Search PubMed⌕ Search

Biomedical subjects

Carl F Schaefer

Publications and source records attributed to Carl F Schaefer.

11 recordsLinked to original sources
PubMed2004

Direct ampholyte-free liquid-phase isoelectric peptide focusing: application to the human serum proteome.

In this study, we utilized a multidimensional peptide separation strategy combined with tandem mass spectrometry (MS/MS) for the identification of proteins in human serum. After enzymatically digesting serum with trypsin, the peptides were fractionated using liquid-phase isoelectric focusing (IEF) in a novel ampholyte-free format. Twenty IEF fractions were collected and analyzed by reversed-phase microcapillary liquid chromatography (microLC)-MS/MS. Bioinformatic analysis of the raw MS/MS spectra resulted in the identification of 844 unique peptides, corresponding to 437 proteins. This study demonstrates the efficacy of ampholyte-free peptide autofocusing, which alleviates peptide losses in ampholyte removal strategies. The results show that the separation strategy is effective for high-throughput characterization of proteins from complex proteomic mixtures.

Blood Proteins↗
PubMed2004

Proteomic analysis of detergent-resistant membrane rafts.

A combined, detergent- and organic solvent-based proteomic method for the analysis of detergent-resistant membrane rafts (DRMR) is described. These specialized domains of the plasma membrane contain a distinctive and dynamic protein and/or lipid complement, which can be isolated from most mammalian cells. Lipid rafts are predominantly involved in signal transduction and adapted to mediate and produce different cellular responses. To facilitate a better understanding of their biology and role, DRMR were isolated from Vero cells as a Triton X-100 insoluble fraction. After detergent removal, sonication in 60% buffered methanol was used to extract, solubilize and tryptically digest the resulting protein complement. The peptide digestate was analyzed by microcapillary reversed-phase liquid chromatography-tandem mass spectrometry. Gas-phase fractionation in the mass-to-charge range was employed to broaden the selection of precursor ions and increase the number of identifications in an effort to detect less abundant proteins. A total of 380 proteins were identified including all known lipid raft markers. A total of 91 (24%) proteins were classified as integral alpha-helical membrane proteins, of which 51 (56%) were predicted to have multiple transmembrane domains.

Amino Acid Sequence↗
PubMed2004

Quantitative proteomic analysis of inorganic phosphate-induced murine MC3T3-E1 osteoblast cells.

Cleavable isotope-coded affinity tag (cICAT) reagents were utilized to identify and quantitate protein expression differences in control and inorganic phosphate-treated murine MC3T3-E1 osteoblast cells. Proteins extracted from control and treated cells were labeled with the light and heavy isotopic versions of cICAT reagents, respectively. The cICAT-labeled samples were combined, proteolytically digested, and the cICAT-derivatized peptides isolated using immobilized avidin chromatography. The cICAT-labeled peptides were resolved into 96 fractions by strong cation-exchange (SCX) liquid chromatography (LC). Analysis of the SCX-LC cICAT peptide fractions by microcapillary reversed-phase LC-tandem mass spectrometry resulted in the identification and quantitation of 7227 unique peptides corresponding to 2501 proteins, or roughly 9% of the proteins currently predicted to be encoded by the mouse genome. A false positive analysis indicated a 98% confidence in the peptide identifications. To corroborate changes in abundance measured by cICAT with those detectable in traditionally prepared cell lysate, we chose to analyze cyclin D1. Cyclin D1 has been previously identified as a phosphate-responsive gene and was likewise identified as a phosphate-responsive protein in the current analysis. The 1.76-fold increase in abundance in cyclin D1 determined from cICAT corresponds well with the 2.41-fold increase as determined by Western blotting. These results demonstrate that quantitative proteomics is capable of providing a quantitative view of thousands of proteins in mammalian cells within a defined set of experiments.

Amino Acid Sequence↗
PubMed2004

Associations of postmenopausal hormone therapy with markers of hemostasis and inflammation and lipid profiles in diabetic and nondiabetic american Indian women: the strong heart study.

OBJECTIVES: To examine the associations of postmenopausal hormone therapy (PHT) with indicators of hemostasis and inflammation and with lipid profiles in American Indian women and to determine if diabetes modifies these associations. METHODS: This report is a cross-sectional analysis of data from 1446 postmenopausal women who were free from cardiovascular disease (CVD) at the second Strong Heart Study examination (1993-1995). Diabetes was diagnosed by WHO criteria. Postmenopausal hormone use was ascertained by review of the medications brought to the examination or by medical record review. Lipoproteins, plasminogen activator inhibitor type 1 (PAI-1), fibrinogen, and C-reactive protein (CRP) were measured in fasting plasma samples. RESULTS: Among nondiabetic women, current PHT users had lower mean fibrinogen, PAI1, and low-density lipoprotein cholesterol (LDLC) levels than those in never users (38.4 mg/dl, 8.68 ng/ml, and 14.16 mg/dl lower, respectively) but higher CRP and triglyceride levels (1.53 mg/l and 31.43 mg/dl higher, respectively). Multivariate adjustment did not alter any of these associations. In diabetic women, current PHT use was associated only with lower PAI-1 (5.48 ng/ml lower) and higher high-density lipoprotein cholesterol (HDLC) levels (3.33 mg/dl higher) compared with never users. CONCLUSIONS: In American Indian women without diabetes, PHT was associated with lower levels of hemostatic markers but higher levels of an inflammatory marker. Associations were less marked in women with diabetes. The relation of PHT with lipid profiles also differed in nondiabetic and diabetic women. These data provide an additional rationale for considering diabetes status when deciding whether or not to use PHT.

Aged↗
PubMed2004

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

Animals↗
PubMed2004

A proteomic characterization of the plasma membrane of human epidermis by high-throughput mass spectrometry.

Membrane proteins are responsible for many critical cellular functions and identifying cell surface proteins on different keratinocyte populations by proteomic approaches would improve our understanding of their biological function. The ability to characterize membrane proteins, however, has lagged behind that of soluble proteins both in terms of throughput and protein coverage. In this study, a membrane proteomic investigation of keratinocytes using a two-dimensional liquid chromatography (LC) tandem-mass spectrometry (MS/MS) approach that relies on a buffered methanol-based solubilization, and tryptic digestion of purified plasma membrane is described. A highly enriched plasma membrane fraction was prepared from newborn foreskins using sucrose gradient centrifugation, followed by a single-tube solubilization and tryptic digestion of membrane proteins. This digestate was fractionated by strong cation-exchange chromatography and analyzed using microcapillary reversed-phase LC-MS/MS. In a set of 1306 identified proteins, 866 had a gene ontology (GO) annotation for cellular component, and 496 of these annotated proteins (57.3%) were assigned as known integral membrane proteins or membrane-associated proteins. Included in the identification of a large number of aqueous insoluble integral membrane proteins were many known intercellular adhesion proteins and gap junction proteins. Furthermore, 121 proteins from cholesterol-rich plasma membrane domains (caveolar and lipid rafts) were identified.

Caveolae↗
PubMed2004

Pathway databases.

Network representations of biological pathways offer a functional view of molecular biology that is different from and complementary to sequence, expression, and structure databases. There is currently available a wide range of digital collections of pathway data, differing in organisms included, functional area covered (e.g., metabolism vs. signaling), detail of modeling, and support for dynamic pathway construction. While it is currently impossible for these databases to communicate with each other, there are several efforts at standardizing a data exchange language for pathway data. Databases that represent pathway data at the level of individual interactions make it possible to combine data from different predefined pathways and to query by network connectivity. Computable representations of pathways provide a basis for various analyses, including detection of broad network patterns, comparison with mRNA or protein abundance, and simulation.

Computational Biology↗
PubMed2002

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov).

Algorithms↗
PubMed2002

An anatomy of normal and malignant gene expression.

A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP) uses serial analysis of gene expression (SAGE). Over 5 million transcript tags from more than 100 human cell types have been assembled. To enhance the utility of this data, the CGAP SAGE project created SAGE Genie, a web site for the analysis and presentation of SAGE data (http://cgap.nci.nih.gov/SAGE). SAGE Genie provides an automatic link between gene names and SAGE transcript levels, accounting for alternative transcription and many potential errors. These informatics advances provide a rapid and intuitive view of transcript expression in the human body or brain, displayed on the SAGE Anatomic Viewer. We report here an easily accessible view of nearly any gene's expression in a wide variety of malignant and normal tissues.

DNA, Mitochondrial↗
PubMed2002

The effect of estrogen use on levels of glucose and insulin and the risk of type 2 diabetes in american Indian postmenopausal women : the strong heart study.

OBJECTIVE: To examine the associations between estrogen use and levels of insulin and glucose as well as the effect of estrogen use on the risk of type 2 diabetes. RESEARCH DESIGN AND METHODS: This report is based on 857 women who were both nondiabetic and postmenopausal at the baseline examination (1989-1992) and who completed a second examination (1993-1995) an average of 4 years later. The participants were divided into three groups: never, past, and current users based on their baseline estrogen use status. ANCOVA was used to compare the insulin and glucose levels among estrogen use groups. Logistic regression was used to evaluate the association between estrogen use and the incidence of type 2 diabetes. RESULTS: Postmenopausal estrogen use was associated with lower fasting glucose (0.2 mmol/l lower) but higher 2-h glucose levels (0.4 mmol/l higher) compared with never users. It was not significantly associated with the risk of type 2 diabetes compared with past and never users, based on American Diabetes Association or World Health Organization definitions of diabetes or on only a 2-h glucose level > or = 11.1 mmol/l. However, the risk of type 2 diabetes increased with increasing duration of estrogen use among current users, with an odds ratio of 1.10 per year of use (95% CI: 1.01-1.19). CONCLUSIONS: The data suggest that estrogen use in American Indian postmenopausal women may relate to deterioration of glucose tolerance. Longer duration of estrogen use among current users may relate to an increased risk of type 2 diabetes.

Blood Glucose↗