Meeting review : ESF workshop on "Impact of nucleic acid chemistry on gene function analysis: antisense, aptamers, ribozymes and RNAi"

The shortage of functional information compared to the abundance of sequence information characterizes today’s situation in functional genomics. For many years the knock-down of a gene’s product has been the most powerful way of analysing its function. In addition to the complete knock-out by homologous recombination, several different techniques have been developed to temporarily knock down gene expression through methods based on specific sequence recognition, such as knockdown by antisense oligonucleotides, ribozymes, aptamers or RNAi. The ESF workshop on ‘Impact of Nucleic Acid Chemistry on Gene Function Analysis’ brought together researchers who use techniques that are different but highly related. It offered an opportunity for an in-depth discussion of recent progress and common problems. Antisense oligonucleotides aptamers and ribozymes are techniques that have been used successfully for many years to validate targets. However, recent developments, such as increased tightness of binding (e.g. locked nucleic acids) or the combination of different methods (e.g. using aptamers to design ribozymes), have continued to improve the existing techniques. RNA interference (RNAi) is a defence mechanism of the cell against viruses. Since the exact mechanism of action within the cell is still unclear, RNAi was a particularly exciting topic at the workshop and was addressed in the largest number of presentations. Predictability of positional effects (accessibility of RNA) is a problem shared by all techniques using sequence-specific recognition and was the subject of quite controversial debates. The meeting comprised over 50 people from 14 countries (13 European countries and the USA)

The genetic defect of the original Norwegian lecithin:cholesterol acyltransferase deficiency families

AbstractThree of the original Norwegian lecithin:cholesterol acyltransferase (LCAT) deficiency families have been investigated for mutations in the gene for lecithin:cholesterol acyltransferase by DNA sequencing of the exons amplified by the polymerase chain reaction. A single T→A transversion in codon 252 in exon 6 converting Met(ATG) to Lys(AAG) was observed in all homozygotes. In spite of the identical mutation, the disease phenotypes differed in severity. This was not reflected in the expression of LCAT in the heterozygotes

Collecting evidence of validity for an assessment tool for Norwegian medical students' non-technical skills (NorMS-NTS): usability and reliability when used by novice raters

Background - The NorMS-NTS tool is an assessment tool for assessing Norwegian medical students’ non-technical skills (NTS). The NorMS-NTS was designed to provide student feedback, training evaluations, and skill-level comparisons among students at different study sites. Rather than requiring extensive rater training, the tool should capably suit the needs of busy doctors as near-peer educators. The aim of this study was to examine the usability and preliminary assess validity of the NorMS-NTS tool when used by novice raters. Methods - This study focused on the usability of the assessment tool and its internal structure. Three raters used the NorMS-NTS tool to individually rate the team leader, a medical student, in 20 video-recorded multi-professional simulation-based team trainings. Based on these ratings, we examined the tools’ internal structure by calculating the intraclass correlation coefficient (ICC) (version 3.1) interrater reliability, internal consistency, and observability. After the rating process was completed, the raters answered a questionnaire about the tool’s usability. Results - The ICC agreement and the sum of the overall global scores for all raters were fair: ICC (3,1) = 0.53. The correlation coefficients for the pooled raters were in the range of 0.77–0.91. Cronbach’s alpha for elements, categories and global score were mostly above 0.90. The observability was high (95%-100%). All the raters found the tool easy to use, none of the elements were redundant, and the written instructions were helpful. The raters also found the tool easier to use once they had acclimated to it. All the raters stated that they could use the tool for both training and teaching. Conclusions - The observed ICC agreement was 0.08 below the suggested ICC level for formative assessment (above 0.60). However, we know that the suggestion is based on the average ICC, which is always higher than a single-measure ICC. There are currently no suggested levels for single-measure ICC, but other validated NTS tools have single-measure ICC in the same range. We consider NorMS-NTS as a usable tool for formative assessment of Norwegian medical students’ non-technical skills during multi-professional team training by raters who are new to the tool. It is necessary to further examine validity and the consequences of the tool to fully validate it for formative assessments

Regulated expression of a transgene introduced on an oriP/EBNA-1 PAC shuttle vector into human cells

<p>Abstract</p> <p>Background</p> <p>Sequencing of the human genome has led to most genes being available in BAC or PAC vectors. However, limited functional information has been assigned to most of these genes. Techniques for the manipulation and transfer of complete functional units on large DNA fragments into human cells are crucial for the analysis of complete genes in their natural genomic context. One limitation of the functional studies using these vectors is the low transfection frequency.</p> <p>Results</p> <p>We have constructed a shuttle vector, pPAC7, which contains both the <it>EBNA-1 </it>gene and <it>ori</it>P from the Epstein-Barr virus allowing stable maintenance of PAC clones in the nucleus of human cells. The pPAC7 vector also contains the <it>EGFP </it>reporter gene, which allows direct monitoring of the presence of PAC constructs in transfected cells, and the <it>Bsr</it>-cassette that allows highly efficient and rapid selection in mammalian cells by use of blasticidin. Positive selection for recombinant PAC clones is obtained in pPAC7 because the cloning sites are located within the SacBII gene. We show regulated expression of the <it>CDH3 </it>gene carried as a 132 kb genomic insert cloned into pPAC7, demonstrating that the pPAC7 vector can be used for functional studies of genes in their natural genomic context. Furthermore, the results from the transfection of a range of pPAC7 based constructs into two human cell lines suggest that the transfection efficiencies are not only dependent on construct size.</p> <p>Conclusion</p> <p>The shuttle vector pPAC7 can be used to transfer large genomic constructs into human cells. The genes transferred could potentially contain all long-range regulatory elements, including their endogenous regulatory promoters. Introduction of complete genes in PACs into human cells would potentially allow complementation assays to identify or verify the function of genes affecting cellular phenotypes.</p