Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases.

The genomes of the spirochaetes Borrelia burgdorferi and Treponema pallidum show strong strand-specific skews in nucleotide composition, with the leading strand in replication being richer in G and T than the lagging strand in both species. This mutation bias results in codon usage and amino acid composition patterns that are significantly different between genes encoded on the two strands, in both species. There are also substantial differences between the species, with T.pallidum having a much higher G+C content than B. burgdorferi. These changes in amino acid and codon compositions represent neutral sequence change that has been caused by strong strand- and species-specific mutation pressures. Genes that have been relocated between the leading and lagging strands since B. burgdorferi and T.pallidum diverged from a common ancestor now show codon and amino acid compositions typical of their current locations. There is no evidence that translational selection operates on codon usage in highly expressed genes in these species, and the primary influence on codon usage is whether a gene is transcribed in the same direction as replication, or opposite to it. The dnaA gene in both species has codon usage patterns distinctive of a lagging strand gene, indicating that the origin of replication lies downstream of this gene, possibly within dnaN. Our findings strongly suggest that gene-finding algorithms that ignore variability within the genome may be flawed.

The effect of needle gauge and lidocaine pH on pain during intradermal injection.

UNLABELLED: Local anesthetics can produce pain during skin infiltration. We designed a randomized, prospective trial to determine whether needle gauge and/or solution pH affect pain during the intradermal infiltration of lidocaine. After approval by our institution's human studies review board, 40 healthy adult volunteers gave their consent to participate in this study. All of the volunteers randomly received four intradermal injections. Each volunteer was blinded as to the content of the intradermal injections and to which needle size was used for each injection. Each volunteer randomly received a 0.25-mL intradermal injection of the following four solutions: 1) lidocaine 2% administered through a 25-gauge needle (lido-25); 2) lidocaine 2% mixed with sodium bicarbonate (4 mL of 2% lidocaine plus 1 mL of sodium bicarbonate, pH 7.26) administered through a 25-gauge needle (lido-bicarb-25); 3) lidocaine 2% administered through a 30-gauge needle (lido-30); and 4) lidocaine 2% mixed with sodium bicarbonate (4 mL of 2% lidocaine plus 1 mL of sodium bicarbonate) administered through a 30-gauge needle (lido-bicarb-30). In each patient, the injection site was in the same region for each of the four injections. The skin wheal was tested for appropriate anesthesia using a 19-gauge needle on the skin wheal. A visual analog pain score was recorded after each intradermal injection. The pain scores were significantly higher in the lido-25 (3.2 +/- 0.2) group than in the lido-30 (2.5 +/- 0.3), lido-bicarb-25 (1.9 +/- 0.2), and lido-bicarb-30 (1.3 +/- 0.2) groups. The lido-bicarb-30 injection was also rated as less painful than the lido-30 injection. We found no differences between the lidobicarb-25 and the lido-bicarb-30 injections. Complete analgesia for the 19-gauge needle pain stimulus was achieved in all patients for each injection. We conclude that, overall, the pain intensity of an intradermal injection of 2% lidocaine is low. The addition of sodium bicarbonate to 2% lidocaine decreases the pain associated with an intradermal skin wheal, and although the use of a 30-gauge needle decreases the pain of injection, the addition of sodium bicarbonate seems to have a greater overall effect than needle size. IMPLICATIONS: Forty volunteers randomly received four intradermal injections consisting of 2% lidocaine with or without sodium bicarbonate via a 25- or 30-gauge needle. The addition of bicarbonate had a greater overall effect than needle size in decreasing the pain associated with the intradermal injection of lidocaine.

DNA sequence evolution: the sounds of silence.

Silent sites (positions that can undergo synonymous substitutions) in protein-coding genes can illuminate two evolutionary processes. First, despite being silent, they may be subject to natural selection. Among eukaryotes this is exemplified by yeast, where synonymous codon usage patterns are shaped by selection for particular codons that are more efficiently and/or accurately translated by the most abundant tRNAs; codon usage across the genome, and the abundance of different tRNA species, are highly co-adapted. Second, in the absence of selection, silent sites reveal underlying mutational patterns. Codon usage varies enormously among human genes, and yet silent sites do not appear to be influenced by natural selection, suggesting that mutation patterns vary among regions of the genome. At first, the yeast and human genomes were thought to reflect a dichotomy between unicellular and multicellular organisms. However, it now appears that natural selection shapes codon usage in some multicellular species (e.g. Drosophila and Caenorhabditis), and that regional variations in mutation biases occur in yeast. Silent sites (in serine codons) also provide evidence for mutational events changing adjacent nucleotides simultaneously.

Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases.

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.

Synonymous codon usage in Kluyveromyces lactis.

The nature and variation of synonymous codon usage in 47 open reading frames from Kluyveromyces lactis have been investigated. Using multivariate statistical analysis, a single major trend among K. lactis genes was identified that differentiates among genes by expression level: highly expressed genes have high codon usage bias, while genes of low expression level have low bias. A relatively minor secondary trend differentiates among genes according to G+C content at silent sites. In these respects, K. lactis is similar to both Saccharomyces cerevisiae and Candida albicans, and the same 'optimal' codons appear to be selected in highly expressed genes in all three species. In addition, silent sites in K. lactis and S. cerevisiae have similar G+C contents, but in C. albicans genes they are more A+T-rich. Thus, in all essential features, codon usage in K. lactis is very similar to that in S. cerevisiae, even though silent sites in genes compared between these two species have undergone sufficient mutation to be saturated with changes. We conclude that the factors influencing overall codon usage, namely mutational biases and the abundances of particular tRNAs, have not diverged between the two species. Nevertheless, in a few cases, codon usage differs between homologous genes from K. lactis and S. cerevisiae. The strength of codon usage bias in cytochrome c genes differs considerably, presumably because of different expression patterns in the two species. Two other, linked, genes have very different G+C content at silent sites in the two species, which may be a reflection of their chromosomal locations. Correspondence analysis was used to identify two open reading frames with highly atypical codon usage that are probably not genes.

Evolution of the recA gene and the molecular phylogeny of bacteria.

The DNA sequences of the recA gene from 25 strains of bacteria are known. The evolution of these recA gene sequences, and of the derived RecA protein sequences, is examined, with special reference to the effect of variations in genomic G + C content. From the aligned RecA protein sequences, phylogenetic trees have been drawn using both distance matrix and maximum parsimony methods. There is a broad concordance between these trees and those derived from other data (largely 16S ribosomal RNA sequences). There is a fair degree of certainty in the relationships among the "Purple" or Proteobacteria, but the branching pattern between higher taxa within the eubacteria cannot be reliably resolved with these data.

Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure.

The recent determination of the complete sequence of chromosome III from the yeast Saccharomyces cerevisiae allows, for the first time, the investigation of the long range primary structure of a eukaryotic chromosome. We have found that, against a background G+C level of about 35%, there are two regions (one in each chromosome arm) in which G+C values rise to over 50%. This effect is seen in silent sites within genes, but not in noncoding intergenic sequences. The variation in G+C content is not related to differential selection of synonymous codons, and probably reflects mutational biases. That the intergenic regions do not exhibit the same phenomenon is particularly interesting, and suggests that they are under substantial constraint. The yeast chromosome may be a model of the structure of the human genome, since there is evidence that it is also a mosaic of long regions of different base compositions, reflected in wide variation of G+C content at silent sites among genes. Two possible causes of this regional effect, replication timing, and recombination frequency, are discussed.

Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae.

Codon usage in a sample of 28 genes from the pathogenic yeast Candida albicans has been analysed using multivariate statistical analysis. A major trend among genes, correlated with gene expression level, was identified. We have focussed on the extent and nature of divergence between C.albicans and the closely related yeast Saccharomyces cerevisiae. It was recently suggested that significant differences exist between the subsets of preferred codons in these two species [Brown et al. (1991) Nucleic Acids Res. 19, 4293]. Overall, the genes of C.albicans are more A + T-rich, reflecting the lower genomic G + C content of that species, and presumably resulting from a different pattern of mutational bias. However, in both species highly expressed genes preferentially use the same subset of 'optimal' codons. A suggestion that the low frequency of NCG codons in both yeast species results from selection against the presence of codons that are potentially highly mutable is discounted. Codon usage in C.albicans, as in other unicellular species, can be interpreted as the result of a balance between the processes of mutational bias and translational selection. Codon usage in two related Candida species, C.maltosa and C.tropicalis, is briefly discussed.

Codon usage in Aspergillus nidulans.

Synonymous codon usage in genes from the ascomycete (filamentous) fungus Aspergillus nidulans has been investigated. A total of 45 gene sequences has been analysed. Multivariate statistical analysis has been used to identify a single major trend among genes. At one end of this trend are lowly expressed genes, whereas at the other extreme lie genes known or expected to be highly expressed. The major trend is from nearly random codon usage (in the lowly expressed genes) to codon usage that is highly biased towards a set of 19-20 "optimal" codons. The G + C content of the A. nidulans genome is close to 50%, indicating little overall mutational bias, and so the codon usage of lowly expressed genes is as expected in the absence of selection pressure at silent sites. Most of the optimal codons are C- or G- ending, making highly expressed genes more G + C-rich at silent sites.

A comparison of the antidepressant action of citalopram and amitriptyline.

The response of patients with major depressive illness to citalopram of amitriptyline was compared in a double-blind multi-centre trial. No differences in efficacy were observed, but citalopram had less hypnotic effect, and a remarkably lower profile of side-effects.

Ontogeny of the nerve growth factor receptor in primary cultures of neural crest cells.

Neural crest cells maintained as primary cultures for 4-7 days demonstrated specific binding of radioiodinated nerve growth factor ([125I]NGF); occasionally, significant binding of ([125I]NGF could be detected in 3-day cultures. Parallel cultures processed for indirect immunofluorescence revealed that the NGF receptor-positive neural crest cells represented a subpopulation of the total cells in culture. Cultures aged 4-7 days demonstrated fluorescent cells which were often grouped as aggregates. Some 3-day cultures contained faintly fluorescent cells. One- and two-day cultures were non-fluorescent. Melanocytes did not appear to bind NGF. Preliminary flow cytofluorometric analysis indicated that ca. 28% of neural crest cells in 5-day cultures possessed specific receptors for NGF.

Mutant allele frequencies in domestic cats of Portugal and the Azores.

The genetic profiles of cat populations of mainland Portugal are basically similar to those of the adjacent Atlantic littoral. The profiles of Azorean populations, while relatively homogeneous among themselves, are strikingly different from the mainland. It is tentatively concluded that some form of selective migration was the most important contributing factor in establishing the differences.

Australopithecus and the origin of the genus Homo: aspects of biometry and systematics with accompanying catalog of tooth metric data.

Having compiled a new comprehensive catalog of length and breadth measurements of hominid teeth, descriptive and range statistics for the six widely accepted extinct hominid species have been calculated. The analysis supports the Gingerich and Schoeninger hypothesis about tooth variability. There is as least as much differentiation in tooth metrics between A. africanus and A. afarensis as between other hominid taxa commonly accorded distinct species status. A strong biometrical argument emerges for considering A. afarensis a distinct species and more closely related to the genus Homo than A. africanus. Differentiation between taxa inhabiting different geographic regions is indicated and support is provided for Wright's population genetic model for semi-isolated groups.