On the reliable identification of plant sequences containing a polyadenylation site.

It is a challenging task to predict with high reliability whether plant genomic sequences contain a polyadenylation (polyA) site or not. In this paper, we solve the task by means of a systematic machine-learning procedure applied on a dataset of 1000 Arabidopsis thaliana sequences flanking polyA sites. Our procedure consists of three steps. In the first step, we extract informative features from the sequences using the highly informative k-mer windows approach. Experiments with five classifiers show that the best performance is approximately 83%. In the second step, we improve performance to 95% by reducing the number of features using linear discriminant analysis, followed by applying the linear discriminant classifier. In the third step, we apply the transductive confidence machines approach and the receiver operating characteristic isometrics approach. The resulting two classifiers enable presetting any desired performance by dealing carefully with sequences for which it is unclear whether they contain polyA sites or not. For example, in our case study, we obtain 99% performance by leaving 26% of the sequences unclassified, and 100% performance by leaving 40% of the sequences unclassified. This is clearly useful for experimental verification of putative polyA sites in the laboratory. The novel methods in our machine-learning procedure should find applications in several areas of bioinformatics.     

The biological properties of bovine parathyroid hormone (1–41), a fragment generated from the native hormone by human leukocytes

Native bovine parathyroid hormone (bPTH) was found to be readily cleaved with human leukocyte elastase to yield the fragments bPTH(1–41) and bPTH(42–84). These were then isolated by reverse-phase HPLC and characterised by gas-phase sequencing and amino acid analysis. The biological activities of these fragments were assessed in an adenylate cyclase bioassay using the rat osteosarcoma cell line UMR106. bPTH(1–41) was found to have approximately twice the molar potency of the native hormone from which it was derived, bPTH(42–84) had no biological activity and did not modulate the adenylate cyclase response to these cells to the native hormone. The possible physiological significance of these observations is discussed.     

Transformation of the forage legume Trifolium repens L. using binary Agrobacterium vectors

A system was established for introducing cloned genes into white clover (Trifolium repens L.). A high regeneration white clover genotype was transformed with binary Agrobacterium vectors containing a chimaeric gene which confers kanamycin resistance. Transformed kanamycin resistant callus was obtained by culturing Agrobacterium inoculated stolon internode segments on selective medium. The kanamycin resistance phenotype was stable in cells and in regenerated shoots. Transformation was confirmed by the expression of an unselected gene, nopaline synthase in selected cells and transgenic shoots and by the detection of neomycin phosphotransferase II enzymatic activity in kanamycin resistant cells. Integration of vector DNA sequences into plant DNA was demonstrated by Southern blot hybridisation.     

Gonadotrophins, fecundity genes and ovarian follicular function

The Booroola Merino is a sheep breed having a major gene(s) (F) influencing its ovulation-rate. Homozygous (FF), heterozygous (F+) and non-carriers (++) of the gene have ovulation-rates of greater than or equal to 5, 3 or 4 and 1 or 2 respectively with the durations of each oestrous cycle and oestrous behaviour being similar in all genotypes. Although the principal site(s) of gene expression are obscure, FF genotypes have mean plasma concentrations of FSH and LH which are higher than in the F+ ewes, which in turn are higher than in the ++ animals. Thus, the FF and F+ animals provide a unique system in which to examine ovarian function under continual exposure to elevated gonadotrophin concentrations. At the ovarian level, F gene-specific differences in follicular development and function were noted. In small follicles (0.1-1.0 mm dia.), the basal levels of cAMP and the in vitro synthesis of cAMP, progesterone, androstenedione and oestradiol-17 beta in response to LH and FSH were significantly influenced by genotype (FF greater than F+ greater than ++; P less than 0.05). In larger follicles (1-4.5 mm dia.) the granulosa cells from FF and F+ ewes were more responsive to FSH and/or LH than in ++ ewes with respect to cAMP synthesis and they also had higher levels of aromatase activity. In vivo, the ovarian secretion-rates of oestradiol from greater than or equal to 5 ("oestrogenic") follicles in FF ewes, 3-4 such follicles in F+ ewes, and 1-2 such follicles in ++ animals during the follicular phase were similar. In FF and F+ ewes, the preovulatory follicles ovulated at a smaller diameter (i.e. 3-5 mm) than in ++ ewes (greater than 5 mm diam.) and also produced smaller corpora lutea. Thus, after continual exposure to elevated levels of gonadotrophins, follicles may synthesize steroid and mature at smaller diameters compared to those exposed to normal levels of FSH and LH.     

Methods for detecting non-randomness in species co-occurrences: a contribution

Summary Comparison of co-occurrences between species on a group of islands with those expected from a randombased null model could provide evidence on community structure. However, it is difficult to decide on the appropriate null model. Gilpin and Diamond proposed a model and a test for departure from it, but this test is shown to indicate significant structure even when applied to a matrix of random numbers. An alternative method is suggested, using the distribution of Gilpin and Diamond's deviation as test statistic, but determining the expected distribution by Monto Carlo simulation, and using many such simulations as a randomisation test of significance. The null model used accepts the observed totals of occurrences for islands and species; it therefore offers a somewhat conservative test. Applied to the Vanuatu bird data that Gilpin and Diamond used, significant departure from a null model is seen, but with an excess of extreme negative associations, the opposite result from that given by Gilpin and Diamond's method. It is not possible to tell whether the negative associations are due to autecology, biogeography, or to interactions between species.     

Effect of high temperature on calcium uptake by suspension-cultured pear fruit cells

Uptake of Ca²⁺ by suspension-cultured pear (Pyrus communis L. cv Passe Crassane) cells and protoplasts was significantly enhanced by exposure to 38°C compared to 25°C. The increased uptake was specific for Ca²⁺ and was not due to cell wall binding. Tissues pretreated at 38°C showed increased uptake even upon return to 25°C. Treatment with carbonylcyanide m-chlorophenylhydrazone, salicylhydroxamic acid + KCN, or arsenite also increased Ca²⁺ content of cells. Results are discussed with regard to membrane permeability changes, the cellular control of Ca²⁺, and heat treatments used to inhibit softening of fruit during postharvest storage.     

Faunal and chemical dynamics of some acid and alkaline New Zealand streams

SUMMARY 1. Water from acid (pH 4.3–5.7), brown water streams was low in alkalinity (0–2.3 g m^?3 CaCO₃) and conductivity (2.5–4.1 mS m^?1) but contained relatively high concentrations of dissolved organic carbon (6.6–16.3 gm^?3). In contrast, alkaline (pH 6.6–8.0), clearwater streams had high CaCO₃ (12.6–57.6 g m^?3) and conductivity (3.7–22.3 mS m^?1) but low dissolved organic carbon concentrations (0.3–4.7 g m^?3). 2. Total reactive aluminium (Al) concentrations were high in acid streams (123–363 mg m?³) but never exceeded 84 mg m?³ in alkaline streams. Acid-soluble and organic monomeric Al were the major Al species in the acid streams (31–168 and 84–178mg m?³, respectively). Concentrations of toxic inorganic monomeric Al were low in all streams (<50mg m?³). 3. Sixty-four invertebrate taxa were collected from the alkaline streams compared to forty-seven from the acid sites. Numbers of taxa in specific insect orders were similar at all sites, however. Benthic faunas at most sites were dominated by the mayfly Deleatidium sp. and chironomids. 4. Overall, mean densities of benthic invertebrates were 2.4–4.8 times higher in alkaline streams than acid streams. No seasonal patterns of abundance were evident at any site. 5. Temporal variability of invertebrate densities was correlated with stream channel stability such that fluctuations in densities declined as stability increased. 6. Sources of dissolved organic carbon and aluminium in acid, brown water streams are discussed. We suggest that changes in the food supply available in acid streams account for the depauperate faunas found there.     

Workshop on algal polysaccharides

Summary This workshop was an impromptu event, but the fact that a number of interesting problems were identified by the participants from the floor may indicate that it is worth repeating. If it is to be repeated, however, it is important that notice be given, and that the scope of the workshop be defined in advance, so that participants can be better informed and bring supporting data. The best approach would be to identify a convenor and define the scope of the workshop prior to the first circular for the next Seaweed Symposium; invitations could then be issued by the convenor for specific topics and data, and a very brief program could be issued with the third circular. Such a procedure may very well allow the identification of new areas for research.