A simple technique for locating the umbilicus in abdominoplasty

A method for locating the umbilicus in abdominoplasty is described. The method utilizes a magnet sutured to the umbilical stalk and a locking device which determines the exact location of the umbilicus.     

A simple method to improve probe set estimates from oligonucleotide arrays

A popular commercially available oligonucleotide microarray technology employs sets of 25 base pair oligonucleotide probes for measurement of gene expression levels. A mathematical algorithm is required to compute an estimate of gene expression from the multiple probes. Previously proposed methods for summarizing gene expression data have either been substantially ad hoc or have relied on model assumptions that may be easily violated. Here we present a new algorithm for calculating gene expression from probe sets. Our approach is functionally related to leave-one-out cross-validation, a non-parametric statistical technique that is often applied in limited data situations. We illustrate this approach using data from our study seeking a molecular fingerprint of STAT3 regulated genes for early detection of human cancer.     

A simple vector system to improve performance and utilisation of recombinant antibodies

Background  

Isolation of recombinant antibody fragments from antibody libraries is well established using technologies such as phage display. Phage display vectors are ideal for efficient display of antibody fragments on the surface of bacteriophage particles. However, they are often inefficient for expression of soluble antibody fragments, and sub-cloning of selected antibody populations into dedicated soluble antibody fragment expression vectors can enhance expression.     

A simple technique to improve recovery and morphology of cells exfoliated into fluids

OBJECTIVE: To devise a simple, inexpensive and effective method for the cytologic study of fluids and to compare the results of the method with the conventional centrifuge smear (CS) method. STUDY DESIGN: We examined 200 fluid samples from various body sites using CS and thick and thin (TT) smears. Cellular yield, cytomorphology and background of the smears were studied and scored. The scores were compared and analyzed with the chi 2 test. RESULTS: TT smears gave a higher cellular yield, better morphologic details and cleaner background. The values of all three features were statistically significant (P < .001). In 38 cases a definitive diagnosis could be made on TT smears and not on CS smears. CONCLUSION: TT smears give significantly better results than CS smears. Simple to prepare and requiring no additional investment in terms of cost, technical skill and sophisticated instruments, this method is ideally suited to small laboratories, especially in developing countries.     

A simple strategy to amplify specifically the HLA-DQ beta gene region with genomic DNA as template

The nature of codon 57 in the HLA-DQ beta gene was recently reported as a potential marker of genetic susceptibility to insulin-dependent diabetes mellitus. When exploring the relevance of this marker by using genomic DNA amplification, we encountered difficulties resulting from the coamplification of the homologous DX beta region. A simple strategy is proposed to amplify the DQ beta region exclusively. It involves the preliminary digestion of genomic DNA with a restriction enzyme which cleaves DX beta specifically, leaving intact the DQ beta sequence. The amplified material is suitable for dot blot analysis and restriction enzyme digestion. This strategy is of general interest when homologous sequences impair the specificity of enzymatic DNA amplification.     

A simple method to improve the precision and accuracy of gas-phase oxygen electrodes.

The precision and accuracy of the measurements using an oxygen gas-phase electrode thermostabilized in an ice bath were evaluated. The precision found was comparable with that obtained with the paramagnetic method and with Scholander analysis. The accuracy was comparable with that of the paramagnetic method.     

A simple modification to improve the accuracy of methylation-sensitive restriction enzyme quantitative polymerase chain reaction

DNA digestion with endonucleases sensitive to CpG methylation such as HpaII followed by polymerase chain reaction (PCR) quantitation is commonly used in molecular studies as a simple and inexpensive solution for assessment of region-specific DNA methylation. We observed that the results of such analyses were highly overestimated if mock-digested samples were applied as the reference. We determined DNA methylation levels in several promoter regions in two setups implementing different references: mock-digested and treated with a restriction enzyme that has no recognition sites within examined amplicons. Fragmentation of reference templates allowed removing the overestimation effect, thereby improving measurement accuracy.     

Aeration: A simple method to control vitrification and improve in vitro culture of rare australian plants

Summary Aeration of tissue cultured rare Australian plantsConostylis wonganensis S.D. Hopper (Haemodoraceae);Diplolaena andrewsii Ostenf.;Drummondita ericoides Harvey (Rutaceae);Eremophila resinosa F. Muell. (Myoporaceae);Eucalyptus ‘graniticola’ (Myrtaceae);Lechenaultia pulvinaris C. Gardner (goodeniaceae); andSowerbaea multicaulis E. Pritzel (Liliaceae) has been found to reduce vitrification in sensitive species as well as significantly improving shoot quality and transfer to soil in most study species. A simple 7-mm hole with a double-layer insert of filter paper in the polypropylene screw lids of the culture vessel decreased shoot vitrification over a 4-wk culture period. The method has implications for facilitating the tissue culture of other rare Australian plants and reducing the occurrence of this developmental abnormality.     

A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia

In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE) was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp) and Aspergillus niger phytase gene phyA (1404 bp). Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.     

3D-Jury: a simple approach to improve protein structure predictions

MOTIVATION: Consensus structure prediction methods (meta-predictors) have higher accuracy than individual structure prediction algorithms (their components). The goal for the development of the 3D-Jury system is to create a simple but powerful procedure for generating meta-predictions using variable sets of models obtained from diverse sources. The resulting protocol should help to improve the quality of structural annotations of novel proteins. Results: The 3D-Jury system generates meta-predictions from sets of models created using variable methods. It is not necessary to know prior characteristics of the methods. The system is able to utilize immediately new components (additional prediction providers). The accuracy of the system is comparable with other well-tuned prediction servers. The algorithm resembles methods of selecting models generated using ab initio folding simulations. It is simple and offers a portable solution to improve the accuracy of other protein structure prediction protocols. AVAILABILITY: The 3D-Jury system is available via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)