Scientific Publications 2005
2005. "Dynamic and Differential in vivo Modifications of the Isoform HMGA1a and HMGA1b Chromatin Proteins." Journal of Biological Chemistry 280(10):8961-8973. doi:10.1074/jbc.M407348200 Abstract Most naturally occurring mammalian cancers and immortalized tissue culture cell lines share a common characteristic, the over-expression of full-length high mobility group A1 (HMGA1) proteins. The HMGA1 proto-oncogene codes for two closely related isoform proteins, HMGA1a and HMGA1b, and causes cancerous cellular transformation when over-expressed in either transgenic mice or “normal” cultured cell lines. Previous work has suggested that the in vivo types and patterns of the HMGA1 post-translational modifications (PTMs) differ between normal and malignant cells. The present study focuses on the important question of whether HMGA1a and HMGA1b proteins isolated from the same cell type have identical or different PTM patterns and also whether these isoform patterns differ between non-malignant and malignant cells. Two independent mass spectrometry methods were used to identify the types of PTMs found on specific amino acid residues on the endogenous HMGA1a and HMGA1b proteins isolated from a non-metastatic, human mammary epithelial cell line, MCF-7, and a malignant, metastatic cell line derived from MCF-7 cells that over-expressed transgenic HMGA1a protein. While some of the PTMs were the same on both the HMGA1a and HMGA1b proteins isolated from a given cell type, many other modifications were present on one but not the other isoform. Furthermore, we demonstrate that both HMGA1 isoforms are dimethylated on arginine and lysine residues. Most importantly, however, the PTM patterns on the endogenous HMGA1a and HMGA1b proteins isolated from nonmetastatic and metastatic cells were consistently different, suggesting that the isoforms likely exhibit differences in their biological functions/activities in these cell types.
2005. "Direct Measurement of Alpha Emitters in Liquids using Passivated Ion Implanted Planar Silicon (PIPS) Diode Detectors." Nuclear Instruments and Methods in Physics Research. Section A, Accelerators, Spectrometers, Detectors and Associated Equipment 537(3):600-609. Abstract The present study evaluated the feasibility of direct measurement of alpha emitting radionuclides in liquids using passivated ion implanted planar silicon (PIPS) diode detectors. The performance characteristics and durability of PIPS diode detectors enabled direct detection of alpha particles from liquid samples by placing the diode detectors in close proximity to the liquid sample. Factors affecting the efficiency and accuracy of direct detection of alpha-emitters in solution and interferences of beta/gamma emitters have been examined. Direct assay of liquid samples using PIPS diode detectors can enable rapid and straightforward detection methodologies suitable for process control applications.
2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomicsbased proteomics." Proteomics 5(12):3120-3130. doi:10.1002/pmic.200401140 Abstract The availability of whole genome sequences has enabled the application of powerful tools for assaying global expression patterns in environmentally relevant bacteria such as Shewanella oneidensis MR-1. A large number of genes in prokaryote genomes, including MR-1, have been annotated as hypothetical indicating that no similar protein has yet been identified in other organisms. Using high-sensitivity mass spectrometry coupled with accurate mass and time (AMT) tag methodology, 1078 tryptic peptides were collectively detected in MR-1 cultures, 671 of which were unique to their parent protein. Using only these unique tryptic peptides and a minimum of 2 peptides per protein, we identified, with high confidence, the expression of 258 hypothetical proteins. These proteins ranged from 3.5 kDa to 139 kDa, with 47 being 100 amino acid residues or less. Using a combination of information including detection in cells grown under specific culture conditions, presence within a specific cell fraction, and predictive algorithms such as PSORT and PSORT-B, possible/plausible functions are proposed for some hypothetical proteins. Further, by applying this approach a number of proteins were found not only to be expressed, but only expressed under certain culturing conditions, thereby suggesting function while at the same time isolating several proteins to distinct locales of the cell. These results demonstrate the utility of the AMT tag methodology for comprehensive profiling of the microbial proteome while confirming the expression of a large number of hypothetical genes.
2005. "MX3- Superhalogens (M=Be, Mg, Ca; X=C1, Br): A Photoelectron Spectroscopic and ab Initio Theoretical Study." Journal of Physical Chemistry A 109(50):11560-11567. Abstract Gas-phase alkaline earth halide anions, MgX3 - and CaX3 - (X ) Cl, Br), were produced using electrospray and investigated using photoelectron spectroscopy at 157 nm. Extremely high electron binding energies were observed for all species and their first vertical detachment energies were measured as 6.60 ( 0.04 eV for MgCl3 -, 6.00 ( 0.04 eV for MgBr3 -, 6.62 ( 0.04 eV for CaCl3 -, and 6.10 ( 0.04 eV for CaBr3 -. The high electron binding energies indicate these are very stable anions and they belong to a class of anions, called superhalogens. Theoretical calculations at several levels of theory were carried out on these species, as well as the analogous BeX3 -. Vertical detachment energy spectra were predicted to compare with the experimental observations, and good agreement was obtained for all species. The first adiabatic detachment energies were found to be substantially lower (by about 1 eV) than the corresponding vertical detachment energies for all the MX3 - species, indicating extremely large geometry changes between MX3 - and MX3. We found that all the MX3 - anions possess D3h (1A1') structures and are extremely stable against dissociation into MX2 and X-. The corresponding neutral species MX3, however, were found to be only weakly bound with respect to dissociation toward MX2 + X. The global minimum structures of all the MX3 neutrals were found to be C2V (2B2), which can be described as (X2 -)(MX+) charge-transfer complexes, whereas the MX2âââX (C2V, 2B1) van der Waals complexes were shown to be low-lying isomers.