system. These channels play a key role in regulating behavior. As a result, the prediction of GABA_ARs from the amino acid sequence would be helpful for research on these receptors. We have developed a method to predict these proteins using the features obtained from Chou's pseudo-amino acid composition concept and support vector machine as a powerful machine learning approach. The predictor efficiency was assessed by five-fold cross-validation. This method achieved an overall accuracy and Matthew's correlation coefficient (MCC) of 94.12% and 0.88, respectively. Furthermore, to evaluate the effect and power of each feature, the minimum Redundancy and Maximum Relevance (mRMR) feature selection method was implemented. An interesting finding in this study is the presence of all six characters (hydrophobicity, hydrophilicity, side chain mass, pK1, pK2 and pI) or combination of the characters among the 5 higher ranked features (pk2 and pI, hydrophobicity and mass, pk1, hydrophilicity and mass) obtained from the mRMR feature selection method. The results show a biologically justifiable ranked attributes of pk2 and pI; hydrophobicity, hydrophilicity and mass; mass and pk1; pk2 and mass. Based on our results, using the concept of Chou's pseudo-amino acid composition and support vector machine is an effective approach for the prediction of GABA_ARs.     

Essential role of stromally induced hedgehog signaling in B-cell malignancies

Interaction of cancer cells with their microenvironment generated by stromal cells is essential for tumor cell survival and influences the localization of tumor growth. Here we demonstrate that hedgehog ligands secreted by bone-marrow, nodal and splenic stromal cells function as survival factors for malignant lymphoma and plasmacytoma cells derived from transgenic Emu-Myc mice or isolated from humans with these malignancies. Hedgehog pathway inhibition in lymphomas induced apoptosis through downregulation of Bcl2, but was independent of p53 or Bmi1 expression. Blockage of hedgehog signaling in vivo inhibited expansion of mouse lymphoma cells in a syngeneic mouse model and reduced tumor mass in mice with fully developed disease. Our data indicate that stromally induced hedgehog signaling may provide an important survival signal for B- and plasma-cell malignancies in vitro and in vivo. Disruption of this interaction by hedgehog pathway inhibition could provide a new strategy in lymphoma and multiple myeloma therapy.     

Enantioselective separation and online affinity chromatographic characterization of R,R- and S,S-fenoterol

BACKGROUND: rac-Fenoterol is a beta2-adrenoceptor agonist (beta2-AR) used in the treatment of asthma. It has two chiral centers and is marketed as a racemic mixture of R,R'- and S,S'-fenoterol (R-F and S-F). Here we report the separation of the R-F and S-F enantiomers and the evaluation of their binding to and activation of the beta2-AR. METHODS: R-F and S-F were separated from the enantiomeric mixture by chiral chromatography and absolute configuration determined by circular dichroism. Beta2-AR binding was evaluated using frontal affinity chromatography with a stationary phase containing immobilized membranes from HEK-293 cells that express human beta2-AR and standard membrane binding studies using the same membranes. The effect of R-F and S-F on cardiomyocyte contractility was also investigated using freshly isolated adult rat cardiomyocytes. RESULTS: Chiral chromatography of rac-fenoterol yielded separated peaks with an enantioselectivity factor of 1.21. The less retained peak was assigned the absolute configuration of S-F and the more retained peak R-F. Frontal chromatography using membrane-bound beta2-AR as the stationary phase and rac-3H-fenoterol as a marker ligand showed that addition of increasing concentrations of R-F to the mobile phase produced concentration-dependent decreases in rac-3H-fenoterol retention, while similar addition of S-F produced no change in rac-3H-fenoterol retention. The calculated dissociation constant of R-F was 472 nM and the number of available binding sites 176 pmol/column, which was consistent with the results from the membrane binding study 460 +/- 55 nM (R-F) and 109,000 +/- 10,400 nM (S-F). In the cardiomyocytes, R-F increased maximum contractile response from (265 +/- 11.6)% to (306 +/- 11.8)% of resting cell length (P < 0.05) and reduced EC50 from -7.0 +/- 0.270 to -7.1 +/- 0.2 log[M] (P < 0.05), while S-F had no significant effect. DISCUSSION: Previous studies have shown that rac-fenoterol acts as an apparent beta2-AR/G(s) selective agonist and fully restores diminished beta2-AR contractile response in cardiomyocytes from failing hearts of spontaneously hypertensive rats (SHR). Here we report the separation of the enantiomers of rac-fenoterol and that R-F is the active component of rac-fenoterol. Further evaluation of R-F will determine if it has enhanced selectivity and specificity for beta2-AR/G(s) activation and if it can be used in the treatment of congestive heart failure.     

Thermal Stability and Decomposition Kinetic Studies of Acyclovir and Zidovudine Drug Compounds

Investigations on thermal behavior of drug samples such as acyclovir and zidovudine are interesting not only for obtaining stability information for their processing in pharmaceutical industry but also for predicting their shelf lives and suitable storage conditions. The present work describes thermal behaviors and decomposition kinetics of acyclovir and zidovudine in solid state, studied by some thermal analysis techniques including differential scanning calorimetry (DSC) and simultaneous thermogravimetry–differential thermal analysis (TG/DTA). TG analysis revealed that thermal degradation of the acyclovir and zidovudine is started at the temperatures of 400°C and 190°C, respectively. Meanwhile, TG–DTA analysis of acyclovir indicated that this drug melts at about 256°C. However, melting of zidovudine occurred at 142°C, which is 100°C before starting its decomposition (242°C). Different heating rates were applied to study the DSC behavior of drug samples in order to compute their thermokinetic and thermodynamic parameters by non-isothermal kinetic methods. Thermokinetic data showed that both drugs at the room temperature have slow degradation reaction rates and long shelf lives. However, acyclovir is considerably more thermally stable than zidovudine.     

The effect of unilateral ureteral obstruction on renal function in pigs measured by diffusion-weighted MRI

The objective of this study was to examine the effect of unilateral ureteral obstruction on the apparent diffusion coefficient (ADC) in pig kidney. Changes in ADC is suggested to reflect changes in the ratio of extracellular to intracellular volume. Thirteen pigs were allocated into three groups: 1) pigs subjected to acute unilateral ureteral obstruction (AUO) (n = 3), 2) pigs subjected to chronic partial unilateral obstruction (CPUO) (n = 3), and 3) control pigs (n = 7). The extra- to intracellular volume ratio was indirectly measured in both the ipsilateral obstructed kidney and contralateral non-obstructed kidney by the ADC of the renal tissue using diffusion-weighted echo-planar magnetic resonance imaging. ADC was 2.07 +/- 0.27 x 10(-3) mm2/s in the cortex and 2.10 +/- 0.24 x 10(-3) mm2/s in the medulla of normal control kidneys. In the obstructed kidney from the AUO group the ADC of the medulla was significantly reduced 24 hours after occlusion of the ureter (1.65 +/- 0.05 x 10(-3) mm2/s vs 2.10 +/- 0.24 x 10(-3) mm2/s; p < 0.05). Similarly ADC decreased slightly in the cortex of the ipsilateral kidney. In contrast, ADC of the ipsilateral kidney of CPUO pigs was increased both in the renal medulla (3.13 +/- 0.21 x 10(-3) mm2/s vs. 2.10 +/- 0.24 x 10(-3) mm2/s; p < 0.05) and cortex (3.09 +/- 0.14 x 10(-3) mm2/s vs. 2.07 x 10(-3) mm2/s, p < 0.05). In conclusion, the results of the present study suggest that diffusion weighted imaging (ADC) may be a useful parameter to incorporate when identifying whether a ureteric obstruction is acute or chronic.