Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “evolvability”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 361 records · Page 20Linked to original sources

Changes in the extracellular envelope glycoprotein of variants that evolve during the course of simian immunodeficiency virus SIVMne infection affect neutralizing antibody recognition, syncytium formation, and macrophage tropism but not replication, cytopathicity, or CCR-5 coreceptor recognition.

Simian immunodeficiency virus SIVMne, like human immunodeficiency virus, evolves from a macrophage-tropic, non-syncytium-inducing virus at early times in infection to a T-cell-tropic, syncytium-inducing, cytopathic virus population over the course of progression to AIDS. Because the viruses isolated late in SIVMne infection of macaques include a complex mixture of variants, the viral determinants of such phenotypic changes have not been defined. To identify genetic changes that are important to virus evolution in the host, we constructed chimeric viruses by introducing variant envelope genes representative of proviruses throughout the course of infection and disease into the SIVMne parental clone (SIVMneCL8) that infected the macaque. The chimeric viruses expressed sequences encoding the surface unit of the envelope glycoprotein (Env-SU) of variants cloned between 35 and 170 weeks postinfection. The chimera with Env-SU from 35 weeks postinfection encoded only four changes in V1 compared to SIVMneCL8, whereas the chimeras encoding Env-SU from variants isolated later in infection encoded progressively more mutations both in V1 and elsewhere. Like SIVMneCL8, the chimeras were infectious for CEMx174 cells and macaque peripheral blood mononuclear cells. However, in contrast to SIVMneCL8, the chimeric viruses did not infect macaque macrophages, although each retained the ability to recognize the CCR-5 coreceptor. Thus, these data provide direct evidence that changes which evolve in Env-SU during the course of SIVMne infection do not alter CCR-5 interactions. Viruses encoding Env-SU from the latest times in infection (121 to 170 weeks postinfection), after disease was apparent, were syncytium inducing. However, these viruses were not highly cytopathic, suggesting that additional viral determinants may be required for the rapidly replicating, cytopathic phenotype of the uncloned mixed variant population. Changes in Env-SU did allow the virus to escape serum neutralizing antibodies that recognized the SIVMneCL8 parent. Moreover, the chimera encoding the Env-SU of a virus from 35 weeks postinfection, which differed from SIVMneCL8 only in V1, was not sensitive to neutralization by infected macaque sera, suggesting that V1 may define a portion of the principal neutralizing determinant for SIVMne. Together, these data suggest that SIV variants with changes in the Env-SU may be selected primarily by virtue of their ability to escape neutralizing antibody recognition.

Amino Acid Sequence↗

Genetic mutations driving ciprofloxacin resistance in laboratory-evolved Salmonella Typhimurium.

Ciprofloxacin resistance in Salmonella Typhimurium is a significant public health concern, and the mechanisms by which the resistance evolves are poorly defined. Here, by serial passaging under antibiotic selection, we isolated ciprofloxacin-resistant S. Typhimurium mutants and subjected them to whole-genome sequencing to reveal the major mutations associated with resistance. The Low CipR mutant acquired four chromosomal mutations in ramR, icdA, lipB, and gyrA, and the High CipR mutant gained additional mutations in gyrB, yaiC, and corA. Functional characterization determined that mutations in ramR resulted in efflux pump upregulation, while disruptions in the TCA cycle caused by mutations in icdA and lipB led to metabolic alterations. These changes indirectly enhanced resistance by increasing the expression of the global regulator MarA and reducing OmpF-dependent membrane permeability. Despite the observation of the G105A substitution in GyrA, enzymatic assays confirmed the failure to support resistance to ciprofloxacin, possibly because the structural alteration remained minimal. GyrB488-489dup was associated with maintained supercoiling under ciprofloxacin and enhanced fluoroquinolone resistance, suggesting a major role in resistance evolution. Other mutations in yaiC impaired biofilm and, in corA, intracellular accumulation of magnesium, possibly stabilizing the bacterial cell envelope under antibiotic pressure. The findings provide novel explanations for the multifaceted mechanisms leading to ciprofloxacin resistance in Salmonella and suggest targets to combat antimicrobial resistance.IMPORTANCEAntibiotic resistance in Salmonella Typhimurium is an increasing public health concern, yet the genetic changes that allow bacteria to become resistant are not fully understood. In this study, we evolved ciprofloxacin-resistant Salmonella in the laboratory and identified the mutations that arise during resistance development. We found that resistance does not result from a single change but from multiple adaptations affecting drug efflux, metabolism, and the antibiotic target. Some mutations increased the activity of pumps that remove antibiotics from the cell, while others altered bacterial metabolism and reduced membrane permeability, making it harder for the drug to enter. A duplication in the DNA gyrase subunit GyrB played a particularly important role in maintaining DNA function under antibiotic stress. Together, these results reveal how diverse genetic changes cooperate to generate ciprofloxacin resistance and provide insights that may help guide strategies to combat drug-resistant Salmonella infections.

DNA gyrase↗

The in situ localization of Adh transcripts in Drosophila species reveals evolved regulatory differences in spatially restricted expression.

Spatial and temporal aspects of Adh expression were examined during oogenesis and embryogenesis of Drosophila melanogaster, D. simulans, and D. virilis by in situ hybridization. In stage 14 and 15 embryos, differences in zygotic expression of Adh in the primordia of the gastric caecae of D. simulans and in the fat body of D. virilis were observed. These zygotic differences appear to be transient because Adh expression is seen in the gastric caecae of stage 16 embryos of D. simulans and in the fat body of stage 17 embryos of D. virilis. Analysis of D. melanogaster x D. simulans hybrids revealed that the parental difference for transcriptional activity of Adh in the primordia of the gastric caecae is under dominant control. These results provide the basis for exploring evolved regulatory differences in Adh expression during oogenesis and embryogenesis of Drosophila, which are until now unexplored. The potential of in situ hybridization in analyzing evolved regulatory differences in gene expression is briefly discussed.

Alcohol Dehydrogenase↗

Evolving digital circuits using hybrid particle swarm optimization and differential evolution.

This paper presents the evolution of combinational logic circuits by a new hybrid algorithm known as the Differential Evolution Particle Swarm Optimization (DEPSO), formulated from the concepts of a modified particle swarm and differential evolution. The particle swarm in the hybrid algorithm is represented by a discrete 3-integer approach. A hybrid multi-objective fitness function is coined to achieve two goals for the evolution of circuits. The first goal is to evolve combinational logic circuits with 100% functionality, called the feasible circuits. The second goal is to minimize the number of logic gates needed to realize the feasible circuits. In addition, the paper presents modifications to enhance performance and robustness of particle swarm and evolutionary techniques for discrete optimization problems. Comparison of the performance of the hybrid algorithm to the conventional Karnaugh map and evolvable hardware techniques such as genetic algorithm, modified particle swarm, and differential evolution are presented on a number of case studies. Results show that feasible circuits are always achieved by the DEPSO algorithm unlike with other algorithms and the percentage of best solutions (minimal logic gates) is higher.

Algorithms↗

Pulsed and parallel-polarization EPR characterization of the photosystem II oxygen-evolving complex.

Photosystem II uses visible light to drive the oxidation of water, resulting in bioactivated electrons and protons, with the production of molecular oxygen as a byproduct. This water-splitting reaction is carried out by a manganese cluster/tyrosine radial ensemble, the oxygen -evolving complex. Although conventional continuous-wave, perpendicular -polarization electron paramagnetic resonance (EPR) spectroscopy has significantly advanced our knowledge of the structure and function of the oxygen-evolving complex, significant additional information can be obtained with the application of additional EPR methodologies. Specifically, parallel-polarization EPR spectroscopy can be use to obtain highly resolved EPR spectra of integer spin Mn species, and pulsed EPR spectroscopy with electron spin echo-based sequences, such as electron spin echo envelope modulation and electron spin echo-electron nuclear double resonance, can be used to measure weak interactions obscured in continuous-wave spectroscopy by inhomogeneous broadening.

Cyanobacteria↗

Serial abnormalities of fibrin turnover in evolving adult respiratory distress syndrome.

We studied the changes of coagulation and fibrinolysis in bronchoalveolar lavage (BAL) and plasma obtained serially at intervals after the onset of adult respiratory distress syndrome (ARDS). BAL procoagulant activity was increased at 3 days and tended to decrease thereafter. Tissue factor associated with factor VII was the major BAL procoagulant. Fibrinopeptide A was increased, indicating increased thrombin-mediated conversion of fibrinogen to fibrin. Fibrinolytic activity was usually undetectable in BAL at 3 days post-ARDS and remained depressed for up to 14 days despite unchanged concentrations of urokinase and variably detectable tissue plasminogen activator. Depressed fibrinolytic activity was associated with increased antiplasmin activity and plasminogen activator inhibitor 1 (PAI-1) while PAI-2 concentrations approximated those of control samples and did not change during evolving ARDS. Evidence of systemic coagulopathy and increased systemic fibrin degradation were commonly found in serial ARDS plasma samples, consistent with accelerated vascular and/or extravascular fibrin deposition in these patients. The data indicate that intra-alveolar as well as systemic derangements of fibrin turnover are common features of evolving ARDS. Concurrent local abnormalities of both coagulation and fibrinolytic pathways favor persistence of alveolar fibrin for up to 14 days after clinical recognition of ARDS.

Adult↗

The good enough calculi of evolving control systems: evolution is not engineering.

In evolved aggregates of accidentally invented elements, retained when statistically good enough to identify limitations of antecedent systems, survival value might favor operators incorporating aspects of, while not identical with, feedback, feedforward, state varible, and "homeostatic" control. Generally, simple organizational increments should predominate. After invention, an internal controller with readily modifiable rules could facilitate evolution of compound inventions, but criteria controlling rule changes would be only indirectly (probably imperfectly) survival referent. Consequent to combination of independent invention with indirect criteria and statistical acceptance, evolved control logic could be: both redundant and incomplete; good enough with malefic aspects; built of loosely linked or autonomous sublogics; and a source of good enough solutions from incomplete information. The partially explicit rules are defined more by rejections than by ratifications. Study of the result based on formal logic, engineering conventions, and familiar coordinate systems could conceive illegitimate illusions of understanding.

Biological Evolution↗

Why did the strepsirhine tooth comb evolve.

The hypothesis that the original strepsirhine tooth comb evolved for scraping gum is examined. The comparative morphology of the anterior dentition does not corroborate this view, and our study suggests that the primitive tooth comb, which was 6-toothed, evolved for the maintenance of the five, evenly distributed narrow spaces in between them. Unlike the incisors of other groups, platyrrhines or catarrhines, for example, the apical extremities in the primitive condition are not closer to one another than the basal portions of these teeth. The biological role responsible for the evolution of the function of the original tooth comb is believed to be fur-combing. Subsequent modifications in numerous lineages altered both morphology and function as a result of new roles, and this tended to obscure the cause of origin of this character complex.

Animals↗

Early and 1-year clinical outcome of patients' evolving non-Q-wave versus Q-wave myocardial infarction after thrombolysis. Results from The TIMI II Study.

BACKGROUND: There are few data comparing clinical outcome and potential indications for routine post-myocardial infarction cardiac catheterization and revascularization of patients who sustain a non-Q-wave versus Q-wave infarct after thrombolytic therapy. METHODS AND RESULTS: A secondary analysis of 2634 patients enrolled in the TIMI II trial with a first myocardial infarction was performed to determine 6-week and 1-year cardiac event rates and identify clinical and angiographic differences between the 1867 patients (70.9%) who evolved a Q-wave infarct and the 767 patients (29.1%) who sustained a non-Q-wave infarct after treatment with intravenous thrombolytic therapy. Male sex (85.3% versus 75.6%; P < .001) and anterior wall infarcts (53.8% versus 43.7%; P < .001) were more frequent in the Q-wave versus the non-Q-wave group. During recombinant tissue-type plasminogen activator (rTPA) infusion, a greater percentage of non-Q-wave patients (37.3% versus 23.5%; P = .001) had normalization of initial ST-segment elevation. Infarct-related artery patency (TIMI flow grade 2 or 3) (P = .02), complete infarct-related artery reperfusion (TIMI 3 flow grade) (P < .001), and the percentage of patients with a predischarge resting left ventricular ejection fraction > 55% (P < .001) were greater in the non-Q-wave group. New congestive heart failure during hospitalization developed more frequently in Q-wave patients (18.9% versus 11.6%; P < .001). After 42 days, the occurrences of reinfarction (P = .76), death (P = .76), and combined death or reinfarction (P = .43) were similar in patients assigned to the invasive or conservative postlytic management strategy, regardless of infarct type. One-year mortality was 3.4% versus 4.4% for non-Q-wave versus Q-wave infarct type, respectively (P = .25). CONCLUSIONS: Angiographic and clinical differences were observed between patients who present with initial ST-segment elevation and evolve early non-Q-wave versus Q-wave myocardial infarcts after treatment with rTPA, heparin, and aspirin. Early mortality and adverse clinical cardiac events in these patients are not significantly different after a conservative compared with an invasive treatment strategy, regardless of whether the infarct type is non-Q wave or Q wave.

Angioplasty, Balloon, Coronary↗

N-acetylcysteine in combination with nitroglycerin and streptokinase for the treatment of evolving acute myocardial infarction. Safety and biochemical effects.

BACKGROUND: N-acetylcysteine (NAC) has been shown to potentiate the effects of nitroglycerin (NTG) and to have antioxidant activity. This is the first study to assess the safety and effect of NAC in the treatment of evolving acute myocardial infarction (AMI). METHODS AND RESULTS: Patients with AMI received either 15 g NAC infused over 24 hours (n = 20) or no NAC (n = 7), combined with intravenous NTG and streptokinase. Peripheral venous plasma malondialdehyde (MDA), reduced (GSH) and oxidized (GSSG) glutathione concentrations, and rate of reperfusion (using continuous ST-segment analysis) were measured. Cardiac catheterization was performed between days 2 and 5. No significant adverse events occurred. Less oxidative stress occurred in patients treated with NAC than in patients not receiving NAC (GSH to GSSG ratio 44 +/- 25 versus 19 +/- 13 at 4 hours, P < .05). NAC concentration (mean 172 +/- 79 mumol/L at 4 hours) was correlated to GSH concentration (P = .006). MDA concentrations were lower (P = .001) over the first 8 hours of treatment with NAC. There was a trend toward more rapid reperfusion (median 58 minutes, 95% confidence interval [CI] 48 to 98 minutes versus median 95 minutes, 95% CI 59 to 106 minutes; P = .17) and better preservation of left ventricular function (cardiac index 3.4 +/- 0.8 versus 2.6 +/- 0.27 L.min.m2, P = .009) with NAC treatment. CONCLUSIONS: NAC in combination with NTG and streptokinase appeared to be safe for the treatment of evolving AMI and was associated with significantly less oxidative stress, a trend toward more rapid reperfusion, and better preservation of left ventricular function.

Acetylcysteine↗

beta-blockade prevents sustained metalloproteinase activation and diastolic stiffening induced by angiotensin II combined with evolving cardiac dysfunction.

Angiotensin II (Ang II)-mediated sympathostimulation may worsen the progression of cardiac failure, although the nature and mechanisms of such interactions are largely unknown. We previously demonstrated that Ang II combined with evolving cardiodepression (48-hour tachycardia pacing, 48hP) induces marked chamber stiffening and increases metalloproteinases (MMPs). Here, we test the hypothesis that both abnormalities stem from sympathostimulatory effects of Ang II. Forty-eight dogs were instrumented to serially assess conscious ventricular mechanics, MMP abundance and activity, and myocardial histopathology. 48hP combined with 5 days of Ang II (15+/-5 ng. kg(-1). min(-1) IV) more than doubled chamber stiffness (end-diastolic pressure >25 mm Hg, P<0.001), whereas stiffness was unchanged by Ang II or 48hP alone. In vitro and in situ zymography revealed increased MMP abundance and activity (principally 92-kDa gelatinase) from Ang II+48hP. Both stiffening and MMP changes were prevented by cotreatment with high-dose atenolol (which nearly fully inhibited isoproterenol-induced inotropy) but not partial beta-blockade. Myocellular damage with fibroblast/neutrophil infiltration from Ang II+48hP was also inhibited by high- but not low-dose atenolol, whereas collagen content was not elevated with either dose. These data support a role of sympathostimulation by Ang II in modulating myocardial MMP abundance and activity and diastolic stiffening in evolving heart failure and suggest a novel mechanism by which beta-blockade may limit chamber remodeling and diastolic dysfunction.

Adrenergic beta-Agonists↗

Connection and coordination: the interplay between architecture and dynamics in evolved model pattern generators.

We undertake a systematic study of the role of neural architecture in shaping the dynamics of evolved model pattern generators for a walking task. First, we consider the minimum number of connections necessary to achieve high performance on this task. Next, we identify architectural motifs associated with high fitness. We then examine how high-fitness architectures differ in their ability to evolve. Finally, we demonstrate the existence of distinct parameter subgroups in some architectures and show that these subgroups are characterized by differences in neuron excitabilities and connection signs.

Animals↗

Fitness landscapes and evolvability.

In this paper, we develop techniques based on evolvability statistics of the fitness landscape surrounding sampled solutions. Averaging the measures over a sample of equal fitness solutions allows us to build up fitness evolvability portraits of the fitness landscape, which we show can be used to compare both the ruggedness and neutrality in a set of tunably rugged and tunably neutral landscapes. We further show that the techniques can be used with solution samples collected through both random sampling of the landscapes and online sampling during optimization. Finally, we apply the techniques to two real evolutionary electronics search spaces and highlight differences between the two search spaces, comparing with the time taken to find good solutions through search.

Biological Evolution↗

Evolving neural networks through augmenting topologies.

An important question in neuroevolution is how to gain an advantage from evolving neural network topologies along with weights. We present a method, NeuroEvolution of Augmenting Topologies (NEAT), which outperforms the best fixed-topology method on a challenging benchmark reinforcement learning task. We claim that the increased efficiency is due to (1) employing a principled method of crossover of different topologies, (2) protecting structural innovation using speciation, and (3) incrementally growing from minimal structure. We test this claim through a series of ablation studies that demonstrate that each component is necessary to the system as a whole and to each other. What results is significantly faster learning. NEAT is also an important contribution to GAs because it shows how it is possible for evolution to both optimize and complexify solutions simultaneously, offering the possibility of evolving increasingly complex solutions over generations, and strengthening the analogy with biological evolution.

Algorithms↗

Self-adaptation in evolving systems.

A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in certain model fitness landscapes. The resultant genotype-phenotype mapping is degenerate in fitness space, there being no direct selective advantage for one probability versus another. Thus there is a "symmetry" between various genotypes that all correspond to the same phenotype. We show that the action of mutation and crossover lifts this degeneracy, that is, the genetic operators induce a breaking of the genotype-phenotype symmetry, thus leading to a preference for those genotypes that propagate most successfully into future generations. We demonstrate that this induced symmetry breaking allows the system to self-adapt in a time-dependent environment.

Adaptation, Physiological↗

Evolving mobile robots in simulated and real environments.

The problem of the validity of simulation is particularly relevant for methodologies that use machine learning techniques to develop control systems for autonomous robots, as, for instance, the artificial life approach known as evolutionary robotics. In fact, although it has been demonstrated that training or evolving robots in real environments is possible, the number of trials needed to test the system discourages the use of physical robots during the training period. By evolving neural controllers for a Khepera robot in computer simulations and then transferring the agents obtained to the real environment we show that (a) an accurate model of a particular robot-environment dynamics can be built by sampling the real world through the sensors and the actuators of the robot; (b) the performance gap between the obtained behaviors in simulated and real environments may be significantly reduced by introducing a "conservative" form of noise; (c) if a decrease in performance is observed when the system is transferred to a real environment, successful and robust results can be obtained by continuing the evolutionary process in the real environment for a few generations.

Algorithms↗

Evolving physically simulated flying creatures for efficient cruising.

The body-brain coevolution of aerial life forms has not been developed as far as aquatic or terrestrial locomotion in the field of artificial life. We are studying physically simulated 3D flying creatures by evolving both wing shapes and their controllers. A creature's wing is modeled as a number of articulated cylinders, connected by triangular films (patagia). The wing structure and its motor controllers for cruising flight are generated by an evolutionary algorithm within a simulated aerodynamic environment. The most energy-efficient cruising speed and the lift and drag coefficients of each flier are calculated from its morphological characteristics and used in the fitness evaluation. To observe a wide range of creature size, the evolution is run separately for creatures categorized into three species by body weight. The resulting creatures vary in size from pigeons to pterosaurs, with various wing configurations. We discuss the characteristics of shape and motion of the evolved creatures, including flight stability and Strouhal number.

Algorithms↗

Solving a real-world problem using an evolving heuristically driven schedule builder.

This work addresses the real-life scheduling problem of a Scottish company that must produce daily schedules for the catching and transportation of large numbers of live chickens. The problem is complex and highly constrained. We show that it can be successfully solved by division into two subproblems and solving each using a separate genetic algorithm (GA). We address the problem of whether this produces locally optimal solutions and how to overcome this. We extend the traditional approach of evolving a "permutation + schedule builder" by concentrating on evolving the schedule builder itself. This results in a unique schedule builder being built for each daily scheduling problem, each individually tailored to deal with the particular features of that problem. This results in a robust, fast, and flexible system that can cope with most of the circumstances imaginable at the factory. We also compare the performance of a GA approach to several other evolutionary methods and show that population-based methods are superior to both hill-climbing and simulated annealing in the quality of solutions produced. Population-based methods also have the distinct advantage of producing multiple, equally fit solutions, which is of particular importance when considering the practical aspects of the problem.

Algorithms↗