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At least 19 recordsLinked to original sources
PubMed1985

Evolve II: a computer model of an evolving ecosystem.

The Evolve II program is a model of an ecosystem in which organisms are allowed to evolve. Organisms are subject to a changeable environment and competition from other organisms for a limited food supply. The gene structure may change through mutation. A feature of Evolve II is that the magnitude of phenotypic change resulting from mutation is itself a property of the gene. The system was studied under a number of environmental variation schemes. We report three significant findings. Two species (lineages with distinctly different survival strategies) evolved and coexisted in the same environmental conditions. Organisms developed a resistance to phenotypic change in response to mutation in slowly varying environments. However, traits which favor survival of the individual at the expense of reproduction could in some cases undergo phenotypic change in response to mutation despite the fact that this did not favor the survival of the offspring. This demonstrates that gene structures can evolve which are advantageous from the standpoint of the lineage, but not advantageous from the standpoint of individual offspring.

Aging↗
PubMedDate not supplied

Changes in the activity and the polypeptide composition of the oxygen-evolving complex in photosystem II of tobacco leaves infected with cucumber mosaic virus strain Y.

The amount of 22- and 23-kDa polypeptides in a 23-kDa protein family, which plays a regulatory role in photosynthetic oxygen evolution, decreased significantly during the progress of appearance of chlorotic spots in cucumber mosaic virus strain Y (CMV[Y])-inoculated tobacco (Nicotiana tabacum 'Ky57') leaves (Plant Mol. Biol. 16:689-698, 1991). The present study was conducted to determine if the amount of other polypeptides of the oxygen-evolving complex and the oxygen-evolving activity also decreased in CMV(Y)-inoculated tobacco leaves. The amount of a 33-kDa polypeptide, which is essential to oxygen evolution, did not decrease in CMV(Y)-inoculated leaves showing early symptoms, although the amount of 22- and 23-kDa polypeptides began to decrease. However, comparative analysis of electron transport in thylakoid membranes indicated that the oxygen-evolving activity in CMV(Y)-inoculated tobacco leaves was only partly reduced, compared with the activity in CMV(O)-inoculated tobacco leaves which did not show clear symptoms. Partial inhibition of the oxygen-evolving activity, by a differential decrease in the amount of polypeptides of the oxygen-evolving complex, seems to be associated with the primary molecular process of symptom expression in CMV(Y)-inoculated tobacco leaves.

Amino Acid Sequence↗
PubMed1988

Comparison of mandelate dehydrogenases from various strains of Acinetobacter calcoaceticus: similarity of natural and 'evolved' forms.

In previous work it had been shown that Acinetobacter calcoaceticus wild-type strain NCIB 8250 had only an L-mandelate deydrogenase but it could give rise to mutants that contained an evolved D-mandelate dehydrogenase; conversely, wild-type strain EBF 65/65 had only a D-mandelate dehydrogenase but gave rise to mutants that possessed an evolved L-mandelate dehydrogenase. Several other wild-type strains of A. calcoaceticus have now been shown to grow on both enantiomers of mandelate. In every case the L-mandelate dehydrogenases were found to be much more heat-stable and insensitive to inhibition by p-chloromercuribenzoate than were the D-mandelate dehydrogenases when measured in bacterial extracts. All the D-mandelate dehydrogenases in the wild-type strains were inactivated to about the same extent by an antiserum that had been raised in a rabbit against an evolved D-mandelate dehydrogenase. An evolved D-mandelate deydrogenase (from a mutant strain derived from strain NCIB 8250) and an original D-mandelate dehydrogenase (from a mutant strain derived from strain EBF 65/65) were purified to homogeneity by the same procedure and were indistinguishable as judged by immunological cross-reactivity of the native and the sodium-dodecyl-sulphate-denatured enzymes, solubility in cholate, net charge at pH 7.5, pI value, salting-out properties, Mr value, apparent K(m) value for D-mandelate, heat-stability and sensitivity to p-chloromercuribenzoate. The most likely explanation for the appearance of evolved mandelate dehydrogenases in strains of A. calcoaceticus is that cryptic genes become expressed.

Acinetobacter↗
PubMed2025

Reproductive Isolation due to Divergent Ecological Selection Is Accompanied by Vast Genomic Instability in Experimentally Evolved Yeast Populations.

Populations evolving independently in divergent environments accumulate genetic differences and potentially evolve reproductive isolation as a by-product of divergence. The speed and mechanisms underlying this process are difficult to investigate because we rarely get the opportunity to witness them in natural settings, and histories of selection and gene flow between populations are often unknown. Here, we experimentally evolved yeast for 1000 generations of evolution in both divergent and parallel environments. At regular time points during experimental evolution, we made crosses between parallel- and divergent-evolving populations to measure postzygotic reproductive isolation (gamete viability). We used whole genome population sequencing to determine the mutational load, the number and types of structural variation, and other genomic features of the parent, F1 and F2 intraspecific hybrids. We found evidence for large-scale phenotypic and genome-wide differentiation in response to divergent laboratory selection. Divergent-selected populations produced hybrids with reduced gamete viability-a classic signature of postzygotic reproductive isolation in the form of hybrid breakdown. Parallel-selected populations, on the other hand, remained more reproductively compatible (with exceptions). We found that F2 hybrid genomes contained vast genomic instability, that is, new structural variants (especially insertions, deletions and interchromosomal translocations) that were not observed in parent and F1 genomes, which is likely a result of chromosome missegregation and recombination errors in hybrid meiosis. Our results provide phenotypic and genomic evidence that partial reproductive isolation evolved due to adaptation to divergent environments, consistent with predictions of ecological speciation theory.

Reproductive Isolation↗
PubMed1985

The role of chloride ion on the photoreactivation of the oxygen-evolving center of tris-washed, 2,6-dichlorophenol indophenol-treated grana.

Chloride ion is found to be an essential factor in photoreactivation of the oxygen-evolving center. Tris-washed, 2,6-dichlorophenol indophenol-treated grana are low in both Mn content and oxygen-evolving activity. These grana can restore high oxygen-evolving activity, however, by incorporating Mn2+ ion under weak light in the presence of chloride and calcium ions with dithiothreitol. This restoration is called photoreactivation. When chloride ion is omitted from the medium for the photoreactivation, the recovery of oxygen-evolving activity is inhibited. Other anions, such as bromide and nitrate anions, could also mediate the reactivation; but, anions of weak acids or polyvalent strong acids were not effective. Chloride ion is also required in the light-induced H+ and Mn2+ uptake of these grana, which are essential partial reactions for the reactivation. It is therefore concluded that chloride ion plays an important role in the photoreactivation.

2,6-Dichloroindophenol↗
PubMed1986

Effects of NaCl and glycerol on photosynthetic oxygen-evolving activity with thylakoid membranes from halophilic green alga Dunaliella tertiolecta.

It is known that the halophilic green alga Dunaliella tertiolecta grows under hypertonic conditions (with NaCl), which induce the intracellular accumulation of high concentrations of glycerol in order to counterbalance the osmotic change. The effects of NaCl and glycerol on the photosynthetic oxygen-evolving activity of thylakoid membranes prepared from D. tertiolecta were investigated in relation to the dissociation of the membranes. It was found that proteins with Mr of 24,000, 17,000, and 13,000 were dissociated from thylakoid membranes of D. tertiolecta by washing with 1 M NaCl, whereas the photosynthetic oxygen-evolving activity was stimulated 2-fold by 0.1-1.5 M NaCl. The antibodies against spinach 24K and 17K proteins did not cross-react with Dunaliella 24K and 17K proteins, respectively. The salt-tolerant feature of the oxygen-evolving activity with Dunaliella thylakoid membranes may be related to the difference of the properties of these two proteins between D. tertiolecta and spinach. When the membranes were washed with 1 M Tris, proteins with Mr of 50,000 and 31,000 were also dissociated in addition to the 24K and 17K proteins described above. The antibody against spinach 33K protein cross-reacted with 31K protein of D. tertiolecta, showing that Dunaliella 31K protein corresponds to spinach 33K protein. When the membranes were treated with a mixture of 1% cholate and 2% deoxycholate, the oxygen-evolving activity was completely depressed, but the depressed activity was significantly restored by organic solvents. Glycerol and dimethylsulfoxide were the most effective for the restoration.(ABSTRACT TRUNCATED AT 250 WORDS)

Chlorophyta↗
PubMed1992

Determination of evolved 14CO2 in decarboxylase reactions with application to measurement of [14C]oxalic acid.

An assay is described for the determination of the radioactive purity of [14C]oxalic acid preparations and the quantity of [14C]oxalic acid in biological samples. In this method oxalate decarboxylase is used to convert oxalate to formate and CO2. The entire procedure is carried out in a scintillation vial. The 14CO2 released in the enzymic reaction is allowed to diffuse off in a fume hood following acidification. Scintillation fluid is added to reacted and unreacted vials and the radioactivity measured. The loss of radioactivity from the reacted versus the unreacted vials provides the quantity of evolved 14CO2. This value is equal to 50% of the [14C]-oxalate (dpm) present. The radioactive purity of four preparations of [U-14C]oxalic acid was 99.0% while a fifth batch had a purity of 88%. A single batch of [U-14C]oxalic acid had a radioactive purity of 99.0% following storage of an aqueous solution, at -20 degrees C for 7 years. Recovery of [14C]oxalic acid from rat fecal extracts was 101.3%. Eight replicate analyses of a [U-14C]oxalic acid preparation gave a coefficient of variation of 0.3%. Following subcutaneous infusion of [U-14C]oxalic acid to rats, 100.2 +/- 2.9%, mean +/- SD, of the 14C in fecal extracts was present as [14C]oxalic acid (n = 10). The procedure provides a rapid, sensitive, and specific method to determine [14C]oxalic acid. It avoids the time consuming and inconvenient procedure for trapping and counting the evolved 14CO2. The approach used to determine the evolved 14CO2 may find application in other radiochemical methods that require its measurement.

Animals↗
PubMed1986

Breast cancer treatment: evolving approaches but stable results.

This report describes the outcome of 530 women with breast cancer diagnosed from 1968 through 1983 and represents a demographic population rather than a referred selected one. The data represents the results of evolving breast cancer treatment approaches during the past 2 decades and is particularly useful as a measure of the total population denominator, free of selection factors that confound reports detailing a surgical, radiation, or chemotherapy experience. During the time interval reviewed, the standard treatment approach of the primary changed from radical mastectomy to biopsy and radiation therapy. Chemotherapy policy evolved from single agent treatment for relapse to multiple drug programs as adjuvant or for relapse. The major findings were: The 5-, 10-, and 15-year survival rates for the intervals 1972-75, 1976-79, and 1980-83 were slightly better than the earliest interval 1968-71, but with no statistically significant improvement. The frequency of favorable disease (Stages Tis, 1) increased from 16 to 31 percent during the interval but the mean age remained the same suggesting that patient education programs, availability of health insurance, or mammography may have lead to identifying patients with more favorable disease. Mastectomy has been replaced by breast conserving surgery and radiation as the most common treatment of the primary. Patients treated by surgery and biopsy/radiation had identical survival outcomes. It was not possible to detect improved survival that could be ascribed to the adoption of multiple agent chemotherapy but the magnitude of the effect is calculated to be on the order of 2% of the total patient population diagnosed. Death due to breast cancer decreases with time after diagnosis but is still 4% per year, 10 years after treatment. The findings suggest that progress has been made in detection, breast conservation, and palliation of symptoms in many subpopulations, but the end results for the total breast cancer population have remained stable during an era when the treatment approach evolved markedly.

Breast Neoplasms↗
PubMed1992

Comparative properties of hydroquinone and hydroxylamine reduction of the Ca(2+)-stabilized O2-evolving complex of photosystem II: reductant-dependent Mn2+ formation and activity inhibition.

Calcium binding to photosystem II slows NH2OH inhibition of O2 evolution; Mn2+ is retained by the O2-evolving complex [Mei, R., & Yocum, C. F. (1991) Biochemistry 30, 7836-7842]. This Ca(2+)-induced stability has been further characterized using the large reductant hydroquinone. Salt-washed photosystem II membranes reduced by hydroquinone in the presence of Ca2+ retain 80% of steady-state O2 evolution activity and contain about 2 Mn2+/reaction center that can be detected at room temperature by electron paramagnetic resonance. This Mn2+ produces a weak enhancement of H2O proton spin-lattice relaxation rates, cannot be easily extracted by a chelator, and is reincorporated into the O2-evolving complex upon illumination. A comparison of the properties of Ca(2+)-supplemented photosystem II samples reduced by hydroquinone or NH2OH alone or in sequence reveals the presence of a subpopulation of manganese atoms at the active site of H2O oxidation that is not accessible to facile hydroquinone reduction. At least one of these manganese atoms can be readily reduced by NH2OH following a noninhibitory hydroquinone reduction step. Under these conditions, about 3 Mn2+/reaction center are lost and O2 evolution activity is irreversibly inhibited. We interpret the existence of distinct sites of reductant action on manganese as further evidence that the Ca(2+)-binding site in photosystem II participates in regulation of the organization of manganese-binding ligands and the overall structure of the O2-evolving complex.

Binding Sites↗
PubMed1991

Nitrogen ligation to manganese in the photosynthetic oxygen-evolving complex: continuous-wave and pulsed EPR studies of photosystem II particles containing 14N or 15N.

The possibility of nitrogen ligation to the Mn in the oxygen-evolving complex from photosystem II was investigated with electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectroscopies using 14N- and 15N-labeled preparations. Oxygen-evolving preparations were isolated from a thermophilic cyanobacterium, Synechococcus sp., grown on a medium containing either 14NO3- or 15NO3- as the sole source of nitrogen. the substructure on the "multiline" EPR signal, which arises from Mn in the S2 state of the enzyme, was measured with continuous-wave EPR. No changes were detected in the substructure peak positions upon substitution of 15N for 14N, indicating that this substructure is not due to superhyperfine coupling from nitrogen ligands. To detect potential nitrogen ligands with superhyperfine couplings of lesser magnitude than could be observed with conventional EPR methods, electron spin-echo envelope modulation experiments were also performed on the multiline EPR signal. The Fourier transform of the light-minus-dark time domain ESEEM data shows a peak at 4.8 MHz in 14N samples which is absent upon substitution with 15N. This gives unambiguous evidence for weak hyperfine coupling of nitrogen to the Mn of the oxygen-evolving complex. Possible origins of this nitrogen interaction are discussed.

Cyanobacteria↗
PubMed2025

Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter.

The in vivo continuous evolution system OrthoRep (orthogonal replication) is a powerful strategy for rapid enzyme evolution in Saccharomyces cerevisiae that diversifies genes at a rate exceeding the endogenous genome mutagenesis rate by several orders of magnitude. However, it is difficult to neofunctionalize genes using OrthoRep partly because of the way selection pressures are applied. Here we combine OrthoRep with optogenetics in a selection strategy we call OptoRep, which allows fine-tuning of selection pressure with light. With this capability, we evolved a truncated form of the endogenous monocarboxylate transporter JEN1 (JEN1t) into a de novo mevalonate importer. We demonstrate the functionality of the evolved JEN1t (JEN1tY180C/G) in the production of farnesene, a renewable aviation biofuel, from mevalonate fed to fermentation media or produced by microbial consortia. This study shows that the light-induced complementation of OptoRep may improve the ability to evolve functions not currently accessible for selection, while its fine tunability of selection pressure may allow the continuous evolution of genes whose desired function has a restrictive range between providing effective selection and cellular viability.

Saccharomyces cerevisiae↗
PubMed2025

The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase.

The polyamine putrescine is synthesized primarily from L-arginine via agmatine in bacteria. There are currently three known routes from agmatine to putrescine, including direct conversion by agmatinase. The other two routes use agmatine deiminase to produce N-carbamoylputrescine from agmatine, then one of two nonhomologous enzymes, putrescine transcarbamylase or N-carbamoylputrescine amidohydrolase (NCPAH), converts N-carbamoylputrescine to putrescine. Here, we functionally identify enzymes from phylogenetically distant bacteria, the ɣ-proteobacterium Shewanella oneidensis, and the actinomycetota species Microterricola gilva, that are novel alternative, nonhomologous, noncanonical NCPAHs that we term AguY, which have emerged by convergent evolution. Kinetic analysis indicates that the AguY enzymes are as efficient as the canonical NCPAH from Pseudomonas aeruginosa in converting N-carbamoylputrescine to putrescine. Genomic evidence suggests that the AguY enzymes may participate in putrescine biosynthetic or agmatine catabolic pathways and are occasionally encoded in genomes that also encode agmatinase. We show that the Type VI secretion system toxin Tse8 from P. aeruginosa has evolved from AguY. It is formally possible that AguY evolved directly or indirectly from the ancient glutamine amidohydrolase GatA, a component of the transamidosome, an RNA/protein complex required for the production of glutamine-charged tRNA. Our study provides a further example of the prevalence of convergent evolution and horizontal gene transfer in polyamine biosynthesis, suggesting pervasive selective pressure to evolve polyamine metabolism in bacteria.

Pseudomonas aeruginosa↗
PubMed1986

Structure of evolving populations of Saccharomyces cerevisiae: adaptive changes are frequently associated with sequence alterations involving mobile elements belonging to the Ty family.

Haploid a and diploid a/alpha and a/a populations of Saccharomyces cerevisiae evolving in laboratory environments for up to 300 generations were analyzed for sequence rearrangements associated with the Ty family of transposable elements. In contrast to results with Escherichia coli, evolving populations of yeast exhibit a high frequency of sequence rearrangements associated with mobile genetic elements. In particular, adaptive shifts in these populations are often associated with such sequence rearrangements. The results are most compatible with the explanation that there is direct selection for some of the sequence rearrangements. In addition, the pattern of changes suggests that the structure of evolving microorganism populations may be more complex than expected.

Adaptation, Biological↗
PubMed1987

Structural localization of the O2-evolving apparatus to multimeric (tetrameric) particles on the lumenal surface of freeze-etched photosynthetic membranes.

Isolated appressed chloroplast membranes, highly enriched in photosystem II (PSII) activity, were examined by freeze-etch electron microscopy. The exposed surfaces of these Triton X-100 solubilized membrane fragments correspond to the lumenal or ESs surface of intact stacked thylakoid membrane regions (Dunahay, T. G., L. A. Staehelin, M. Seibert, P. D. Ogilvie, and S. P. Berg. 1984. Biochim. Biophys. Acta. 764:179-193). The sequential removal from this sample of three extrinsic proteins (17, 23, and 33 kD) associated with the O2-evolving apparatus and the concomitant loss of O2 evolution, was related to subtle changes in the height and substructure of characteristic multimeric (often tetrameric) particles that protrude from the ESs membrane surface. After removal of these proteins, the multimeric particles disappeared and dimeric particles of similar diameter but of lesser height (6.1 vs. 8.2 nm in the controls) were observed. Reconstitution of the depleted membrane fragments with the extrinsic proteins led to rebinding of the three proteins, to a 63% recovery of the control rates of O2 evolution, and to the reappearance of the larger multimeric particles. Analysis of the structural changes associated with the loss and rebinding of the extrinsic proteins is consistent with a stoichiometry of one PSII complex for either one or two copies of the 17-, 23-, and 33-kD proteins, and these are symmetrically arranged on the lumenal surface of the complex. These results demonstrate that the multimeric ESs particles correspond to part of the intact O2-evolving apparatus of PSII, thus confirming previous indirect studies relating these particles to PSII. The dimeric particles probably contain the rest of the O2-evolving complex.

Chlorophyll↗
PubMed1991

Identification of adaptive changes in an evolving population of Escherichia coli: the role of changes with regulatory and highly pleiotropic effects.

A population of Escherichia coli initiated with a single clone developed extensive morphological and physiological polymorphism after being maintained for 773 generations in glucose-limited continuous culture. To understand the mechanisms of adaptation to this environment, total protein patterns of four adaptive clones and of the parent strains were examined by two-dimensional gel electrophoresis. Approximately 20% of the proteins (approximately 160 in absolute numbers) showed significantly different levels of expression in pairwise comparisons of parent and adapted clones. The extent of these changes points to the importance of mutations with regulatory and/or highly pleiotropic effects in the adaptive process. The four evolved clones all expressed fewer proteins than did the parent strain, supporting the hypothesis of energy conservation during evolutionary change. Forty-two proteins that could be assigned to known cellular functions were identified. The changes in some of them indicated that the evolved clones developed different adaptive mechanisms to glucose-limited environment. Changes were observed in the expression levels of proteins associated with translation, membrane composition, shock response, and active transport. A fraction of the changes could not be either explained or predicted from a consideration of the nature of the environment in which the clones evolved.

Adaptation, Biological↗
PubMedDate not supplied

Thromboxane A2 does not contribute to arrhythmogenesis during evolving canine myocardial infarction.

During the healing phase of evolving myocardial infarction, inflammatory cells invade the affected region and produce metabolites that may influence electrophysiological parameters and the genesis of malignant arrhythmias. We have recently shown an increased synthetic capacity within an evolving infarct for thromboxane A2 (TXA2), a metabolite that has been implicated in arrhythmias associated with early ischemia. The present study used both in vivo and in vitro procedures to define the electrophysiological and arrhythmogenic effects, if any, of thromboxane during evolving myocardial infarction. Thirty-three dogs divided into three groups were studied 3-7 days after transient left anterior descending coronary artery ligation. One group (n = 24) was examined by programmed electrical stimulation in the conscious state and, of the five dogs in this group with sustained ventricular tachycardia (VT), none demonstrated consistent limitation of inducibility by selective inhibition of thromboxane synthetase using three different agents. In the second group, (n = 5) regional conduction velocity was assessed using detailed three-dimensional activation analysis from 232 simultaneous intramyocardial sites, and no change was induced by the thromboxane synthetase inhibitor OKY-1581 in either normal or infarcted myocardial zones during sinus rhythm or with pacing. In the third group (n = 4), isolated ventricular muscle was studied in vitro using both intracellular transmembrane action potential recordings and surface extracellular maps from 48 simultaneous points. Neither intracellular action potential parameters nor extracellularly recorded activation patterns were altered by superfusion with the stable thromboxane analog STA2, the activity of which was verified by bioassay. Thus, despite increased synthetic capacity for thromboxane generation, the presence of TXA2 does not directly influence either electrophysiological indices or arrhythmogenesis.

Action Potentials↗
PubMed2025

Multi-Omics Analysis of Experimentally Evolved Candida auris Isolates Reveals Modulation of Sterols, Sphingolipids, and Oxidative Stress in Acquired Amphotericin B Resistance.

Clinical isolates of Candida auris show a high prevalence of resistance to Amphotericin B (AmB)-an uncommon trait in most Candida species. Alterations in ergosterol biosynthesis can contribute to acquired AmB resistance in C. auris laboratory strains but are rarely seen in clinical isolates. In this study, we experimentally evolved two drug-susceptible Clade II isolates of C. auris to develop AmB resistance. The evolved strains displayed a four to eight fold increase in MIC50 compared to the parental cells. We analyzed changes in their karyotype, genome, lipidome, and transcriptome associated with this acquired resistance. In one lineage, AOX2 was upregulated, and its deletion reversed the AmB resistance phenotype. The aox2Δ mutant also failed to evolve AmB resistance under experimental conditions. In the same lineage, restoring the UPC2 S332R and RTG3 S101T mutations to the wild-type allele restored AmB susceptibility. In another lineage, the ergosterol and sphingolipid pathways were observed to play a critical role, and upregulation of the ERG genes elevated the total sterol content, while significant downregulation of HSX11 (glucosylceramide synthase) resulted in lower levels of glucosylceramides. To our knowledge, this study is the first to show that AmB resistance in C. auris can be acquired through mechanisms both dependent on or independent of sterol content modulation, highlighting Aox2 and Upc2 as key regulators of amphotericin resistance.

Amphotericin B↗
PubMed1991

Do women and men speak in different voices? A comparative study of self-evolvement.

A comparative study of women's and men's levels of self evolvement was conducted based on Kegan's Constructive-Developmental Theory. The samples for the study were drawn from groups of American women and men in military service in Europe and their dependents, as well as civilians employed by the American military. The participants level of self evolvement was determined by Kegan's Subject-Object Interview. The results indicated that there were no gender differences in levels of self evolvement. Hence, the orientation toward individuation and increased autonomy, which is stereotypically masculine, and the orientation toward attachment and dependence, which is stereotypically feminine, are not necessarily based on innate male or female characteristics. The tendency towards separateness or inclusion may be related more to individual differences and other factors such as the social and cultural environment.

Adult↗