Molecular Biology Commons^™

Quality Control And Peak Finding For Proteomics Data Collected From Nipple Aspirate Fluid Using Surface Enhanced Laser Desorption And Ionization., Jeffrey S. Morris, Kevin R. Coombes, Herbert A. Fritsche, Charlotte Clarke, Jeng-Neng Chen, Keith A. Baggerly, Lian-Chun Xiao, Mien-Chie Hung, Henry M. Kuerer

Jeffrey S. Morris

Background: Recently, researchers have been using mass spectroscopy to study cancer. For use of proteomics spectra in a clinical setting, stringent quality-control procedures will be needed.

Methods: We pooled samples of nipple aspirate fluid from healthy breasts and breasts with cancer to prepare a control sample. Aliquots of the control sample were used on two spots on each of three IMAC ProteinChip® arrays (Ciphergen Biosystems, Inc.) on 4 successive days to generate 24 SELDI spectra. In 36 subsequent experiments, the control sample was applied to two spots of each ProteinChip array, and the resulting spectra were analyzed to determine how …

A Comprehensive Approach To The Analysis Of Maldi-Tof Proteomics Spectra From Serum Samples., Keith A. Baggerly, Jeffrey S. Morris, Jing Wang, David Gold, Lian-Chun Xiao, Kevin R. Coombes

Jeffrey S. Morris

For our analysis of the data from the First Annual Proteomics Data Mining Conference, we attempted to discriminate between 24 disease spectra (group A) and 17 normal spectra (group B). First, we processed the raw spectra by (i) correcting for additive sinusoidal noise (periodic on the time scale) affecting most spectra, (ii) correcting for the overall baseline level, (iii) normalizing, (iv) recombining fractions, and (v) using variable- width windows for data reduction. Also, we identified a set of polymeric peaks (at multiples of 180.6 Da) that is present in several normal spectra (B1–B8). After data processing, we found the intensities …

Perilipin A Is Essential For The Translocation Of Hormone-Sensitive Lipase During Lipolytic Activation. J Cell Biol, John Tansey

Chemistry Faculty Scholarship

A key step in lipolytic activation of adipocytes is the translocation of hormone-sensitive lipase (HSL) from the cytosol to the surface of the lipid storage droplet. Adipocytes from perilipin -null animals have an elevated basal rate of lipolysis compared with adipocytes from wild-type mice, but fail to respond maximally to lipolytic stimuli. This defect is downstream of the -adrenergic receptor–adenylyl cyclase complex. Now, we show that HSL is basally associated with lipid droplet surfaces at a low level in perilipin nulls, but that stimulated translocation from the cytosol to lipid droplets is absent in adipocytes derived from embryonic fibroblasts of …

Bayesian Shrinkage Estimation Of The Relative Abundance Of Mrna Transcripts Using Sage, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes

Jeffrey S. Morris

Serial analysis of gene expression (SAGE) is a technology for quantifying gene expression in biological tissue that yields count data that can be modeled by a multinomial distribution with two characteristics: skewness in the relative frequencies and small sample size relative to the dimension. As a result of these characteristics, a given SAGE sample may fail to capture a large number of expressed mRNA species present in the tissue. Empirical estimators of mRNA species’ relative abundance effectively ignore these missing species, and as a result tend to overestimate the abundance of the scarce observed species comprising a vast majority of …

Genetic Variation Within And Among The Suminoe Oyster (Crassostrea Ariakensis) Populations And Stocks As Assessed By Molecular Markers, Qian Zhang

Dissertations, Theses, and Masters Projects

No abstract provided.

A Mycobacterium-Inducible Nramp In Striped Bass Morone Saxatilis, Erin Jeffrey Burge

Dissertations, Theses, and Masters Projects

In mammals, the natural resistance-associated macrophage protein 1 gene, Nramp1, plays a major role in resistance to mycobacterial infections. Chesapeake Bay (USA) striped bass, Morone saxatilis, are currently experiencing an epizootic of mycobacteriosis that threatens the health of this ecologically and economically important species. This dissertation characterizes an Nramp gene in this species (MsNramp ) and provide evidence for induction following Mycobacterium exposure. The striped bass MsNramp gene and 554 amino acid sequence contain all the signal features of the Nramp family, including a topology of 12 transmembrane domains (TM), the transport protein specific 'binding-protein-dependent transport system inner membrane component …

Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen

Mathematics & Statistics Faculty Publications

We report our results in classifying protein matrix-assisted laser desorption/ionizationtime of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation studies …