The use of plant growth promoting bacterial inoculants as live microbial biofertilizers provides a promising alternative to chemical fertilizers and pesticides. Inorganic phosphate solubilization is one of the major mechanisms of plant growth promotion by plant associated bacteria. This involves bacteria releasing organic acids into the soil which solubilize the phosphate complexes converting them into ortho-phosphate which is available for plant up-take and utilization. The study presented here describes the ability of endophytic bacteria to produce gluconic acid (GA), solubilize insoluble phosphate, and stimulate the growth of Pisum sativum L. plants. This study also describes the genetic systems within three of these endophyte strains thought to be responsible for their effective phosphate solubilizing abilities. The results showed that many of the endophytic strains produced GA (14–169 mM) and have moderate to high phosphate solubilization capacities (~400–1300 mg L−1). When inoculated into P. sativum L. plants grown in soil under soluble phosphate limiting conditions, the endophytes that produced medium-high levels of GA displayed beneficial plant growth promotion effects.

Synonymous codon usage varies considerably among Caenorhabditis elegans genes. Multivariate statistical analyses reveal a single major trend among genes. At one end of the trend lie genes with relatively unbiased codon usage. These genes appear to be lowly expressed, and their patterns of codon usage are consistent with mutational biases influenced by the neighbouring nucleotide. At the other extreme lie genes with extremely biased codon usage. These genes appear to be highly expressed, and their codon usage seems to have been shaped by selection favouring a limited number of translationally optimal codons. Thus, the frequency of these optimal codons in a gene appears to be correlated with the level of gene expression, and may be a useful indicator in the case of genes (or open reading frames) whose expression levels (or even function) are unknown. A second, relatively minor trend among genes is correlated with the frequency of G at synonymously variable sites. It is not yet clear whether this trend reflects variation in base composition (or mutational biases) among regions of the C.elegans genome, or some other factor. Sequence divergence between C.elegans and C.briggsae has also been studied.

Antimicrobial peptides (AMPs) are essential components of innate immunity in a range of species fromDrosophila to humans and are generally thought to act by disrupting the membrane integrity of microbes. In order to discover novel AMPs in the chicken, we have implemented a bioinformatic approach that involves the clustering of more than 420,000 chicken expressed sequence tags (ESTs). Similarity searching of proteinspredicted to be encoded by these EST clusters-for homology to known AMPs has resulted in the in silico identification of full-length sequences for seven novel gallinacins (Gal-4 to Gal-10), a novel cathelicidin and a novel liver-expressed antimicrobial peptide 2 (LEAP-2) in the chicken. Differential gene expression of these novel genes has been demonstrated across a panel of chicken tissues. An evolutionary analysis of the gallinacin family has detected sites-primarily in the mature AMP-that are under positive selection in these molecules. The functional implications of these results are discussed.

When the neutral theory of molecular evolution [ 11 was first proposed, silent (that is, synonymously variable) sites in codons were considered to be ideal candidates for truly neutral evolution [Z]. However, as the DNA sequences of numerous genes were determined, it became apparent that the usage of alternative codons for different amino acids was neither uniform nor random. Furthermore, codonusage patterns were found to vary both among species and among genes from the same genome [ 31. This non-random codon usage was interpreted as evidence of selective differences between codons. Codon selectionThe first species in which patterns of codon usage were elucidated was Escherichia coli, with critical evidence coming from knowledge of the abundance, and anticodon sequence, of the various tRNAs present in the cell [4]. Optimal codons were identified as those best recognized (1) by the most abundant tRNAs (2). Highly expressed genes have a highly biased codon usage, with a very high frequency of the optimal codons, while lowly expressed genes have a more random codon usage [4, 51. To illustrate point (Z), consider the six codons for arginine. These are translated by three tRNAs: one (decoding CGU, CGC and CGA) is one of the most abundant tRNAs in E. coli; the other two are of minor abundance, and are rarely