Methods for discovering novel motifs in nucleic acid sequences

We describe a computer tool to aid the discovery of new motifsin nucleic acid sequences. A typical use would be to analysea set of upstream regions from a family of related genes inorder to find possible control sequences. The heart of the methodis the creation of dictionaries of related subsequences. Thesedictionaries can then be analysed to look for the commonestor best-defined subsequences, those that occur in the highestnumber of different sequences, or for those in equivalent positionswithin the family. We show the application of the method toa set of E. coli promoter sequences. Received on May 9, 1989; accepted on July 27, 1989     

Butenolide from plant-derived smoke enhances germination and seedling growth of arable weed species

We tested the applicability of the recently identified major germination cue from smoke (a butenolide 3-methyl-2Hfuro[2,3-c]pyran-2-one) on 18 weed species from non-fire prone environments. For the study species we compared the relative effectiveness of alternating temperatures, KNO₃, GA₃, smoke water and the butenolide on germination percentage, germination rate and seedling mass. We found that while smoke stimulated germination in a number of species it also had negative impacts on other species. In addition, the butenolide was effective on the widest range of species in terms of enhancing germination percentage, rate and seedling mass. However, none of the treatments, including butenolide were effective on all species. Our data demonstrate that butenolide may have wide applicability as a germination and seedling growth stimulant irrespective of whether the species come from fire-prone habitats.     

Polyamines and carnation flower senescence: Endogenous levels and the effect of applied polyamines on senescence

The polyamines putrescine and spermine were effective in delaying the senescence of carnation buds, but were ineffective when applied to flowers of which the petals had already opened, and were 90° with respect to the stem. Higher levels of endogenous putrescine were detected in the open flowers than in the buds, and this may explain the negative effect obtained when polyamines were applied to open flowers that were picked for commercial distribution.Abbreviations AOA amino-oxyacetic acid - AVG amino-ethoxyvinyl-glycine - SAM S-adenosyl methionine - STS silver thiosulphate     

A molecular mechanics study of spermine complexation to DNA: a new model for spermine-poly(dG-dC) binding.

Molecular mechanics calculations of the binding of spermine to a number of solvated DNA helices have led to the development of a new model for spermine complexation. The structural details of the complexes formed with d(GCGCGCGCGC)2 and d(ATATATATAT)2 decamers allowed a rationalization of the observed experimental differences for binding to these two helices. For d(ATATATATAT)2 it was concluded that spermine remains in a cross-major groove binding site. Conversely, for d(GCGCGCGCGC)2 spermine reorientation via specific ligand-base-pair hydrogen-bond formation allows complexation along the major groove. The solvent plays an important role in differentiating the two binding modes. A mechanism of spermine complexation to natural DNA is postulated from these results. Past experimental data are also considered in the context of the new model.     

Plant-derived smoke solutions stimulate the growth of Lycopersicon esculentum roots in vitro

Aqueous extracts of smoke, derived from Themeda triandra, a fire-climax grass, and Passerina vulgaris, a fynbos plant, stimulated the growth of primary root sections of tomato roots in suspension culture. The optimal dilution for both extracts was 1:2000. Several of the fractions obtained from TLC separation of the Themeda and the Passerina extracts significantly promoted primary root growth. The auxins naphthaleneacetic acid (NAA), indolebutyric acid (IBA) and indoleacetic acid (IAA) were found to stimulate the growth of the primary root axis, with IAA and NAA significantly promoting lateral root number. Similarly, the naturally occurring cytokinins, zeatin and its derivatives (zeatin-O-glucoside; dihydrozeatin and zeatin riboside) stimulated primary root length. Zeatin and dihydrozeatin promoted secondary root growth, but only at very low concentrations.