The argRB of Escherichia coli is rare in isolates obtained from natural sources

A single nucleotide polymorphism between Escherichia coli strains K12 and B is known to alter the mechanism by which the arginine repressor regulates arginine biosynthesis, from a regulated system in E. coli K12 to a deregulated system in E. coli B. Laboratory experiments have demonstrated that the different regulatory strategies are selectively favored under different environmental conditions. In this study we analyzed 537 E. coli strains and show that the argR allele in E. coli B, which causes deregulation, is rare in isolates obtained from natural sources. Moreover, sequence analysis of 85 strains shows no evidence of selection at the arginine repressor locus. This illustrates that analysis of sequence data is insufficient to detect selection of uncommon alleles in rare environments.     

The potential for the formation of the arginine biosynthetic enzymes and its masking during evolution

The present account spans the history of arginine regulation from its discovery in 1955 until the present. In 1957 I demonstrated that not only added arginine but also internally produced arginine represses enzyme formation and that the potential for enzyme synthesis is in excess of what is required for growth. In 1959 I located the regulatory gene argR encoding the arginine repressor. An unusual feature of this research was the finding that in E. coli B, in contrast to E. coli K12, arginine synthesis is permanently repressed, independent of arginine. This was due to a single amino acid difference between the two repressors. Recent studies showed that, in natural populations of E. coli, K12-type regulation is much more frequent than B-type regulation, and that E. coli B evolved from a strain with K12-type regulation. In competition experiments, E. coli K12 was found to be favored in the presence of arginine and E. coli B in its absence, showing that contrary to expectations permanently turned off regulation is favored over negative regulation in some environments.     

Breeding systems and pollination inVigna minima (Leguminosae,Papilionoideae)

Four types of floral breeding systems—(i) chasmogamy, (ii) aerial pseudocleistogamy, (iii) subterranean pseudocleistogamy and (iv) obligate subterranean true cleistogamy—are observed in the populations ofVigna minima inhabiting the Western Ghats (India). Five categories of phenotypes are recognized based on the number and kinds of floral breeding systems found in a given individual. The frequencies of different categories of phenotypes not only show intra- and interpopulation variation, but also fluctuate from generation to generation suggesting differences in the genetic structure of populations. This polymorphism in the breeding system of a single species is unique and may be adaptive. Obligate subterranean true cleistogamy and amphicarpy appear to be adaptations to jungle fires and soil erosion.—The flowers are of the flag-blossom type and insect visitors act as tripping agents. The tripping mechanism together with the polymorphic floral breeding system result in a balanced mixture of selfing and outcrossing. Such a recombination system may enhance the fitness ofV. minima which is essentially a colonizing species.     

Relationships among analytical methods used to study genotypic variation and genotype-by-environment interaction in plant breeding multi-environment experiments

Following the recognition of the importance of dealing with the effects of genotype-by-environment (G ×E) interaction in multi-environment testing of genotypes in plant breeding programs, there has been substantial development in the area of analytical methodology to quantify and describe these interactions. Three major areas where there have been developments are the analysis of variance, indirect selection, and pattern analysis methodologies. This has resulted in a wide range of analytical methods each with their own advocates. There is little doubt that the development of these methodologies has greatly contributed to an enhanced understanding of the magnitude and form ofG ×E interactions and our ability to quantify their presence in a multi-environment experiment. However, our understanding of the environmental and physiological bases of the nature ofG ×E interactions in plant breeding has not improved commensurably with the availability of these methodologies. This may in part be due to concentration on the statistical aspects of the analytical methodologies rather than on the complementary resolution of the biological basis of the differences in genotypic adaptation observed in plant breeding experiments. There are clear relationships between many of the analytical methodologies used for studying genotypic variation andG ×E interaction in plant breeding experiments. However, from the numerous discussions on the relative merits of alternative ways of analysingG ×E interactions which can be found in the literature, these relationships do not appear to be widely appreciated. This paper outlines the relevant theoretical relationships between the analysis of variance, indirect selection and pattern analysis methodologies, and their practical implications for the plant breeder interested in assessing the effects ofG ×E interaction on the response to selection. The variance components estimated from the combined analysis of variance can be used to judge the relative magnitude of genotypic andG ×E interaction variance. Where concern is on the effect of lack of correlation among environments, theG ×E interaction component can be partitioned into a component due to heterogeneity of genotypic variance among environments and another due to the lack of correlation among environments. In addition, the pooled genetic correlation among all environments can be estimated as the intraclass correlation from the variance components of the combined analysis of variance. WhereG ×E interaction accounts for a large proportion of the variation among genotypes, the individual genetic correlations between environments could be investigated rather than the pooled genetic correlation. Indirect selection theory can be applied to the case where the same character is measured on the same genotypes in different environments. Where there are no correlations of error effects among environments, the phenotypic correlation between environments may be used to investigate indirect response to selection. Pattern analysis (classification and ordination) methods based on standardised data can be used to summarise the relationships among environments in terms of the scope to exploit indirect selection. With the availability of this range of analytical methodology, it is now possible to investigate the results of more comprehensive experiments which attempt to understand the nature of differences in genotypic adaptation. Hence a greater focus of interest on understanding the causes of the interaction can be achieved.     

Fitness of resprouters versus seeders in relation to nutrient availability in two Plantago species

Two contrasting strategies of plants from disturbed areas are reported to depend on nutrient availability. Resprouters, investing into storage and capable of vegetative regeneration after disturbance, are predicted to be enhanced in nutrient poor environments. This contrasts to seeders, which invest preferentially into seed production and regenerating only from seeds, and are thought to prevail in nutrient rich environments. To test such predicted dichotomy, we set up an experiment with two facultative resprouters with contrasting nutrient demands and assessed the fitness of individuals regenerated from seeds and root fragments in differently productive environments. We hypothesized that 1) plants with higher nutrient demands have a higher fitness as seeders irrespectable of nutrient availability and/or 2) both species will have a higher fitness as resprouters under lower nutrient availability and as seeders when nutrient availability is higher. Nutrient availability was also manipulated prior to and after disturbance to evaluate the impact of changing nutrient availability on the strategy of resprouting. The results of our pot experiment with Plantago lanceolata and Plantago media supported the first but not the second hypothesis. Moreover, high nutrient availability prior to disturbance negatively affected resprouting success, but the growth and fitness of successfully regenerated individuals were enhanced under higher nutrient availability. We concluded that resprouting from roots after disturbance is affected by nutrient availability, but this effect considerably differs between individual life-history stages.     

Mutations affecting regulation of the anabolic argF and the catabolic aru genes in Pseudomonas aeruginosa PAO

Summary The nucleotide sequence required for a fully functional promoter and operator of the Pseudomonas aeruginosa argF gene (argF _po), the arginine-repressible gene for anabolic ornithine carbamoyltransferase, was defined within a 160 by region. The streptomycin (Sm) resistance genes strAB of plasmid RSF1010 were fused to argF _po. This construct in P. aeruginosa strain PAO conferred resistance to Sm. Mutants of strain PAO were selected which were resistant to Sm in the presence of arginine due to constitutive expression of argF _po —strAB. These mutants were designated argR. They were unable to grow or grew poorly on arginine or ornithine as the sole carbon and nitrogen source. This growth defect (Aru^–/Oru^– phenotype) was correlated with a reduced level of N-succinylornithine aminotransferase, an enzyme participating in the major aerobic pathway for arginine and ornithine catabolism in this organism. The argR mutants were classified into four groups by transduction analysis and three argR mutations were mapped on the PAO chromosome. argR9901 and argR9902 were co-transducible with car-9 (at 1 min) and thus close to the oru-310 locus; argR9906 was localized in the oruI (=aru) gene cluster (67 min). Some aru mutants, which have been isolated previously and which produce very low amounts of all enzymes in the arginine succinyltransferase pathway, were unable to repress the argF gene in an arginine medium. Thus, P. aeruginosa PAO appears to have multiple genes that are involved in the regulation of both the anabolic argF and the catabolic aru genes.Abbreviations Arg^– arginine auxotrophy - Aru arginine utilization - Oru ornithine utilization     

HLA antigens in Brazilian patients with paracoccidioidomycosis

Eighty patients with paracoccidioidomycosis were typed for 43 HLA specificities from loci A, B, C and DR. A highly significant increased frequency of HLA-B40 (relative risk 29.2) and HLA-Cw 1 (relative risk 8.8) were found in patients compared to control subjects. The frequencies HLA-A2, B7 and B21 were also increased in patients and haplotypes-B40-Cw1 and -A2-B40 were positively correlated with the disease. DR antigen frequencies were not significantly altered in the patients and evidence of a protective effect was not found for any of the 43 antigens tested. These findings further support the involvement of the HLA system in the genetic susceptibility to paracoccidioidomycosis and the importance of ethnic variability in this association.     

Age-specific fitness components and their temporal variation in the barn owl

Theory predicts that temporal variability plays an important role in the evolution of life histories, but empirical studies evaluating this prediction are rare. In constant environments, fitness can be measured by the population growth rate lambda, and the sensitivity of lambda to changes in fitness components estimates selection on these traits. In variable environments, fitness is measured by the stochastic growth rate lambda(S), and stochastic sensitivities estimate selection pressure. Here we examine age-specific schedules for reproduction and survival in a barn owl population (Tyto alba). We estimated how temporal variability affected fitness and selection, accounting for sampling variance. Despite large sample sizes of old individuals, we found no strong evidence for senescence. The most variable fitness components were associated with reproduction. Survival was less variable. Stochastic simulations showed that the observed variation decreased fitness by about 30%, but the sensitivities of lambda and lambda(S) to changes in all fitness components were almost equal, suggesting that temporal variation had negligible effects on selection. We obtained these results despite high observed variability in the fitness components and relatively short generation time of the study organism, a situation in which temporal variability should be particularly important for natural selection and early senescence is expected.     

Growth and mineral nutrition of six rapid-cycling Brassica species in response to seawater salinity

The growth of six rapid-cycling lines of Brassica species, B. napus, B. campestris, B. nigra, B. juncea, B. oleracea and B. carinata was inhibited by seawater salinity. Based on the change in dry matter reduction relative to the control at varying concentrations of salts (4, 8 and 12 dS m^-1), the relative salt tolerance of these species was evaluated. B. napus and B. carinata were the most tolerant and most sensitive species, respectively, while the other four species were moderately tolerant. The influence of seawater on the concentrations of 12 elements including macronutrients and micronutrients in the shoots of these Brassica plants was characterized to determine the relationship between nutritional disturbance and relative salt tolerance. It was found that seawater salinity had a significant effect on the concentrations of Ca, Mg, K, Cl, Na and total N in the shoots of these plants but only the change in Ca concentration was significantly related to the relative salt tolerance of these six rapid-cycling Brassica species according to a rank analysis of the data. This finding indicates that Ca may play a regulatory role in the responses of Brassica species to saline conditions.     

Cloning and characterization of argR, a gene that participates in regulation of arginine biosynthesis and catabolism in Pseudomonas aeruginosa PAO1.

Gel retardation experiments indicated the presence in Pseudomonas aeruginosa cell extracts of an arginine-inducible DNA-binding protein that interacts with the control regions for the car and argF operons, encoding carbamoylphosphate synthetase and anabolic ornithine carbamoyltransferase, respectively. Both enzymes are required for arginine biosynthesis. The use of a combination of transposon mutagenesis and arginine hydroxamate selection led to the isolation of a regulatory mutant that was impaired in the formation of the DNA-binding protein and in which the expression of an argF::lacZ fusion was not controlled by arginine. Experiments with various subclones led to the conclusion that the insertion affected the expression of an arginine regulatory gene, argR, that encodes a polypeptide with significant homology to the AraC/XylS family of regulatory proteins. Determination of the nucleotide sequence of the flanking regions showed that argR is the sixth and terminal gene of an operon for transport of arginine. The argR gene was inactivated by gene replacement, using a gentamicin cassette. Inactivation of argR abolished arginine control of the biosynthetic enzymes encoded by the car and argF operons. Furthermore, argR inactivation abolished the induction of several enzymes of the arginine succinyltransferase pathway, which is considered the major route for arginine catabolism under aerobic conditions. Consistent with this finding and unlike the parent strain, the argR::Gm derivative was unable to utilize arginine or ornithine as the sole carbon source. The combined data indicate a major role for ArgR in the control of arginine biosynthesis and aerobic catabolism.     

Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity

There is considerable understanding about how laboratory populations respond to predictable (constant or deteriorating environment) selection for single environmental variables such as temperature or pH. However, such insights may not apply when selection environments comprise multiple variables that fluctuate unpredictably, as is common in nature. To address this issue, we grew replicate laboratory populations of Escherichia coli in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen peroxide (H₂O₂) were randomly changed daily. After ~170 generations, the fitness of the selected populations had not increased in any of the three selection environments. However, these selected populations had significantly greater fitness in four novel environments which have no known fitness‐correlation with tolerance to pH, NaCl or H₂O₂. Interestingly, contrary to expectations, hypermutators did not evolve. Instead, the selected populations evolved an increased ability for energy‐dependent efflux activity that might enable them to throw out toxins, including antibiotics, from the cell at a faster rate. This provides an alternate mechanism for how evolvability can evolve in bacteria and potentially lead to broad‐spectrum antibiotic resistance, even in the absence of prior antibiotic exposure. Given that environmental variability is increasing in nature, this might have serious consequences for public health.     

The resource balance of Milium effusum with emphasis on environmental resource supply

Summary Growth of the broad-leaved graminoid Milium effusum, occurring in shady deciduous forests, was matched with periods of high light influx through the tree canopy in spring and autumn. Fertile shoots grew faster than sterile shoots. Leaves on flowering shoots were fully developed when the budbreak started on the trees, whereas nonflowering shoots had fully developed leaves when the tree canopy closed. Leaf concentrations of N and P were high (6.1 and 0.74% respectively) in spring but decreased as the leaves expanded. Maximum pool sizes of N and P in whole tillers were reached about one month after the onset of spring growth, whereas maximum spring pools of K, Mg, and Ca were timed with peak biomass about one month later. The leaves lost nutrients during summer when no growth took place. Since leaching losses were negligible, nutrients were probably allocated from the leaves to support root growth. Autumn reallocation to winter stores was low. The pattern of growth and nutrient use suggests that light availability, i.e., the resource in relatively lowest supply, regulates the investment of the resource in highest supply, i.e., nutrients. This is consistent with previously reported observations on Eriophorum vaginatum, a graminoid of low nutrient — high light environments. This species utilizes nutrients efficiently at the expense of less efficient acquisition of carbon. We suggest that selection for efficient utilization of the resource in lowest relative supply has been a strong driving force behind the physiological adaptation of both species to their environments.     

Isolation and partial characterization of an argR mutant of Salmonella typhimurium.

An arginine regulatory mutant (i.e., mutated in the argR gene) has been isolated from a strain of Salmonella typhimurium LT2. The argR mutant was found to excrete arginine into the growth medium with glycerol but not glucose as carbon source. Constitutive synthesis of arginine biosynthetic enzymes was observed. Whereas previous results (A. T. Abd-E1-A1 and J. L. Ingraham, Abstr. Annu. Meet. Am. Soc. Microbiol. 1975, K169, p. 175) have shown constitutive synthesis of carbamyl phosphate synthetase in the argR mutant, the regulation of the synthesis of the last five enzymes of the pyrimidine pathway was unaffected. However, in pyrH mutants, known to exhibit derepressed synthesis of the pyrimidine enzymes, a 10-fold derepression of ornithine transcarbamylase was observed.     

Effect of nitrogen and fiber content on the decomposition of the waterhyacinth (Eichhornia crassipes [Mart.] Solms)

In situ rates of waterhyacinth decomposition were found to vary with tissue nitrogen and fiber content. High nitrogen (2.8%), low fiber (49%) waterhyacinth aerial tissues collected from a eutrophic site decomposed more rapidly than low nitrogen (1.3%), high fiber (58%) aerial tissues collected from a nutrient-poor site. In addition, waterhyacinth roots (65% fiber) decomposed much more slowly than aerial waterhyacinth tissues (49% fiber). Because the biomass distribution (aerial/root) and nitrogen and fiber content of waterhyacinths fluctuate both seasonally and with nitrogen availability, considerable temporal and site-to-site variability in decomposition dependent processes (e.g., sedimentation, mineralization) exist in aquatic systems infested by this species.     

Intraspecific variability in Karlodinium veneficum: Growth rates, mixotrophy, and lipid composition

We isolated eleven strains of the harmful algal bloom (HAB)-forming dinoflagellate Karlodinium veneficum during a bloom event in the NW Mediterranean coastal waters and we studied the inter-strain variability in several of their physiological and biochemical traits. These included autotrophic growth parameters, feeding capabilities (mixotrophy), lipid composition, and, in some cases, their responses to biotic and abiotic factors. The strains were found to differ in their growth rates (0.27–0.53 d⁻¹) and in the maximum cell concentrations achieved during stationary phase (6.1 × 10⁴–8.6 × 10⁴ cells mL⁻¹). Their ingestion performance, when offered Rhodomonas salina as prey, was also diverse (0.22–1.3 cells per K. veneficum per day; 8–52% of their daily ration). At least two strains survived for several months under strict heterotrophic conditions (no light, low inorganic nutrients availability, and R. salina as food source). These strains also showed very distinct fatty acid compositions, with very low contents of monounsaturated and polyunsaturated fatty acids. According to a Bray Curtis similarity analysis, three or four strain groups able to perform different roles in bloom development were identified. We further analyzed one strain from each of the two most distinct groups with respect to prey concentration, light intensity, nutrient availability, and we determined the functional responses (growth and feeding rates) to food concentration. Taken together, the results served to highlight the role of mixotrophy and clone variability in the formation of HABs.     

Population growth kinetics and bulk membrane lipid alterations in Tetrahymena pyriformis: exposure to pentachlorophenol

This study describes effects of exposure of the freshwater ciliate Tetrahymena pyriformis to the "classic" weak acid respiratory uncoupler pentachlorophenol (PCP) on the population growth kinetics and membrane lipid profiles. The assessment of growth kinetics of naive populations exposed to PCP, at concentrations eliciting <50% growth inhibition, showed generation times of exposed cultures similar to generation times of controls but preceded by a short lag phase (<2 h). Assessment of exposed cultures exhibiting >50% growth inhibition revealed generation times that increased with increasing concentrations of toxicant. In addition, the relative percentages of selected fatty acid methyl esters (FAMEs) in both pellicle and mitochondrial membranes were examined. Upon exposure to PCP the relative percentages of FAMEs 12:0, 14:0, 16:0, 16:1, and 18:0 did not change. However, with exposure to PCP a decrease was observed for FAMEs 15:0 and 17:0. Conversely, with PCP exposure there was an increase in FAME 18:1. A comparison of these results with those elicited upon exposure to the model narcotic 1-octanol reveals marked differences in both growth kinetics and fatty acid shifts. This revised version was published online in July 2006 with corrections to the Cover Date.     

Perturbation of gene frequencies in a natural population of Drosophila melanogaster: evidence for selection at the Adh locus

The cellar population of Drosophila melanogaster at the Chateau Tahbilk Winery (Victoria, Australia) was perturbed for alcohol dehydrogenase (Adh) gene frequencies. Phenol oxidase (Phox) frequencies were also perturbed and monitored as a control. Subsequent gene frequency changes, together with information on population structure, indicated that selection acted on the chromosome regions of both loci. Adh gene frequencies returned to preperturbation levels in a predictable manner. A model in which the relative fitness of Adh phenotypes was determined by temperature-dependent specific activities of enzymes of Adh genotypes adequately accounts for the rate of gene frequency change at this locus. Thus temperature behaves as a selective agent in modulating Adh gene frequencies in this cellar environment.     

QTL x environment interactions in rice. I. heading date and plant height

One hundred twenty six doubled-haploid (DH) rice lines were evaluated in nine diverse Asian environments to reveal the genetic basis of genotype × environment interactions (GEI) for plant height (PH) and heading date (HD). A subset of lines was also evaluated in four water-limited environments, where the environmental basis of G × E could be more precisely defined. Responses to the environments were resolved into individual QTL × environment interactions using replicated phenotyping and the mixed linear-model approach. A total of 37 main-effect QTLs and 29 epistatic QTLs were identified. On average, these QTLs were detectable in 56% of the environments. When detected in multiple environments, the main effects of most QTLs were consistent in direction but varied considerably in magnitude across environments. Some QTLs had opposite effects in different environments, particularly in water-limited environments, indicating that they responded to the environments differently. Inconsistent QTL detection across environments was due primarily to non- or weak-expression of the QTL, and in part to significant QTL × environment interaction effects in the opposite direction to QTL main effects, and to pronounced epistasis. QTL × environment interactions were trait- and gene-specific. The greater GEI for HD than for PH in rice were reflected by more environment-specific QTLs, greater frequency and magnitude of QTL × environment interaction effects, and more pronounced epistasis for HD than for PH. Our results demonstrated that QTL × environment interaction is an important property of many QTLs, even for highly heritable traits such as height and maturity. Information about QTL × environment interaction is essential if marker-assisted selection is to be applied to the manipulation of quantitative traits.Communicated by G. Wenzel     

Selection methods in bacilli for recombinants and transformants of intra- and interspecific fused protoplasts

The intraspecific fusion frequencies obtained with the direct selection method on a semi-synthetic regeneration medium between strains of B. subtilis and B. licheniformis were distribution from 9.9×10^-2 to 4.5×10^-3, which was one or two orders higher than those of interspecific recombinations between B. subtilis and B. licheniformis.The regeneration media were also useful for selecting interspecific transformants from plasmid carrier to non-carrier. This selection could be used as a primary selection method for inter-and intraspecific recombinants obtained by protoplast fusion.Abbreviations NTG N-methyl-N-nitro-N-nitrosoguanidine - Cm chloramphenicol - SMM 0.5 M sucrose-0.02 M MgCl₂-0.02 M maleate buffer, pH 6.5