PubMed · 12977117
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S MOORE, W H STEIN. 1952. [Chromatography].. https://doi.org/10.1146/annurev.bi.21.070152.002513
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We present improvements on a previously reported method (Vernille JP, Schneider JW. 2004. Biotechnol Prog 20(6):1776-1782) to purify DNA oligomers by attachment of peptide nucleic acid amphiphiles (PNAA) to particular sequences on the oligomers, followed by their separation from unbound oligomers using hydrophobic interaction chromatography (HIC). Use of alkyl-modified HIC media (butyl and octyl sepharose) over phenyl-modified media (phenyl sepharose) reduced the elution time of unbound DNA while not affecting the elution time of the PNAA/DNA complex. Modifying the alkane tail length for PNAA from C(12) to C(18) increased slightly the retention of PNAA/DNA duplexes. By combining these two refinements, we show that sequence-specific purifications of DNA oligomers 60 bases in length or more can be achieved with high resolution, even when the PNAA alkane is attached to the center of the target strand. The insensitivity of the PNAA/DNA duplex binding to choice of HIC media appears to be due to a surface-induced aggregation phenomenon that does not occur in the case of untagged DNA. We also report on the use of batch HIC as an adequate predictor of elution profiles in linear gradient HIC, and its potential to considerably reduce purification times by applying step gradients.
BACKGROUND: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. RESULTS: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. CONCLUSION: JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.
Recent studies have shown that various semi- and non-volatile organohalogen compounds are ubiquitous in the environment: these include halogenated dioxins including chlorinated dioxins, other persistent organic pollutants (POPs), brominated flame retardants (BFRs), and perfluorooctane sulfonate (PFOS). However, monitoring and assessment of these compounds by the analyses of individual compounds and their isomers is onerous because of their low environmental concentrations and large number of compounds. In this study, we have developed a new method that is capable of screening and monitoring an array of organohalogen compounds efficiently by combustion ion chromatography (CIC) - the new analyzer that serially connects combustion furnace and ion chromatograph. Analyzer performance was evaluated in terms of its applicability, reproducibility, and sensitivity as limit of detection (LOD). Recoveries of organochlorine, organobromine, and organoiodine compounds by the CIC were between 97 and 105%; those of organofluorine compounds were from 86 to 91%. In all cases, the relative standard deviation of five analyses was 4% or smaller. The analyzer would exhibit good sensitivity for various environmental matrices (e.g., 2.8-31ng-X/g-soil, 1.4-16ng-X/L-water, and 9.2-100ng-X/m3N-gas). The method is fast and can provide information regarding the occurrence of organohalogen compounds within 1 or 2 days after sampling. Applicability of the new method for the assessment of contamination in flue gas and fly ash was also demonstrated. Our results show that the method is efficient to investigate emission sources and areas contaminated by organohalogen compounds.