RNA cleavage without hydrolysis. Splitting the catalytic activities of binase with Asn101 and Thr101 mutations

Members of the microbial guanyl-specific ribonuclease family catalyse the endonucleolytic cleavage of single-stranded RNA in a two-step reaction involving transesterification to form a 2',3'-cyclic phosphate and its subsequent hydrolysis to yield the respective 3'-phosphate. The extracellular ribonuclease from Bacillus intermedius (binase, RNase Bi) shares a common mechanism for RNA hydrolysis with mammalian RNases. Two catalytic residues in the active site of binase, Glu72 and His101, are thought to be involved in general acid-general base catalysis of RNA cleavage. Using site-directed mutagenesis, binase mutants were produced containing amino acid substitutions H101N and H101T and their catalytic properties towards RNA, poly(I), poly(A), GpC and guanosine 2',3'- cyclic phosphate (cGMP) substrates were studied. The engineered mutant proteins are active in the transesterification step which produces the 2',3'-cyclic phosphate species but they have lost the ability to catalyse hydrolysis of the cyclic phosphate to give the 3' monophosphate product.      

A single-headed dimer of Escherichia coli ribosomal protein L7/L12 supports protein synthesis

During protein synthesis, the two elongation factors Tu and G alternately bind to the 50S ribosomal subunit at a site of which the protein L7/L12 is an essential component. L7/L12 is present in each 50S subunit in four copies organized as two dimers. Each dimer consists of distinct domains: a single N-terminal ("tail") domain that is responsible for both dimerization and binding to the ribosome via interaction with the protein L10 and two independent globular C-terminal domains ("heads") that are required for binding of elongation factors to ribosomes. The two heads are connected by flexible hinge sequences to the N-terminal domain. Important questions concerning the mechanism by which L7/L12 interacts with elongation factors are posed by us in response to the presence of two dimers, two heads per dimer, and their dynamic, mobile properties. In an attempt to answer these questions, we constructed a single-headed dimer of L7/L12 by using recombinant DNA techniques and chemical cross-linking. This chimeric molecule was added to inactive core particles lacking wild-type L7/L12 and shown to restore activity to a level approaching that of wild-type two-headed L7/L12.     

The absence of a triphasic renovascular response by the multicalyceal kidney of the primate in reaction to acute, complete, unilateral, ureteric obstruction

The early renovascular response by the ipsilateral kidney to acute, total, unilateral, ureteric obstruction was investigated in the adult male chacma baboon (Papio ursinus). Complete occlusion was effected by ligating the ureter at the brim of the bony pelvis ("N"=10). Sham studies were enacted using the same method but the ureter was not obstructed ("N"=11). Haemodynamic reactions were monitored for 12 hours. Compared with the sham-occluded set, the renal pelvic pressures in the obstructed group were significantly increased (P<0.05) from the second hour of the inquiry. However, there were no significant differences in renal blood flow, either between or within the respective cohorts. In this study, the renovascular response to acute ureteric occlusion was similar to that displayed by the multicalyceal kidney of other species under identical conditions. This reaction was fundamentally different to that exhibited by the unicalyceal kidney under similar circumstances.     

An evaluation of current and alternative systems for quality grading carcasses of mature slaughter cows

Strip loins from 354 female bovine carcasses, selected to represent 30 skeletal maturity (A, B, C, D, and E) x marbling score (SA/MA/AB, MD, MT, SM, SL, and TR/PD) subclasses, were used to evaluate current and alternative systems for classifying cow carcasses into expected-palatability groups. Strip loins were vacuum-packaged, stored for 14 d postmortem at 2 degrees C, and frozen (-27 degrees C). Five steaks from each strip loin, each cooked to a different internal temperature (60, 66, 71, 77, or 82 degrees C), were used for shear force determinations. Two steaks from each strip loin, one cooked to 66 degrees C and the other to 77 degrees C, were used for sensory evaluation. Increased carcass maturity was associated with decreased tenderness and juiciness, increased flavor intensity, and a higher incidence of flavors described as "painty," "fishy," and "grassy." Position of a carcass within a maturity group had a negligible effect on palatability. Increased marbling was associated with greater tenderness and juiciness, a lower incidence of steaks with a "grassy" flavor, and a higher incidence of steaks with a flavor described as "fatty." Relationships between marbling and beef palatability traits were consistent across all maturity groups. Carcasses of maturities A through E were most effectively stratified according to differences in palatability when marbling scores were grouped as follows: 1) MD and higher; 2) SL, SM, MT; and 3) TR/PD. Among mature (C, D, and E maturity) carcasses, yellow-colored fat was associated with greater beef toughness and higher detection rates for "grassy" and "fishy" flavors. Higher end-point temperatures were associated with higher shear force values and lower ratings for muscle fiber tenderness, connective tissue amount, overall tenderness, and juiciness. Two alternative grading approaches (one involving current quality grading factors and the other involving the use of fat color as an additional grade factor) were developed for possible use in classification of cow carcasses into expected-palatability groups. Both alternative systems provided a more effective stratification of cow carcasses according to palatability differences than did the current USDA quality grading system.     

Testing the theory of relative defect proneness for closed-source software

Recent studies on open-source software (OSS) products report that smaller modules are proportionally more defect prone compared to larger ones. This phenomenon, referred to as the Theory of Relative Defect Proneness (RDP), challenges the traditional QA approaches that give a higher priority to larger modules, and it attracts growing interest from closed-source software (CSS) practitioners. In this paper, we report the findings of a study where we tested the theory of RDP using ten CSS products. The results clearly confirm the theory of RDP. We also demonstrate the useful practical implications of this theory in terms of defect-detection effectiveness. Therefore, this study does not only make research contributions by rigorously testing a scientific theory for a different category of software products, but also provides useful insights and evidence to practitioners for revising their existing QA practices.     

MLiT: mixtures of Gaussians under linear transformations

The curse of dimensionality hinders the effectiveness of density estimation in high dimensional spaces. Many techniques have been proposed in the past to discover embedded, locally linear manifolds of lower dimensionality, including the mixture of principal component analyzers, the mixture of probabilistic principal component analyzers and the mixture of factor analyzers. In this paper, we propose a novel mixture model for reducing dimensionality based on a linear transformation which is not restricted to be orthogonal nor aligned along the principal directions. For experimental validation, we have used the proposed model for classification of five “hard” data sets and compared its accuracy with that of other popular classifiers. The performance of the proposed method has outperformed that of the mixture of probabilistic principal component analyzers on four out of the five compared data sets with improvements ranging from 0.5 to 3.2%. Moreover, on all data sets, the accuracy achieved by the proposed method outperformed that of the Gaussian mixture model with improvements ranging from 0.2 to 3.4%.     

The unique relationship between swell percent and swell pressure of compacted clays

Expansive soils exhibit high volumetric deformations, posing a serious threat to the stability of structures and foundations. However, measurement of swelling properties is time consuming and requires special and expensive equipment. This study made an attempt to investigate the relationship between these parameters and easily obtained soil properties using various clay mineral mixtures to obtain soils in a wide range of plasticity indices. Free swell percent was correlated to clay percent, water content, dry unit weight, plasticity index, liquidity index and cation exchange capacity using multiple regression analyses. A very high (R = 0.94) fit was also found for a proposed relationship between the percent swell and swell pressure values for samples having a swell pressure ≤300 kPa. It is concluded that the proposed equations offer a rapid and inexpensive substitute for laboratory testing of swell percent/swell pressure in the preliminary stages of site investigations.