The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

Ancient cells must have possessed small gene content. Primitive enzymes may have possessed broad specificity and undeveloped regulation mechanisms. The considerable substrate ambiguity of these enzymes resulted in the formation of minor amounts of erroneous products. Fortuitous formation of metabolites offered ancient cells maximum biochemical flexibility with minimal gene content. Gene duplication provided the opportunity for increased gene content and increased specialization of the diverging enzymes, the substrate specialization being further reinforced by the development of regualtory mechanisms. Recuritment of enzymes for new pathways did not necessarily require the sequential and backwardly evolving progression of evolutionary steps required by the hypothesis of retrograde evolution of biochemical pathways. Substrate ambiguity remains a conspicuous feature of many contemporary proteins, and evolutionary exploitation of substrate ambiguity in a variety of organisms is still apparent.

We have characterized expression of the familial breast and ovarian cancer gene, BRCA1, in cases of non-hereditary (sporadic) breast cancer and analyzed the effect of antisense inhibition of BRCA1 on the proliferative rate of mammary epithelial cells. BRCA1 mRNA levels are markedly decreased during the transition from carcinoma in situ to invasive cancer. Experimental inhibition of BRCA1 expression with antisense oligonucleotides produced accelerated growth of normal and malignant mammary cells, but had no effect on non-mammary epithelial cells. These studies suggest that BRCA1 may normally serve as a negative regulator of mammary epithelial cell growth whose function is compromised in breast cancer either by direct mutation or alterations in gene expression.

NIH sponsored a meeting of medical and veterinary pathologists with mammary gland expertise in Annapolis in March 1999. Rapid development of mouse mammary models has accentuated the need for de®nitions of the mammary lesions in genetically engineered mice (GEM) and to assess their usefulness as models of human breast disease. The panel of nine pathologists independently reviewed material representing over 90% of the published systems. The GEM tumors were found to have: (1) phenotypes similar to those of non-GEM; (2) signature phenotypes speci®c to the transgene; and (3) some morphological similarities to the human disease. The current mouse mammary and human breast tumor classi®cations describe the majority of GEM lesions but unique morphologic lesions are found in many GEM. Since little information is available on the natural history of GEM lesions, a simple morphologic nomenclature is proposed that allows direct comparisons between models. Future progress requires rigorous application of guidelines covering pathologic examination of the mammary gland and the whole animal. Since the phenotype of the lesions is an essential component of their molecular pathology, funding agencies should adopt policies ensuring careful morphological evaluation of any funded research involving animal models. A pathologist should be part of each research team. Oncogene (2000) 19, 968 ± 988.

The authors thank the more than 70 clinicians and pathologists who provided clinical follow-up information, Sandy Olson for discussions, Julia Smith and Robena Ross for technical support, and Jean McClure for assistance with the article.

Background. The stratification of ductal carcinoma in situ (DCIS) of the human breast into prognostically relevant categories by size and histologic pattern is a current concern. Few studies have been able to follow women after the identification of any type of DCIS when they have had biopsy only. Methods. This is an extension of a follow‐up study of a group of 28 women with small, noncomedo ductal carcinomas in situ that were excised by biopsy only, published in 1982. All these women have now been successfully followed for an average of almost 30 years. Results. The overall risk of development of invasive carcinoma for these women over almost 30 years is nine times that of the general population (95% confidence interval, 4.7–17). This is similar to the 11‐fold elevation in relative risk that was determined after about 15 years of follow‐up. All invasive carcinomas have developed in the same area in the same breast. There were two women in whom invasive carcinoma developed between 20 and 30 years after initial biopsy. One other woman had an extensive noncomedo DCIS that was identified 25 years after her initial biopsy, but had no evidence of invasive disease. Conclusion. The natural history of small, noncomedo DCIS can last over at least 2 decades, with invasive carcinoma developing at the same site in which DCIS was previously discovered in a significant percentage of women (broadly, between 25%–50%). This is quite different from the natural history of comedo DCIS or any type of DCIS treated purposefully by surgery alone.

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The breast cancer predisposition genes, BRCA1 and BRCA2, are responsible for the vast majority of hereditary breast cancer. Although BRCA2 functions to help the cell repair double-stranded DNA breaks, the function of BRCA1 remains enigmatic. Here, we develop a human genetic system to study the role of BRCA1 in oxidative DNA damage. We show that human cancer cells containing mutated BRCA1 are hypersensitive to ionizing radiation. This hypersensitivity can be reversed by the expression of forms of BRCA1 that are not growth suppressing. Reversal of hypersensitivity requires the ring finger of BRCA1, its transactivation domain, and its BRCT domain. Lastly, we show that unlike BRCA2, BRCA1 does not function in the repair of doublestranded DNA breaks. Instead, it functions in transcription-coupled DNA repair (TCR). TCR ability correlated with radioresistance as cells containing BRCA1 showed both increased TCR and radioresistance, whereas cells without BRCA1 showed decreased TCR and radiosensitivity. These findings give physiologic significance to the interaction of BRCA1 with the basal transcription machinery.BRCA1 and BRCA2, the breast cancer 1 and 2 genes, are responsible for over 90% of hereditary breast cancers (1-4). Although BRCA2 has been shown to affect the repair of doublestranded DNA breaks reviewed in Ref. 9), a clear consensus has not been reached on the function of BRCA1. Unfortunately, BRCA1Ϫ/Ϫ mice die at day 6.5 to day 8.5 of embryonic gestation because of lack of proliferation of the mouse blastocyst (10 -12). Despite this embryonic lethality, work in the mouse systems has resulted in two suggestive findings. First, when BRCA1 Ϫ/Ϫ mice are mated with p53mice to generate BRCA1 Ϫ/Ϫ p53 Ϫ/Ϫ mice, these double-knock out mice show reduced embryonic lethality (13,14), suggesting that BRCA1 and p53 may lie on a common functional pathway. The second finding is that cells from BRCA1 Ϫ/Ϫ mice have a defect in transcription-coupled DNA repair (TCR) 1 (15), implying that BRCA1 may be involved in DNA repair and/or the stress response of the cell.Despite these suggestive findings in the mouse system, there are such large differences in mouse and human BRCA1 biology that it is unclear whether the DNA repair function of mouse BRCA1 is applicable to human BRCA1. Mouse BRCA1 is only 57% homologous to human BRCA1 (10 -12), and BRCA1 appears to function differently in the two systems. Although BRCA1 has been shown to be required for cellular proliferation during mouse development, BRCA1 has been shown to be a powerful growth suppressor in both yeast and human systems (16 -20). Although there are reports of living humans who are homozygous for BRCA1 mutations (21), mice carrying homozygous BRCA1 mutations die early in gestation. Lastly, DNA repair in a mouse cell is not necessarily indicative of repair in a human cell (22)(23)(24). Mouse and human cells show differences in the amount of damage sustained per given DNA-damaging dose, in the kinetics of DNA repair, and in cellular survival at a given dose of a DNA-damaging ...