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171.
Genomic islands (GIs) are genomic regions that are originally transferred from other organisms. The detection of genomic islands in genomes can lead to many applications in industrial, medical and environmental contexts. Existing computational tools for GI detection suffer either low recall or low precision, thus leaving the room for improvement. In this paper, we report the development of our Ensemble algorithm for Genomic Island Detection (EGID). EGID utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between our ensemble algorithm and existing programs have shown that our ensemble algorithm is better than any other program. EGID was implemented in Java, and was compiled and executed on Linux operating systems. EGID is freely available at http://www5.esu.edu/cpsc/bioinfo/software/EGID. 相似文献
172.
173.
Equilibrium unfolding by guanidinium hydrochloride (GuHCl) and urea as well as evolutionary trends of two homologous albumins,
pig serum albumin (PSA) and rabbit serum albumin (RSA), has been studied with circular dichroism, tryptophanyl fluorescence
and bioinformatics. GuHCl cannot distinguish the contribution of electrostatic interactions to the proteins which were otherwise
effectively monitored by urea. Higher differences in free energy changes due to urea than GuHCl show electrostatic interactions
among charged amino acids are possibly responsible for higher structural stability of RSA in comparison to PSA. From the sequence
of HSA and RSA, deletion of arginine at position 117 and the presence of one extra tryptophan at position 135 may possess
some clue for lesser stability of PSA. Here, for comparison, chemical unfolding data of HSA and BSA had been taken into consideration.
We found that thermodynamically RSA and PSA are closer to HSA and BSA, respectively, in accordance with their sequence homologies.
Taxonomically, rabbit belongs to lagomorph which is closer to hominids than ungulates. Hence, on the basis of these thermodynamic
data of protein denaturation of different species we can use this new approach to analyze the phylogenetic relationship among
the major clades of eutherian mammals to obtain their evolutionary trends. 相似文献
174.
Gul M Dogan E Kirecci E Ucmak H Dirican E Karadag A 《Acta microbiologica et immunologica Hungarica》2011,58(3):235-238
Serratia ficaria was first described in 1979 as a Gram-negative facultative anaerobic rod. S. ficaria was found in figs, but also isolated from human specimens in a few cases. We now report an isolate of S. ficaria from sputum specimen.A 46-year-old man was suffering from a chronic renal failure of five years, four months of peritoneal dialysis and one week of fever due to respiratory tract infection, accompanied by cough. Sputum culture yielded a Gram-negative rod. It was identified as S. ficaria and the antibiotic susceptibility test was performed by automated Vitek II (bioMerieux). The tested S. ficaria strain was susceptible to amikacin, gentamicin, cefepime, trimethoprim-sulfamethoxazole, imipenem, meropenem, tigecycline and ciprofloxacin. This strain was resistant to ampicillin, amoxicillin-clavulanic acid, cephalothin, cefoxitine, cefuroxime and ceftriaxone. The patient was treated successfully (80 mg trimethoprim/400 mg sulfamethoxazole twice daily for 7 days)S. ficaria is an opportunistic pathogen responsible for intestinal colonization or serious infections such as septicaemia, gall bladder empyema in immunocompromised patients. The fig tree and fig play an important role in human colonization. It should be remembered that S. ficaria infections may be encountered frequently especially in fig tree culture zones. 相似文献
175.
Ledesma MC Jung-Hynes B Schmit TL Kumar R Mukhtar H Ahmad N 《Molecular medicine (Cambridge, Mass.)》2011,17(1-2):134-143
Various formulations of selenium and vitamin E, both essential human dietary components, have been shown to possess a therapeutic and preventive effect against prostate cancer. Fortuitous results of clinical trials also implied a risk-reduction effect of selenium and vitamin E supplements. The Selenium and Vitamin E Cancer Prevention Trial (SELECT), using oral selenium and vitamin E supplementation in disease-free volunteers, was designed to test a prostate cancer chemoprevention hypothesis. SELECT was terminated early because of both safety concerns and negative data for the formulations and doses given. Here, we review and discuss the studies done before and since the inception of SELECT, as well as the parameters of the trial itself. We believe that there is a lack of appropriate in vivo preclinical studies on selenium and vitamin E despite many promising in vitro studies on these agents. It seems that the most effective doses and formulations of these agents for prostate cancer chemoprevention have yet to be tested. Also, improved understanding of selenium and vitamin E biology may facilitate the discovery of these doses and formulations. 相似文献
176.
177.
Hossein Vaheed Seyed Abbas Shojaosadati Hasan Galip 《Journal of industrial microbiology & biotechnology》2011,38(1):101-111
In this research, ethanol production from carob pod extract (extract) using Zymomonas mobilis with medium optimized by Plackett–Burman (P–B) and response surface methodologies (RSM) was studied. Z. mobilis was recognized as useful for ethanol production from carob pod extract. The effects of initial concentrations of sugar, peptone,
and yeast extract as well as agitation rate (rpm), pH, and culture time in nonhydrolyzed carob pod extract were investigated.
Significantly affecting variables (P = 0.05) in the model obtained from RSM studies were: weights of bacterial inoculum, initial sugar, peptone, and yeast extract.
Acid hydrolysis was useful to complete conversion of sugars to glucose and fructose. Nonhydrolyzed extract showed higher ethanol
yield and residual sugar compared with hydrolyzed extract. Ethanol produced (g g−1 initial sugar, as the response) was not significantly different (P = 0.05) when Z. mobilis performance was compared in hydrolyzed and nonhydrolyzed extract. The maximum ethanol of 0.34 ± 0.02 g g−1 initial sugar was obtained at 30°C, initial pH 5.2, and 80 rpm, using concentrations (g per 50 mL culture media) of: inoculum
bacterial dry weight, 0.017; initial sugar, 5.78; peptone, 0.43; yeast extract, 0.43; and culture time of 36 h. 相似文献
178.
Uremic syndrome results from malfunctioning of various organ systems due to the retention of uremic toxins which, under normal conditions, would be excreted into the urine and/or metabolized by the kidneys. The aim of this study was to elucidate the mechanisms underlying the renal elimination of uremic toxin creatinine that accumulate in chronic renal failure. Quantitative investigation of the plausible correlations was performed by spectroscopy, calorimetry, molecular docking and accessibility of surface area. Alkalinization of normal plasma from pH 7.0 to 9.0 modifies the distribution of toxin in the body and therefore may affect both the accumulation and the rate of toxin elimination. The ligand loading of HSA with uremic toxin predicts several key side chain interactions of site I that presumably have the potential to impact the specificity and impaired drug binding. These findings provide useful information for elucidating the complicated mechanism of toxin disposition in renal disease state. 相似文献
179.
180.
Gommet C Billecocq A Jouvion G Hasan M Zaverucha do Valle T Guillemot L Blanchet C van Rooijen N Montagutelli X Bouloy M Panthier JJ 《PLoS neglected tropical diseases》2011,5(12):e1421