Subspecies-specific distribution of intervening sequences in the Bacillus subtilis prophage ribonucleotide reductase genes

A collection of 212 gram-positive bacilli isolated from natural habitats was screened for the presence of intervening sequences (introns and intein-coding sequences) in the SPbeta prophage-related ribonucleotide reductase genes bnrdE and bnrdF. Three novel configurations were identified on the basis of the presence of (i) intervening sequences in bnrdE and bnrdF, and (ii) an ORF in the bnrdE-bnrdF spacer. Analysis of the cell wall genetic determinants as well as of the incorporation of radio-labelled glycerol into cell wall allowed newly and previously identified B. subtilis strains with different configurations of bnrdE/bnrdF intervening sequences to be assigned to one of two subspecies. Strains apparently belonging to the subsp. subtilis contain three intervening sequences many of which are associated with the putative homing endonuclease activity. Strains of the subsp. spizizenii contain only one or two ORF-less group I introns. Introns occupying bnrdF are confined to the subspecies subtilis.     

Performance analysis of MPI collective operations

Previous studies of application usage show that the performance of collective communications are critical for high-performance computing. Despite active research in the field, both general and feasible solution to the optimization of collective communication problem is still missing. In this paper, we analyze and attempt to improve intra-cluster collective communication in the context of the widely deployed MPI programming paradigm by extending accepted models of point-to-point communication, such as Hockney, LogP/LogGP, and PLogP, to collective operations. We compare the predictions from models against the experimentally gathered data and using these results, construct optimal decision function for broadcast collective. We quantitatively compare the quality of the model-based decision functions to the experimentally-optimal one. Additionally, in this work, we also introduce a new form of an optimized tree-based broadcast algorithm, splitted-binary. Our results show that all of the models can provide useful insights into various aspects of the different algorithms as well as their relative performance. Still, based on our findings, we believe that the complete reliance on models would not yield optimal results. In addition, our experimental results have identified the gap parameter as being the most critical for accurate modeling of both the classical point-to-point-based pipeline and our extensions to fan-out topologies.

Alchemilla viridiflora Rothm.: the potent natural inhibitor of angiotensin I-converting enzyme

Molecular and Cellular Biochemistry - Alchemilla viridiflora Rothm., Rosaceae is a herbaceous plant widespread in central Greece, Bulgaria, North Macedonia and Serbia with Kosovo. Liquid...     

In Vitro Reassembly of the Ribose ATP-binding Cassette Transporter Reveals a Distinct Set of Transport Complexes

Bacterial ATP-binding cassette (ABC) importers are primary active transporters that are critical for nutrient uptake. Based on structural and functional studies, ABC importers can be divided into two distinct classes, type I and type II. Type I importers follow a strict alternating access mechanism that is driven by the presence of the substrate. Type II importers accept substrates in a nucleotide-free state, with hydrolysis driving an inward facing conformation. The ribose transporter in Escherichia coli is a tripartite complex consisting of a cytoplasmic ATP-binding cassette protein, RbsA, with fused nucleotide binding domains; a transmembrane domain homodimer, RbsC₂; and a periplasmic substrate binding protein, RbsB. To investigate the transport mechanism of the complex RbsABC₂, we probed intersubunit interactions by varying the presence of the substrate ribose and the hydrolysis cofactors, ATP/ADP and Mg²⁺. We were able to purify a full complex, RbsABC₂, in the presence of stable, transition state mimics (ATP, Mg²⁺, and VO₄); a RbsAC complex in the presence of ADP and Mg²⁺; and a heretofore unobserved RbsBC complex in the absence of cofactors. The presence of excess ribose also destabilized complex formation between RbsB and RbsC. These observations suggest that RbsABC₂ shares functional traits with both type I and type II importers, as well as possessing unique features, and employs a distinct mechanism relative to other ABC transporters.     

An Investigation into the Influence of Experimental Conditions on <Emphasis Type="Italic">In Vitro</Emphasis> Drug Release from Immediate-Release Tablets of Levothyroxine Sodium and Its Relation to Oral Bioavailability

The aim of this study was to investigate the influence of experimental conditions on levothyroxine sodium release from two immediate-release tablet formulations which narrowly passed the standard requirements for bioequivalence studies. The in vivo study was conducted as randomised, single-dose, two-way cross-over pharmacokinetic study in 24 healthy subjects. The in vitro study was performed using various dissolution media, and obtained dissolution profiles were compared using the similarity factor value. Drug solubility in different media was also determined. The in vivo results showed narrowly passing bioequivalence. Considering that levothyroxine sodium is classified as Class III drug according to the Biopharmaceutics Classification System, drug bioavailability will be less sensitive to the variation in its dissolution characteristics and it can be assumed that the differences observed in vitro in some of investigated media probably do not have significant influence on the absorption process, as long as rapid and complete dissolution exists. The study results indicate that the current regulatory criteria for the value of similarity factor in comparative dissolution testing, as well as request for very rapid dissolution (more than 85% of drug dissolved in 15 min), are very restricted for immediate-release dosage forms containing highly soluble drug substance and need further investigation. The obtained results also add to the existing debate on the appropriateness of the current bioequivalence standards for levothyroxine sodium products.     

Deficiency of a Niemann-Pick, type C1-related protein in toxoplasma is associated with multiple lipidoses and increased pathogenicity

Several proteins that play key roles in cholesterol synthesis, regulation, trafficking and signaling are united by sharing the phylogenetically conserved 'sterol-sensing domain' (SSD). The intracellular parasite Toxoplasma possesses at least one gene coding for a protein containing the canonical SSD. We investigated the role of this protein to provide information on lipid regulatory mechanisms in the parasite. The protein sequence predicts an uncharacterized Niemann-Pick, type C1-related protein (NPC1) with significant identity to human NPC1, and it contains many residues implicated in human NPC disease. We named this NPC1-related protein, TgNCR1. Mammalian NPC1 localizes to endo-lysosomes and promotes the movement of sterols and sphingolipids across the membranes of these organelles. Miscoding patient mutations in NPC1 cause overloading of these lipids in endo-lysosomes. TgNCR1, however, lacks endosomal targeting signals, and localizes to flattened vesicles beneath the plasma membrane of Toxoplasma. When expressed in mammalian NPC1 mutant cells and properly addressed to endo-lysosomes, TgNCR1 restores cholesterol and GM1 clearance from these organelles. To clarify the role of TgNCR1 in the parasite, we genetically disrupted NCR1; mutant parasites were viable. Quantitative lipidomic analyses on the ΔNCR1 strain reveal normal cholesterol levels but an overaccumulation of several species of cholesteryl esters, sphingomyelins and ceramides. ΔNCR1 parasites are also characterized by abundant storage lipid bodies and long membranous tubules derived from their parasitophorous vacuoles. Interestingly, these mutants can generate multiple daughters per single mother cell at high frequencies, allowing fast replication in vitro, and they are slightly more virulent in mice than the parental strain. These data suggest that the ΔNCR1 strain has lost the ability to control the intracellular levels of several lipids, which subsequently results in the stimulation of lipid storage, membrane biosynthesis and parasite division. Based on these observations, we ascribe a role for TgNCR1 in lipid homeostasis in Toxoplasma.     

Oxidative stress biomarker monitoring in elite women volleyball athletes during a 6-week training period

The objectives of this study were to determine (a) if reactive oxygen metabolites (ROMs) are a reliable parameter for monitoring oxidative stress in athletes alone or in association with other parameters of oxidative stress and depending on whether antioxidant supplements are taken or not; (b) the level of oxidative stress in athletes before the competition season; and (c) if oxidative status could be improved in volleyball athletes. Sixteen women athletes (supplemented group) received an antioxidant cocktail containing vitamin E, vitamin C, zinc gluconate, and selenium as a dietary supplement during a 6-week training period, whereas 12 of them (control group) received no dietary supplement. Blood samples were taken before and after the training period. The following parameters were measured: ROMs, superoxide anion (O2??), malondialdehyde (MDA), advanced oxidation protein products (AOPP), lipid hydroperoxide (LOOH), biological antioxidative potential (BAP), paraoxonase activity toward paraoxon (POase) and diazoxon (DZOase), superoxide dismutase(SOD), total sulfydryl group concentration (SH groups), and lipid status. Reactive oxygen metabolites were taken as the dependent variable and MDA, O2??, AOPP, and LOOH as independent variables. In the group of athletes who have received supplementation, linear regression analysis revealed that the implemented model had a lower influence on dROMs (70.4 vs. 27.9%) after the training period. The general linear model showed significant differences between parameters before and after training/supplementation (Wilks' lambda = 0.074, F = 11.76, p < 0.01). At the partial level, significant increases in ROM levels (p <0.05, 95% confidence interval [CI]: 286-337), SOD activity (CI: 113-144), and BAP (CI: 2,388-2,580) (p < 0.01) were observed. The association between ROMs and other parameters of oxidative stress was reduced in athletes who received supplements. During the precompetition training period, treatment with dietary supplements prevented the depletion of antioxidative defense in volleyball athletes.     

Kinesin molecular motor Eg5 functions during polypeptide synthesis

The kinesin-related molecular motor Eg5 plays roles in cell division, promoting spindle assembly. We show that during interphase Eg5 is associated with ribosomes and is required for optimal nascent polypeptide synthesis. When Eg5 was inhibited, ribosomes no longer bound to microtubules in vitro, ribosome transit rates slowed, and polysomes accumulated in intact cells, suggesting defects in elongation or termination during polypeptide synthesis. These results demonstrate that the molecular motor Eg5 associates with ribosomes and enhances the efficiency of translation.