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PubMed1987

Hydrogen peroxide as an alternate substrate for the oxygen-evolving complex.

Photosystem II reaction centers evolve O2 in the dark when H2O2 is added as a substrate. Although some of this activity can be attributed to catalase, as much as 75% of the activity was not affected by the addition of 1 mM KCN. Several lines of evidence demonstrate that this KCN-insensitive O2 evolution from H2O2 in the dark is catalyzed by the cycling of S states in the oxygen-evolving complex including: inactivation of H2O2-mediated O2 evolution by Ca/EDTA washing; susceptibility of the activity to inhibition by amines like ammonia and Tris; inhibition by CCCP which is known to accelerate the rate of deactivation of the S2 state and; a direct dependence of the rate of O2 evolution on the presence of calcium and chloride.

Calcium↗
PubMed1994

Expression of the 23 kDa protein from the oxygen-evolving complex of higher plants in Escherichia coli.

The 23 kDa protein from the oxygen-evolving complex of higher plants regulates the binding of one Ca2+ ion, which is an essential cofactor of water splitting. In this report its expression in Escherichia coli is described. The 23 kDa protein was expressed and secreted to the periplasm where it accumulated in a soluble form. After purification by cation exchange chromatography the recombinant protein was found to NaCl-washed Photosystem II. Detailed analysis of oxygen-evolving activity demonstrates its function in Ca2+ binding identical to the spinach 23 kDa protein. This expression system opens the way for mutational analysis and isotopic labelling in order to study its function in water splitting.

Amino Acid Sequence↗
PubMed1992

Glycinebetaine stabilizes the association of extrinsic proteins with the photosynthetic oxygen-evolving complex.

The photosynthetic oxygen-evolving activity of the photosystem 2 complex, prepared from spinach, was labile when the complex was exposed to high-salt conditions under which the extrinsic proteins were dissociated from the complex. Glycinebetaine prevented the dissociation of the 18-kDa and the 23-kDa extrinsic proteins from the photosystem 2 complex in the presence of 1 M NaCl. It also prevented the dissociation of the 33-kDa extrinsic protein from the complex in the presence of 1 M MgCl2 or 1 M CaCl2. The oxygen-evolving activity of the photosystem 2 complex was stabilized by glycinebetaine when the complex was subjected to treatment with NaCl and MgCl2.

Betaine↗
PubMed1990

A single copy gene for chicken chromosomal protein HMG-14b has evolutionarily conserved features, has lost one of its introns and codes for a rapidly evolving protein.

The evolutionary origins and common features of the genes coding for the HMG-14/-17 family of chromosomal proteins have been studied by isolating and sequencing the chicken HMG-14b gene, the true homolog of the human and calf HMG-14 gene. Comparison of the structure of this gene to that of the human HMG-14 gene and to the human and chicken HMG-17 genes indicates that the HMG-14 and HMG-17 genes evolved from a common ancestor. We postulate that the ancestral gene consisted of six exons. In all genes the first exon codes for the entire 5' untranslated region and for the first four amino acids, which are invariant among all the known members of the HMG-14/-17 protein family. The last exon codes for ten to 16 amino acids and for the entire 3' untranslated region, which, for each gene, constitutes over 70% of the transcript. The DNA-binding domain of the proteins is encoded by two distinct exons. The genes are characterized by 5' regions that are highly enriched in G + C residues and have features characteristic of "housekeeping" genes. The HMG-17 genes are distinct from the HMG-14 in that the 5' regulatory region of the former has two TATA boxes while the HMG-14 genes have no such regulatory element. The chicken HMG-14b gene is a single-copy gene and produces a unique transcript. In this gene, exons II and III are fused and intron 2 is missing. The fusion of the two exons produced a codon for valine in a position that, among all HMG-14/-17 proteins, is unique to HMG-14b. The possible consequences of a valine insertion at the N-terminal end of the DNA-binding domains are discussed. The HMG-14 proteins evolve significantly faster than HMG-17, suggesting that the proteins are subject to different evolutionary pressure. However, certain amino acids are conserved among all the known members of the HMG-14/-17 protein family, suggesting that they are part of the functional domain of this family of chromosomal proteins.

Amino Acid Sequence↗
PubMed1991

Cellular response of the evolving myocardial infarction after therapeutic coronary artery reperfusion.

This study describes the cellular response of the evolving myocardial infarction in humans after early coronary artery reperfusion by one or more of the following therapies: streptokinase, percutaneous transluminal coronary angioplasty, tissue plasminogen activator, and/or coronary artery bypass graft surgery. Postmortem histologic changes were compared in two groups (n = 43 pairs) of human hearts with acute myocardial infarction matched for clinical age and left ventricular location of the infarct. The treatment group received one or more of the forms of reperfusion therapy. The control group received conventional therapy. The treatment group was judged to have an older histologic age infarct, P less than 0.002, compared with documented clinical age. For example, infarcts that were clinically 4 days old or less were judged histologically to be 1 day older. The treatment group had a higher Cellular Response Index, P less than 0.017; more hemorrhage within the infarct, P less than 0.001; a greater extent of selective myocardial cell necrosis, and a lesser extent of coagulation necrosis, P less than 0.05; more patchy, nontransmural distribution of necrosis, P less than 0.04; and a more florid cellular response, specifically more macrophages, P less than 0.034, and reactive stromal cells, P less than 0.05. In infarcts less than 3 days old clinically, the treatment group had hemorrhage and a cellular response which were wide-spread throughout the lesion, P less than 0.05, n = 18 pairs. In infarcts 3 to 4 days old clinically, the treatment group had a florid cellular response due to more macrophages, P less than 0.05, n = 9 pairs. In infarcts 5 to 10 days old, the treatment group had more macrophages, P less than 0.01; and more phagocytosis, P less than 0.003. In infarcts 10 to 40 days old clinically, the treatment group had scar formation that was patchy, P less than 0.05. In conclusion, this study demonstrates that early therapeutic coronary artery reperfusion after an acute myocardial infarction alters the pattern of injury and the cellular response to the evolving myocardial infarction so that the classical criteria for infarcts need to be modified.

Aged↗
PubMed1992

Telomeric associations evolving to ring chromosomes in a recurrent pleomorphic xanthoastrocytoma.

Telomeric associations observed in a recurrent untreated pleomorphic xanthoastrocytoma were apparently the primary cytogenetic events that evolved by fusion and breakage events, resulting in subclones with ring chromosomes. The telomeric fusions between chromosomes 15pter and 20qter, and between an extra copy of the long arm of chromosome 1 and chromosome 22qter, evolved in a stepwise fashion to ring chromosomes 20 and 22. The findings in this tumor demonstrate that telomeric association is one mechanism that can initiate chromosome instability by generating subclones with unstable chromosome intermediates and result in ring chromosomes and subsequent chromosome loss.

Adolescent↗
PubMed1996

Evolving cooperation: strategies as hierarchies of rules.

To better understand the evolutionary dynamics of cooperative strategies and their behavioral components in populations subjected to individual selection, a new classifier-system model (EvA) was developed. In EvA, strategies are encoded as algorithms composed of a fixed number of rules relating behavior remembered from the recent past to the present action to be taken. Each algorithm is the genotype of an individual within the population, and these individuals play the Iterated Prisoner's Dilemma game against each other to determine their relative contributions to the next generation. The rules are hierarchical, with more specific rules, when they apply, overriding more general rules. Maximal mutual cooperation was obtained when interaction sequences for each pair of individuals playing the game were long, when only the immediately preceeding plays in the game were remembered, and when the algorithms consisted of an intermediate number of rules (20-40). Under other conditions, mutual cooperation was reduced--even becoming less frequent than would be expected if behavior were completely random, with very few rules per algorithm. The algorithms that evolved could sometimes be recognized as Tit-For-Tat, Simpleton, or other well-known strategies; but when memory of several previous events was invoked by algorithms based on a substantial number of rules, the resulting strategies were considerably more complex. This approach shows considerable promise for providing a much deeper understanding of how cooperation may evolve in nature. Moreover, classifier-system models could prove to be broadly useful for addressing many optimization questions in biology.

Algorithms↗
PubMed1996

Evolving cooperation: the role of individual recognition.

To evaluate the role of individual recognition in the evolution of cooperation, we formulated and analyzed genetic algorithm model (EvCo) for playing the Iterated Prisoner's Dilemma (IPD) game. Strategies compete against each other during each generation, and successful strategies contribute more of their attributes to the next generation. Each strategy is encoded on a 'chromosome' that plays the IPD, responding to the sequences of most recent responses by the interacting individuals (chromosomes). The analysis reported in this paper considered different memory capabilities (one to five previous interactions), pairing continuities (pairs of individuals remain together for about one, two, five, or 1000 consecutive interactions), and types of individual recognition (recognition capability was maximal, nil, or allowed to evolve between these limits). Analysis of the results focused on the frequency of mutual cooperation in pairwise interactions (a good indicator of overall success in the IPD) and on the extent to which previous responses by the focal individual and its partner were associated with the partner's identity (individual recognition). Results indicated that a fixed, substantial amount of individual recognition could maintain high levels of mutual cooperation even at low pairing continuities, and a significant but limited capability for individual recognition evolved under selection. Recognition generally increased mutual cooperation more when the recent responses of individuals other than the current partner were ignored. Titrating recognition memory under selection using a fitness cost suggested that memory of the partner's previous responses was more valuable than memory of the focal's previous responses. The dynamics produced to date by EvCo are a step toward understanding the evolution of social networks, for which additional benefits associated with group interactions must be incorporated.

Algorithms↗
PubMed2005

Evidence for the role of the oxygen-evolving manganese complex in photoinhibition of Photosystem II.

Photoinhibition of PSII occurs at the same quantum efficiency from very low to very high light, which raises a question about how important is the rate of photosynthetic electron transfer in photoinhibition. We modulated electron transfer rate and light intensity independently of each other in lincomycin-treated pea leaves and in isolated thylakoids, in order to elucidate the specific effects of light and PSII electron transport on photoinhibition. Major changes in the rate of electron transport caused only small changes in the rate of photoinhibition, suggesting the existence of a significant photoinhibitory pathway that contains an electron-transfer-independent phase. We compared the action spectrum of photoinhibition with absorption spectra of PSII components that could function as photoreceptors of the electron-transfer-independent phase of photoinhibition and found that the absorption spectra of Mn(III) and Mn(IV) compounds resemble the action spectrum of photoinhibition, showing a steep decrease from UV-C to blue light and a low visible-light tail. Our results show that the release of a Mn ion to the thylakoid lumen is the earliest detectable step of both UV- and visible-light-induced photoinhibition. After Mn release from the oxygen-evolving complex, oxidative damage to the PSII reaction center occurs because the Mn-depleted oxygen-evolving complex cannot reduce P680+ normally.

Cucurbita↗
PubMed2006

Artificial model of photosynthetic oxygen evolving complex: catalytic O2 production from water by di-mu-oxo manganese dimers supported by clay compounds.

Adsorption of [(OH(2))(terpy)Mn(mu-O)(2)Mn(terpy)(OH(2))](3+) (terpy=2,2':6',2"-terpyridine) (1) onto montmorillonite K10 (MK10) yielded catalytic dioxygen (O(2)) evolution from water using a Ce(IV) oxidant. The Mn K-edge X-ray absorption near edge structure (XANES) of the 1/MK10 hybrid suggested that the oxidation state of the di-mu-oxo Mn(2) core could be Mn(III)-Mn(IV). However the pre-edge peak in the XANES spectrum of 1 adsorbed on MK10 is different from the neat 1 powder. The kinetic analysis of O(2) evolution showed that the catalysis requires cooperation of two equivalents of 1 adsorbed on MK10. The reaction of the [(bpy)(2)Mn(mu-O)(2)Mn(bpy)(2)](3+) (bpy=2,2'-bipyridine) (2)/MK10 hybrid with a Ce(IV) oxidant evolved O(2). However, the turnover number value was less than unity for 2/MK10, showing that 2 adsorbed on MK10 does not work as a catalyst. The terminal water ligands could be an important for the catalysis by adsorbed 1. The mechanism of O(2) production by photosynthetic oxygen evolving complex is discussed based on catalytic O(2) evolution by 1 adsorbed on MK10.

Adsorption↗
PubMedDate not supplied

Modelling biological evolvability: implicit context and variation filtering in enzyme genetic programming.

This paper describes recent insights into the role of implicit context within the representations of evolving artefacts and specifically within the program representation used by enzyme genetic programming. Implicit context occurs within self-organising systems where a component's connectivity is both determined implicitly by its own definition and is specified in terms of the behavioural context of other components. This paper argues that implicit context is an important source of evolvability and presents experimental evidence that supports this assertion. In particular, it introduces the notion of variation filtering, suggesting that the use of implicit context within representations leads to meaningful variation filtering whereby inappropriate change is ignored and meaningful change is encouraged during evolution.

Algorithms↗
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↗
PubMed2005

Robustness, evolvability, and optimality of evolutionary neural networks.

In a typical optimization problem, the main goal is to search for the appropriate values of the variables that provide the optimal solution of the given function. In artificial neural networks (ANN), this translates to the minimization of the error surface during training such that misclassification is minimized during generalization. However, since optimal training performance does not necessarily imply optimal generalization due to the possibility of overfitting or underfitting, we developed SEPA (Structure Evolution and Parameter Adaptation) which addressed these issues by simultaneously evolving ANN structure and weights. Since SEPA primarily relies on the perturbation function to bring variation in its population, this follow-up study aims to find out SEPAs evolvability, optimality, and robustness in other perturbation functions. Our findings indicate that SEPAs optimal generalization performances are stable and robust from the effect of the different perturbation functions. This is due to the feedback loop between its architecture evolution and weight adaptation such that any shortcoming of the former is compensated by the latter, and vice versa. Our results strongly suggest that proper ANN design requires simultaneous adaptation of ANN structure and weights to avoid one-sided or bias convergence to either the weight or architecture space.

Algorithms↗
PubMed2005

Advances in classification of EEG signals via evolving fuzzy classifiers and dependant multiple HMMs.

Two novel approaches to the problem of brain signals (electroencephalogram (EEG)) classification are introduced in the paper. The first method is based on a modular probabilistic network architecture that employs multiple dependant hidden Markov models (DM-HMM-D) on the input features (channels). The second method, eClass, is based on an on-line evolvable fuzzy rule base of EEG signal prototypes that represent each class and take into consideration the spatial proximity between input signals. Both approaches use supervised learning but differ in their mode of operation. eClass is designed recursively, on-line, and has an evolvable structure, while DM-HMM-D is trained off-line, in a block-based mode, and has a fixed architecture. Both methods have been extensively tested on real EEG data that is recorded during several experimental sessions involving a single female subject who is exposed to mild pain induced by a laser beam. Experimental results illustrate the viability of the proposed approaches and their potential in solving similar classification problems.

Adult↗
PubMed2006

Why did the acquired immune system of vertebrates evolve?

Rapidly expanding genomic information offers important insights into the mechanisms of acquired immunity and has fostered progress in comparative immunology. However, the question of why the acquired immune system, a trait restricted to jawed vertebrates, evolved has rarely been addressed. Here, I will examine three unique features of early vertebrate evolution, during the 50 million years when the acquired immune system evolved: co-evolution with specialised parasites, increased metabolic rates and genomic instability. These combine to shape a powerful multi-level and multi-causal selective scenario that I propose could have moulded the acquired immune system.

Animals↗
PubMed2005

Clinically significant cancer evolves from transient mutated and/or aneuploid neoplasia by cell fusion to form unstable syncytia that give rise to ecologically viable parasite species.

Following the idea of Duesberg and Rasnick (Cell Motil Cytoskeleton 2000; 47:81-107) that cancer is a separate species of organism, the ecology of cancer as a parasite is examined. The most important ecological feature of cancer is its ability to evolve. The mutation hypothesis and the "unstable genome" hypothesis of cancer evolution are considered but neither of these current hypotheses is believed to adequately explain how cancer successfully evolves. In particular, either of these processes alone should lead to extinction of the cell line before a clinically significant neoplasm is achieved. Moreover, the term "unstable genome" probably should be replaced by "labile genome" because cancer genomes must be stable enough to reproduce themselves through many generations if the clone is to expand. The key step in productive evolution of undetectable neoplasia into clinically significant cancer is hypothesized to be sex-like resorting of chromosomes from different cells (e.g., normal and abnormal cells). The sex-like process begins with cell fusion to form a syncytium, which may be stable (producing multinucleated giant cells seen in many tumors) or which may undergo "mitotic catastrophe" to produce polyploidy cells. The nuclei of polyploid cells may undergo a process called "neosis" in which they form buds and undergo karyokinesis followed by cytokinesis to yield karyoplasts (small cells with little cytoplasm) that found new cancer clone lines. Although both mutations and unstable (aneuploid) genomes are seen as dead ends in cancer evolution (i.e., using only these modes of genome modification, cancers would not likely advance to clinical significance before becoming extinct), they each produce transient genetic material, which can be incorporated into stable genomes with aggressive (i.e., ecologically fit) phenotypes by cell fusion. It is proposed that inhibition of cell fusion (or other steps in this sex-like process) concurrent with classical chemotherapy might prevent evolution of the clones and recurrence of the cancer. Similarly, active suppression of viruses or other conditions that catalyze cell fusion should also slow down evolution of cancer clones.

Adaptation, Physiological↗
PubMed2004

Structure of photosystem II and molecular architecture of the oxygen-evolving centre.

Photosynthesis utilizes light energy to oxidize water molecules to molecular oxygen at the oxygen-evolving centre of photosystem II. The structure of photosystem II from the cyanobacterium Thermosynechococcus elongatus has been reported at 3.5A resolution and, for the first time, the complete molecular structure of this 650 kDa complex, including the oxygen-evolving centre, has been revealed.

Cyanobacteria↗
PubMed1998

An investigation into the composition of products evolved during heating of hot melt adhesives.

The major chemical components generated by a selection of fourteen hot melt adhesives during heating have been identified. This information is required so that the possible health consequences of occupational exposure can be assessed and advice on controls developed. Details are also given of the test apparatus and standard testing procedure devised for this investigation. Analysis of the evolved material indicates the presence of a wide range of chemical compounds, including resin acids, volatile terpenes, aliphatic aldehydes, aliphatic and aromatic hydrocarbons and isocyanates. Some components, including resin acids and formaldehyde, are common to several types of adhesive, whereas others, such as acrolein and isocyanates, are specific to just one. There is no component which is characteristic of fume from all fourteen adhesives. Concentrations of individual chemical components show significant variation, both between different types of adhesive, and between samples of the same adhesive heated to different temperatures or for different periods of time. For individual adhesives, concentrations of evolved material tend to increase as the temperature of the glue is raised, with the highest levels being observed in samples taken directly after commencement of heating.

Adhesives↗