Age of diagnosis and evaluation of consequences of submucous cleft palate.

OBJECTIVES: To evaluate the frequency of submucous cleft palate (SMCP) in a group of children with clefts. The reason for suspecting submucous cleft, age of diagnosis, effect of age on speech development, problems in speech, hearing and swallowing were compared with previous literature. METHODS: Retrospective chart review: Out of 33 patients with SMCP, registered by the Groninger cleft team over approximately 20 years (1990 until July 2012), 28 non-syndromic patients with a proven diagnosis of SMCP were included: 17 males and 11 females. Speech and hearing were examined and the number of patients with SMCP and age at time of diagnosis were evaluated. The percentages of problems in resonance, articulation and hearing, present at time of diagnosis, were compared with the percentages of problems found after surgery. RESULTS: Out of 800 patients with clefts, 28 patients (3,5%) were diagnosed with SMCP at a mean age of 3;9 years. All patients presented one or more symptomatic complaints at time of diagnosis: hypernasality (65%), problems in articulation (46%), conductive hearing loss (39%) and/or swallowing problems (32%). A bifid uvula was found in 92%. Following surgery, hypernasal speech and swallowing problems were no longer observed. The articulation problems remained after surgery. Age of diagnosis seems no predictor of articulation problems. An improvement in hearing was observed but normal hearing was not achieved. Pharyngoplasty appeared to be a successful and save treatment of hypernasality. CONCLUSIONS: SMCP is a rare cleft palate which is, despite the presence of a bifid uvula and symptoms of velopharyngeal insufficiency, often diagnosed late. In children with a bifid uvula and mild problems in speech, hearing and swallowing, it is important to be alert to SMCP because SMCP may account for these persistent mild complaints. Therefore, early detecting of SMCP can yield profits.

Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions.

The simian retrovirus-1 (SRV-1) gag-pro frameshift signal was identified in previous work, and the overall structure of the pseudoknot involved was confirmed (ten Dam E, Brierley I, Inglis S, Pleij C, 1994, Nucleic Acids Res 22:2304-2310). Here we report on the importance of specific elements within the pseudoknot. Some mutations in stem S1 that maintain base pairing have reduced frameshift efficiencies. This indicates that base pairing in itself is not sufficient. In contrast, frameshifting correlates qualitatively with the calculated stability of mutations in S2. The stems thus play different roles in the frameshift event. The nature of the base in L1 has little influence on frameshift efficiency. It is however required to bridge S2; deleting it lowers frameshifting from 23 to 9%. In L2, frameshift efficiency was not affected in a mutant that changed 10 to 12 bases. This makes it unlikely that the primary sequence of L2 plays a role in -1 frameshifting, in contrast to readthrough in Moloney murine leukemia virus (Wills N, Gesteland R, Atkins J, 1994, EMBO J 13:4137-4144). Deletions of 2 and 3 bases gave more frameshifting than the wild type, probably reflecting the increased stability of the pseudoknot due to a shorter loop L2. Deleting even more bases reduces frameshifting compared to wild-type levels. At this point, stress will build up in L2, and this will reduce overall pseudoknot stability.

Identification and analysis of the pseudoknot-containing gag-pro ribosomal frameshift signal of simian retrovirus-1.

The pro and pol genes of simian retrovirus-1 (SRV-1) are expressed as parts of a fusion protein generated by -1 ribosomal frameshifting. To investigate the requirements for frameshifting at the gag-pro overlap, we have inserted a stretch of 58 nucleotides containing the proposed frameshift signal into a plasmid that allows monitoring of translation in all three reading frames. In vitro translation of mRNAs derived from this plasmid indicated that the 58 nucleotides from the SRV-1 gag-pro overlap were sufficient to induce an efficient -1 shift in a heterologous context. Mutational analysis demonstrated that the slip site is formed at the heptanucleotide G GGA AAC. The frameshift efficiency of the wild type sequence in rabbit reticulocyte lysate was 23%. A second component of the frameshift signal is formed by a pseudoknot seven bases downstream of the slip site. The presence of this pseudoknot was confirmed by mutational analysis, employing complementary and compensatory base changes, and by probing the structure of short RNA transcripts containing the frameshift signal. Adding increasing amounts of an SRV-1 pseudoknot containing RNA transcript to a translation reaction programmed with an SRV-1 frameshift reporter mRNA had no effect on the frameshift efficiency, arguing against the role of a specific pseudoknot-recognising factor in the frameshifting process.

RNA pseudoknots: translational frameshifting and readthrough on viral RNAs.

Ribosomal frameshifting on retroviral RNAs has been proposed to be mediated by slippage of two adjacent tRNAs into the -1 direction at a specific heptanucleotide sequence. Here we report a computer-aided analysis of the structure around the established or putative frameshift sites in a number of retroviral, coronaviral, toroviral, and luteoviral RNAs and two dsRNA yeast viruses. In almost all cases a stable hairpin was predicted four to nine nucleotides downstream of the shifty heptanucleotide. More than half of the resulting hairpin loops give rise to potential pseudoknotting with sequences downstream of this hairpin. Especially in the case of the shifty heptanucleotides U UUA AAC and G GGA AAC, stable downstream pseudoknots are present. Indications were also found for the presence of pseudoknots downstream of amber stop condons at readthrough sites in some retroviral RNAs.