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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.

Background: Results of several studies have suggested that diet during adolescence may influence the risk of breast cancer in adulthood. We evaluated whether an intervention to lower fat intake among adolescent girls altered their serum concentrations of sex hormones that, in adults, are related to breast cancer development., Methods: We conducted an ancillary hormone study among 286 of the 301 girls who participated between 1988 and 1997 in the Dietary Intervention Study in Children, in which healthy, prepubertal, 8- to 10-year-olds with elevated low-density lipoprotein cholesterol were randomly assigned to usual care or to a behavioral intervention that promoted a low-fat diet. Median time on the intervention was 7 years. Blood samples collected before randomization and at the year 1, year 3, year 5, and last visits were assayed to determine the girls' serum levels of sex hormones. All P values are two-sided., Results: At the year 5 visit, girls in the intervention group had 29.8% (95% confidence interval [CI] = 5.4% to 47.9%; P =.02) lower estradiol, 30.2% (95% CI = 7.0% to 47.7%; P =.02) lower non-sex hormone binding globulin-bound estradiol, 20.7% (95% CI = 4.7% to 34.0%; P =.02) lower estrone, and 28.7% (95% CI = 5.1% to 46.5%; P =.02) lower estrone sulfate levels during the follicular phase of the menstrual cycle and 27.2% (95% CI = 5.7% to 53.1%; P =.01) higher testosterone levels during the luteal phase of the menstrual cycle than did girls in the usual care group. At the last visit, the luteal phase progesterone level was 52.9% (95% CI = 20.0% to 72.3%) lower for girls in the intervention group than for girls in the usual care group (P =.007)., Conclusion: Modest reductions in fat intake during puberty are associated with changes in sex hormone concentrations that are consistent with alterations in the function of the hypothalamic-pituitary-ovarian axis. Whether these changes influence breast cancer risk is currently unknown.

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.

Concern has been raised about the adequacy of radioimmunoassays to measure steroid sex hormones in population studies. We compared steroid sex hormone measurements in serum by radioimmunoassay with mass spectrometry. Four male and four female serum pools with known relative concentrations of steroid sex hormones were measured multiple times by both methods. Because measurements are expected to increase linearly with concentration for each sex, we examined whether the linear regressions of hormone measurements on concentration were the same for radioimmunoassay and mass spectrometry. Estradiol, estrone, androstenedione, testosterone, and dehydroepiandrosterone sulfate were measured in female pools; testosterone, dihydrotestosterone, androstenedione, and dehydroepiandrosterone sulfate were measured in male pools. Regression slopes for radioimmunoassay and mass spectrometry measurements were comparable for all hormones except androstenedione, which had a steeper slope when measured by mass spectrometry (P < or = 0.02). Intercepts for radioimmunoassay and mass spectrometry were similar and close to zero for estradiol, androstenedione, dehydroepiandrosterone sulfate, and in male samples, testosterone. For testosterone in female samples, estrone, and dihydrotestosterone, radioimmunoassay and mass spectrometry intercepts differed significantly. Standard deviations of individual measurements by radioimmunoassay and mass spectrometry differed by hormone and serum concentration; neither method consistently measured hormone concentrations with less variability. Our findings suggest that although absolute concentrations may differ for some hormones, radioimmunoassay and mass spectrometry can yield similar estimates of between subject differences in serum concentrations of most steroid sex hormones commonly measured in population studies. Relative power of studies using radioimmunoassay and mass spectrometry will depend on the hormones measured and their serum concentrations.

Using a general strategy for evaluating clinical tissue specimens, we found that 70% ethanol fixation and paraffin embedding is a useful method for molecular profiling studies. Human prostate and kidney were used as test tissues. The protein content of the samples was analyzed by one-dimensional gel electrophoresis, immunoblot, two-dimensional gel electrophoresis, and layered expression scanning. In each case, the fixed and embedded tissues produced results similar to that obtained from snap-frozen specimens, although the protein quantity was somewhat decreased. Recovery of mRNA was reduced in both quantity and quality in the ethanol-fixed samples, but was superior to that obtained from formalin-fixed samples and sufficient to perform reverse transcription polymerase chain reactions. Recovery of DNA from ethanol-fixed specimens was superior to formalin-fixed samples as determined by one-dimensional gel electrophoresis and polymerase chain reaction. In conclusion, specimens fixed in 70% ethanol and embedded in paraffin produce good histology and permit recovery of DNA, mRNA, and proteins sufficient for several downstream molecular analyses. Complete protocols and additional discussion of relevant issues are available on an accompanying website (http://cgap-mf.nih.gov/).

Researchers working collaboratively in Brazil and the United States have assembled an International Database of Cancer Gene Expression. Several strategies have been employed to generate gene expression data including expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and open reading-frame expressed sequence tags (ORESTES). The database contains six million gene tags that reflect the gene expression profiles in a wide variety of cancerous tissues and their normal counterparts. All sequences are deposited in the public databases, GenBank and SAGEmap. A suite of informatics tools was designed to facilitate in silico analysis of the gene expression datasets and are available through the NCI Cancer Genome Anatomy Project web site (http://cgap.nci.nih.gov).

The Cancer Genome Anatomy Project (CGAP) was designed and implemented to provide public datasets, material resources and informatics tools to serve as a platform to support the elucidation of the molecular signatures of cancer. This overview of CGAP describes the status of this effort to develop resources based on gene expression, polymorphism identification and chromosome aberrations, and we describe a variety of analytical tools designed to facilitate in silico analysis of these datasets.

Cytochrome b5 spontaneously binds to liposomes in a 'loose', or transferable form, whereas in vivo b5 binds post-translationally to the ER in the 'tight' or nontransferable form. The mechanism of tight insertion is unknown, except that it does not require SRP or energy input. The present study shows that prolonged incubation of b5 with large unilamellar vesicles (LUVs) of phosphatidylcholine results in slow conversion of the loose to the tight form, with a halftime of days. However, the process is complex. When the b5-LUVs are depleted of loose b5, by transfer of b5 to sonicated vesicles, the tight b5 is found to be concentrated to near saturating levels in a small fraction of the LUVs. If the LUVs devoid of tight b5 are recovered and then reincubated with fresh b5, the same slow transformation recurs. Apparently, a new population of vesicles, containing tight b5, is generated during the prolonged incubation with the protein. The b5-enriched LUVs contain about the same level of trapped sucrose as does the original vesicle preparation, indicating that vesicle integrity is maintained throughout the process. When fresh b5 is added to these tight b5-containing LUVs, all the freshly bound protein rapidly inserts (< 2 h) into the tight configuration. Apparently, the newly formed tight-b5/LUV vesicle population is 'insertion-active'. A model for these complex transformations is proposed.

The ability of the glycolipid photoprobe, 12-(4-azido-2-nitrophenoxy)-stearoyl[1-14C]glucosamine (12-APS-GlcN), to undergo transbilayer flip-flop and intermembrane transfer between liposomes was examined. It was found that probe which was incorporated into membranes during the preparation of large unilamellar vesicles (LUVs) could be rapidly and completely extracted by incubation of these donor vesicles (in the liquid-crystalline state) with probe-free acceptor vesicles.

Cytochrome b5 is an amphipathic integral membrane protein that spontaneously inserts, post-translationally, into intracellular membranes. When added to preformed phospholipid vesicles, it binds in a so-called "loose," or transferable, configuration characterized by the ability of the protein to rapidly equilibrate between vesicles. A heterogeneous dispersion of sonicated phosphatidylcholine vesicles, 212 to about 350 A in diameter, was prepared by differential centrifugation. When cytochrome b5 was incubated with these vesicles (1 mol of protein/833 mol of phospholipid, in 0.01 M NaHCO3, 0.1 M NaCl, 10(-4) M EDTA, pH 7.4) and the mixture was subjected to molecular sieve chromatography on Sepharose 2B-CL, the cytochrome b5 was found to elute preferentially with the smaller vesicles. Subsequently, a fresh preparation of heterogeneous vesicles was subfractionated by gel filtration, and the individual fractions were incubated with the protein. Molecular sieve chromatography of these complexes showed that cytochrome b5 favors the smallest over the largest vesicles by a factor of at least 20. This result suggests that formation of highly curved regions in biological membranes may cause accumulation of certain membrane proteins at those sites.

Cytochrome b5 is an amphipathic integral membrane protein that spontaneously inserts, post-translationally, into intracellular membranes. When added to preformed phospholipid vesicles, it binds in a so-called "loose" or transferable configuration, characterized by the ability of the protein to rapidly equilibrate between vesicles. In a preliminary report we showed that the distribution of cytochrome b5 among a heterogeneous population of small sonicated phosphatidylcholine vesicles (212 to about 350 A in diameter) lies in favor of the smallest vesicles by a factor of at least 20 (Greenhut, S.F. and Roseman, M.A. (1985) J. Biol. Chem. 260, 5883-5886). In the present studies we have attempted to determine the maximal extent to which bilayer curvature can influence the intervesicle distribution of cytochrome b5, by measuring the distribution of the protein between a population of limit-size vesicles 212 A in diameter and a population of large unilamellar vesicles approximately 1000 A in diameter. (The effect of bilayer curvature on the physical properties of the lipids in the large vesicles is considered to be negligible.) The results show that cytochrome b5 favors the small vesicle population by a factor of about 200. This observation suggests that the formation of highly curved regions in biological membranes (or the formation of regions in which the physical state of the lipids is similar to that in small vesicles) may cause the accumulation of certain membrane proteins at those sites. We also observed that a significant fraction (11-20%) of the cytochrome b5, when added directly to the large vesicles, spontaneously inserts into the "tight," physiologically proper configuration. A possible mechanism is discussed.

Cytochrome b5 induced flip-flop of phosphatidylethanolamine (PE) in sonicated vesicles prepared from a 9:1 mixture of phosphatidylcholine (PC) to phosphatidylethanolamine was determined as follows. First, vesicles having a nonequilibrium distribution of PE across the bilayer were prepared by amidinating the external amino groups with isethionyl acetimidate. Amidinated cytochrome b5 was then added, and after the protein was completely bound, the rate of appearance of fresh PE on the outer surface was determined by removing aliquots at timed intervals and titrating the external amino groups with trinitrobenzenesulfonic acid. The results show an initial rapid phase of flip-flop (especially in the presence of salt) followed by a very slow phase, at 25 degrees C. Similar results were obtained when cytochrome b5 was introduced into the amidinated vesicles by spontaneous transfer from PC donor vesicles. These results indicate that the accumulation of the transferable ("loose") form of cytochrome b5 on the outer surface of a vesicle causes a transient, global destabilization of the bilayer that is relieved by lipid flip-flop. We speculate that this mechanism may be a significant driving force for the transfer of amphipathic molecules across membranes.