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.

Improved RNA quality and TaqMan ® Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials

Abstract: Archival formalin-fixed paraffin-embedded (FFPE) tissues represent an abundant source of clinical specimens; however their use is limited in applications involving analysis of gene expression due to RNA degradation and modification during fixation and processing. This study improved the quality of RNA extracted from FFPE by introducing a heating step into the selected extraction protocols. Further, it evaluated a novel pre-amplification system (PreAmp) designed to enhance expression analysis from tissue samples using assays with a range of amplicon size (62–164 bp). Results from the Bioanalyzer and TaqMan® data showed improvement of RNA quality extracted using the modified protocols from FFPE. Incubation at 70°C for 20 minutes was determined to be the best condition of those tested to disrupt cross-links while not compromising RNA integrity. TaqMan® detection was influenced by master mix, amplicon size and the incorporation of a pre-amplification step. TaqMan® PreAmp consistently achieved decreased CT values in both snap frozen and FFPE aliquots compared with no pre-amplification. Modification to extraction protocols has facilitated procurement of RNA that may be successfully amplified using QRT-PCR. TaqMan® PreAmp system is a robust and practical solution to limited quantities of RNA from FFPE extracts.

New fragmentation mechanisms in matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry of carbohydrates

Abstract: The spectra recorded by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS/MS) of complex carbohydrates from human milk are presented Besides ions originating from glycosidic cleavages and from sugar ring fragmentations, these spectra show intense peaks that may be assigned to ions produced by three new fragmentation pathways involving a six-atom rearrangement These ions, together with the A fragments from sugar ring fragmentations, open the possibility of obtaining a complete mapping of the linkage positions present in the carbohydrates investigated by MALDI-TOF/TOF

Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia

Abstract: More than half of all deaths in Western society are related to arteriosclerotic cardiovascular diseases. Inherited disturbances in the low-density-lipoprotein (LDL) receptor and similar lipid-related defects account for the majority of these deaths. Testing procedures thus far rely on total cholesterol, LDL cholesterol, high-density-lipoprotein cholesterol, and triglyceride determinations. These tests are not able to provide any genetic information. We have developed an oligonucleotide ligation assay (OLA) that enables us to screen for high-risk individuals by testing for 19 common mutations in the LDL receptor and the apolipoprotein B genes using an automated genotyping-based two-step protocol. The novel OLA uses oligomeric pentaethyleneoxide mobility modifiers. The automated test will be useful in screening large populations for genetic data to distinguish relative from absolute risk, as well as for cost-effective familial analysis.