Genomic mapping by fingerprinting random clones: a mathematical analysis

Results from physical mapping projects have recently been reported for the genomes of Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans, and similar projects are currently being planned for other organisms. In such projects, the physical map is assembled by first "fingerprinting" a large number of clones chosen at random from a recombinant library and then inferring overlaps between clones with sufficiently similar fingerprints. Although the basic approach is the same, there are many possible choices for the fingerprint used to characterize the clones and the rules for declaring overlap. In this paper, we derive simple formulas showing how the progress of a physical mapping project is affected by the nature of the fingerprinting scheme. Using these formulas, we discuss the analytic considerations involved in selecting an appropriate fingerprinting scheme for a particular project.     

Expression of mRNA encoding basic fibroblast growth factor (bFGF) in bovine corpora lutea and cultured luteal cells.

A radiolabelled cRNA was synthesized using a 1.4 kb cDNA complementary to mRNA encoding bovine basic fibroblast growth factor (bFGF) as a template, and used as a probe to investigate the expression of mRNA encoding bFGF in bovine ovarian tissue, and luteal cells in primary culture. Northern analysis of poly(A +)RNA prepared from follicles and corpora lutea of various stages revealed a major mRNA species of 7 kb in corpora lutea of all stages, the amount of which was higher late in the luteal phase. No hybridizable message was detectable in follicles of any size. When luteal cells were established in primary culture, expression of the 7 kb mRNA species was maintained. This expression was increased markedly when cells were treated with LH/hCG or Bt2cAMP. Prostaglandin F-2 alpha treatment caused a marked decrease in the basal content of this 7 kb mRNA, and also severely impaired the ability of LH to stimulate this expression.     

Import and processing of P-450SCC and P-450(11) beta precursors by corpus luteal mitochondria: a processing pathway recognizing homologous and heterologous precursors

Maturation of the precursor forms of bovine cholesterol side-chain cleavage cytochrome P-450 (P-450SCC) and 11 beta-hydroxylase cytochrome P-450 (P-450(11)beta) was investigated using mitochondria from bovine corpus luteum. The results show that both precursors, whose synthesis was directed by bovine adrenocortical RNA, can be imported and proteolytically processed to their corresponding mature forms by bovine corpus luteal mitochondria, even though P-450(11)beta is not expressed in this tissue. Furthermore, the efficiency of processing of pre-P-450(11)beta by corpus luteal mitochondria is similar to that of pre-P-450SCC, an endogenous enzyme of these mitochondria. However, the P-450(11)beta precursor is not processed by mitochondria from a nonsteroidogenic tissue (heart), a result observed previously for the P-450SCC precursor (M. F. Matocha and M. R. Waterman (1984) J. Biol. Chem. 259, 8672-8678). This discriminatory processing of pre-P-450(11)beta by heterologous mitochondria suggests that the precursor forms of P-450SCC and P-450(11)beta are processed via a common pathway in steroidogenic mitochondria and that this pathway is absent in nonsteroidogenic mitochondria.     

The influence of drainage and soil phosphorus on the vegetation of Douala-Edea Forest Reserve,Cameroun

All living trees (30 cm gbh) were enumerated in 104 80×80 m plots arranged along four transects in the Douala-Edea Forest Reserve Cameroun, a system of low-lying ancient coastal sand dunes interspersed by numerous streams and swamps. The extent of permanent and seasonal swamps was recorded for each plot. Two hundred thirty taxa were recognized of which 63% were identified to species. Mean tree density was 376 ha^–1, basal area 31.0 m² ha^–1 and number of species per plot 39. The Olacaceae were the most abundant family in terms of basal area, but the Euphorbiaceae the most frequently represented. The most abundant species wasCoula edulis (Olacaceae). Twenty-two plots had most of their area permanently or seasonally swamped. Percentage sand, silt and clay ranged between 32–100, 0–64, 0–21% respectively. The ranges for other variables recorded were: pH (2.7–5.4), organic carbon (1.5–12.4%), available phosphorus (7–90 ppm) and potassium (28–188 ppm), and nitrogen (ammonium 4–40 ppm, nitrate 1–12 ppm).Classification of the plots on the basis of six soil variables provided three large distinct groups: swamp plots and non-swamp plots, the latter divided into plots of low and high available soil phosphorus. Swamp plots were distinguished by high abundances ofProtomegabaria stapfiana andLibrevillea klainei, though correspondence ordination of plots in these groups showedP. stapfiana associated with more clayey soils andLibrevillea klainei (andGluema ivorensis) on the very sandy soils. Direct gradient analysis highlighted several species associated with these lower phosphorus soils. Available soil phosphorus is not as low at Douala-Edea as in parts of Korup, and the association of these Douala-Edea soils with the Caesalpinioideae is correspondingly weaker.Nomenclature follows Aubréville (1963–1983).The field work was supported by grant numbers RR00167-14, RR00167-15 and RR0167-16 from the National Institutes of Health for the operation of the Wisconsin Regional Primate Research Center, and N.A.T.O. Scientific Affairs grant number 1748 (to PGW and JSG). It was greatly facilitated by the skill and dedication of Ferdinand Namata. R. M. Polhill and D. W. Thomas assisted considerably in the identification of plant species. Sue Gartlan collected and collated the meteorological data, besides other field support. In the field phase J.S.G., P.G.W. and D.B.McK. were researches attached to the National Office of Scientific and Technical Research (ONAREST), Yaoundé. We thank M. D. Swaine for comments on earlier drafts, R. Letouzey for checking species nomenclature, the Computer Unit at Stirling University for facilities, M. Burnett for the typing at Stirling, and the Department of Soil Science, University of Wisconsin, for undertaking the soil chemical analyses.Reprint requests to D.McC.N. at Stirling.Publication No. 23-025 of the Wisconsin Regional Primate Center.     

3 Beta-hydroxysteroid dehydrogenase-isomerase activity in bovine adrenocortical cells in culture: lack of response to ACTH treatment

Primary cultures of bovine adrenocortical cells (BAC) were used to determine whether the adrenal microsomal 3 beta-hydroxysteroid dehydrogenase-isomerase complex (3 beta-HSD), like the 17 alpha-hydroxylase (17-OHase), responded to ACTH treatment with an increase in activity. Both enzymes influence the steroidogenic path leading to 17 alpha-hydroxyprogesterone formation and thus could affect adrenal androgen biosynthesis. 3 beta-HSD Activity in postmitochondrial supernatant fluid, homogenates or cell monolayers remained unchanged after cells had been maintained in 1 microM ACTH up to 48 h. Since ACTH exposure led to a marked increase in 17-OHase activity over the same time period, it is concluded that, under the conditions used, the 3 beta-HSD-isomerase complex in BAC is nonresponsive to tropic hormone treatment.     

Multiple sequence alignment by consensus.

An algorithm for multiple sequence alignment is given that matches words of length and degree of mismatch chosen by the user. The alignment maximizes an alignment scoring function. The method is based on a novel extension of our consensus sequence methods. The algorithm works for both DNA and protein sequences, and from earlier work on consensus sequences, it is possible to estimate statistical significance.     

Statistical characterization of nucleic acid sequence functional domains

It has long been recognized that various genome classes were distinguishable on the basis of base composition and nearest neighbor frequencies. In addition Grantham et al. (8) have recently presented evidence that these distinctions are preserved at the level of codon usage. As discussed in this report it is now clear that these and related statistics can uniquely characterize the various functional domains of the genome. In particular peptide coding, intervening segments, structural RNA coding and mitochondrial domains of the vertebrate genome are uniquely characterizable. The statistical measures not only reflect understood functional differences among these domains but suggest others. The ability of these simple statistics of nucleic acid sequences to reflect so much of the encoded complex pattern information and/or effects of selective constraints is somewhat surprising. Here, we investigated the statistical measures most distinctive of the various domains and then linked them to our current understandings in so far as possible.