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PubMed2003

A comparison of directed evolution approaches using the beta-glucuronidase model system.

Protein engineers can alter the properties of enzymes by directing their evolution in vitro. Many methods to generate molecular diversity and to identify improved clones have been developed, but experimental evolution remains as much an art as a science. We previously used DNA shuffling (sexual recombination) and a histochemical screen to direct the evolution of Escherichia coli beta-glucuronidase (GUS) variants with improved beta-galactosidase (BGAL) activity. Here, we employ the same model evolutionary system to test the efficiencies of several other techniques: recursive random mutagenesis (asexual), combinatorial cassette mutagenesis (high-frequency recombination) and a versatile high-throughput microplate screen. GUS variants with altered specificity evolved in each trial, but different combinations of mutagenesis and screening techniques effected the fixation of different beneficial mutations. The new microplate screen identified a broader set of mutations than the previously employed X-gal colony screen. Recursive random mutagenesis produced essentially asexual populations, within which beneficial mutations drove each other into extinction (clonal interference); DNA shuffling and combinatorial cassette mutagenesis led instead to the accumulation of beneficial mutations within a single allele. These results explain why recombinational approaches generally increase the efficiency of laboratory evolution.

Directed Molecular Evolution↗
PubMed1979

The evolution of an immune system.

A model for the molecular evolution of an imune system is presented. It suggests how a system of cell surface-fixed antigen receptors, called FR, to be thought of as "primitive" but still functional antibodies, could evolve into the "modern" labile T cell and antibody system, the receptors for which may be called CER (clonal expansion receptors). Perhaps the most significant insight to be gained from the theory concerns the conclusion that the immune system of an embryo may be primed by the interaction between two types of cells with complementary surface specificities. In the first type of cell the interacting molecule is an FR molecule coded by a gene of the Major Histocompatibility Complex (MHC) which has undergone a somatic mutation; in the second type it is a CER molecule also coded by a gene which has undergone a recent somatic mutation. It is believed that this insight eliminates some of the problems experienced in understanding generation of diversity, and renders unnecessary some of the more complex hypotheses about immune networks. The mechanism of action of immune response genes is easily explained by the theory.

Adaptation, Physiological↗
PubMed1999

A potential model for early stages of chromosomal evolution via concentric Robertsonian fans: a large area of polymorphism in southern short-tailed shrews (Blarina carolinensis).

Western Tennessee contains unusually highly polymorphic populations of southern short-tailed shrews (Blarina carolinensis). We previously documented eight Robertsonian translocations (ROBs) accounting for a variation in diploid number from 46 in most of this species' range to 34-40 in western Tennessee. We have now expanded our study to include data from adjacent areas in Tennessee and Mississippi, 10 localities in all. The new data show a variation in diploid number ranging from 31 to 41, four new ROBs (for a total of 12), and the novel finding of monobrachial translocations in this group. All animals collected from this large area (extending over 12, 000 km(2)) had some level of ROBs, and none represented the 2n = 46 form seen in other parts of the range of this species. Because other species of shrews (genus Sorex) are not affected in the same area, the factors and/or selective forces causing this extensive polymorphism in B. carolinensis must be unique to this species and to this geographic area. Some ROBs were found throughout this large area of over 12,000 km(2). Other translocations (including those with monobrachial homology) were located in one or two localities in this large area, and still other translocations were intermediate in their distribution. There was a concentric pattern to the evolution and presumed spreading of the ROBs. This allowed us to expand the concept of a Robertsonian "fan," introduced by Matthey (1970), to that of concentric evolution of multiple fusion fans: ROBs likely arose independently, separated temporally and geographically, and radiated into surrounding populations to create this complex zone of polymorphism. This is an active process in its infancy, and it is not as mature as that seen in European studies of Mus and Sorex.

Animals↗
PubMed1997

Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera.

Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprinid fish Cyprinella spiloptera. Variation at different nucleotide positions in individual repeats supported different models of repeat evolution. One set of characters included several nucleotide variants found in all copies from a limited number of individuals, while the other set included an 8-bp deletion found in a limited number of copies in all individuals. The deletion and an associated nucleotide change appear to be the result of a deterministic, rather than stochastic, mutation process. Parallel origins of repeat arrays in different mitochondrial lineages, possibly coupled with a homogenization mechanism, best explain the distribution of nucleotide variation.

Animals↗
PubMed2004

Model development and application for surfactant biodegradation in an acclimatising activated sludge system.

A model for the biodegradation of non-ionic surfactants in an activated sludge system during acclimatisation was developed, based on respirometric and titrimetric experimental data. The data were obtained in a sequencing batch reactor (SBR) using a non-ionic surfactant as sole carbon source and sludge previously acclimatised to a different surfactant. The model was successfully applied to successive SBR-cycles of sludge acclimatisation processes subjected to two ethoxylated surfactants. The model was validated using the corresponding total organic carbon data. The evolution of the model parameters along the acclimatisation process was examined. An acclimatisation model was developed using the evolution of two of these parameters (affinity constant and inhibition constant), supported by two independently calculated acclimatisation indicators. This acclimatisation model was then applied to determine an optimal surfactant concentration sequence to feed non-acclimatised sludge during a period of 41 days, in order to induce pre-acclimatisation to this surfactant before it replaces another one in the wastewater. The model was also useful in the economical assessment of this and alternative procedures to cope with frequent changes in activated sludge feed composition.

Biodegradation, Environmental↗
PubMed1995

Learning and evolution: a quantitative genetics approach.

Recent models of the interactions between learning and evolution show that learning increases the rate at which populations find optima in fixed environments. However, learning ability is only advantageous in variable environments. In this study, quantitative genetics models are used to investigate the effects of individual learning on evolution. Two models of populations of learning individuals are constructed and analyzed. In the first model, the effect of learning is represented as an increase in the variance of selection. Dynamical equations and equilibrium conditions are derived for a population of learning individuals under fixed and variable environmental selection. In the second model, the amount of individual learning effort is regulated by a second gene specifying the duration of a critical learning period. The second model includes a model of the learning process to determine the individual fitness costs and benefits accrued during the learning period. Individuals are then selected for the optimal learning investment. The similarities of the results from these two models suggest that the net effects of learning on evolution are relatively independent of the mechanisms underlying the learning process.

Animals↗
PubMed2003

A transition probability model for amino acid substitutions from blocks.

Substitution matrices have been useful for sequence alignment and protein sequence comparisons. The BLOSUM series of matrices, which had been derived from a database of alignments of protein blocks, improved the accuracy of alignments previously obtained from the PAM-type matrices estimated from only closely related sequences. Although BLOSUM matrices are scoring matrices now widely used for protein sequence alignments, they do not describe an evolutionary model. BLOSUM matrices do not permit the estimation of the actual number of amino acid substitutions between sequences by correcting for multiple hits. The method presented here uses the Blocks database of protein alignments, along with the additivity of evolutionary distances, to approximate the amino acid substitution probabilities as a function of actual evolutionary distance. The PMB (Probability Matrix from Blocks) defines a new evolutionary model for protein evolution that can be used for evolutionary analyses of protein sequences. Our model is directly derived from, and thus compatible with, the BLOSUM matrices. The model has the additional advantage of being easily implemented.

Amino Acid Substitution↗
PubMed2000

Evolution of the thyroid hormone-binding protein, transthyretin.

Transthyretin (TTR) belongs to a group of proteins, which includes thyroxine-binding globulin and albumin, that bind to and transport thyroid hormones in the blood. TTR is also indirectly implicated in the carriage of vitamin A through the mediation of retinol-binding protein (RBP). It was first identified in 1942 in human serum and cerebrospinal fluid and was formerly called prealbumin for its ability to migrate faster than serum albumin on electrophoresis of whole plasma. It is a single polypeptide chain of 127 amino acids (14,000 Da) and is present in the plasma as a tetramer of noncovalently bound monomers. The major sites of synthesis of TTR in eutherian mammals, marsupials, and birds are the liver and choroid plexus but in reptiles it is synthesised only in the choroid plexus. The observation that TTR is strongly expressed in the choroid plexus but not in the liver of the stumpy-tailed lizard and the strong conservation of expression in the choroid plexus from reptiles to mammals have been taken as evidence to suggest that extrahepatic synthesis of TTR evolved first. The identification and cloning of TTR from the liver of an amphibian, Rana catesbeiana, and a teleost fish, Sparus aurata, and its absence from the choroid plexus of both species suggest an alternative model for its evolution. Protein modelling studies are presented that demonstrate differences in the electrostatic characteristics of the molecule in human, rat, chicken, and fish, which may explain why, in contrast to TTR from human and rat, TTR from fish and birds preferentially binds triiodo-l-thyronine.

Amino Acid Sequence↗
PubMed2004

Acquisition and performance of delayed-response tasks: a neural network model.

We study the time evolution of a neural network model as it learns the three stages of a visual delayed-matching-to-sample (DMS) task: identification of the sample, retention during delay, and matching of sample and target, ignoring distractors. We introduce a neurobiologically plausible, uncommitted architecture, comprising an "executive" subnetwork gating connections to and from a "working" layer. The network learns DMS by reinforcement: reward-dependent synaptic plasticity generates task-dependent behaviour. During learning, working layer cells exhibit stimulus specialization and increased tuning of their firing. The emergence of top-down activity is observed, reproducing aspects of prefrontal cortex control on activity in the visual areas of inferior temporal cortex. We observe a lability of neural systems during learning, with a tendency to encode spurious associations. Executive areas are instrumental during learning to prevent such associations; they are also fundamental for the "mature" network to keep passing DMS. In the mature model, the working layer functions as a short-term memory. The mature system is remarkably robust against cell damage and its performance degrades gracefully as damage increases. The model underlines that executive systems, which regulate the flow of information between working memory and sensory areas, are required for passing tests such as DMS. At the behavioural level, the model makes testable predictions about the errors expected from subjects learning the DMS.

Animals↗
PubMed2003

Fitness distributions in exponentially growing asexual populations.

We explore a mean-field model for the evolution of exponentially growing populations of mutating replicators. Motivated by recent in vitro experiments devised to analyze phenotypic properties of bacterial and viral populations subjected to serial population transfers, we allow our in silico individuals to undergo unrestricted growth before applying bottleneck events. Different dynamical regimes of our model can be mapped to different experimental situations. Numerical and analytical results for fitness distributions calculated at the statistically stationary states of the dynamics compare favorably with available experimental data. Our model and results provide a common framework to better understand populations evolving under different selection pressures.

Biological Evolution↗
PubMed2000

The evolution of homoerotic behavior in humans.

This paper presents a theoretical model for the evolution of same-sex sexual behavior, or homoerotic behavior, in humans. Contrary to the traditional study of the topic, the emphasis is on homoerotic behavior itself, irrespective of sexual orientation. It is an inferential model drawn from cross-species evidence, cross-cultural evidence, and current evolutionary theory. It is posited that humans evolved a disposition for homoerotic behavior because it increased same-sex affiliation among peripheralized hominids and indirectly influenced rates of survival and reproductive success. The implications for the conceptualization of same-sex sexual behavior and future research are indicated.

Adaptation, Physiological↗
PubMed1993

Temporal evolution of endothelial dysfunction in a rat model of chronic heart failure.

OBJECTIVES: The goal of this study was to investigate the evolution of endothelial dysfunction and plasma renin activity in a rat model of heart failure. BACKGROUND: Endothelial dysfunction has been demonstrated in heart failure and may play a significant role in this pathophysiologic process. Studies have also suggested a physiologic interaction between the renin-angiotensin system and endothelium-derived relaxing factor. However, the evolution of endothelial dysfunction and plasma renin activity in heart failure has not been studied to date. METHODS: Endothelium-dependent and -independent relaxations were studied at 1, 4 and 16 weeks after coronary artery ligation in a rat model of heart failure. Thoracic aortic rings were placed in isolated organ baths and acetylcholine and sodium nitroprusside concentration response curves were generated. Plasma renin activity was assessed at each time point. RESULTS: Aortic rings from rats with heart failure demonstrated no evidence of endothelial dysfunction at week 1, although progressive rightward shifts in the acetylcholine curves and decreasing maximal relaxation over time compared with findings in sham-operated control rats were evident at weeks 4 and 16. The sodium nitroprusside curves were not different between rats with heart failure and sham-operated rats. Plasma renin activity was elevated at week 1 and progressively increased through week 16, even though it correlated poorly with endothelial dysfunction. CONCLUSIONS: This study suggests that endothelial dysfunction in heart failure is a progressive time-dependent process that probably plays a minor role early in heart failure. Although plasma renin activity increased significantly in rats with heart failure, it was poorly predictive of endothelial dysfunction.

Acetylcholine↗
PubMed1996

The rate of compensatory evolution.

A two-locus model is presented to analyze the evolution of compensatory mutations occurring in stems of RNA secondary structures. Single mutations are assumed to be deleterious but harmless (neutral) in appropriate combinations. In proceeding under mutation pressure, natural selection and genetic drift from one fitness peak to another one, a population must therefore pass through a valley of intermediate deleterious states of individual fitness. The expected time for this transition is calculated using diffusion theory. The rate of compensatory evolution, kappa c, is then defined as the inverse of the expected transition time. When selection against deleterious single mutations is strong, kappa c becomes independent on the recombination fraction r between the two loci. Recombination generally reduces the rate of compensatory evolution because it breaks up favorable combinations of double mutants. For complete linkage, kappa c is given by the rate at which favorable combinations of double mutants are produced by compensatory mutation. For r > O, kappa c decreases exponentially with r. In contrast, kappa c becomes independent of r for weak selection. We discuss the dynamics of evolutionary substitutions of compensatory mutants in relation of WRIGHT's shifting balance theory of evolution and use our results to analyze the substitution process in helices of mRNA secondary structures.

Evolution, Molecular↗
PubMed2000

Multiregional, not multiple origins.

Multiregional evolution is a model to account for the pattern of human evolution in the Pleistocene. The underlying hypothesis is that a worldwide network of genic exchanges, between evolving human populations that continually divide and reticulate, provides a frame of population interconnections that allows both species-wide evolutionary change and local distinctions and differentiation. "Multiregional" does not mean independent multiple origins, ancient divergence of modern populations, simultaneous appearance of adaptive characters in different regions, or parallel evolution. A valid understanding of multiregional evolution would go a long way toward reducing the modern human origins controversy.

Animals↗
PubMed1995

Temporal evolution of neuropathologic changes in an immature rat model of cerebral hypoxia: a light microscopic study.

The sequential evolution of neuropathologic changes was studied in an immature model of cerebral hypoxia-ischemia. According, 7-day postnatal rats were subjected to unilateral common carotid artery ligation combined with 2 h of hypoxia (breathing in 8% oxygen) and their brains were examined by light microscopy at recovery intervals ranging from 0 to 3 weeks. Immediately following hypoxia, a large area with a pale staining border was noted occupying most of the cerebral hemisphere ipsilateral (IL) to the occluded common carotid artery; in approximately half of the brains the dorsomedial cortex of the contralateral (CL) hemisphere was also involved. Most neurons in the pale area had nuclei containing a coarse granular condensation of chromatin. Within a few hours, the majority of neurons in the IL hemisphere had developed pyknotic nuclei and clear or eosinophilic perikarya. After 24 h these changes had evolved in the majority of brains into coagulation necrosis (infarction) in the IL hemisphere and foci of selective neuronal necrosis in the CL cortex. Within a few days infarcts became partially cavitated, and by 3 weeks a smooth-walled cystic infarct had developed. Activated microglia/macrophages and reactive astrocytes were first seen at 4 and 24 h, respectively. No parenchymal neutrophilic infiltrate was seen at any time point.

Animals↗
PubMed1995

A photothrombotic 'ring' model of rat stroke-in-evolution displaying putative penumbral inversion.

BACKGROUND AND PURPOSE: To facilitate reproducible and rigorous study of a tissue zone at risk of encroaching ischemic damage, we propose a new model in which the potentially compromised tissue lies within rather than perifocal to an ischemic locus. The perimeter of the "zone at risk" is defined by a photothrombotically produced cortical lesion in the shape of a toroid (or "ring"). METHODS: The exposed crania of erythrosin B-injected rats were irradiated with a 514.5-nm laser beam, configured as a 5-mm-diameter ring, to yield a ring-shaped lesion caused by photochemically induced platelet occlusion of cortical vasculature. Developing perfusion deficits in the interior region were revealed by carbon black infusion. Tissue damage and infarct volumes were assessed by light and electron microscopy, and blood-brain barrier integrity was assessed with Evans blue dye and horseradish peroxidase as tracers. RESULTS: For rats injected with 17 mg/kg erythrosin B and irradiated for 2 minutes with a ring beam intensity of 0.92 W/cm2 (beam power of 65 mW), carbon black infusion at times up to 4 hours demonstrated a shallow cortical ring lesion encircling a fully patent zone at risk, which by 24 hours evinced an essentially complete perfusion deficit. At times up to 24 hours, the ring lesion was penetrated at the pial surface by distal branches of the middle cerebral and anterior cerebral arteries. Stereotaxically based histopathological assessment showed that by 24 hours the lesion spanned the cortical thickness. Lesion volume increased from 14.5 +/- 8.0 mm3 (mean +/- SD) (n = 8) to 46.2 +/- 15.6 mm3 (n = 8) between 4 and 24 hours after irradiation (P < .01), but the anteroposterior lesion diameter did not change significantly between 4 hours (6.00 +/- 1.03 mm; n = 9) and 24 hours (6.75 +/- 1.15 mm; n = 9). CONCLUSIONS: The present model of slowly developing but inevitable cortical tissue death in a sequestered area should facilitate more precise observations of the evolution of tissue metabolic responses, from the impending onset of ischemia to the threshold of irreversible damage. This system may prove efficient for evaluating treatments intended to salvage a penumbral region.

Animals↗
PubMed2004

Eigen model as a quantum spin chain: exact dynamics.

We map the Eigen model of biological evolution [Naturwissenschaften 58, 465 (1971)] into a quantum spin model with non-Hermitian Hamiltonian. Based on such a connection, we derive exact relaxation periods for the Eigen model to approach static energy landscape from various initial conditions. We also study a simple case of dynamic fitness function.

Biological Evolution↗