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M A Riley

Publications and source records attributed to M A Riley.

At least 37 records · Page 2Linked to original sources
PubMed2000

The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification.

Two evolutionary mechanisms have been proposed in the process of protein diversification of the large family of antimicrobial toxins of Escherichia coli, known as the colicins. Data from previous studies suggest that the relatively rare nuclease colicins appear to diversify primarily through the action of positive selection, whilst the more abundant pore-former colicins appear to diversify through the action of recombination. The complete DNA sequence of the newly characterized colicin plasmid, pCol-Let, isolated from a Yanomama Indian of South America, is presented here. This plasmid encodes a newly identified pore-former colicin, colicin Y. DNA and protein sequence comparisons of the colicin Y gene cluster and the encoded proteins with those of published pore-former colicins provide the first evidence that positive selection may also act to increase pore-former colicin diversity.

Colicins↗
PubMed1999

Recurrence quantification analysis of postural fluctuations.

A technique (recurrence quantification analysis; RQA) for analyzing center of pressure (COP) signals is presented and applied to data obtained by having participants stand with the head forward or sideways and with eyes open or closed. RQA is suitable for short, nonstationary signals and quantifies dynamical (deterministic) structure and nonstationarity. Results indicated that vision affects the deterministic structure (in degree and complexity) of COP motions and that differential optical flow structure (radial versus lamellar flow) induced by spontaneous sway under different head orientations affects COP nonstationarity. Implications of these findings and the sensitivity of RQA to subtle time-evolutionary properties of the COP are discussed.

Adolescent↗
PubMed1999

The ecological role of bacteriocins in bacterial competition.

Bacteriocins are an abundant class of antimicrobial molecules that appear to mediate population dynamics within species. The bacteriocins of Escherichia coli have served as a model for exploring the ecological role of these potent toxins. Studies suggest that colicins provide a competitive edge in nutrient-poor environments and that there might be a trade-off between the costs and benefits of colicin production.

Bacteriocins↗
PubMed1999

Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages.

In prokaryotes, lateral gene transfer across chromosomal lineages may be mediated by plasmids, phages, transposable elements, and other accessory DNA elements. However, the importance of such transfer and the evolutionary forces that may restrict gene exchange remain largely unexplored in native settings. In this study, tests of phylogenetic congruence are employed to explore the range of horizontal transfer of symbiotic (sym) loci among distinct chromosomal lineages of native rhizobia, the nitrogen-fixing symbiont of legumes. Rhizobial strains isolated from nodules of several host plant genera were sequenced at three loci: symbiotic nodulation genes (nodB and nodC), the chromosomal housekeeping locus glutamine synthetase II (GSII), and a portion of the 16S rRNA gene. Molecular phylogenetic analysis shows that each locus generally subdivides strains into the same major groups, which correspond to the genera Rhizobium, Sinorhizobium, and Mesorhizobium. This broad phylogenetic congruence indicates a lack of lateral transfer across major chromosomal subdivisions, and it contrasts with previous studies of agricultural populations showing broad transfer of sym loci across divergent chromosomal lineages. A general correspondence of the three rhizobial genera with major legume groups suggests that host plant associations may be important in the differentiation of rhizobial nod and chromosomal loci and may restrict lateral transfer among strains. The second major result is a significant incongruence of nod and GSII phylogenies within rhizobial subdivisions, which strongly suggests horizontal transfer of nod genes among congenerics. This combined evidence for lateral gene transfer within, but not between, genetic subdivisions supports the view that rhizobial genera are "reproductively isolated" and diverge independently. Differences across rhizobial genera in the specificity of host associations imply that the evolutionary dynamics of the symbiosis vary considerably across lineages in native settings.

Base Sequence↗
PubMed1998

Molecular mechanisms of bacteriocin evolution.

Microorganisms are engaged in a never-ending arms race. One consequence of this intense competition is the diversity of antimicrobial compounds that most species of bacteria produce. Surprisingly, little attention has been paid to the evolution of such extraordinary diversity. One class of antimicrobials, the bacteriocins, has received increasing attention because of the high levels of bacteriocin diversity observed and the use of bacteriocins as preservatives in the food industry and as antibiotics in the human health industry. However, little effort has been focused on evolutionary questions, such as what are the phylogenetic relationships among these toxins, what mechanisms are involved in their evolution, and how do microorganisms respond to such an arsenal of weapons? The focus of this review is to provide a detailed picture of our current understanding of the molecular mechanisms involved in the process of bacteriocin diversification.

Bacteriocins↗
PubMed1997

Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum.

Lateral transfer of bacterial plasmids is thought to play an important role in microbial evolution and population dynamics. However, this assumption is based primarily on investigations of medically or agriculturally important bacterial species. To explore the role of lateral transfer in the evolution of bacterial systems not under intensive, human-mediated selection, we examined the association of genotypes at plasmid-encoded and chromosomal loci of native Rhizobium, the nitrogen-fixing symbiont of legumes. To this end, Rhizobium leguminosarum strains nodulating sympatric species of native Trifolium were characterized genetically at plasmid-encoded symbiotic (sym) regions (nodulation AB and nodulation CIJT loci) and a repeated chromosomal locus not involved in the symbiosis with legumes. Restriction fragment length polymorphism analysis was used to distinguish genetic groups at plasmid and chromosomal loci. The correlation between major sym and chromosomal genotypes and the distribution of genotypes across host plant species and sampling location were determined using chi2 analysis. In contrast to findings of previous studies, a strict association existed between major sym plasmid and chromosomal genetic groups, suggesting a lack of successful sym plasmid transfer between major Rhizobium chromosomal types. These data indicate that previous observations of sym plasmid transfer in agricultural settings may seriously overestimate the rates of successful conjugation in systems not impacted by human activities. In addition, a nonrandom distribution of Rhizobium genotypes across host plant species and sampling site demonstrates the importance of both factors in shaping Rhizobium population dynamics.

Biological Evolution↗
PubMed1997

Common effects of touch and vision on postural parameters.

Subjects stood upright with the index finger of the right hand either touching a nearby surface gently or not touching it at all and with the eyes either open or closed. Trajectories of the center of pressure (COP) were analyzed as fractional Brownian motion. The extracted parameters were the effective diffusion (D) coefficients and Hurst (H) exponents for short-term time intervals (corresponding to positively correlated random walks) and long-term time intervals (corresponding to negatively correlated random walks). Gentle tactile contact reduced the effective stochastic activity measured by D to the same extent as the availability of vision. Further, touch interacted with time interval in the same way as vision, with the correlated activity closer to H = 0.5 at both time scales when the finger contacted the nearby surface. The results corroborate and extend major features of recent investigations of haptic influences on posture and recent analyses of vision's influence on the fractional Brownian motions of the COP. Discussion focused on (a) the equivalence of expropriospecific information (about the body's orientation to the environment) registered haptically and visually and (b) the possibility that postural sway may reflect exploratory motions in the short term (obtaining information about the postural system) and performatory motions in the long term (using this information).

Adolescent↗
PubMed1997

Chaos in Human Rhythmic Movement.

Rhythmic movements typical of locomotory actions are usually modeled as limit cycle dynamics, and their deviations from pure periodicity are attributed to stochastic physiological noise. In the present study, the dynamics of human rhythmic movements were found to contain more than the 2 dynamically active variables expected from limit cycle dynamics; the number depended upon the size of the limb oscillator. Observed positive Lyapunov exponents and fractal attractor dimensions indicated that the gross variability of human rhythmic movements may stem largely from low-dimensional chaotic motion on strange attractors.

degrees of freedom↗
PubMed1997

Nucleotide polymorphism in colicin E2 gene clusters: evidence for nonneutral evolution.

To explore the molecular mechanisms behind the diversification of colicin gene clusters, we examined DNA sequence polymorphism for the colicin gene clusters of 14 colicin E2 (ColE2) plasmids obtained from natural isolates of Escherichia coli. Two types of ColE2 plasmids are revealed, with type II gene clusters generated by recombination between type I ColE2 and ColE7 gene clusters. The levels and patterns of DNA polymorphism are different between the two types. Type I polymorphism is distributed evenly along the gene cluster, while type II accumulates polymorphism at an elevated rate in the 5' end of the colicin gene. These differences may be explained by recombinational origins of type II gene clusters. The pattern of divergence between the ColE2 gene cluster and its close relative ColE9 is not correlated with the pattern of polymorphism within ColE2, suggesting that this gene cluster is not evolving in a neutral fashion. A statistical test confirms significant departures from the predictions of neutrality. These data lend further support to the hypothesis that colicin gene clusters may evolve under the influence of nonneutral forces.

Base Sequence↗
PubMed1996

Asymmetries generated by transcription-coupled repair in enterobacterial genes.

Although certain replication errors occur at different frequencies on each of the complementary strands of DNA, it remains unclear whether this bias is prevalent enough during chromosome replication to affect sequence evolution. Here, nucleotide substitutions in enteric bacteria were examined, and no difference in mutation rates was detected between the leading and lagging strands, but in comparing the coding and noncoding strands, and excess of C-->T changes was observed on the coding strand. This asymmetry is best explained by transcription-coupled repair on the noncoding strand. Although the vast majority of mutations are thought to arise from spontaneous errors during replication, this result implicates DNA damage as a substantial source of mutations in the wild.

Chromosome Mapping↗
PubMed1996

Low synonymous site variation at the lacY locus in Escherichia coli suggests the action of positive selection.

We have determined the nucleotide sequences of seven lacY alleles isolated from natural isolates of Escherichia coli. Nucleotide heterozygosity estimates for this locus were compared to those obtained from previous studies of intraspecific variation at chromosomal loci, revealing that lacY has unusually low synonymous site variation. The average pairwise heterozygosity of synonymous sites (Ks = 0.0112 +/- 0.0100) is the second lowest reported and the lowest for loci that have an equivalent level of nonsynonymous variation. We consider several hypotheses to explain how different forces in evolution could act to create the observed pattern of polymorphism, including selection for translational efficiency and positive selection. Our analysis most strongly supports the hypothesis that positive selection has acted on the lacY locus in E. coli.

Alleles↗
PubMed1996

Rapid invasion by colicinogenic Escherichia coli with novel immunity functions.

Bacteriocins have been suggested to play an important role in the invasion dynamics of bacteria. Recently, the 'diversifying selection' hypothesis has been proposed, which addresses the origin and diversification of one group of bacteriocins, the colicins of Escherichia coli. According to this hypothesis, novel colicin gene clusters arise from mutations generating expanded immunity functions. Positive selection, favouring these novel immunities, then rapidly drives strains carrying the evolved colicin gene clusters to fixation in the local population. To test this fixation step driven by selection, invasion experiments were carried out by introducing novel colicinogenic strains into established colicinogenic populations. In all cases, invasion by strains expressing novel immunity functions occurred rapidly, even when initial frequencies of the invader were quite low. These invasions were attributed primarily to colicin killing effect. Other factors, such as growth rate, level of colicin production and stationary-phase survival rate, were shown to play very minor roles in the invasion process. These results provide direct evidence for the hypothesis of diversifying selection acting on colicin gene clusters and shed light on the ecological role of colicins.

Colicins↗
PubMed1996

Homology among nearly all plasmids infecting three Bacillus species.

We have surveyed naturally occurring plasmids in strains of Bacillus subtilis and the closely related species B. mojavensis and B. licheniformis. Previous studies have failed to find host-benefitting functions for plasmids of these species, suggesting that these plasmids are nonmutualistic. Only one type of plasmid was found in each plasmid-bearing strain, suggesting that most of the plasmids infecting these Bacillus species are in the same incompatibility group. A sample of 18 plasmids from these species ranged in size from 6.9 to 16 kb, with all but 6 plasmids falling into three size groups. These groups differed in the sizes of their host ranges and geographical ranges. All but 1 of the 18 plasmids from these three host species are homologous with one another. The cryptic plasmids from these three species are far less diverse than are plasmids (from other species) that are known to benefit their bacterial hosts. The low-level diversity among these cryptic plasmids is consistent with the hypothesis that host-benefitting adaptations play an important role in fostering the coexistence of plasmid populations, but other explanations for the low-level plasmid diversity are possible. Comparison of the phylogenies of the plasmids with those of their hosts suggests that Bacillus plasmids are horizontally transferred in nature at a low rate similar to that found for the colicin plasmids of Escherichia coli.

Bacillus↗
PubMed1996

MR imaging of anterior cruciate ligament injury: independent value of primary and secondary signs.

OBJECTIVE: The purpose of this blinded study was to test the value of primary and secondary signs, independent of each other, for diagnosis of a tear of the anterior cruciate ligament (ACL) by means of MR imaging. MATERIALS AND METHODS: MR images of the knee in 74 patients who had the status of the ACL confirmed arthroscopically were blindly reviewed for status of the ACL three times: with primary signs masked, with secondary signs masked, and with no signs masked. On the basis of the observed signs at each session, the status of the ACL was predicted and the confidence in that prediction was noted. The MR imaging predictions were compared with the arthroscopic findings. The results were analyzed with receiver operating characteristic curves and stepwise discriminant analysis. RESULTS: We found no difference in diagnostic performance when only primary signs were used and when both primary and secondary signs were used. When using primary signs only, our observers performed significantly better than when using secondary signs alone. However, with secondary signs alone, our observers performed better than if left to chance for predicting ACL status. Of the secondary signs, our statistical analysis found bone contusion, anterior translation of the tibia, and an uncovered posterior horn of the lateral meniscus to be the most useful for diagnosis. CONCLUSION: Secondary signs do have value for deciding ACL status independent of primary signs. However, our observers performed much better when using primary signs instead of secondary signs. In the clinical setting, secondary signs do not help significantly in the diagnosis of ACL tears by means of MR imaging.

Anterior Cruciate Ligament↗
PubMed1995

Can phage defence maintain colicin plasmids in Escherichia coli?

We examined the role of plasmid-based phage defence in maintaining plasmids, using colicin plasmids in Escherichia coli as a model system. Experimental data indicated that the possession of a colicin plasmid can confer limited protection against bacteriophages. A continuous culture model, using these experimental values, indicated that the observed limited protection alone could selectively maintain colicin plasmids, without requiring a competitive advantage due to colicinogeny. Phage defence might explain the current maintenance of colicin plasmids, given the naturally occurring high levels of resistance to colicins. This model also suggests that many plasmids might be maintained in natural populations, in part, by phage resistance, including 'cryptic' plasmids for which no phenotype is known.

Bacteriocin Plasmids↗
PubMed1994

Nucleotide polymorphism in colicin E1 and Ia plasmids from natural isolates of Escherichia coli.

We examined DNA sequence polymorphism for the colicin gene clusters of seven ColE1 and six ColIa plasmids obtained from natural isolates of Escherichia coli. These gene clusters harbor levels of nucleotide diversity ranging from 0.006 (ColIa) to 0.054 (ColE1). This level of diversity is similar to that observed for chromosomally encoded E. coli genes. However, the variance associated with these estimates is severalfold higher for the plasmid-encoded genes. This increased variance may be due to the differing plasmid population sizes. The pattern of colicin gene cluster polymorphism suggests that the two colicins are evolving in different fashions. ColE1 accumulates polymorphism at an elevated rate in the central domain of the colicin protein, while ColIa polymorphism is distributed evenly along the gene cluster. Comparison of the patterns of divergence between colicin and related proteins of ColIa and Ib and patterns of polymorphism within ColIa suggest that this gene cluster is not evolving in a neutral fashion. These data lend support to the hypothesis that colicin gene clusters may evolve under the influence of diversifying selection.

Bacteriocin Plasmids↗
PubMed1994

Evaluation of cold-adapted, reassortant influenza B virus vaccines in elderly and chronically ill adults.

The safety and immunogenicity of two recent cold-adapted reassortant influenza B viruses were evaluated in persons at high risk for influenza-related morbidity and mortality. Ambulatory adults > 65 years old or with chronic high-risk conditions were randomly assigned to receive parenteral trivalent inactivated influenza vaccine containing either influenza B/Ann Arbor/86 or B/Yamagata/88 hemagglutinin antigens, cold-adapted reassortant influenza B/Ann Arbor/1/86 or B/Yamagata/16/88 viruses (10(7.2) TCID50), or placebo in double-blind fashion. Cold-adapted vaccine viruses were well tolerated, with similar rates of respiratory symptoms in all groups. There were no changes in spirometry or oxygen saturation following vaccination. Immune responses to both types of vaccine were modest, with serum antibody responses occurring significantly more frequently and with higher magnitude in those receiving inactivated than in those receiving cold-adapted vaccine. Cold-adapted, reassortant influenza B vaccines are safe in the elderly and those with chronic illness but are not optimally immunogenic in this group.

Aged↗