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Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria.

The extent to which a population diverges from its ancestor through adaptive evolution depends on variation supplied by novel beneficial mutations. Extending earlier work, recent theory makes two predictions that seem to be robust to biological details: the distribution of fitness effects among beneficial mutations before selection should be (i) exponential and (ii) invariant, meaning it is always exponential regardless of the fitness rank of the wild-type allele. Here we test these predictions by assaying the fitness of 665 independently derived single-step mutations in the bacterium Pseudomonas fluorescens across a range of environments. We show that the distribution of fitness effects among beneficial mutations is indistinguishable from an exponential despite marked variation in the fitness rank of the wild type across environments. These results suggest that the initial step in adaptive evolution--the production of novel beneficial mutants from which selection sorts--is very general, being characterized by an approximately exponential distribution with many mutations of small effect and few of large effect. We also document substantial variation in the pleiotropic costs of antibiotic resistance, a result that may have implications for strategies aimed at eliminating resistant pathogens in animal and human populations.

Biological Evolution↗

Nongeometric conditional phase shift via adiabatic evolution of dark eigenstates: a new approach to quantum computation.

We propose a new approach to quantum phase gates via the adiabatic evolution. The conditional phase shift is neither of dynamical nor geometric origin. It arises from the adiabatic evolution of the dark state itself. Taking advantage of the adiabatic passage, this kind of quantum logic gates is robust against moderate fluctuations of experimental parameters. In comparison with the geometric phase gates, it is unnecessary to drive the system to undergo a desired cyclic evolution to obtain a desired solid angle. Thus, the procedure is simplified, and the fidelity may be further improved since the errors in obtaining the required solid angle are avoided. We illustrate such a kind of quantum logic gates in the ion trap system. The idea can also be realized in other systems, opening a new perspective for quantum information processing.

Journal Article↗

Experimental compaction of anisotropic granular media.

We report on experiments to measure the temporal and spatial evolution of packing arrangements of anisotropic and weakly confined granular material, using high-resolution gamma-ray adsorption. In these experiments, the particle configurations start from an initially disordered, low-packing-fraction state and under vertical solicitations evolve to a dense state. We find that the packing fraction evolution is slowed by the grain anisotropy but, as for spherically shaped grains, can be well fitted by a stretched exponential. For a given type of grains, the characteristic times of relaxation and of convection are found to be of the same order of magnitude. On the contrary, compaction mechanisms in the media strongly depend on the grain anisotropy.

Journal Article↗

Redox control in development and evolution: evidence from colonial hydroids

Redox chemistry, involving the transfer of electrons and hydrogen atoms, is central to energy conversion in respiration, and the control of gene expression by redox state commonly occurs in bacteria, allowing rapid responses to environmental changes, for instance, in the food supply. Colonial metazoans often encrust surfaces over which the food supply varies in time or space; hence, in these organisms, redox control of the development of feeding structures and gastrovascular connections could be similarly adaptive, allowing colonies to adjust the timing and spacing of structures in response to a variable food supply. To investigate the possibility of redox control of colony development, the redox states of hydractiniid hydroid colonies were manipulated experimentally. As in many colonial animals, hydractiniid hydroids display a range of morphological variation from sheet-like forms (i.e. closely spaced polyps with high rates of stolon branching) to runner-like forms (i. e. widely spaced polyps with low rates of stolon branching). In the runner-like Podocoryna carnea, azide, a blocker of the electron transport chain, and dinitrophenol, an uncoupler of oxidative phosphorylation, diminished the largely polyp-driven gastrovascular flow to a similar extent. Measures of the redox state of the polyp epitheliomuscular cells using the fluorescence of NAD(P)H suggest that azide shifts the redox state in the direction of reduction, while dinitrophenol shifts the redox state in the direction of oxidation. Colony development corresponds to redox state in that azide-treated colonies were more runner-like, while dinitrophenol-treated colonies were more sheet-like. Nevertheless, the functional role of polyps in feeding and generating gastrovascular flow probably contributed to a trade-off between polyp number and size such that azide-treated colonies had few large polyps, while dinitrophenol-treated colonies had many small polyps. Regardless of the treatment, P. carnea colonies developed to maturity and produced swimming medusae in the normal fashion. In the sheet-like Hydractinia symbiolongicarpus, treatment with azide resulted in complete suppression of the development of both the stolonal mat and the blastostyles, the reproductive polyps. Azide-treated H. symbiolongicarpus colonies therefore developed in a juvenilized, runner-like manner and much resembled colonies of P. carnea. Following cessation of azide treatment in H. symbiolongicarpus, normal colony development ensued, and both a stolonal mat and blastostyles formed. In both hydroid species, relative oxidization favors sheet-like growth, while relative reduction favors runner-like growth. Since feeding triggers strong contractions of polyp epitheliomuscular cells and results in relative oxidation, this experimental evidence supports the hypothesis of adaptive redox control of colony development and evolution.

Journal Article↗

Spreading of Surfactant Solutions over Hydrophobic Substrates.

The spreading of surfactant solutions over hydrophobic surfaces is considered from both theoretical and experimental points of view. Water droplets do not wet a virgin solid hydrophobic substrate. It is shown that the transfer of surfactant molecules from the water droplet onto the hydrophobic surface changes the wetting characteristics in front of the drop on the three-phase contact line. The surfactant molecules increase the solid-vapor interfacial tension and hydrophilize the initially hydrophobic solid substrate just in front of the spreading drop. This process causes water drops to spread over time. The time of evolution of the spreading of a water droplet is predicted and compared with experimental observations. The assumption that surfactant transfer from the drop surface onto the solid hydrophobic substrate controls the rate of spreading is confirmed by our experimental observations. Copyright 2000 Academic Press.

Journal Article↗

The evolution strategy--a search strategy used in individual optimization of electrical parameters for therapeutic carotid sinus nerve stimulation.

Optimization problems, arising in the search for parameters and/or techniques of functional electrostimulation (FES), disproportionally increase when multiple electrodes, electrode configurations, electrical parameters, and stimulation modes may be applied. When computational or investigational effort precludes systematic studies in FES, we propose to apply and evaluate Rechenberg's evolution strategy, which in technical use and numerical optimization has been valid in comparison to more traditional methods. This strategy implements mutation and selection processes in analogy to biological evolution. The effect of combined multiple input variables on a quality function (Q) is experimentally evaluated. The actual computed value of Q serves as a selection criterion for those input variable combinations which lead Q to approach a target value (maximization), similar to a hill-climbing procedure. In radiofrequency controlled, therapeutic electrical carotid sinus nerve stimulation (CSNS), we varied (mutated) combinations of pulse frequency and pulse amplitude parameters, according to the evolution strategy, in individual patients. CSNS lowers blood pressure and decreases heart rate. Q was computed from blood pressure and heart rate responses to CSNS. The strategy individually optimized electrical parameters to achieve large depressor responses upon CSNS. Although, in contrast to technical usage, only two input variables were investigated, and biomedical experience with the evolution strategy is limited so far, its potential use in other fields of FES, especially when more input variables are to be optimized, is discussed and encouraged.

Algorithms↗

Impaired hyaloidal circulation function and uncoordinated ocular growth patterns in experimental retinopathy of prematurity.

PURPOSE: To test the hypotheses that, in the newborn rat model of retinopathy of prematurity (ROP), the hyaloidal circulation is functionally impaired and its development is not well coordinated with that of other ocular structures. METHODS: The functional response of the hyaloidal circulation to a carbogen inhalation challenge was noninvasively evaluated using magnetic resonance imaging (MRI) in day 12 rats raised under either variable oxygen conditions (experimental ROP, n = 8) or room air (control, n = 8). A similar MRI examination was performed in separate experiments using either day 18 newborn control rats (n = 3) or adult rats (n = 9). For each experiment, the hyaloidal circulation perfusion response to carbogen, the functional spatial extent of the hyaloidal circulation in vitreous, and the volumes of vitreous and lens were estimated from MRI enhancement maps. RESULTS: The hyaloidal perfusion response to carbogen breathing in the newborn rats decreased as follows: control day 12 > experimental day 12 > control day 18; no measurable hyaloidal function was found in the adult rat. Regression analysis indicated a relatively poorer superior-inferior correlation in the temporal response to carbogen inhalation for the experimental animals than in the control newborn rats. The vitreous volume decreased in control rats as expected (adult rat > day 18 > day 12). Good agreement was found between the MRI-determined adult rat vitreous volume (56 +/- 2 microliters) and that of previous reports. Functional hyaloidal volumes during carbogen breathing were not significantly different (P > 0.05) between day 18, day 12 control, and experimental newborn rats. The ratio of this functional hyaloidal circulation extent volume to vitreous volume was significantly different (P < 0.05) between these groups. Covariance analysis revealed a relatively less coordinated development between the functional hyaloidal volume and the vitreous volume in experimental animals than in age-matched control animals, whereas there was coordinated evolution of the hyaloidal circulation and the lens in all the animals. CONCLUSIONS: Carbogen-enhanced MRI appears to be a powerful new and noninvasive approach for assessing the functionality of the hyaloidal circulation (that is, its ability to respond to a carbogen challenge) and quantitatively comparing the functional hyaloidal extent to other ocular volumes in the same eye during development and during the disease process. Evidence is presented here for the first time that supports the authors' hypotheses that the function of the hyaloidal circulation in experimental ROP is impaired and that the growth of ocular components are less coordinated.

Animals↗

The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens.

The "survival of the fittest" is the paradigm of Darwinian evolution in which the best-adapted replicators are favored by natural selection. However, at high mutation rates, the fittest organisms are not necessarily the fastest replicators but rather are those that show the greatest robustness against deleterious mutational effects, even at the cost of a low replication rate. This scenario, dubbed the "survival of the flattest", has so far only been shown to operate in digital organisms. We show that "survival of the flattest" can also occur in biological entities by analyzing the outcome of competition between two viroid species coinfecting the same plant. Under optimal growth conditions, a viroid species characterized by fast population growth and genetic homogeneity outcompeted a viroid species with slow population growth and a high degree of variation. In contrast, the slow-growth species was able to outcompete the fast species when the mutation rate was increased. These experimental results were supported by an in silico model of competing viroid quasispecies.

Chrysanthemum↗

Founder-effect speciation theory: failure of experimental corroboration.

The theory of founder-effect speciation proposes that colonization by very few individuals of an empty habitat favors rapid genetic changes and the evolution of a new species. We report here the results obtained in a 10-year-long and large-scale experiment with Drosophila pseudoobscura designed to test the theory. In our experimental protocol, populations are established with variable numbers of very few individuals and allowed to expand greatly for several generations until conditions of severe competition for resources are reached and the population crashes. A few random survivors are then taken to start a new population expansion and thus initiate a new cycle of founding events, population flushes, and crashes. Our results provide no support for the theories proposing that new species are very likely to appear as by-products of founder events.

Animals↗

A model of extravascular bubble evolution: effect of changes in breathing gas composition.

Observations of bubble evolution in rats after decompression from air dives (O. Hyldegaard and J. Madsen. Undersea Biomed. Res. 16: 185-193, 1989; O. Hyldegaard and J. Madsen. Undersea Hyperbaric Med. 21: 413-424, 1994; O. Hyldegaard, M. Moller, and J. Madsen. Undersea Biomed. Res. 18: 361-371, 1991) suggest that bubbles may resolve more safely when the breathing gas is a heliox mixture than when it is pure O(2). This is due to a transient period of bubble growth seen during switches to O(2) breathing. In an attempt to understand these experimental results, we have developed a multigas-multipressure mathematical model of bubble evolution, which consists of a bubble in a well-stirred liquid. The liquid exchanges gas with the bubble via diffusion, and the exchange between liquid and blood is described by a single-exponential time constant for each inert gas. The model indicates that bubbles resolve most rapidly in spinal tissue, in adipose tissue, and in aqueous tissues when the breathing gas is switched to O(2) after surfacing. In addition, the model suggests that switching to heliox breathing may prolong the existence of the bubble relative to breathing air for bubbles in spinal and adipose tissues. Some possible explanations for the discrepancy between model and experiment are discussed.

Adipose Tissue↗

Evolution of action potential propagation and repolarization in cultured neonatal rat ventricular myocytes.

INTRODUCTION: Cultured neonatal rat ventricular myocytes (NRVM) reestablish gap junctions as they form synchronously and spontaneously beating monolayers, thus providing a useful model for studying activation and repolarization. METHODS AND RESULTS: We used the multielectrode array data acquisition system with 60 unipolar electrodes to investigate the functional organization of cultured NRVM, by determining propagation and repolarization patterns. Activation maps were constructed from the local activation times at each electrode. During days 3 to 8 in culture, QRS amplitude and dV/dt(max) increased with age. Concomitantly, with the culture maturation, QT interval (representing action potential duration) decreased, and T wave amplitude and slopes of the T wave ascending and descending limbs progressively increased. The changes in conduction velocity were different than those of the electrogram properties, slightly increasing during the first 3 to 5 days and gradually declining toward day 8 in culture. CONCLUSION: Establishment of uniform activation patterns in spontaneously firing or driven myocytes in monolayer cultures is accompanied by organization of activation and repolarization whose evolution appears in concert with that of a mature connexin43 staining pattern. The experimental techniques developed in this study provide useful tools to investigate the complex relations among gap junctions, conduction velocity, and propagation patterns, as well as a means to learn how gap junctional remodeling under pathophysiologic conditions predisposes the myocardium to arrhythmias.

Action Potentials↗

Epidemiology, hypermutation, within-host evolution and the virulence of Neisseria meningitidis.

Many so-called pathogenic bacteria such as Neisseria meningitidis, Haemophilus influenzae, Staphylococcus aureus and Streptococcus pneumoniae are far more likely to colonize and maintain populations in healthy individuals asymptomatically than to cause disease. Disease is a dead-end for these bacteria: virulence shortens the window of time during which transmission to new hosts can occur and the subpopulations of bacteria actually responsible for disease, like those in the blood or cerebral spinal fluid, are rarely transmitted to new hosts. Hence, the virulence factors underlying their occasional pathogenicity must evolve in response to selection for something other than making their hosts sick. What are those selective pressures? We address this general question of the evolution of virulence in the context of phase shifting in N. meningitidis, a mutational process that turns specific genes on and off, and, in particular, contingency loci that code for virulence determinants such as pili, lipopolysaccharides, capsular polysaccharides and outer membrane proteins. We use mathematical models of the epidemiology and the within-host infection dynamics of N. meningitidis to make the case that rapid phase shifting evolves as an adaptation for colonization of diverse hosts and that the virulence of this bacterium is an inadvertent consequence of short-sighted within-host evolution, which is exasperated by the increased mutation rates associated with phase shifting. We present evidence for and suggest experimental and retrospective tests of these hypotheses.

Biological Evolution↗

Easy approach to DNA shuffling: its potential implication in health sciences.

Directed evolution experiments rely on the cyclical application of mutagenesis, screening and amplifications in a test tube. During the laboratory evolution of biological molecules, recombination has been used to generate novel sequences in a process known as DNA shuffling. DNA shuffling is a recently developed technique that allows accelerated and directed protein evolution for desired properties in vitro, which recombines and evolves genes to rapidly obtain molecules with improved biological activity and fitness. DNA shuffling is generally achieved by DNaseI treatment and by PCR. This has led to the creation of novel proteins for a wide range of applications. The use of improved enzymes for medical, industrial and environmental purposes is prevalent today, and will be expanding. New applications in vaccine development and disease diagnosis are among the key features of DNA shuffling. However, directed evolution currently requires an uncertain, typically large number of labor-intensive and expensive experimental cycles before proteins with improved function are identified. A simplified and low-cost DNA shuffling protocol for random recombination of homologous genes in vitro is described here.

DNA Shuffling↗

[Electrophysiology of transmissible encephalopathies].

The purpose of electrophysiological studies during the evolution of spongiform encephalopathies or prion diseases is to describe the changes of spontaneous or evoked electroencephalographic activity in natural and experimental diseases (natural and experimental scrapie, Kuru and Creutzfeldt-Jakob (CJ) disease in man and in different animal models) and to establish or to propose an action mechanism of the infectious agents. In the aim, the changes of electroencephalogram (EEG) and evoked potentials are described. Generally these modifications constitute an excellent and early marker of the initial phases of pathological mechanisms, replication of the agent and the cell membranes alterations. The changes of the sleep organisation occur generally later with the beginning of the clinical phase, just at the end of incubation period. The typical changes of EEG during the human CJ disease are rare in the experimental diseases. However, with animal models, it is possible to demonstrate the very univocal character of these diseases, creating pathophysiological modifications whose nature, origin and evolution are very comparable, with characteristic triade (loss of neurons, gliosis and spongiosis) and specific alterations of gabaergic, dopaminergic and inhibitory processes.

Animals↗

A general theory for the evolutionary dynamics of virulence.

Most theory on the evolution of virulence is based on a game-theoretic approach. One potential shortcoming of this approach is that it does not allow the prediction of the evolutionary dynamics of virulence. Such dynamics are of interest for several reasons: for experimental tests of theory, for the development of useful virulence management protocols, and for understanding virulence evolution in situations where the epidemiological dynamics never reach equilibrium and/or when evolutionary change occurs on a timescale comparable to that of the epidemiological dynamics. Here we present a general theory similar to that of quantitative genetics in evolutionary biology that allows for the easy construction of models that include both within-host mutation as well as superinfection and that is capable of predicting both the short- and long-term evolution of virulence. We illustrate the generality and intuitive appeal of the theory through a series of examples showing how it can lead to transparent interpretations of the selective forces governing virulence evolution. It also leads to novel predictions that are not possible using the game-theoretic approach. The general theory can be used to model the evolution of other pathogen traits as well.

Animals↗

Glomerular cells and macrophages in the progression of experimental focal and segmental glomerulosclerosis.

To determine the characteristics of glomerular cell involvement in experimental focal and segmental glomerulosclerosis (FGS) in rats induced by repeated injections of aminonucleoside of puromycin (PAN) and protamine sulfate (PS), glomeruli were isolated and grown in tissue culture. When compared with saline controls the FGS rats had decreased rates of glomerular attachment and significantly reduced outgrowths of type 1 (epithelial) and type II (mesangial) cells. However, the FGS rats had greater numbers of type III cells (macrophages) present in the outgrowths than controls. The production of interleukin-1 (IL-1) in the glomerular culture supernatant, measured by thymocyte stimulating activity, was determined at various stages throughout the evolution of FGS and in saline controls. The FGS glomeruli early in the disease course (day 10) had higher levels of IL-1 activity than glomerular outgrowths from control rats but significantly lower levels of IL-1 were produced late in the disease (day 80). Glomerular macrophages were present throughout the evolution of the disease but in greater numbers early (day 10). In this experimental model of FGS, IL-1 production, has been demonstrated early in the disease process, could originate from macrophages and/or mesangial cells, and could be involved in the progressive glomerulosclerosis.

Animals↗

Application of information theory and extreme physical information to carcinogenesis.

Cellular information dynamics during somatic evolution of the malignant phenotypes are complex and poorly understood. Accumulating, random genetic mutations and, therefore, loss of genomic information appears necessary for carcinogenesis. However, additional control parameters can be inferred because unconstrained mutagenesis would ultimately produce cellular information degradation incompatible with life. Similarly, the stability of some genomic segments, such as those controlling proliferation and metabolism, indicates the presence of selective mutational constraints. By applying Information Theory and Extreme Physical Information (EPI) analysis, we demonstrate that the phenotypic characteristics and growth pattern of cancer populations are emergent properties resulting from the nonlinear dynamics of accumulating, random genetic mutations and tissue selection factors. Maximum quantitative loss of transgenerational information is demonstrated in genomic segments encoding negative or neutral evolutionary properties. This is most evident in the progressive dedifferentiation observed during carcinogenesis and may terminate in a differentiation "information catastrophe" producing decoherent cellular morphology and function. In contrast, microenvironmental selection pressures preserve genomic information controlling properties that confer selective growth advantages even in the presence of a high background mutation rate. Thus, phenotypic traits characteristically retained by tumor populations can be identified as critical selection parameters favoring clonal proliferation. The information model of carcinogenesis is tested by applying EPI analysis to predict tumor growth dynamics. We found that cellular proliferation attributable to information degradation will produce power law tumor growth with an exponent of 1.62. Data from six published studies that use sequential mammograms to measure the volume of small, untreated human breast cancers demonstrate power law tumor growth with a mean exponent value of 1.73 +/- 0.23. Other predictions including exponential growth of tumor cells in vitro are also supported by experimental observations. The nonlinear dynamics of stochastic information loss constrained by somatic evolution indicate that carcinogenesis will not be associated with any predictable, fixed sequence of genomic alterations. Rather, sporadic clinical cancers are emergent structures produced by multiple, fundamentally nondeterministic genetic pathways.

Animals↗

Why are phenotypic mutation rates much higher than genotypic mutation rates?

The evolution of genotypic mutation rates has been investigated in numerous theoretical and experimental studies. Mutations, however, occur not only when copying DNA, but also when building the phenotype, especially when translating and transcribing DNA to RNA and protein. Here we study the effect of such phenotypic mutations. We find a maximum phenotypic mutation rate, umax, that is compatible with maintaining a certain function of the organism. This may be called a phenotypic error threshold. In particular, we find a minimum phenotypic mutation rate, umin, with the property that there is (nearly) no selection pressure to reduce the rate of phenotypic mutations below this value. If there is a cost for lowering the phenotypic mutation rate, then umin is close to the optimum phenotypic mutation rate that maximizes the fitness of the organism. In our model, there is selective pressure to decrease the rate of genotypic mutations to zero, but to decrease the rate of phenotypic mutations only to a positive value. Despite its simplicity, our model can explain part of the huge difference between genotypic and phenotypic mutation rates that is observed in nature. The relevant data are summarized.

Animals↗