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PubMed2006

Discrete polymorphisms due to disruptive selection on a continuous trait--I: the one-locus case.

We have investigated, numerically and analytically, long-term evolution under frequency-dependent disruptive selection of a continuous trait varying in a finite range and controlled by one diploid mendelian locus. We found that evolution converges towards a unique long-term equilibrium where only two extreme phenotypes are present with frequencies identical to those of the mixed strategy that would be the unique ESS of the game defined by the basic fitness function of the model. As long as this precise phenotypic composition is preserved, any genetic configuration of the polymorphism is equally acceptable (selectively neutral) at the equilibrium. Thus the number of alleles and their dominance pattern may vary considerably among different equilibrium populations. If genetic expression of the trait is variable but the amount of variability is genetically modifiable, disruptive selection, acting on such modifiers, produces a steady increase of expression variability before the equilibrium is attained. In this case a population at the long-term equilibrium might even be genetically monomorphic, with the phenotypic dimorphism resulting from purely random individual variation.

Alleles↗

PubMed2004

Communication and interoperability for serial comparison in continuous health care--the new challenges.

The evolution of information technology and of telematics and increasing efforts to establish an electronic health record stimulate the development and introduction of new concepts in health care. However, compared to other application areas, e.g., tourism, banking, commerce etc. the use of information technology in health care is still of limited success. In hospitals as well in ambulatory medicine (General Practitioner systems) computers are often only used for administrative purposes. Fully operational Hospital Information Systems (HIS) are rare and often island solutions. The situation is somewhat better for department systems (DIS), e.g., where image analysis, processing of biochemical data or of biosignals is in the clinical focus. Even before we have solved the various problems in health care data processing and management within the "conventional" care institutions new challenges are coming up with concepts of telemedicine for assisted and non-assisted home care for patients with chronic diseases or people at high risk. The major challenges for provision of tele-monitoring and alarming services are improvement of communication and interoperability of devices and care providers. A major obstacle in achieving such goals are lack of standards for devices as well for procedures and a lack of databases with information on "normal" variability of many medical parameters to be monitored by serial comparison in continuous medical care. Some of these aspects will be discussed in more detail.

Biosensing Techniques↗

PubMed2003

Pathogenicity mechanisms of prokaryotic cells: an evolutionary view.

The success of pathogenic microbes depends on their ability to colonize host tissues and to counter host defense mechanisms. Microorganisms can produce overwhelming infection because of their relatively short generation times, and because they have evolved powerful mechanisms for generating phenotypic diversity as an efficient strategy for adapting to rapidly responding immune system defenses and the broad range of polymorphisms characteristic of different host tissues. Bacterial evolution may not be a continuous process, but more of a succession of temporally spaced major events. These events cause a non-gradual sequence of adaptations to a given environment. The pathogenicity islands are genetically unstable elements, and many of the genes coding for the adhesins, toxins and other virulence factors are present in pathogenicity islands, which almost certainly had former lives as accessory elements or as parts thereof, or were borne on functional accessory elements. Novel genes are also acquired by transduction (mediated by bacteriophages, plasmids or transposons), by conjugation (DNA transfer between cells) or by transformation (natural DNA uptake). Horizontal gene transfer from other species is a major source of variation and is fundamental to the genetic theory of adaptive evolution in prokaryotes.

Bacteria↗

PubMed1977

Growth of Klebsiella aerogenes on xylitol: implications for bacterial enzyme evolution.

When Klebsiella aerogenes was grown in continuous culture with xylitol. an unnatural pentitol, as the growth limiting substrate, the structural gene which codes for ribitol dehydrogenase, an enzyme which gratuitously catalyzes the oxidation of xylitol to D-xylulose, was duplicated. It appears that the duplication mechansim only duplicates the gene which is subjected to selective pressure and not any of the other closely linked genes. The degree to which the ribitol dehydrogenase gene is duplicated does not appear to be strictly correlated with the ability to grow faster on xylitol. Duplication mutants do, in fact, grow faster than their parent strain, but when challenged to grow at even higher growth rates there is a catabolic repression of enzyme activity. Thus a situation is created in which a structural gene is duplicated in response to selective pressure; these mutants can grow faster on the new substrate, but faster growth results in a "silencing" of a portion of the genes by catabolite repression.

Alcohol Oxidoreductases↗

PubMed1989

Traveling waves of in vitro evolving RNA.

Populations of short self-replicating RNA variants have been confined to one side of a reaction-diffusion traveling wave front propagating along thin capillary tubes containing the Q beta viral enzyme. The propagation speed is accurately measurable with a magnitude of about 1 micron/sec, and the wave persists for hundreds of generations (of duration less than 1 min). Evolution of RNA occurs in the wavefront, as established by front velocity changes and gel electrophoresis of samples drawn from along the capillary. The high population numbers (approximately equal to 10(11], their well-characterized biochemistry, their short generation time, and the constant conditions make the system ideal for evolution experiments. Growth is monitored continuously by excitation of an added RNA-sensitive fluorescent dye, ethidium bromide. An analytic expression for the front velocity is derived for the multicomponent kinetic scheme that reduces, for a high RNA-enzyme binding constant, to the Fisher form v = 2 square root of kappa D, where D is the diffusion constant of the complex and kappa is the low-concentration overall replication rate coefficient. The latter is confirmed as the selective value-determining parameter by numerical solution of a two-species system.

Biological Evolution↗

PubMed2005

DNA assembly with gaps (Dawg): simulating sequence evolution.

MOTIVATION: Relationships amongst taxa are inferred from biological data using phylogenetic methods and procedures. Very few known phylogenies exist against which to test the accuracy of our inferences. Therefore, in the absence of biological data, simulated data must be used to test the accuracy of methods which produce these inferences. Researchers have limited or non-existent options for simulations useful for studying the impact of insertions, deletions, and alignments on phylogenetic accuracy. RESULTS: To satisfy this gap I have developed a new algorithm of indel formation and incorporated it into a new, flexible, and portable application for sequence simulation. The application, called Dawg, simulates phylogenetic evolution of DNA sequences in continuous time using the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of indel formation. On completion, Dawg produces the true alignment of the simulated sequences. Unlike other applications, Dawg allows indel lengths to be explicitly distributed via a biologically realistic power law. Many options are available to allow users to customize their simulations and results. Because simulating with indels would be problematic if biologically realistic parameters could not be estimated, a script is provided with Dawg that can estimate the parameters of indel formation from sequence data. Dawg was applied to the sequences of four chloroplast trnK introns. It was used to parametrically bootstrap an estimation of the rate of indel formation for the phylogeny. Because Dawg can assist in parametric bootstrapping of sequence data it is useful beyond phylogenetics, such as studying alignment algorithms or parameters of molecular evolution. AVAILABILITY: Dawg 1.0.0 can be obtained at the following websites: http://www.genetics.uga.edu/sw/ or http://scit.us/dawg/. The package includes source code, example files, a brief manual and helper scripts. Binary distributions are available for Windows and Macintosh OS X. A development page for Dawg exists at http://scit.us/dawg/, with links to a Subversion repository, mailing lists and updated versions.

Base Sequence↗

PubMed1996

Long-term evolution of multilocus traits.

We analyze monomorphic equilibria of long-term evolution for one or two continuous traits, controlled by an arbitrary number of autosomal loci and subject to constant viability selection. It turns out that fitness maximization always obtains at long term equilibria, but in the case of two traits, linkage determines the precise nature of the fitness measure that is maximized. We then consider local convergence to long term equilibria, for two multilocus traits subject to either constant or frequency dependent selection. From a model of long-term dynamics near an equilibrium we derive a criterion of local long-term stability for 2-dimensional equilibria. It turns out that mutation can be a decisive factor for stability.

Animals↗

PubMed2006

The gain and loss of genes during 600 million years of vertebrate evolution.

BACKGROUND: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years. RESULTS: We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication (whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost. CONCLUSION: Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication (probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates.

Animals↗

PubMed2000

Discrepancies in Epstein-Barr virus association at presentation and relapse of classical Hodgkin's disease: impact on pathogenesis.

BACKGROUND: Though Epstein-Barr virus (EBV) has been linked to classical Hodgkin's disease (cHD), only a proportion of cHD cases show EBV-association. While there has been evidence to suggest a crucial role for EBV in the early phase of cHD evolution, we are unclear whether continued presence of EBV is essential for the maintenance of the neoplasm. We have addressed this issue by investigating the EBV-association in paired samples of cHD obtained at presentation and relapse. MATERIALS AND METHODS: We have analysed lymph node biopsy samples from 23 cases of cHD at presentation and relapse. In situ hybridization with EBER-1 probe and immunostaining with anti latent membrane protein-1 (LMP-1) antibody was performed on the paraffin sections. PCR for EBNA 3C gene was performed for EBV subtype analysis on the DNA extracted from paraffin sections. RESULTS: EBV-association was documented in both the presentation and relapse samples of 14 cases. One case showed loss of EBV-association at relapse. PCR analysable DNA was obtained from both presentation and relapse samples in four of the EBV-associated cases. The EBNA 3C amplimer corresponded to type A strain of EBV in all the samples. CONCLUSION: Loss of EBV-association between presentation and relapse seen in one case implies a hit and run mechanism in EBV-induced lymphomagenesis. Though EBV may be essential early in the evolution of cHD, it may not be required for maintenance of the neoplastic clone. Our study also brings out a speculation that a proportion of EBV-negative cHD could represent loss of EBV in the tumour prior to clinical presentation. Alternatively, an unidentified lymphotropic virus other than EBV might play a pathogenetic role in EBV-negative cHD.

Burkitt Lymphoma↗

PubMed1992

Factors affecting the in vitro evolution of a myeloma cell line.

A continuously growing plasma cell line has been established from the bone marrow of a multiple myeloma patient. Initial growth of the cells was dependent on the presence of bone marrow stromal cells. Following initial outgrowth the cells were maintained by transfer onto non-autocthonous bone marrow stromal cultures. Following approximately one year of continuous growth, a subline was derived which could be grown independently of feeder cells. These stromal-cell-independent myeloma cells nevertheless retained dependence for a growth factor present in stromal-cell-conditioned media. The relevant factor in the conditioned media was determined to be interleukin-6 (IL-6). The cells also ultimately became independent of the conditioned media. These latter cells were shown to contain mRNA for IL-6 and eventually began to secrete IL-6. This cell line has thus progressed from complete dependence on stromal cells to IL-6-dependent growth in the absence of stromal cells to complete self sufficient growth. This in vitro progression may reflect an in vivo pattern of myeloma development.

Bone Marrow↗

PubMed2004

Evolution and stability of the G-matrix on a landscape with a moving optimum.

In quantitative genetics, the genetic architecture of traits, described in terms of variances and covariances, plays a major role in determining the trajectory of evolutionary change. Hence, the genetic variance-covariance matrix (G-matrix) is a critical component of modern quantitative genetics theory. Considerable debate has surrounded the issue of G-matrix constancy because unstable G-matrices provide major difficulties for evolutionary inference. Empirical studies and analytical theory have not resolved the debate. Here we present the results of stochastic models of G-matrix evolution in a population responding to an adaptive landscape with an optimum that moves at a constant rate. This study builds on the previous results of stochastic simulations of G-matrix stability under stabilizing selection arising from a stationary optimum. The addition of a moving optimum leads to several important new insights. First, evolution along genetic lines of least resistance increases stability of the orientation of the G-matrix relative to stabilizing selection alone. Evolution across genetic lines of least resistance decreases G-matrix stability. Second, evolution in response to a continuously changing optimum can produce persistent maladaptation for a correlated trait, even if its optimum does not change. Third, the retrospective analysis of selection performs very well when the mean G-matrix (G) is known with certainty, indicating that covariance between G and the directional selection gradient beta is usually small enough in magnitude that it introduces only a small bias in estimates of the net selection gradient. Our results also show, however, that the contemporary G-matrix only serves as a rough guide to G. The most promising approach for the estimation of G is probably through comparative phylogenetic analysis. Overall, our results show that directional selection actually can increase stability of the G-matrix and that retrospective analysis of selection is inherently feasible. One major remaining challenge is to gain a sufficient understanding of the G-matrix to allow the confident estimation of G.

Adaptation, Biological↗

PubMed2002

Antigenic drift and variability of influenza viruses.

Annual influenza epidemics are caused by rapid evolution of the viral genome. Continuous and extensive antigenic variation has been shown for hemagglutinin (HA), the principal immunizing antigen of the virus. Monitoring of the antigenicity of circulating influenza viruses is necessary for selection of the most suitable vaccine strains. In this study, characterization of influenza A/H3N2 and influenza B viruses recently circulating in Germany was performed by molecular and antigenic analysis. Sequencing and phylogenetic analysis of the HA1 gene revealed that two distinct groups of H3N2 viruses co-circulated during 1997/1998. The majority of isolates clustered with the new drift variant A/Sydney/5/97, as was also shown by antigenic characterization. A noteworthy genetic drift of H3N2 viruses was evident during the winter 1998/1999. However, serological characterization using hemagglutinin inhibition tests did not result in detection of viruses belonging to different groups as confirmed by molecular analysis. Influenza B viruses isolated during 1996/1997 were antigenically closely related to the prototype vaccine strains B/Beijing/184/93 or B/Harbin/7/94. Molecular analysis demonstrated that our German 1996/1997 isolates differed by nine amino acids from B/Harbin/7/94 and represented a group of viruses that was completely different from the Harbin strain. Retrospective studies revealed the circulation of B/Yamanshi/166/98-like viruses in Germany already during the 1996/1997 season. Our results suggest that molecular analysis of the HA gene is important to complement the antigenic characterization for a better selection of appropriate vaccine strains.

Amino Acid Sequence↗

PubMedDate not supplied

Evolving beyond perfection: an investigation of the effects of long-term evolution on fractal gene regulatory networks.

This paper continues a theme of exploring algorithms based on principles of biological development for tasks such as pattern generation, machine learning and robot control. Previous work has investigated the use of genes expressed as fractal proteins to enable greater evolvability of gene regulatory networks (GRNs). Here, the evolution of such GRNs is investigated further to determine whether evolution exhibits natural tendencies towards efficiency and graceful degradation of developmental programs. Experiments where "perfect" GRNs are evolved for a further thousand generations without the addition of any further selection pressure, confirm this hypothesis. After further evolution, the perfect GRNs operate in a more efficient manner (using fewer proteins) and show an improved ability to function correctly with missing genes. When the algorithm is applied to applications (e.g. robot control) this equates to efficient and fault-tolerant controllers.

Algorithms↗

PubMed1988

Back muscle function during bipedal walking in chimpanzee and gibbon: implications for the evolution of human locomotion.

The evolution of erect posture and locomotion continues to be a major focus of interest among paleoanthropologists and functional morphologists. To date, virtually all of our knowledge about the functional role of the back muscles in the evolution of bipedalism is based on human experimental data. In order to broaden our evolutionary perspective on the vertebral region, we have undertaken an electromyographic (EMG) analysis of three deep back muscles (multifidus, longissimus thoracis, iliocostalis lumborum) in the chimpanzee (Pan troglodytes) and gibbon (Hylobates lar) during bipedal walking. The recruitment patterns of these three muscles seen in the chimpanzee closely parallel those observed in the gibbon. The activity patterns of multifidus and longissimus are more similar to each other than either is to iliocostalis. Iliocostalis recruitment is clearly related to contact by the contralateral limb during bipedal walking in both species. It is suggested that in both the chimpanzee and gibbon, multifidus controls trunk movement primarily in the sagittal plane, iliocostalis responds to and adjusts movement in the frontal plane, while longissimus contributes to both of these functions. In many respects, the activity patterns shared by the chimpanzee and gibbon are quite consistent with recent human experimental data. This suggests a basic similarity in the mechanical constraints placed on the back during bipedalism among these three hominoids. Thus, the acquisition of habitual bipedalism in humans probably involved not so much a major change in back muscle action or function, but rather an improvement in the mechanical advantages and architecture of these muscles.

Animals↗

PubMed1989

Olduvai Hominid 7 trapezial metacarpal 1 articular morphology: contrasts with recent humans.

A consideration of the metacarpal 1 articulation of the Olduvai Hominid 7 trapezium shows that, although it is generally similar to those of recent humans, it is considerably flatter radioulnarly and dorsopalmarly than those of modern humans and similar in its degree of dorsopalmar flattening to those of Upper Pleistocene late archaic humans. Even though this flattening may have slightly limited flexion-extension at the pollical carpometacarpal joint, it is most likely related to the apparently elevated levels of axial joint reaction force through the thumbs of archaic members of the genus Homo. It also documents the continuation of human carpometacarpal articular evolution through the Pleistocene.

Animals↗

PubMed1994

Combined transsylvian-subtemporal exposure of cerebral aneurysms involving the basilar apex.

The surgical repair of cerebral aneurysms involving the apex of the basilar artery continues to undergo refinement and evolution. The inherent difficulty in accessing the basilar apex as well as the complexities of the microanatomy render this area a notoriously hazardous and technically challenging region in which to perform microsurgical clipping of cerebral aneurysms. Several operative approaches have been described and are constantly undergoing a state of evolution in the hopes of optimizing the exposure of the distal basilar artery and minimizing the inherent risks of surgery. The consistent decline in operative morbidity has paralleled improved understanding of the microvascular anatomy, both in this region and along the various corridors of approach. No single operative approach is universally superior, considering the wide variability of individual patient anatomy and vascular configurations. Each approach has strengths, weaknesses, and potential complications that must be considered in the though process of planning an operative attack on a basilar apex aneurysm. Intimate familiarity with the microvasculature and the microsurgical anatomy of the region is an imperative prerequisite for the application of any surgical approach to this region. This paper outlines a detailed review of the microsurgical anatomy that is pertinent to microsurgery of aneurysms in this region, and describes an approach referred to as the combined transsylvian-subtemporal approach. We have found this operative approach particularly useful in aneurysm surgery of the basilar apex but do not mean to imply that this single approach is suitable for all surgeons or all patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Basilar Artery↗

PubMed1997

Characterization of an extremely thermophilic and oxygen-stable membrane-bound hydrogenase from a marine hydrogen-oxidizing bacterium Hydrogenovibrio marinus.

The membrane-bound hydrogenase from a marine hydrogen-oxidizing bacterium Hydrogenovibrio marinus was characterized as highly oxygen-tolerant, extremely thermophilic and thermostable in its membrane-bound form. The optimum temperatures for H2 oxidation and H2 evolution were 90 and 80 degrees C, respectively. The enzyme retained 90% of its activity after heating at 70 degrees C for 50 min under air and retained full activity at 90 degrees C for 80 min under hydrogen. The optimum pH values were 5.5 (H2 evolution) and 9.4 (H2 oxidation), and the activity ratio (H2 evolution/H2 oxidation) was high (50.3) at pH 5.5. The hydrogen evolution from reduced methyl viologen continued at high temperatures and acidic pH with the continuous addition of sodium dithionite.

Cell Membrane↗

PubMed1999

Line narrowing of I = 12 spins coupled to quadrupolar nuclei in liquids: effects of weak decoupling fields

In this paper an exact description of the observed transverse magnetization of spin 12 nuclei, coupled to quadrupolar spins which are subjected to RF irradiation, is presented. It is shown that for on-resonance CW decoupling at weak to intermediate irradiation levels, the transverse decay of the spin 12 magnetization is modulated with a period of 1/nu(2), where nu(2) is the amplitude of the decoupling irradiation. When the spin 12 signal is created as a spin echo, and the quadrupolar resonance continuously irradiated during the echo evolution, the echo amplitudes experience much stronger modulation with period 2/nu(2). In previous treatments of such spin systems, the regime of weak decoupling power was usually neglected, and approximate analytical expressions seeking to define the "adequate" or "minimal" decoupling power, necessary to achieve the collapse of the spin 12 multiplet into a single narrow line, were derived. It is demonstrated here, both by experiments and by simulations using a full Redfield formalism, that simple analytical predictions for the T(2) decay of the spin 12 magnetization are still possible, even when the scalar relaxation is not in the "fast exchange" limit and the transverse decay is considerably modulated due to insufficient decoupling power. In this case, the expected single exponential decay rate is obtained for the nonmodulated component of the signal. The theoretical solution for spin I = 12 coupled to S = 3 is derived, and results for the proton decay in (10)B-enriched sodium borocaptate in aqueous solution are presented. The effects of irradiation by several composite pulse decoupling sequences are also considered. Copyright 1999 Academic Press.

Journal Article↗