Genetic homologies among nocardiae and other actinomycetes

1973 ◽  
Vol 19 (8) ◽  
pp. 1007-1014 ◽  
Author(s):  
S. G. Bradley ◽  
G. H. Brownell ◽  
Josephine Clark
Keyword(s):  
Dna Hybridization ◽  
Genetic Recombination ◽  
Nucleotide Sequences ◽  
Dna Reassociation ◽  
Hybrid Molecules ◽  
Nearly Neutral Mutations ◽  
Neutral Mutations ◽  
Incubation Temperatures ◽  
Duplex Formation ◽  
Discrete Populations

The extent of association between deoxyribonucleic acid (DNA) from various actinomycetes with reference DNA samples from two strains of Nocardia erythropolis has been used as an index of relatedness. N. erythropolis, N. canicruria, and particular cultures designated as N. corallina and N. opaca constitute a genospecies, on the bases of ability to form DNA hybrid molecules and ability to participate in genetic recombination. The lack of reciprocity in the DNA reassociation assays involving selected strains of N. erythropolis indicates that the DNA from particular lineages possesses unique nucleotide sequences. The taxon Mycobacterium rhodochrous is heterogeneous and contains at least two discrete populations. The present results do not clarify the relationships of the N. erythropolis genospecies to the other nocardiae, streptomycetes, or mycobacteria. The differences in extent of hybrid DNA duplex formation at exacting and non-exacting incubation temperatures reflect the degree of matching between the compared nucleotide sequences. On this basis, actinomycete DNA samples differ from one another by nucleotide alterations dispersed throughout the genome. DNA hybridization is a sensitive assay for molecular evolution and may be able to detect neutral and nearly neutral mutations that are not recognized phenotypically.

scholarly journals Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus ϕ6

Genetics ◽  
2007 ◽  
Vol 176 (1) ◽  
pp. 467-476 ◽  
Author(s):  
Christina L. Burch ◽  
Sebastien Guyader ◽  
Daniel Samarov ◽  
Haipeng Shen
Keyword(s):  
Rna Virus ◽  
Experimental Estimate ◽  
Nearly Neutral Mutations ◽  
Neutral Mutations

scholarly journals Recombinant hepatitis C virus in experimentally infected chimpanzees

2007 ◽  
Vol 88 (1) ◽  
pp. 143-147 ◽  
Author(s):  
Fengxiang Gao ◽  
Omana V. Nainan ◽  
Yuri Khudyakov ◽  
Jinfeng Li ◽  
Ying Hong ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Sequence Analysis ◽  
Factor Viii ◽  
Genetic Recombination ◽  
Nucleotide Sequences ◽  
Recombinant Hepatitis ◽  
Rt Pcr ◽  
Crossover Region ◽  
Different Strains

Genetic recombination between different strains of Hepatitis C virus (HCV) was investigated in three chimpanzees inoculated experimentally with factor VIII concentrate containing HCV subgenotypes 1a, 1b, 2b and 3a. A 750 bp long fragment from the HCV envelope region was amplified by RT-PCR and quasispecies were isolated by plasmid cloning. Nucleotide sequences derived from isolated quasispecies were screened for the presence of inter-subgenotypic recombination by using sequence analysis. Recombination between HCV subgenotype 1a and 1b was found in two animals; each recombinant variant differed by location of predicted crossover region or order of subgenotype 1a and 1b sequences.

scholarly journals LIMITS OF ADAPTATION: THE EVOLUTION OF SELECTIVE NEUTRALITY

Genetics ◽  
1985 ◽  
Vol 111 (3) ◽  
pp. 655-674 ◽  
Author(s):  
Daniel L Hartl ◽  
Daniel E Dykhuizen ◽  
Antony M Dean
Keyword(s):  
Enzyme Activity ◽  
Natural Selection ◽  
Concave Function ◽  
Neutral Evolution ◽  
Favorable Effect ◽  
Effective Population ◽  
Population Number ◽  
Selective Neutrality ◽  
Nearly Neutral Mutations ◽  
Neutral Mutations

ABSTRACT Many enzymes in intermediary metabolism manifest saturation kinetics in which flux is a concave function of enzyme activity and often of the Michaelis-Menten form. The result is that, when natural selection favors increased enzyme activity so as to maximize flux, a point of diminishing returns will be attained in which any increase in flux results in a disproportionately small increase in fitness. Enzyme activity ultimately will reach a level at which the favorable effect of an increase in activity is of the order 1/(4Ne) or smaller, where Ne is the effective population number. At this point, many mutations that result in small changes in activity will result in negligible changes in fitness and will be selectively nearly neutral. We propose that this process is a mechanism whereby conditions for the occurrence of nearly neutral mutations and gene substitutions can be brought about by the long-continued action of natural selection. Evidence for the hypothesis derives from metabolic theory, direct studies of flux, studies of null and other types of alleles in Drosophila melanogaster and chemostat studies in Escherichia coli. Limitations and complications of the theory include changes in environment or genetic background, enzymes with sharply defined optima of activity, overdominance, pleiotropy, multifunctional enzymes and branched metabolic pathways. We conclude that the theory is a useful synthesis that unites many seemingly unrelated observations. The principal theoretical conclusion is that the conditions for the occurrence of neutral evolution can be brought about as an indirect result of the action of natural selection.

scholarly journals Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes

2010 ◽  
Vol 60 (1) ◽  
pp. 154-165 ◽  
Author(s):  
Javier Pascual ◽  
M. Carmen Macián ◽  
David R. Arahal ◽  
Esperanza Garay ◽  
María J. Pujalte
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Multilocus Sequence Analysis ◽  
Direct Pcr ◽  
Practical Advantage ◽  
Core Group ◽  
Dna Reassociation ◽  
Species Pairs ◽  
Identification Tool

The central clade of the genus Vibrio, also called the Vibrio core group, comprises six species that are tightly related (DNA–DNA reassociation values are very close to 70 % for most species pairs). Identification of novel strains to the species level within this group is troublesome and results are quite often dependent on the methodology employed. Therefore, this group represents an excellent framework to test the robustness of multilocus sequence analysis (MLSA) not only for inferring phylogeny but also as an identification tool without the need for DNA–DNA hybridization assays. The genes selected, 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR, were amplified by direct PCR from 44 Vibrio core-group strains. Subsequent analysis allowed us to recognize toxR and rpoD as the most resolving individual genes and showed that concatenated sequences of rpoD, rctB and toxR were more useful than concatenated sequences of all seven genes. To validate our conclusions, MLSA similarities have been correlated with DNA–DNA relatedness values obtained in this study and values taken from the literature. Although the seven concatenated genes gave the best correlation, the concatenated sequences of rpoD, rctB and toxR have the practical advantage of showing a considerable gap between the maximal interspecies similarity and the minimal intraspecies similarity recorded, meaning that they can be used quite conveniently for species identification of vibrios.

scholarly journals Reduced-stringency DNA reassociation: sequence specific duplex formation

1982 ◽  
Vol 10 (2) ◽  
pp. 719-733 ◽  
Author(s):  
Henry E. Burr ◽  
Robert T. Schimke
Keyword(s):  
Dna Reassociation ◽  
Duplex Formation

scholarly journals Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles

1968 ◽  
Vol 11 (3) ◽  
pp. 247-270 ◽  
Author(s):  
Motoo Kimura
Keyword(s):  
Amino Acids ◽  
Finite Population ◽  
Exact Formula ◽  
Effective Size ◽  
Approximation Formula ◽  
Synonymous Mutations ◽  
Dna Base ◽  
Nearly Neutral Mutations ◽  
Image Position ◽  
Neutral Mutations

1. The average and the effective numbers of alleles maintained in a finite population due to mutational production of neutral isoalleles were studied by mathematical analysis and computer simulation.2. The exact formula was derived for the effective number (ne) of alleles maintained in a population of effective size Ne, assuming that there are K possible allelic states and mutation occurs with equal frequency in all directions. If the number of allelic states is so large that every mutation is to a new, not pre-existing, allele, we have ne = 4Neu+1 − 2Neu2, where u is the mutation rate. Thus, the approximation formula, ne = 4Neu+1, given by Kimura & Crow (1964) is valid as long as 2Neu2 ≪ 1.3. The formula for the average number of alleles (na) maintained in a population of actual size N and effective size Ne was derived by using the method of diffusion approximation. If every mutation is to a new, not pre-existing, allele, we obtainwhere M = 4Neu. The average number of alleles as a function of M and N is listed in Table 1.4. In order to check the validity of the diffusion approximations, Monte Carlo experiments were carried out using the computer IBM 7090. The experiments showed that the approximations are satisfactory for practical purposes.5. It is estimated that among the mutations produced by DNA base substitutions, synonymous mutations, that is, those which cause no alterations of amino acids, amount roughly to 0·2–0·3 in vertebrates. Incompletely synonymous mutations, that is, those which lead to substitution of chemically similar amino acids at a different position of the polypeptide chain from the active site and therefore produce almost no phenotypic effects, must be very common. Together with synonymous mutations, they might constitute at least some 40% of all mutations. These considerations suggest that neutral and nearly neutral mutations must be more common than previously considered.

Sign in / Sign up

Export Citation Format

Share Document