Six RNA aptamers that bind to yeast phenylalanine tRNA were identified by in vitro selection from a random-sequence pool. The two most abundantly represented aptamers interact with the tRNA anticodon loop, each through a sequence block with perfect Watson-Crick complementarity to the loop. It was possible to truncate one of these aptamers to a simple hairpin loop that forms a classical 'kissing complex' with the anticodon loop. Three other aptamers have nearly complete complementarity to the anticodon loop. The sixth aptamer has two sequence blocks, one complementary to the tRNA T loop and the other to the D loop; this aptamer binds better to a mutant tRNA that disrupts the normal D-loop/T-loop tertiary interaction than to the wild-type tRNA. Selection of complements to tRNA loops occurred despite an attempt to direct binding to tertiary structural features of tRNA. This serves as a reminder of how special the RNA-RNA interactions are that are not based on complementarity. Nonetheless, these aptamers must present the tRNA complement in some special structural context; the simple single-strand complement of the anticodon loop did not bind tRNA effectively. Keywords: in vitro selection/kissing complex/RNA-RNA interactions/RNA stem-loop/tRNA
The global production of sulfur, which is currently obtained almost exclusively as an involuntary byproduct of the oil and gas industry, is exceeding the market demand so that long term storage or even definitive disposal of elemental sulfur is often needed to handle production surplus. The storage of large quantities of elemental sulfur calls for solidifying liquid sulfur in huge blocks, hundred meters wide on each side and as high as 20 meters. Sulfur, in presence of water and air, can be oxidized to sulfuric acid by a ubiquitous microorganism: Thiobacillus. On large blocks, this natural phenomenon may lead to soil and water acidification. Research projects have addressed suppression of Thiobacilli activity to prevent acidification, but no industrial applications have been reported. This work describes the inhibition of sulfur biological oxidation attainable by exposing sulfur to a high ionic strength environment. The bacteriostatic action is produced by contacting sulfur with a solution of an inorganic salt, such as sodium chloride, having an ionic strength similar to sea water. Possible ways to exploit the inhibitory effect to prevent the generation of acidity from sulfur storage blocks are suggested.
The aim of the study is to analyze the biodegradation capacity of a biosurfactant exopolysaccharide (EPS 2003 ) by heterotrophic marine bacterial strains. During the initial screening performed in two sites located at the harbor of Messina for analyzing the response of marine bacterial population with the presence of biosurfactant EPS 2003 , ten bacterial strains capable to degrade this substance were isolated. Between the bacterial strains isolated, two representative bacterial strains, isoDES-01, clustered with Pseudoalteromonas sp. A28 (100%), and isoDES-07, closely related to Vibrio proteolyticus (98.9%), were chosen for mineralization and respirometry test, performed to evaluate biodegradability potential of EPS 2003 . Assays of bacterial growth and measure of concentration of total RNA were also performed. More than 90% of EPS 2003 was mineralized by the isoDE01 strain for biomass formation and respiration, while EPS 2003 mineralization by the isoDE-07 strain was less effective, reaching 60%. This approach combines the study of the microbial community with its functional aspects (i.e., mineralization and respirometry test) allowing a more precise assessment of biosurfactant degradation. These results enhance our knowledge of microbial ecology of EPSdegrading bacteria and the mechanisms by which this biodegradation occurs. This will prove helpful for predicting the environmental fate of these compounds and for developing practical EPS 2003 bioremediation strategies from future marine hydrocarbon pollution.
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