[A PhD completed. Predictability and long-term effects of MAD treatment of obstructive sleep apnea]. / Serie: Hora est. Voorspelbaarheid en langetermijneffecten van MRA-behandeling bij obstructieve slaapapneu.

Obstructive sleep apnea is a sleep-related breathing disorder, characterized by repetitive obstruction of the upper airway during sleep. Obstructive sleep apnea can be treated with a mandibular advancement device (MAD), which advances the mandibula into a forward position, thus preventing obstruction of the upper airway. Different MAD designs are available, however, clinically significant differences in effectiveness have not been found. Besides this, a randomized crossover study found the effectiveness of a new 'boil and bite' MAD to be equal to that of the custom MAD. After a 10-year follow-up, too, the MAD has been proven to be a successful treatment option. However, attention must be paid to minimalizing dental side effects, such as tooth repositioning.

Rok1p is a putative RNA helicase required for rRNA processing.

The synthesis of ribosomes involves many small nucleolar ribonucleoprotein particles (snoRNPs) as transacting factors. Yeast strains lacking the snoRNA, snR10, are viable but are impaired in growth and delayed in the early pre-rRNA cleavages at sites A0, A1, and A2, which lead to the synthesis of 18S rRNA. The same cleavages are inhibited by genetic depletion of the essential snoRNP protein Gar1p. Screens for mutations showing synthetic lethality with deletion of the SNR10 gene or with a temperature-sensitive gar1 allele both identified the ROK1 gene, encoding a putative, ATP-dependent RNA helicase of the DEAD-box family. The ROK1 gene is essential for viability, and depletion of Rok1p inhibits pre-rRNA processing at sites A0, A1, and A2, thereby blocking 18S rRNA synthesis. Indirect immunofluorescence by using a ProtA-Rok1p construct shows the protein to be predominantly nucleolar. These results suggest that Rok1p is required for the function of the snoRNP complex carrying out the early pre-rRNA cleavage reactions.

A system for the analysis of yeast ribosomal DNA mutations.

To develop a system for the analysis of eucaryotic ribosomal DNA (rDNA) mutations, we cloned a complete, transcriptionally active rDNA unit from the yeast Saccharomyces cerevisiae on a centromere-containing yeast plasmid. To distinguish the plasmid-derived ribosomal transcripts from those encoded by the rDNA locus, we inserted a tag of 18 base pairs within the first expansion segment of domain I of the 26S rRNA gene. We demonstrate that this insertion behaves as a neutral mutation since tagged 26S rRNA is normally processed and assembled into functional ribosomal subunits. This system allows us to study the effect of subsequent mutations within the tagged rDNA unit on the biosynthesis and function of the rRNA. As a first application, we wanted to ascertain whether the assembly of a 60S subunit is dependent on the presence in cis of an intact 17S rRNA gene. We found that a deletion of two-thirds of the 17S rRNA gene has no effect on the accumulation of active 60S subunits derived from the same operon. On the other hand, deletions within the second domain of the 26S rRNA gene completely abolished the accumulation of mature 26S rRNA.

Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes.

We have measured the removal of UV-induced pyrimidine dimers from DNA fragments of the adenosine deaminase (ADA) and dihydrofolate reductase (DHFR) genes in primary normal human and xeroderma pigmentosum complementation group C (XP-C) cells. Using strand-specific probes, we show that in normal cells, preferential repair of the 5' part of the ADA gene is due to the rapid and efficient repair of the transcribed strand. Within 8 h after irradiation with UV at 10 J m-2, 70% of the pyrimidine dimers in this strand are removed. The nontranscribed strand is repaired at a much slower rate, with 30% dimers removed after 8 h. Repair of the transcribed strand in XP-C cells occurs at a rate indistinguishable from that in normal cells, but the nontranscribed strand is not repaired significantly in these cells. Similar results were obtained for the DHFR gene. In the 3' part of the ADA gene, however, both normal and XP-C cells perform fast and efficient repair of either strand, which is likely to be caused by the presence of transcription units on both strands. The factor defective in XP-C cells is apparently involved in the processing of DNA damage in inactive parts of the genome, including nontranscribed strands of active genes. These findings have important implications for the understanding of the mechanism of UV-induced excision repair and mutagenesis in mammalian cells.

All three functional domains of the large ribosomal subunit protein L25 are required for both early and late pre-rRNA processing steps in Saccharomyces cerevisiae.

Mutational analysis has shown that the integrity of the region in domain III of 25S rRNA that is involved in binding of ribosomal protein L25 is essential for the production of mature 25S rRNA in the yeast Saccharomyces cerevisiae. However, even structural alterations that do not noticeably affect recognition by L25, as measured by an in vitro assay, strongly reduced 25S rRNA formation by inhibiting the removal of ITS2 from the 27S(B) precursor. In order to analyze the role of L25 in yeast pre-rRNA processing further we studied the effect of genetic depletion of the protein or mutation of each of its three previously identified functional domains, involved in nuclear import (N-terminal), RNA binding (central) and 60S subunit assembly (C-terminal), respectively. Depletion of L25 or mutating its (pre-)rRNA-binding domain blocked conversion of the 27S(B) precursor to 5.8S/25S rRNA, confirming that assembly of L25 is essential for ITS2 processing. However, mutations in either the N- or the C-terminal domain of L25, which only marginally affect its ability to bind to (pre-)rRNA, also resulted in defective ITS2 processing. Furthermore, in all cases there was a notable reduction in the efficiency of processing at the early cleavage sites A0, A1 and A2. We conclude that the assembly of L25 is necessary but not sufficient for removal of ITS2, as well as for fully efficient cleavage at the early sites. Additional elements located in the N- as well as C-terminal domains of L25 are required for both aspects of pre-rRNA processing.

Rat RL23a ribosomal protein efficiently competes with its Saccharomyces cerevisiae L25 homologue for assembly into 60 S subunits.

The large subunit protein RL23a from rat liver ribosomes shows 62% sequence identity with the primary rRNA-binding ribosomal protein L25 from Saccharomyces cerevisiae. In vitro binding studies indicated that both r-proteins are able to recognise the L25 binding site on yeast 25 S rRNA and its structural homologue on mammalian 28 S rRNA with equal efficiency. To determine whether the two r-proteins are also functionally equivalent in vivo, a single plasmid-borne copy of either the wild-type L25 gene or the RL23a cDNA, driven by the L25 promoter, was introduced into a yeast strain in which the chromosomal L25 gene is under control of the glucose-repressible GALI-10 promoter. No difference in growth rate could be detected between the two types of transformants when cultured on glucose-based medium. In cells that co-express epitope-tagged versions of L25 and RL23a from single-copy genes, approximately 35% of the 60 S subunits contained the heterologous protein as determined by Western analysis. This value could be increased to 55% by overexpressing RL23a using a multi-copy plasmid. These data demonstrate that rat RL23a can act as a highly efficient substitute for its yeast counterpart in the assembly of functional yeast ribosomes even in the presence of the endogenous L25 protein.

Mutational analysis of the C-terminal region of Saccharomyces cerevisiae ribosomal protein L25 in vitro and in vivo demonstrates the presence of two distinct functional elements.

A previous analysis of yeast ribosomal protein L25 implicated an evolutionarily conserved motif of seven amino acids near the C terminus (positions 120 to 126) in specific binding of the protein to domain III of 26 S rRNA. We analyzed the effect of various point mutations in this amino acid sequence on the capacity of the protein to interact in vitro with its binding site on the rRNA. Most of the mutations tested, including some conservative replacements, strongly reduced or abolished rRNA binding, further supporting a pivotal role for the motif in the specific interaction between L25 and 26 S rRNA. We have also determined the ability of the various mutant L25 species to complement in vivo for the absence of wild-type protein in cells that conditionally express the chromosomal L25 gene. Surprisingly, up to a fivefold reduction in the in vitro binding capacity of L25 is tolerated without affecting the ability of the mutant protein to support (virtually) wild-type rates of 60 S subunit formation and cell growth. Mutations that completely abolish recognition of 26 S rRNA, however, block the formation of 60 S particles, demonstrating that binding of L25 to this rRNA is an essential step in the assembly of the large ribosomal subunit. Using the same combination of approaches we identified an element, located between positions 133 and 139, that is indispensable for the ability of L25 to support a normal rate of 60 S subunit formation, but plays a relatively minor role in determining the rRNA-binding capacity of the protein. In particular, the presence of a hydrophobic amino acid at position 135 was found to be highly important. These results indicate that the element in question is crucial for a step in the assembly of the 60 S subunit subsequent to association of L25 with 26 S rRNA.

Evolutionarily conserved structural elements are critical for processing of Internal Transcribed Spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA.

Structural features of Internal Transcribed Spacer 2 (ITS2) important for the correct and efficient removal of this spacer from Saccharomyces cerevisiae pre-rRNA were identified by in vivo mutational analysis based upon phylogenetic comparison with its counterparts from four different yeast species. Compatibility between ITS2 structure and the S. cerevisiae processing machinery was found to have been maintained over only a short evolutionary distance, in contrast to the situation for ITS1. Nevertheless, cis-acting elements required for correct and efficient processing are confined predominantly to those regions of the spacer that show the highest degree of evolutionary conservation. Mutation or deletion of each of these regions severely reduced production of mature 26 S, but not 17 S rRNA, mainly by impeding processing of the 29 SB precursor. In some cases, however, conversion of 29SA into 29 SB pre-rRNA also appeared to be affected. Deletion of non-conserved segments, on the other hand, caused little or no disturbance in processing. Surprisingly, some combinations of such individually neutral deletions had a severe negative effect on the removal of ITS2, suggesting a requirement for a higher-order structure of ITS2. Finally, even structural alterations of ITS2 that did not noticeably affect processing, significantly reduced the growth rate of cells that exclusively express the mutant rDNA units. We take this as further evidence for a direct role of ITS2 in the formation of fully functional 60 S ribosomal subunits.

Domain III of Saccharomyces cerevisiae 25 S ribosomal RNA: its role in binding of ribosomal protein L25 and 60 S subunit formation.

Domain III of Saccharomyces cerevisiae 25 S rRNA contains the recognition site for the primary rRNA-binding ribosomal protein L25, which belongs to the functionally conserved EL23/L25 family of ribosomal proteins. The EL23/L25 binding region is very complex, consisting of several irregular helices held together by long-distance secondary and tertiary interactions. Moreover, it contains the eukaryote-specific V9 (D7a) expansion segment. Functional characterisation of the structural elements of this site by a detailed in vitro and in vivo mutational analysis indicates the presence of two separate regions that are directly involved in L25 binding. In particular, mutation of either of two conserved nucleotides in the loop of helix 49 significantly reduces in vitro L25 binding, thus strongly supporting their role as attachment sites for the r-protein. Two other helices appear to be primarily required for the correct folding of the binding site. Mutations that abolish in vitro binding of L25 block accumulation of 25 S rRNA in vivo because they stall pre-rRNA processing at the level of its immediate precursor, the 27 S(B) pre-rRNA. Surprisingly, several mutations that do not significantly affect L25 binding in vitro cause the same lethal defect in 27 S(B) pre-rRNA processing. Deletion of the V9 expansion segment also leads to under-accumulation of mature 25 S rRNA and a twofold reduction in growth rate. We conclude that an intact domain III, including the V9 expansion segment, is essential for normal processing and assembly of 25 S rRNA.

The inheritance of chilling tolerance in tomato (Lycopersicon spp.).

During the past 25 years, chilling tolerance of the cultivated (chilling-sensitive) tomato Lycopersicon esculentum and its wild, chilling-tolerant relatives L. peruvianum and L. hirsutum (and, less intensively studied, L. chilense) has been the object of several investigations. The final aim of these studies can be seen in the increase in chilling tolerance of the cultivated genotypes. In this review, we will focus on low-temperature effects on photosynthesis and the inheritance of these traits to the offspring of various breeding attempts. While crossing L. peruvianum (male symbol) to L. esculentum (female symbol) so far has brought the most detailed insight with respect to physiological questions, for practical purposes, e.g., the readily cross ability, crossing programmes with L. hirsutum as pollen donor at present seem to be a promising way to achieve higher chilling-tolerant genotypes of the cultivated tomato. This perspective is due to the progress that has been made with respect to the genetic basis of chilling tolerance of Lycopersicon spp. over the past five years.

Hierarchies of DNA repair in mammalian cells: biological consequences.

Mammalian cells exposed to genotoxic agents exhibit heterogeneous levels of repair of certain types of DNA damage in various genomic regions. For UV-induced cyclobutane pyrimidine dimers we propose that at least three levels of repair exist: (1) slow repair of inactive (X-chromosomal) genes, (2) fast repair of active housekeeping genes, and (3) accelerated repair of the transcribed strand of active genes. These hierarchies of repair may be related to chromosomal banding patterns as obtained by Giemsa staining. The possible consequences of defective DNA repair in one or more of these levels may be manifested in different clinical features associated with UV-sensitive human syndromes. Moreover, molecular analysis of hprt mutations reveals that mutations are primarily generated by DNA damage in the poorly repaired non-transcribed strand of the gene.

(6-4) photoproducts and not cyclobutane pyrimidine dimers are the main UV-induced mutagenic lesions in Chinese hamster cells.

A partial revertant (RH1-26) of the UV-sensitive Chinese hamster V79 cell mutant V-H1 (complementation group 2) was isolated and characterized. It was used to analyze the mutagenic potency of the 2 major UV-induced lesions, cyclobutane pyrimidine dimers and (6-4) photoproducts. Both V-H1 and RH1-26 did not repair pyrimidine dimers measured in the genome overall as well as in the active hprt gene. Repair of (6-4) photoproducts from the genome overall was slower in V-H1 than in wild-type V79 cells, but was restored to normal in RH1-26. Although V-H1 cells have a 7-fold enhanced mutagenicity, RH1-26 cells, despite the absence of pyrimidine dimer repair, have a slightly lower level of UV-induced mutagenesis than observed in wild-type V79 cells. The molecular nature of hprt mutations and the DNA-strand specificity were similar in V79 and RH1-26 cells but different from that of V-H1 cells. Since in RH1-26 as well as in V79 cells most hprt mutations were induced by lesions in the non-transcribed DNA strand, in contrast to the transcribed DNA strand in V-H1, the observed mutation-strand bias suggests that normally (6-4) photoproducts are preferentially repaired in the transcribed DNA strand. The dramatic influence of the impaired (6-4) photoproduct repair in V-H1 on UV-induced mutability and the molecular nature of hprt mutations indicate that the (6-4) photoproduct is the main UV-induced mutagenic lesion.

Ibuprofen: plasma concentrations in man.

The plasma levels of ibuprofen were measured in five healthy subjects who took 600 mg tablets of ibuprofen twice daily, three times daily and four times daily in a crossover study. Peak plasma levels were obtained 1 hour after the first dose in all but one subject (slow absorber), the mean peak value being 51.3 micrograms X ml-1 (range 39.4-63.7 micrograms X ml-1). After the repeated dose regimens of two, three or four times daily of ibuprofen, the peak levels achieved were in a similar range to those seen after the first dose: Twice daily 39.4-66.4 micrograms X ml-1; Three times daily 43.6-63.3 micrograms X ml-1; Four times daily 44.1-58.4 micrograms X ml-1. There was no evidence of accumulation of the drug and no side-effects occurred during the trial.

Relationship between DNA-adduct formation, DNA repair, mutation frequency and mutation spectra.

DNA-adduct formation by a series of ethylating agents was determined and correlated with induction of gene mutations. This approach gave information concerning the DNA-adduct(s) likely to be responsible for the observed mutations. A methodology has been developed which is used for the DNA sequence analysis of point mutations in the HPRT gene of mammalian cells. This method can be used to obtain mutation spectra and to determine whether the base-pair changes do occur at those sites where DNA-adducts are likely to occur. Measurements of DNA repair in specific DNA sequences show that actively transcribed genes are repaired faster than the genome overall. This stresses the importance of studying removal DNA-adducts in the gene that is used for the analysis of mutation induction.

Ribosome synthesis in Saccharomyces cerevisiae.

The synthesis of ribosomes is one of the major metabolic pathways in all cells. In addition to around 75 individual ribosomal proteins and 4 ribosomal RNAs, synthesis of a functional eukaryotic ribosome requires a remarkable number of trans-acting factors. Here, we will discuss the recent, and often surprising, advances in our understanding of ribosome synthesis in the yeast Saccharomyces cerevisiae. These will underscore the unexpected complexity of eukaryotic ribosome synthesis.

RRP5 is required for formation of both 18S and 5.8S rRNA in yeast.

Three of the four eukaryotic ribosomal RNA molecules (18S, 5.8S and 25-28S) are synthesized as a single precursor which is subsequently processed into the mature rRNAs by a complex series of cleavage and modification reactions. In the yeast Saccharomyces cerevisiae, the early pre-rRNA cleavages at sites A0, A1 and A2, required for the synthesis of 18S rRNA, are inhibited in strains lacking RNA or protein components of the U3, U14, snR10 and snR30 small nucleolar ribonucleoproteins (snoRNPs). The subsequent cleavage at site A3, required for formation of the major, short form of 5.8S rRNA, is carried out by another ribonucleoprotein, RNase MRP. A screen for mutations showing synthetic lethality with deletion of the non-essential snoRNA, snR10, identified a novel gene, RRP5, which is essential for viability and encodes a 193 kDa nucleolar protein. Genetic depletion of Rrp5p inhibits the synthesis of 18S rRNA and, unexpectedly, also of the major short form of 5.8S rRNA. Pre-rRNA processing is concomitantly impaired at sites A0, A1, A2 and A3. This distinctive phenotype makes Rrp5p the first cellular component simultaneously required for the snoRNP-dependent cleavage at sites A0, A1 and A2 and the RNase MRP-dependent cleavage at A3 and provides evidence for a close interconnection between these processing events. Putative RRP5 homologues from Caenorhabditis elegans and humans were also identified, suggesting that the critical function of Rrp5p is evolutionarily conserved.

Processing of pre-ribosomal RNA in Saccharomyces cerevisiae.

Post-transcriptional processing of precursor-ribosomal RNA comprises a complex pathway of endonucleolytic cleavages, exonucleolytic digestion and covalent modifications. The general order of the various processing steps is well conserved in eukaryotic cells, but the underlying mechanisms are largely unknown. Recent analysis of pre-rRNA processing, mainly in the yeast Saccharomyces cerevisiae, has significantly improved our understanding of this important cellular activity. Here we will review the data that have led to our current picture of yeast pre-rRNA processing.