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 73 records · Page 4Linked to original sources
PubMed2003

Smoldering multiple myeloma: natural history and recognition of an evolving type.

Patients with smoldering multiple myeloma (SMM) meet the diagnostic criteria of multiple myeloma (MM) but are asymptomatic. Between January 1978 and July 2001, 53 patients (median age 63 years) were diagnosed with SMM. The median serum M-protein and proportion of bone marrow plasma cells were 36 g/l and 27% respectively. Two subsets of SMM were identified: (i) evolving SMM (n = 22), characterized by a progressive increase in serum M-protein, a previously recognized monoclonal gammopathy of undetermined significance (MGUS) and a significant higher proportion of IgA type and (ii) non-evolving SMM (n = 26) with stable M-protein that abruptly increases when symptomatic MM develops. Thirty-four patients developed symptomatic MM. The median time to progression in the overall series was 3.2 years and the only feature associated with a shorter time to progression was the evolving versus non-evolving type (1.3 vs. 3.9 years respectively, P = 0.007). The pattern of progression consisted of anaemia, lytic bone lesions or both, without renal failure, hypercalcaemia or extramedullary plasmacytomas. Fifty-seven per cent of patients that required chemotherapy showed no or minimal response. The median survival from diagnosis and from progression was 8.2 and 3.5 years respectively.

Adult↗
PubMedDate not supplied

A mechanistic study of evolvability using the mitogen-activated protein kinase cascade.

Evolvability is a function of the way genetic variation interacts with the mechanisms that produce the phenotype. We explore an explicitly mechanistic way of studying the evolvability of phenotypes that are produced by a relatively simple genetic mechanism, the mitogen-activated protein kinase (MAPK) cascade. We developed a quantitative model of MAPK activation that can be used to study the effects of genetic variation on the various components of this signaling cascade. We show how some standard tools of applied mathematics, such as steady-state formulations and nondimensionalization, can be used to elucidate the relative importance of variation in each gene of this mechanism. We also give insights into non-intuitive patterns of dependence and trade-off among the genes. The mechanism produces several different phenotypes (ultrasensitivity to stimulation, switch-like behavior, amount of MAPK-PP delivered, persistence of MAPK-PP activity), each of which is sensitive to different (but partially overlapping) combinations of genes. We show that the mechanism imposes clear limitations on the evolvability of each of the different phenotypes of the pathway, even in the presence of genetic variation in the components of the mechanism. This approach to the study of evolvability is generally applicable and complements the traditional approach through statistical genetics by providing a mechanistic understanding of the genetic interactions that produce the phenotype.

Biological Evolution↗
PubMed2005

Rapidly evolving genes of Drosophila: differing levels of selective pressure in testis, ovary, and head tissues between sibling species.

Investigations of rapidly evolving sex- and reproduction-related genes are expected to reveal important information about the process of speciation and species divergence. We screened testis, ovary, and head tissues to identify and characterize rapidly evolving genes (REGs) between closely related species. The results show differential patterns of evolution of genes expressed in reproductive and nonreproductive tissues. (1) There is a differential distribution of REGs in the Drosophila genome, with most REGs localized in the testis, followed by ovary, and then head. (2) Sequence analysis indicates that differential selective pressures are driving the rapid evolution of genes expressed in sex and nonsex tissues. Testis REGs from our data, on average, yielded higher rates of nonsynonymous substitutions relative to transcripts in ovary and head, indicating stronger selective pressures on the male reproductive system. (3) We identified REGs in the testis, ovary, as well as in head tissue that show evidence of evolving under positive selection. Identification of rapidly evolving sex genes is important for detailed investigations of cryptic female choice, sexual conflict, and faster male evolution and is pertinent to our understanding of the process of species divergence and speciation.

Animals↗
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↗
PubMed2006

Natural history as a predictor of protein evolvability.

Natural selection generally produces specific and efficient enzymes. In contrast, directed evolution experiments usually produce enzyme variants with broadened substrate specificity or enhanced catalytic promiscuity. Some proteins may be more evolvable than others, but few workers consider this problem when choosing starting points for laboratory evolution. Here, we review the variables associated with enzyme evolvability, namely promiscuity and mutational robustness. We present a qualitative model of adaptive evolution and recommend that protein engineers exploit their knowledge of natural history to identify evolvable wild-type proteins. Three examples of 'generalist' proteins that evolved in the laboratory into 'specialists' are described to illustrate the practical utility of this point.

Animals↗
PubMed2005

Efficacy of an evolved Escherichia coli phytase in diets of broiler chicks.

An evolved Escherichia coli-derived phytase was evaluated for its efficacy in improving growth performance and nutrient utilization of broiler chicks. One hundred forty-four 7-d-old male broiler chicks were grouped by weight into 6 blocks of 6 cages with 4 birds per cage. Six corn-soybean meal-based mash diets were randomly assigned to cages within each block. The 6 diets were adequate P (7.7 g of P/kg of diet), low P (3.9 g of P/kg of diet), low P diet plus 0.75 or 1.5 g of inorganic P from monosodium phosphate, and low P diet plus the evolved Escherichia coli phytase at 500 or 1,000 units/kg of diet. The chicks were fed the experimental diets from 8 to 22 d of age. The evolved Escherichia coli phytase improved weight gain (P < 0.05), feed intake (P < 0.01), percentage tibia ash (P < 0.01), and retention of P (P < 0.001), Ca (P < 0.01), N (P < 0.05), and a number of amino acids (P < 0.05). The evolved Escherichia coli phytase was, therefore, efficacious in improving broiler growth performance, bone characteristics, and retention of P, Ca, N, and a number of amino acids.

6-Phytase↗
PubMed2005

Prognostic value of a simple evolving disseminated intravascular coagulation score in patients with severe sepsis.

OBJECTIVE: We postulated that the coagulopathy initiated by the inflammatory response to severe sepsis would be reflected by changes in the platelet count and prothrombin time that convey prognostic information. To examine this hypothesis, we looked at the utility of a simple evolving disseminated intravascular coagulation (DIC) score that awarded 1 point for each of the following: a) an absolute platelet count <100 x 10/L; b) a prothrombin time >15.0 secs; c) a 20% decrease in platelets; and d) a >0.3-sec increase in prothrombin time in predicting outcome in patients with severe sepsis. DESIGN: Prospective observational study. SETTING: Intensive care units of university medical center. PATIENTS: Patients were 163 critically ill severe sepsis patients. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Patients were clinically classified as having capillary leak syndrome (n = 24), multiple organ failure with death from sepsis (n = 37), or multiple organ failure with recovery (n = 57) or as well (n = 45) if they showed rapid improvement in their modified Multiple Organ Dysfunction Syndrome (MODS) score (which did not score for thrombocytopenia). Patients with capillary leak syndrome had the highest Acute Physiology and Chronic Health Evaluation II score, modified MODS, and prothrombin time and the lowest platelet counts, whereas well patients had the most normal values. The simple evolving DIC score increased with worsening clinical class and was associated with worsening organ failure (increased modified MODS). Mortality rate increased from 10% for a simple evolving score of 0 to 73% for a score of 4 (p < .01). Overall, 86% of those with a score < or =1 survived, whereas 85% of those with a score of > or =2 developed multiple organ failure and half of them died from sepsis. CONCLUSIONS: The simple evolving DIC score calculated in the first 48 hrs from two readily available global coagulation markers appears to reflect the severity of the underlying disorder. It can be easily calculated at the bedside and provides useful prognostic information for the patient with severe sepsis.

Adult↗
PubMed1981

Structure of an experimentally evolved gene duplication encoding ribitol dehydrogenase in a mutant of Klebsiella aerogenes.

We have previously described a system of experimental evolution in which many of the mutants of Klebsiella aerogenes selected for faster growth on xylitol ('evolvants') synthesized elevated levels of ribitol dehydrogenase and have presented genetic evidence implicating gene duplication in the enzyme superproduction in some of the evolvants. Here we describe a physical approach to the screening for gene duplications and subsequent structure determination. Nick-translated, cloned ribitol operon (rbt) DNA was used as a hybridization probe to identify fragments containing rbt operon sequences in restriction digests of total bacterial DNA. Whilst several of the evolvants probably harbour duplications spanning the entire rbt operon, one of the spontaneously arising evolvants (strain A3) was shown to harbour a small (5.8 kilobase pairs) direct DNA repeat which encodes the dehydrogenase (but not the kinase) of the closely linked D-arabitol operon as well as the dehydrogenase (but not the kinase) of the rbt operon. The hybridization data suggest that there are 4 to 5 copies of the repeat arranged contiguously on the chromosome. The genetic instability of strain A3, the rbt fragment hybridization pattern of an A3 segregant and the activities of the pentitol catabolic enzymes in A3 are all consistent with the proposed gene duplication structure.

Base Sequence↗
PubMed2006

Generalized disjunction decomposition for evolvable hardware.

Evolvable hardware (EHW) refers to self-reconfiguration hardware design, where the configuration is under the control of an evolutionary algorithm (EA). One of the main difficulties in using EHW to solve real-world problems is scalability, which limits the size of the circuit that may be evolved. This paper outlines a new type of decomposition strategy for EHW, the "generalized disjunction decomposition" (GDD), which allows the evolution of large circuits. The proposed method has been extensively tested, not only with multipliers and parity bit problems traditionally used in the EHW community, but also with logic circuits taken from the Microelectronics Center of North Carolina (MCNC) benchmark library and randomly generated circuits. In order to achieve statistically relevant results, each analyzed logic circuit has been evolved 100 times, and the average of these results is presented and compared with other EHW techniques. This approach is necessary because of the probabilistic nature of EA; the same logic circuit may not be solved in the same way if tested several times. The proposed method has been examined in an extrinsic EHW system using the (1 + lambda) evolution strategy. The results obtained demonstrate that GDD significantly improves the evolution of logic circuits in terms of the number of generations, reduces computational time as it is able to reduce the required time for a single iteration of the EA, and enables the evolution of larger circuits never before evolved. In addition to the proposed method, a short overview of EHW systems together with the most recent applications in electrical circuit design is provided.

Algorithms↗
PubMed2003

Is evolvability involved in the origin of modular variation?

Lipson et al. (2002) presented an elegant linear algebraic formalism to define and study the evolution of modularity in an artificial evolving system. They employed simulation data to support their suggestion that modularity arises spontaneously in temporally fluctuating systems in response to selection for enhanced evolvability. We show analytically and by simulation that their correlate of modularity is itself under selection and so is not a reliable indicator of selection for modularity per se. In addition, we question the relation between modularity and evolvability in their simulations, suggesting that this modularity cannot confer enhanced evolvability.

Biological Evolution↗
PubMed2003

The evolution of the evolvability properties of the yeast prion [PSI+].

Saccharomyces cerevisiae's ability to form the prion [PSI+] may increase the rate of evolvability, defined as the rate of appearance of heritable and potentially adaptive phenotypic variants. The increase in evolvability occurs when the appearance of the prion causes read-through translation and reveals hidden variation in untranslated regions. Eventually the portion of the phenotypic variation that is adaptive loses its dependence on the revealing mechanism. The mechanism is reversible, so the restoration of normal translation termination conceals the revealed deleterious variation, leaving the yeast without a permanent handicap. Given that the ability to form [PSI+] is known to be fixed and conserved in yeast, we construct a mathematical model to calculate whether this ability is more likely to have become fixed due to chance alone or due to its evolvability characteristics. We find that evolvability is a more likely explanation, as long as environmental change makes partial read-through of stop codons adaptive at a frequency of at least once every million years.

Adaptation, Biological↗
PubMed1993

Complex telomere-associated repeat units in members of the genus Chironomus evolve from sequences similar to simple telomeric repeats.

The dipteran Chironomus tentans has complex tandemly repeated 350-bp DNA sequences at or near the chromosome ends. As in Drosophila melanogaster, short simple repeats with cytosines and guanines in different strands have never been observed. We were therefore interested in learning whether the Chironomus repeats could have evolved from simple sequence telomeric DNA, which might suggest that they constitute a functional equivalent. We screened for repeat units with evolutionarily ancient features within the tandem arrays and recovered two clones with a less-evolved structure. Sequence analysis reveals that the present-day 350-bp unit probably evolved from a simpler 165-bp unit through the acquisition of transposed sequences. The 165-bp unit contains DNA with a highly biased distribution of cytosine and guanine between the two strands, although with the ratios inverted in two minor parts of the repeat. It is largely built up of short degenerate subrepeats for which most of the sequence can be reconstructed. The consensus for the subrepeat sequence is similar to the simple telomeric repeat sequences of several kinds of eukaryotes. We propose that the present-day unit has evolved from telomeric, simple sequence, asymmetric DNA from which it has retained some original sequence features and possibly functions.

Animals↗
PubMed2004

Differential effects of apolipoprotein A-I-mimetic peptide on evolving and established atherosclerosis in apolipoprotein E-null mice.

BACKGROUND: Apolipoprotein (apo) A-I and apoA-I-mimetic peptides showed promise to prevent atherosclerosis development. Using a bypassed vein graft model in apoE-null mice, we evaluated the effects of oral or intraperitoneal administration of an apoA-I-mimetic peptide on evolving atherosclerotic lesions in the vein graft and compared such effects on the established atherosclerotic lesions in aortic sinus in the same mice. METHODS AND RESULTS: We used apoE-null mice in which a segment of inferior vena cava was grafted into the right carotid artery at 16 weeks of age. Native aortic atherosclerotic lesions (established atherosclerosis) and vein-graft atherosclerotic lesions (evolving atherosclerosis) were assessed 4 weeks after daily oral (0.3 mg/mL) or intraperitoneal (50 microg in 200 microL saline) administration of an apoA-I-mimetic peptide, D4F. Mice receiving saline or water without D4F served as controls. Both oral and intraperitoneal administration of D4F reduced vein-graft atherosclerotic (evolving lesions) plaque size by 43% and 42%, plaque lipid by 70% and 49%, and macrophage immunoreactivity by 63% and 62%, respectively, compared with controls. In contrast, D4F had no effect on the native aortic sinus atherosclerotic lesions (established lesions). CONCLUSIONS: Oral and intraperitoneal administration of the apoA-I-mimetic peptide D4F significantly reduced rapidly evolving atherosclerotic lesions in vein grafts but not established atherosclerotic lesions in aortic sinus. These observations suggest that the type of atherosclerotic lesions and the time of initiation during the course of lesion evolution modulate the beneficial effects of apoA-I-mimetic peptides on atherosclerosis.

Administration, Oral↗
PubMed2000

Talking helps: evolving communicating agents for the predator-prey pursuit problem.

We analyze a general model of multi-agent communication in which all agents communicate simultaneously to a message board. A genetic algorithm is used to evolve multi-agent languages for the predator agents in a version of the predator-prey pursuit problem. We show that the resulting behavior of the communicating multi-agent system is equivalent to that of a Mealy finite state machine whose states are determined by the agents' usage of the evolved language. Simulations show that the evolution of a communication language improves the performance of the predators. Increasing the language size (and thus increasing the number of possible states in the Mealy machine) improves the performance even further. Furthermore, the evolved communicating predators perform significantly better than all previous work on similar prey. We introduce a method for incrementally increasing the language size, which results in an effective coarse-to-fine search that significantly reduces the evolution time required to find a solution. We present some observations on the effects of language size, experimental setup, and prey difficulty on the evolved Mealy machines. In particular, we observe that the start state is often revisited, and incrementally increasing the language size results in smaller Mealy machines. Finally, a simple rule is derived that provides a pessimistic estimate on the minimum language size that should be used for any multi-agent problem.

Algorithms↗
PubMed2002

Genetic redundancy in evolving populations of simulated robots.

A number of authors have argued that redundancy in biological organisms contributes to their evolvability. We investigate this hypothesis via the experimental manipulation of genetic redundancy in evolving populations of simulated robots controlled by artificial neural networks. A genetic algorithm is used to simulate the evolution of robots with the ability to perform a previously studied task. Redundancy is measured using systematic lesioning. In our experiments, populations of robots with larger genotypes achieve systematically higher fitness than populations whose genotypes are smaller. It is shown that, in principle, robots with smaller genotypes have enough computational power to achieve optimal fitness. Populations with larger (redundant) genotypes appear, however, to be more evolvable and display significantly higher diversity. It is argued that this enhanced evolvability is a direct effect of genetic redundancy, which allows populations of redundant robots to explore neutral networks spanning large areas of genotype space. We conjecture that, where cost considerations allow, redundancy in functional or potentially functional components of the genome may make a valuable contribution to evolution in artificial and perhaps in biological systems. The methods described in the article provide a practical way of testing this hypothesis for the artificial case.

Models, Genetic↗
PubMed2005

Evolvability suppression to stabilize far-sighted adaptations.

The opportunistic character of adaptation through natural selection can lead to evolutionary pathologies--situations in which traits evolve that promote the extinction of the population. Such pathologies include imprudent predation and other forms of habitat overexploitation, or the tragedy of the commons, adaptation to temporally unreliable resources, cheating and other antisocial behavior, infectious pathogen carrier states, parthenogenesis, and cancer, an intraorganismal evolutionary pathology. It is known that hierarchical population dynamics can protect a population from invasion by pathological genes. Can it also alter the genotype so as to prevent the generation of such genes in the first place, that is, suppress the evolvability of evolutionary pathologies? A model is constructed in which one locus controls the expression of the pathological trait, and a series of modifier loci exist that can prevent the expression of this trait. It is found that multiple evolvability checkpoint genes can evolve to prevent the generation of variants that cause evolutionary pathologies. The consequences of this finding are discussed.

Adaptation, Physiological↗
PubMed1995

Evolving brain lesions in the first 12 hours after head injury: analysis of 37 comatose patients.

From January 1, 1990, to April 30, 1994, 412 patients were admitted to our intensive care unit in coma after head injuries. Our study group consisted of 37 patients who were retrospectively identified as harboring lesions or developing new lesions within a 12-hour period from the time of admission. We defined the evolution of a lesion as an increase or decrease in the size of an already present hematoma or as the appearance of a totally new lesion. There were 25 male and 12 female patients (mean age, 34.9 yr), and the cause of trauma was road traffic accidents in 32 patients. Nine patients presented with shock, and six had evidence of abnormal coagulation at admission. Patients were divided into two different groups. In Group 1, 15 patients harbored lesions that evolved toward reabsorption. In Group 2, 22 patients harbored hematomas that evolved toward lesions requiring surgical removal. Fifteen of these patients had initial diagnoses of diffuse injury that evolved in this manner, whereas the remaining seven patients had already been operated upon and had developed second, noncontiguous, surgical lesions. Patients with lesions that required surgical evacuation had their computed tomographic (CT) scans obtained earlier and had a higher incidence of clinical deterioration. There was a significant difference in the evolution of the different lesions (P < 0.001), with subdural hematomas being more prone to reabsorption and intracerebral and extradural hematomas being more likely to increase in size or to appear as new lesions. Second CT scans were obtained because of clinical deterioration in 10 patients and because of increase in intracranial pressure in 5 patients. Scheduled CT scans were obtained in 13 patients, whereas in the remaining 9 patients, the diagnosis emerged from a combination of scheduled CT scans and intracranial pressure monitoring. There was a trend toward a poorer result among the patients with clinical deterioration, which, however, was not significant. A significant proportion of post-traumatic patients, particularly those who are unconscious, harbor early evolving intracranial lesions. When the first CT scan is performed within 3 hours after injury, a CT scan should be repeated within 12 hours.

Adolescent↗
PubMed2002

[Clinical characteristics of chronic subdural hematoma evolving from traumatic subdural effusion].

OBJECTIVE: To probe into the incidence, mechanism and clinical characteristics of chronic subdural hematoma (CSDH) evolving from traumatic subdural effusion (TSE). METHODS: The clinical materials of 32 patients with CSDH evolving from TSH were analyzed retrospectively and the correlative literature was reviewed. RESULTS: 16.7% of the patients with TSH evolved into CSDH. The time of evolution was 22 - 100 days after head injury. All patients were cured with hematoma drainage. CONCLUSIONS: TSE is one of the origins of CSDH. The clinical characteristics of TSE evolving into CSDH include polarization of patient age, and chronic small effusion. The patients are usually injured deceleratedly and accompanied with mild cerebral damage.

Adolescent↗