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Nonsense-mediated mRNA decay (NMD) is an essential eukaryotic process regulating transcript quality and abundance, and is involved in diverse processes including brain development and plant defenses. Although some of the NMD machinery is conserved between kingdoms, little is known about its evolution. Phosphorylation of the core NMD component UPF1 is critical for NMD and is regulated in mammals by the SURF complex (UPF1, SMG1 kinase, SMG8, SMG9 and eukaryotic release factors). However, since SMG1 is reportedly missing from the genomes of fungi and the plant Arabidopsis thaliana, it remains unclear how UPF1 is activated outside the metazoa. We used comparative genomics to determine the conservation of the NMD pathway across eukaryotic evolution. We show that SURF components are present in all major eukaryotic lineages, including fungi, suggesting that in addition to UPF1 and SMG1, SMG8 and SMG9 also existed in the last eukaryotic common ancestor, 1.8 billion years ago. However, despite the ancient origins of the SURF complex, we also found that SURF factors have been independently lost across the Eukarya, pointing to genetic buffering within the essential NMD pathway. We infer an ancient role for SURF in regulating UPF1, and the intriguing possibility of undiscovered NMD regulatory pathways.

Autochthonous microorganisms inhabiting hydrocarbon polluted marine environments play a fundamental role in natural attenuation and constitute promising resources for bioremediation approaches. Alcanivorax spp. members are ubiquitous in contaminated surface waters and are the first to flourish on a wide range of alkanes after an oil-spill. Following oil contamination, a transient community of different Alcanivorax spp. develop, but whether they use a similar physiological, cellular and transcriptomic response to hydrocarbon substrates is unknown. In order to identify which cellular mechanisms are implicated in alkane degradation, we investigated the response of two isolates belonging to different Alcanivorax species, A. dieselolei KS 293 and A. borkumensis SK2 growing on n-dodecane (C12) or on pyruvate. Both strains were equally able to grow on C12 but they activated different strategies to exploit it as carbon and energy source. The membrane morphology and hydrophobicity of SK2 changed remarkably, from neat and hydrophilic on pyruvate to indented and hydrophobic on C12, while no changes were observed in KS 293. In addition, SK2 accumulated a massive amount of intracellular grains when growing on pyruvate, which might constitute a carbon reservoir. Furthermore, SK2 significantly decreased medium surface tension with respect to KS 293 when growing on C12, as a putative result of higher production of biosurfactants. The transcriptomic responses of the two isolates were also highly different. KS 293 changes were relatively balanced when growing on C12 with respect to pyruvate, giving almost the same amount of upregulated (28%), downregulated (37%) and equally regulated (36%) genes, while SK2 transcription was upregulated for most of the genes (81%) when growing on pyruvate when compared to C12. While both strains, having similar genomic background in genes related to hydrocarbon metabolism, retained the same capability to grow on C12, they nevertheless presented very different physiological, cellular and transcriptomic landscapes.

Method and computer system for constructing a decision tree for use in address lookup of a requested address in an address space. The address space is arranged as a set of basic address ranges. Each basic address range is defined by a lower and an upper bound address, and an address in the address space is represented by a predetermined number of bits.

Contains fulltext : 105076.pdf (Publisher’s version ) (Open Access) A. Gerlo Marnixi Epistulae. De briefwisseling van Marnix van Sint-Aldegonde. Een kritische uitgave, delen 1-3 Brussel:Brussel University Press ,1997

Since the initiation of dialysis, nephrologists have sought an index (or indices) for the adequacy of toxic solute removal. This quest has been characterized by a gradual shift in thinking, ending with a preference for dynamic parameters such as clearances normalized for body size (Kt/V). The threshold Kt/V, however, has changed over the years. While present guidelines suggest 1.2 with single-pool kinetics, higher levels might be proposed in the future. In spite of the known relation between Kt/V and survival, the accuracy of this parameter as a representative of the removal of the whole spectrum of compounds that are responsible for uremia is problematic. Kt/V only assesses the removal of a water-soluble compound from the body water through mostly hydrophilic membranes to the dialysate water. Furthermore, the small size of urea means that convective and/or diffusive transfer through a given semipermeable membrane is unlikely to be representative of larger molecules, especially if dialyzers with a small pore size are applied. Urea kinetics are also poorly representative of the removal of small protein-bound molecules and intracellular solutes with cell membrane-limited clearance. Finally, it should be realized that the Kt/V concept has been developed in a specific population, that is, a group of renal failure patients with few comorbidities, submitted to short intermittent hemodialysis with small-pore bioincompatible membranes very likely using dialysate of lower quality than that used today. Kt/V might well become less accurate and useful in predicting outcomes as different dialysis conditions are pursued, such as dialysis with biocompatible and/or large-pore membranes, (ultra) pure dialysate, alternative time frames, high levels of convection, and/or in populations with a different distribution of body mass.

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