The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias

Genes sequences from Escherichia coli, Salmonella typhimurium, and other members of the Enterobacteriaceae show a negative correlation between the degree of synonymous-codon usage bias and the rate of nucleotide substitution at synonymous sites. In particular, very highly expressed genes have very biased codon usage and accumulate synonymous substitutions very slowly. In contrast, there is little correlation between the degree of codon bias and the rate of protein evolution. It is concluded that both the rate of synonymous substitution and the degree of codon usage bias largely reflect the intensity of selection at the translational level. Because of the high variability among genes in rates of synonymous substitution, separate molecular clocks of synonymous substitution might be required for different genes.      

Reductive dechlorination of tetrachloroethene by two compost samples with different maturity

This study sets up microcosms using two types of compost samples, bagasse/manure compost, and yard-trimming compost with different maturity, to evaluate their capacity for reductive dechlorination of tetrachloroethene (PCE). The experimental results show that less matured compost samples could reduce 300 μM of PCE to ethene within 180 days of incubation. Decreasing initial PCE concentration and removing dissolved oxygen from the solution could enhance reducing efficiency. The solution remains near neutral pH throughout the experiment, and ethene emerged when the redox potential dropped to below -150 mV. Different microbial inhibition agents, such as 2-bromoethanesulfonic acid and sodium molybdate 2-hydrate, exhibit different effects on the dechlorination efficiency. The potential advantages of using compost to remove PCE are discussed. Overall, due to their high carbon content, diverse microbial activity, high buffer capacity, and complex physical structure, compost samples could serve as suitable media for dechlorinating PCE.     

Structure-activity studies on the inhibition of gamma-aminobutyric acid uptake in brain slices by compounds related to nipecotic acid.

Various N-methyl derivatives of nipecotic acid and related compounds were tested as inhibitors of gamma-aminobutyric acid (GABA) uptake into mini slices. N-Methylnipecotic acid, N,N-dimethylnipecotic acid, N-methylguvacine, and N-methylnicotinic acid were effective inhibitors. None of them, however, were as potent as nipecotic acid itself. All the effective inhibitors, including nipecotic acid, also inhibited the uptake of L-proline, but to a much lesser extent. Four of the test compounds produced a depressant action on cerebral cortical neurons, but even N-methylisoguvacine, the most potent in this respect, was considerably less active than GABA. None of the test compounds caused any clearly discernible changes in the gross behaviour or appearance of mice in the 1-h period following intramuscular injection. It was concluded that methylation of the N atom of nipecotic acid and its derivatives was unlikely to lead to the development of agents with greater experimental or therapeutic potential than that of nipecotic acid itself, if the action of the agent was dependent on its effects on GABA uptake.     

Immunosuppressive antilymphocyte serum: IV. Characterization of a T-cell-specific antibody that shifts T-lymphocyte subpopulations in vivo

We have characterized a biologically active antibody present in immunosuppressive but not nonimmunosuppressive antilymphocyte serum. This antibody when administered to rats induced a dose-dependent fall in the numbers of one subpopulation of T lymphocytes while leaving a second subpopulation relatively untouched. When absorption studies were performed, the active antibody was shown to be T-cell specific and could be absorbed preferentially by a subpopulation of thymus lymphocytes which were steroid resistant. The data revealed that the relevant antigen was found in highest concentration on a minority of thymus cells.     

Two- and three-dimensional image reconstructions from stained and autoradiographed histological sections

A complete system has been developed to utilize histologicalserial sections for two- and three-dimensional image reconstructions.Eighty to 120 sections are digitized using a personal computingsystem augmented with a imaging board and CCD camera. The imagefiles are transmitted to a VAX computer for processing and imagereconstruction, and the processed images are transmitted backto the personal computer for display and recording using a filmrecorder or PostScript printer. The software developed for thesystem allows serial sections to be placed into proper registrationin a 256³ array, 256 grey levels. Autoradiographs of the sectionsare obtained in the presence of appropriate standards whichare used to recalibrate grey levels to represent linearly theradioactivity of each pixel in the sections and scale the valuesto allow maximum use of the grey scale. Starting from coronallysectioned material the system has been used to analyse and reconstructrat nasal turbinates. In two dimensions horizontal and sagittalsections have been obtained while in three dimensions back-to-frontand surface-rendered images have been constructed. Useful renderingof differential metabolic activity within an organ of complexgeometry has been obtained, and there appears to be no reasonwhy the system cannot be used for any material for which serialsectioning is appropriate. Received on November 29, 1989; accepted on February 28, 1990     

An efficient phage plaque screen for the random mutational analysis of the interaction of HIV-1 gp120 with human CD4.

A lambda phage expression methodology was adapted to dissect protein/ligand interactions efficiently through the creation and rapid screening of large numbers of mutants. Here we describe the method and its specific application to the interaction between the external envelope glycoprotein of the human immunodeficiency virus (HIV-1), gp120, and the human cell surface protein CD4. Random substitutions were introduced throughout the gp120 binding region (amino acids 38-62) in the amino-terminal domain of CD4 by oligonucleotide mutagenesis. These mutations were expressed within phage plaques and directly screened for their effect on binding of gp120 using a modified phage plaque lift procedure. Plaques showing increased, decreased, and no effect on binding were identified and mutations were verified by sequence analysis. In this manner, 25 unique mutations were identified that altered CD4 binding to gp120. A new site was identified at which mutations reduced binding to gp120 and several novel amino acid substitutions were defined at sites previously implicated in binding. Of particular interest, this in vitro genetic approach identified a mutation which significantly increased binding to gp120. The phenotypes of several of these mutants were further characterized by quantitative measurement of their binding affinity. The results confirmed the accuracy of the phenotypic selection and demonstrated that the sensitivity of the system allowed detection of a 3-4-fold increase or decrease in affinity. In the context of the recently determined atomic structure of CD4, these results further implicate residues in the CDR2-like region and in an adjacent loop in recognition of gp120. This methodology should be generally applicable to other high affinity protein/ligand interactions that are compatible with expression in Escherichia coli.