Lack of pseudouridine 38/39 in the anticodon arm of yeast cytoplasmic tRNA decreases in vivo recoding efficiency

Many different modified nucleotides are found in naturally occurring tRNA, especially in the anticodon region. Their importance for the efficiency of the translational process begins to be well documented. Here we have analyzed the in vivo effect of deleting genes coding for yeast tRNA-modifying enzymes, namely Pus1p, Pus3p, Pus4p, or Trm4p, on termination readthrough and +1 frameshift events. To this end, we have transformed each of the yeast deletion strains with a lacZ-luc dual-reporter vector harboring selected programmed recoding sites. We have found that only deletion of the PUS3 gene, encoding the enzyme that introduces pseudouridines at position 38 or 39 in tRNA, has an effect on the efficiency of the translation process. In this mutant, we have observed a reduced readthrough efficiency of each stop codon by natural nonsense suppressor tRNAs. This effect is solely due to the absence of pseudouridine 38 or 39 in tRNA because the inactive mutant protein Pus3[D151A]p did not restore the level of natural readthrough. Our results also show that absence of pseudouridine 39 in the slippery tRNA(UAG)(Leu) reduces +1 frameshift efficiency. Therefore, the presence of pseudouridine 38 or 39 in the tRNA anticodon arm enhances misreading of certain codons by natural nonsense tRNAs as well as promotes frameshifting on slippery sequences in yeast.     

A P-stable exponentially-fitted method for the numerical integration of the Schrödinger equation

In this paper we present a P-stable exponentially-fitted four-step method for the numerical integration of the radial Schrödinger equation. More specifically we present a method than satisfies the property of P-stability and also integrates exactly any linear combination of the functions {1, x, exp( ± w x), x exp( ± w x), x ²exp( ± w x)}. We tested the efficiency of our newly developed scheme against well known methods, with excellent results. The numerical illustration showed that our method is considerably more efficient compared to well‐known methods used for the numerical integration of resonance problem of the radial Schrödinger equation.     

Fractionation of proteins and carbohydrates of extracellular polymeric substances in a membrane bioreactor system

The major operational problem associated with membrane bioreactors (MBR) is membrane fouling, for which extracellular polymeric substances (EPS) are primarily responsible. In this work both the soluble and bound EPS (i.e. SMP and EPS) produced in an MBR system operating under sludge retention times (SRT) of 10, 15, 20 and 33 days were fractionized by means of membranes having variable molecular weight cutoffs (300 kDa, 100 kDa, 10 kDa & 1 kDa). The results show that increasing the SRT leads to a reduction of SMP and EPS and that these reductions are more pronounced for the SRTs in the range 10–20 days. This reduction is more significant for carbohydrates than for proteins. The decrease of SMP and EPS with increasing SRT from 10 to 20 days led to a significant decrease of the level of fouling. The further increase of SRT to 33 days did not significantly impact on the level of fouling as the SMP and EPS concentrations did not change much.     

Yeast Los1p Has Properties of an Exportin-Like Nucleocytoplasmic Transport Factor for tRNA

Saccharomyces cerevisiae Los1p, which is genetically linked to the nuclear pore protein Nsp1p and several tRNA biogenesis factors, was recently grouped into the family of importin/karyopherin-β-like proteins on the basis of its sequence similarity. In a two-hybrid screen, we identified Nup2p as a nucleoporin interacting with Los1p. Subsequent purification of Los1p from yeast demonstrates its physical association not only with Nup2p but also with Nsp1p. By the use of the Gsp1p-G21V mutant, Los1p was shown to preferentially bind to the GTP-bound form of yeast Ran. Furthermore, overexpression of full-length or N-terminally truncated Los1p was shown to have dominant-negative effects on cell growth and different nuclear export pathways. Finally, Los1p could interact with Gsp1p-GTP, but only in the presence of tRNA, as revealed in an indirect in vitro binding assay. These data confirm the homology between Los1p and the recently identified human exportin for tRNA and reinforce the possibility of a role for Los1p in nuclear export of tRNA in yeast.     

A modified phase-fitted and amplification-fitted Runge-Kutta-Nyström method for the numerical solution of the radial Schrödinger equation

A new Runge-Kutta-Nyström method, with phase-lag and amplification error of order infinity, for the numerical solution of the Schrödinger equation is developed in this paper. The new method is based on the Runge-Kutta-Nyström method with fourth algebraic order, developed by Dormand, El-Mikkawy and Prince. Numerical illustrations indicate that the new method is much more efficient than other methods derived for the same purpose.     

Intra-peritoneal application of catechins and EGCG as in vivo inhibitors of ozone-induced oxidative stress

Oxidative stress is considered as a prominent feature of many acute and chronic diseases as well as of the normal aging process. We examined the effects of intra-peritoneal administration of catechins and EGCG as in vivo inhibitors of oxidative stress induced by ozone administration in two groups of Wistar rats. The first group was treated by intra-peritoneal administration of catechins and EGCG after the administration of ozone and the second group was pretreated by intra-peritoneal administration of catechins and EGCG prior to ozone administration. We determined in blood the activity of the enzymes superoxide dismutase and glutathione peroxidase, total antioxidant capacity, levels of copper and zinc and in urine malonaldehyde contents. Ozone administration resulted in significant reduction of glutathione peroxidase activity, plasma zinc levels and plasma and Red Blood Cells antioxidant capacity. Catechins and EGCG upregulate superoxide dismutase activity and maintain plasma and Red Blood Cells antioxidant capacity. Malonaldehyde levels at the end of the study were significantly increased only in the first group. Our data demonstrate that treatment with catechins and EGCG cannot reverse or prevent the effects of oxidative stress although some modulation occurs.     

Transfer RNA biogenesis: A visa to leave the nucleus

Only correctly folded and mature tRNAs can leave the nucleus and enter the cytoplasm. Surprisingly, tRNA-aminoacylation has been found to occur, not only in the cytosol, but also inside the nucleus, where it may act as an additional proofreading step and facilitate the export of 'ready-to-function' aminoacyl-tRNAs.