Applied Biosystems

About: Applied Biosystems is a based out in . It is known for research contribution in the topics: Mass spectrometry & Nucleic acid. The organization has 1521 authors who have published 1579 publications receiving 285423 citations.

Analysis of chlorothalonil by liquid chromatography/mass spectrometry using negative-ion atmospheric pressure photoionization.

Abstract: A highly sensitive and simple method for the analysis of chlorothalonil was presented using a liquid chromatograph/mass spectrometer equipped with an atmospheric pressure photoionization (APPI) source Chlorothalonil is one of the most extensively used fungicides The major degraded product of chlorothalonil, 4-hydroxy-2,5,6-trichloroisonaphthonitrile (4OH-TPN), was also quantified with sensitivity similar to that of chlorothalonil The method was applied to the determination of chlorothalonil in aqueous environment and food samples The method detection limits (MDLs) of chlorothalonil for aqueous samples and cucumber were determined to be 018 and 32 ng g(-1), respectively At several estuarial locations, chlorothalonil was detected with a maximum of 11 ng L(-1) On the other hand, 4OH-TPN was detected not from estuaries but from rivers with a maximum of 14 ng L(-1)

Systematic identification of pseudogenes through whole genome expression evidence profiling

Abstract: The identification of pseudogenes is an integral and significant part of the genome annotation because of their abundance and their impact on the experimental analysis of functional genes. Most of the computational annotation systems are not optimized for systematic pseudogene recognition, often annotating pseudogenes as functional genes, and users then propagate these errors to subsequent analyses and interpretations. In order to validate gene annotations and to identify pseudogenes that are potentially mis-annotated, we developed a novel approach based on whole genome profiling of existing transcript and protein sequences. This method has two important features: (i) equally detects both processed and non-processed pseudogenes and (ii) can identify transcribed pseudogenes. Applying this method to the human Ensembl gene predictions, we discovered that 2011 (9% of total) Ensembl genes in the categories of known and novel might be pseudogenes based on expression evidence. Of these, 1200 genes are found to have no existing evidence of transcription, and 811 genes are found with transcription evidence but contain significant translation disruption. Approximately 40% of the 2011 identified pseudogenes presented a multi-exon structure, representing non-processed pseudogenes. We have demonstrated the power of whole genome profiling of expression sequences to improve the accuracy of gene annotations.

An improved synthesis of oligodeoxynucleotide N3′→P5′ phosphoramidates and their chimera using hindered phosphoramidite monomers and a novel handle for reverse phase purification

Abstract: Oligodeoxynucleotide N3'-->P5' phosphoramidates are promising candidates for antisense therapeutics, as well as for diagnostic applications. We recently reported a new method for the synthesis of these oligonucleotide analogs which makes use of a phosphoramidite amine-exchange reaction in the key coupling step. We report herein an improved set of monomers that utilize a more reactive, hindered phosphoramidite to produce optimal yields in a single coupling step followed by oxidation, thereby eliminating the need for the previously reported couple-oxidize-couple-oxidize approach. On the 10 micromol scale, the synthesis is performed using only 3.6 equivalents (equiv.) of monomer. An improved oxidation reagent consisting of hydrogen peroxide, water, pyridine and THF is also introduced. Reported here for the first time is the use of a reverse-phase purification methodology employing a ribonucleotide purification handle that is removed under non-acidic conditions, in contrast to the conventional dimethoxytrityl group. The synthesis and purification of uniformly modified N3'-->P5' phosphoramidate oligodeoxy-nucleotides, as well as their chimera containing phosphodiester and/or phosphorothioate linkages at predefined positions, using these new methodologies are included herein. The results of31P NMR studies that led to this improved amine-exchange methodology are also described.