Electronic data publishing and GenBank.

GenBank, the national repository for nucleotide sequence data, has implemented a new model of scientific data management, which we term electronic data publishing. In traditional publishing, both scientific conclusions and supporting data are communicated via the printed page, and in electronic journal publishing, both types of information are communicated via electronic media. In electronic data publishing, by contrast, conclusions are published in a journal while data are published via a network-accessible, electronic database.

Identifying potential tRNA genes in genomic DNA sequences.

We have developed an algorithm that automatically and reproducibly identifies potential tRNA genes in genomic DNA sequences, and we present a general strategy for testing the sensitivity of such algorithms. This algorithm is useful for the flagging and characterization of long genomic sequences that have not been experimentally analyzed for identification of functional regions, and for the scanning of nucleotide sequence databases for errors in the sequences and the functional assignments associated with them. In an exhaustive scan of the GenBank database, 97.5% of the 744 known tRNA genes were correctly identified (true-positives), and 42 previously unidentified sequences were predicted to be tRNAs. A detailed analysis of these latter predictions reveals that 16 of the 42 are very similar to known tRNA genes, and we predict that they do, in fact, code for tRNA, yielding a false-positive rate for the algorithm of 0.003%. The new algorithm and testing strategy are a considerable improvement over any previously described strategies for recognizing tRNA genes, and they allow detections of genes (including introns) embedded in long genomic sequences.

Characterization of the distribution of potential short restriction fragments in nucleic acid sequence databases. Implications for an alternative to chemical synthesis of oligonucleotides.

We have searched the GenBank nucleic acid sequence database for potential short restriction fragments. All possible oligonucleotides up to length five are found at least once flanked by known restriction recognition patterns. Thus, searches in the database for a specific sequence corresponding to a desired oligonucleotide would often point to one or more sources of short, retrievable fragments containing that sequence. These results underscore the potential of nucleic acid sequence databases in planning experiments.

Limitations of the lipid state hypothesis for atherosclerosis are revealed by X-ray diffraction measurements.

The lipid state hypothesis proposes that liquid crystalline states of cholesteryl esters play a role in the development and persistence of the fatty streak lesions characteristic of atherosclerosis. We have tested several corollaries suggested by this hypothesis and find that the ensemble of droplets in atherosclerotic tissue are predominantly in the isotropic (fluid) state at 37.0 degrees C. Furthermore, the liquid-crystalline state transition behavior of these droplets is not influenced significantly by the distribution of component cholesteryl ester species. There are no significant correlations between the transition behavior of the droplets and the age, sex, or race of the subjects from which tissue samples were taken. These results show that the lipid state hypothesis is weak, and that the origin and persistence of fatty streak lesions in humans is probably dominated by other factors.

A program for computer-assisted scoring of Southern blots.

SCORE, a program for computer-assisted scoring of Southern blots of clone DNA, retains the use of expert human judgment while taking over much of the drudgery of the scoring task. The primary functions of the program are to help make an aligned overlay of the fluorescence gel image and the autoradiogram blot image, to keep track of band and lane locations and to store the resulting data directly into a database. Use of SCORE has resulted in greatly increased efficiency and accuracy.

DNA structural patterns and nucleosome positioning.

There is no clear picture to date of the mechanisms determining nucleosome positioning. Generally, local DNA sequence signals (sequence-dependent positioning) or non-local signals (e.g. boundary effects) are possible. We have analyzed the DNA sequences of a series of positioned and mapped nucleosome cores in a systematic search for local sequence signals. The data set consists of 113 mapped nucleosome cores, mapped in vivo, in situ, or in reconstituted chromatin. The analysis focuses on the periodic distribution of sequence elements implied by each of six different published DNA structural models. We have also investigated the periodic distribution of all mono-, di-, and trinucleotides. An identical analysis was performed on a set of isolated chicken nucleosome cores (nucleosome data from the literature) that are presumably positioned due to local sequence signals. The results show that the sequences of the isolated nucleosome cores have a number of characteristic features that distinguish them clearly from randomly chosen reference DNA. This confirms that the positioning of these nucleosomes is mainly sequence-dependent (i.e., dependent on local octamer-DNA interactions) and that our algorithms are able to detect these patterns. Using the same algorithms, the sequences of the mapped nucleosome cores, however, are on average very similar to randomly chosen reference DNA. This suggests that the position of the majority of these nucleosomes can not be attributed to the sequence patterns implemented in our algorithms. The arrangement of positioned nucleosomes seems to be the result of a dynamic interplay of octamer-DNA interactions, nucleosome-nucleosome interactions and other positioning signals with varying relative contributions along the DNA.

A quantitative measure of DNA curvature enabling the comparison of predicted structures.

A growing body of data indicates that the equilibrium structures of some DNA fragments are curved and that curvature is sequence-directed. We describe a quantitative measure of DNA curvature that can be used for evaluating and comparing current proposed models for the molecular basis of DNA curvature. We demonstrate that this measure, in conjunction with any given prediction model, enables both the comparison of experimental data to predictions and the scanning of nucleotide sequence databases for potential curved regions.

Partial purification of plasma phenoloxidase of the yellow fever mosquito Aedes aegypti L. (Diptera: Culicidae).

A nitrocellulose-based assay was developed using a dot-blot apparatus to detect phenoloxidase activity in column fractions. Using this assay, plasma phenoloxidase was partially purified from Aedes aegypti larvae using hydrophobic interaction chromatography, gel filtration, and ion-exchange chromatography. The molecular weight (M(r)) native enzyme was 130,000, and it contained subunits of 76,000, 62,000, and 58,000. Two phenoloxidase peaks were observed by ion exchange chromatography, and these fractions had distinct polypeptide profiles as detected by SDS-PAGE.

Schedule-induced polydipsia: are response-dependent schedules a limiting condition?

The collateral water intake of albino rats was measured when the inter-pellet intervals in fixed-ratio and fixed-time schedules were equated. Fixed-ratio and fixed-time inter-pellet intervals were equated by dividing the average fixed-ratio session time of each subject by 150 (food pellets). The average inter-pellet interval obtained then defined the subsequent fixed-time schedule for each individual subject. Shifts to fixed-time schedules followed the completion of each fixed-ratio 20, 40, and 80 schedule. This procedure permitted an assessment of the extent to which excessive collateral drinking was associated with inter-pellet interval length or adventitious food reinforcement. For both the fixed-ratio and fixed-time schedules, drinking progressively increased as a function of increasing the duration of the inter-pellet interval and was a post-pellet event under the control of variables other than adventitious food reinforcement.

Cardiovascular risks: among Black and White rural-urban low income women.

The purpose of this descriptive comparative pilot study was to determine if there are rural-urban and racial differences in the prevalence of four modifiable risk factors (blood pressure, serum cholesterol, diabetes and smoking) for cardiovascular disease among low income Black and White women. Of the 163 low income women who participated in the study, it was found that Black women had a significantly higher prevalence of elevated blood pressure and serum cholesterol levels than White women. The observed rates for smoking and diabetes were highest among rural White women. Implications for health education and continued research are presented.

Unusual pheromone chemistry in the navel orangeworm: novel sex attractants and a behavioral antagonist.

Using molecular- and sensory physiology-based approaches, three novel natural products, a simple ester, and a behavioral antagonist have been identified from the pheromone gland of the navel orangeworm, Amyelois transitella Walker (Lepidoptera: Pyralidae). In addition to the previously identified (Z,Z)-11,13-hexadecadienal, the pheromone blend is composed of (Z,Z,Z,Z,Z)-3,6,9,12,15-tricosapentaene, (Z,Z,Z,Z,Z)-3,6,9,12,15-pentacosapentaene, ethyl palmitate, ethyl-(Z,Z)-11,13-hexadecadienoate, and (Z,Z)-11,13-hexadecadien-1-yl acetate. The C(23) and C(25) pentaenes are not only novel sex pheromones, but also new natural products. In field tests, catches of A. transitella males in traps baited with the full mixture of pheromones were as high as those in traps with virgin females, whereas control and traps baited only with the previously known constituent did not capture any moths at all. The navel orangeworm sex pheromone is also an attractant for the meal moth, Pyralis farinalis L. (Pyralidae), but (Z,Z)-11,13-hexadecadien-1-yl acetate is a behavioral antagonist. The new pheromone blend may be highly effective in mating disruption and monitoring programs.

Molecular Biology Database List.

Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list (http://www.oup.co.uk/nar/Volume_27/Issue_01/summary/ gkc105_gml.html) which includes links both to source Web sites and to on-line versions of articles describing the databases.