Applied Biosystems

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

Maldi plate with removable magnetic insert

Abstract: A sample plate structure (10) is provided including a retainer plate (11) having a central recess (12) with a trough (13) along its periphery, a sample insert plate (14) which fits into and rests on contact surface of the recess, and a magnet (16) that is held below the contact surface. A portion of the bottom surface (15) of the insert is formed of a magnetic material. The magnet (16) provides sufficient force to retain the insert plate (14) in the retainer plate (11) during MALDI MS analysis. The sample insert plate 814) is provided with a peripheral configuration, which assures that the sample insert plate is properly oriented within the sample plate support structure and is held flat. A hole (18) for a protrusion allows easy insert installation and alignment against the orientation feature in the recess as well as easy removal of the insert simply by pushing up from underneath the retainer plate. While the insert sample plate (14) can be a consumable, the remaining portion of the apparatus can be reused.

Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells

Abstract: We previously analyzed human embryonic kidney (HEK) cell lines for the effects that simian virus 40 (SV40) small tumor antigen (ST) has on gene expression using Affymetrix U133 GeneChips. To cross-validate and extend our initial findings, we sought to compare the expression profiles of these cell lines using an alternative microarray platform. METHODS: We have analyzed matched cell lines with and without expression of SV40 ST using an Applied Biosystems (AB) microarray platform that uses single 60-mer oligonucleotides and single-color quantitative chemiluminescence for detection. RESULTS: While we were able to previously identify only 456 genes affected by ST with the Affymetrix platform, we identified 1927 individual genes with the AB platform. Additional technical replicates increased the number of identified genes to 3478 genes and confirmed the changes in 278 (61%) of our original set of 456 genes. Among the 3200 genes newly identified as affected by SV40 ST, we confirmed 20 by QRTPCR including several components of the Wnt, Notch, and Hedgehog signaling pathways, consistent with SV40 ST activation of these developmental pathways. While inhibitors of Notch activation had no effect on cell survival, cyclopamine had a potent killing effect on cells expressing SV40 ST. CONCLUSIONS: These data show that SV40 ST expression alters cell survival pathways to sensitize cells to the killing effect of Hedgehog pathway inhibitors.

Error-tolerant EST database searches by tandem mass spectrometry and multiTag software.

Abstract: The MultiTag method (Sunyaev et al., Anal. Chem. 2003 15, 1307-1315) employs multiple error-tolerant searches with peptide sequence tags (Mann and Wilm, Anal. Chem. 1994, 66, 4390-4399) for the identification of proteins from organisms with unsequenced genomes. Here we demonstrate that the error-tolerant capabilities of MultiTag increased the number of peptide alignments and improved the confidence of identifications in an EST database. The MultiTag outperformed conventional database searching software that only utilizes stringent matching of tandem mass spectra to nucleotide sequences of ESTs.